CELLMOL

MAY 2, 2024 - ZOOM

INTRODUCTION TO CELL BIOLOGY
THE CELL THEORY: A BRIEF HISTORY
➢ Robert Hooke (1665):
○ Observed compartments in cork, under a
microscope, and first named cells (the basic
unit of biology).
○ Observations were limited by low
magnification power (30x enlargement).
■ Know that there are cells but haven’t
had a clear vision of them.
○ Antonie van Leeuwenhoek: produced better
lenses that magnify up to 300x.

EARLY PROGRESS IN CELL BIOLOGY WAS SLOW

➢ Two factors restricted progress in early cell biology:
○ Microscopes had limited resolution (ability to
see fine detail).
○ The descriptive nature of cell biology; the focus
was on observation, with little emphasis on
explanation.
■ Presence was observed but the Guide Questions
details were not further elaborated 1. Who formulated the cell theory? Schwann and Virchow
2-3. What does the cell theory state?
MICROSCOPES: ESSENTIAL TOOLS IN EARLY CELL BIOLOGY All organisms consist of one or more cells.
➢ By the 1830s, compound microscopes were used (two The cell is the basic unit of structure for all organisms.
lenses). All cells arise only from preexisting cells.
○ Increased magnification and resolution.
○ Structures only 1 micrometer in size could be THE EMERGENCE OF MODERN CELL BIOLOGY
seen. ➢ Three historical strands weave together into modern cell
➢ Robert Brown: identified the nucleus inside plant cells biology, each with important contributions to
using a compound microscope. understanding cells:
➢ Matthias Schleiden: concluded that all plant tissues are ➢ To understand cell biology, one must understand the
composed of cells. concepts of cytology, biochemistry, and genetics
➢ Thomas Schwann: concluded that all animal tissues are ○ Cytology: focuses mainly on cellular structure
composed of cells. and optical techniques.
○ Biochemistry: focuses on cellular function.
○ Genetics: focuses on information flow and
heredity.

THE CELL THEORY

➢ Schwann (1839): postulated the cell theory.
○ All organisms consist of one or more cells.
○ The cell is the basic unit of structure for all
organisms.
➢ Rudolf Virchow (1855): added
○ All cells arise only from preexisting cells.

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➢ Cytology came first given that structures must be

understood first to know the cellular functions that they
correspond to. While biochemistry shows processes,
reactions, and functions, genetics gives further details on
structures far smaller than what’s tackled in cytology.

THE CYTOLOGICAL STRAND DEALS WITH CELLULAR STRUCTURE

➢ Historically, cytology deals primarily with cell structure
and observation using optical techniques.

THE LIGHT MICROSCOPE

➢ Earliest tool of cytologists.
➢ Allowed identification of organelles within cells.
➢ Organelles: membrane-bound structures, such as nuclei,
mitochondria, and chloroplasts.

Guide Questions
4-6. What are the 3 strands important to understanding cells?
Genetics, Biochemistry, Cytology

USEFUL TOOLS IN EARLY MICROSCOPY

➢ Microtome: (mid-1800s) allowed preparation of very thin
slices of samples.
○ Looks like a small guillotine to cut the
specimens into smaller and thinner samples.
➢ A variety of dyes for staining cells began to be used ➢ Naked eye: 10 μm - 1mm
around the same time. ➢ Light microscope: 1.5 cm - 1 μm
○ Parafilm was also used to preserve the integrity ➢ Electron microscope: 100 μm - 0.1 nm
of the structures of the specimen.
➢ These improved the limit of resolution (how far apart
objects must be to appear as distinct).
➢ The smaller the limit resolution the microscope has, the
greater its resolving power.

VISUALIZATION OF CELLS
➢ The light microscopy so far described is called brightfield
microscopy, as white light is passed through a specimen.
➢ Some preparations (fixing, staining, embedding in
plastic) may distort tissues.
○ Fixing - specimen is put under chloroform or
alcohol to preserve the cells and structures
○ Staining - different stains are used based on the
type of cell and structure to visualize and
differentiate them.
○ Embedding in plastic - to preserve and harden
the specimen in order to have a firmer sample
for easy slicing under the microtome without
damaging the structures. ➢ Brightfield (unstained specimen): Passes light directly
➢ Various types of microscopy have been developed to through specimen; unless the cell is naturally pigmented
allow observation of living cells. or artificially stained, the image has little contrast.
➢ Brightfield (stained specimen): Staining with various dyes
VISUALIZING LIVING CELLS enhances contrast, but most staining procedures require
➢ Phase contrast/differential interference contrast that cells be fixed (preserved).
microscopy: exploit differences in the phase of light ➢ Fluorescence: Shows the locations of specific molecules
passing through a structure with a refractive index in the cell. Fluorescent substances absorb ultraviolet
different from the surrounding medium. radiation and emit visible light. The fluorescing molecules
➢ Fluorescence microscopy: detects fluorescent dyes, or may occur naturally in the specimen but more often are
labels, to show locations of substances in the cell. made by tagging the molecules of interest with
➢ Confocal scanning: uses a laser beam to illuminate a fluorescent dyes or antibodies.
single plane of a fluorescently labeled specimen. ➢ Phase contrast: Enhances contrast in unstained cells by
amplifying variations in refractive index within specimen;
especially useful for examining living, unpigmented cells.
➢ Differential interference contrast: Also uses optical
modifications to exaggerate differences in refractive
index.
➢ Confocal: Uses lasers and special optics to focus the
illuminating beam on a single plane within the
specimen. Only those regions within a narrow depth of
focus are imaged. Regions above and below the
selected plane of view appear black rather than blurry.

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THE ELECTRON MICROSCOPE DEVELOPMENTS IN EARLY BIOCHEMISTRY

➢ Uses a beam of electrons rather than light. ➢ Louis Pasteur (1860s) showed that yeasts could ferment
➢ Major breakthrough for cell biology. sugar into alcohol.
➢ The limit resolution of an electron microscope is around ➢ Buchners (1897) showed that yeast extracts could do
0.1-0.2 nm. the same.
➢ Magnification is much higher than light microscopes-up ➢ Led to the discovery of enzymes, biological catalysts.
to 100,000x. ○ Break down agents

ELECTRON MICROSCOPY EARLY DISCOVERIES IN BIOCHEMISTRY

➢ Transmission electron microscopy (TEM), electrons are ➢ Steps of the pathways of fermentation and others were
transmitted through the specimen. elucidated in the 1920s and 1930s.
➢ Scanning electron microscopy (SEM), the surface of a ➢ Gustav Embden and Otto Meyerhof described the steps
specimen is scanned, by detecting electrons deflected of glycolysis (the Embden-Meyerhof pathway) in the
from the outer surface. early 1930s.
➢ Specialized approaches in electron microscopy allow ➢ The Krebs cycle was described soon after.
for visualization of specimens in three dimensions, and ➢ Both pathways are important in energy metabolism.
one allows visualization of individual atoms.
IMPORTANT ADVANCES IN BIOCHEMISTRY
➢ Radioactive isotopes: to trace the fate of specific atoms
and molecules (led to elucidation of the Calvin cycle,
1950s).
➢ Subcellular fractionation: such as centrifugation to
separate/isolate different structures and
macromolecules.
○ Fractionation separates/isolates different
structures with varying sizes from the other parts
of the specimen
➢ Ultracentrifuges: capable of very high speeds (over
100,000 revolutions per minute).
➢ Chromatography: techniques to separate molecules
from a solution based on size, charge, or chemical
affinity.
➢ Electrophoresis: uses an electrical field to move proteins,
DNA or RNA molecules through a medium based on
size/charge.
○ An electric current is used to move the
molecules through a gel or other matrix.
➢ Mass spectrometry: to determine the size and
composition of individual proteins.

THE GENETIC STRAND FOCUSES ON INFORMATION FLOW

➢ The genetic strand has important roots in the 19 th
century.
➢ Gregor Mendel’s experiment with peas (1866) laid the
foundation for understanding the passage of
“hereditary factors” from parents to offspring.
➢ The hereditary factors are now known to be genes.

CHROMOSOMES AND THE GENETIC MATERIAL

➢ Walther Flemming (1880) saw the threadlike bodies in
the nucleus called chromosomes.
➢ He called the process of cell division mitosis.
➢ Wilhelm Roux (1883) and August Weisman (shortly after)
suggested that chromosomes carried the genetic
material.

THE CHROMOSOMES THEORY

➢ 3 geneticists formulated the chromosome theory of
heredity, proposing that Mendel’s hereditary factors are
located on chromosomes.
➢ Morgan, Bridges, and Sturtevant (1920s) were able to
THE BIOCHEMICAL STRAND COVERS THE CHEMISTRY OF connect specific traits to specific chromosomes in the
BIOLOGICAL STRUCTURE AND FUNCTION model organism, Drosophila melanogaster (the
➢ Around the same time cytologists were studying cells common fruit fly).
microscopically, others began to explore cellular
function. PROGRESS IN UNDERSTANDING DNA
➢ Much of biochemistry dates from the work of Fredrich
➢ Friedrich Miescher (1869) first isolated DNA, which he
Wohler (1828), who showed that a compound made in
called nuclein.
a living organism could be synthesized in the lab.
➢ DNA:

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○ Known to be a component of chromosomes ○ In silico: using computer analysis of large

by 1914. amounts of data.
○ Known to be composed of only 4 different ■ uses bioinformatics
nucleotides by the 1930s.
■ ATGC
○ Proteins, composed of 20 different amino
acids, thought more likely to be genetic
material.

DNA IS THE GENETIC MATERIAL

➢ Experiments with bacteria and viruses in the 1940s began
to implicate DNA as the genetic material.
➢ Beadle and Tatum formulated the one gene-one
enzyme concept (each gene is responsible for the
production of a single protein).
➢ 1953 – Watson and Crick, with assistance from Rosalind
Franklin, proposed the double helix model for DNA
structure.
➢ 1960s – many advances toward understanding DNA
replication, RNA production, and the genetic code.
○ Start of the concept of central dogma

IMPORTANT TECHNIQUES IN GENETICS

➢ Ultracentrifugation and electrophoresis: for separating
DNA and RNA molecules.
➢ Nucleic acid hybridization: a variety of techniques that
use the ability of nucleic acid bases to bind to each
other.
➢ Recombinant DNA technology, restriction enzymes cut
DNA at specific places allowing scientists to create
recombinant DNA molecules, with DNA from different HOW WE EXPLAIN OBSERVATIONS
sources. ➢ Hypothesis: statement consistent with most of the data,
○ DNA scissors may take the form of a model (an explanation that
➢ DNA sequencing, methods for rapidly determining the appears to account for the data); must be testable.
base sequences of DNA molecules. ➢ Theory: a hypothesis that has been extensively tested by
➢ It is now possible to sequence entire genomes (entire many investigators, using different approaches, widely
DNA content of a cell). accepted.
➢ Bioinformatics: merges computer science with biology ➢ Law: a theory that has been tested and confirmed over
to organize and interpret enormous amounts of a long period of time with virtually no doubt of its validity.
sequencing and other data.
➢ Yeast two-hybrid system allows determination of how Guide Questions
proteins interact within a cell. 9. Which laboratory approach uses live cells or organisms? In vivo
➢ Nanotechnology, development of tiny tools, sensors and 10. ___ is a theory that has been tested and confirmed over a long
computer-aided analysis of the results. period of time with virtually no doubt of its validity. Law
○ Future of science

Guide Questions
7. ___ is a technique used to separate molecules from a solution
based on size, charge, or chemical affinity. Chromatography
8. T or F. The DNA has a double helix structure. True

“FACTS” AND THE SCIENTIFIC METHOD

➢ In science, “facts” are tenuous and dynamic.
➢ The scientific method is used to assess new information.
○ Scientists formulate a hypothesis (tentative
explanation or model that can be tested).
○ Data is collected and interpreted, and the
model is accepted or rejected.
○ Occam’s razor states that the simplest
explanation consistent with the observations is
most likely to be correct.
○ Nowadays, rejected hypotheses and negative
results are still considered as accepted

RESEARCH APPROACHES IN CELL BIOLOGY

➢ Research in laboratories may be:
○ In vitro: using purified chemicals and cellular
components.
■ produced in laboratories
○ In vivo: using live cells or organisms.
■ use animal models

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MAY 6, 2024 - ZOOM ➢ They are considered to have descended from a

common ancestor that also gave rise to eukaryotes long
PART 1: CELLS AND ORGANELLES after diverging from bacteria
PROPERTIES AND STRATEGIES OF CELLS
➢ Several general characteristics of cells:
○ organizational complexity
○ molecular components
○ sizes and shapes
○ specialization

All Organisms Are Bacteria, Archaea, or Eukaryotes ➢ Archaea and Eukarya has a common ancestor which
means that they are much more related as compared
➢ Biologists recognized two types of cells
○ the mentioned above are three main domains to archaea and bacteria
of the organism but they were first classified
into two types A COMPARISON OF SOME PROPERTIES OF BACTERIAL,
➢ The simpler type is characteristic of bacteria ARCHAEAL, AND EUKARYOTIC CELLS
(prokaryotes) and the more complex type characteristic
of plants, animals, fungi, algae and protozoa
(eukaryotes)
➢ The main distinction between the two cells types is the
membrane-bounded nucleus of eukaryotic cells

A CHANGING VIEW OF PROKARYOTES

➢ Recently, the term prokaryote is unsatisfactory in
describing the non-nucleated cells
➢ Sharing of a gross structural feature is not necessarily
evidence of relatedness
○ so that is why they don’t use the term
prokaryotes anymore
➢ Based on rRNA sequence analysis, prokaryotic cells can
be divided into the widely divergent bacteria and
archaea

THREE DOMAINS
LIMITATIONS ON CELL SIZE
➢ Bacteria and archaea are as divergent from one
another as humans and bacteria are ➢ Cells come in various sizes and shapes
○ they have differences even though they are ➢ Some of the smallest bacteria are about 0.2 - 0.3 μm in
prokaryotes diameter
➢ Biologists now recognize three domains, the archaea, ➢ Some highly elongated nerve cells may extend a meter
bacteria and eukarya (eukaryotes) or more
➢ Despite the extremes, cells in general fall into
GUIDE QUESTIONS predictable size ranges
➢ 1-3. What are the 3 domains? Bacteria, archaea,
SIZE RANGES
eukarya
➢ 4. T or F. The main distinction between the two cell types ➢ Bacteria cells normally range from 1 to 5 μm in diameter
is the presence of membrane-bounded nucleus of ➢ Animal cells have dimensions in the range of 10-100 μm
eukaryotic cells. T ➢ Cells are usually very small
➢ There are three main limitations on cell size
BACTERIA
➢ These include most of the commonly encountered LIMITATIONS ON CELL SIZE
single-celled, non-nucleated organisms traditionally ➢ Cell size is limited by:
called bacteria ○ The need for adequate surface area relative to
➢ Examples include (which are disease-causing): volume
○ Escherichia coli ○ The rates at which molecules can diffuse
○ Pseudomonas ○ The need to maintain adequate local
○ Streptococcus (popular as it is known to cause concentrations of substances required for
pimples) necessary cellular functions

ARCHAEA SURFACE AREA/VOLUME RATIO

➢ Archaea were originally called archebacteria before ➢ In most cases, the major limit on cell size is set by the
they were discovered to be so different from bacteria need to maintain an adequate surface area/volume
○ so more likely they are NOT bacteria ratio
➢ They include many species that live in extreme habitats ○ there should be a limit on the cell size
and have diverse metabolic strategies ➢ Surface area is important because exchanges between
➢ Types of archaea include: the cell and its surrounding stake place there
○ methanogens - obtain energy from hydrogen ○ surface area should be adequate to the cell
and convert CO2 into methane size so that there’s space for its function—site
○ halophiles - occupy extremely salty of exchange
environments ➢ The cell's volume determines the amount of exchange
○ thermoacidophiles - thrive in acidic hot springs that must take place, across the available surface area

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THE PROBLEM OF MAINTAINING ADEQUATE SURFACE DIFFUSION RATES OF MOLECULES

AREA/VOLUME RATIO ➢ Many molecules move through the cell by diffusion, the
➢ The volume of a cell increases with the cube of its length unassisted movement of a substance from a region of
➢ But the surface area of the cell increases with the square high concentration to a region of low concentration
of its length, so larger cells have proportionately smaller ➢ The rate of diffusion of molecules decreases as the size
surface areas of the molecule increases, so the limitation is most
➢ Beyond a certain threshold a large cell would not have important for macromolecules like proteins and nucleic
a large enough surface area to allow for intake of acids.
enough nutrients and release of enough wastes ○ The bigger the molecules, the slower the rate
of diffusion.
➢ Volume stays the same, but surface area increases
○ we can see that larger cells have smaller ratios
AVOIDING LIMITATIONS OF RATES OF DIFFUSION
compared to smaller cells
➢ Eukaryotic cells can avoid the problem of slow diffusion
rates by using carrier proteins to actively transport
materials through the cytoplasm.
➢ Some cells use cytoplasmic streaming (cyclosis in
plants) to actively move cytoplasmic contents
➢ Other cells move molecules through the cell in vesicles
that are transported along microtubules

THE NEED FOR ADEQUATE CONCENTRATIONS OF REACTANTS AND

CATALYSTS
➢ For a reaction to occur, the appropriate reactants must
collide with and bind to a particular enzyme
➢ The frequency of such collisions is greatly increased by
higher concentrations of enzymes and reactants
➢ As cell size increases, the number of molecules increase
proportionately with volume
○ these happen simultaneously

Eukaryotic Cells Use Organelles to Compartmentalize Cellular

Function
➢ A solution to the concentration problem is the
compartmentalization of activities within specific regions
of the cell
*For a cube having a side with length s, volume = s³ and surface ○ it disperses the activity within compartments
area = 6s² ➢ Most eukaryotic cells have a variety of organelles,
membrane-bounded compartments that are
CELL SPECIALIZED FOR ABSORPTION specialized for specific functions
➢ Cells that are specialized for absorption have ➢ e.g. cells in a plant leaf have most of the materials
characteristics to maximize surface area/volume ratio needed for photosynthesis compartmentalized into
➢ E.g., cells lining the small intestine have microvilli, structures called chloroplasts.
fingerlike projections that increase the surface area
○ this can help the surface of small intestines GUIDE QUESTIONS
absorb more nutrients even though they have ➢ 5. ____ occupy extremely salty environments. Halophiles
an increased surface area ➢ 6. T or F. Eukaryotic cells can avoid the problem of slow
diffusion rates by using carrier proteins to actively
transport materials through the cytoplasm. T

BACTERIA, ARCHAEA, AND EUKARYOTES DIFFER FROM EACH

OTHER IN MANY WAYS
➢ There are shared characteristics among cells of each of
the domains, bacteria, archaea and eukarya
➢ However, each type of cell has a unique set of
distinguishing properties

PRESENCE OF A MEMBRANE-BOUNDED NUCLEUS

➢ A eukaryotic cell has a true, membrane-bounded
nucleus
➢ The nuclear envelope consists of two membranes
➢ The nucleus also includes the nucleolus, the site of
ribosomal RNA synthesis and ribosome assembly

*these are the microvilli that helps the intestinal mucosal cell to
absorb more nutrients in the lumen of the intestine

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*Plant cell - has large vacuoles, cell wall, plasmodesmata, and

chloroplasts
*the rest are found in the animal cell

THE CYTOSKELETON
➢ Several nonmembranous, proteinaceous structures for
➢ The genetic information of a bacterial or archaeal cell is cellular contraction, motility and support are found in
folded into a compact structure called the nucleoid the cytoplasm of eukaryotic cells
and is attached to the cell membrane (since ➢ These include: microtubules, microfilaments, and
archaea/bacteria does not have a nucleus or intermediate filaments, all key components of the
nucleoplasm) cytoskeleton, which imparts structure and elasticity to
○ their genetic material is scattered throughout most eukaryotic cells
the cell ➢ The cytoskeleton also provides scaffolding for transport
of vesicles within the cell

EXOCYTOSIS AND ENDOCYTOSIS

➢ Eukaryotic cells are able to exchange materials
between compartments within the cell and the exterior
of the cell
➢ This is possible through exocytosis and endocytosis,
processes involving membrane fusion events unique to
eukaryotic cells
➢ exo: outside; endo: inside
EUKARYOTE ORGANELLES
➢ Nearly all eukaryotes make extensive use of internal ORGANIZATION OF DNA
membranes to compartmentalize specific functions and BACTERIAL DNA circular molecule
have numerous organelles
➢ E.g., endoplasmic reticulum, Golgi complex,
mitochondria, chloroplasts, lysosomes, peroxisomes and associated with a few proteins
various types of vacuoles and vesicles
➢ Each organelle contains the materials and molecular
machinery needed to carry out the functions for which EUKARYOTIC DNA organized into linear molecules
the structure is specialized

complexed with large amounts of

proteins (histones)

ARCHAEAL DNA circular molecule

complexed with proteins similar to

eukaryotic histone proteins

DNA PACKAGING
➢ The circular DNA of bacteria or archaea is much longer
than the cell itself
○ it must be folded and packed tightly.
○ It is equivalent to packing about 60 feet of
thread into a thimble.
*Animal cell - has an outer membrane, nuclear envelope which
➢ Most eukaryotic cells have more than 1000 times more
inside has the nucleolus, lysosomes, centrioles (important for cell
DNA than prokaryotes and encode only 5-10 times more
division), rough endoplasmic reticulum, plasma membrane, golgi
proteins
complex, cytosol, peroxisomes, and smooth endoplasmic
reticulum ➢ JUNK DNA: the excess noncoding DNA but it may have
important functions in gene regulation and evolution

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CHROMOSOMES must carry out all the have cells which are
necessary functions in one specialized for particular
cell functions

since they are not each cell has a specific

compartmentalized, the function
functions are together

GUIDE QUESTIONS
➢ 7. ____ provides scaffolding for transport of vesicles within
the cell. Cytoskeleton
➢ 8. T or F. Chromosomes contain equal amounts of
histones and DNA. T

THE EUKARYOTIC CELL IN OVERVIEW

➢ The structural complexity of eukaryotic cells is illustrated
by the typical animal and plant cells
➢ A typical eukaryotic cell has:
○ plasma membrane
○ nucleus
➢ The problem of DNA packaging is solved among ○ membrane-bounded organelles
eukaryotes by organizing the DNA into chromosomes ○ cytosol interlaced by a cytoskeleton
➢ Chromosomes contain equal amounts of histones and ➢ In addition, plant and fungal cells have a rigid cell wall,
DNA surrounded by an extracellular matrix
○ since there’s a lot of DNA, these are folded and
compressed into chromosomes CHAPTER CROSS-REFERENCES FOR CELLULAR STRUCTURES AND
TECHNIQUES USED TO STUDY CELLS
SEGREGATION OF GENETIC INFORMATION
➢ Prokaryotes and eukaryotes differ in how genetic
information is allocated to daughter cells upon division

BACTERIAL + ARCHAEAL CELLS EUKARYOTIC CELLS

Replicate their DNA and Replicate DNA and then

divide by binary fission with distribute their chromosomes
one molecule of the into daughter cells by mitosis
replicated DNA and the and meiosis, followed by
cytoplasm going into each cytokinesis (the division of the
daughter cell. cytoplasm).

Its DNA is replicated and the From each parent cell, only
exact copy is passed down half of its DNA is passed down
to its daughter cell to its daughter cell

EXPRESSION OF DNA
➢ Eukaryotic cells transcribe genetic information in the
nucleus into large RNA molecules which are processed
and transported into the cytoplasm for protein synthesis
○ DNA → RNA → cytoplasm → protein synthesis
○ Each RNA molecule typically encodes one
polypeptide
➢ Bacteria transcribe genetic information into RNA and PLASMA MEMBRANE
the RNA molecules produced may contain information ➢ Functions:
for several polypeptides ○ It surrounds every cell
○ DNA → RNA → information for several ○ Ensures that the cells contents are retained
polypeptides ○ Consist of lipids including phospholipids and
➢ In both bacteria and archaea, RNA molecules become proteins and is organized into two layers
involved in protein synthesis before transcription is ➢ Amphipathic membrane components
complete ○ Each phospholipid molecule consists of two
hydrophobic “tails” and a hydrophilic
CELL SPECIALIZATION DEMONSTRATES THE UNITY “head”—an amphipathic molecule.
AND DIVERSITY OF BIOLOGY ○ LIPID BILAYER: formed when the hydrophilic
➢ All cells resemble one another in fundamental ways heads face outward and the tails face inward
➢ However, they differ from one another in important ○ Membrane proteins are also amphipathic,
aspects some with polysaccharides attached to them
are called glycoproteins

UNICELLULAR ORGANISMS MULTICELLULAR ORGANISMS

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disease is associated with the lysosomes, and I-

cell disease with the Golgi bodies.

MITOCHONDRION
➢ It is found in all eukaryotic cells, which are sites of aerobic
respiration for the cell to function
➢ They are comparable in size to bacteria (small)
➢ Most eukaryotic cells contain hundreds of mitochondria,
each of which is surrounded by an inner and outer
mitochondrial membrane
➢ Mitochondrial similarity to bacterial cells:
○ Mitochondria contain small circular molecules
of DNA
■ That’s why they are sometimes used
for forensics.
○ Its chromosomes encode some RNAs and
proteins needed for mitochondrial function
➢ The photo above shows where the plasma membrane is ○ They also have their own ribosomes, to carry
cut—looking like a sandwich—where the hydrophobic out protein synthesis
region is inside the cell, while the hydrophilic region is ■ They are like cells within a cell since
towards the outside. they have their own proteins and
ribosomes that can function
➢ We can also see proteins that are bound to the outside.
○ Most membrane proteins have at least one
hydrophobic membrane-spanning domain
○ The proteins in the plasma membrane are
typically glycoproteins with short carbohydrate
side chains towards the outside of the cell.

PROTEINS IN THE PLASMA MEMBRANE

➢ Roles:
○ Enzymes catalyze reactions associated with
the membranes, such as cell wall synthesis
○ Others serve as anchors for structural
components of the cytoskeleton
➢ Transmembrane proteins and their roles:
○ TRANSPORT PROTEINS: move substances across
the membrane
○ RECEPTORS: for external signals trigger ➢ Functions:
processes within the cell. ○ Oxidation of sugars and other fuel molecules in
○ They can carry information from the outside of mitochondria extracts energy from food and
the cell. stores it in ATP.
○ Most molecules for mitochondrial function are
NUCLEUS localized on the cristae (infoldings of the inner
➢ Information center and the most prominent structure mitochondrial membrane) or the matrix (the
➢ It contains the DNA fluid that fills the inside of the mitochondrion).
➢ NUCLEAR ENVELOPE: surrounds the nucleus, composed ➢ Varied number and location:
of inner and outer membranes ○ Number and location vary among cells
○ PORES: numerous openings in the nuclear according to their role in that cell type.
envelope, each of which is a transport ○ Tissues with high demand for ATP have many
channel, lined with a nuclear pore complex. mitochondria, located within the cell at the site
➢ CHROMOSOMES: most easily visualized during mitosis, of greatest energy needs
whereas during interphase, they are dispersed as ■ e.g. sperm and muscle cells since
chromatin and difficult to visualize. they need more energy to create
○ The number of chromosomes in the nucleus is movement to function
a species-specific characteristic
○ During interphase, we still don’t call them
chromosomes. They are like intertwined
threads inside the cell and therefore, hard to
visualize.
➢ NUCLEOLI: also present in the nucleus, which is darker
stained when observed in the microscope.

INTRACELLULAR MEMBRANES AND ORGANELLES

➢ CYTOPLASM: the internal volume of the cell outside the
nucleus and is occupied by organelles and the semifluid
cytosol CHLOROPLAST
➢ a number of heritable human disorders are caused by ➢ The site of photosynthesis in plants and algae
malfunctions of specific organelles ➢ They are large, and can be quite numerous in the cells
○ e.g. MELAS Syndrome is caused by the of green plants
malfunction of the mitochondria, Pompe

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➢ They are surrounded both inner and outer membranes ➢ rRNA sequences, ribosome size, sensitivities to inhibitors
and contain a system of flattened membranous sacs of RNA and protein synthesis, and type of protein factors
called thylakoids, stacked into grana used in protein synthesis are all similar.
➢ Both resemble bacteria in size and shape and are
surrounded by double membranes, the inner of which
has bacterial-type lipids.

ENDOSYMBIONT THEORY
➢ This theory suggests that mitochondria and chloroplasts
originated from prokaryotes.
➢ These gained entry into single-celled organisms called
protoeukaryotes.
➢ Protoeukaryotes may have ingested bacteria by
phagocytosis without then digesting them, allowing a
symbiotic relationship to develop. (it's like ingesting a
parasite, but the eukaryote can acquire something from
that bacteria, so it lodged or settled there!)

GUIDE QUESTIONS
➢ 9. ____ is the site of photosynthesis in plants and algae.
Chloroplast
➢ The grana has stacks of thylakoids, which can be ➢ 10. T or F. The endosymbiont theory suggests that
compared to electrical posts and are also considered mitochondria and chloroplasts originated from
stock for energy prokaryotes. T
➢ Functions:
○ Site of photosynthesis, a process that uses solar
energy and CO2 to produce sugars and other
organic compounds
○ This process is the reverse of the mitochondrial
reactions that oxidize glucose into CO2
○ They are found in photosynthesis cells and
contain most of the enzymes needed for
photosynthesis.
○ Reactions that depend on solar energy take
place in or on the thylakoid membranes.
○ Reactions involved in the reduction of CO 2 to
sugar occur within the stroma—a semifluid in
the interior of the chloroplast.
○ Like mitochondria, they contain their own
ribosomes and a small circular DNA molecule
that encodes some RNAs and proteins needed
in the chloroplast.
➢ Other functions:
○ Reduces nitrogen from NO3- in soils, to
ammonia NH3, the form needed for protein
synthesis
○ SO42- is reduced to H2S (hydrogen sulfide) also
needed for protein synthesis
○ One of the several types of plastids found in
plant cells
➢ Plastids are specialized for particular functions:
○ CHROMOPLASTS: responsible for coloration in
flowers, fruits, and other plant structures
○ AMYLOPLASTS: specialized for storing starch
(amylose and amylopectin)

DID MITOCHONDRIA AND CHLOROPLASTS EVOLVE

FROM ANCIENT BACTERIA?
➢ Both have their own DNA and ribosomes and can
produce some of their own proteins
➢ However, most of the proteins needed in these
organelles are encoded by nuclear genes
➢ Overall, there are many similarities between processes in
mitochondria and chloroplasts and those in bacteria

SIMILARITIES BETWEEN MITOCHONDRIA,

CHLOROPLASTS, AND BACTERIA
➢ All three have circular DNA molecules without
associated histones.

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MAY 9, 2024 - ZOOM ○ These are commonly found in the muscles.

CELLS AND ORGANELLES PART 2
THE ENDOPLASMIC RETICULUM
➢ Almost every eukaryotic cell has a network of
membranes in the cytoplasm called the endoplasmic
reticulum (ER).
➢ It consists of tubular membranes and flattened sacs
called cisternae.
➢ The internal space of the ER is called the lumen.
○ The endoplasmic reticulum is continuous with
the other membranes in the cell since it is found
inside the cell.
➢ There are two types of endoplasmic reticulum:
○ Rough ER: includes free ribosomes.
○ Smooth ER: no ribosomes are present.

THE GOLGI COMPLEX

➢ The Golgi complex, closely related to the ER in proximity
and function, consists of a stack of flattened vesicles
known as cisternae.
➢ It plays an important role in processing and packaging
secretory proteins and complex polysaccharide
synthesis.
○ Sorting center, which processes the deliveries
(proteins and polysccharides) from the
endoplasmic reticulum.
➢ It accepts vesicles that bud off of the ER.
The Golgi Complex is like a Processing Station
➢ The contents of vesicles from the ER are modified and
processed in the Golgi complex.
○ E.g., secretory and membrane proteins are
mainly glycosylated (the addition of short-
ROUGH ENDOPLASMIC RETICULUM
chain carbohydrates.), a process that begins in
➢ Rough ER is studded with ribosomes on the cytoplasmic the ER and is completed in the Golgi complex.
side of the membrane, responsible for protein synthesis. ➢ The processed substances then move to other locations
➢ These ribosomes synthesize polypeptides that in the cell through vesicles that bud off the Golgi
accumulate within the membrane or are transported to complex.
the lumen. ○ From the Golgi complex, which is the sorting
➢ Free ribosomes are not associated with the ER center, the proteins and polysccharides will
○ They are just located in the cytoplasmic side, have a new address where it will be delivered
attached in that area – which is why they are to its real location.
called the rough endoplasmic reticulum.

SECRETORY VESICLES
➢ Once processed by the Golgi complex, materials to be
exported from the cell are packaged into secretory
vesicles.
○ The vehicle that delivers the proteins to those
cells who are in need of.
SMOOTH ENDOPLASMIC RETICULUM ➢ These move to the plasma membrane and fuse with it,
releasing their contents outside the cell.
➢ Smooth ER has no free ribosmes and plays a role in
➢ The ER, Golgi, secretory vesicles, and lysosomes make up
protein synthesis.
the endomembrane system of the cell, responsible for
➢ It is involved in synthesizing lipids and steroids, such as trafficking substances through the cell.
cholesterol and its derivatives. ○ The control center that maintains and
➢ Smooth ER is responsible for inactivating and detoxifying manages the proteins in the cell.
potentially harmful substances.
➢ The sarcoplasmic reticulum has critical functions in
contraction.

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GUIDE QUESTIONS
1. T or F. Both rough and smooth endoplasmic reticulum
are involved in protein synthesis. F
2. T or F. The endoplasmic reticulum, Golgi, secretory Other functions of Peroxisomes
vesicles, and lysosomes make up the endomembrane ➢ Peroxisomes detoxify other harmful compounds and
system of the cell. T catabolize unusual substances.
THE LYSOSOME ➢ In animals, they play roles in the oxidative breakdown of
fatty acids, especially longer-chain fatty acids (up to 22
➢ Lysosomes are single membrane organelles that store
carbon atoms).
hydrolases, enzymes that can digest any kind of
biological molecule. ➢ Some serious human diseases result from defects in one
○ Enzymes are those that break down and digest or more peroxisomal enzymes, normally involved in
any kind of biomolecules. degrading long-chain fatty acids.
➢ These enzymes are sequestered to prevent them from Peroxisomes in Plants
digesting the contents of the cell. ➢ During the germination of fat-storing seeds, specialized
○ A special carbohydrate coating on the inner peroxisomes called glyoxysomes play a role in
lysosome membrane protects it from digestion. converting the stored fat into carbohydrates.
■ Only the unwanted and floating ➢ Leaf peroxisomes are prominent in photosynthetic tissue
substances will be digested. because of their role in photorespiration, the light-
dependent uptake of oxygen, and the release of
carbon dioxide.
○ This is located near the chloroplast.

THE PEROXISOME
➢ Peroxisomes resemble lysosomes in size and
appearance.
VACUOLES
➢ They are surrounded by a single membrane and perform
➢ Vacuoles are found in both plants and animal cells.
several functions depending on the cell type.
➢ Some cells contain a membrane-bounded vacuole.
➢ Peroxisomes are especially prominent in the liver and
➢ In animal and yeast cells, they are used as temporary
kidney cells of animals.
storage or transport.
Hydrogen peroxide ➢ Phagocytosis leads to the formation of a membrane-
➢ Hydrogen peroxide is highly toxic to cells but can be bound particle called a phagosome.
formed into water and oxygen by the enzyme catalase. ➢ When this type of vacuole fuses with a lysosome,
○ This happened through breaking down. producing phagolysosomes, and its contents are
➢ Eukaryotic cells have metabolic processes that produce hydrolyzed to provide nutrients to a cell.
this. Plant Vacuoles
➢ These reactions are confined to peroxisomes that
➢ Most mature plant cells contain a single large vacuole
contain catalase so that cells are protected from the
called a central vacuole.
harmful effects of peroxide.
○ These are only specific for reactions producing ➢ The main function of the central vacuole is to maintain
hydrogen peroxide since it is very toxic to other the turgor pressure that keeps the plant from wilting.
cells. ○ This is important so that the plant would still
○ Catalase is responsible for breaking down this maintain its original form (not watery).
so that it won’t harm its neighboring cells. ➢ Tissues wilt when the central vacuole no longer presses
against the cell contents (fails to provide adequate
pressure).
○ When the vacuole is punctured, its contents will
leak, releasing the pressure, causing it to wilt.
○ Imagine a balloon in a plastic bag, when the
balloon pops out, the plastic bag will collapse.

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➢ The central vacuole has a very large space in the center The Cytoskeleton
of the plant cell. ➢ The cytoskeleton is a three-dimensional array of
interconnected microfilaments, microtubules, and
intermediate filaments.
➢ It gives a cell its distinctive shape and internal
organization.
➢ It also plays a role in cell movements and cell division.
➢ The cytoskeleton are those found in the center providing
the framework of the cell.

GUIDE QUESTIONS
3. ______ are single membrane organelles that store
hydrolases. lysosomes
4. T or F. The main function of the central vacuole is to
maintain the turgor pressure. T
RIBOSOMES
➢ Ribosomes are not really organelles because they are
not enclosed by a membrane.
➢ They are found in all cells but differ slightly in bacteria,
archaea, and eukarya in their size and composition.
➢ Each cell type has a unique type of ribosomal RNA.
Plant Vacuoles
➢ Ribosomes can only be seen under the electron
microscope. ➢ The cytoskeleton serves a framework for positioning and
➢ They have sedimentation coefficients in keeping with moving organelles and macromolecules within the cell.
their small size. ➢ It may do the same for ribosomes and enzymes.
➢ Sedimentation coefficients – a measure of how rapidly a ➢ Even some of the water within the cell (20–40%) may be
particle sediments in an ultracentrifuge, expressed in bound to microfilaments and microtubules.
Svedberg units (S). ➢ There are three structural elements of the cytoskeleton:
○ Sediments in Ultracentrifuge are the ○ Microtubules
precipitates that are settled down in the lower ○ Microfilaments
part of the tube. ○ Intermediate filaments
➢ Ribosomes have values of 80S (eukaryotes) or 70S (Cytoskeleton) Microtubules
(bacteria and archaea)
➢ Microtubules are the largest structural elements of the
Ribosome Subunits cytoskeleton.
➢ Ribosomes have two subunits, the large and small ➢ The axoneme of cilia and flagella is a microtubule-
subunits, with sedimentation coefficients of 60S and 40S, based structure.
respectively. ➢ Microtubules also form the mitotic spindle fibers that
○ If it is smaller, then it is faster. separate chromosomes prior to cell division.
➢ Bacteria and archaea have large and small subunits of ➢ Microtubules play a role in the organization of the
50S and 30S, respectively. cytoplasm:
➢ The S values of large and small subunits does not add up ○ Overall shape of the cell, distribution of
to the value for the complete ribosome, because S organelles
values depend on both size and shape. ○ Movement of macromolecules and other
○ They are completely different. substances within the cell
Ribosome are Numerous and Ubiquitous ○ Distribution of microfilaments and intermediate
filaments
➢ Ribosomes are much more numerous than most other
➢ Structure:
cellular structure (prokaryotic cells contain thousands,
○ Microtubules are cylinders of longitudinal
eukaryotic cells may contain millions).
arrays of protofilaments with a hollow center
➢ Ribosomes in mitochondria and chloroplasts are similar called a lumen.
size and composition to those of bacteria. ○ Each protofilament is a linear polymer of
➢ This is particularly true of the nucleotide sequences of tubulin with inherent polarity.
their rRNAs. ○ Tubulin is a dimeric protein consisting of alpha-
CYTOPLASM tubulin and beta-tubulin.
➢ The cytoplasm of a eukaryotic cell is the interior of the
cell not occupied by the nucleus.
○ Anything that surrounds the nucleus.
➢ The cytosol is the semifluid substance in which the
organelles are suspended.
○ The liquid where the organelles floats.
○ Located in the cytoplasm.
➢ The synthesis of fats and proteins and the initial steps in
releasing energy from sugars takes place in the cytosol.
➢ The cytosol is permeated by the cytoskeleton.
○ Cytoskeleton provides an internal framework
and structure of the cell – scaffoldings.

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(a) A microtubule. A diagram of a microtubule, showing 13 (b) A microfilament. A diagram of a microfilament, showing a
protofilaments forming a hollow cylinder. Each protofilament is a strand of F-actin twisted into a helical structure. The F-actin
polymer of tubulin dimers. All tubulin dimers are oriented in the polymer consists of monomers of G-actin, all oriented in the same
same direction, giving polarity to the protofilament and hence to direction to give the microfilament its inherent polarity.
the entire microtubule. (Cytoskeleton) Intermediate Filaments
(Cytoskeleton) Microfilaments ➢ Intermediate filaments are larger in diameter than
➢ Microfilaments are the smallest components of the microfilaments but smaller than microtubules.
cytoskeleton. ➢ They are the most stable and least soluble components
➢ They can form connections with the plasma membrane of the cytoskeleton.
to affect movement. ➢ They may have a tension-bearing role in some cells
➢ They produce the cleavage furrow in cell division. because they are found in areas subject to mechanical
➢ They contribute to cell shape. stress.
➢ Structure:
○ Intermediate filaments differ in protein
composition from tissue to tissue.
○ There are six classes of intermediate filaments,
➢ Structure: and animal cells from different tissues can be
○ Microfilaments are polymers of the protein distinguished on the basis of the types of
actin. intermediate filaments they contain.
○ Actin is synthesized as a monomer called G- ○ This is referred to as intermediate filament
actin (globular). typing.
○ These subunits are polymerized into F-actin ➢ Common features of intermediate filament proteins:
(filamentous), with a helical appearance. ○ Though heterogeneous in size and chemical
○ Microfilaments have polarity. properties, intermediate filament proteins are
similar in that they all have a central rodlike
segment.
○ They differ in N-terminal and C-terminal
segments.
○ Protofilaments are tetramers that interact with
one another to form an intermediate filament.

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➢ In vertebrates, collagen is the most abundant protein in

the animal body, as it is also found in tendons, cartilage,
and bone.
➢ Processes regulated by the ECM may include:
○ Cell motility and migration
○ Cell division
○ Cell recognition and adhesion
○ Cell differentiation during embryonic
development
The Plant Cell Wall
➢ The wall laid down during cell division is the primary cell
wall, which consists mainly of cellulose fibrils embedded
in a polysaccharide matrix.
➢ It is flexible and extensible to allow for increases in cell
size.
➢ Once the cell reaches its final size and shape, the rigid
secondary cell wall forms by deposition of additional
cellulose and lignin on the inner surface of the primary
cell wall.
Cell Communication
➢ Plant cells are connected to neighboring cells by
cytoplasmic bridges called plasmodesmata, which pass
through the cell wall.
➢ Plasmodesmata are large enough to allow for passage
(c) An intermediate filament. A diagram of an intermediate of water and small solutes from cell to cell.
filament. The structural unit is the tetrameric protofilament, ➢ Animal cells also communicate with one another
consisting of two pairs of coiled polypeptides. Protofilaments through intercellular connections called gap junctions.
assemble by end-to-end and side-to-side alignment, forming an ➢ Tight junctions and adhesion junctions also connect
intermediate filament that is thought to be eight protofilaments animal cells.
thick at any point.
GUIDE QUESTIONS
5. T or F. Ribosomes are organelles enclosed in the
membrane. F
6. What are the three structural elements of the
cytoskeleton? Microtubules, microfilaments,
intermediate filaments
7. ^
8. ^
EXTRACELLULAR MATRIX & CELL WALL
➢ Most cells are characterized by extracellular structures.
➢ For many animal cells, these structures are called the
extracellular matrix (ECM) and consist mainly of
collagen fibers and proteoglycans.
➢ For plant and fungal cells, these are cell walls, consisting
mainly of cellulose microfibrils.
Bacterial Cell Walls
➢ Bacterial cell walls are composed of peptidoglycans,
long chains of GlcNAc and MurNAc.
➢ These are held together by peptide bonds between a
small number of amino acids, forming a netlike structure.
➢ There are additional substances specific to cell walls of
major groups of bacteria.
Motility & the ECM
➢ Plant cells are nonmotile and thus suited to the rigidity
that cell walls confer on an organism. VIRUSES, VIROIDS, AND PRIONS: AGENTS THAT INVADE CELLS
➢ Animal cells are motile and therefore are surrounded by ➢ There are several types of agents that invade cells,
a strong but elastic network of collagen fibers. disrupt cell function, and even kill the host cell.
➢ Bacteria and archaea may be motile or not; their cell ➢ These include the viruses and the less understood viroids
walls provide protection from bursting due to osmotic and prions.
differences between the cell and the surrounding Virus
environment.
➢ A virus consists of a DNA or RNA core surrounded by a
The ECM protein coat.
➢ The primary function of the ECM is support, but the types ➢ Viruses are noncellular parasitic particles incapable of a
of materials and patterns in which they are deposited free-living existence.
regulate a variety of processes. ➢ They have no cytoplasm, organelles, or ribosomes, and
➢ In animal cells, a network of proteoglycans surrounds the consist of only a few different molecules of nucleic acid
collagen fibers. and protein.

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➢ They invade and infect cells, using the synthetic Prions

machinery to produce more virus particles. ➢ Prions are proteinaceous infective particles that are
➢ Viruses are responsible for many diseases in humans, responsible for neurological diseases like scrapie, kuru,
animals, and plants. and mad cow disease.
➢ They are also important as research tools for cell and ○ Scrapie in sheep and goats causes infected
molecular biologists. animals to rub against trees, scraping off their
➢ They are typically named after the disease they cause. wool in the process.
➢ Viruses that infect bacteria are bacteriophages or ○ Kuru is a progressive, degenerative disease of
phages. the CNS in humans.
➢ Structure: ○ Mad cow disease affects cattle.
○ Viruses are small; the smallest are about the ➢ Prions are abnormally folded versions of normal cellular
size of a ribosome, while the largest are about proteins.
one quarter the size of a bacterial cell. ➢ Prions cannot be destroyed by cooking or boiling.
○ Each virus has a characteristic shape, defined ➢ In regions where the prion disease, chronic wasting
by its protein capsid. disease, is found in deer and elk, hunters must have
○ Viruses are chemically quite simple, consisting meat tested for the prion before eating it.
of a coat (capsid) of protein surrounding a
GUIDE QUESTIONS
core, containing DNA or RNA, depending on 9. T or F. Viruses have no cytoplasm, organelles, or
the type of virus.
ribosomes. T
○ Some viral capsids consist of a single type of
10. What are known as the smallest infectious agents?
protein, while more complex viruses have
Viroids
capsids with a number of different proteins.
○ Some viruses are surrounded by a membrane
and are called enveloped viruses; HIV (Human
immunodeficiency virus) is an example.

➢ Are viruses living?

○ Living things have the fundamental properties
of:
■ Metabolism (cellular reactions, in
pathways)
■ Irritability (ability to perceive and
respond to external stimuli)
■ Ability to reproduce
○ Viruses do not satisfy the first two, and though
they reproduce, they can only do so via the
machinery of a living cell.
Viroids
➢ Viroids, found in some plant cells, are even simpler than
viruses.
➢ They are small, circular RNA molecules, and the smallest
known infectious agents.
➢ Viroids cause several diseases of crop plants, such as
cadang-cadang disease in coconut palms.
➢ Viroids don’t exist freely and are transmitted when the
surfaces of adjacent plant cells are damaged.

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MAY 13, 2024 - ZOOM FOUR LEVELS OF BIOMOLECULES

PART 1 BIOCHEMISTRY OF CELLS
BIOMOLECULES
➢ All living organisms require several compounds to
continue to live.
➢ We call these compounds biomolecules. All of these
biomolecules are organic, which means that they
contain carbon.
○ Carbon has 4 valence electrons, which means
this element forms strong covalent bonds with
many other elements.
○ Mas humahaba yung elements and they can
form big biomolecules.

MONOMERS OF BIOMOLECULES

➢ Level 1: Monomeric units

○ most basic and smallest.
○ nucleotides, amino acids, sugars
○ form bonds to create bigger molecules.
➢ Level 2: Macromolecules
○ DNA, protein, cellulose
➢ Level 3: Supramolecular complexes
○ chromosome, plasma membrane, cell wall
○ where macromolecules are found.
○ will eventually form the cell and its organelles.
➢ Level 4: The cell and its organelles

BIOMOLECULES (CONT'D)
➢ Biomolecules are formed by joining many small units
➢ All of our biomolecules are classified into 4 groups:
(monomeric units) together to form a long chain.
○ carbohydrates
➢ This process is called synthesis. Often, a water molecule
○ lipids
is removed in the process.
○ proteins
○ nucleic acids ○ When this happens, we call it dehydration
synthesis (tinatanggal yung water molecule so
➢ Each of these classes have different structures and
that the small units will be joined together).
functions.
➢ They are composed of carbon and they can form bonds
HYDROLYSIS
that can make the structure bigger.
➢ Reverse process of dehydration synthesis.
➢ In dehydration synthesis, water is lost to create a bigger
molecule.
➢ In hydrolysis, water is ADDED, and a bigger molecule is
broken down into smaller pieces.
○ Hydrolysis = hydro (water) and lysis (break
down).

BREAKING DOWN POLYMERS

➢ Hydrolysis breaks a covalent bond by adding OH and H
from a water molecule (H2O).

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DEHYDRATION VS. HYDROLYSIS

AMINO ACIDS
➢ Dehydration synthesis: removal of water to form a ➢ Every amino acid has the same basic structure.
covalent bond. ➢ Each has a unique side chain, called an R group.
➢ Hydrolysis: addition of water to break a covalent bond. ➢ All amino acids except glycine have an asymmetric α
carbon atom.
BIOMOLECULES (CONT’D) ➢ The specific properties of amino acids depend on the
➢ The smallest functioning unit of a biomolecule is a nature of their R groups.
monomer. ➢ Usually, an amino acid has a carboxyl group, amino
○ “Mono” = one. group, and R group.
➢ Put two monomers together and you get a dimer. ➢ Its plane of symmetry can either be L or D.
○ “Di” = two. ○ If the R group is on the right side, then the
➢ Once several monomers are put together, we get a amino group is on the left side (L).
polymer. ○ If the R group is on the left side, then the amino
○ “Poly” = many. group is on the right side (D).

PROTEINS
➢ Proteins are extremely important macromolecules in all
organisms, occurring nearly everywhere in the cell.
➢ Proteins fall into nine different classes.

CLASSES OF PROTEINS

Classes of Proteins Function

Enzymes function as catalysts,

increasing the rates of
chemical reactions (breaks
down).

Structural proteins physical support (rigidity) and

shape

Motility proteins contraction and movement

Regulatory proteins control and coordinate cell

function

Transport proteins move substances in and out

of cells

Hormonal proteins communication between

cells

Receptor proteins enable cells to respond to

chemical stimuli from the
environment.

Defensive proteins protect against disease.

Storage proteins reservoirs of amino acids

THE MONOMERS ARE AMINO ACIDS
➢ Only 20 kinds of amino acids are used in protein
synthesis.
➢ Some contain additional amino acids, usually the result
of modification.
➢ No two different proteins have the same amino acid
sequence.

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DIFFERENT AMINO ACID GROUPS BASED ON HYDROPHOBICITY

➢ Group A: Nonpolar Amino Acids (Hydrophobic) THE POLYMERS ARE POLYPEPTIDES AND PROTEINS
○ glycine (gly) ➢ Amino Acids are linked together stepwise into a linear
○ alanine (ala) polymer by dehydration (or condensation) reactions.
○ valine (val) ➢ As the three atoms comprising H2O are removed, a
○ leucine (leu) covalent C-N bond (a peptide bond) is formed.
○ isoleucine (ile) ➢ Amino acids form peptide bonds when linked together.
○ methionine (met)
○ phenylalanine (phe) DIRECTIONALITY OF POLYPEPTIDES
○ tryptophan (trp)
○ proline (pro) ➢ Because of the way peptide bonds are formed,
➢ Group B: Polar, Uncharged Amino Acids (Hydrophilic) polypeptides have a directionality.
○ serine (ser) ➢ The end with the amino group is called the N-terminus or
○ threonine (thr) amino terminus.
○ cysteine (cys) ➢ The end with the carboxyl group is called the C-terminus
○ tyrosine (tyr) or carboxyl terminus.
○ asparagine (asn) ➢ Peptide bonds form between the C and N terminus.
○ glutamine (gln)
➢ Group C: Polar, Charged Amino Acids (Hydrophilic)
○ aspartate (asp)
○ glutamate (glu)
○ lysine (lys)
○ arginine (arg)
○ histidine (his)

CLASSES OF R GROUPS
➢ Nine amino acids have nonpolar, hydrophobic R groups.
➢ The remaining eleven amino acids are hydrophilic, with
R groups that are either polar, or charged at cellular pH.
➢ Acidic amino acids are negatively charged, whereas
basic amino acids are positively charged.
➢ Polar amino acids tend to be found on the surface of
proteins (can bind).

➢ C terminus of glycine + N terminus of alanine =

glycylalanine.

PROTEINS AND POLYPEPTIDES

➢ The process of elongating a chain of amino acids is
called protein synthesis.
➢ However, the immediate product of amino acid
polymerization is a polypeptide.
➢ A polypeptide does not become a protein until it has
assumed a unique, stable three-dimensional shape and
is biologically active.

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MONOMERIC AND MULTIMERIC PROTEINS ➢ Hydrogen bond acceptors (e.g., carbonyl or sulfhydryl
➢ Proteins that consist of a single polypeptide are groups) have an electronegative atom that attracts the
monomeric proteins, whereas multimeric proteins donor hydrogen.
consist of two or more polypeptides. ➢ Donors and acceptors are complementary to each
➢ Proteins consisting of two or three polypeptides are other.
called dimers or trimers, respectively.
➢ Hemoglobin is a tetramer, consisting of two αlpha IONIC BONDS
subunits and two β subunits. ➢ Ionic bonds, or electrostatic interactions, form between
positively and negatively charged R groups.
➢ They exert attractive forces over longer distances than
some of the other noncovalent interactions.
➢ Because they depend on the charge on the R groups,
changes in pH can disrupt ionic bonds.

VAN DER WAALS INTERACTIONS

➢ Molecules with nonpolar covalent bonds may have
transient positively and negatively charged regions.
➢ These are called dipoles and two molecules with these
will be attracted to one another if they are close enough
together.
➢ This transient is called a Van der Waals interaction or
force.

HYDROPHOBIC INTERACTIONS
➢ A hydrophobic interaction is the tendency of
hydrophobic molecules or parts of molecules to be
excluded from interactions with water.
picture of hemoglobin
➢ Amino acids with hydrophobic side chains tend to be
found within proteins.
SEVERAL KINDS OF BONDS AND INTERACTIONS ARE IMPORTANT IN
➢ Protein folding is a balance between the tendency of
PROTEIN FOLDING AND STABILITY
hydrophilic groups to interact with water and of
➢ Both covalent bonds and noncovalent interactions are
hydrophobic groups to avoid interaction with water.
needed for a protein to adopt its proper shape or
conformation.
DIFFERENT BONDS
➢ These same bonds and interactions are required for
polypeptides to form multimeric proteins.
➢ The interactions involve carboxyl, amino, and R groups
of the amino acids, called amino acid residues once
incorporated into a polypeptide.

DISULFIDE BONDS
➢ Covalent disulfide bonds form between the sulfur atoms
of two cysteine residues.
➢ They form through the removal of two hydrogen ions
(oxidation) and can only be broken by the addition of
two hydrogens (reduction).
➢ Once formed, disulfide bonds confer considerable
stability to the protein conformation.

CATEGORIES OF DISULFIDE BONDS

➢ Intramolecular disulfide bonds: form between cysteines
in the same polypeptide.
➢ Intermolecular disulfide bonds: form between cysteines
in two different polypeptides.
➢ They link the two polypeptides together.
PROTEIN STRUCTURE DEPENDS ON AMINO ACID SEQUENCE AND
NONCOVALENT BONDS AND INTERACTIONS INTERACTIONS
➢ These include the hydrogen and ionic bonds, van der ➢ The overall shape and structure of a protein are
Waals, and hydrophobic interactions. described in terms of four levels of organization.
➢ These are individually weaker than covalent bonds but ○ Primary structure: amino acid sequence
collectively can strongly influence protein structure and (linear)
stability. ○ Secondary structure: local folding of
HYDROGEN BONDS polypeptides (beta pleated sheets)
➢ Hydrogen bonds form in water and between amino ○ Tertiary structure: three-dimensional
acids in a polypeptide chain via their R groups. conformation (subunits)
○ Quaternary structure: interactions between
➢ Hydrogen bond donors (e.g., hydroxyl or amino groups)
monomeric proteins to form a multimeric unit
have hydrogen atoms covalently linked to more
(interaction of two or more subunits = more
electronegative atoms.
stable).

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THE α HELIX
➢ The α helix is spiral in shape, consisting of the
peptide backbone, with R groups jutting out from
the spiral
➢ There are 3.6 amino acids per turn of the helix
➢ A hydrogen bond forms between the NH group of
one amino acid and the CO group of a second
amino acid that is one turn away from the first.

PRIMARY STRUCTURE
➢ Primary structure is the formal designation of the amino
acid sequence.
➢ By convention, amino acid sequences are written from
the N-terminus to the C-terminus, the direction in which
the polypeptide was synthesized.
➢ The first protein to have its amino acid sequence
determined was the hormone insulin.
➢ Insulin consists of one alpha and one beta subunit with
THE β SHEET
21 and 30 amino acids, respectively.
➢ The β sheet is an extended sheetlike conformation
with successive atoms of the polypeptide chain
located at “peaks” or “troughs”
➢ The R groups jut out on alternating sides of the
sheet
➢ Because of the formation of peaks and troughs, it
is sometimes referred to as a β-pleated sheet
DETERMINING AMINO ACID SEQUENCE ➢ The β sheet, like the α helix, is characterized by a
➢ Sanger obtained the Nobel Prize for his work on the maximum of hydrogen bonding, but β sheet
insulin protein sequence. formation may involve different polypeptides or
➢ He cleaved the protein into smaller fragments and different regions of a single polypeptide
analyzed the amino acid order within individual ➢ If the parts of polypeptides forming the β sheet
overlapping fragments. have the same polarity (relative to the N- and C-
➢ Sanger’s work paved the way for the sequencing of termini) they are called parallel
hundreds of other proteins, and for advancements in the
methods used for sequencing proteins. ➢ If the parts of polypeptides forming the β sheet
have opposite polarity they are called antiparallel
THE IMPORTANCE OF PRIMARY STRUCTURE
➢ Primary structure is important genetically because the
sequence is specified by the order of nucleotides in the
corresponding messenger RNA.
➢ It is important structurally because the order and identity
of amino acids directs the formation of the higher-order
(secondary and tertiary) structures.

SECONDARY STRUCTURE
➢ The secondary structure of a protein describes local
regions of structure that result from hydrogen bonding
between NH and CO groups along the polypeptide
backbone
➢ These result in two major patterns, the α helix and the
β sheet

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TERTIARY STRUCTURE
➢ The tertiary structure reflects the unique aspect of
the amino acid sequence because it depends on
interactions of the R groups
➢ Tertiary structure is neither repetitive nor easy to
predict
AMINO ACID SEQUENCE AND SECONDARY STRUCTURE
➢ It results from the sum of the hydrophobic residues
➢ Certain amino acids (e.g., leucine, methionine,
avoiding water, hydrophilic residues interacting
glutamate) tend to form α helices whereas others
with water, the repulsion of similarly charged
(e.g., isoleucine, valine, phenylalanine) tend to
residues, and attraction between oppositely
form β sheets
charged residues
➢ Proline cannot form hydrogen bonds and tends to
disrupt α helix structures by introducing a bend in NATIVE CONFORMATION
the helix
➢ The most stable possible three-dimensional
MOTIFS structure of a particular polypeptide is called the
native conformation
➢ Certain combinations of the α helices and β sheets
➢ Proteins can be divided into two broad categories
have been identified in many proteins
○ Fibrous proteins
➢ These units of secondary structure consist of short ○ Globular proteins
stretches of α helices and β sheets and are called
motifs FIBROUS PROTEINS
➢ Examples include the β-α-β, the hairpin loop, and
➢ Fibrous proteins have extensive regions of
the helix-turn-helix motifs
secondary structure, giving them a highly ordered
repetitive structure
➢ Some examples include:
○ fibroin proteins of silk
○ keratin proteins of hair and wool
○ collagen found in tendons and skin
○ elastin found in ligaments and blood
vessels

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MANY GLOBULAR PROTEINS HAVE DOMAINS

➢ A domain is a discrete locally folded unit of tertiary
structure, usually with a specific function
➢ A domain is typically 50-350 amino acids long,
with regions of α helices and β sheets packed
GLOBULAR PROTEINS together
➢ Most proteins are globular proteins, that are ➢ Proteins with similar functions often share a
folded into compact structures common domain
➢ Each type of globular protein has its own unique ➢ Proteins with multiple functions usually have a
tertiary structure separate domain for each function, like modular
➢ Globular proteins may be mainly α helical, mainly units from which globular proteins are constructed
β sheet, or a mixture of both

PREDICTION OF TERTIARY STRUCTURE

➢ It is known that primary structure determines the
final folded shape of a protein
➢ However, we are still not able to predict exactly
how a given protein will fold, especially for larger
proteins

QUATERNARY STRUCTURE
➢ The quaternary structure of a protein is the level of
organization concerned with subunit interactions
and assembly
➢ Therefore, the term applies specifically to
multimeric proteins
➢ Some proteins consist of multiple identical
subunits; others, like hemoglobin, contain two or
more types of polypeptides

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MAINTENANCE OF THE QUATERNARY STRUCTURE THE STRUCTURE OF GLUCOSE

➢ The bonds and forces maintaining quaternary ➢ D-glucose is the most stable form of glucose
structure are the same as those responsible for though many other stereoisomers are possible
tertiary structure ➢ D-glucose is often depicted as a linear molecule,
➢ The process of subunit formation is usually, but not as in the Fischer projection, in which the H and OH
always, spontaneous groups intended to project out of the plant of the
➢ Sometimes, molecular chaperones are required diagram
to assist the process ➢ In the cell, D-glucose exists in a dynamic
equilibrium between the linear and ring form
HIGHER LEVELS OF ASSEMBLY ➢ The Haworth projection shows the ring form of the
➢ A higher level of assembly is possible in the case of molecule
proteins (often enzymes) that are organized into
multiprotein complexes
➢ Each protein in the complex may be involved
sequentially in a common multistep process
➢ One example is the pyruvate dehydrogenase
complex, in which three enzymes and five other
proteins form a multienzyme complex

GUIDE QUESTIONS
➢ 1. Amino acids are bound together by ___ bonds.
Peptide
➢ 2-5. What are the 4 levels of organizations of
proteins? Primary, Secondary, Tertiary, Quaternary

POLYSACCHARIDES
➢ Polysaccharides are long chain polymers of sugar
derivatives that are not informational molecules
➢ They usually consist of a single kind of repeating
unit, or sometimes an alternating pattern of two TWO RING FORMS OF D-GLUCOSE
kinds ➢ The formation of a ring by D-glucose can result in
➢ Short polymers, oligosaccharides, are sometimes two alternative forms
attached to cell surface proteins
➢ These depend on the spatial orientation of the
hydroxyl group on carbon number 1
THE MONOMERS ARE MONOSACCHARIDES
➢ These forms are designated α (hydroxyl group
➢ Repeating units of polysaccharides are
downward) and β (hydroxyl group upward)
monosaccharides
➢ A sugar may be an aldehyde, aldosugars with a
terminal carbonyl group, or ketone, ketosugars
with an internal carbonyl group
➢ Sugars within these groups are named generically
based on how many carbon atoms they contain

CLASSIFICATION OF SUGARS
➢ Most sugars have between 3 and 7 carbons and
are classified as
○ trioses (3 carbons)
○ tetroses (4 carbons)
○ pentoses (5 carbons)
○ hexoses (6 carbons)
○ heptoses (7 carbons)

GLUCOSE
➢ The single most common monosaccharide is the
aldohexose D-glucose (C6H12O6)
➢ The formula CnH2nOn is common for sugars and led GLUCOSE ALSO EXISTS AS DISACCHARIDES
to the general term carbohydrate
➢ Glucose exists as disaccharides, in which two
➢ For every molecule of CO2 incorporated into a
monosaccharide units are covalently linked
sugar, one water molecule is consumed
➢ Common disaccharides include:
➢ The carbons of glucose (and other organic
○ maltose, two glucose units
molecules) are numbered from the more oxidized,
○ lactose, one glucose linked to one
carbonyl, end
galactose

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○ sucrose, one glucose linked to one

fructose

DISACCHARIDES
➢ The linkage of disaccharides is a glycosidic bond,
formed between two monosaccharides by the
elimination of water
➢ Glycosidic bonds involving the α form of glucose
are called α glycosidic bonds (e.g., maltose);
those involving the β form are called β glycosidic
bonds (e.g., lactose)

THE POLYMERS ARE STORAGE AND STRUCTURAL

POLYSACCHARIDES
➢ The most familiar storage polysaccharides are
starch in plant cells and glycogen in animal cells STARCH
and bacteria ➢ Starch is the glucose reserve commonly found in
➢ Both consist of α-D-glucose units linked by α- plant tissue
glycosidic bonds, involving carbons 1 and 4 (1→4) ➢ It occurs both as unbranched amylose (10-30%)
➢ Occasionally α(1→6) bonds may form, allowing for and branched amylopectin (70-90%)
the formation of side chains (branching) ➢ Amylopectin has α(1→6) branches once every 12-
25 glucose units, and longer side chains than
GLYCOGEN
glycogen
➢ Glycogen is highly branched, the branches
➢ Starch is stored as starch grains within the plastids
occurring every 8-10 glucose units along the ○ Chloroplasts, the sites of carbon fixation
backbone and sugar synthesis in photosynthesis
➢ Glycogen is stored mainly in the liver (as a source ○ Amyloplasts, which are specialized for
of glucose) and muscle tissues (as a fuel source starch storage
for muscle contraction) of animals
➢ Bacteria also store glycogen as a glucose reserve

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STRUCTURAL POLYSACCHARIDES
➢ The best-known structural polysaccharide is the
cellulose found in plant cell walls
➢ Cellulose, composed of repeating monomers of β-
D-glucose, is very abundant in plants
➢ Mammals cannot digest cellulose (some have
microorganisms in their digestive systems that can)

CHITIN
➢ The polysaccharide chitin consists of GlcNAc units
only, joined by β(1→4) bonds
➢ Chitin is found in insect cytoskeletons, crustacean
shells, and fungal cell walls

OTHER STRUCTURAL POLYSACCHARIDES

➢ The cellulose of fungal cell walls differs from that of
plants, and may contain either β(1→4) or β(1→3)
linkages
➢ Bacterial cell walls contain two kinds of sugars
GlcNAc (N-acetylglucosamine) and MurNAc (N-
acetylmuramic acid)
➢ Both are derivatives of β-glucosamine, and are
linked alternately in cell walls
POLYSACCHARIDE STRUCTURE DEPENDS ON THE TYPE OF
GLYCOSIDIC BONDS INVOLVED
➢ α- and β-glycosidic bonds are associated with
marked structural differences
➢ Starch and glycogen (α polysaccharides) form
loose helices that are not highly ordered due to
the side chains
➢ Cellulose (that forms β linkages) exists as rigid
linear rods that aggregate into microfibrils, about
5-20 nm in diameter

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➢ Plant and fungal cells walls contain these rigid

microfibrils in a noncellulose matrix containing
other polymers (hemicellulose, pectin) and a
protein called extensin.

GUIDE QUESTIONS
➢ 6. ____ formed between two monosaccharides by the
elimination of water. Glycosidic bonds
➢ 7. T or F. The most familiar storage polysaccharides
are glycogen in plant cells and starch in animal cells
and bacteria. F
➢ 8-10. Examples of common disaccharides. Maltose,
lactose, sucrose

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MAY 16, 2024 - FACE-TO-FACE ○ Other small interfering RNAs (siRNAs) come
from exogenous sources, such as viruses, and
NUCLEIC ACIDS can inhibit transcription or translation
INTRODUCTION
➢ Nucleic acids are of paramount importance to the
THE MONOMERS ARE NUCLEOTIDES
cells because they store, transmit, and express genetic
➢ RNA and DNA each consist of only four different types
information
of nucleotides, the monomeric units
➢ They are linear polymers of nucleotides
➢ Each nucleotide consists of a five-carbon sugar, to
➢ DNA is deoxyribonucleic acid; RNA is ribonucleic acid
which a phosphate group and N-containing aromatic
base are attached
DIFFERENCES BETWEEN DNA AND RNA
➢ Each base is either a purine or a pyrimidine
➢ DNA and RNA differ chemically and in their cellular role
○ RNA contains the 5-carbon sugar ribose, and
DNA contains the related sugar, deoxyribose
○ DNA serves as the repository of genetic
information, whereas RNA plays several roles
in expressing that information

DNA RNA

Nucleus only Nucleus and cytoplasm

(ribosome)

Double Stranded Single Stranded

ATCG AUCG

Deoxyribose Sugar Ribose sugar

1 type only 3 main types

● mRNA - messenger
● tRNA - transfer
● rRNA - ribosomal TYPES OF NUCLEOTIDES

RNA AND POLYPEPTIDE SYNTHESIS PURINES PYRIMIDINES

➢ DNA resides mainly in the nucleus
➢ The nucleus is the major site of RNA synthesis adenine (A) DNA: thymine (T)
1. TRANSCRIPTION: a segment of DNA known as RNA: uracil (U)
a gene directs the synthesis of a
complementary molecule of messenger RNA guanosine (G) cytosine (C)
(mRNA)
➢ NUCLEOSIDE: the sugar-base portion without the
2. mRNA EXPORT: after processing, the mRNA
phosphate group
exits the nucleus through tiny nuclear pores
➢ Translation (polypeptide synthesis) takes place in the
NOMENCLATURE
cytoplasm
3. TRANSLATION: a ribosome, a complex of ➢ Nucleosides with one phosphate group can be thought
ribosomal RNA (rRNA) and proteins, attaches of as nucleoside monophosphates (example:
to the mRNA to read the coded information, adenosine monophosphate, AMP)
whereas transfer RNA (tRNA) molecules bring ➢ Adenosine diphosphate (ADP) has two phosphate
the correct amino acids to add to the groups and adenosine triphosphate (ATP) has three
polypeptide chain

OTHER TYPES OF RNA

➢ Several new types of RNA have been recently
discovered
○ Most (or all) eukaryotic cells contain a variety
of smallRNAs (20-30 nucleotides long) that
function as regulatory molecules
○ Micro RNAs (miRNAs), small, endogenous
RNAs, down-regulate expression of specific
genes

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THE BASES, NUCLEOSIDES, AND NUCLEOTIDES OF RNA AND DNA COMPLEMENTARY BASE PAIRING
➢ Complementary base pairing allows A to form two
hydrogen bonds with T and G to form three hydrogen
bonds with C
➢ This base pairing is a fundamental property of nucleic
acids

THE POLYMERS ARE DNA AND RNA

➢ Nucleic acids are linear polymers of nucleotides linked
by a 3'-5' phosphodiester bridge, a phosphate group
linked to two adjacent nucleotides via two
phosphodiester bonds
➢ The polynucleotide formed by this process has a
directionality with a 5' phosphate group at one end
and a 3' hydroxyl group at the other
➢ Nucleotide sequences are conventionally written in the
5' to 3' direction

THE DNA MOLECULE IS A DOUBLE-STRANDED HELIX

➢ Francis Crick and James Watson postulated the double
helix structure of DNA in 1953
➢ The structure accounted for the known physical and
chemical properties of DNA
➢ It also suggested a mechanism for DNA replication
➢ The double helix consists of two anti-parallel and
complementary strands of DNA twisted around a
common axis to form a right-handed spiral
structure(B-DNA, the main form in cells)

NUCLEIC ACID SYNTHESIS

➢ A preexisting molecule is used to ensure that new
nucleotides (NTPs for RNA, dNTPs for DNA) are added in
the correct order
➢ This molecule is called a template and correct base
pairing between the template and the incoming
nucleotide is required to specify correct order
➢ A complementary relationship exists between certain
purines and pyrimidines

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BASE PAIRING AND RNA

➢ RNA is normally single stranded
➢ RNA structure also depends on base pairing
➢ However, the pairing is usually between bases in
different areas of the same molecule and is less
extensive than that of DNA

LIPIDS
➢ Lipids are not formed by the same type of linear
polymerization as proteins, nucleic acids, and
polysaccharides
➢ However, they are regarded as macromolecules
because of their high molecular weight and their
importance in cellular structures, particularly
membranes

FEATURES OF LIPIDS
➢ Although heterogeneous, all have a hydrophobic
nature, and thus little affinity for water; they are readily
soluble in nonpolar solvents such as chloroform or ether
➢ They have relatively few polar groups, but some are
amphipathic, having polar and nonpolar regions
➢ Functions include energy storage, membrane structure, TRANS FATS
or specific biological functions such as signal
➢ Trans fats are a type of unsaturated fatty acid with a
transmission
particular type of double bond that causes less of a
bend in the chain
THE MAIN CLASSES OF LIPIDS
➢ They are relatively rare in nature and are produced
➢ The lipids can be divided into six classes based on their artificially in shortening and margarine
structure ➢ They have been linked to increased risk of heart
○ Fatty acids disease and elevated cholesterol levels
○ Triacylglycerols
○ Phospholipids
○ Glycolipids
○ Steroids
○ Terpenes

FATTY ACIDS ARE THE BUILDING BLOCKS OF SEVERAL

CLASSES OF LIPIDS
➢ Fatty acids are components of several other kinds of
lipids
➢ A fatty acid is a long amphipathic, unbranched
hydrocarbon chain with a carboxyl group at one end
➢ The polar carboxyl group is the "head" and the
nonpolar hydrocarbon chain is the "tail"

FATTY ACID STRUCTURE

➢ The hydrocarbon tails are variable in length, but usually
12 to 20 carbons long
➢ Even numbers of carbons are favored because fatty TRIACYLGLYCEROLS ARE STORAGE LIPIDS
acid synthesis occurs via the stepwise addition of ➢ Triacylglycerols, also known as triglycerides, consist of a
two-carbon units to the growing chain glycerol molecule with three fatty acids attached to it
➢ Fatty acids are highly reduced and so yield a large ➢ Glycerol is a three-carbon alcohol with a hydroxyl
amount of energy upon oxidation group on each carbon
➢ In saturated fatty acids, each carbon atom in the chain ➢ Fatty acids are linked to glycerol, one at a time, by
is bonded to the maximum number of hydrogens ester bonds, formed by the removal of water
➢ These have long straight chains that pack together well
➢ Unsaturated fatty acids have one or more double TRIACYGLYCEROL STRUCTURE
bonds, so have bends in the chains and less tight ➢ Monoacylglycerols contain a single fatty acid
packing ➢ Diacylglycerols have two
➢ The three fatty acids on a triacylglycero/ may vary in
length and degree of saturation

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TRIACYLGLYCEROL FUNCTION
➢ The main function of triacylglycerols is energy storage
and some animals store triacylglycerols under the skin
as a protection against cold
➢ Triacylglycerols containing mostly saturated fats are
usually solid or semisolid at room temperature and are
called fats
➢ Triacylglycerols in plants are liquid at room temperature
(e.g., vegetable oil) and are predominantly
unsaturated

PHOSPHOLIPIDS ARE IMPORTANT IN MEMBRANE STRUCTURE

➢ Phospholipids are important to membrane structure
due to their amphipathic nature
➢ Phospholipids can be divided into phosphoglycerides
or sphingolipids, depending on their chemistry

PHOSPHOGLYCERIDES
➢ Phosphoglycerides are the predominant phospholipids
in most membranes
➢ The basic component of phosphoglycerides is
phosphatidic acid, which has two fatty acids and a
phosphate group attached to a glycerol
➢ Membrane phosphoglycerides invariably have a small
hydrophilic alcohol linked to the phosphate by an ester
bond
➢ The alcohol is usually serine, ethanolamine, choline, or
inositol, which contributes to the polar nature of the
phospholipid head group GLYCOLIPIDS ARE SPECIALIZED MEMBRANE COMPONENTS
➢ Typical phosphoglycerides often have one saturated ➢ Glycolipids are lipids containing a carbohydrate
and one unsaturated fatty acid instead of a phospholipid and are often derivatives of
➢ The length and degree of saturation of the fatty acids sphingosine and glycerol (glycosphingolipids)
have profound effects on membrane fluidity ➢ Carbohydrate groups attached to a glycolipid may be
one to six sugar units (D-glucose, D-galactose, or
N-acetyl-D-galactosamine)
➢ Glycolipids occur largely on the outer monolayer of the
plasma membrane

SPHINGOLIPIDS
➢ Sphingolipids are based on the amine sphingosine,
which has a long hydrocarbon chain with a single site
of unsaturation near the polar end
➢ Sphingosine can form an amide bond to a long-chain
fatty acid, resulting in a molecule called a ceramide
➢ A whole family of sphingolipids exists, with different
polar groups attached to the hydroxyl group of the
ceramide STEROIDS ARE LIPIDS WITH A VARIETY OF FUNCTIONS
➢ Sphingolipids are predominantly found in the outer ➢ Steroids are derivatives of a four-ringed hydrocarbon
leaflet of the plasma membrane bilayer, often in lipid skeleton, which distinguishes them from other lipids
rafts, localized domains within a membrane ➢ They are relatively nonpolar and therefore hydrophobic
➢ Lipid rafts are important in communication between a ➢ Steroids differ from one another in the positions of
cell and its external environment double bonds and functional groups
➢ The most common steroid in animal cells is cholesterol

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A VARIETY OF STEROLS OTHER ISOPRENE-BASED COMPOUNDS

➢ Cholesterol is insoluble and found primarily in plasma ➢ The isoprene-based compounds, dolichols, are
membranes of animal cells and most membranes of involved in activating sugar compounds
organelles ➢ Electron carriers such as coenzyme Q and
➢ Similar molecules are found in plant cells (stigmasterol plastoquinone are also isoprene derivatives
and sitosterol), and fungal cells (ergosterol) ➢ Polyisoprenoids, polymers of isoprene, are found in cell
membranes of the Archaea
STEROID HORMONES
➢ Cholesterol
○ the starting material for synthesis of steroid
hormones, including male and female sex
hormones, glucocorticoids, and
mineralocorticoids
➢ Sex hormones
○ estrogens produced by the ovaries of females
(e.g., estradiol)
○ androgens produced by male testes (e.g.,
testosterone)
➢ Glucocorticoids
○ a family of hormones that promote synthesis
of glucose and suppress inflammation
○ e.g., cortisol
➢ Mineralocorticoids
○ regulate ion balance by promoting
reabsorption of sodium, chloride, and
bicarbonate ions by the kidney
○ e.g., aldosterone

GUIDE QUESTIONS
➢ Compare and contrast DNA and RNA.
➢ Give 5 classes of lipids based on their structure.

TERPENES ARE FORMED FROM ISOPRENE

➢ Terpenes are synthesized from the five-carbon
compound isoprene and are sometimes called
isoprenoids
➢ Isoprene and its derivatives are joined in various
combinations to produce substances such as vitamin A
and carotenoid pigments

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MAY 20, 2024 Membranes are SITES of specific proteins and therefore of
SPECIFIC FUNCTIONS.
PART 1: CELL MEMBRANE
➢ Membranes are associated with specific functions
MEMBRANES: THEIR STRUCTURE, FUNCTION, AND CHEMISTRY
because the molecules responsible for these functions
➢ Membranes define the boundaries of a cell and its
are embedded in or localized on membranes.
internal compartments.
➢ The specific enzymes associated with particular
➢ Membranes play multiple roles in the life of a cell.
membranes can be used as markers to identify the
membranes during isolation.

Membrane proteins REGULATE the TRANSPORT of solutes.

➢ Membrane proteins carry out and regulate the
transport of substances across the membrane.
➢ Cells and organelles take up nutrients, ions, gasses,
water, and other substances, as well as expel products
and wastes.
➢ Some substances diffuse directly across membranes,
whereas others must be moved by specific transporters.

Membrane proteins detect and TRANSMIT electrical and

chemical SIGNALS.
➢ A cell receives information from its environment as
electrical or chemical signals at its surface.
➢ Signal Transduction:
○ Mechanisms by which signals are transmitted
from the outer surface to the interior of a cell.
○ The binding of signal molecules to their
receptors triggers chemical events on the
inner membrane surface that ultimately lead
to changes in cell function.
○ Membrane receptors allow cells to recognize,
transmit, and respond to a variety of specific
signals in nearly all cell types.
➢ Chemical signal molecules usually bind to membrane
proteins—i.e., receptors—on the outer surface of the
plasma membrane.
○ Once the receptor receives a signal, a
cascade of processes occurs in the cell based
THE FUNCTIONS OF MEMBRANES on that signal.
➢ Define boundaries of a cell and organelles and act as ○ e.g., Inflammation
permeability barriers ■ When we eat something we’re
➢ Serve as sites for biological functions such as electron allergic to, the receptor detects the
transport foreign object and since allergic
➢ Possess transport proteins that regulate the movement tayo don, magpproduce siya ng
of substances into and out of cells and organelles cascade of signals sa cell that
➢ Contain protein molecules that act as receptors to produces symptoms of inflammation.
detect external signals
Membrane proteins mediate cell adhesion and CELL-TO-CELL
➢ Provide mechanisms for cell-to-cell contact, adhesion,
COMMUNICATION.
and communication (through the aforementioned
protein molecules) ➢ Most cells in multicellular organisms are in contact with
other cells.
Membranes define boundaries and serve as PERMEABILITY ➢ Cell-to-cell contacts—critical in animal
BARRIERS. development—are often mediated by cadherins.
➢ Membranes separate the interior and exterior of cells ➢ Cadherins:
and organelles. ○ Have extracellular amino acid sequences that
➢ They are effective permeability barriers due to their bind calcium and promote adhesion
hydrophobic interior. between similar cell types in a tissue.
➢ The plasma membrane surrounds the whole cell, ○ Membrane proteins responsible for cell
whereas intracellular membranes compartmentalize adhesion and communication.
functions within the cell. ➢ Other types of junctions between cells in animal tissues:
○ Adhesive junctions hold cells together.
○ Tight junctions form seals that block the
passage of fluids between cells.

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○ Gap junctions allow for communication ○ He reasoned that they must orient on water
between adjacent animal cells. with the hydrophobic tails away from the
■ In plants, plasmodesmata perform a water.
similar function.
GORTER & GRENDEL: The basis of membrane structure is a
BILAYER.
➢ 1925: These physiologists extracted lipids from RBCs and
spread the lipids in a monolayer on a water surface.
➢ The film on the water was twice the surface area of the
blood cells.
○ This suggested that lipids on the cell surface
consisted of two layers.
➢ They suggested that the most favorable structure would
be a lipid bilayer, with the nonpolar regions facing
inward.

DAVSON & DANIELLI: Membranes also contain PROTEINS.

➢ Davson and Danielli showed that the bilayer alone
could not account for all membrane properties,
especially:
○ Surface tension
○ Solute permeability
Different functions of cell membrane: ○ Electrical resistance
1. Boundary and permeability barrier ➢ They suggested that proteins are present in membranes
2. Organization and localization of function as thin sheets coating the lipids.
3. Transport processes
4. Signal detection ROBERTSON: All membranes share a COMMON UNDERLYING
5. Cell-to-cell interactions STRUCTURE.
➢ Using electron microscopy, biologists could verify the
GUIDE QUESTIONS (1–5) presence of membranes around cells and organelles.
1. Give at least five functions of the cell membrane. ➢ A trilaminar structure, visible under the TEM, was
- Define boundaries of a cell and organelles and act as observed for all membranes.
permeability barriers ○ This led to the suggestion of a common
- Serve as sites for biological functions such as electron membrane structure—the unit membrane.
transport
- Possess transport proteins that regulate the movement
of substances into and out of cells and organelles
- Contain protein molecules that act as receptors to
detect external signals
- Provide mechanisms for cell-to-cell contact, adhesion,
and communication (through the aforementioned
protein molecules)

MODELS OF MEMBRANE STRUCTURE: AN EXPERIMENTAL

APPROACH
➢ The development of electron microscopy in the 1950s
was important for understanding membrane structure.
➢ The fluid mosaic model is thought to be descriptive of
all biological membranes. Major Shortcomings of the Davson-Danielli Model
➢ The model envisions a membrane as:
➢ Electron microscopy revealed that there was not
○ Two fluid lipid layers; with
enough space to either side of the bilayer for an
○ Proteins within and on the layers.
additional layer of protein.
OVERTON & LANGMUIR: LIPIDS are important membrane ➢ The Davson-Danielli model also did not account for the
components. chemical distinctiveness of particular types of
membranes, especially the protein/lipid ratio.
➢ 1890s: Overton observed the easy penetration of
○ Different membrane types have differing
lipid-soluble substances into cells.
protein/lipid ratios.
○ He concluded that the cell surface had some
kind of lipid “coat” on it.
➢ Langmuir studied phospholipids and found that they
were amphipathic (i.e., has polarity).

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➢ Membranes are susceptible to digestion by

phospholipases.
○ This suggested that membrane lipids are
exposed and not covered by a protein layer.
➢ Scientists were unable to isolate “surface” proteins from
membranes unless organic solvents or detergents were
used.
(b) An integral membrane protein with multiple α-helical
○ This suggested that there were no proteins on
transmembrane segments. Many integral membrane proteins of
top of the lipid bilayer.
the plasma membrane have carbohydrate side chains attached
SINGER & NICHOLSON: A membrane consists of a MOSAIC OF to the hydrophilic segments on the outer membrane surface.
PROTEINS in a fluid lipid bilayer.
THE FLUID NATURE OF THE BILAYER
➢ The fluid mosaic bilayer model accounts for all the
➢ Lipids in the bilayer are in constant motion.
inconsistencies with previous models.
➢ Proteins are also able to move laterally within the
➢ The model has two key features:
membrane, though some are anchored to internal
○ A fluid lipid bilayer,
structural elements.
○ A mosaic of proteins attached to or
➢ Anchored proteins have restricted mobility.
embedded in the bilayer.
UNWIN & HENDERSON: Most membrane proteins contain
TRANSMEMBRANE proteins.
➢ Most integral membrane proteins have one or more
hydrophobic segments that span the lipid bilayer.
➢ These transmembrane segments anchor the protein to
the membrane.
➢ Bacteriorhodopsin was the first membrane protein
shown to possess this structural feature.

Recent findings further refine our understanding of membrane

structure.
➢ Membranes are:
○ Not homogeneous, but freely mixing;
○ Ordered through dynamic microdomains
(a) Singer and Nicholson's fluid mosaic model envisions the called lipid rafts.
membrane as a fluid bilayer of lipids with a mosaic of associated ➢ Most cellular processes that involve membranes
proteins. Integral membrane proteins are anchored to the depend on structural complexes of specific lipids and
hydrophobic interior of the membrane by hydrophobic proteins.
transmembrane segments (light purple), while hydrophilic
segments (dark purple) extend outward on one or both sides of MEMBRANE LIPIDS: THE “FLUID” PART OF THE MODEL
the membrane. Peripheral membrane proteins are associated ➢ Membrane lipids are important components of the
with the membrane surface by weak electrostatic forces. “fluid” part of the fluid mosaic model.
➢ Membranes contain several major classes of lipids:
3 CLASSES OF MEMBRANE PROTEINS ○ Phospholipids
➢ Integral membrane proteins are embedded in the lipid ○ Glycolipids
bilayer due to their hydrophobic regions. ○ Sterols
➢ Peripheral proteins are hydrophilic and located on the ➢ The fluid mosaic model of membrane structure retains
bilayer surface. the lipid bilayer of earlier models.
➢ Lipid-anchored proteins are hydrophilic and attached ➢ However, there is a greater diversity and fluidity of lipids
to the bilayer by covalent attachments to lipid than originally thought.
molecules embedded in the bilayer.
PHOSPHOLIPIDS
➢ Phospholipids are the most abundant lipids in the
membrane.

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○ Structure: Glycerol and two fatty acid

backbone.
➢ They include glycerol-based phosphoglycerides and
sphingosine-based sphingolipids.
○ This depends on what the backbone is.
○ Structure: Sphingosine backbone and one
fatty acids.
➢ The kinds and relative proportions of phospholipids vary
greatly among types of membranes.

STEROLS
➢ The membrane of most eukaryotes contains significant
amounts of sterols
○ Structure: Rings are prominent.
➢ The main sterol in the animal cell membrane is
cholesterol, which is needed to stabilize and maintain
membranes.
➢ Plant cell membranes contain small amounts of
phytosterols, whereas fungal cell membranes contain
ergosterol, similar to the cholesterol of the animal cell.

PRESENCE OF PHOSPHOLIPIDS
HOW ARE LIPIDS ISOLATED?
➢ Lipids can be isolated, separated, and studied using
nonpolar solvents such as acetone and chloroform.
➢ Thin layer chromatography is an important technique
for Lipid Analysis
○ Thin layer chromatography is used to separate
different kinds of lipids based on their relative
polarities.
○ With TLC, we can isolate, separate, and also
study using nonpolar solvents, acetone, or
➢ Depending on the membranes' different structures, chloroform.
there are different amounts and components of ➢ How do we use this?
phospholipids. ○ A glass plate is coated with silicic acid, and
lipids are spotted onto a position near the
GLYCOLIPIDS bottom of the plate called the origin.
➢ Glycolipids are formed by adding carbohydrates to
lipids. Principle of Separating Lipids via TLC
○ Structure: A monosaccharide and can have a ➢ A nonpolar organic solvent moves up the plate by
sphosine backbone and fatty acid. capillary action, taking different lipids with it to varying
➢ Some are glycerol-based, and some are degrees.
sphingosine-based, the glycosphingolipids. ➢ Nonpolar lipids have little affinity for the silicic acid on
○ The most common glycosphingolipids are the plate and so move readily with the solvent near the
cerebrosides and gangliosides. solvent front.
■ These are often seen in the brain ○ These can move farther near the solvent front.
and the nerve cells. ➢ Polar lipids will interact variably (depending on how
polar they are) with the silicic acid, and their
CEREBROSIDE AND GANGLIOSIDES
movement will be slowed proportionately.
➢ Cerebrosides are neutral glycolipids; each molecule ○ These move variably; hence, movement is
has an uncharged sugar as its head group slowed proportionately.
➢ A ganglioside has an oligosaccharide head group with
one or more negatively charged sialic acid residues.
➢ Cerebrosides and gangliosides are especially
prominent in brain and nerve cells.

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Separating Lipids via TLC LIPIDS

➢ Most lipids are distributed unequally between the two
monolayers.
➢ Membrane asymmetry is the difference between the
monolayers regarding the kinds of lipids present and
the degree of saturation of fatty acids in the
phospholipids.
➢ Most of the glycolipids in the plasma membrane of
animal cells are in the outer layer.
➢ Membrane asymmetry is established during the
synthesis of the membrane.

Membrane Asymmetry tends to be Maintained

➢ Once established, membrane asymmetry does not
1. The less polar ones are moved closer to the solvent
change much
front – fast movement going up.
➢ The movement of lipids from one monolayer to another
a. Cholesterol is less polar
requires their hydrophilic heads to move all the way
2. The more polar ones are near the solvent system,
through the hydrophobic interior of the bilayer.
meaning they are not going upwards.
➢ The transverse diffusion or flip-flop is relatively rare.
a. Serine is more polar

Lipids move freely within their Monolayer

FATTY ACIDS
➢ Lipids are mobile within their monolayer
➢ Fatty acids are essential to membrane structure and
➢ Rotation of phospholipids about their axes can occur a
function as it is a component of all membrane lipids
➢ Phospholipids can also move within the monolayer via
except the sterols.
lateral diffusion.
➢ Their long hydrocarbon tails provide a barrier to the
➢ Transverse diffusion is outside the layer “flip-flop.”
diffusion of polar solutes.
➢ Both types of movement are rapid and random.
➢ The sizes of membrane fatty acids range between
12-20 carbons long, which is optimal for bilayer
formation and dictates the usual thickness of
membranes (6-9nm).

Fatty Acids vary in Degree of Saturation

➢ Fatty acids vary considerably in the presence and
number of double bonds.
➢ Saturated fatty acids are those without double bonds
and more carbon: Palmitate (16C) and stearate (18C)
are common saturated fatty acids.
○ They have more C, which tends to be more
stable
➢ Unsaturated fatty acids are those with double bonds
Transverse Diffusion does Occur
but less carbon: Oleate (one double bond) and
➢ Though rare, phospholipid flip-flop does occur in
linoleate (two double bonds) are 18C unsaturated fatty
natural membranes
acids.
➢ Some membranes, in particular the smooth ER
○ Double bonds are seen, which tend to have
membrane, have proteins that catalyze the flip-flop of
more fluid.
membrane lipids.
➢ These proteins are called phospholipid translocators or
flippases, which facilitate the flip-flop movement.

THE LIPID BILAYER

➢ The lipid bilayer behaves as a fluid that permits the
movement of lipids and proteins.
➢ Lipids can move as much as several um per second
within the monolayer.
➢ Lateral diffusion can be demonstrated using
fluorescence recovery after photobleaching (FRAP).

Measuring Lipid Mobility with FRAP

1. Investigators label lipid molecules in a membrane with
a fluorescence dye.
2. A laser beam is used to bleach the dye in a small area,
creating a dark spot on the membrane.

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3. The membrane is observed afterward to determine

how long it takes for the dark spot to disappear, a
measure of how quickly new fluorescent lipids move in.

Membranes Function
➢ Membranes function properly only in the fluid state.
➢ Membrane fluidity changes with temperature,
decreasing as temperature falls and vice versa.
➢ Every lipid bilayer has a characteristic transition
temperature (™), the temperature at which it becomes
fluid.
○ This state change is called a phase transition, Effects of Fatty Acid Composition on Membrane Fluidity
in this case, from solid to liquid.
➢ Fluidity of a membrane depends mainly on the fatty
○ e.g., oil becomes solid if it is called.
acids that it contains.
➢ Below the ™, any functions that rely on membrane
○ Depending if saturated or unsaturated.
fluidity will be disrupted.
➢ The length of fatty acid chains and the degree of
○ If the fluid becomes solid in state, the
saturation both affect the fluidity of the membrane.
membrane function will disappear.
➢ Long-chain and saturated fatty have higher Tm,
Measuring the transition temperature of a membrane whereas short-chain and unsaturated fatty acids have
➢ The transition temperature can be measured by lower ™.
differential scanning calorimetry.
➢ The membrane is placed inside a calorimeter, and heat
uptake is measured as temperature increases.
➢ The ™ is the point of maximum heat absorption as the
membrane changes from the gel to the fluid state.
○ (a) Normal Membrane: A peak of heat
absorption marks the gel-to-fluid transition
temperature.
○ (b) Membranes enriched in unsaturated or
saturated fatty acid: Transition point differs,
more unsaturated becomes more fluid (16C),
while more saturated has less fluid (70c),
which needs a higher temperature to change
in state.
■ More fluid: Low temperature
■ Less fluid: High temperature Fatty Acid Saturation and Membrane Fluidity
➢ Saturated fatty acids pack together well in the
membrane.
➢ Unsaturated Fatty acids with one or more double
bonds have bends in the chains that prevent them
from packing together nearly.
➢ Thus, unsaturated fatty acids are more fluid than
saturated fatty acids and have lower ™.

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Membrane Composition
➢ Most plasma membrane fatty acids vary in chain
length and degree of saturation.
➢ This helps to ensure that membranes are fluid at
physiological temperatures so that their functions are
maintained.
➢ Most unsaturated fatty acids have cis double bonds,
unlike the commercially produced trans fats, which
pack together as saturated fats do, which is why trans
fats are considered to be bad.

Effects of Sterols on Membrane Fluidity

➢ Membrane fluidity is influenced by sterols.
➢ The intercalation of rigid cholesterol molecules into a
membrane decreases its fluidity and increases the ™.
➢ However, cholesterol also prevents hydrocarbon chains
of phospholipids from packing together tightly,
reducing the tendency of membranes to gel upon
cooling.
○ Therefore, cholesterol is a fluidity buffer; sterols
in organisms may function similarly.

Most Organisms can Regulate Membrane Fluidity

➢ Most organisms can regulate membrane fluidity by
varying the lipid composition of the membranes.
➢ This is most important in poikilotherms, organisms that
cannot regulate their body temperature.
○ Poikilotherms use homeoviscous adaptation,
compensating for changes in temperature by
altering the length and degree of saturation
of fatty acids in their membranes.

Oxygen and Desaturase Enzyme

➢ Some organisms have a desaturase enzyme, which
introduces double bonds into fatty acids as needed,
making them unsaturated.
➢ In plants and yeasts, temperature-related fluidity
changes are tied to the increased solubility of oxygen
at lower temperatures.
Other effects of sterols on membranes ➢ More oxygen is available at low temperatures, and
➢ Sterols decrease the permeability of membranes to ions oxygen acts as a substrate for desaturase, allowing for
and small polar molecules. maintenance of membrane fluidity at lower
➢ This is likely because they fill spaces between the temperatures.
hydrocarbon chains of phospholipids.
➢ This effectively blocks the routes that ions and small
THE LIPID RAFTS
molecules would take through the membrane, also
➢ Lipid rafts are localized regions of membrane lipids that
forming the hydrogen bond.
are involved in cell signaling
➢ Localized regions of membrane lipids in association
with specific proteins are called lipid microdomains or
lipid rafts.
➢ These are dynamic, changing composition as lipids and
proteins move into and out of them.
➢ Lipid rafts in the outer monolayer of animal cells have
elevated levels of cholesterol and glycosphingolipids
and are less fluid than the rest of the membrane.

Functions of Lipid Rafts

➢ Lipid rafts are thought to have roles in detecting and
responding to extracellular signals.
➢ For example, lipid rafts have roles in

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○ Transport of nutrients and ions across

membranes.
○ Binding of activates immune system cells to
their microbial targets.
○ Transport of cholera toxin into intestinal cells.
Receptors in Lipid Rafts
➢ When a receptor molecule on the outer surface of the
plasma binds its ligand, it can move into lipid rafts also
located in the outer monolayer.
➢ Lipid rafts containing receptors are coupled to lipid
rafts on the inner monolayer.
➢ Some lipid rafts contain kinases, enzymes that generate
second messengers in a cell via phosphorylation of
target molecules.

GUIDE QUESTIONS 6-10

➢ Which is the best among the membrane structure
models? Why? The fluid mosaic bilayer model accounts
for all the inconsistencies with previous models.

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MAY 23, 2024 - FACE TO FACE

PART 2: CELL MEMBRANE
MEMBRANE PROTEINS: THE MOSAIC PART OF THE MODEL
➢ The mosaic part of the fluid mosaic model includes lipid
rafts and other lipid domains.
➢ However, it is membrane proteins that are the main
components.

EVIDENCE FROM FREEZE-FRACTURE MICROSCOPY

➢ The membrane consists of a mosaic of proteins.
➢ Support for the fluid mosaic model came from studies
involving freeze-fracturing.
➢ A bilayer or membrane is frozen and then hit sharply
with a diamond knife.
➢ The resulting fracture often follows the plane between
the two layers of membrane lipid.

➢ Surface view of monolayers.

○ This sketch of a freeze-fractured membrane
shows electron micrographs of the E and P
faces from the plasma membrane of a mouse
kidney tubule cell. Individual proteins
embedded in either face show up as small
particles (TEMs).
➢ The E face is smoother than the P phase.

➢ Separation of membrane monolayers.

○ Notice how the fracture plane has passed
through the hydrophobic interior of the FREEZE-FRACTURE ANALYSIS OF MEMBRANES
membrane, revealing the inner surfaces of the ➢ When a fracture plane splits a membrane into its two
two monolayers. layers, particles the size and shape of globular proteins
○ Integral membrane proteins that remain with can be seen.
the outer monolayer are seen on the E ➢ The E surface is the exoplasmic face and the P surface
(exoplasmic) face, whereas those that remain is the protoplasmic face.
with the inner monolayer are seen on the P ➢ Artificial bilayers without added protein show no
(protoplasmic) face. particles.

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MEMBRANES CONTAIN INTEGRAL, PERIPHERAL, AND ➢ Some are arranged as a closed beta sheet called a
LIPID-ANCHORED PROTEINS beta barrel.
➢ Membrane proteins have different hydrophobicites and
so occupy different positions in or on membranes. SINGLEPASS MEMBRANE PROTEINS
➢ This, in turn, determines how easily such proteins can be ➢ Singlepass membrane proteins have the C-terminus
extracted from membranes. extending from one surface of the membrane and the
➢ Membrane proteins fall into three categories: N-terminus from the other.
○ Integral ➢ For example, glycophorin is a singlepass protein on the
○ Peripheral erythrocyte plasma membrane that is oriented so the
○ Lipid-anchored C-terminus is on the inner surface and the N-terminus is
on the outer.

THE ERYTHROCYTE PLASMA MEMBRANE

➢ The erythrocyte (red blood cell) membrane has been
one of the most widely studied.
➢ This is because of the wide availability of red blood cells
and how easily plasma membranes can be isolated
from them.

INTEGRAL MEMBRANE PROTEINS

➢ Most membrane proteins possess one or more
hydrophobic regions with an affinity for the interior of
the lipid bilayer.
➢ These are integral membrane proteins, with MULTIPASS MEMBRANE PROTEINS
hydrophobic regions embedded in the interior ➢ Multipass membrane proteins have 2-20 (or more)
membrane bilayer. transmembrane proteins.
➢ They are difficult to remove from membranes by ○ For example, band 3 protein (anion exchange
standard isolation procedures. protein) is present in the erythrocyte
➢ Some integral membrane proteins, called integral membrane and has at least 6 transmembrane
monotropic proteins, are embedded in just one side of segments.
the bilayer. ○ For example, bacteriorhodopsin has 7
➢ However, most are transmembrane proteins that span transmembrane segments positioned to form
the membrane and protrude on both sides. a channel.
➢ Transmembrane proteins cross either once (singlepass
proteins) or several times (multipass proteins).

TRANSMEMBRANE PROTEINS
➢ Most transmembrane proteins are anchored to the lipid
bilayer by one or more hydrophobic transmembrane
segments.
➢ In most cases, the polypeptide chain appears to span
the membrane in an alpha-helical conformation about
20-30 amino acids long.

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GUIDE QUESTIONS
➢ 1-3. What are the 3 types of proteins found on
membranes? Integral, peripheral, and lipid-anchored
proteins.

PROTEINS CAN BE SEPARATED BY SDS-POLYACRYLAMIDE GEL

ELECTROPHORESIS
➢ Membrane proteins must be solubilized and extracted
from membranes so that they can be studied.
➢ They are separated by electrophoresis.

ISOLATION OF MEMBRANE PROTEINS

➢ Peripheral membrane proteins are usually easy to
isolate by altering pH or ionic strength.
➢ Chelating (cation binding) agents are also used to
solubilize peripheral membrane proteins.
➢ Lipid-anchored proteins are isolated by similar means.

ISOLATING INTEGRAL MEMBRANE PROTEINS

➢ Integral membrane proteins are difficult to isolate from
membranes.
➢ Often detergents are used that disrupt hydrophobic
interactions and dissolve the lipid bilayer.
○ For example, sodium dodecyl sulfate (SDS), a
strong ionic detergent, is used to isolate and
PERIPHERAL MEMBRANE PROTEINS
fractionate integral membrane proteins, but
➢ Membrane proteins that lack discrete hydrophobic
alters their function.
regions do not penetrate the lipid bilayer.
➢ These peripheral membrane proteins are bound to
SDS-POLYACRYLAMIDE GEL ELECTROPHORESIS
membrane surfaces through weak electrostatic forces
➢ Electrophoresis: group of techniques that use an
and hydrogen bonds.
electric field to separate charged molecules.
➢ Some hydrophobic residues play a role in anchoring
➢ How quickly a molecule moves during electrophoresis
them to the membrane surface.
depends on both charge and size.
➢ Peripheral membrane proteins are easily separated
➢ Electrophoresis uses various support media most
from membranes by changing pH or ionic strength.
commonly polyacrylamide or agarose.
➢ The main peripheral membrane proteins of erythrocytes
➢ SDS gel is harder to load compared to agarose. This is
are spectrin, ankyrin, and band 4.1.
because agarose has certain angles that have holes in
➢ These are on the inner surface of the plasma
them, unlike in SDS where you can’t see the buffer.
membrane.

ELECTROPHORESIS OF MEMBRANE PROTEINS

LIPID-ANCHORED MEMBRANE PROTEINS
➢ The polypeptide chains of lipid-anchored membrane ➢ Membrane fragments are solubilized in SDS, which
proteins are located on the surfaces of membranes. disrupts protein-protein and protein-lipid associations.
➢ They are covalently bound to lipid molecules ➢ The proteins are thus coated with negatively charged
embedded in the bilayer. detergent molecules.
➢ Proteins bound to the inner surface of the plasma ➢ The proteins are loaded onto a polyacrylamide gel and
membrane are linked to fatty acids, or isoprenyl groups. an electric potential applied.
➢ The negatively charged proteins run toward the
TYPES OF LIPID-ANCHORED MEMBRANE PROTEINS positively charged bottom of the gel.
➢ Polypeptides move through the gel with the smallest
➢ Fatty acid anchored membrane proteins:
moving fastest.
○ Attached to a saturated fatty acid, usually
➢ The gel is stopped when the smallest proteins reach the
myristic acid (14C) or palmitic acid (16C).
bottom, and is stained with a dye such as Coomassie
➢ Isoprenylated membrane proteins:
brilliant blue to show the proteins.
○ Synthesized in the cytosol and then modified
by addition of multiple isoprenyl groups (5C)
usually farnesyl (15C) or geranygeranyl (20C)
groups.
➢ GPI-anchored membrane proteins:
○ Covalently linked to
glycosylphosphatidylinositol.

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ADDITIONAL TECHNIQUES USING ELECTROPHORESIS

➢ Two-dimensional SDS-PAGE (polyacrylamide gel
electrophoresis) separates proteins in two dimensions,
first by charge and then by size.
➢ Following electrophoresis, polypeptides can be
identified by Western blotting.
➢ In this technique, proteins are transferred to a
membrane and bound by specific antibodies.

➢ (A) Hydropathy plot of connexin.

DETERMINING THE THREE-DIMENSIONAL STRUCTURE OF MEMBRANE
○ The hydropathy index on the vertical axis is a
PROTEINS IS BECOMING MORE FEASIBLE
numerical measure of the relative
➢ X-ray crystallography can be used to determine the
hydrophobicity of successive segments of the
structure of proteins that can be isolated in crystalline
polypeptide chain based on its amino acid
form.
sequence.
➢ Membrane proteins are hard to isolate and crystallize.
➢ (B) Transmembrane structure of connexin.
➢ An alternative approach called hydropathic analysis
○ Connexin has four distinct hydrophobic
can be used.
regions, which correspond to the four
alpha-helical segments that span the plasma
X-RAY CRYSTALLOGRAPHY
membrane.
➢ X-ray crystallography is widely used to determine the
three-dimensional structure of proteins. GUIDE QUESTIONS
➢ Integral membrane proteins are difficult to isolate and
➢ 4. ___ is a group of techniques that use an electric field
crystallize, but recent techniques have improved.
to separate charged molecules. Electrophoresis.
➢ Now, over 200 proteins have been studied using this
➢ 5. T or F. X-ray crystallography can be used to
method.
determine the structure of proteins that can be isolated
in crystalline form. T
HYDROPATHY ANALYSIS
➢ T or F. Southern blot uses the technique where proteins
➢ The number and location of transmembrane segments are transferred to a membrane and bound by specific
in a membrane protein can be predicted if the protein antibodies. F
sequence is known.
➢ A hydropathy (or hydrophobicity) plot is used for this. MOLECULAR BIOLOGY HAS CONTRIBUTED GREATLY TO OUR
➢ A computer program identifies clusters of hydrophobic UNDERSTANDING OF MEMBRANE PROTEINS
residues, calculating a hydropathy index for successive ➢ Within the past three decades, the study of membrane
“windows” along the protein. proteins has been revolutionized by DNA sequencing
and recombinant DNA technology.
➢ Amino acid sequence can be deducted from DNA
sequence.

MEMBRANE PROTEINS HAVE A VARIETY OF FUNCTIONS

➢ Some membrane proteins are enzymes, which
accounts for the localization of particular functions to
specific membranes.

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➢ Electron transport proteins such as cytochromes and ○ The enzyme galactose oxidase (GO) can be
iron-sulfur proteins are closely related to enzymes in used to label carbohydrate side chains
function. attached to membrane proteins and lipids

SOLUTE TRANSPORT ACROSS MEMBRANES A METHOD FOR LABELING PROTEINS EXPOSED ON ONE OR BOTH
➢ Transport proteins facilitate the movement of nutrients SURFACES OF A MEMBRANE VESICLE
across membranes
➢ Channel proteins provide hydrophilic passageways
through hydrophobic membranes
➢ Transport ATPases use the energy of ATP to transport
ions across membranes

SIGNALING ACROSS MEMBRANES

➢ Receptors recognize and mediate the effects of
specific chemical signals on the surface of the cell
➢ Hormones, neurotransmitters, and growth-promoting
substances are examples of chemical signals

COMMUNICATION BETWEEN CELLS

➢ Membrane proteins involved with intercellular
communication include
○ proteins that form connexons at gap junctions
in animal cells
○ proteins that make up plasmodesmata in ➢ (a) In the presence of 125|, lactoperoxidase (LP) labels
plant cells membrane proteins exposed on the outer surface of
membrane vesicles (that is, proteins A and B). If
MEMBRANE PROTEINS PLAY ROLES IN OTHER CELL FUNCTIONS membrane vesicles are (b) first incubated in a
➢ Membrane proteins play roles in uptake and secretion hypotonic medium to make them permeable to LP and
of substances by endocytosis and exocytosis (c ) then transferred to an isotonic solution containing
➢ They also take part in targeting, sorting, and 125| but no external LP, the membrane proteins
modification of proteins in the endoplasmic reticulum exposed on the inner membrane surface (that is,
and Golgi complex proteins B and C) become labeled.
➢ They also participate in autophagy, the digestion of a
cell’s own organelles or structures MANY MEMBRANE PROTEINS ARE GLYCOSYLATED
➢ Glycoproteins are membrane proteins with
STABILIZING AND SHAPING THE CELL MEMBRANE carbohydrate chains covalently linked to amino acid
➢ Membrane-associated proteins play structural roles in side chains
stabilizing and shaping the cell membrane ➢ The addition of a carbohydrate side chain to a protein
➢ In erythrocytes, examples include spectrin, ankyrin, and is called glycosylation
band 4.1 protein ➢ Glycosylation occurs in the ER and Golgi compartments
➢ The spectrin-based network gives the red blood cells its
distinctive shape GLYCOSYLATION
➢ Glycosylation involves linkage of the carbohydrate to
MEMBRANE PROTEINS ARE ORIENTED ASYMMETRICALLY ACROSS ○ The nitrogen atom of an amino group
THE LIPID BILAYER (N-linked glycosylation), of an asparagine
➢ Membrane proteins exhibit asymmetric orientation with residue, or
respect to the lipid bilayer ○ The oxygen atom of a hydroxyl group
➢ Once in place, in or on one of the monolayers, proteins (O-linked glycosylation) of a serine, threonine,
cannot move across the membrane from one surface or modified lysine or proline residue
to the other
➢ All the molecules of a particular protein are oriented
the same way in the membrane

DETECTING PROTEINS ON SPECIFIC MEMBRANE PROTEINS

➢ Radioactive labeling procedures are used to distinguish
between proteins on inner and outer surfaces of
membrane vesicles
○ The enzyme lactoperoxidase (LP) can be used
to attach l125 to proteins

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CARBOHYDRATE CHAINS ATTACHED TO PROTEINS

➢ Carbohydrate chains attached to peptides can be

either straight or branched and range in length from 2
to about 60 sugar units
➢ The most common sugars are galactose, mannose,
N-acetylglucosamine, and sialic acid

ROLES OF GLYCOPROTEINS

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➢ Glycoproteins are most prominent in plasma ➢ Antibodies are immune system proteins that bind
membranes, where they play a role in cell-cell specific antigens, such as cell surface proteins
recognition
➢ The carbohydrate groups protrude on the outer surface THE FRYE AND EDIDIN EXPERIMENTS
of the cell membrane
➢ Lectins are plant proteins that bind specific sugar
groups very tightly, and can be used to study
membrane glycoproteins

GLYCOCALYX

➢ Frye and Edidin fused human and mouse cells and

used two fluorescent antibodies, each with a differently
colored dye linked to it
➢ The anti-mouse antibodies were linked to fluorescein, a
green dye, and the anti-human antibodies were linked
to rhodamine, a red dye
➢ Within a few minutes of fusion, the red and green
region proteins began to intermix

RANDOM DISTRIBUTION OF PROTEINS

➢ In animal cells, the carbohydrate groups of plasma

membrane glycoproteins and glycolipids from a
surface coat called a glycocalyx
➢ The carbohydrate groups on the cell surface are
components of the recognition sites of membrane
receptors involved in antibody-antigen reactions
➢ When plasma membranes are examined in
freeze-fracture micrographs, the embedded proteins
GUIDE QUESTIONS
appear to be randomly distributed
➢ 7. ____ is the addition of a carbohydrate chain to a ➢ The same is true for other types of membranes
protein. Glycosylation
➢ 8. T or F. Glycoproteins play a role in cell to cell EXPERIMENTAL EVIDENCE FOR RESTRICTED MOBILITY
recognition. T ➢ Although many types of membrane proteins do move
freely through the bilayer, their rates of movement vary
MEMBRANE PROTEINS VARY IN THEIR MOBILITY ➢ Photobleaching recovery experiments can be used to
➢ Membrane proteins are more variable than lipids in determine diffusion rates
their ability to move freely within the membrane ➢ Membrane proteins are much more variable in diffusion
➢ Some proteins can move freely, whereas others are rates than lipids are
constrained because they are anchored to protein
complexes MEMBRANE DOMAINS
➢ Diffusion of many membrane proteins is restricted to a
EXPERIMENTAL EVIDENCE FOR PROTEIN MOBILITY
limited area of the membrane
➢ Evidence for mobility of some membrane proteins
➢ So, some membranes consist of separate membrane
comes from cell fusion experiments
domains that differ in protein composition and
➢ Frye and Edidin fused cells from two different species
therefore in function
and labeled specific proteins on the surfaces with
antibodies

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MECHANISMS FOR RESTRICTING PROTEIN MOBILITY

➢ Membrane proteins aggregate within the membrane,
forming large, slow-moving complexes
➢ Membrane proteins also form structures that become
barriers to diffusion, creating membrane domains

MEMBRANE PROTEIN ANCHORING

➢ The most common restraint on mobility of membrane
proteins is anchoring of such proteins to structures to
one side of the membrane or the other
➢ For example, many proteins of the plasma membrane
are anchored to either cystoskeleton or to extracellular
structures

GUIDE QUESTIONS
➢ 9. T or F. Some proteins can move freely, whereas
others are constrained because they are anchored to
protein complexes. T
➢ 10. ____ are immune system proteins that bind specific
antigens, such as cell surface proteins. Antibodies

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MAY 27, 2024 - ZOOM ○ Aquaporins - for the transport of water

through pores.
PART 3: TRANSPORT ACROSS THE CELL MEMBRANE ○ Proteins digested from the Lysozyme - will go
OVERCOMING THE PERMEABILITY BARRIER
out as amino acids, which will be nutrients for
➢ Overcoming the permeability barrier of cell
the cell
membranes is crucial to the proper functioning of the
○ Chloroplasts - exchange of gasses (O2 and
cell
CO2), which are important in photosynthesis
➢ Specific molecules and ions need to be selectively
○ Ions (Sodium-Potassium Pump) - exchange of
moved into and out of the cell or organelle
sodium and potassium ions in and out of the
➢ Membranes are selectively permeable—hindi lahat
cell
nakakapasok at nakakalabas ng cell membrane.
SOLUTES CROSS MEMBRANES BY SIMPLE DIFFUSION,
CELLS AND TRANSPORT PROCESSES
FACILITATED DIFFUSION, AND ACTIVE TRANSPORT
➢ Cells and cellular compartments are able to
➢ Three quite different mechanisms are involved in
accumulate a variety of substances in concentrations
moving solutes across membranes.
that are very different from those of the surroundings.
○ There should be a balance within those
SIMPLE DIFFUSION
substances to achieve the same
➢ A few molecules cross membranes by simple diffusion,
concentration in and out of the cell.
the direct unaided movement dictated by differences
➢ Most substances that move across membranes are
in concentration of the solute on the two sides of the
dissolved gasses, ions, and small organic molecules;
membrane
solutes.
○ It doesn’t need anything that helps it to
transport the molecules.
TRANSPORT IS CENTRAL TO CELL FUNCTION
○ It’s just the movement of substances based on
➢ A central aspect of cell function is selective transport,
the difference in concentration.
the movement of ions or small organic molecules
➢ However, most solutes cannot cross the membrane this
(metabolites; components of metabolic pathways)
way.

TRANSPORT PROTEINS
➢ Transport proteins assist most solute across membranes
➢ These integral membrane proteins recognize the
substances to be transported with great specificity
○ Hindi basta-basta—they are very specific and
they only bind to the proteins that they can
recognize.

FACILITATED DIFFUSION
➢ Some move solutes to regions of lower concentration;
this facilitated diffusion (or passive transport) uses no
energy.
➢ They transfer from high concentration to low
concentration.

ACTIVE TRANSPORT
➢ In other cases, transport proteins move solutes against
the concentration gradient.
➢ Active transport requires energy such as that released
by the hydrolysis of ATP or by the simultaneous transport
of another solute down an energy gradient.

THE MOVEMENT OF A SOLUTE ACROSS A MEMBRANE IS

DETERMINED BY ITS CONCENTRATION GRADIENT OR ITS
ELECTROCHEMICAL POTENTIAL
➢ The movement of a molecule with no net charge is
➢ There are different substances that are transported
determined by its concentration gradient.
inside and outside of the cell:
➢ Simple or facilitated diffusion involves exergonic
○ Example: Glucose - they need to have carrier
movement "down" the concentration gradient
proteins to be transported
(negative ΔG)
○ There are times when there are transport
➢ Active transport involves endergonic movement "up"
proteins to be transported into the nucleus.
the concentration gradient (positive ΔG)

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THE ELECTROCHEMICAL POTENTIAL protein facilitates the reciprocal transport of

➢ The movement of an ion is determined by its chloride (CI-) and bicarbonate (HCO3-).
electrochemical potential, the combined effect of its ○ (c) mediated by channel proteins. Aquaporin
concentration gradient, and the charge gradient channel proteins can facilitate the rapid
across the membrane. inward or outward movement of water
➢ The active transport of ions across a membrane creates molecules.
a charge gradient or membrane potential (Vm) across ➢ Active transport: (d) driven by the hydrolysis of ATP, the
the membrane Na+/K+ pump moves three sodium ions outward for
every two potassium ions moved inward, establishing
ACTIVE TRANSPORT OF IONS an electrochemical potential across the plasma
membrane for both ions.
➢ Most cells have an excess of negatively charged
solutes inside the cell
SIMPLE DIFFUSION: UNASSISTED MOVEMENT DOWN THE GRADIENT
➢ This charge difference favors the inward movement of
➢ The most straightforward way for a solute to cross a
cations such as Nat and the outward movement of
membrane is through simple diffusion, the unassisted
anions such as Cl
net movement of a solute from high to lower
➢ In all organisms, active transport of ions across the
concentration
plasma membrane results in asymmetric distribution of
➢ Typically, this is only possible for gasses, nonpolar
ions inside and outside the cell
molecules, or small polar molecules such as water,
➢ We need to balance out the ions—kung alin yung
glycerol, or ethanol
lumabas, ganun din dapat ang pumasok.

OXYGEN AND THE FUNCTION OF ERYTHROCYTES

GUIDE QUESTIONS
➢ Oxygen gas traverses the lipid bilayer readily by simple
1-3. What are the 3 types of cell transport? Simple diffusion,
diffusion
facilitated diffusion, active transport
➢ Erythrocytes take up oxygen in the lungs, where oxygen
concentration is high, and release it in the body tissues,
THE ERYTHROCYTE PLASMA MEMBRANE PROVIDES EXAMPLE OF
where oxygen concentration is low
TRANSPORT MECHANISMS
○ They deliver oxygen to different parts of the
➢ The transport proteins of the erythrocyte plasma
body.
membrane are among the best understood of all such
proteins
➢ The membrane potential is maintained by the active
transport of potassium ions inward and sodium ions
outward—the Sodium-Potassium Pump
➢ Special pores or channels allow water and ions to enter
or leave the cell rapidly as needed

➢ (a) In the capillaries of body tissues (low O2 and high

➢ Simple diffusion: (a) oxygen, carbon dioxide, and water
CO2 relative to the erythrocytes outward to mee tissue
diffuse directly across the plasma membrane in
by carbonic anhydrase in the cytosol. Bicarbonate ions
response to their relative concentrations inside and
are transported outward by the anion exchange
outside the cell.
protein, accompanied by the inward movement of
➢ Facilitated diffusion:
chloride ions to maintain charge balance. Carbon
○ (b) mediated by carrier proteins. The
dioxide, therefore, returns to the lungs as bicarbonate
movement of glucose across the plasma
ions.
membrane is facilitated by a specific glucose
➢ (b) In the capillaries of the lungs (high O2 and low CO2
transporter called GLUT1. An anion exchange
relative to the erythrocytes), O2 diffuses inward and

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binds to hemoglobin. Bicarbonate moves inward from concentration). Equilibrium is reached when the solute
the blood plasma, accompanied by an outward concentration is the same in both chambers.
movement of chloride ions. Incoming bicarbonate is ➢ (RIGHT) Osmosis occurs when the membrane between
converted into CO2, which diffuses out of the the two chambers is not permeable to the dissolved
erythrocytes and into the cells that line the capillaries of solute, represented by the black triangles. Because
the lungs. The CO2 is now ready to be expelled from the solute cannot cross the membrane, water diffuses from
body. chamber B, where the solute concentration is lower
(more water), to chamber A, where the solute
DIFFUSION ALWAYS MOVES SOLUTES TOWARD EQUILIBRIUM concentration is higher (less water). At equilibrium, the
➢ Diffusion always tends to create a random solution in solute concentration will be equal on both sides of the
which the concentration is the same everywhere membrane.
➢ Solutes will move toward regions of lower concentration
until the concentrations are equal TONICITY OF CELLS
➢ Thus, diffusion is always a movement toward equilibrium

DIFFUSION TENDS TOWARD MINIMUM FREE ENERGY

➢ Chemical reactions and physical processes proceed in
the direction of decreasing free energy.
➢ Diffusion is the same: free energy is minimized as
molecules move down their concentration gradients
➢ So, diffusion always proceeds from regions of higher to
lower free energy

OSMOSIS IS THE DIFFUSION OF WATER ACROSS A

SELECTIVELY PERMEABLE MEMBRANE
➢ The properties of water cause it to behave in a special
way
➢ Water molecules are uncharged and so are not
affected by the membrane potential
➢ ISOTONIC SOLUTION: When a cell is in an isotonic
➢ Water concentration is not appreciably different on
solution, the solute concentration inside the cell is equal
opposite sides of a membrane
to the solute concentration outside the cell. This
equilibrium results in no net movement of water, and
THE DIRECTION OF DIFFUSION OF WATER
the cell maintains its normal shape and volume.
➢ Solute molecules that are dissolved in water disrupt the
➢ HYPERTONIC SOLUTION: If a cell is placed in a
interactions that normally occur between water
hypertonic solution, where the solute concentration
molècules
outside the cell is higher than inside, water will move
➢ This decreases the free energy of the solution.
out of the cell. This causes the cell to lose water and
➢ Water thus moves from regions of low to high solute
shrink, or shrivel.
concentration, moving toward the region of lowest free
➢ HYPOTONIC SOLUTION: If a cell is placed in a hypotonic
energy.
solution, where the solute concentration outside the
cell is lower than inside, water will move into the cell.
OSMOSIS
This causes the cell to gain water and swell, becoming
➢ If two solutions are separated by a selectively turgid.
permeable membrane, permeable to the water but
not the solutes, the water will move toward the region GUIDE QUESTIONS
of higher solute concentration.
4. T or F. Water moves from regions of low to high solute
➢ This movement is called osmosis
concentration, moving toward the region of lowest free
➢ For most cells, water tends to move
energy. T
5. _____ is the movement of water toward the region of
higher solute concentration. Osmosis

SIMPLE DIFFUSION IS LIMITED TO SMALL, NONPOLAR MOLECULES

➢ Scientists use membrane models to study diffusion
➢ Bangham and colleagues discovered that when lipids
➢ (LEFT) Simple diffusion occurs when the membrane from cell membranes are dispersed in water, they form
separating chambers A and B is permeable to liposomes
molecules of dissolved solute, represented by the black ➢ These are small vesicles forming a closed spherical lipid
dots. The net movement of solute molecules across the bilayer lacking proteins
membrane is from chamber A to B (high to low solute

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THE USE OF LIPOSOMES TO STUDY DIFFUSION THE RATE OF SIMPLE DIFFUSION IS DIRECTLY PROPORTIONAL TO THE
➢ Bangham trapped solutes inside liposomes and CONCENTRATION GRADIENT
measured the rate at which they diffused out ➢ Thermodynamically, simple diffusion is always an
➢ Ions were trapped inside the liposomes for days, and exergonic process, requiring no input of energy
small uncharged molecules such as oxygen diffused ➢ Kinetically, the net rate of transport for a substance is
too rapidly to measure proportional to its concentration difference across the
➢ Factors affecting diffusion: size, polarity, and charge membrane

SOLUTE SIZE VINWARD (VELOCITY INWARD)

➢ In general, lipid bilayers are more permeable to small
molecules-water, oxygen, carbon dioxide-than larger
ones
➢ But without a transporter, even these small molecules
move more slowly than in the absence of a membrane
➢ Still, water diffuses more rapidly than would be
expected for a polar molecule

DIFFUSION OF WATER
➢ It is thought that membranes contain tiny pores that
allow water to diffuse more rapidly than predicted
➢ Simple diffusion has a linear relationship between
based on its polarity
inward flux of solute and the concentration gradient of
➢ Alternatively, perhaps membrane lipid movement
the solute
creates temporary "holes" through which the water can
move
➢ There is little evidence for these hypotheses

SOLUTE POLARITY
➢ Lipid bilayers are more permeable to nonpolar
substances than to polar ones
➢ Nonpolar substances dissolve readily into the
hydrophobic region of the bilayer
➢ Large nonpolar molecules such as estrogen and
testosterone cross membranes easily despite their large
size

A MEASURE OF SOLUTE POLARITY

➢ The polarity of a solute can be measured by the ratio of
its solubility in an organic solvent to its solubility in water
➢ This is called the partition coefficient
➢ In general, the more nonopolar (hydrophobic) a FACILITATED DIFFUSION: PROTEIN-MEDIATED MOVEMENT DOWN
substance is, the higher the partition coefficient THE GRADIENT
➢ Most substances in the cell are too large or too polar to
cross membranes by simple diffusion
SOLUTE CHARGE ➢ These can only move in and out of cells with the
➢ The relative impermeability of polar substances, assistance of transport proteins
especially ions, is due to their association with water ➢ If the process is exergonic, it is called facilitated
molecules diffusion; the solute diffuses as dictated by its
➢ The molecules of water form a shell of hydration around concentration gradient
polar substances
➢ For these substances to move into a membrane, the TRANSPORT PROTEINS IN FACILITATED DIFFUSION
water molecules must be removed, which requires ➢ No input of energy is needed in facilitated diffusion
energy ➢ The role of the transport proteins is just to provide a
path through the lipid bilayer, allowing the "downhill"
SOLUTE CHARGE — RELEVANCE TO CELL FUNCTION movement of a polar or charged solute
➢ Every cell must maintain an electrochemical potential
across its plasma membrane to function CARRIER PROTEINS AND CHANNEL PROTEINS FACILITATE
➢ In most cases, this potential is a gradient of either DIFFUSION BY DIFFERENT MECHANISMS
sodium ions (animal cells) or protons (other cells) ➢ Transport proteins are large, integral membrane
➢ Membranes must still be able to allow ions to cross the proteins with multiple transmembrane segments
bilayer in a controlled manner ➢ Carrier proteins (transporters or permeases) bind solute
molecules on one side of a membrane, undergo a

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conformation change, and release the solute on the ➢ So, carrier-facilitated transport (like enzyme catalysis)
other side of the membrane exhibits saturation kinetics
➢ Channel proteins form hydrophilic channels through the
membrane to provide a passage route for solutes SATURATION KINETICS OF CARRIER PROTEINS
➢ Carrier-facilitated transport has an upper limiting
CHANNELS velocity, Vmax, and a constant Km corresponding to
➢ Some channels are large and nonspecific, such as the the concentration of solute needed to achieve
pores on the outer membranes of bacteria, ½(Vmax)
mitochondria, and chloroplasts ➢ The initial rate of solute transport can be described as
➢ Pores are formed by transmembrane proteins called follows:
porins that allow passage of solutes up to a certain size
to pass (600D)
➢ Most channels are smaller and highly selective

ION CHANNELS
➢ Most of the smaller channels are involved in ion
transport and are called ion channels
➢ The movement of solutes through ion channels is much
faster than transport by carrier proteins COMPETITIVE INHIBITION OF CARRIER PROTEINS
➢ This is likely because conformation changes are not ➢ Competitive inhibition of carrier proteins can occur in
required the presence of molecules or ions that are structurally
related to the correct substrate
CARRIER PROTEINS ALTERNATE BETWEEN TWO ➢ For example, the transport of glucose by glucose carrier
CONFORMATIONAL STATES proteins can be inhibited by the other
➢ The alternating conformation model states that a carrier monosaccharides that the carrier accepts (such as
protein is an allosteric protein and alternates between mannose and galactose)
two conformational states
➢ In one state, the solute binding site of the protein is CARRIER PROTEINS TRANSPORT EITHER ONE OR TWO SOLUTES
accessible on one side of the membrane ➢ When a carrier protein transports a single solute across
➢ The protein shifts to the alternate conformation, with the membrane, the process is called uniport
the solute binding site on the other side of the ➢ A carrier protein that transports a single solute is called
membrane, triggering solute release a uniporter
➢ When two solutes are transported simultaneously and
CARRIER PROTEINS ARE ANALOGOUS TO ENZYMES IN THEIR their transport is coupled, the process is called coupled
SPECIFICITY AND KINETICS transport
➢ Carrier proteins are analogous to enzymes
○ Facilitated diffusion involves binding a
substrate on a specific solute-binding site
○ The carrier protein and solute form an
intermediate
○ After the conformational change, the
"product" is released (the transported solute)
○ Carrier proteins are regulated by external
factors

SPECIFICITY OF CARRIER PROTEINS

➢ Carrier proteins share the property of high specificity
with enzymes, too
➢ Transport proteins are often highly specific for a single
compound or a small group of closely related COUPLED TRANSPORT
compounds ➢ If the two solutes are moved across a membrane in the
➢ The carrier protein for glucose in erythrocytes is specific same direction, it is referred to as symport (or
to a few monosaccharides and is stereospecific for only cotransport)
their D-isomers ➢ If the solutes are moved in opposite directions, it is
called antiport (or countertransport)
KINETICS OF CARRIER PROTEINS ➢ Transporters that mediate these processes are
➢ Carrier proteins can become saturated as the symporters and antiporters
concentration of the solute rises
➢ This is because the number of carrier proteins is limited,
and each functions at a finite maximum velocity

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TRANSPORT BY GLUT1 IS REVERSIBLE

➢ A carrier protein can facilitate transport in either
direction
➢ The direction of transport is dictated by the relative
solute concentrations outside and inside the cell
➢ Glucose concentration is kept low inside most animal
cells

PHOSPHORYLATION OF GLUCOSE

➢
➢ The immediate phosphorylation of glucose upon entry
into the cell keeps the concentration of glucose low
➢ Once phosphorylated, glucose cannot bind the carrier
THE ERYTHROCYTE GLUCOSE TRANSPORTER AND ANION protein any longer and is effectively locked into the cell
EXCHANGE PROTEIN ARE EXAMPLES OF CARRIER PROTEINS
➢ The glucose transporter is a uniport carrier for glucose THE ERYTHROCYTE ANION EXCHANGE PROTEIN:
➢ The anion exchange protein is an antiport anion carrier AN ANTIPORT CARRIER
for Cl- and HCO3- ➢ The anion exchange protein (also called the
➢ Both are found in the plasma membrane of chloride-bicarbonate exchanger) facilitates reciprocal
erythrocytes exchange of Cl- and HCO3- ions only
➢ The exchange will stop if either anion is absent
THE GLUCOSE TRANSPORTER: A UNIPORT CARRIER ➢ The ions are exchanged in a strict 1:1 ratio
➢ The erythrocyte is capable of glucose uptake by
facilitated diffusion because the level of blood glucose The "ping-pong" mechanism
is much higher than that inside the cell
➢ The anion exchange protein is thought to alternate
➢ Glucose is transported inward by a glucose transporter
between two conformational states
(GLUT; GLUT1 in erythrocytes)
➢ In the first, it binds a chloride ion on one side of the
➢ GLUT1 is an integral membrane protein with 12
membrane, which causes a change to the second
transmembrane segments, which form a cavity with
state
hydrophilic side chains
➢ In the second state, the chloride is moved across the
membrane and released
MECHANISM OF TRANSPORT BY GLUT1
➢ The release of chloride causes the protein to bind to
➢ GLUT1 is thought to transport glucose through the
bicarbonate
membrane by the alternating confirmation mechanism
➢ The binding of bicarbonate causes a shift back to the
➢ One conformational state, T1, has the binding site for
first conformation
glucose open on the outside of the cell
➢ In this conformation, bicarbonate is moved out of the
➢ The other conformational state, T2, has the binding site
cell, allowing the carrier to bind chloride again
open to the inside of the cell

MECHANISM OF TRANSPORT BY GLUT1

BIOLOGICAL RELEVANCE OF ANION EXCHANGE
1. D-glucose collides with and binds to GLUT1 in the T1 ➢ In tissues, waste CO2 diffuses into the erythrocytes,
conformation where it is converted to HCO3- by the enzyme carbonic
2. GLUT1 shifts to the T2, conformation anhydrase
3. The conformational change causes the release of ➢ As the concentration of bicarbonate rises, it moves out
glucose of the cell, coupled with the uptake of Cl to prevent a
4. GLUT1 returns to the T1, conformation net charge imbalance
➢ In the lungs, the entire process is reversed

GUIDE QUESTIONS
6-8. What are the factors affecting diffusion? Size, polarity,
charge
9. _________ is the process when a carrier protein transports a
single solute across the membrane. uniport
10. _________ is an enzyme that converts CO2 to HCO3- carbonic
anhydrase

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JUNE 3, 2024 - ZOOM PORIN OF AN E.COLI

PART 4: TRANSPORT ACROSS CELL MEMBRANES

CHANNEL PROTEINS FACILITATE DIFFUSION BY FORMING
HYDROPHILIC TRANSMEMBRANE CHANNELS
➢ Channel proteins form hydrophilic transmembrane
channels that allow specific solutes to cross the
membrane directly.
➢ There are three types of channels: ion channels, porins,
and aquaporins.

ION CHANNELS
➢ Transmembrane proteins that allow rapid passage of
specific ions.
➢ Tiny pores lined with hydrophilic atoms are
remarkably selective.
➢ Because most allow passage of just one ion, there
are separate proteins needed to transport Na+, K+,
Ca2+, and Cl-, etc. ➢ The porin end view is open to allow passage.
➢ Selectivity is based on both binding sites involving
amino acid side chains and a size filter.
AQUAPORINS
➢ Transmembrane channels that allow rapid passage of
GATED CHANNELS
water.
➢ Most ion channels are gated, meaning that they open ➢ Movement of water across cell membranes in some
and close in response to some stimulus. tissues is faster than expected given the polarity of
○ Voltage-gated channels open and close in the water molecule.
response to changes in membrane potential. ➢ Aquaporin (AQP) was discovered only in 1992.
○ Ligand-gated channels are triggered by the ➢ Aquaporins allow rapid passage of water through
binding of certain substances to the channel membranes of erythrocytes and kidney cells in
protein. animals, and root cells and vacuolar membranes in
○ Mechanosensitive channels respond to plants.
mechanical forces acting on the membrane.
STRUCTURE OF AQUAPORINS
FUNCTIONS OF ION CHANNELS
➢ All aquaporins are tetrameric integral membrane
➢ Ion channels play roles in many types of cellular proteins.
communication, such as muscle contraction and ○ Tetrameric: 4 monomeric subunits that are
electrical signaling of nerve cells. similar.
➢ Ion channels are also needed for maintaining salt ➢ The identical monomers associate with their 24
balance in cells and airways linking the lungs. transmembrane segments oriented to form four
○ A chloride ion channel, the cystic fibrosis central channels.
transmembrane conductance regulator ➢ The channels, lined with hydrophilic side chains, are
(CFTR), helps maintain the proper Cl- just large enough for water molecules to pass through
concentration in lungs; defects in the protein one at a time.
cause cystic fibrosis. ○ Not bidirectional.

PORINS
➢ Transmembrane proteins that allow rapid passage of
various solutes.
➢ Pores on outer membranes of bacteria, mitochondria,
and chloroplasts are larger and less specific than
ion channels.
➢ The pores are formed by multipass transmembrane
proteins called porins.
➢ The transmembrane segments of porins cross the
membrane as beta barrels.

STRUCTURE OF PORINS
➢ The beta barrel has a water-filled pore at its center.
➢ Polar side chains line the inside of the pore,
allowing passage of many hydrophilic solutes.
➢ The outside of the barrel contains many nonpolar
side chains that interact with the hydrophobic interior
of the membrane.

➢ Lipid molecule at the center blocks other solutes or

ions present in the molecule.

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GUIDE QUESTIONS
➢ 1-3. What are the 3 types of channels? Ion channels,
porins, and aquaporins.

ACTIVE TRANSPORT: PROTEIN-MEDIATED MOVEMENT UP THE

GRADIENT
➢ Facilitated diffusion is important, but only accounts for
movement of molecules down a concentration
gradient, toward equilibrium.
○ Facilitated diffusion moves from high to low
concentration only to achieve equilibrium.
➢ Sometimes a substance must be transported against
a concentration gradient.
➢ In this case active transport is used to move solutes
up a concentration gradient, away from equilibrium.

FUNCTIONS OF ACTIVE TRANSPORT

➢ Active transport couples endergonic transport to an
exergonic process, usually ATP hydrolysis.
➢ Active transport performs three important cellular
functions: ➢ (a) Direct active transport: involves a transport
○ Uptake of essential nutrients system coupled to an exergonic chemical reaction,
○ Removal of wastes most commonly the hydrolysis of ATP. As shown, ATP
○ Maintenance of non-equilibrium hydrolysis drives the outward transport of protons,
concentrations of certain ions. thereby establishing an electrochemical potential for
protons across the membrane.
NON-EQUILIBRIUM CONDITIONS
➢ Active transport allows the creation and maintenance INDIRECT ACTIVE TRANSPORT
of an internal cellular environment that differs greatly ➢ Depends on the simultaneous transport of two
from the surrounding environment. solutes.
➢ Many membrane proteins involved in active transport ➢ Favorable movement of one solute down its gradient
are called pumps, because energy is required to drives the unfavorable movement of the other up its
move substances against their concentration gradient.
gradients. ➢ This can be a symport or an antiport, depending on
whether the two molecules are transported in the
ACTIVE TRANSPORT IS UNIDIRECTIONAL same or different directions.
➢ Active transport differs from diffusion (both simple and ○ Symport: movement of two solutes in the
facilitated) in the direction of transport. SAME direction.
➢ Diffusion is nondirectional with respect to the ○ Antiport: movement of two solutes in an
membrane and proceeds as directed by the OPPOSITE direction.
concentrations of the transported substances.
➢ Active transport has an intrinsic directionality.

COUPLING OF ACTIVE TRANSPORT

➢ The coupling of active transport to an energy source
may be direct or indirect.
➢ Active transport mechanisms can be divided based on
the sources of energy and whether or not two solutes
are transported at the same time.
➢ Active transport is categorized as direct or indirect.

DIRECT ACTIVE TRANSPORT

➢ In direct active transport (or primary active transport),
the accumulation of solute molecules on one side of
the membrane is coupled directly to an exergonic
chemical reaction.
➢ This is usually hydrolysis of ATP.
○ ATP is broken down into ADP and Pi
(phosphate).
➢ Transport proteins driven by ATP hydrolysis are called ➢ (b) Indirect active transport: involves the coupled
transport ATPases or ATPase pumps. transport of a solute S and ions-protons, in this case.
The exergonic inward movement of protons provides
the energy to move the transported solute, S, against
its concentration gradient or electrochemical potential.
➢ The picture shows a SYMPORT movement.

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GUIDE QUESTIONS ○ A peripheral component that juts out from

➢ 4. T or F. Active transport is bidirectional. F the membrane surface.
➢ 5. T or F. Active transport differs from diffusion (both ➢ Keeps pH of compartment low, which activates
simple and facilitated) in the direction of transport. T hydrolytic enzymes.

DIRECT ACTIVE TRANSPORT DEPENDS ON FOUR TYPES OF F-TYPE ATPases

TRANSPORT ATPases ➢ Found in bacteria, mitochondria, and chloroplasts.
➢ Four types of transport ATPases have been identified: ➢ They transport protons and have two components:
○ P-type ○ A transmembrane pore (F0)
○ V-type ○ A peripheral membrane component (F1) that
○ F-type contains the ATP binding site
○ ABC-type ➢ Remember Biochemistry 2 lesson sa F0 andF1.
➢ They differ in structure, mechanism, location, and ➢ Both are multisubunit components.
roles. ➢ F-type ATPases also function in reverse. It can
*A table of summary is found in the book. facilitate the reverse process.
○ In this case, ATP is synthesized, driven by
P-TYPE ATPases the exergonic flow of protons down their
gradients.
➢ Members of a large family, and are reversibly
○ In the reverse direction, the ATPases are
phosphorylated by ATP on a specific aspartic acid
more accurately called ATP synthases.
residue.
➢ F-type ATPases illustrate an important principle
➢ They have 8-10 transmembrane segments in a single
because of the way F-type ATPases function. The
polypeptide, which crosses the membrane multiple
principles are the following:
times.
○ Not only can ATP be used as an energy
➢ They are sensitive to inhibition by vanadate, VO43-,
source to generate ion gradients, but such
which resembles phosphate, PO43-.
gradients can be used as an energy source
○ They use vanadate to detect certain types of
to synthesize ATP.
P-type ATPases because they are very
○ This is true of all eukaryotes and most
sensitive to vanadate. So if you put
prokaryotes.
vanadate, you will know the P-type ATPase
present.
ABC-TYPE ATPases
➢ P-type ATPases fall into five subfamilies:
○ P1-ATPases are found in all organisms and ➢ The ABC-type ATPases are also called ABC (ATP
transport heavy metal ions. Binding Cassette) transporters.
○ P2-ATPases are responsible for maintaining ➢ The term cassette describes the catalytic domain that
gradients of ions (Na+, K+, H+ Ca2+) across binds ATP as part of the transport process.
plasma membranes of eukaryotic cells. ➢ ABC-type ATPases comprise a very large family of
■ They play roles in muscle transport proteins found in all organisms.
contraction (sodium-potassium ➢ Importers and exporters:
pump in P2) and the acidification of ○ Most of the ABC transporters initially
gastric juices in the stomach discovered from bacteria were importers,
(hydrogen pump in P2). involved in uptake of nutrients.
■ These are the ones targeted by ○ But many are now known to be exporters,
proton pump inhibitors found in some of which are medically important.
acidic people to lessen acidity. ➢ Structure of ABC-type ATPases:
○ P3-ATPases of plants and fungi pump ○ ABC transporters typically have four protein
protons out across the plasma membrane, domains, two of which are highly
acidifying the external medium. hydrophobic.
■ Similar to P2 but P2 is found in ○ These are embedded in the membrane.
eukaryotic cells while P3 is found in ○ The other two domains are peripheral, and
plants and fungi (eukaryotes pa rin associated with the cytoplasmic side of the
lol). membrane.
○ P4-ATPases pump hydrophobic molecules ➢ Structure and function of ABC-type ATPases:
such as cholesterol and fatty acids, and do ○ The peripheral domains bind ATP and couple
not transport them all the way across the its hydrolysis to transport
bilayer, but act as flippases. ○ The embedded domains each consist of six
■ Flippases: flips the lipids in the membrane-spanning segments that form a
bilayer. channel through which solutes can pass
○ P5-ATPases are not well characterized, but ○ Sometimes all four domains are found on a
some are known to transport cations. single polypeptide but usually they are
separate polypeptides
V-TYPE ATPases ➢ Medical Significance of ABC-type ATPases
○ ABC transporters are medically important
➢ Pump protons into organelles such as vacuoles,
because some of them pump antibiotics or
vesicles, lysosomes, endosomes, and the Golgi
drugs out of cells, rendering the cell resistant
complex.
to the drug
➢ They have two multisubunit components:
○ Some human tumors are resistant to drugs
○ An integral component embedded in the
that normally inhibit growth of tumors; the
membrane.
resistant cells have high concentrations of an

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ABC transporter called MDR (multidrug ➢ Light-driven proton transport in some bacteria is an
resistance) transport protein example of an unusual type of transport

MDR Transport Protein Direct Active Transport: The Na+/K+ Pump Maintains
➢ MDR transport protein pumps hydrophobic drugs out Electrochemical Ion Gradients
of cells, reducing the cytoplasmic concentration and ➢ In a typical animal cell, [K+]inside/[K+]outside is about 35:1
hence their effectiveness and [Na+]inside/[Na+]outside is around 0.08:1
➢ Unlike most ABC transporters, MDR protein ➢ The electrochemical potentials for sodium and
transports a wide range of chemically dissimilar drugs potassium are essential as a driving force for coupled
➢ The MDR protein of some bacteria render them transport and for transmission of nerve impulses
resistant to antibiotics by a similar mechanism
Requirement for energy
Indirect Active Transport Is Driven by Ion Gradients
➢ The pumping of both Na+ and K+ ions against their
➢ Indirect active transport (or secondary active
gradients requires energy
transport) is not powered by ATP hydrolysis
➢ The pump that is responsible, the Na+/K+ ATPase (or
➢ The inward transport of molecules up their
pump), uses the exergonic hydrolysis of ATP to drive
electrochemical gradients is often coupled to and
the transport of both ions
driven by simultaneous inward movement of Na+
➢ It is responsible for the asymmetric distribution of ions
(animals) or protons (plant, fungi, bacteria) down their
across the plasma membrane of animal cells
gradients
Structure of the Na+/K+ ATPase
Support mechanisms of indirect active transport
➢ The pump is a tetrameric transmembrane protein with
➢ Most cells pump either sodium ions or protons out of
two α and two β subunits
the cell (e.g., the Na+/K+ pump in animals)
➢ The α subunits contain binding sites for sodium and
➢ The resulting high extracellular concentration of Na+
ATP on the cytoplasmic side and potassium and ATP
is a driving force for the uptake of sugars and amino
on the external side
acids
➢ Three sodium ions are moved out and two potassium
➢ This is indirectly related to ATP because the pump
ions moved in per molecule of ATP hydrolysed
that maintains the sodium ion gradient is driven by
ATP

Proton gradients drive indirect active transport in many Structure of the Na+/K+ ATPase
organisms ➢ The Na+/K+ pump has two alternative conformational
➢ Most organisms rely on proton gradients rather than states, E1 and E2
the Na+ gradients used by animals ➢ The E1 conformation is open to the inside of the cell
➢ For example, fungi and plants use proton symport for and has high affinity for Na+ ions
the uptake of organic solutes, with ATP driving the ➢ The E2 conformation is open to the outside of the cell
proton pump that creates and maintains the proton and has high affinity for K+ ions
electrochemical potential
➢ Proton or ion gradients can be used for export as well Mechanism of the Na+/K+ pump
as import ➢ 1. Three Na+ ions bind to the E1 conformation
➢ 2. This triggers phosphorylation of the a subunit by
Example of Active Transport ATP
➢ The Na+/K+ ATPase (or pump) in all animal cells is a ➢ 3. The pump undergoes a shift to the E2 conformation,
well-understood example of direct active transport by causing release of the Na+ ions on the outside of the
a P-type ATPase cell
➢ The Na+/gucose symporter is an example of indirect ➢ 4. Two K+ ions bind to the E2 conformation on the
active transport outside of the cell

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➢ 5. This triggers dephosphorylation of the α subunit by

ATP and a return to the E1 conformation
➢ 6. In the conformational change, K+ ions are carried
to the inside of the cell and released

The Bacteriorhodopsin Proton Pump Uses Light Energy to

Transport Protons
➢ Bacteriorhodopsin is a small integral membrane
protein in the plasma membrane of archaea of the
genus Halobacterium
Indirect Active Transport: Sodium Symport Drives the Uptake of ➢ It uses energy from photons of light to drive active
Glucose transport of protons out of the cells
➢ Although most glucose into and out of our cells occurs ➢ It creates an electrochemical proton gradient that
by facilitated diffusion, some cells use a Na+/glucose powers synthesis of ATP by an ATP synthase
symporter ➢ The light-absorbing pigment is retinal, which is related
➢ For example, the cells lining the intestine take up to vitamin A
glucose and some amino acids even when their ➢ Retinal makes the bacteria purple, so halobacteria are
concentrations are much lower outside than inside the also called purple synthetic bacteria
cells ➢ Bacteriorhodopsin has seven α-helical
membrane-spanning segments forming a cylindrical
Uptake of glucose via sodium symport requires energy
shape
➢ A steep Na+ gradient that is maintained across the
plasma membrane (via the Na+/K+ pump) is used to
provide the energy needed
➢ The proteins responsible for sodium symport are
called sodium-dependent glucose transporters, or
SGLT proteins

Mechanism for the Na+/glucose symporter

➢ 1. Two external Na+ ions bind their sites on the
symporter, which is open to the exterior
➢ 2. This allows one molecule of glucose to bind
➢ 3. A conformational change in the proteins exposes
the glucose and Na+ inside the cell
➢ 4. The two Na+ ions dissociate in response to the low
internal Na+ concentration
➢ 5. This locks the symporter in its inward-facing
conformation until the glucose dissociates
➢ 6. The loss of glucose frees the symporter to return to
the outward-facing conformation

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Bacteriorhodopsin function
➢ The retinal chromophore is normally present in an
all-trans conformation, covalently linked to a lysine
side chain at position 216
➢ When the retinal absorbs a photon, one of its double
bonds isomerases to a cis form, activating the
bacteriorhodopsin molecule
➢ The photoactivated molecule then transfers protons to
the outside of the cell
➢ The proton gradient produced by pumping protons out
of the cell is used to produce ATP
➢ Protons flow back into the cell down their
concentration gradient, using ATP synthases to
produce ATP
➢ This mechanism is being researched for the relatively
new field of biomolecular electronics

The Energetics of Transport

➢ Every transport event in the cell is an energy
transaction
➢ For uncharged solutes, the only variable is the
concentration gradient across the membrane
➢ For charged solutes, both concentration and electrical
potential are relevant

Guide Questions
➢ 6-9. What are the 4 types of ATPases? P-type,
V-type, F-type, ABC-type
➢ 10. ____ pumps hydrophobic drugs out of cells,
reducing the cytoplasmic concentration. MDR
transport protein

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JUNE 6, 2024 Membrane Biosynthesis

Fatty acids for membrane phospholipids are
CELL AND MOLECULAR BIOLOGY ➢
synthesized in the cytoplasm and incorporated into the
THE ENDOMEMBRANE SYSTEM – PART 1
ER membrane on the cytosolic side.
➢ Rough and smooth endoplasmic reticulum and the
➢ They are transferred to the lumenal side of the bilayer
Golgi complex are sites for protein synthesis,
by enzymes called phospholipid translocators
processing, and sorting.
(flippases).
➢ Endosomes carry and sort material brought into the
➢ The type of phospholipid molecules transferred across
cell.
the membrane depends on the particular translocator
➢ Lysosomes digest ingested material and unneeded
present, leading to membrane asymmetry.
cellular components.
➢ The distinct composition of cytosolic and lumenal
➢ These form the endomembrane system.
monolayers established in the ER is transferred to other
cellular membranes.
➢ Movement of phospholipids from ER to mitochondria,
chloroplasts, or peroxisomes is problematic.
➢ Phospholipid exchange proteins (phospholipid transfer
proteins) convey specific phospholipids to these
organelles.

PEROXISOMES
➢ Peroxisomes house hydrogen peroxide-generating
reactions.
➢ They also perform diverse metabolic functions.
➢ Kasama sa nag-bbreakdown.

THE ENDOPLASMIC RETICULUM

➢ The endoplasmic reticulum (ER) is a continuous network
of flattened sacs, tubules, and vesicles through the
cytoplasm of a eukaryotic cell.
➢ The membrane-bound sacs are called ER cisternae and A striking feature of the plasma membrane of hepatocytes is the relatively
low amount of phosphoglycerides and high cholesterol, sphingomyelin,
the space inside them is the ER lumen.
and glycolipids.
Functions of the Endoplasmic Reticulum
Cholesterol
➢ The enzymes associated with the ER are involved in
➢ Cholesterol, cortisol, and steroid hormones share a
synthesis of proteins for:
four-ring structure, but differ in the number and
○ Incorporation into the plasma membrane
arrangement of carbon side chains and hydroxyl
○ Organelles of the endomembrane system
groups.
○ Export from the cell
➢ Hydroxymethylglutaryl/-CoA reductase (HMG-CoA
➢ The ER is also involved in lipid synthesis:
reductase) is the committed step in cholesterol
○ The smooth endoplasmic reticulum
biosynthesis.
The ER Plays a Central Role in the Biosynthesis of Membranes ➢ It is found in smooth ER of liver cells and is targeted by
cholesterol-lowering drugs called statins.
➢ In eukaryotic cells, the ER is the primary source of
membrane lipids, with a few exceptions. TYPES OF ENDOPLASMIC RETICULUM
➢ Mitochondria synthesize phosphatidylethanolamine. Rough Endoplasmic Reticulum
➢ Peroxisomes synthesize cholesterol.
1. Ribosomes on the cytosolic side of the RER synthesize
➢ Chloroplasts contain enzymes for chloroplast-specific
both membrane-bound and soluble proteins for the
lipids.
endomembrane system.

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2. Newly synthesized proteins are inserted into the are associated with spontaneous
endomembrane system through a pore complex as cancers in mice.
they are synthesized (cotranslationally). iii. Cigarette smoke is a potent inducer
3. Rough ER is the site for: of aryl hydrocarbon carboxylase.
○ The initial steps of addition of carbohydrates 2. Carbohydrate metabolism
to glycoproteins; a. Smooth ER is involved in breakdown of stored
○ The folding of polypeptides; glycogen; it contains glucose-6-phosphatase,
○ Recognition and removal of misfolded an enzyme unique to smooth ER.
proteins; and b. Glucose-6-phosphatase hydrolyzes the
○ Assembly of multimeric protein complexes. phosphate from glucose-6-phosphate to form
4. Rough ER has a role in quality control. free glucose.
○ In ER-associated degradation (ERAD), proteins
that are incorrectly folded, modified, or
assembled are exported for degradation. 3. Regulation of Glucose
○ Degradation occurs in cytosolic proteasomes. ○ The liver stores glucose as glycogen in
5. A subdomain of rough ER, the transitional elements granules associated with smooth ER.
(TEs), plays a role in the formation of transition vesicles ○ When glucose is needed, glycogen is broken
that shuttle lipids and proteins from the ER to the Golgi down by phosphorylysis, producing
complex. glucose-6-phosphate.
○ This must be converted to free glucose in
Smooth Endoplasmic Reticulum order to leave the cell and enter the
➢ The smooth endoplasmic reticulum lacks ribosomes and bloodstream.
has other roles in the cell:
1. Drug Detoxification
a. Drug detoxification often involves
hydroxylation.
i. Adding hydroxyl groups to
hydrophobic drugs increases their
solubility, making them easier to
excrete from the body.
b. Hydroxylation is catalyzed by a member of
the cytochrome P-450 family of proteins, also
called monooxygenases.
c. Hydroxylation occurs via electron transport. Figure 12-2 The Role of the Smooth ER in the Catabolism of Liver Glycogen. (a) This
i. Electrons from NADPH or NADH are electron micrograph of a liver cell shows numerous granules of glycogen closely
associated with smooth ER (b) Glycogen degradation produces glucose-1-phosphate
transferred to a heme group in (glucose-1-P), which is converted to glucose-6-phosphate (glucose- 6-P). Production
cytochrome P-450. of free glucose from glucose-6-P requires glucose-6-phosphatase, an enzyme
ii. An electron is donated to O2, where associated with the smooth ER membrane. Free glucose is then transported out of the
liver cell by a glucose transporter in the plasma membrane.
one oxygen atom forms H2O and the
other is added to the substrate as a
4. Calcium Storage
hydroxyl group.
○ The sarcoplasmic reticulum of muscle cells is
iii. RH + NAD(P)H + H+ + O2 → ROH +
an example of smooth ER that specializes in
NAD(P)+ + H2O
calcium storage.
d. Drug Tolerance
○ The ER lumen contains high concentrations of
i. Injection of phenobarbitol into rats
calcium-binding proteins.
causes rapid increases in the
○ Calcium ions are pumped into the ER by
barbiturate-detoxifying enzymes and
ATP-dependent calcium ATPases and are
a proliferation of smooth ER.
released when needed for muscle
ii. This means that higher doses of the
contraction.
drug are needed to achieve the
5. Steroid Biosynthesis
same effect, a phenomenon known
○ Smooth ER in some cells is the site of
as tolerance.
cholesterol and steroid hormone synthesis.
iii. The enzymes involved can decrease
○ Large amounts of smooth ER are found in cells
the effectiveness of other drugs as
that synthesize these.
well.
○ Smooth ER has also been found associated
e. Drug Detoxification in the Smooth ER
with plastids in some plants. It may also be
i. Another cytochrome P-450 is part of
involved in phytohormone synthesis.
a complex called aryl hydrocarbon
hydroxylase, which metabolizes
Distinguishing RER from SER
polycyclic hydrocarbons.
ii. The products can be more toxic ➢ Rough and smooth ER are easily distinguished.
than the original compounds; some ➢ Rough ER membranes form large flattened sheets.

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➢ Smooth ER membranes form tubular structures.

The Golgi Network
➢ Transitional elements of the rough ER are an exception;
they resemble the smooth ER. ➢ Proteins and lipids leave the Golgi in transport vesicles
that continuously bud from the tips of the TGN.
➢ Between the TGN and CGN are medial cisternae,
where much of the processing of proteins occurs.
➢ Each compartment shows biochemical polarity,
containing specific proteins unique to each portion of
the network.

Variation in Amounts of Rough and Smooth ER

➢ Both types of ER are present in most cells, but there is
variation in the relative amounts.
➢ Cells involved in synthesis of secretory proteins have
prominent rough ER networks.
➢ Cells producing steroid hormones tend to have
extensive networks of smooth ER.

Microsomes
➢ When tissue is homogenized, the ER membranes can
break into smaller fragments and form sealed vesicles
called microsomes.
➢ These can be useful for studying both types of ER.
(a) A Golgi stack in an animal cell
➢ Microsomes do not form naturally in cells.

THE GOLGI COMPLEX

➢ The Golgi complex is functionally and physically linked
to the ER.
➢ Here, glycoproteins and membrane lipids from the ER
undergo further processing and are sorted and
packaged for transport.
➢ Thus, the Golgi complex plays a central role in
membrane and protein trafficking in eukaryotic cells.

The Golgi Complex Consists of a Series of

Membrane-Bound Cisternae
➢ The Golgi complex is a series of flattened
membrane-bounded cisternae.
➢ A series of cisternae, usually 3-8, is called a Golgi stack.
○ Some cells have one large stack, and others,
especially secretory cells, have hundreds or
thousands of stacks.
➢ Transport Vesicles:
○ Both ER and the Golgi complex are
surrounded by numerous transport vesicles
Two Models Depict the Flow of Lipids and Proteins Through the
that carry lipids and proteins from the ER to
Golgi Complex
the Golgi complex and then to various
destinations in the cell. ➢ Two models have been proposed to explain the
○ The Golgi complex lumen (intracisternal movement of lipids and proteins from the Golgi.
space) is part of the endomembrane system. ➢ These are:
1. The stationary cisternae model
The Two Faces of the Golgi Stack ■ In this model, each cisterna in the
➢ Each Golgi stack has two distinct sides, or faces. Golgi stack is a stable structure.
➢ The cis face is oriented toward the ER. The Golgi ■ Transport of materials from one
compartment on this side is called the cis-Golgi cisterna to another is mediated by
network (CGN). shuttle vesicles.
➢ The opposite side is called the trans face and the ■ These bud off from one cisterna and
compartment on this side is called the trans-Golgi fuse with the next cisterna in a cis- to
network (TGN). trans- sequence.

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2. The cisternal maturation model

○ In this model, the Golgi cisternae are transient
compartments.
○ These gradually change from CGN through
medial cisternae to TGN.
○ Enzymes not needed in later compartments
are returned to earlier compartments in
vesicles.
➢ These two models are not mutually exclusive.
○ Both models involve the formation of transport
vesicles containing sorted cargo targeted for
various destinations.
○ Experimental evidence suggests that these
models are not mutually exclusive.
○ Experiments involve tracking the movement of
substances between the compartments and
time-lapse fluorescence microscopy.

Anterograde Transport
➢ Movement of material toward the plasma membrane is
called anterograde transport.
➢ As a secretory granule fuses with the plasma
membrane and discharges its contents (exocytosis), a
bit of membrane from the ER becomes part of the
plasma membrane.
➢ This flow of lipids toward the plasma membrane must
be balanced.

Retrograde Transport
➢ Retrograde transport is the flow of vesicles from Golgi
cisternae back to the ER.
Compartmentalization of the Steps of Glycosylation and Subsequent
➢ This allows the cell to balance the flow of lipids toward Modification of Proteins. Enzymes that catalyze specific steps of
the plasma membrane. glycosylation and further modification of proteins reside in different
➢ It also ensures a supply of materials for forming new compartments of the ER and Golgi apparatus. Processing occurs
vesicles. sequentially as proteins travel from the ER to the CGN and on to the TGN.
These potential modifications do not necessarily occur with all
glycoproteins.
ROLES OF THE ER & GOLGI IN PROTEIN GLYCOSYLATION
➢ Much of the protein processing carried out in the ER
and Golgi involves glycosylation—the addition of 1. Glycosylation begins as dolichol phosphate, an
carbohydrate side chains to proteins. oligosaccharide carrier, is inserted into the ER
➢ Enzyme-catalyzed reactions involving the resulting membrane.
glycoproteins then modify the oligosaccharide side 2. GlcNAc and mannose groups are then added to the
chain. phosphate group.
3. The growing core oligosaccharide is translocated to
Two General Kinds of Glycosylation the ER lumen by a flippase.
4. Once inside the lumen, more mannose and glucose
➢ N-linked glycosylation (N-glycosylation) involves the
are added.
addition of an oligosaccharide to the nitrogen atom of
5. The completed core oligosaccharide is transferred from
certain arginine residues.
dolichol to the asparagine residue of the recipient
➢ O-linked glycosylation involves the addition of the
protein.
oligosaccharide to the oxygen atom on the hydroxyl
6. The core oligosaccharide attached to the protein is
group of certain serine or threonine residues.
trimmed and modified.
Initial Glycosylation Occurs in the ER
➢ The initial steps of N-glycosylation take place on the
cytosolic surface of the ER membrane.
➢ Later steps take place in the ER lumen.
➢ All carbohydrate side chains initially have a common
core oligosaccharide consisting of:
○ 2 units of N-acetylglucosamine,
○ 9 mannose units, and
○ 3 glucose units.

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Proper Folding in the ER

➢ A glucosyl transferase, UDP-glucose:glycoprotein
glucotransferase (UGGT), binds to improperly folded
proteins.
➢ It adds back a single glucose unit, making the protein a
substrate for CNX/CRT binding.
➢ Once proper conformation is achieved, UGGT no
longer binds the new glycoprotein, which moves on to
the Golgi.

Further Glycosylation Occurs in the Golgi Complex

➢ Further processing of N-glycosylated proteins occurs in
the Golgi complex as the glycoproteins move from the
cis face through to the trans face.
➢ These terminal glycosylations are variable and create
great diversity.
○ Terminal glycosylation involves the removal of
a few units of the core oligosaccharide and
sometimes, nothing more.
○ In some cases, more complex
oligosaccharides are generated by adding
GlcNAc or other monosaccharides.
○ Sometimes, galactose units are added by
galactosyl transferases.
○ The ER and Golgi contain hundreds of
different glycosyl transferases.

GUIDE QUESTIONS
➢ 1-5. What forms the endomembrane system? Rough ER,
1. Dolichol phosphate in the ER membrane acts as the carrier of
oligosaccharide units for protein glycosylation. In mammals, it
Smooth ER, Golgi complex, Endosomes, Lysosomes
usually equals 18. ➢ 6. Movement of material toward the plasma
2. Core oligosaccharide synthesis begins in the cytoplasm as membrane is called ____. Anterograde Transport
N-acetylglucosamine (N) and mannose (M) units are added to ➢ 7. _____ is the flow of vesicles from Golgi cisternae back
dolichol phosphate. to the ER. Retrograde Transport
3. Translocation of the oligosaccharide from the cytosol to the ER
➢ 8-9. What are the 2 general kinds of glycosylation?
lumen is catalyzed by a phospholipid translocator (flippase).
N-linked glycosylation and O-linked glycosylation
4. Completion of the core oligosaccharide occurs in the ER lumen
as more mannose and glucose (G) units are added.
➢ 10. T or F. Cotranslational glycosylation helps promote
5. Transfer of the completed core oligosaccharide to an proper protein folding. T
asparagine residue of the recipient protein is catalyzed by an
oligosaccharyl transferase.
6. Final processing involves the removal of certain glucose and
mannose units in the ER before transfer of the glycoprotein to
the Golgi.

Cotranslational Glycosylation
➢ Usually, the oligosaccharide is added to the recipient
protein as the polypeptide is being synthesized.
○ This is called cotranslational glycosylation.
➢ It helps to promote proper protein folding.

Two Proteins Assist with Proper Folding

➢ Two ER proteins, calnexin (CNX) and calreticulin (CRT),
bind to monoglucosylated proteins and promote
disulfide bond formation.
➢ This occurs via a complex that includes a thiol
reductase known as ERp57.
➢ The complex dissociates, and the final glucose is
removed by glucosidase II.

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JUNE 10, 2024 ● (3) Retrograde traffic returns compartment-specific

proteins to earlier compartments.
PART 2: ENDOMEMBRANE SYSTEM
Roles of the ER and Golgi Complex in Protein Trafficking
***ORIGINAL SCREENSHOT OF THE PPT SLIDE
➢ Proteins synthesized in the rough ER must be directed to
a variety of locations
➢ Once a protein reaches its destination, it must be
prevented from leaving
➢ Each protein contains a specific "tag," targeting it to a
transport vesicle that will take it to the correct location

PROTEIN TAGS
➢ Depending on the protein and destination, a tag may
be an amino acid sequence, a hydrophobic domain,
or oligosaccharide side chain, or some other feature
➢ Tags can also be used to exclude material from certain
vesicles.

LIPID TAGS
➢ Membrane lipids may also be tagged to help vesicles
reach their destinations
➢ Lipid tags can be one or more phosphate groups
attached to positions 3, 4, and/or 5 of a membrane OVERVIEW OF TRAFFICKING
phosphatidyl inositol ➢ Sorting of proteins begins in the ER and early
compartments of the Golgi
OVERVIEW OF HOW THEY DELIVER THE PROTEINS OR LIPIDS ➢ There are mechanisms to retrieve or retain
compartment-specific proteins
➢ The final sorting of material that will leave the Golgi
complex occurs in the TGN

ER-SPECIFIC PROTEINS CONTAIN RETENTION AND RETRIEVAL TAGS

➢ Protein composition in the ER is maintained by
preventing some proteins from escaping the ER and by
retrieving others from the Golgi
➢ Some proteins localized to the ER contain the
sequence RXR (Arg-X-Arg; X is any amino acid)
➢ This is a retention tag, and is also found in some proteins
that are destined for the plasma membrane

THE RXR TAG

➢ The N-methyl-D-aspartate (NMDA) receptor, important
in mammalian neurotransmission, has the RXR tag
➢ It is thought that the individual subunits of the the
● (1) As ribosomes of the rough ER synthesize proteins, the
receptor must be retained in the ER until assembly is
proteins enter the ER lumen, where initial glycosylation
complete
steps occur
➢ The RXR tag must be masked to allow the assembled
● (2) Transition vesicles carry glycosylated proteins and
complex to leave the ER
newly synthesized lipids to the CGN.
● (3) Lipids and proteins move through the cisternae of
RETRIEVAL TAGS
the Golgi stack.
➢ Some proteins returned from the Golgi to the ER
● (4A) At the TGN, some vesicles form secretory vesicles,
contain retrieval tags
which release their contents at the plasma membrane
➢ The tags are short C-terminal sequences such as KDEL
by exocytosis.
(Lys-Asp-Glu-Leu) or KKXX in mammals and HDEL
● (4B) Other vesicles bud from the TGN to form
(His-Asp-Glu-Leu) in yeast
endosomes that help make lysosomes.
➢ When a protein with this tag binds a receptor, the
receptor-ligand complex is packaged into a transport
● (1) At the same time, proteins and other materials can
vesicle for return to the ER
be taken into the cell by endocytosis, forming vesicles
that fuse with early endosomes.
● (2) Early endosomes containing this material for
digestion mature to form late endosomes and then
lysosomes.

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EVIDENCE REGARDING RETRIEVAL TAGS

➢ Evidence about the importance of retrieval tags comes
from experiments involving chimeric proteins (fusion
proteins)
➢ These are made by joining the DNA sequences for two
polypeptide segments to allow production of a hybrid
protein
➢ Proteins normally secreted from the cell that are altered
to contain the retrieval tag end up in the ER

GOLGI COMPLEX PROTEINS MAY BE SORTED ACCORDING TO THE

LENGTHS OF THEIR MEMBRANE-SPANNING DOMAINS
➢ Some proteins resident to the Golgi complex also
contain retention or retrieval tags
➢ Large complexes that are excluded from transport
vesicles may play a role in maintaining the protein
composition of the Golgi complex
➢ A third mechanism involves hydrophobic regions of
Golgi proteins

GOLGI-SPECIFIC PROTEINS ARE INTEGRAL MEMBRANE PROTEINS

➢ All Golgi-specific proteins are integral membrane
proteins with one or more hydrophobic
membrane-spanning domains
THE MANNOSE-6-PHOSPHATE TAG
➢ The length of the hydrophobic domains may determine
into which cisternae each protein is incorporated ➢ Phosphorylation of mannose is catalyzed by two
➢ The thickness of cellular membranes increases Golgi-specific enzymes
progressively from the ER (5nm) to the plasma ➢ The first is a phosphotransferase that adds
membrane (8nm) GIcNAc-1-phosphate to carbon 6 of mannose in an
early Golgi compartment
LENGTH OF HYDROPHOBIC DOMAINS IS CORRELATED WITH ➢ The second, in a mid-Golgi compartment, removes
LOCATION IN THE GOLGI COMPLEX GIcNAc, leaving behind the mannose-6-phosphate
reside
➢ The thickness of membranes in the Golgi increases from
the CGN to the TGN
DESTINATION OF LYSOSOMAL PROTEINS
➢ Proteins move from compartment to compartment until
the membrane thickness exceeds the length of the ➢ Tagged lysosomal proteins bind to
transmembrane domains mannose-6-phosphate receptors (MPRs)
➢ This blocks further migration ➢ The receptor-ligand complexes are packaged into
transport vesicles and conveyed to an endosome
TARGETING OF SOLUBLE LYSOSOMAL PROTEINS TO ENDOSOMES ➢ In animal cells, lysosomal enzymes are transported from
AND LYSOSOMES IS A MODEL FOR PROTEIN SORTING IN THE TGN the TGN to organelles known as late endosomes
➢ Soluble lysosomal enzymes in the ER and early Golgi ➢ Dissociation of the lysosomal enzymes prevents the
compartments undergo N-glycosylation followed by retrograde movement of the enzymes back to the
removal of glucose and mannose units Golgi with the receptors
➢ The mannose residues on the side chains are ➢ The late endosome matures to form a new lysosome, or
phosphorylated within the Golgi complex, forming an delivers its contents to an active lysosome
oligosaccharide containing mannose-6-phosphate ➢ In the human genetic disorder, I-cell disease, lysosomal
➢ This tag ensures delivery of lysosomal proteins to the enzymes are misdirected
lysosomes
SECRETORY PATHWAYS TRANSPORT MOLECULES TO THE EXTERIOR
OF THE CELL
➢ Secretory pathways move proteins from the ER through
the Golgi complex to secretory vesicles and secretory
granules
➢ The secretory granules then discharge their contents to
the exterior of the cell
➢ Experiment using electron microscopy autoradiography
shows the movement of proteins through secretory
pathways

RESULTS OF THE EXPERIMENT

➢ Proteins were radioactively labeled briefly

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➢ After three minutes, the proteins could be seen primarily REGULATED SECRETION
in the rough ER ➢ Secretory vesicles involved in regulated secretion
➢ A few minutes later, the proteins began to appear in accumulate in the cell and only fuse with the plasma
the Golgi complex membrane in response to specific signals
➢ An important example is neurotransmitter release
➢ Regulated secretory vesicles form by budding from the
TGN as immature secretory vesicles
➢ Maturation of secretory proteins involves their
concentration, called condensation, and sometimes
proteolytic processing
➢ The mature secretory vesicles move close to the site of
secretion and remain there until receiving a signal
➢ The signal triggers vesicles to release their contents by
fusion with the plasma membrane

EXCLUDING NONSECRETORY PROTEINS FROM VESICLES

➢ Evidence suggests that high concentrations of
secretory proteins leads to formation of protein
aggregates
➢ These aggregates, formed in the TGN, act to exclude
nonsecretory proteins from the forming secretory
vesicles
➢ Proteins that do not form aggregates or enter secretory
vesicles would be transported elsewhere
➢ After 37 minutes, the protein was detected in vesicles
budding from the Golgi (named condensing vacuoles ZYMOGEN GRANULES
by the researchers) ➢ Zymogen granules are a type of mature regulated
➢ After 117 minutes, the protein began to accumulate secretory vesicle that are usually quite large and
zymogen granules, vesicles that discharge their contain highly concentrated protein
contents out of the cell

CONSTITUTIVE SECRETION
➢ After budding from the TGN, some vesicles move
directly to the cell surface and immediately fuse with
the plasma membrane
➢ This unregulated process is continuous and
independent of external signals
➢ It is called constitutive secretion; one example is mucus
secretion by the intestinal lining EXOCYTOSIS AND ENDOCYTOSIS: TRANSPORTING MATERIAL
ACROSS THE PLASMA MEMBRANE
CONSTITUTIVE SECRETION, BY DEFAULT? ➢ Two methods (unique to eukaryotes) for transporting
➢ Constitutive secretion was once thought to be a materials across the plasma membrane are
default pathway for proteins synthesized by rough ER ○ Exocytosis, the process by which secretory
➢ It was thought that proteins destined to stay in the vesicles release their contents outside the cell
endomembrane system must have a tag to avoid ○ Endocytosis, the process by which cells
constitutive secretion internalize external materials
➢ Current evidence suggests that some tags may be
required for constitutive secretion

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EXOCYTOSIS RELEASES INTRACELLULAR MOLECULES

OUTSIDE THE CELL
➢ In exocytosis, proteins in a vesicle are released to the
exterior of the cell as the vesicle fuses with the plasma
membrane
➢ Animal cells secrete hormones, mucus, milk proteins,
and digestive enzymes this way
➢ Plant and fungal cells secrete enzyme and structural
proteins for the cell wall

THE PROCESS OF EXOCYTOSIS

➢ In the photo, we can see on the right the secretory

vesicle (SV) incorporating itself to the plasma
membrane (PM). This exposes the glycoproteins and
glycolipids towards outside.

MECHANISM OF EXOCYTOSIS
➢ The mechanism of the movement of exocytotic vesicles
to the cell surface is not clear
➢ Evidence points to the involvement of microtubules in
vesicle movement
➢ Vesicle movement stops when cells are treated with
colchicine, a microtubule assembly inhibitor

THE ROLE OF CALCIUM IN TRIGGERING EXOCYTOSIS

➢ Fusion of regulated secretory vesicles with the plasma
membrane is generally triggered by an extracellular
signal
➢ In the photo:
➢ In most cases a hormone or neurotransmitter binds
1. Vesicles containing products for secretion
receptors on the cell surface and triggers a second
move to the cell surface.
messenger inside the cell
2. The membrane of the vesicle fuses with the
➢ A transient elevation in Ca2+ appears to be an essential
plasma membrane.
step in the signaling cascade
3. Fusion with the plasma membrane discharges
➢ Note:
the contents of the vesicle.
○ The first signal involves the hormones and
4. The membrane of the vesicle becomes part of
neurotransmitters.
the cell membrane.
○ Once bounded to the receptor, it will be
considered as the first signal, which will now
ORIENTATION OF MEMBRANE signal the second messenger inside the cell.
➢ When the vesicle fuses with the plasma membrane ○ Before the signalling cascade, calcium levels
○ The lumenal (inner) membrane of the vesicle must be increased in order to function
becomes part of the outer surface of the exocytosis.
plasma membrane.
○ So, glycolipids and glycoproteins that were POLARIZED SECRETION
formed in the ER and Golgi lumens will face ➢ In many cases, exocytosis of specific proteins is limited
the extracellular space. to a specific surface of the cell
➢ For example, intestinal cells secrete digestive enzymes
only on the side of the cell that faces into the intestine
➢ This is called polarized secretion
○ There is only a specific surface of the cell
where it can secrete proteins and enzymes.

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ENDOCYTOSIS IMPORTS EXTRACELLULAR MOLECULES BY PHAGOCYTES IN IMMUNE FUNCTION

FORMING VESICLES FROM THE PLASMA MEMBRANE ➢ In humans, two types of white blood cells use
➢ Most eukaryotic cells carry out one or more forms of phagocytosis as a means of defense
endocytosis for uptake of extracellular material ○ Neutrophils and macrophages engulf and
digest foreign materials or invasive
microorganisms found in the bloodstream or
injured tissues
○ Macrophages are also scavengers, ingesting
cellular debris and damaged cells.
■ They eat off damaged cells that
were degraded in a wound.

PHAGOCYTES IN THE AMOEBA

➢ Phagocytosis is most extensively studied in amoebae,
which use it for nutrition
➢ Contact with food or other particles triggers the
formation of pseudopods, folds of membrane
➢ These surround the object and engulf it, forming an
intracellular phagocytic vacuole (phagosome)

➢ In the photo:
1. A small segment of the plasma membrane
folds inward (1)
2. Then it pinches off to form an endocytic
vesicle containing ingested substances or
particles (2-4)
➢ This is the direct opposite of exocytosis.
○ EXOCYTOSIS: from the inside, the vesicle will
bind to the plasma membrane, it will fuse,
then rupture, releasing its contents.
○ ENDOCYTOSIS: the small segment of the PM
will fold inward and it will pinch off to form the
endocytic vesicle which contains the ingested
particles.

MEMBRANE FLOW
➢ Endocytosis and exocytosis have opposite effects, in
terms of membrane flow
➢ Exocytosis adds lipids and proteins to the plasma
membrane, whereas endocytosis removes them
➢ The steady-state composition of the plasma membrane
results from a balance between the two processes

PHAGOCYTOSIS ➢ In the photo:

➢ The ingestion of large particles up to and including 1. The phagosome fuses with a late endosome
whole cells or microorganisms is called phagocytosis or matures directly into a lysosome
➢ For many unicellular organisms it is a means of 2. In the lysosome, the engulfed material is
acquiring food digested
➢ For more complex organisms, it is usually restricted to ➢ In the human immune system phagocytes generate
specialized cells called phagocytes toxic amounts of oxidants in the phagosome to kill
○ This is usually used as a defense mechanism microorganisms
for humans in order to fight off foreign
substances.

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PROCESS OF RECEPTOR-MEDIATED ENDOCYTOSIS

➢ In the photo, the pseudopod eats the bacterium, and it

will eat it off. A phagosome will then form and as the
bacterium is being engulfed, it will also become larger.

RECEPTOR-MEDIATED ENDOCYTOSIS
➢ Cells acquire some substances by receptor-mediated
endocytosis (or clathrin-dependent endocytosis)
➢ Cells use receptors on the outer cell surface to
internalize many macromolecules 1. Specific molecules (ligands) bind to their receptors on
➢ Mammalian cells can ingest hormones, growth factors, the outer surface of the cell. (1)
serum proteins, enzymes, cholesterol, antibodies, iron, 2. As the receptor-ligand complexes diffuse laterally they
viruses, bacterial toxins encounter specialized regions called coated pits, sites
for collection and internalization of these complexes.(2)
LOW-DENSITY LIPOPROTEIN 3. In a typical mammalian cell, coated pits occupy about
20% of the total surface area.
➢ Low-density lipoproteins (LDL) are internalized by
4. Accumulation of complexes in the pits triggers the
receptor-mediated endocytosis
accumuration of additional proteins on the cytosolic
○ They are regarded as bad cholesterols.
surface of the membrane
➢ The internalization of LDL carries cholesterol into cells
5. These proteins-adaptor protein, clathrin, dynamin—
➢ The study of hypercholesterolemia and connection to
induce curvature and invagination of the pit (3)
heart disease led to the discovery of
6. Eventually the pit pinches off (4), forming a coated
receptor-mediated endocytosis and a Nobel Prize for
vesicle
Brown and Goldstein
7. The clathrin coat is released, leaving an uncoated
vesicle (5)
8. Coat proteins and dynamin are recycled to the plasma
membrane and the uncoated vesicle fuses with an
early endosome (6)
9. The process is very rapid and coated pits can be very
numerous in cells

➢ In the photo:
1. Yolk particles accumulate in a coated pit—a
shallow invagination of the plasma

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membrane with a clathrin coat on its inner AFTERNATIVE FATES FOR LIGAND-RECEPTOR COMPLEXES
surface.
2. A deeper coated pit forms as more clathrin is
added, forcing the membrane to curve and
trapping additional free particles of yolk.
3. Additional curvature leads to the formation of
a coated vesicle, shown here just prior to
budding from the plasma membrane.
4. A complete coated vesicle has just formed
below the plasma membrane and still has an
intact clathrin coat.

SEVERAL VARIATIONS OF RECEPTOR-MEDIATED ENDOCYTOSIS

➢ Epidermal growth factor undergoes endocytosis and is
a signal that stimulates cell division
➢ As EGF receptors are internalized, the cell becomes less
responsive to EGF, desensitization (hindi na siya
gagaya—similar to hindi na magkakaroon ng
resistance)
➢ Defective desensitization through failure to endocytose
the receptor can lead to excess cell proliferation and
possible tumor formation

VARIATIONS OF RECEPTOR-MEDIATED ENDOCYTOSIS

➢ Receptors may be concentrated in coated pits ➢ In the photo:
independent of ligand binding 1. Some complexes are carried to a lysosome for
➢ In this case, ligand binding triggers internalization degradation
➢ In another variation (e.g., LDL receptors) receptors are 2. Some complexes are carried to the TGN,
constitutively concentrated and constitutively where they enter a variety of pathways
internalized independent of ligand binding 3. Complexes can also travel by transport
vesicles to a different region of the plasma
AFTER INTERNALIZATION membrane, where they are secreted
(transcytosis)
➢ Uncoated vesicles fuse with vesicles budding from the
➢ These are the three (3) alternative fates:
TGN to form early endosomes
○ expelled out (ilabas)
➢ Early endosomes are sites for sorting and recycling of
○ digested
materials brought into the cell
○ recycled
➢ Early endosomes continue to acquire lysosomal
proteins from the TGN and mature to form late
CLATHRIN-INDEPENDENT ENDOCYTOSIS
endosomes, which then develop into lysosomes
➢ Fluid-phase endocytosis is a type of pinocytosis for
nonspecific internalization of extracellular fluid
RECYCLING PLASMA MEMBRANE RECEPTORS
➢ This process does not concentrate the ingested
➢ Receptors from the plasma membrane are recycled material, and contents are routed to early endosomes
due to acidification of the early endosome ○ They do not need the coating and uncoating
➢ The pH gradually lowers as the endosome matures, before fusion with the endosome.
facilitated by an ATP-dependent proton pump ➢ It proceeds fairly constantly and compensates for
➢ The lower pH dissociates ligand and receptors, allowing membrane segments added by exocytosis.
receptors to be returned to the membrane
GUIDE QUESTIONS
1. What are the major steps in trafficking through the
membrane? (5pts)
2. What are the similarities and differences of exocytosis
and endocytosis? (5pts)

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JUNE 18, 2024 - ZOOM ○ These radiate from a central vertex, with the
light chains associated with the inner half of
ENDOMEMBRANE SYSTEM PART 3 each “leg”
COATED VESICLES IN CELLULAR TRANSPORT
○ Triskelions assemble into the hexagons and
➢ Most vesicles in protein and lipid transport are called
pentagons of the lattice around
coated vesicles because of the layers of proteins
clathrin-coated pits and vesicles.
covering their systolic surfaces.
➢ Coated vesicles are involved in vesicular traffic
throughout the endomembrane system, as well as in
exocytosis and endocytosis.
➢ There are several types of coat proteins.

COAT PROTEINS
➢ Most studied coat proteins: clathrin, COPI, and COPII.
➢ The type of coat protein on a vesicle helps to
determine the destination of the vesicle.
➢ They also induce curvature needed for the formation of
the vesicles and prevent nonspecific fusion of the
vesicle with another membrane.

GUIDE QUESTIONS
➢ 1-3. Give at least 3 most studied coat proteins. clathrin,
COPI, COPII
➢ 4. What is the basic unit of clathrin lattices? triskelion.

CAVEOLAE ADAPTOR PROTEINS

➢ A recently discovered protein is caveolin. ➢ The adaptor protein was identified by its ability to
➢ Caveolin-coated vesicles are caveolae. promote assembly of clathrin coats and is sometimes
➢ They are a type of lipid raft rich in cholesterol and called assembly protein.
sphingolipids and may be involved in cholesterol ➢ There are four types of AP complexes, each composed
uptake by cells. of four polypeptides; 2 of adaptin; 1 medium chain,
and 1 small chain.
CLATHRIN-COATED VESICLES ARE SURROUNDED BY LATTICES ➢ Each polypeptide binds to a different receptor.
COMPOSED OF CLATHRIN AND ADAPTOR PROTEIN
➢ Clathrin-coated vesicles are surrounded by coats THE ASSEMBLY OF CLATHRIN COATS DRIVES THE FORMATION OF
made of two multimeric proteins: clathrin and adaptor VESICLES FROM THE PLASMA MEMBRANE AND TGN
protein (AP). ➢ Binding of AP complexes to the plasma membrane and
➢ The shape of clathrin proteins and the way they concentration of receptors or receptor-ligand
assemble provides the driving force to induce a flat complexes require ATP and GTP.
membrane to form a spherical vesicle. ➢ The assembly of the clathrin coat appears to provide
➢ The basic unit of clathrin lattices is a triskelion. some of the driving force for vesicle formation.

CLATHRIN COAT ASSEMBLY

➢ Initially, all clathrin units are hexagonal and form a
planar structure.
➢ As more triskelions are incorporated into the growing
lattice, some pentagons are formed.
➢ The mixture of pentagons and hexagons allows the
new coat to curve around the budding vesicle.

➢ Structure of a triskelion:
○ Each is a multimeric protein composed of
three heavy chains and three light chains.

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COPI- AND COPII-COATED VESICLES TRAVEL BETWEEN THE ER AND

GOLGI COMPLEX CISTERNAE
➢ COPI-coated vesicles are found in all eukaryotic cells
examined and are involved in retrograde transport from
the Golgi back to the ER.
○ pwedeng bumalik.
➢ The vesicles are coated with COPI and an ADP
ribosylation factor (ARF), with a small GTP-binding
protein.
➢ Assembly coat is mediated by ARF.

ROLE OF ARF
➢ In the cytosol, it exists as part of an ARF-GDP complex.
➢ Upon meeting a guanine nucleotide exchange factor
associated with the membrane, the GDP is exchanged
for GTP.
➢ The resulting conformational change in ARF attaches it
to the lipid bilayer.
➢ Once firmly anchored, ARF binds COPI multimers.
➢ Assembly of coat drives vesicle formation.
➢ Once the vesicle is formed, a protein in the donor
membrane triggers hydrolysis of GTP to GDP, a
conformational change in ARP and release of the coat.

COPII-COATED VESICLES
➢ COPII-coated vesicles have a role in transport from the
ER to the Golgi.
➢ In yeast, the COPII coat is assembled from two protein
complexes (Sec 13/31 and Sec 23/24) and a small
GTP-binding protein called Sar1.
➢ Sar1 is similar to ARF and the process of coat formation
is similar to COPI-coated vesicles.
DYNAMIN
SNARE PROTEINS MEDIATE FUSION BETWEEN VESICLES AND TARGET
➢ As clathrin accumulates around the budding vesicle,
MEMBRANES
dynamin is required for constricting and closing the
➢ Once vesicles form, additional proteins ensure delivery
vesicle.
to the correct destination.
➢ Dynamin is a systolic GTPase; as GTP is hydrolyzed,
➢ The SNARE hypothesis explains specificity.
dynamin rings tighten and separate the vesicle from
➢ The hypothesis states that sorting and targeting of
the plasma membrane.
vesicles involves two families of SNARE (SNAP receptor)
proteins.
UNCOATING THE VESICLE
➢ A mechanism is required to remove the clathrin coat SNARE PROTEINS
(uncoat) from the newly formed vesicle.
➢ v-SNAREs (vesicle-SNAP receptors) are found on
➢ Clathrin dissociates rapidly once the vesicle is formed.
vesicles.
➢ Uncoating requires energy, provided by an uncoating
○ v = vesicle (Lazada metaphor: ito daw yung
ATPase.
packages)
➢ t-SNARE (target-SNAP receptors) are found on target
CLATHRIN CAGES
membranes.
➢ In acidic conditions, with calcium present, clathrin can ○ t = target (Lazada metaphor: bahay kung
spontaneously form empty shells called clathrin cages. saan daw dadalhin yung package)
➢ Assembly and disassembly occur very quickly. ➢ v- and t-SNAREs are complementary molecules that
allow recognition between vesicles and their targets.
GUIDE QUESTIONS
➢ 5. What is another name for adaptor proteins?
assembly protein.
➢ 6. _____ required for constricting and closing the vesicle.
dynamin.

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LYSOSOMES ISOLATE DIGESTIVE ENZYMES FROM THE REST OF THE

CELL
➢ Lysosomes contain acid phosphatase and several other
hydrolytic enzymes
➢ They vary in size and shape but are usually about 0.5
μm in diameter, bound by a single membrane
➢ The lumenal side of the membrane is coated with
glycoproteins to protect the membrane from
degradation

RAB GTPases
➢ When a vesicle reaches its destination, Rab GTPases
(specific for different destinations) lock the
complementary SNARE proteins together.
➢ This facilitates membrane fusion.

RELEASE OF SNAREs
➢ Following vesicle fusion, N-ethylmaleimide-sensitive
factor (NSF) and a group of soluble NSF attachment
proteins (SNAPs) mediate release of the SNAREs of the
donor and target membranes.
➢ ATP hydrolysis may be needed, though its role is
unclear. LYSOSOMES ARE HIGHLY ACIDIC INSIDE
➢ NSF and SNAPs are nonspecific.
➢ Lysosomes maintain an acidic environment (pH 4.0-5.0)
inside
SNAREs MAY NOT BE THE WHOLE STORY
➢ ATP-dependent proton pumps in the membrane are
➢ Recent research suggests that SNAREs are not solely
responsible for this
responsible for targeting specificity.
➢ There are numerous enzymes inside lysosomes; all are
➢ Tethering proteins act over longer distances and attach
acid hydrolases
vesicles to their targets before the SNAREs interact.
➢ Chemical blocking of SNARE complex formation does
FINAL STEP OF LYSOSOME DEVELOPMENT
not abolish vesicle-target interaction.
➢ The last step in development of a lysosome is activation
of the acid hydrolases
TETHERING PROTEINS
➢ This occurs as the internal environment becomes more
➢ Two main groups of tethering proteins:
acidic
○ coiled-coil proteins
➢ This occurs through the pumping of protons or through
○ multisubunit complexes
fusion with an existing lysosome
➢ Coiled-coil proteins such as golgins are important in
recognition and binding of COPI or COPII vesicles to
the Golgi.
➢ Multisubunit complexes such as the exocyst complex
are important for protein secretion.

OTHER MULTISUBUNIT PROTEIN COMPLEXES

➢ COG (conserved oligomeric Golgi) complex
➢ GARP (Golgi-associated retrograde protein) complex.
➢ TRAPP (transport protein particle) complex.
➢ All are implicated in initial recognition and specificity of
vesicle-target interaction.

LYSOSOMES AND CELLULAR DIGESTION

➢ The lysosome is an organelle of the endomembrane
system that contains digestive enzymes
➢ It is capable of degrading all the major classes of
biological macromolecules ➢ Phagocytic vacuoles are transformed into lysosomes by
fusing with early endosomes (pathway A).

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➢ Vesicles containing material brought into a cell by

receptor-mediated endocytosis also form early
endosomes (pathway B).
➢ The digestion of old or unwanted organelles or other
cell structures is called autophagy (pathway C).
➢ In some cases lysosomes discharge their enzymes to the
outside of the cell by exocytosis, resulting in
extracellular digestion (pathway D).

LYSOSOMES DEVELOP FROM ENDOSOMES

➢ Lysosomal enzymes are synthesized by ribosomes on
rough ER, and translocated inside
➢ Lysosomal enzymes are delivered from the TGN to
endosomes in transport vesicles
➢ Over time endosomes mature into late endosomes,
with all the enzymes, but not engaged in digestion

LYSOSOMAL ENZYMES ARE IMPORTANT FOR SEVERAL DIFFERENT

DIGESTIVE PROPERTIES
➢ Lysosomes have multiple origins EXTRACELLULAR DIGESTION
➢ Those containing substances that originated outside ➢ Most lysosomal digestion occurs inside the cell
the cell are called heterophagic lysosomes ➢ In some cases, lysosomes discharge their contents
➢ Those with materials that originated inside the cell are outside the cell, resulting in extracellular digestions
called autophagic lysosomes ➢ For example, the head of a sperm releases digestive
enzymes to degrade barriers protecting an egg
PHAGOCYTOSIS AND RECEPTOR-MEDIATED ENDOCYTOSIS:
LYSOSOMES IN DEFENSE AND NUTRITION LYSOSOMAL STORAGE DISEASES ARE USUALLY CHARACTERIZED BY
➢ The degradation of external materials brought into the THE ACCUMULATION OF INDIGESTIBLE MATERIAL
cell occurs by phagocytosis and receptor-mediated ➢ Over 40 lysosomal storage diseases are known, in
endocytosis which certain lysosomal proteins are absent
➢ Phagocytic vacuoles become lysosomes by fusion with ➢ The diseases are characterized by the accumulation of
endosomes substances like that cannot be broken down as
➢ Vesicles formed by receptor-mediated endocytosis needed
fuse with vesicles of the TGN containing acid hydrolases ➢ Most are not treatable yet

AFTER DIGESTION IS COMPLETE EXAMPLES OF LYSOSOMAL STORAGE DISEASES

➢ Eventually indigestible material is all that remains in a ➢ Type Il glycogenesis - accumulation of excessive
lysosome glycogen
➢ The lysosome becomes a residual body when digestion ➢ Hurler syndrome, Hunter syndrome - accumulation
ceases ➢ of glycosaminoglycans
➢ Some cells release the contents by exocytosis; in others, ➢ Tay-Sachs disease - accumulation of a ganglioside in
accumulation of debris may contribute to cellular the nervous system
aging
THE PLANT VACUOLE: A MULTIFUNCTIONAL ORGANELLE
AUTOPHAGY: A BIOLOGICAL RECYCLING SYSTEM ➢ Plant cells have acidic vacuoles that perform the
➢ Cellular structures that are damaged or unneeded function of lysosomes
must be broken down, via autophagy ➢ However, these have additional roles as well
➢ Macrophagy: an organelle is wrapped in a double ➢ Vacuole development is similar to that of lysosomes,
membrane derived from the ER, forming an autophagic with coated vesicles conveying materials for the
vacuole (autophagosome) vacuole to a provacuole, similar to an endosome
➢ Microphagy: a much smaller vacuole is formed,
surrounded by a single-membrane bilayer ADDITIONAL FUNCTIONS OF VACUOLES
➢ Vacuoles mature to form a structure that can fill up to
90% of the cell's total volume
➢ Vacuoles maintain turgor pressure, the osmotic pressure
preventing plant cells from collapsing
➢ They regulate cytosolic pH, using ATP-dependent
proton pumps
➢ They serve as a storage compartment
○ Seed storage proteins
○ Malate (in CAM plants)
○ Anthocyanins

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○ Soluble and insoluble waste

GUIDE QUESTIONS
7. ______is an organelle of the endomembrane system that
contains digestive enzymes. LYSOSOME
8. T or F. v- and t-SNAREs are noncomplementary molecules that
allow recognition between vesicles and their targets. F

PEROXISOMES
➢ Peroxisomes are bounded by single membranes but
are not derived from ER
➢ Thus they are not part of the endomembrane system
➢ The defining characteristic of peroxisomes is the
presence of catalase, for degrading H2O2

THE DISCOVERY OF PEROXISOMES DEPENDED ON INNOVATION IN

EQUILIBRUM DENSITY CENTRIFUGATION
➢ Researchers used a gradient of sucrose concentration
MOST PEROXISOMAL FUNCTIONS ARE LINKED TO HYDROGEN
to isolate specific cellular components
PEROXIDE METABOLISM
➢ They identified a region distinct from known organelles
➢ The essential roles of proxisomes include
that contained the enzyme urate oxidase
○ Hydrogen peroxide metabolism
➢ This region of the gradient contained peroxisomes
○ Detoxification of harmful compounds
○ Oxidation of fatty acids
PEROXISOME STRUCTURE
○ Metabolism of nitrogen-containing
➢ Animal peroxisomes contain a crystalline core,
compounds
consisting of crystalline urate oxidase
○ Catabolism of unusual substances
➢ Plant peroxisomes contain crystalline catalase
➢ Peroxisomes without the crystalline cores may be
HYDROGEN PEROXIDE METABOLISM
difficult to identify, microscopically
➢ Oxidases generate H2O2 in peroxisomes
○ RH2 + O2 → R + H2O2
➢ The hydrogen peroxide is detoxified by catalase
○ 2H2O2 → O2 + 2H2O

HYDROGEN PEROXIDE CAN BE DETOXIFIED ANOTHER WAY

➢ Alternatively, catalase can function as peroxidase
○ R’H2 + H2O2 → R’ + 2H2O
➢ The result is the same in either case – hydrogen
peroxide is degraded while still inside the peroxisome

DETOXIFICATION OF HARMFUL COMPOUNDS

➢ Peroxisomes detoxify reactive oxygen species
-
➢ (H2O2, O2 )
➢ If these accumulate they can cause oxidative stress;
superoxide dismutase and other peroxisome enzymes
detoxify them
➢ Catalase uses a variety of other toxic substances as
electron donors

OXIDATION OF FATTY ACIDS

CHEMICAL IDENTIFICATION OF PEROXISOMES IN PLANT CELLS
➢ Peroxisomes contain enzymes for ß-oxidation of fatty
Catalase oxidizes diaminobenzidine (DAB) to a form
acids
➢

that causes deposition of osmium ions

➢ In animal cells, they oxidize long-chain fatty acids;
These electron-dense deposits can be seen via
once the fatty acids are fewer than 16 carbons in
➢

electron microscopy
length, the rest of the oxidation occurs in mitochondria
➢ In plants and yeast, fatty acids are completely oxidized
in peroxisomes

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METABOLISM OF NITROGEN-CONTAINING COMPOUNDS ➢ These structures on plant roots are involved in nitrogen
➢ Most animals (not primates) require urate oxidase to fixation
oxidize urate, formed during catabolism of nucleic ➢ The peroxisomes in these structures are involved in
acids and some proteins processing the fixed nitrogen
○ urate + O2 → allantoin + H2O2
PEROXISOME BIOGENESIS OCCURS BY DIVISION OF PREEXISTING
AMINOTRANSFERASES PEROXISOMES
➢ Aminotransferases catalyze the transfer of amino ➢ Peroxisomes increase in number as cells grow and
groups from amino acids to a-ketoacids in the divide; this proliferation is biogenesis
degradation and synthesis of amino acids ➢ Proteins required for this process are peroxins

PEROXISOME BIOGENESIS
➢ Membrane components, matrix enzymes, and
cofactors from the cytosol are incorporated into
peroxisomes (1-3)
➢ Then, new peroxisomes are formed by division of a
preexisting one (4)
➢ Some peroxisomes may obtain materials or form de
novo from vesicles derived from the ER (5)

CATABOLISM OF UNUSUAL SUBSTANCES

➢ D-amino acids are rare substances for which the cell
has no degradative pathways, except in the
peroxisome
➢ In some cells peroxisomes also contain enzymes that
break down xenobiotics, compounds foreign to living
organisms
➢ This includes short-chain hydrocarbons such as alkanes

PEROXISOMAL DISORDERS
➢ A large number of disorders arise from defects in
peroxisomal proteins
➢ The most common is X-linked adrenoleukodystrophy
➢ The defective protein in this case may be responsible
for transporting long-chain fatty acids into the SIGNALS THAT TARGET SOME PROTEINS TO PEROXISOMES
peroxisome for degradation
➢ The signal that targets at least some proteins to
peroxisomes is SKL (Ser-Lys-Leu), called PTS-1
PLANT CELLS CONTAIN TYPES OF PEROXISOMES NOT FOUND IN
(peroxisomal targeting signal-1) on the C-terminus
ANIMAL CELLS
➢ It is both necessary and sufficient to direct proteins to
➢ In plants and algae peroxisomes are involved in several peroxisomes
aspects of cell energy metabolism, as already ➢ A second signal, PTS-2, is found on the N-terminus of
described some proteins

LEAF PEROXISOMES GUIDE QUESTIONS

➢ Cells of photosynthetic tissues contain leaf peroxisomes 9. T or F. Peroxisomes are part of the endomembrane system. F
in close contact with mitochondria and chloroplasts 10. T or F. Peroxisomes can detoxify reactive oxygen species. T
➢ They are involved in the glycolate pathway

GLYOXYSOMES
➢ Glyoxysomes occur transiently in seedlings
➢ They contain enzymes needed to convert stored
triacyglycerols to sucrose, β oxidation of fatty acids,
and the glyoxylate cycle
➢ They are only found in tissues where fat is stored, and
when no longer needed are converted to peroxisomes

OTHER TYPES OF PLANT PEROXISOMES

➢ Another kind of specialized peroxisome is found in
nodules

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JUNE 20, 2024

PART 1: CELL CYCLE REGULATION, APOPTOSIS, CANCER
THE CELL CYCLE, DNA REPLICATION, AND MITOSIS
➢ Cell growth is generally accompanied by cell division,
whereby one cell gives rise to two new daughter cells.
➢ All the genetic information in the nucleus must be
accurately duplicated and carefully distributed to the
daughter cells.
➢ In doing this, a cell passes through a series of stages
known as the cell cycle.

OVERVIEW OF THE CELL CYCLE

➢ The cell cycle begins when two new cells are formed
by division of a parent cell and ends when one of these
cells divides again.
➢ M phase is when the cells actually divide; the nucleus
MITOTIC INDEX
first, followed by the cytoplasm.
➢ The percentage of time in the M phase is called the
➢ Nuclear division is mitosis, and division of the cytoplasm
mitotic index.
is cytokinesis.
➢ It can be determined by examining a group of cells
and determining the proportion that are in mitosis at
CHROMOSOMES IN MITOSIS
any point in time.
➢ At the beginning of mitosis, chromatin folds and
➢ For cultured mammalian cells, it is 3-5% or 30-45
condenses to produce visible chromosomes.
minutes.
➢ DNA has replicated, so each chromosome is
composed of two sister chromatids.
G PHASES
➢ The microtubules of the mitotic spindle will distribute the
➢ G1 is quite variable depending on cell type; G2 is
chromatids to opposite ends of the cell.
shorter and less variable.
➢ During G1, a major decision is made, whether a cell will
divide again; cells that arrest in G1, waiting for a signal
to divide, are said to be in G0.
➢ Cells that exit the cell cycle are said to undergo
terminal differentiation.

DNA REPLICATION
➢ DNA replication is a central event in the cell cycle
➢ The underlying mechanism depends on the
GUIDE QUESTIONS double-helical structure of DNA
1. T or F. Cell cycle begins when two new cells are formed ➢ One strand of every new DNA molecule is derived from
by division of a parent cell and ends when one of these the parent molecule, and the other is new:
cells divides again. semiconservative replication
2. T or F. In M phase, the cytoplasm divides first, then the
nucleus.
3. Nucleus: mitosis; Cytoplasm: cytokinesis.

MITOSIS IS A RELATIVELY SHORT PART OF THE CELL CYCLE

➢ Cells spend very little time in the M phase.
➢ Most of the time is spent in the interphase, which is
composed of the G1 phase, the S phase (when DNA is
replicated), and the G2 phase.
➢ The overall length of the cell cycle is called the
generation time; in cultured mammalian cells, this is
about 18-24 hours

➢ In the figure above, one strand would be the template

strand—from the parent—while the other strand is
formed as the new strand.

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EQUILIBRIUM DENSITY CENTRIFUGATION SHOWS THAT DNA ➢ These are formed where replication begins and then
REPLICATION IS SEMICONSERVATIVE proceeds in a bidirectional fashion away from the
➢ Meselson and Stahl (with Vinograd) showed that origin.
replication is semiconservative by using 14N and 15N to
distinguish newly formed DNA strands from old
➢ Bacterial cells were grown in a 15N medium for many
generations to incorporate heavy nitrogen into their
DNA, then transferred to a 14N medium
➢ he strands were distinguished by equilibrium density
centrifugation.

RESULTS OF THE EXPERIMENT

➢ After one cycle of replication in the 14N medium, a
band was observed intermediate between the heavy
and light strands.
➢ If the hybrid DNA was heated to separate the strands,
one strand was "heavy," and the other was "light"
➢ These results were consistent with semiconservative
replication.

➢ Replication forks are the starting point of DNA

replication.

BACTERIAL REPLICATION
➢ Replication forks move away from the origin, unwind
the DNA, and copy both strands as they proceed.
➢ This is called theta (θ) replication and is observed in the
replication of circular DNA molecules.
➢ The two copies of the replicating chromosome bind to
the plasma membrane at their origins; when replication
is complete, the cell divides by binary fission.

➢ In the figure above, we can see that the bacteria

grown in 15N developed heavy DNA.
○ When they were transferred to the 14N, their
first generation had the hybrid DNA, which
contains the light DNA, seen in (b).
○ When they have grown the second
generation, we can see the heavy chain from
the original DNA, as well as the light chain
from the 14N.
○ As seen in (c), we now developed two light
chains, signifying that these ones are formed
from the hybrid first generations of the DNA.

DNA REPLICATION IS USUALLY BIDIRECTIONAL ➢ In Figure 19-4B, the upper left shows oriC, the origin of
➢ DNA replication is especially well-understood in replication in bacterial DNA. Replication begins at this
Escherichia coli point, creating two replication forks that proceed
➢ Saccharomyces cerevisiae and the virus SV40 are used bidirectionally. The DNA unwinds, and new strands are
in studies of eukaryotic replication synthesized simultaneously at each fork, leading to the
➢ Replication is very similar in prokaryotes and eukaryotes formation of two identical circular DNA molecules.

EARLY EXPERIMENTS IN REPLICATION

➢ Cairns studied replication in E. coli; he grew cells in a
medium containing 3H-thymidine.
➢ He visualized the circular chromosomes by
autoradiography; he observed replication forks.

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➢ In the figure above, replicons are located at different

sites; therefore, in a single DNA strand. there could be a
lot of replicons present.
○ It will then produce replication bubbles where
replication forms can be seen to start the
replication process and create a new DNA
strand.
○ Once two bubbles enlarge and come close
to one another, they will fuse to form one
replicon.
○ The process continues until a double helix
DNA is formed.

RATES OF REPLICATION
➢ S phase is very rapid in embryonic cells, where cell
➢ In Figure 19-4C, we see that replication forks form in a
divisions occur in quick succession but slower in adult
cell, leading to the separation of the DNA strands and
cells, in which fewer and more widely spaced replicons
their replication. Once replication is complete, binary
are used.
fission occurs, where the membrane growth pushes the
○ That’s why kids have faster development than
chromosomes apart, creating another cell with the
adults. For them, replication is rapid, but as
same circular DNA.
they grow, their replication slows down.
➢ During the S phase in eukaryotes, not all replicons are
EUKARYOTIC DNA REPLICATION INVOLVES MULTIPLE REPLICONS
activated at the same time; some are replicated early,
➢ In eukaryotes, replication of linear chromosomes is
and others later.
initiated at multiple sites, creating replication units
➢ Genes that are transcriptionally active are replicated
called replicons.
earlier than inactive genes.
➢ At the center of each replicon is a DNA sequence
called an origin of replication, where synthesis is
GUIDE QUESTIONS
initiated by several groups of initiator proteins.
4. When bacterial replication is complete, the cell divides
➢ First, a multisubunit protein complex called the origin
by binary fission.
recognition complex (ORC) binds the replication origin.
5. Replication forks are formed where replication begins
➢ Next, the minichromosome maintenance (MCM)
and then proceeds in a bidirectional fashion away from
proteins bind the origin
the origin.
➢ The MCM proteins include several DNA helicases that
unwind the double helix; a set of proteins called
REPLICATION LICENSING ENSURES THAT DNA MOLECULES ARE
helicase loaders recruit the MCM proteins
DUPLICATED ONLY ONCE PRIOR TO EACH CELL DIVISION
➢ At this point, all the DNA-bound proteins make up the
➢ Licensing is provided by binding of MCM proteins to the
pre-replication complex, and the DNA is "licensed" for
origin, which requires both ORC and helicase loaders.
replication
➢ It ensures that after DNA is replicated at each origin,
the DNA cannot be licensed for replication again until
ORIGINS OF REPLICATION
after mitosis.
➢ DNA sequences that act as replication origins are
➢ After replication begins, the MCM proteins are
greatly varied in eukaryotes
removed from the origins and cannot bind again.
➢ Sequences that confer the ability to replicate when
introduced into DNA molecules are called
ROLE OF CYCLIN-DEPENDENT KINASE (CDK)
autonomously replicating sequences or ARS
➢ Cyclin-dependent kinase, CDK, has many roles in the
➢ After replication begins, two replication forks synthesize
cell cycle
DNA in opposite directions, forming a replication
➢ One form produced early in the S phase activates DNA
bubble that grows as replication proceeds.
synthesis at licensed origins and prevents origins from
being licensed again
➢ It catalyzes the phosphorylation of ORC proteins and
helicase loaders.

GEMININ
➢ Multicellular eukaryotes contain an additional inhibitor
of relicensing called geminin.
➢ It is made during the S phase that blocks the binding of
MCM proteins to DNA.
➢ When the cell completes mitosis, geminin is degraded,
and Cdk activity falls so that licensing can occur for the
next cycle.

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OBSERVATIONS ON TEMPERATURE-SENSITIVE BACTERIA

➢ Bacterial strains have been identified in which DNA
polymerase Ill functions normally at 37°C but loses its
ability to replicate when the temperature is raised to
42°C.
➢ The observations indicate that DNA polymerase Ill is
central to bacterial DNA replication.
➢ However, a variety of other proteins is needed for
replication.

➢ IN FIGURE 19-6, Licensing of DNA Replication During the EUKARYOTE DNA POLYMERASE
Eukaryotic Cell Cycle. ➢ Eukaryotic cells contain several types of DNA
○ DNA is licensed for replication during G1 by polymerase; more than a dozen.
the binding of MCM proteins to replication ➢ Of these, DNA polymerase α, δ, and ε are involved in
origins, an event that requires both ORC and nuclear DNA replication.
helicase loaders. ➢ DNA polymerase γ is used in mitochondrial DNA
○ The licensing system is turned off at the end of replication.
G1 by the production of CDK and/or geminin, ➢ Those types remaining are involved in DNA repair or
whose activities block the functions of the replication across regions of DNA damage.
proteins required for licensing (ORC, helicase
loaders, and MCM). BIOTECHNOLOGY FUNCTIONS OF DNA POLYMERASES
○ After the cell completes mitosis, geminin is ➢ DNA polymerases have practical applications in
degraded, and CDK activity falls, so the biotechnology
licensing system becomes active again for the ➢ The polymerase chain reaction is a technique in which
next cell cycle. a DNA polymerase is used to amplify tiny samples of

DNA POLYMERASES CATALYZE THE ELONGATION OF DNA CHAINS DNA IS SYNTHESIZED AS DISCONTINUOUS SEGMENTS THAT ARE
➢ DNA polymerase is an enzyme that can copy DNA JOINED TOGETHER BY DNA LIGASE
molecules ➢ DNA is synthesized in the 5' to 3' direction, but the two
➢ Incoming nucleotides are added to the 3' hydroxyl end strands of the double helix are oriented in opposite
of the growing DNA chain, so elongation occurs in the directions
5' to 3' direction ➢ One strand (the lagging strand) is synthesized in
➢ Several other forms of DNA polymerase have been discontinuous fragments called Okazaki fragments.
identified; the original is now called DNA polymerase I ➢ The other (the leading strand) is synthesized in a
continuous chain.

OKAZAKI’S EXPERIMENTS
➢ Okazaki isolated DNA from bacteria that were briefly
exposed to a radioactive substrate incorporated into
newly made DNA
➢ Much of the radioactivity was located in small
fragments about 1000 nucleotides long
➢ With longer labeling, the radioactivity became
associated with longer molecules; this conversion did
not take place in bacteria lacking DNA ligase

OKAZAKI'S OBSERVATIONS ILLUSTRATE HOW LAGGING

STRAND SYNTHESIS OCCURS
➢ DNA synthesis from the lagging strand is synthesized in
Okazaki fragments
➢ These are then joined by DNA ligase to form a
TEMPERATURE-SENSITIVE MUTATIONS continuous new 3' to 5' DNA strand
➢ It is difficult to grow and study mutant strains that lack ➢ Okazaki fragments are 1000-2000 nucleotides long in
important functions such as DNA replication. bacteria and viruses, but about one-tenth this length in
➢ One approach involves using temperature-sensitive eukaryotic cells
mutants, which produce proteins that function properly
at 37°C but lose their function when the temperature is
raised to 42°C.

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DNA SYNTHESIS REQUIRES RNA PRIMERS

➢ The observations led to the conclusion that DNA
synthesis is initiated by the formation of short RNA
primers
➢ These are synthesized by primase using a single DNA
strand as the template
➢ In E. coli, primase is inactive unless accompanied by six
other proteins, forming a complex called a primosome

➢ This is an unwinded DNA

○ Leading strand is where it is replicated
continuously
○ Lagging strand is replicated in Okazaki
fragments—discontinuous
■ which will be sealed by the DNA
ligase

PROOFREADING IS PERFORMED BY THE 3'→ 5' EXONUCLEASE

ACTIVITY OF DNA POLYMERASE
➢ About 1 of every 100,000 nucleotides incorporated
during DNA replication is incorrect.
➢ Such mistakes are usually fixed by a proofreading
mechanism
➢ Almost all DNA polymerases have a 3' → 5'
exonuclease activity

PROOFREADING
➢ Exonucleases degrade nucleic acids from the ends of
the molecules
➢ Endonucleases make internal cuts in nucleic acid
molecules
➢ The exonuclease activity of DNA polymerase allows it to
remove incorrectly base-paired nucleotides and
incorporate the correct base

RNA PRIMERS INITIATE DNA REPLICATION

THE PROCESS OF DNA SYNTHESIS
➢ DNA polymerase can only add nucleotides to the 3'
➢ Once the RNA primer is made, DNA polymerase Ill (or
end of an existing nucleotide chain
DNA polymerase α, followed by δ or ε, in eukaryotes)
➢ Researchers implicated RNA in the initiation process
adds deoxynucleotides to the 3' end of the primer.
based on several observations.
➢ For the leading strand, just one primer is needed, but
➢ Observations about RNA involvement in DNA
the lagging strand needs a series of primers to initiate
replication
each Okazaki fragment.
1. Okazaki fragments usually have short stretches
➢ When the DNA chain reaches the next Okazaki
of RNA at their 5' ends
fragment, the RNA is degraded and replaced with
2. DNA polymerase is able to add nucleotides to
DNA; adjacent fragments are joined together by DNA
RNA chains as well as DNA chains
ligase.
3. Cells contain an enzyme called primase that
synthesizes short (~10 nt) chains of RNA using
UNWINDING THE DNA DOUBLE HELIX REQUIRES DNA
DNA as a template
HELICASES, TOPOISOMERASES, AND SINGLE-STRANDED
4. Primase is able to initiate RNA strands without
DNA-BINDING PROTEINS
a pre-existing chain to add to
➢ During DNA replication, the two strands of the double
helix must unwind at each replication fork
➢ Three classes of proteins facilitate the unwinding: DNA
helicases, topoisomerases, and single-stranded
DNA-binding proteins

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➢ DNA helicases are responsible for unwinding the DNA,

using energy from ATP hydrolysis

HELICASES
➢ The DNA double helix is unwound ahead of the
replication fork, the helicases breaking the hydrogen
bonds as they go.
➢ In E. coli, at least two different helicases are involved;
one attaches to the lagging strand and moves 5' → 3',
whereas the other attaches to the leading strand and
moves 3' → 5'
➢ Both are part of the primosome.

TOPOISOMERASES
➢ The unwinding of the helix would create too much
supercoiling if not for topoisomerases. (1) Initiator protein binds to double-stranded DNA at the
➢ These enzymes create swivel points in the DNA origin of replication and, using ATP energy slightly
molecule by making and then quickly sealing unwinds the DNA.
double-strand or single-stranded breaks. (2) DNA helicase binds to the unwound DNA and
➢ Of the ~10 topoisomerases in E. coli, the key enzyme for continues the unwinding. Meanwhile, DNA gyrase
DNA replication is gyrase. promotes strand separation by inducing negative
supercoiling in front of the DNA helicase. Strand
separation is maintained by molecules of
SINGLE-STRANDED DNA BINDING PROTEIN single-stranded DNA binding protein (SSB), which
➢ Once strand separation has begun, molecules of SSB stabilize the unwound region and allow the separated
(single-stranded DNA binding protein) move in quickly strands to serve as templates. A replication fork is now
and attach to the exposed single-strands. in evidence.
➢ They keep the DNA unwound and accessible to the (3) Primase binds to the first initiating sequence on the
replication machinery. leading strand template and synthesizes a short RNA
➢ When a segment of DNA has been replicated, the SSB primer that is complementary to the DNA template.
molecules fall off and are recycled. (4) DNA polymerase III (polymerase a followed by
polymerase & or & in eukaryotes) uses the primer to
initiate DNA synthesis by adding deoxyribonucleotides
to its 3' end. The leading strand requires only one
priming event because DNA synthesis is continuous in
the 5' → 3' direction.

PUTTING IT ALL TOGETHER: DNA REPLICATION IN SUMMARY

➢ Starting at the origin of replication, the machinery at
the replication fork adds proteins required for
synthesizing DNA.
➢ These are DNA helicase, DNA gyrase, SSB, primase, DNA
(5) An RNA primer is made for the lagging strand, and DNA
polymerase, and DNA ligase.
polymerase then extends the strand. In E. coli, the
➢ Several other proteins are used to improve the
primase is part of the primosome, a protein complex
efficiency, e.g., a ring-shaped sliding clamp keeps DNA
that includes the DNA helicase.
polymerase firmly attached to DNA.
(6) For the lagging strand, DNA synthesis is discontinuous
and requires a series of RNA primers (shown in red).
DNA is synthesized at the 3' end of each primer,
generating an Okazaki fragment that grows until it
meets the adjacent fragment. The RNA primer is then
removed by the 5' → 3' exonuclease activity of DNA

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polymerase I and replaced with DNA by the

polymerase activity of the same enzyme.
(7) DNA ligase links together adjacent Okazaki fragments.
Hereafter, DNA ligase, polymerase I, polymerase III,
primase, DNA helicase, and DNA gyrase will be working
simultaneously in the vicinity of the replication fork.

THE REPLISOME
➢ Proteins involved in DNA replication are all closely
associated in one large complex called a replisome.
➢ The activity and movement of the replisome is powered
by nucleoside triphosphate hydrolysis.
➢ As the replisome moves along the DNA, it must
accommodate the fact that DNA is being produced
on both leading and lagging strands.

GUIDE QUESTIONS
6. ____ is an enzyme that can copy DNA molecules. DNA
polymerase
7. ____ degrade nucleic acids from the ends of the molecules.
Exonucleases
8. ____ are responsible for unwinding the DNA, using energy from
ATP hydrolysis. DNA helicases (1) DNA replication is initiated at the origin; the replication
bubble grows as the two replication forks move in
EUKARYOTIC DNA REPLICATION opposite directions.
➢ Eukaryotes have much of the same replication (2) Finally, only one primer (red) remains on each daughter
machinery found in prokaryotes DNA molecule.
➢ E.g. a DNA clamp protein acts along with DNA (3) The last primers are removed by a 5' → 3' exonuclease,
polymerase; one of these is called proliferating nuclear but no DNA polymerase can fill the resulting gaps
cell antigen (PCNA) because there is no 3' OH available to which a
➢ PCNA is a clamp protein for DNA polymerase δ nucleotide can be added.
(4) Each round of replication generates shorter and shorter
TELOMERES SOLVE THE DNA END-REPLICATION PROBLEM DNA molecules.
➢ Linear DNA molecules have a problem in completing
DNA replication on the lagging strand because primers TELOMERES AND TELOMERASE
are required.
➢ Human telomeres have 100 to 1500 copies of TTAGGG
➢ Each round of replication would end with the loss of
at the ends of chromosomes
some nucleotides from the ends of each linear
➢ These noncoding sequences ensure that the cell will
molecule.
not lose important genetic information if DNA
➢ Eukaryotes solve this problem with telomeres, highly
molecules shorten during replication.
repeated sequences at the ends of chromosomes.
➢ A polymerase called telomerase can catalyze the
addition of repeats to chromosome ends.

TELOMERASE FUNCTION
➢ Telomerase is composed of protein and RNA.
➢ In the protozoan Tetrahymena, the RNA component of
the telomerase (3'-AACCCC-5') is complementary to
the telomere repeat sequence (5'-TTGGGG-3')
➢ This enzyme-bound RNA acts as a template for adding
the DNA repeat sequence to the telomere ends.

PROTECTING CHROMOSOME ENDS

➢ After telomeres are lengthened by telomerase,
telomere capping proteins bind to the exposed 3' end
to protect from degradation
➢ In many eukaryotes, the 3' ends of the DNA also loop
back and base-pair with the opposite strand to form a
protective closed loop.

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➢ In multicellular organisms, telomerase function is focuses on one end of a DNA molecule from
restricted to germ cells and a few other types of Tetrahymena, whose telomeric repeat unit is TTGGGG.
actively proliferating cells. The 3' end of the DNA extends beyond the 5' end and is
the substrate for telomerase, an enzyme composed of
protein and RNA. The RNA portion of Tetrahymena
telomerase is 159 nucleotides long and contains a
9-base sequence complementary to 1.5 telomeric
repeat units.

MOST CELLS HAVE A LIMITED LIFESPAN

➢ Telomere shortening occurs with each cell division in
most cells
➢ As a result, telomere length is a counting device for
how many times a cell has divided; if a cell divides too
many times, telomeres could be lost
➢ Cells at risk of loss of telomeres undergo apoptosis,
programmed cell death

DNA DAMAGE AND REPAIR

➢ DNA must be accurately passed on to daughter cells
➢ In addition to ensuring that replication is faithful, this
also means that DNA alterations must be repaired
➢ DNA alterations, or mutations, can arise spontaneously
or through exposure to environmental agents

DNA DAMAGE CAN OCCUR SPONTANEOUSLY OR IN

RESPONSE TO MUTAGENS
➢ During DNA replication, some types of mutations occur
through spontaneous hydrolysis reactions.
➢ Depurination is the loss of a purine base (A or G)
➢ Deamination is the removal of a base's amino group,
changing its base-pairing properties.
○ Deamination may involve A, G, or, most often,
C.

(1) Telomerase 1 binds to the 3' end of the telomeric DNA,

positioning itself so the last few bases of the DNA are
base-paired with part of the 9-base RNA sequence.
(2) The telomerase then catalyzes the addition of
nucleotides to the 3' end of the DNA strand, with the
remainder of the 9-base RNA sequence serving as a
template.
(3) Next, the telomerase advances along the DNA strand
in the 3' direction and repeats steps 1 and 3 several
times.
(4) Meanwhile, the standard DNA replication machinery
synthesizes a lagging strand complementary to the
DNA DAMAGE BY CHEMICAL MUTAGENS
strand elongated by telomerase.
➢ Base analogs resemble nitrogenous bases and are
(5) In some eukaryotes, the lengthened telomeric DNA
incorporated into DNA
folds back upon itself, creating a loop that caps the
➢ Base-modifying agents react chemically with DNA
end of the chromosome. The electron micrograph
bases to alter their structures, forming DNA adducts
shows such a loop in chromatin isolated from chicken
➢ Intercalating agents insert themselves between
erythrocytes.
adjacent bases, distorting DNA structure
➢ Telomeres are stretches of repeated DNA located at
the ends of eukaryotic chromosomes. This figure

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DNA DAMAGE BY RADIATION

➢ Ultraviolet radiation alters DNA by triggering pyrimidine
dimer formation - covalent bonds between adjacent
pyrimidine bases.
➢ X-rays and related types of radiation, called ionizing
radiation, remove electrons from molecules and
generate highly reactive intermediates that damage.

GUIDE QUESTIONS
9. T or F. Cells at risk of loss of telomeres undergo apoptosis. T
10. ____ are mutation-causing agents. mutagens

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JUNE 17, 2024

CELL CYCLE AND MITOSIS
NUCLEAR AND CELL DIVISION
➢ The two copies of each chromosome made during the
S phase are distributed into daughter cells during the M
phase.
○ M phase includes nuclear division (mitosis)
and cytoplasmic division (cytokinesis)
■ The formation of two daughter cells.

Mitosis is Subdivided into Prophase, Prometaphase,

Metaphase, Anaphase, and Telophase
➢ Mitosis is divided into five stages based on the
changing appearance and behavior of chromosomes.
○ Prophase
○ Prometaphase
○ Metaphase
○ Anaphase
○ Telophase
➢ Events during each stage are directed toward the
correct distribution of one copy of each chromosome
into daughter nuclei.

GUIDE QUESTIONS
➢ What are the 5 stages of mitosis?

STAGES OF MITOSIS
PROPHASE
➢ After DNA replication, cells exit the S phase and enter
the G2 phase. This is where final preparations are made
for entry into mitosis.
○ Toward the end of G2, chromosomes begin to
condense into more compact, folded
structures.
■ Figure A: The chromosomes become
thicker as compared to the
interphase.
○ The G2 → prophase transition is not sharply
defined but cells are in prophase when
individual chromosomes become visible.
■ Figure B: From chromatins, it will now
become a chromosome once it
enters prophase. PROMETAPHASE
➢ In prophase, each chromosome has two chromatids. ➢ The onset of prometaphase is marked by the
○ In animal cell nucleoli disperse, but in plant fragmentation of the membranes of the nuclear
cells nucleoli may still be visible. envelope.
➢ The centrosomes near the nucleus, which function as ○ The membrane is slowly breaking down.
microtubules organizing centers (MTOC), begin to ➢ Centrosomes complete their movement to opposite
migrate away from each other. sides of the nucleus and the spindle MTs contact the
○ As centrosomes move, they act as nucleation condensed chromosomes.
sites for microtubules (MTs), destined to form ○ MTs attach to chromosomes in the
the mitotic spindle. centromere region.
■ A dense starburst of MT called asters ➢ Figure: The chromosomes are slowly moving to the
forms near each centrosome. center where the astral MTsand the kinetchores are
● These are found in the connecting in the chromosomes’ MT.
poles of the cells that are ○ As they move towards it, spaces are now
“kumikinang and sinag.” visible as shown in figure B.
○ Within the centrosomes are microtubule –
CENTROMERES AND KINETOCHORES
containing structures called centrioles.
➢ DNA in centromeres consists of simple, tandemly
repeated CEN sequences, with considerable variation
among species.

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➢ A common feature among species is the presence of a METAPHASE

special histone H3 called CENP–A in humans. ➢ A cell is in metaphase when the fully condensed
○ CENP-A recruits additional proteins to the chromosome are all aligned at the metaphase plate.
centromere to form the kinetochore, to which ○ Metaphase plane is a plane equidistant
MTs attach. between the two poles of the spindle.
➢ Kinetochore proteins begin to assemble on ➢ Agents that interfere with spindle function (e.g.,
centromeres shortly after S phase. colchicine) are used to arrest cells at metaphase.
○ During prometaphase spindle MTs bind the ○ Colchicine is used to create a karyotype, so
kinetochores associated with each chromatid that the choromosomes found in the middle
○ Forces exerted by these kineochore of the cell won’t move (arrested.
microtubules gradually move chromosomes ➢ Examining metaphase cells allows chromosomes to be
toward the center of the cell; this is called identifies, generating a karyotype.
congression. ➢ Figure: This is aligning of the chromosomes at the center
of the cell. They are composed of metaphase plate at
the center.
○ In plant cells, they are easily identifiable as the
chromosomes are found at the center.
○ When the cells are at rest, we can identify the
chromosomes since they are organized and
we can make a karyotype to check if the
chromosomes found in one person is correct.
■ These are used in studying many
diseases: trisomy 21, wherein there
are three chromosomes in
chromosome 21.

TWO OTHER TYPES OF MICROTUBULES

➢ Polar microtubules interact with microtubules from the
opposite pole of the cell
➢ Astral microtubules are shorter and form the asters at
each pole, (small and parang sinag lang)
○ Some of the astral microtubules interact with
proteins loining the plasma membrane.

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ANAPHASE
➢ Anaphase is the shortest phase of mitosis
○ The two sister chromatids of each
chromosome abruptly separate and move
toward opposite poles.
➢ In anaphase A, the chromosomes are pulled toward
spindle poles as kinetochore MTs get shorter.
➢ In anaphase B, the spindle poles themselves move
away from each other as polar MTs lengthen.
➢ Depending on the cell type, anaphase A nad B may
take place at the same time, or anaphase B may follow
anaphase A.
➢ Figure: In both plant and animal cells, these are easily
identifiable with each chromosome moving towards
the poles of the cell.
○ Chromosome – pull movement: Chromosomes
→ Pole → Anaphase B → Separation of the
two.

TELOPHASE
➢ At the beginning of telophase, the daughter
chromosomes arrive at the poles of the spindle.
○ Chromosomes uncoil into interphase
chromatin.
○ Nucleoli reappear and nuclear envelopes
reform.
➢ During this period, cytokinesis also takes place.

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DIFFERENT STAGES OF MITOSIS MITOSIS IN ONION ROOTS

GUIDE QUESTIONS
➢ T or F. During anaphase, the two sister chromatods of
each chromosome abruptly separate and move
toward opposite poles.
➢ T or F. Nucleoli reappear and nuclear envelopes
reforms during anaphase B.
➢ At which stage is best to identify chromosomes and
make a karyotype?

THE MITOTIC SPINDLE IS RESPONSIBLE FOR

CHROMOSOME MOVEMENTS DURING MITOSIS
➢ The microtubule-containing apparatus responsible for
the separation of chromatids into daughter cells is the
mitotic spindle.

SPINDLE ASSEMBLY AND CHROMOSOME ATTACHMENT

➢ Microtubules have an inherent polarity.
○ The two ends have different chemical
properties.
1. Interphase – The centrioles are still found above the ➢ The end where microtubule (MT) assembly is initiated
cell, nuclear envelope is still visible, and the chromatin (the centrosome in the case of the spindle) is the minus
is present. or negative end.
2. Prophase – The centrioles are slowly moving towards ➢ The end where most growth occurs is the plus or
the opposite ends of the cell and the asters are now positive end.
visible. While the nucleolus are starting to disappear
and the chromosomes are formed (by condesing) to
now develop sister chromatids.
3. Prometaphase – The chromosomes are slowly moving
towards the center of the cell, and different
microtubules are seen attached to the kinetochore.
4. Metaphase – The chromosomes will align at the center
and the MTs are now more visible.
5. Anaphase
a. Anaphase a – It is where the chromosomes
initiates the separation.
b. Anaphase b – It is where the chromosomes The microtubules consist of tubulin subunits which are gained or lost as the
are slowly being separated from pole to pole. microtubules lengthen or shorten.
i. Pulling away from sides to sides.
6. Telophase – This is where the nucleolus will once again Spindle Assembly
form and the cleavage furrow will slowly now appear ➢ During late prophase, MT growth speeds up
forming two daughter cells. dramatically. Initiation of new MTs at centrosomes
increases.
➢ When the nuclear envelope disintegrates, kinetochores
and microtubules can come into contact.
➢ When the plus end of MTs and the kinetochore bind,
the MT becomes a kinetochore MT (i.e., differentiation).

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Kinetochores ➢ One kinesin-like motor is at the plus end of the

➢ Each kinetochore is a three-layered structure made of MT, embedded in the kinetochore, and
proteins attached to CEN sequences at the moves the chromosome as it “chews up” the
centromere. MT.
➢ The two kinetochores are located at opposite sides of a ➢ The other kinesin-like motor is located at the
chromosome, so they usually attach to MTs from minus end of the kinetochore MTs.
opposite spindle poles. ○ It is embedded in the spindle pole
➢ The polar MRs make contact with the MTs from the and induces depolymerization there,
opposite pole at the same time. “reeling in” the microtubules and the
attached chromosomes.

Mitotic Motors.
(a) A model for mitotic chromosome movement based on
The kinetochore is very important because dito nakadikit yung three roles played by motor proteins. Motor proteins are
microtubules so that the chromosomes will be pulled apart. shown in red, and the red arrows indicate direction of
movement generated by these motors. Motor proteins
are associated with three types of MTs: kinetochore
Cells without Centrosomes
MTs, polar MTs, and astral MTs.
➢ Cells without centrosomes can still form spindles using a (i) Kinetochore MTs have motor proteins
different mechanism promoted by chromosomes. associated with both their plus (embedded in
➢ This requires the involvement of Ran, the GTP-binding the chromosomal kinetochore) and minus
protein. ends (located in the centrosome of the
➢ Ran binds to GTP due to a protein associated with spindle pole). The motor proteins located at
mitotic chromosomes, then binds importin and releases the kinetochore “chew up” (i.e.,
proteins that promote MT assembly. depolymerize) the plus ends of the
kinetochore MTs. This way, the chromosome is
CHROMOSOME ALIGNMENT AND SEPARATION pulled toward the spindle pole as the
➢ Chromosomes migrate to the central region of the kinetochore MTs are shortened through the
spindle through a series of movements generated by loss of tubulin subunits. Simultaneously, motor
pulling and pushing forces from the microtubules. proteins located at the spindle pole
➢ Chromosomes reach the central region and stay there depolymerize the minus ends of the
as a result of precisely balanced forces pulling them kinetochore MTs, reeling in the MTs and their
toward opposite poles. attached chromosomes.
➢ Chromatid separation requires action of topoisomerase (ii) Motor proteins crosslink the polar MTs and
II and changes in adhesive proteins. cause them to slide apart, thereby forcing the
spindle poles away from each other. As the
MOTOR PROTEINS AND CHROMOSOME MOVEMENT polar MTs slide apart, they are lengthened by
➢ Several motor proteins play active roles in mitosis. the addition of tubulin subunits to their plus
➢ They use energy from ATP to change shape and exert ends where they overlap near the spindle
force that causes movement of attached structures. center.
➢ Motor proteins play at least three distinct roles in the (iii) Astral MT motor proteins link the plus ends of
movement of anaphase chromosomes. astral MTs to the cell cortex and exert a pull
on the spindle poles by inducing astral MT
Roles of Motor Proteins in Chromosome Movement depolymerization at their plus ends.
1. Chromosomes are moved—kinetochores first—toward
the spindle poles during anaphase A.
➢ This is driven by kinesins associated with
kinetochore MTs.

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CYTOKINESIS IN ANIMAL CELLS

➢ Cytoplasmic division is called cleavage.
○ It begins with a slight puckering of the cell
surface that deepens into a cleavage furrow.
➢ The furrow continues to deepen until opposite surfaces
make contact and split the cell in two.
➢ The furrow deepens along a plane passing through the
spindle equator.

(b) The two electron micrographs provide evidence for the

sliding of polar MTs driven by polar MT motors. During
metaphase, the polar MTs from opposite ends of the
cell overlap significantly. During anaphase, the polar
MT motors cause these two groups of MTs to slide away
from each other, thereby resulting in a reduced region
Cytokinesis
of overlap.
➢ Signals emanating from the central part of the spindle,
the spindle midzone, are important for completing
2. Motor proteins play a role in the movement of the
cytokinesis.
spindle poles away from each other during anaphase
➢ Cleavage depends on a beltlike bundle of actin
B.
microfilaments (i.e., the contractile ring) that form just
➢ Bipolar kinesin motors bind to overlapping
below the plasma membrane in early anaphase.
polar MTs from opposite spindle poles, forcing
➢ As cleavage progresses, the ring tightens around the
the poles away from each other.
cytoplasm.
3. Cytoplasmic dynein is associated with astral MTs that
are connected to the cell cortex.
● The cell cortex is a layer of actin
microfilaments lining the inner surface of the
plasma membrane.
● The dynein moves toward the minus ends of
the MTs and appears to move the spindle
toward the cortex.

CYTOKINESIS DIVIDES THE CYTOPLASM

➢ After the chromosomes have separated, cytokinesis
divides the cytoplasm in two.
➢ It usually starts in late anaphase or early telophase.
➢ Certain cell types undergo many rounds of nuclear
division without cytokinesis, forming a syncytium
(multinucleated cell).

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Myosin and Cleavage

➢ Contraction of the ring is generated by interactions CELL DIVISION IS SOMETIMES ASYMMETRIC
between actin and the motor protein myosin. ➢ Cytokinesis is not always symmetric; sometimes, the
➢ Members of Rho-GTP binding proteins regulate spindle forms in an asymmetrical fashion.
assembly and activation of the contractile ring. ➢ This can result in one large and one small cell.
➢ RhoA is recruited to the cleavage furrow to activate ➢ These occur frequently during embryonic
proteins needed for actin polymerization and stimulate development; sometimes, cells formed in this way have
myosin activation. differing developmental potentials.

CYTOKINESIS IN PLANT CELLS

➢ Plant cells cannot form a contractile ring because of
the rigid cell wall.
➢ They assemble a plasma membrane and a cell wall
between the two daughter nuclei.
➢ In late anaphase or early prophase, a group of small
vesicles from the Golgi complex align themselves
across the equatorial region of the spindle.
➢ The vesicles contain polysaccharides and glycoproteins
for cell wall formation and are guided to the spindle
equator by the phragmoplast.
○ This is an array of MTs derived from polar MTs.
➢ The vesicles fuse together to form a cell plate, which
expands outward from the cell wall.

REGULATION OF THE CELL CYCLE

➢ Variations are observed in:
○ Overall length of the cell cycle
○ Relative length of time spent in various phases
○ How closely mitosis and cytokinesis are
coupled
➢ The cell cycle is regulated to meet the needs of each
cell type and organism.

CELL CYCLE LENGTH VARIES AMONG

DIFFERENT CELL TYPES
➢ At one extreme are cells that divide continuously to
replace cells that are constantly lost or destroyed.
○ e.g., cells involved in sperm formation; stem
cells
➢ At the other extreme are extremely slow-growing tissues
or even some (mature nerve or muscle cells) that do
not divide at all.
○ Which is why as we grow older, the functions
of these nondividing cells can become
affected
➢ Some cells do not divide unless stimulated.
○ Depends on factors found in the environment

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VARIATIONS IN GENERATION TIME

➢ Most of the variations in generation time are based on
differences in the length of G1, though S and G2 can
also vary.
➢ Cells that divide very slowly may spend days, months,
or years in the offshoot of G1 called G0.
➢ Cells that divide very rapidly have a short G1 or may
skip it entirely.

CELL GROWTH AND THE CELL CYCLE

➢ Although in some cases cell growth is not essential to
the cell cycle, the two are generally linked.
➢ A protein kinase called TOR (target of rapamycin) plays
a role in the signaling network that controls cell size and
coordinates it with cell cycle progression.
➢ The network activates TOR in the presence of nutrients
and growth factors.
➢ Activated TOR stimulates molecules that control the
rate of protein synthesis, leading to increased cell mass.
➢ Some of the molecules also facilitate entry into the S
phase.
➢ TOR is therefore an important regulator of both cell size
and cell cycle progression.

GUIDE QUESTIONS
➢ _____ divides the cytoplasm in two.
➢ _____ is an important regulator of both cell size and cell
cycle progression.

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JULY 1, 2024
PART 3: CELL CYCLE REGULATION, APOPTOSIS,
CANCER
PROGRESSION THROUGH THE CELL CYCLE IS CONTROLLED AT
SEVERAL KEY TRANSITION POINTS
➢ Control of the cell cycle must
○ [1] ensure that events of each phase are
carried out in the correct order and at the
appropriate time.
○ [2] ensure that each phase is completed
before the next one begins.
○ [3] respond to external conditions.

KEY TRANSITION POINTS

➢ At key transition points in the cell cycle, conditions in
the cell determine whether or not it will proceed.
○ Kailangan makuha nila ang tamang
condition ng cell bago mag-proceed. ➢ Restriction point (start) is influenced by:
➢ The first control point occurs in late G1; the G1 → S ○ growth factors
progression is called Start in yeast. ○ nutrients
➢ In animal cells, the comparable control point is called ○ cell size
the restriction point; the ability to pass it is influenced by ○ DNA damage
the presence of extracellular growth factors. Note: need masatisfy muna yan bago magproceed sa G2.
➢ G2-M transition is influenced by:
THE RESTRICTION POINT ○ cell size
○ DNA damage
➢ Cells that successfully pass the restriction point are
○ DNA replication
committed to the S phase.
➢ Metaphase-Anaphase transition is influenced by:
➢ Those that do not pass the restriction point enter into
○ chromosome attachments to spindle
G0 and reside there until a signal allows them to reenter
Note: need masatisfy mga yan bago magprogress with cell
G1 and pass through the restriction points.
cycle (yan sabi ni miss sa vid).

A SECOND TRANSITION POINT

GUIDE QUESTIONS
➢ Another transition point occurs at the G2 → M
➢ 1. T or F. The restriction points are influenced by growth
boundary, where the commitment is made to enter
factors. T
mitosis.
➢ 2. T or F. Cells that have successfully passed the
➢ In some cell types, the cell can be arrested in G2
restriction point are committed to M phase. F
indefinitely and the cell enters a state analogous to G0.
○ nagkakaroon ng cell cycle arrest.
STUDIES INVOLVING CELL FUSION AND CELL CYCLE MUTANTS LED
➢ In most cells the G1 arrest is the more prevalent type of
TO THE IDENTIFICATION OF MOLECULES THAT CONTROL THE CELL
control, but in some, such as frog eggs, the G2 arrest is
CYCLE
more important.
➢ Cell fusion experiments in the 1970s gave hints about
the identity of molecules that drive the cycle.
A THIRD TRANSITION POINT
➢ Two cultured mammalian cells were fused to form a
➢ A third important transition point is during M phase, cell with two nuclei–a heterokaryon.
between metaphase and anaphase. ➢ If one cell is in S phase and the other in G1, the G1
➢ Here the commitment is made to move the two sets of nucleus quickly begins DNA replication, suggesting that
chromosomes in the new cells. S phase cells contain molecules that trigger the G1 → S
➢ Before cells can begin anaphase, all the chromosomes progression.
must be properly attached to the spindle. ○ Kahit magkaiba yung stage ng cells, pag
nagfuse sila, maiinfluence yung activity ng
cells. For example, one cell is in S phase and
the other is in G1. The cell in S phase will
influence the cell in G1 phase when they fuse,
leading to both cells to undergo S phase.

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○ Mitotic cyclins: required for the G2 → M

transition and bind mitotic Cdks.
○ G1 cyclins: required for passage through the
G1 restriction point (or Start) and the Cdks to
which they bind are called G1 Cdks.
○ S cyclins: required for DNA replication.

MITOTIC CDK-CYCLIN
➢ Mitotic cdk-cyclin drives progression through the G2 →
OTHER OBSERVATIONS M transition by phosphorylation key proteins involved in
➢ Fusion of cells in M phase with cells in G1, S, or G2 the early stages of mitosis.
causes the interphase nuclei to immediately begin ➢ Evidence of a control molecule triggering mitosis came
mitosis. from experiments involving frog eggs (evidence from
○ Kung sino yung phase na mas advanced, yun Masui).
ang sinusunod. ➢ Mature eggs develop from oocytes through meiosis
○ When a G1 cell is fused with an M cell, G1 cell ○ The oocyte arrests shortly after meiosis begins
will immediately proceed to mitosis, instead of until a hormone signal is received.
undergoing S and G2 phases. ➢ Injecting the cytoplasm of a mature egg into an
➢ These experiments suggest that molecules in the immature oocyte causes it to immediately proceed
cytoplasm drive cells from G1 to S or G2 to M. through meiosis.
➢ Yeast cells were used to try to identify the molecules.

➢ Just like in the topic a while ago, the cell follows the
TEMPERATURE-SENSITIVE CELL CYCLE MUTANTS IN BUDDING YEAST
more advanced stage. So, the immature oocyte will
➢ Yeasts carrying a temperature-sensitive mutation
also follow the phase of cytoplasm of the mature egg,
affecting the cell cycle can be grown at a lower
causing it to immediately proceed through meiosis.
(permissive) temperature.
➢ Their cell cycles will be blocked at high temperatures.
MATURATION-PROMOTING FACTOR
➢ Hartwell and colleagues identified many genes
➢ Masui hypothesized that a cytoplasmic chemical that
involved in cell cycle regulation using this type of
he named maturation-promoting factor (MPF) induced
mutation.
oocyte maturation.
○ Other references call it a mitosis-promoting
SIMILAR WORK IN FISSION YEAST
factor.
➢ Nurse carried out similar research with the fission yeast,
➢ Subsequent experiments showed that MPF triggered
Schizosaccharomyces pombe.
mitosis when injected into fertilized frog eggs.
➢ He identified a gene called cdc2 (cell division cycle 2),
➢ Comparable molecules were soon detected in a
whose activity is needed for the G2 → M transition.
broad range of organisms.
➢ cdc2 was soon found to have counterparts in all
○ By this time, they already know that certain
eukaryotic cells studied; it was found to encode a
molecules are needed to trigger mitosis faster.
protein kinase.
➢ MPF is a mitotic Cdk-cyclin complex.
○ Important for mitosis.
○ MPF was shown to be composed of a cyclin
and a Cdk (a Cdk-cyclin complex).
PROGRESSION THROUGH THE CELL CYCLE IS CONTROLLED BY
○ The mitotic Cdk portion of the complex is
CYCLIN-DEPENDENT KINASES (Cdks)
almost identical to the protein product of the
➢ Phosphorylation of target proteins by protein kinases
yeast cdc2 gene.
and dephosphorylation by protein phosphatases is a
○ Yeast cells with a defective cdc2 gene can
common mechanism for controlling the cell cycle.
function perfectly well if the human
➢ Cell cycle progression is driven by protein kinases that
equivalent is provided to them.
are active only when bound to a cyclin.
➢ These kinases are cyclin-dependent kinases (Cdks).
CONTROL OF CDK-CYCLIN COMPLEXES
➢ Mitotic Cdk is found consistently throughout the cell
CYCLINS
cycle.
➢ The concentration of cyclins varies with phases of the
➢ It is active only when bound to mitotic cyclin and the
cell cycle.
concentration of mitotic cyclin gradually increases

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through G1, S, G2 until it reaches a crucial threshold at

the end of G2.
➢ Halfway through mitosis, it is abruptly degraded.

ACTIVATION OF MITOTIC CDK

➢ Activation of mitotic Cdk involves phosphorylation and

dephosphorylation. ➢ Active mitotic Cdk-cyclin stimulates:
○ [1] The binding of mitotic cyclin to mitotic Cdk ○ nuclear envelope breakdown
forms a cyclin-Cdk complex that is initially ○ chromosome condensation
inactive. ○ mitotic spindle formation
○ [2] Inhibiting kinases phosphorylates two sites ○ targeted protein degradation
on the Cdk, blocking the active site.
○ [3] An activating phosphate is then added by ANAPHASE-PROMOTING COMPLEX
an activating kinase, but the Cdk remains ➢ The anaphase-promoting complex coordinates key
inactive as long as the inhibitory phosphate mitotic events by targeting specific proteins for
groups are present. destruction.
○ [4] The final step is the removal of the ➢ Mitotic Cdk-cyclin phosphorylates and contributes to
inhibiting phosphates by a specific activation of the anaphase-promoting complex.
phosphatase enzyme, thereby activating the ➢ The anaphase-promoting complex functions as a
mitotic Cdk-cyclin complex. ubiquitin ligase, which adds ubiquitin to proteins to
➢ Once the phosphatase begins removing the target the, for destruction.
phosphates, activated Cdk stimulates the ➢ One target is securin, an inhibitor of sister chromatid
phosphatase, amplifying activation. separation.
➢ Function of securin:
ONSET OF MITOSIS ○ Prior to anaphase, sister chromatids are held
➢ Once activated, the Cdk-cyclin phosphorylates lamin together by adhesive proteins called
proteins of the nuclear lamina. cohesins.
➢ This causes the lamina breakdown and destabilization ○ Securin maintains this attachment by inhibiting
of the nuclear envelope. the separase protein that would otherwise
➢ It also phosphorylates condensin, which is involved in degrade the cohesins.
chromosome condensation, and ○ When the anaphase-promoting complex
microtubule-associated proteins to facilitate assembly triggers destruction of securin, separase
of the mitotic spindle. cleaves cohesin, freeing the sister chromatids.
➢ Other activities of the anaphase-promoting complex:
○ The anaphase-promoting complex targets
mitotic cyclin for destruction, causing the
kinase activity of mitotic Cdk to fall.
○ Many changes associated with exit from
mitosis–cytokinesis, chromosome
decondensation, nuclear envelope
assembly–depend on degradation of mitotic
cyclin.

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➢ While Rb remains bound to E2F, the E2F molecule is

inactive and the cell cannot enter the S phase.
➢ But when cells are stimulated to divide by growth
factors (which activates the Ras pathway), G1
Cdk-cyclin is activated and phosphorylates Rb.
➢ Rb releases E2F, which initiates transcription of genes
needed for entry of S phase.

GUIDE QUESTIONS
➢ 3. What do you call a cell with 2 nuclei fused from 2
cultured mammalian cells? heterokaryon
➢ 4. Sister chromatids are held together by adhesive
proteins called cohesins,

CHECKPOINT PATHWAYS MONITOR CHROMOSOME-TO-SPINDLE

ATTACHMENTS, COMPLETION OF DNA REPLICATION, AND DNA
DAMAGE
➢ If cells proceeded from one phase of the cell cycle to
the next without completing each step, daughter cells
might be abnormal.
○ E.g., aneuploidy: incorrect number of
chromosomes.
➢ Cells use a series of checkpoints that ensure each
phase is completed properly before the next one
begins.

THE MITOTIC SPINDLE CHECKPOINT

➢ The mitotic spindle checkpoint or spindle assembly
checkpoint (SAC) prevents anaphase from beginning
before the chromosomes are all attached to the
spindle.
G1 CDK-CYCLIN ➢ Kinetochores that remain unattached to microtubules
➢ G1 Cdk-cyclin regulates progression through the produce a “wait” signal that inhibits the
restriction point by phosphorylating the Rb protein. anaphase-promoting complex.
○ G1 Cdk-cyclin phosphorylates the key target ➢ Members of the Mad and Bub protein families are
Rb protein. involved.
➢ Nonphosphorylated Rb binds the E2F transcription
factor. MAD AND BUB
➢ Unbound E2F activates transcription of genes coding ➢ One model suggests that Mad and Bub proteins
for proteins that initiate DNA replication. accumulate at unattached kinetochores
➢ They are converted into a multiprotein complex that
inhibits the anaphase-promoting complex by blocking
the action of Cdc20 protein (essential activator)
➢ Once all the components are attached, Mad and Bud
are no longer converted and the inhibition is lifted

➢ Rb bound to E2F if not phosphorylated.

➢ If Rb is phosphorylated, Rb separates from E2F. E2F will
be activated = activated gene transcription, mRNA
translation, and DNA replication.

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THE DNA REPLICATION CHECKPOINT ○ 1. An autonomous clock goes through a fixed

➢ The DNA replication checkpoint ensures that DNA cycle over and over again via the synthesis
synthesis is complete before the cell exits G2 and and degradation of cyclins
begins mitosis ○ 2. The clock is adjusted as needed
➢ Cells that are prevented from completing DNA
replication fail to undergo the final dephosphorylation
step in the activation of mitotic Cdk-cyclin

THE DNA DAMAGE CHECKPOINT

➢ A multiple series of DNA damage checkpoints monitor
DNA for damage and halt the cell cycle at various
points (late G1, S, and late G2) by inhibiting different
Cdk-cyclin complexes
➢ p53 protein, the “guardian of the genome,” plays a
central role in these checkpoint pathways

RESPONSE TO DOUBLE-STRANDED DNA BREAKS

➢ Breaks in DNA trigger activation of an enzyme called
the ATM (ataxia telangiectasia mutated) protein kinase
➢ ATM phosphorylates checkpoint kinases, which then
phosphorylate p53 (and other targets)
➢ Phosphorylated p53 is unable to bind to Mdm2; Mdm2
GUIDE QUESTIONS
marks p53 for destruction
5. _______ is a protein that plays a central role in DNA damage
➢ Phosphorylated p53 is protected from degradation and
checkpoints. p53
activates two types of events: cell cycle arrest and cell
6. T or F. p53 activates genes needed to trigger cell death by
death
apoptosis after repairing DNA damage. F
➢ p53 activates the gene coding for p21, a protein that
halts the progression of the cell cycle by inhibiting the
GROWTH FACTORS AND CELL PROLIFERATION
activity of different Cdk-cyclins
➢ In simple unicellular organisms presence of nutrients in
➢ ATR (ATM-related) acts similarly in response to
the environment is the primary factor determining
single-stranded DNA breaks
whether cells grow and divide
➢ In multicellular organisms extracellular signaling
CELL DEATH
proteins, growth factors, control the rate of cell
➢ p53 stimulates production of enzymes involved in DNA
proliferation
repair
➢ Growth factors are called mitogens
➢ But if the damage cannot be repaired, p53 activates
genes needed to trigger cell death by apoptosis
STIMULATORY GROWTH FACTORS ACTIVATES THE RAS PATHWAY
➢ A key protein in this pathway is called Puma (p53
➢ Mammalian cells with plenty of nutrients but no growth
upregulated modulator of apoptosis), which inactivates
factors arrest in G1
Bcl-2, an apoptosis inhibitor
➢ Growth and division can be triggered by adding blood
serum, which contains several stimulatory growth
factors, such as PDGF (platelet-derived growth factor)
➢ Another is epidermal growth factor (EGF)

ACTION OF GROWTH FACTORS

➢ Growth factors such as PDGF and EGF act by binding
receptors on the plasma membrane
➢ This activates the tyrosine kinase activity of the
receptors, which triggers a complex cascade of events
that ends with the cell passing the restriction point
➢ The Ras pathway plays a central role in these events

THE RAS PATHWAY IN THE CELL CYCLE

➢ Binding of a growth factor to its receptor leads to Ras
activation (1)
➢ Activated Ras leads to phosphorylation and activation
of a protein kinase called Raf, which starts a
PUTTING IT ALL TOGETHER: THE CELL CYCLE REGULATION MACHINE phosphorylation cascade (2)
➢ The “machine” that regulates the eukaryotic cell cycle ➢ Raf phosphorylates a proteins kinase called MEK, which
involves two interacting mechanisms phosphorylates a group of MAP kinases
(mitogen-activated protein kinases)

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INHIBITION OF CELL CYCLE ARREST

➢ Akt inhibits cell cycle arrest through activation of a
monomeric G protein called Rheb
➢ This leads to activation of TOR, a key regulator of cell
growth
➢ The net effect of the P13-kinase-Akt signaling pathway
is to promote cell survival and proliferation

INHIBITORY GROWTH FACTORS ACT THROUGH CDK INHIBITORS

➢ Some growth factors inhibit cell proliferation, e.g.,
transforming growth factor β (TGF β)
➢ TGF β binding to its receptor phosphorylates Smad
proteins that move into the nucleus and activate
expression of genes coding for proteins that inhibit
proliferation
➢ Two Cdk inhibitors that block cell cycle progression are
p15 and p21

GUIDE QUESTIONS
➢ Activated MAPKs enter the nucleus and phosphorylate
specific genes, including Jun and members of the Ets 7-8. The net effect of the P13-kinase-Akt signaling pathway is to
family of transcription factors (3) promote cell survival and proliferation.
➢ These transcription factors turn on transcription of “early
genes” APOPTOSIS
➢ The early genes code for production of other ➢ Damaged or diseased cells need to be eliminated
transcription factors including Myc, Fos, and Jun ➢ In such cases, the process must not damage
➢ Genes such as Myc, Fos, and Jun activate transcription surrounding cells
of a family of “delayed genes” ➢ Multicellular organisms accomplish this through a
➢ One of these encodes the E2F transcription factor, programmed cell death — apoptosis
covered earlier
➢ The delayed genes include several genes coding for APOPTOSIS AND NECROSIS
Cdk or cyclin molecules that form Cdk-cyclin ➢ Cell death called necrosis sometimes follows tissue
complexes that phosphorylate Rb and trigger G1 → S injury
transition ➢ Necrosis involves swelling and rupture of injured cells,
whereas apoptosis involves a specific series of events
STIMULATORY GROWTH FACTORS CAN ALSO ACTIVATE THE that lead to dismantling of the cell contents
P13K-Akt PATHWAY
➢ Activated growth factor receptors may trigger other STEPS OF APOPTOSIS
pathways besides Ras ➢ The cell’s DNA segregates near the periphery of the
➢ One is the P13-kinase-Akt pathway, that begins with nucleus and the cytoplasm decreases (1)
receptor-induced activation of phosphatidyl-inositol ➢ The cell produces small cytoplasmic extensions and the
3-kinase which catalyzes formation of PIP3 nucleus begins to fragment (2)
(phosphatidylinositol-3,4,5-triphosphate) ➢ DNA is cleaved by an apoptosis-specific endonuclease
➢ It leads ultimately to Akt phosphorylation and and the cell is dismantled into small pieces called
activation and suppression of apoptosis by Akt apoptotic bodies

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➢ Inactivation of a phospholipid translocator (flippase) THE SECOND TYPE OF APOPTOSIS

causes accumulation of phosphatidylserine in the outer ➢ Mitochondria trigger apoptosis by releasing
leaflet of the plasma membrane cytochrome c into the cytosol after accumulation of
➢ This serves as a signal for the remnants of the affected pro-apoptotic proteins lead to formation of channels in
cell to be engulfed by nearby cells via phagocytosis (3) the outer mitochondrial membrane
➢ Cytochrome c stimulates calcium release from
mitochondria and ER, where it binds IP3 receptors
➢ It also activates an initiator procaspase, procaspase-9,
which then activates caspase-3

DAMAGED CELLS CAN TRIGGER THEIR OWN APOPTOSIS

➢ If a cell suffers such damage that it can’t repair itself, it
may trigger its own demise
CASPASES ➢ It can enter apoptosis through the activity of p53,
➢ Apoptosis proceeds through the activation of a series which acts through the protein Puma, which binds and
of enzymes called caspases inhibits Bcl-2
➢ They are produced as inactive precursors called
procaspases and are cleaved to create active
enzymes

APOPTOSIS IS TRIGGERED BY DEATH SIGNALS OR WITHDRAWAL OF

SURVIVAL FACTORS
➢ There are two main routes by which cells can activate
caspases and enter apoptosis
➢ Activation can occur directly, e.g., when human cells
are infected by viruses, cytotoxic T lymphocytes are
inactivated and induce apoptosis
➢ This is triggered when cells receive cell death signals

APOPTOSIS IN CELL INFECTED BY VIRUSES

➢ Two death signals are tumor necrosis factor and
CD95/Fas
➢ CD95 is a protein on the surface of infected cells;
lymphocytes have a protein on their surfaces that binds
CD95, causing it to aggregate GUIDE QUESTIONS
➢ Adaptor proteins attach to the CD95, which recruits 9. CD95 is a protein on the surface of infected cells.
procaspase-8 to the sites of clustering 10. Mitochondria trigger apoptosis by releasing cytochrome c

INITIATOR AND EXECUTIONER CASPASES

➢ When the procaspase is activated it acts as an initiator
caspase, initiating the cascade
➢ Initiator caspases also activate an executioner
caspase, caspase-3, which is important for activating
many steps in apoptosis

THE SECOND TYPE OF APOPTOSIS

➢ One of the best-studied cases of the second type of
apoptosis involves survival factors
➢ When survival factors are withdrawn, a cell may enter
apoptosis
➢ The site of action is the mitochondrion
➢ Healthy cells have several anti-apoptotic proteins in the
outer mitochondrial membrane
➢ The proteins are structurally related to a protein called
Bcl-2 which, together with other proteins, counteracts
proteins that promote apoptosis (pro-apoptotic
proteins)
➢ When cellular signals shift in balance toward
pro-apoptotic proteins, the cell is more likely to
undergo apoptosis
➢ One pro-apoptotic protein is called Bad
(Bcl-2-associated death promoter)

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JULY 4, 2024
CANCER CELLS
➢ Cancer, the second leading cause of death, is an
example of a disease that arises from abnormalities in
cell function.
➢ Gene mutations and changes in gene expression play
a central role in cancer development.
➢ Investigating the biology of cancer cells has deepened
our understanding of normal cells.

Uncontrolled Cell Proliferation and Survival

➢ The term cancer was coined to describe diseases in
which tissues grow and spread abnormally.
➢ Cancers are grouped into categories depending on
the cell type involved:
○ Carcinomas arise from epithelial cells that
cover external and internal body surfaces
(e.g., lung, breast, colon cancer).
○ Sarcomas develop from supporting tissues
such as bone, cartilage, fat, and muscle.
○ Lymphomas and leukemias arise from cells of
lymphatic and blood origin, respectively.
Benign & Malignant Tumors
Tumors Arise When the Balance between Cell Division and ➢ As the abnormal dividing cells accumulate, the normal
Differentiation or Death is Disrupted organization and function of the tissue is disrupted.
➢ A cancer is an abnormal type of tissue growth in which ➢ Benign tumors grow in a confined local area and are
some cells divide and accumulate in an uncontrolled, rarely dangerous.
relatively autonomous way. ➢ Malignant tumors can invade surrounding tissues and
➢ The resulting mass of growing tissue is called a tumor (or spread throughout the body.
neoplasm). ➢ Cancer refers to any malignant tumor.
➢ Tumors lack the normal balance between cell division
and differentiation or death. Cancer Cell Proliferation is Anchorage-Dependent
and Insensitive to Population Density
Differentiation of Skin Cell ➢ Cancer cells that are injected into nude mice (which
➢ Each time a basal cell divides, one of the two cells have no functional immune system) will proliferate and
produced loses the ability to divide and undergoes form tumors.
differentiation as it moves toward the skin surface. ○ Normal human cells will not grow.
➢ During differentiation, it flattens out and begins to make ➢ Normal cells won’t grow well in culture without a solid
keratin. surface to attach to.
➢ Eventually, the cell dies and is shed from the skin ➢ Cancer cells grow in culture with or without solid
surface. support.

Balance of Cells in the Basal Layer

➢ Whenever a cell divides in the basal layer, once cell
differentiates and the other remains in the basal layer
and retain its ability to divide
➢ This arrangement ensures that there is no increase in
the number of dividing cells
➢ In tumors this finely balanced arrangement is disrupted,
so that some divisions give rise to cells that both
continue to divide

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Cancer Cell Proliferation Cancer Arises Through a Multistep Process

➢ Cancer cells exhibit anchorage-independent growth. ➢ The development of cancer requires multiple steps:
➢ Most normal cells anchor to the substrate through 1. Normal cells are converted to a precancerous
integrins. state, which sensitizes them to further changes
➢ If integrins are inhibited, the cells lose the ability to that lead to cancer in a process known as
divide and self-destruct by apoptosis. initiation.
➢ Cancer cells circumvent this process. 2. There is a long, gradual process of promotion,
➢ Normal cells grown in culture divide until the vessel involving repeated exposure of sensitized cells
surface is covered by a single layer of cells (i.e., the to cancer-promoting agents.
monolayer stage). 3. Finally, once a tumor has formed, the tumor
○ This is called density-dependent inhibition of grows and differentiates in the process of
growth. tumor progression.
➢ Cancer cells show reduced sensitivity to
density-dependent growth.

Cancer Cells are Immortalized by Mechanisms

that Maintain Telomere Length
➢ Normal cells in culture divide a limited number of times.
➢ They stop dividing, undergo degenerative changes,
and may die.
➢ Cancer cells under similar conditions exhibit no
limitation, continuing to divide.
○ e.g., HeLa cells, first isolated in 1951, are still
growing in culture.

Telomeric Sequences
➢ Telomeric sequences are lost from the tips of each
chromosome with every DNA replication.
➢ If a normal cell divides too many times, the telomeres
become too short to protect the ends of the
chromosomes, and a pathway to halt cell division is
initiated.
➢ Cancer cells express telomerase, an enzyme that
maintains telomere length.

Defects in Signaling Pathways, Cell Cycle Controls, and

Apoptosis Contribute to Uncontrolled Proliferation
➢ Proliferation is regulated by growth factors that bind
cell surface receptors and activate signaling pathways
in the target cells.
➢ Normal cells do not divide unless stimulated by the
proper signals.
Oncogenes & Tumor Suppressor Genes
➢ Cancer cells alter signaling pathways to create a
constant signal to divide. ➢ DNA mutations in cancer originate in different ways.
➢ However, the mutations always affect genes that
Disruptions in Cell Cycle Control control cell proliferation and survival.
➢ The commitment to proceed through the cell cycle is ➢ There are two main classes:
made at the restriction point (G1 to S progression). ○ Oncogenes
➢ Under suboptimal conditions, normal cells arrest at the ○ Tumor suppressor genes
restriction point (i.e., cease dividing).
➢ Under comparable conditions, cancer cells continue to Oncogenes are Genes Whose Products Can
divide due to defects in cell cycle controls. Trigger the Development of Cancer
➢ An oncogene is a gene whose presence can trigger
Apoptosis
cancer.
➢ Cell death is controlled mainly by pathways that trigger ○ Some are introduced by cancer-causing
apoptosis to remove unnecessary or defective cells. viruses.
➢ Cancer cells are defective and unnecessary but elude ○ Others arise from mutation of normal genes.
apoptosis by blocking the pathway. ➢ The first oncogene discovered was in the Rous sarcoma
➢ In some cancers, uncontrolled growth arises more from virus.
failure to undergo apoptosis than from increased cell ➢ Viruses with defects in the src gene can infect cells but
division. don’t cause cancer.

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Oncogenes in Cancers Not Caused by Viruses ○ This causes the protein product to be
➢ DNA from human cancer cells was introduced into produced in excess although the protein
cultured mouse 3T3 cells. produced is normal.
➢ DNA was administered under conditions that stimulate ○ e.g., some breast and ovarian cancers have
transfection, or the uptake of foreign DNA into cells and amplified copies of the ERBB2 gene, which
incorporation into chromosomes. encodes a growth factor receptor; multiple
➢ After transfection, some 3T3 cells proliferated copies lead to excessive cell proliferation.
excessively.
➢ The abnormal 3T3 cells were injected into mice, which
then developed cancer.
○ This suggests that a human gene taken up by
the cells caused the cancer.
➢ This resulted in the identification of RAS, the human
oncogene identified of which more than 200 are now
known.

Single Oncogenes are Not Sufficient to Cause Cancer

➢ The RAS oncogene only caused cancer because of a
3. Chromosomal Translocation
preexisting cell cycle mutation in the 3T3 cells.
○ In chromosomal translocation, a part of one
➢ In normal cells, the RAS oncogene alone will not cause
chromosome is joined to another
cancer, but the RAS oncogene combined with
chromosome
oncogenes that target the p53 pathway will.
■ E.g., in Burkitt lymphoma, EBV
➢ Multiple mutations are usually required to convert a
stimulates cell proliferation but
normal cell into a cancer cell.
cannot cause cancer by itself
○ Cancer arises when a translocation involving
Proto-oncogenes are Converted into Oncogenes
chromosomes8 and 14 occurs in one of the
by Several Distinct Mechanisms
proliferating cells
➢ Oncogenes arise by mutation from normal cellular
genes called proto-oncogenes.
➢ They are normal cellular genes that contribute to the
regulation of cell growth and survival.
➢ When their structure or activity is disrupted by mutation
(through several mechanisms), the mutant form of the
gene can cause cancer.

1. Point Mutation
○ The simplest mechanism for converting a
proto-oncogene into an oncogene is a point ○ The translocation in Burkitt lymphoma
mutation. ■ The translocation in Burkitt lymphoma
○ This is a single nucleotide substitution that often moves the MYC gene from
causes a single amino acid change in the chromosome 8 to a highly active
protein product. region of chromosome 14, coding for
○ e.g., point mutations in RAS create abnormal, antibody molecules.
hyperactive forms of the Ras protein that lead ■ This leads to overproduction of the
to excessive cell proliferation. Myc protein—a transcription factor
that stimulates cell proliferation.

2. Gene Amplification
○ Gene amplification increases the number of
○ The Philadelphia chromosome
copies of a proto-oncogene.
■ The Philadelphia chromosome is a
translocation chromosome that
involves chromosomes 9 and 22 and

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is associated with chronic 5. Insertional Mutagenesis

myelogenous leukemia. ○ Retroviruses can sometimes cause cancer by
■ The translocation creates an integrating their own genes into a host
oncogene called BCR-ABL, a fusion chromosome in a region where a
of two genes (BCR and ABL), the proto-oncogene is located
oncogene produces a fusion protein ○ This is called insertional mutagenesis; the
that functions abnormally. proto-oncogene is converted into an
oncogene by causing it to be overexpressed.
4. Local DNA Rearrangements
○ Local rearrangements alter base sequences
of proto-oncogenes by deletions, insertions,
inversions, or transpositions
■ E.g., two genes, NTRK1 and TPM3,
reside on the same chromosome
○ In some cancers a DNA inversion causes one
end of the TPM3 gene to fuse to the opposite
end of the NTRK1 gene.

GUIDE QUESTIONS
➢ What are the 5 mechanisms where protooncogenes
are converted to oncogenes?

Most Oncogenes Code for Components

of Growth-Signaling Pathways
➢ More than 200 oncogenes have been identified, and
many of them encode proteins in one of six categories.
➢ Each of the six categories is related to steps in
growth-signaling pathways.
○ The TRK oncogene
■ The resulting gene is called the TRK
oncogene, which fuses the tyrosine
kinase part of the receptor (NTRK1)
to a region of the tropomyosin
molecule.
■ This fusion protein creates a
permanently activated tyrosine
kinase

1. Growth Factor
○ Normal cells will not divide unless they have
been stimulated by the appropriate growth
factor
○ But if a cell possesses an oncogene that
produces the growth factor, it can stimulate
its own proliferation
○ The v-sis gene (found in the simian sarcoma
virus) encodes a mutant form of
platelet-derived growth factor (PDGF)
■ PDGF
■ When the virus infects a monkey cell
that is normally controlled by PDGF,

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the PDGF produced by v-sis ■ The enzymes that catalyze these

stimulates the cell's proliferations. intracellular phosphorylations are
■ A PDGF-related oncogene has also nonreceptor protein kinases
been detected in some human ■ E.g., in the Ras pathway, activated
sarcomas. Ras phosphorylates Raf protein
■ These have a translocation that joins kinase
part of the PDGF gene to part of the ○ Several oncogenes code for protein kinases
collagen gene resulting in involved in the phosphorylation cascade
uncontrolled production of PDGF. triggered by Ras.
○ BRAF codes for a mutant Raf protein in a
2. Receptors
variety of human cancers.
○ Oncogenes sometimes code for mutant
○ Oncogenes coding for non receptor protein
versions of receptors with permanently
kinases in other pathways have also been
activated tyrosine kinase activity, even in the
identified. Included in this group are
absence of a growth factor
oncogenes that produce abnormal versions
■ E.g., the v-erb-b oncogene is found
of Src, Jak, and Abl protein kinases
in a virus that causes red blood cell
cancer in chickens 5. Transcription Factors
○ It produces an altered version of the ○ Receptor tyrosine kinase activation triggers
epidermal growth factor (EGF) receptor that changes in transcription factors, altering gene
remains constitutively active expression.
○ Oncogenes that produce mutant forms or
excessive amounts of various transcription
factors have been detected in many types of
cancers.
○ Among the most common are oncogenes
coding for Myc transcription factors that
control genes involved in survival and
proliferation.

6. Cell Cycle and Apoptosis Regulators

○ Transcription factors activate genes that code
for proteins controlling cell proliferation and
survival.
○ The activated genes include those coding for
cyclins and cyclin-dependent kinases (Cdks)
that trigger passage through key steps of the
cell cycle.
○ Overproduction of receptors
○ Several human oncogenes produce proteins
■ Other oncogenes produce normal
of this type.
receptors, but in excessive quantities
■ e.g., CDK4 is amplified in some
■ The presence of too many receptors
sarcomas, and the cyclin gene,
causes a magnified response to
CYCD1, is commonly amplified in
growth factor and hence
breast cancers.
overproliferation
■ An example is the human ERBB2 Inhibition of Apoptosis
gene.
➢ Some oncogenes contribute to accumulation of
● Amplification of the ERBB2
proliferating cells by inhibiting apoptosis.
gene in certain breast and
➢ One example involves the gene that encodes the
ovarian cancers causes it
apoptosis-inhibiting protein Bcl-2. Some cancers are
to overproduce a growth
associated with translocations that result in
factor receptor.
overproduction of Bcl-2.
3. Plasma Membrane GTP-Binding Proteins
➢ MDM2, which codes for a protein that targets p53 for
○ Oncogenes coding for mutant Ras (plasma
destruction, can also cause failure of apoptosis when it
membrane GTP-binding protein) are one of
is amplified or overexpressed.
the most common genetic abnormalities
found in human cancers. GUIDE QUESTIONS
○ The mutations that create RAS oncogenes are ➢ _______ encodes a mutant form of platelet-derived
usually point mutations that lead to hyperactive
growth factor (PDGF).
Ras that remain in a permanently active
➢ T or F. Oncogenes contribute to accumulation of
4. Nonreceptor Protein Kinases proliferating cells by inhibiting apoptosis.
○ Protein phosphorylation is a common feature
of many growth-signaling pathways.

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JULY 8, 2024 ➢ However, during many cell divisions, a retinal cell may
occasionally acquire a mutation in the same region
CANCER CELLS
TUMOR SUPPRESSOR GENES ARE GENES WHOSE LOSS OR
INACTIVATION LEADS TO CANCER
➢ The loss or inactivation of tumor suppressor genes can
also lead to cancer
➢ The normal function of such genes is to restrict cell
proliferation; the first understanding that such genes
exist came from cell fusion experiments
➢ Fusion of cancer cells with normal cells usually
produces hybrid cells that behave normally; providing
evidence that cells contain genes whose products can
suppress tumor growth

IDENTIFICATION OF THE RB GENE

➢ The pattern of development of the disease suggests
that
1. Chromosome 13 contains a gene that
normally inhibits proliferation
2. 2. Deletion or disruption of both copies must
occur before cancer develops
➢ The RB gene was identified as the missing gene

ROLE OF RB
THE HYBRID CELLS DON’T STAY NORMAL
➢ The product of the RB gene, Rb protein controls the G1
➢ Over time, the hybrid cells can revert to malignant
to S phase progression in the cell cycle
uncontrolled growth
➢ Rb is part of a mechanism that prevents cells from
➢ Reversion to malignancy is associated with the loss of
passing G1 unless an appropriate signal from a growth
certain chromosomes, suggesting that these
factor is received
chromosomes had tumor suppressor genes on them
➢ Disrupting both copies of RB opens the door to
uncontrolled proliferation
HEREDITARY CANCERS
➢ One approach to identification of tumor suppressor RB IN OTHER CANCERS
genes is through the study of families at high risk for
➢ Mutations in the RB gene have been detected in
cancer
nonhereditary cancers as well
➢ About 10-20% of cancers can be traced to inherited
➢ The Rb protein is a target of HPV, which contains an
mutations
oncogene that produces E7 protein
➢ Susceptibility to developing cancer can be inherited;
➢ E7 binds RB and prevents it from properly controlling the
the susceptibility is related to defects in tumor
cell cycle
suppressor genes
➢ In hereditary cancers, one copy of a tumor suppressor
gene is mutated; if the wild-type copy is also mutated,
the cell can begin the progression toward cancer

THE RB TUMOR SUPPRESSOR GENE WAS DISCOVERED BY STUDYING

FAMILIES WITH HEREDUTARY RETINOBLASTOMA
➢ In hereditary retinoblastoma, a rare eye cancer
develops in young children with a family history of the
disease
➢ Children with this condition inherit à deletion in part of
chromosome 13; the deletion alone does not cause
cancer

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The APC Tumor Suppressor Gene Codes for a Protein That

The p53 Tumor Suppressor Gene Is the Most Frequently Inhibits the Wnt Signaling Pathway
➢ The APC gene is associated with an inherited disease
Mutated Gene in Human Cancers
called familial adenomatous polyposis
➢ One of the most important tumor suppressor genes
➢ Individuals who inherit a mutation in the gene are
identified is the p53 gene (TP53 in humans)
susceptible to developing polyps (benign tumors) in the
➢ About 50% of all cancers have p53 mutations
colon if the second copy of APC is mutated
➢ p53 responds to DNA damage by arresting the cell
➢ APC mutations can also arise spontaneously or be
cycle to allow DNA repair, and triggering apoptosis if
triggered by mutagens
repairs cannot be made

APC AND Wnt SIGNALING

p53 IN CANCER
➢ The APC gene produces a protein involved in the Wnt
➢ Inactivation of p53 leads to a failure of apoptosis, and
pathway, which plays a role in controlling proliferation
allows defective cells to continue to divide
and differentiation during embryonic development
➢ An inherited condition, Li-Fraumeni syndrome, is
➢ The central component is ß-catenin, which is regulated
caused by a defective copy of the p53 gene and is
by a multiprotein destruction complex (APC, axin, and
characterized by the development of various types of
GSK3)
cancers by early adulthood
➢ The destruction complex targets ß-catenin for
➢ These are caused by mutations in the second copy of
destruction
p53

ACTIVATION OF Wnt
p53 IS A TARGET FOR CERTAIN CANCER VIRUSES
➢ The Wnt pathway is turned on by Wnt signaling proteins
➢ HPV has a second oncogene that produces the E6
that bind and activate cell surface Wnt receptors
protein
➢ The activated receptors bind axin, and prevent
➢ E6 directs attachment of ubiquitin to p53 and targets it
assembly of the destruction complex
for destruction
➢ ß-catenin enters the nucleus, binds the TCT transcription
➢ Therefore, HPV blocks the action of both the Rb and
factor, and activates genes (e.g., MYC, CYCD1) that
p53 proteins
stimulate proliferation

APC AND CANCER

➢ Defects in the APC gene prevent the formation of the
destruction complex, leading to constitutive Wnt
signaling
➢ Thus cells receive a continuous signal to divide

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a) Normal cell (without Wnt proteins) c) Cancer cell (regardless of the presence or absence of
In the absence of growth-signaling Wnt proteins, Wnt proteins).
B-catenin is targeted for degradation by the Some cancer cells have loss-of-function mutations in
axin-APC-GSK3 destruction complex, which catalyzes the APC gene. In the absence of functional APC
the phosphorylation of B-catenin. The phosphorylated protein, the destruction complex cannot form and
-catenin is linked to ubiquitin, thereby marking the B-catenin therefore accumulates, entering the nucleus
phosphorylated B-catenin for degradation by and locking the Wnt pathway in the ON position.
proteasomes. The resulting absence of B-catenin
maintains the Wnt pathway in the OFF position.

b) Normal cell (with Wnt proteins)

The Wnt pathway is turned ON by Wnt proteins, which
activate cell surface Wnt receptors. The activated
GENETIC INSTABILITY
receptors bind to axin, thereby preventing assembly of
➢ Genetic instability refers to the fact that mutation rates
the destruction complex and thus halting B-catenin
in cancer cells are thousands of times higher than
degradation. The B-catenin enters the nucleus and
normal
binds to the TCF transcription factor, forming a complex
➢ This state can arise in several ways
that activates a variety of genes that control cell
➢ One group of mechanisms involves disruptions in DNA
proliferation, including MYC and CYCD1 (a cyclin
repair (e.g., HNPCC and Xeroderma pigmentosum)
gene).

FACULTY DNA REPAIR AND BREAST CANCER

➢ Most hereditary forms of breast cancer arise in women
who inherit a mutant copy of either BRCA1 or BRCA2
➢ Both of these genes code for proteins involved in repair
of double-strand DNA breaks
➢ Breast and ovarian cells with these mutations exhibit
chromosomal rearrangements
➢ Women inheriting BRCA mutations exhibit a 40-80%
lifetime risk for breast cancer and a 15-65% risk for
ovarian cancer
➢ Genetic testing is available for women with a family
history of breast cancer

GENETIC INSTABILITY
➢ Most cancers are not hereditary but still exhibit genetic
instability
➢ In some cases, the instability can be traced to
mutations in DNA repair genes
➢ The p53 pathway is defective in most cancer cells,
removing an important protective mechanism against
genetic instability

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COMBINATIONS OF MUTATIONS
DEFECTS IN MITOSIS ➢ The common mutations in cancers involve the
➢ Genetic instability can arise from defects that cause inactivation of tumor suppressor genes and the
disruptions in chromosome sorting during cell division. conversion of proto-oncogenes to oncogenes.
➢ This results in broken chromosomes and aneuploidy ➢ The most common pattern detected in colon cancer is
(abnormal number of chromosomes) active KRAS oncogene plus a mutation in tumor
➢ Sometimes, extra centrosomes are present (structures suppressor genes APC, SMAD4, and p53.
that guide spindle formation) ○ When there is this combination of genes, it is
most likely to develop into colon cancer.
MITOTIC SPINDLE CHECKPOINT ➢ Benign tumors have two of these; rapidly growing
➢ Cancer cells may exhibit defects in the mitotic spindle cancers have all four.
checkpoint, which normally prevents anaphase until all
the chromosomes are correctly attached to the STEPWISE DEVELOPMENT OF COLON CANCER
spindle. ➢ The earliest mutation to be routinely detected is loss of
➢ Loss of this checkpoint due to mutations in the genes function of APC, often in small polyps before cancer
that regulate it (e.g., Mad, Bub) can lead to has arisen.
chromosome missegregation. ➢ Mutations in KRAS and SMAD4 are seen when polyps
grow larger.
GATEKEEPERS AND CARETAKERS ➢ Mutations in p53 accompany the development of
➢ Tumor suppressor genes such as APC, RB, and p53 are cancer (the steps do not always occur in this order nor
called gatekeepers; their loss directly opens the gates involve the exact set of genes).
to excessive proliferation and formation of tumors.
➢ Genes involved in DNA repair and chromosome sorting
are called caretakers because they maintain genetic
stability but are not directly involved in controlling
proliferation.

➢ In the figure above, it shows an illustration of how colon

cancer starts and develops.
○ We can see that in APC mutation, early
benign tumors are developed.
○ However, as each set of gene mutations is
added, the proliferation of cells worsens, thus
leading to more severe and aggressive tumor
growth.
○ This progression continues with the
accumulation of additional mutations in other
key genes, such as KRAS, SMAD4, p53, and
other mutations and epigenetic changes that
drive the transition of genetic instability—from
benign to malignant stages—ultimately
resulting in invasive and metastatic colon
cancer.

THE TGFβ-SMAD PATHWAY

CANCERS DEVELOP THE STEPWISE ACCUMULATION OF MUTATIONS ➢ The TGFβ-Smad pathway is frequently disrupted in
INVOLVING ONCOGENES AND TUMOR SUPPRESSOR GENES colon cancer; this pathway inhibits epithelial cell
➢ ACCUMULATION? :o proliferation.
○ When mutations occur simultaneously in both ➢ Loss of function mutations in this pathway disrupt the
oncogenes and tumor suppressor genes, inhibitory function and are commonly detected in
cancer develops. colon cancers.
○ It is the uncontrolled proliferation of cells when ➢ That’s why when epithelial cell proliferation is not
there is no regulation. inhibited, it continues to increase, eventually
➢ Sequencing studies show that a given type of cancer developing into a mass that leads to a tumor.
typically involves mutations in 50-75 genes.
➢ A few of these are mutated frequently in samples from EPIGENETIC CHANGES IN GENE EXPRESSION INFLUENCE THE
different people; the commonly mutated genes affect PROPERTIES OF CANCER CELLS
about a dozen different pathways. ➢ Epigenetic changes alter a gene's expression but not its
sequence.

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➢ E.g., DNA methylation at -CG- sites near promoters can ➢ Six traits have been described as the hallmarks of
silence the adjacent genes, resulting in epigenetic cancer; these traits uncouple cancer cells from the
silencing. normal limits on proliferation and growth.
➢ Epigenetic silencing of numerous genes (tumor
suppressor genes) occurs in cancer cells, where THE HALLMARKS OF CANCER
methylation levels are very high. 1. Self-sufficiency in growth signals
- Normal cells require growth cells to proliferate,
EPIGENETIC CHANGES AND CANCER PREDISPOSITION but cancer cells escape this requirement.
➢ People can inherit methylated genes. 2. Insensitivity to antigrowth signals
➢ Inheritance of methylated tumor suppressor genes is - Normal tissues are protected from
associated with a predisposition to cancer overproliferation by a variety of inhibitory
➢ For example, the inheritance of methylated MLH1, a signals, but cancer cells are insensitive to
DNA repair gene, is associated with susceptibility to these.
many types of cancer. 3. Self-sufficiency in growth signals
- Apoptosis is used by normal cells to prevent
MICRO-RNAS AND CANCER PREDISPOSITION damaged or defective cells from continuing
➢ MicroRNAs bind to and silence the translation of to divide; apoptosis is inhibited or disrupted in
thousands of mRNAs; cancer cells produce excessive cancer cells.
amounts of some miRNAs and insufficient amounts of 4. Limitless replicative potential
others. - Normal cells have limited replicative potential
➢ Overproduced miRNAs that act as oncogenes include due to telomere loss; cancer cells contain
miR-155, miR-17-92, and miR-21 active telomerase (or other mechanisms) to
➢ Underproduced miRNAs that act as tumor suppressors maintain telomeres.
include let-7, miR-29, and miR-15a/miR-16-1 5. Sustained angiogenesis
- Tumor cells cannot grow beyond a few mm
OVERPRODUCED miRNAs without a blood supply; cancer cells trigger
angiogenesis by activating genes coding for
➢ miR-17-92 inhibits the translation of PTEN, a
angiogenesis stimulators and inhibiting genes
phosphatase that inhibits P13K-Akt signaling
coding for angiogenesis inhibitors.
pathways—an important pathway in cell proliferation.
6. Tissue invasion and metastasis
➢ Overproduction of miR-17-92 in cancer cells leads to
- Cancer cells lose adhesiveness with
constitutive activation of the P13K-Akt signaling
neighbors, invade nearby tissues, and
pathway and consequent enhancement of cell
eventually metastasize around the body via
proliferation.
the circulatory system.
○ Nothing is inhibiting the pathway once again,
so cell proliferation continues unchecked,
THE CRUCIAL ENABLING TRAIT: GENETIC INSTABILITY
leading to the formation of another tumor.
➢ To acquire the six traits that lead to cancer, cells must
accumulate more mutations that could be generated
UNDERPRODUCED miRNAs
by normal mutation rates.
➢ The miR-15a/miR-16-1 cluster is often deleted in certain
➢ Genetic instability arises most frequently from disruption
forms of leukemia
of the p53 pathway, but also occurs due to mutations
➢ One of the functions of these miRNAs is to inhibit the
affecting DNA repair and chromosome sorting.
synthesis of Bcl-2, a protein that inhibits apoptosis.
○ There should be a combination—in the
➢ Too little miR-15a/miR-16-1 leads to less inhibition of
beginning, there is a mutation affecting the
Bcl-2 and thus less ability of a cell to carry out apoptosis
inhibition of proliferation.
if the need arises.
○ Once a tumor forms, there's also a mutation in
the p53 pathway, so the damaged cells
miRNAs AND HISTONES
continue to proliferate unchecked until
➢ Some miRNAs influence histone modifications reaching the end stage of cancer.
➢ miR-101 is frequently deleted in prostate cancer; this
miRNA normally inhibits synthesis of EZH2, a protein that
catalyzes histone methylation
➢ Loss of miR-101 is therefore associated with increased
histone methylation and the silencing of tumor
suppressor genes

SUMMING UP: CARCINOGENESIS AND THE HALLMARKS OF ➢ In the figure above, we can see the factors that affect
CANCER the DNA—radiation, chemicals, infectious agents, and
➢ Carcinogenesis is the multistep process that converts heredity. It then produces mutations, which activate
normal cells into cancer cells. the oncogenes and tumor suppressor genes, thus
➢ The four main causes of cancer are chemicals, creating genetic instability. The accumulation of
radiation, infectious agents, and heredity.

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genetic and epigenetic changes can have the

hallmarks of cancer.

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JULY 15, 2024 Application of Four Signals

SIGNAL TRANSDUCTION MECHANISMS

MESSENGERS AND RECEPTORS
➢ In the second major means of intercellular
communication, the signal is transmitted by regulatory
chemical messengers.
➢ Receptors are located on receiving cells that can be
quite distant from the secreting cell.
➢ In order to have a cell function, they need certain
signals and receptors to perform a certain function.

CHEMICAL SIGNALS AND CELLULAR RECEPTORS

➢ Cells produce signals, in some cases by displaying
molecules on their surfaces or by releasing a chemical
signal.
1. Hormones - It involves the Endocrine pathway, in which
➢ Multicellular organisms can control the activities of
the signal will move through the bloodstream before it
specialized cells through release of chemical
will be delivered in their target cell.
messengers.
2. Local mediators - It is short range that involves:
a. Juxtacrine: Require physical contact
Different Types of Chemical Signals can be Received by Cells
b. Autocrine: The signals released will also affect
➢ Signaling molecules are often classified based on the themselves
distance between the site of production and the target c. Paracrine: They need to be in short distance,
○ Endocrine signals are produced far from the found within the same area to deliver their
target tissues, which they reach via the signals.
circulatory system.
○ Paracrine signals are diffusible and act over a GUIDE QUESTION
short range. ➢ 1-4. Give the different types of signals.
■ The signal will be only transmitted ○ Endocrine
within the area. Hence this type of ○ Paracrine
signaling will stay here and will not ○ Juxtacrine
be transported in far locations. ○ Autocrine

Types of Signals LIGANDS AND RECEPTORS

➢ Classification of signaling molecules: ➢ When a messenger reaches its target, it binds to
○ Juxtacrine signals require physical contact receptors on the surface of the target cell.
between sending and receiving cells. ○ Awaits the ligands inside the cell,
■ They need to be together before it ➢ A messenger that binds a target receptor is called a
sends out cells. ligand; it may bind a receptor on the surface or inside
● Analogy: Phone (AirDrop), the target cell.
they need to be near each ○ In either case, the ligand is the primary
other so that there will be messenger, which is the first signal that will
exchange of signals. bind with the receptor.
○ Autocrine signals act on the same cell that
produces. Secondary Messengers
■ The signal secreted from the inducer ➢ Ligand binding may trigger production of molecules in
will also affect their own selves the receiving cell.
● They can be activated ○ Once it binds with the receptor, it signals the
through their own signals. cells to perform a certain function, which in
this case is the production of different
molecules.
➢ These small molecules or ions that relay signals from one
location to another in the cell are called second
messengers.
➢ A cascade of changes may be induced in the
receiving cell.
○ Exhibits a domino effect where:
■ Primary messenger → Ligand →
Receptor → Secondary messenger.

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Signal Transduction Receptor Down-regulation

➢ The ability of a cell to respond to ligand-receptor ➢ Cells are geared to sense ligand concentration
binding by altering its behavior or gene expression is changes rather than fixed concentrations.
called signal transduction. ➢ When receptors are occupied for prolonged periods,
○ The ability of the cell to respond in the ligand the cell adapts to no longer respond to the ligand.
receptor binding. ➢ Such changes are called receptor down-regulation,
■ The cell will have alteration that will which can be accomplished in two ways.
change its gene expression.
Mechanisms of Receptor Down-regulation
➢ Cells can down-regulate receptors in two ways:
○ Cells reduce the density of receptors on their
surfaces via receptor-mediated endocytosis.
○ Cells can adapt to signals by desensitization,
alterations to the receptor that lower its
affinity for the ligand.
■ Common method of desensitization
is phosphorylation.

Agonists and Antagonists

➢ It is possible to make synthetic ligands that bind even
more tightly or selectively than the real ligand.
➢ Agonists: drugs that activate the receptor they are
bound to.
➢ Antagonists: bind receptors without triggering a
change, and prevent the naturally occurring
Receptor Binding Involves Specific Interactions messenger from activating the receptor.
Between Ligands and their Receptors
➢ Messengers bind to receptors in a highly specific way, Receptor Binding Activates a Sequence of Signal
through several noncovalent bonds. Transduction Events Within the Cell
➢ This is achieved through: ➢ When a ligand binds to its cognate receptor it either
○ The binding site (or binding pocket) on the induces a change in receptor conformation or causes
receptor that fits the messenger very closely receptors to cluster.
○ The necessary amino acid side chains, ➢ Once this takes place, a preprogrammed sequence of
positioned to form chemical bonds with the events is initiated inside the cell.
messenger.
Signal Integration

Receptor-Ligand Interactions ➢ Cells can be exposed to a multitude of signals at any

given moment.
➢ In most cases the binding of a receptor and ligand
➢ Cells must integrate these signals to produce
resembles the binding of an enzyme and its substrate
appropriate responses.
➢ The receptor specific for a certain ligand is called the
➢ A single receptor can activate multiple pathways, or
cognate receptor
multiple pathways can converge onto the same
➢ A receptor bound to its ligand is said to be occupied.
molecules.

Receptor Affinity
➢ The relationship between the [ligand] in solution and
the number of receptors occupied can be described in
terms of receptor affinity.
➢ The dissociation constant, Kd, is the [free ligand]
needed to produce a state in which half the receptors
are occupied.
➢ Receptors with high ligand affinity have low Kg and
vice versa.

Coreceptors
➢ Receptor-ligand interactions can be affected by
coreceptors on the cell surface.
➢ They help to facilitate receptor-ligation interaction via
physical interaction with the receptor.
➢ One well-studied class of such molecules is heparan
sulfate proteoglycans including glypicans and
syndecans.

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Crosstalk Many Seven-Membrane Spanning Receptors Act via G Proteins

➢ Sometimes activated components from one pathway ➢ A portion of an activated G protein binds a target
affect components of another pathway. protein, altering its activity.
○ This is called signaling crosstalk. ➢ A class of receptors of great clinical importance is the
➢ Signaling is more of a network of biochemical opioid receptors, to which narcotic drugs such as
pathways than a linear sequence of events. morphine bind.
○ They are now illegal because its usage was
SIgnal Amplification abused by the users.
➢ Very small quantities of ligand are often sufficient to
elicit a response from a target cell. The Structure of G Protein-Linked Receptors
➢ At each step in the resulting cascade of events, a ➢ G protein-linked receptors have a similar structure but
signaling intermediate stimulates the production of quite different amino acid sequence.
many molecules needed for the next step. ➢ The receptor forms seven transmembrane a helices
➢ This multiplication of the effect of the signal is called connected by alternating cytosolic or extracellular
signal amplification. loops.
➢ The extracellular portion of each receptor has a unique
messenger-binding site.

Regulation of G Protein-Linked Receptors

➢ G protein-linked receptors can be regulated in several
ways.
Categories of Receptors
➢ One is via phosphorylation of amino acids in the
➢ Receptors can be classified into several basic
cytosolic domain, carried out by G protein-linked
categories:
receptor kinases (GRKs), which act on activated
○ Ligand-gated channels
receptors.
○ Plasma membrane receptors of two types:
➢ B-arrestin binds phosphorylated B-adrenergic receptors
■ Those linked to G proteins
and inhibits them.
■ Those linked to protein kinases
○ Protein Kinase A (PKA) is activated by G
protein-mediated signaling.
GUIDE QUESTION
a. PKA can phosphorylate other amino
➢ 5-7. Give 3 categories of receptors.
acids on the receptor and inhibit it.
○ ligand-gated channels
b. This is a good example of negative
○ plasma membrane receptors linked to G
feedback during cell signaling.
proteins
○ plasma membrane receptors linked to protein
The Structure, Activation, and Inactivation of G Proteins
kinases
➢ G proteins act like molecular switches whose on and off
states depend on whether they are bound to GTP or
G Protein-Linked Receptors
GDP.
➢ The G protein-linked receptor family is so named
➢ There are large heterotrimeric G proteins and small
because ligand binding causes a change in receptor
monomeric G proteins.
conformation that activates a particular G protein.
➢ The heterotrimeric G proteins mediate signal
○ G protein: guanine-nucleotide binding protein
transduction through G protein-linked receptors and
■ The receptor family activates the
have Ga, Gb, and Gy subunits.
g-protein.

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G Protein Structure G Protein Inactivation

➢ Ga is the largest subunit of Gaby, and binds to GDP ➢ G proteins remain active as long as the G alpha subunit
and GTP. is bound to GTP and separate from the G beta and
○ When it binds to GTP it detaches from the Gby gamma subunit.
subunits which are permanently bound ➢ Once the G alpha subunit has hydrolyzed GTP to GDP,
together. it reassociates with G beta and gamma.
➢ Gs are stimulators of signal transduction; Gi are ➢ Some G alpha proteins are not very efficient at GTP
inhibitors. hydrolysis.
Regulation of G Proteins
G Protein Function ➢ G protein activity (for GTP hydrolysis) is greatly
➢ When a messenger binds to a G protein-linked receptor enhanced by regulators of G protein-signaling (RGS)
the resulting change in receptor conformation causes proteins.
a G protein to associate with it and release its GDP. ○ RGS ang nagccheck kung hindi magaling
➢ The Ga then binds a new GTP molecule and detaches yung G proteins sa GTP hydrolysis.
from the complex. ➢ These GTPase activating proteins (GAPs) are important
➢ Either the Ga or the Gby initiates signal transduction regulators of G protein function.
depending on the G protein. ➢ The most important G protein function is release or
formation of second messengers.

Cyclic AMP is a Secondary Messenger

Whose Production is Regulated by Some G Proteins
➢ Cyclic adenosine monophosphate (cAMP) is formed
from cytosolic ATP by adenylyl cyclase, an enzyme
that is anchored in the plasma membrane.
➢ The enzyme is inactive until bound to activated G
stimulatory alpha (by receptor-ligand stimulated
acquisition of GTP and release from G stimulatory beta
and gamma).
➢ G inhibitor alpha inhibits adenylyl cyclase.

1. In resting state, the receptor is not bound by the

ligand, so the G alpha subunit is still bound to the GTP
and still associated with the beta-gamma complex.
2. When the ligands bind to the receptor, the receptor
binds to the G protein, and then the G alpha now
releases the GTP and gets or acquires the GTP.
3. So now the Galpha associated with GTP dissociates
and separates from beta and the gamma, activating The Activation of Cyclic AMP. When adenylyl cyclase is in the
the G protein subunits or inhibiting target proteins, activated form, it will activate cyclic AMP. cAMP will be
initiating the signal transduction events. inactivated through hydrolysis by phosphodiesterase,
a. So it will bind to whom is available. transforming it into AMP again.
b. The G alpha subunit hydrolyses its bound GTP
to GDP becoming inactive again.
i. Once it’s used and not bounded
anymore, GDP will now be acquired
becoming GDP, recombining with
the beta-gamma subunit.
ii. This inactivates the G protein.

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2. The GTP-G stimulatory alpha complex then binds to

and activates membrane-bound adenylyl cyclase (A),
which synthesizes cAMP.
3. Activation ends when the ligand leaves the receptor,
the GTP is hydrolyzed to GDP by the GTPase activity of
the G stimulatory alpha subunit, and the G stimulatory
alpha dissociates from adenylyl cyclase.
4. Adenylyl cyclase then reverts to the inactive form, the
G stimulatory alpha reassociates with the G stimulatory
beta and gamma complex, and…
5. cAMP molecules in the cytosol are hydrolyzed to AMP
by the phosphodiesterase.

G Proteins are Active for Only a Short Time

➢ Because G proteins remain active for a very short time,
they can respond quickly to changing conditions.
➢ Once a G protein becomes inactive, adenylyl cycles
stop making new cAMP.
➢ The cAMP that remains is degraded by
phosphodiesterase.

cAMP Function
➢ cAMP is important in many cellular events.
➢ Its main target is protein kinase A (PKA), which it
regulates by separating the regulatory and catalytic
subunits.
➢ PKA phosphorylates a variety of proteins on ser or thr
residues using ATP as the source of phosphate.

The Roles of G Proteins and Cyclic AMP in Signal Transduction. In

the inactive state, the alpha, beta, and gamma subunits are
present as a complex, with GDP bound to the alpha subunit.
When a ligand (L) binds its receptor (R), it binds and activates a
G stimulatory protein.
1. When a receptor is activated by ligand binding, the
receptor-ligand complex associates with the G
stimulatory protein, causing the displacement of GDP
by GTP and the dissociation of the G stimulatory
alpha-GTP complex.

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➢ Whooping cough:
○ Bordetella pertussis secretes pertussis toxin
that acts on Gi so that it can no longer inhibit
adenylyl cyclase.
○ This causes an accumulation of fluid in the
lungs and the persistent cough associated
with the disease.

Many G Proteins Use Inositol Trisphosphate and

Diacylglycerol as Second Messengers
➢ Inositol-1,4,5-trisphosphate (IP3) functions as a second
messenger.
➢ It is generated from PIP2 when the enzyme
phospholipase C is activated.
➢ It cleaves PIP2 into IP3 and diacylglycerol, both of which
are second messengers in a variety of cellular events.

(Very important functions)

The Activation of Protein Kinase A by Cyclic AMP.

1. PKA is composed of 2 catalytic and 2 regulatory
subunits. The regulatory subunits inhibit the catalytic
subunits in the absence of cAMP.
2. cAMP activates PKA by binding to the regulatory
subunits, causing the regulatory subunits to change
conformation.
3. The catalytic subunits detach. They are now activated
and can phosphorylate target proteins in the cell.

Disruption of G Protein Signaling Causes

Several Human Diseases
➢ Some bacteria cause their diseases through their
effects on heterotrimeric G proteins.
➢ Cholera:
○ When Vibrio cholerae colonizes the gut, it
secretes cholera toxin.
○ This toxin modifies Gs so that it cannot
How DAG and IP3 are formed. Phospholipase C cleaves PIP2,
hydrolyze GTP.
resulting in DAG and IP3. IP3 is in the cytosol, while DAG is by the
○ This alters secretion of salts and fluids in the
plasma membrane.
intestine and can cause death by
dehydration.

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IP3 and Diacylglycerol in Signaling 1. A receptor is activated by the binding of the ligand.
➢ A ligand binds its membrane receptor, leading to the The receptor-ligand complex associates with the G
activation of a G protein, Gq. protein Gq, causing displacement of GDP by GTP and
➢ Gq activates a phospholipase C called C beta, dissociation of the alpha and beta-gamma subunits.
generating both IP3 and diacylglycerol. 2. The GTP-G alpha complex then binds to phospholipase
➢ IP3 diffuses through the cytosol and binds a C (P), activating it and causing cleavage of PIP2 into IP3
ligand-gated calcium channel: the IP3 receptor and DAG.
channel. 3. IP3 is released into the cytosol, where it triggers calcium
➢ When IP3 binds the receptor, calcium is released into release.
the cytosol. 4. DAG remains in the membrane, where it activates
➢ Calcium and diacylglycerol activate members of the protein kinase C.
protein kinase C (PKC) family, which then
phosphorylate ser and thr residues on a variety of The Release of Calcium ions is a Key Event
target proteins. in Many Signaling Processes
➢ Calcium-sensitive fluorescent dyes (calcium indicators)
can be used to demonstrate the importance of
calcium release in signaling.
➢ Treating cells with calcium ionophores results in the
release of calcium in the absence of stimulus.
○ This further implicates calcium as an
intermediary in IP3 signaling.

Based on the color, we can see which part has increased

calcium concentration.

Calcium in Signaling
➢ Calcium concentrations can be released by opening
calcium channels in the plasma membrane, as in
neuronal signaling.
➢ Calcium can also be released from storage in the ER
through the IP3 receptor channel.
➢ The IP3 receptor channel and the ryanodine receptor
channels are sensitive to calcium.
➢ A rapid increase in calcium ions can cause the
ryanodine receptor channels to open, allowing
calcium to enter the cytoplasm from the ER.
○ This is termed calcium-induced calcium
release.

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Calcium Binding Activates Many Effector Proteins

➢ Calcium can bind directly to effector proteins, altering
their activity.
➢ The protein calmodulin mediates calcium-activated
processes in the cell.
➢ Calmodulin has an armlike structure with a hand at
each end; each binds two Ca2+.

An Overview of Calcium Regulation in Cells. Cytotoxic Ca2+

concentration is lowered by the actions of the ER calcium
ATPase, the plasma membrane calcium ATPase, Na+/Ca2+
exchangers, and mitochondria. Ca2+ concentration increases in
the cytosol because of the opening of Ca2+ channels in the
plasma membrane and the release of Ca2+ through the IP3 or
ryanodine receptor channels in the ER membrane.
Calmodulin Function
(blue numbers = calcium is increased, red numbers = calcium is
➢ Two Ca2+ bind at each “hand,” inducing a
decreased)
conformational change and forming the active
calcium-calmodulin complex. [1,2]
Calcium Release Following Fertilization of Animal Eggs
➢ In the presence of a protein with a calmodulin binding
➢ Animal sperm are activated by the release of calcium.
site, calmodulin binds it by wrapping around the
➢ Activated sperm then bind to the surfaces of mature
binding site. [3]
eggs and unite with them, triggering the release of
➢ Calmodulin binding can dramatically alter the protein’s
Ca2+ from internal stores.
activity.
➢ Ca2+ release begins at the site of sperm entry, then
spreads across the egg surface like a wave.

Roles of Calcium in Fertilization

➢ Calcium release is necessary for two crucial events:
○ It stimulates vesicles called cortical granules
to release their contents and alter the
properties of the vitelline envelope (slow
block to polyspermy).
○ It induces egg activation, the resumption of
metabolic processes and reorganization of
egg contents, which is necessary for
embryonic development to proceed.

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The Beta-Gamma Subunits of G Proteins Can Also Receptor Tyrosine Kinases

Transduce Signals ➢ Several growth factors stimulate receptor tyrosine
➢ G beta-gamma can also engage in signaling. kinases:
○ G protein receptor kinases are activated by ○ Insulin
the dissociated (from G alpha) G ○ Insulin-like growth factor-1
beta-gamma subunit. ○ Fibroblast growth factor
➢ e.g., The muscarinic acetylcholine receptor, when ○ Epidermal growth factor
bound to acetylcholine, triggers release of the G ○ Nerve growth factor
beta-gamma subunit from G alpha.
➢ The subunit causes K+ channels to open.

Receptor Tyrosine Kinases Aggregate and Undergo

Autophosphorylation
1. In the absence of acetylcholine (Ach), a G protein ➢ Many receptor tyrosine kinases (RTKs) trigger a chain of
associated with the muscarinic Ach receptor is bound events in the cell that culminate in cell growth,
to GDP. proliferation, or specialization.
2. Binding of Ach results in activation of the G protein. The
beta-gamma subunit interacts with a K+ ion channel, The Structure of Receptor Tyrosine Kinases
causing it to open. ➢ RTKs often consist of a single polypeptide chain with just
one transmembrane segment.
Protein Kinase-Associated Receptors ➢ The extracellular part of the receptor contains the
➢ Protein kinase-associated receptors are not only ligand-binding domain.
receptors, but also function as kinases (enzymes). ➢ On the cytosolic side is the tyrosine kinase domain.
➢ Ligand binding stimulates their kinase activities.
➢ Signaling of these receptor protein kinases is
transmitted through a phosphorylation cascade.
➢ Kinases are either tyrosine kinases or serine/threonine
kinases.

Growth Factors Often Bind

Protein Kinase-Associated Receptors
➢ For cells to divide, they need enough nutrients for
growth and signals to stimulate cell growth.
➢ Cultured cells in vitro will not grow, even with enough
nutrients, unless blood serum is provided.
➢ Messengers in the serum that stimulate growth are
called growth factors.

Components of Blood Plasma and Serum

The Structure and Activation of a Receptor Tyrosine Kinase (RTK).
➢ Plasma is whole blood.
a. The receptor for epidermal growth factor (EGF) is
○ It includes platelets, which contain clotting
typical of many RTKs. These receptors often have only
components, BUT…
one transmembrane segment. The extracellular portion
○ Excludes red and white blood cells.
of the receptor binds to the ligand (in this case, EGF).
○ It cannot support cell growth.
Inside the cell, a portion of the receptor has tyrosine
➢ Serum is the clear fluid remaining after blood has
kinase activity. The remainder of the receptor contains
clotted, during which the platelets secrete growth
a series of tyrosine residues that are substrates for the
factors.
tyrosine kinase.
b. The activation of RTKs starts with ligand binding, causing
Platelet-Derived Growth Factor
receptor clustering. Once the receptors aggregate,
➢ The growth factors secreted by platelets stimulate they cross-phosphorylate each other at a number of
fibroblasts to form new connective tissue. tyrosine residues. The formation of tyrosine phosphate
➢ The serum that remains after clotting contains large (Tyr-P) residues on the receptor creates binding sites for
amounts of platelet-derived growth factor (PDGF). cytosolic proteins that contain SH2 domains.
➢ The receptor for PDGF is a receptor tyrosine kinase. c. This shows the dimerization of EGF receptors after they
bind EGF.

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➢ Sometimes, the receptor and tyrosine kinase are two

separate proteins.
➢ In this case, the nonreceptor tyrosine kinase binds to
the receptor and is activated in response to ligand
binding.
➢ e.g., Src was the first nonreceptor tyrosine kinase
discovered.

The Activation of Receptor Tyrosine Kinases

➢ Signal transduction is initiated upon ligand binding that
causes aggregation of RTKs.
➢ In some cases, receptors dimerize upon ligand binding
and phosphorylate each other.
➢ Because they phosphorylate the same type of receptor
as themselves, this is called autophosphorylation.

GUIDE QUESTION
➢ 8-10. Give 3 growth factor families.
○ Epidermal growth factor (EGF)
○ Transforming growth factor alpha (TGFa)
Platelet-derived growth factor (PDGF)
○ Transforming growth factor beta (TGFb)
○ Fibroblast growth factor (FGF)
○ Interleukin-2 (IL-2)
○ Colony-stimulating factor-1 (CSF-1)
○ Wnts
○ Hedgehogs

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JULY 15, 2024 ➢ It is a small monomeric G protein.

PART 2: CELL SIGNALING ➢ Ras and other such molecules can bind GDP or GTP,
but are active only when bound to GTP.
RECEPTOR TYROSINE KINASES
➢ Ras requires assistance from a guanine-nucleotide
➢ Receptor tyrosine kinases initiate a signal transduction
exchange factor (GEF) called Sos to acquire a GTP
cascade involving Ras and MAP Kinase.
molecule.

picture of Ras/step 1 of receptor tyrosine kinase signal

transduction cascade

RAS SIGNALING
➢ (2) For Sos to become active, it must bind the receptor
through another protein called GRB2, which has an SH2
domain.
➢ (3) Sos then stimulates Ras to release Ras to release
GDP and bind a GTP molecule, which activates Ras.
➢ (5) Activated Ras triggers a series of phosphorylations.
(Note: nakalagay sa ppt step 5 ito. Si step 4 ibang
signaling pathway siya which will be discussed as you
read further).

➢ (1) Once autophosphorylation of the receptors occurs,

the receptor recruits cytosolic proteins.
○ The cytosolic proteins have amino acid
stretches (domains) that recognize the
phosphotyrosine and nearby residues on the
receptor.
○ One such domain is called the SH2 domain
because the residues are similar to sequences
on Src (SH = Src Homology).

RAS picture of Ras signaling/steps of receptor tyrosine kinase signal

➢ Important in regulating growth of cells. transduction cascade

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➢ The first protein phosphorylated is Raf, a protein kinase.

➢ Raf phosphorylates serine and threonine residues in a
protein kinase called MEK.
➢ (6) MEK in turn phosphorylates ser,thr residues in a class
of proteins called mitogen-activated protein kinases
(MAP kinases).
○ MAPKs are activated in response to a signal to
grow and divide, sometimes called a
mitogen.
➢ (7) MAPKs phosphorylate transcription factors that enter
the nucleus to alter gene expression.
➢ (8) E.g. Jun and Ets family members regulate the
expression of genes needed for growth and division.
➢ Ste 5 increases the efficiency of signaling by recruiting
all of the kinases in the cascade into a large complex
INACTIVATION OF RAS
➢ Other similar scaffolding complexes have been
➢ Once Ras is in the active state, it must be inactivated to identified in yeast and other organisms
avoid continual stimulation of the Ras pathway. ➢ E.g., one important class of proteins that function, this
➢ This is accomplished by a GTPase activating protein way is the 14-3-3 proteins
(GAP) that facilitates GTP hydrolysis.
➢ (9) GDP bound Ras is now inactive.

picture of Ras inactivation/steps of receptor tyrosine kinase

signal transduction cascade

RECEPTOR TYROSINE KINASES ACTIVATE A VARIETY OF OTHER

SIGNALING PATHWAYS
➢ Receptor tyrosine kinases can also activate DOMINANT NEGATIVE MUTANT RECEPTORS ARE IMPORTANT TOOLS
phospholipase C (4), leading to production of IP3 and FOR STUDYING RECEPTOR FUNCTION
DAG. ➢ One approach to studying receptor function involves
➢ The phospholipase Cy (C-gamma) in this case contains introducing mutations into the receptor to determine
an SH2 domain and must bind to the receptor. the effect
➢ RTKs can also activate enzymes such as PI3-kinase ➢ E.g., fibroblast growth factors (FGFs) and their receptor
(phosphatidylinositol-3-kinase). tyrosine kinases (FGFRs)
➢ Normal FGFs undergo autophosphorylation in response
SCAFFOLDING COMPLEXES CAN FACILITATE CELL SIGNALING to ligand binding
➢ Signaling components such as those in the Ras
pathway are sometimes assembled into large
multiprotein complexes that make cascades more
efficient.
➢ E.g., in yeast, cells of mating type a secrete a signal
called “a factor”, which can bind to G protein-linked
receptors on nearby a (alpha) cells.
➢ The a (alpha) cells secrete a (alpha) factor.

CELL SIGNALING AND YEAST MATING

➢ The mating factor signaling between a and α cells
results in large-scale changes including polarized
discretion, cytoskeletal changes, and gene expression
changes
➢ The signaling is mediated through the activated Gβγ
subunit of a G protein, which recruits Ste5, a large
scaffolding protein, to the plasma membrane

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DOMINANT NEGATIVE RECEPTOR MUTATIONS

➢ Some types of mutant FGFRs can bind ligands but
cannot undergo autophosphorylation
➢ These mutant receptors interfere with normal receptor
function because they can dimerize with normal
receptors
➢ A mutant that overrides normal function in this way is
called a dominant negative mutation

CONSTITUTIVE MUTATIONS
➢ Some mutations make FGFRs active in signaling, even
when not bound to ligand
➢ These mutations are called constitutively active
mutations because they cause the receptor to stay
switched “on” all the time

FGFR FUNCTION
➢ Dominant negative mutations of FGFR can be made
artificially and then introduced into frog embryos,
which then fail to develop correctly in the trunk and tail
➢ In humans, a dominant mutation in FGFR-3 causes a
form of dwarfism called achondroplasia

OTHER GROWTH FACTORS TRANSDUCE THEIR SIGNALS VIA

RECEPTOR SERINE-THREONINE KINASES
➢ A major class of serine-threonine kinases is a family of
proteins that bind transforming growth factor β(TGFβ)
family members
➢ This family regulates many cell functions including cell
proliferation, programmed cell death, specialization,
and key embryonic events

TGFβ SIGNALING
➢ Upon ligand binding, the type Il receptor
➢ TGFβ signaling begins when the growth factor binds the phosphorylates the type I receptor, which then initiates
transmembrane receptor (1,2) a signal transduction cascade.
➢ There are type I and type II receptors in the receiving ➢ It phosphorylates a class of proteins called Smads
cell ➢ There are three types of Smads.
➢ Some TGFβ family members dimerize before binding
the receptors

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TYPES OF SMADS
➢ Some are phosphorylated by a complex of
anchoring proteins and receptors and are called
receptor-regulated, or R-Smads (3)
➢ Smad 4 forms a multiprotein complex with
phosphorylated R-Smads; the whole complex
can then enter the nucleus (4)
➢ Other Smads act at various points to inhibit the
TGF-β pathway.

DISRUPTIONS OF GROWTH FACTOR SIGNALING

CAN LEAD TO CANCER
➢ Some cancers can result from the loss of
regulation of growth factor signaling
➢ E.g., mutations in Ras are often associated with
cancer

GROWTH FACTOR RECEPTOR PATHWAYS

SHARE COMMON THEMES
➢ Several common themes are involved in growth
factor signaling
➢ Ligand binding often results in activation and/or
clustering of receptors, followed by a cascade of
events, often phosphorylation
➢ Phosphorylation may be catalyzed by the
receptor, or by Janus-activated kinase, when
activated by a receptor

HORMONE SIGNALING
➢ Plants and animals use secreted chemical signals
called hormones to coordinate the function of
cells and tissues over long distances.
➢ Hormones differ in many ways.
➢ Animal hormones are better understood than
plant hormones.

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○ Lipid-like hormones such as steroids (e.g.,

testosterone)

CONTROL OF GLUCOSE METABOLISM IS A GOOD

EXAMPLE OF ENDOCRINE REGULATION
➢ Adrenergic hormones, epinephrine and
norepinephrine, function to put body functions
on hold and redirect resources to the heart and
skeletal muscles in dangerous or stressful
situations.
HORMONES CAN BE CLASSIFIED BY THE DISTANCE THEY
➢ They bind to a family of G protein-linked
TRAVEL AND BY THEIR CHEMICAL PROPERTIES
receptors, adrenergic receptors, classified as a-
➢ Endocrine hormones travel from sending to
and β-adrenergic receptors.
receiving cells via the circulatory system.
➢ They are synthesized by endocrine tissues and
ADRENERGIC RECEPTORS
are secreted directly into the bloodstream, with a
➢ α-adrenergic receptors bind epinephrine and
life span ranging from a few seconds to many
norepinephrine; these receptors are located on
hours.
smooth muscles, regulating flow to visceral
➢ As they circulate, they encounter their receptors
organs
in target tissues.
➢ β-adrenergic receptors bind epinephrine better
than norepinephrine and are located on smooth
muscles associated with arterioles feeding the
heart, lungs, and skeletal

ADRENERGIC RECEPTORS AND G PROTEINS

➢ α- and β-adrenergic receptors are associated

with different G proteins and so stimulate
different signal transduction pathways
➢ E.g., a1-adrenergic receptors are Gq, proteins,
whereas the β-adrenergic receptors activate GS
➢ GS stimulates the CAMP signal transduction
pathway, inducing relaxation of certain smooth

INTRACELLULAR EFFECTS OF ADRENERGIC HORMONAL

CONTROL OF GLYCOGEN DEGRADATION
➢ In the figure above, when the adrenal gland
➢ The breakdown of glycogen is facilitated by the
secretes epinephrine, it will travel toward two
enzyme glycogen phosphorylase, resulting in
organs: the heart or liver.
release of a glucose-1-phosphate
○ Heart Cell: It will trigger a cascade of
➢ Glycogen degradation begins when an
actions that will result to the increased
epinephrine molecule binds to a
heart rate.
beta-adrenergic receptor on a liver or muscle
○ Liver Cell: It will trigger the breakdown of
cell
liver glycogen.
➢ The receptor activates a neighboring Gs protein
CHEMICAL CLASSIFICATION OF ENDOCRINE HORMONES that in turn stimulates adenylyl cyclase

➢ Endocrine hormones fall into four categories

ADRENERGIC RECEPTORS AND G PROTEINS
○ Amino acid derivatives (e.g.,
➢ Adenylyl cyclase generates CAMP from ATP; the
epinephrine)
cAMP increase activates protein kinase A (1)
○ Peptides (e.g., vasopressin)
○ Proteins (e.g., insulin)

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➢ PKA activates another cascade of events starting

with phosphorylation of the enzyme
phosphorylase kinase (2)
➢ This leads to a conversion of the less active b
form to the more active a form

α-Adrenergic Receptors and the IP3 Pathway

➢ a1-adrenergic receptors stimulate formation of
IP3 and DAG
➢ When the receptors are stimulated, the formation
of IP3 causes an increase in intracellular [Ca2+]
➢ The activation of glycogen phosphorylase a ➢ Elevated calcium causes smooth muscle
leads to an increased rate of glycogen contraction, constricting blood vessels and
breakdown (4) reducing blood flow

➢ CAMP also stimulates the inactivation of the

Insulin Signaling Acts through PI 3-Kinase to Regulate
enzyme system responsible for synthesis of
Resting Glucose Levels
glycogen
➢ Specialized cells in the pancreas called the islets
➢ PKA also phosphorylates glycogen synthase, and
of Langerhans secrete two peptide hormones
inactivates it that regulate normal glucose levels
➢ Glucagon acts to increase blood glucose
through glycogen breakdown
➢ Insulin reduces blood glucose levels by
stimulating uptake into muscle and adipose cells,
and stimulating glycogen synthesis.

DIABETES

➢ Type I diabetes results in loss of insulin-producing

cells in the islets of Langerhans
➢ It can be successfully treated with insulin
➢ Type Il diabetes appears to result from resistance
to insulin and so is not effectively treated with
insulin

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INSULIN ➢ Activation of Akt has two important

➢ Insulin has rapid and longer-lasting effects on a consequences
variety of cells ○ Activation of Akt leads to movement of
➢ Insulin binds to receptor tyrosine kinases, which a glucose transporter, GLUT4, to the
have two a and two & subunits plasma membrane, allowing glucose
➢ When insulin binds the receptor, the ß subunits uptake
phosphorylate insulin receptor substrate I (IRS-1) ○ Also, Akt can phosphorylate glycogen
synthase kinase 3 (GSK3), reducing its
activity
■ This leads to an increase in the
amount of the active form of
glycogen synthase, enhancing
glycogen production

Steroid Hormone Receptors Act Primarily in the Nucleus,

Not the Cell Surface
➢ Steroid receptor proteins mediate the actions of
steroid hormones such as progesterone,
estrogen, testosterone, and glucocorticoids
➢ Steroid hormones are lipid signaling molecules
➢ The hormone enters the target cell and binds its
receptor, triggering a cascade of events that
(1) When the insulin receptor binds insulin, the
activate (sometimes inhibit) transcription of a set
activated receptor phosphorylates the IRS-1
of target genes
protein. IRS-1 can lead to recruitment of GRB2,
activating the Ras pathway.
(2) IRS-1 activates Pl 3-kinase, which catalyzes the
addition of a phosphate group to the membrane
lipid PIP2, thereby converting it to PIP3. PTEN can
convert PIP3, back to PIP2
(3) PIP3, binds a protein kinase called Akt, which is
activated by other protein kinases.
(4) Akt catalyzes phorphorylation of key proteins,
leading to an increase in glycogen synthase
activity and recruitment of the glucose
transporter, GLUT4, to the membrane

INSULIN SIGNALING

➢ Phosphorylated IRS-1 stimulates two different ➢ Mare-recognize siya ng receptor so it will trigger
pathways a response sa loob ng nucleus → transcription
➢ IRS-1 can recruit GRB2, activating the Ras
GUIDE QUESTION
pathway (1)
➢ Give your comments and suggestions for the
➢ IRS-1 can also bind phosphatidylinositol-3-kinase
course.
(PI 3-kinase), which converts PIP2 into PIP3 (2)
➢ PIP3 binds a protein called Akt (or protein kinase
B) (3)
➢ An enzyme that opposes P1 3-kinase is PTEN, a
phosphatase that removes a phosphate from
PIP3, preventing activation of Akt

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