BBO - Cell biology

Jade Tang
Cell structure
nucleus

nuclear envelope: the two membranes, situated nucleolus: one or more of which is found inside the nucleus;
close together its function is to manufacture ribosomes using the
information in its own DNA
nuclear pores: pores found in the nuclear
envelope which control the exchange of materials - deeply staining area
-main functions is to make ribosomes =rRNA+protein
Ribosomes

ribosome: a tiny organelle found in large numbers in all cells; prokaryotic ribosomes(70S) are about 20 nm in
diameter while eukaryotic ribosomes(80S) are about 25 nm in diameter

ribosome=ribosomal RNA (rRNA) +protein

Ribosomes allow all the interacting molecules involved in protein synthesis, such as mRNA,
tRNA, amino acids and regulatory proteins, to gather together in one place

*not visible with a light microscope

 nucleolus (plural, nucleoli)

ribosomal RNA (rRNA)

in the nucleolus, proteins imported from the cytoplasm are

assembled with rRNA into large and small subunits of
ribosomes. These subunits then exit the nucleus through the
nuclear pores to the cytoplasm, where a large and a small
subunit can assemble into a ribosome.

- free ribosomes
suspended in the cytosol
- bound ribosomes
attached to the outside of the endoplasmic reticulum or nuclear envelope, so bound ribosomes
generally make proteins that are destined for insertion into membranes, for packaging within certain
organelles such as lysosomes
The Endoplasmic Reticulum: Biosynthetic Factory
Endoplasmic reticulum (ER): a network of flattened sacs running through the cytoplasm of
eukaryotic cells; ER is continuous with the outer membrane of the nuclear envelope.

The ER membrane separates the internal compartment of the ER, called the ER lumen (cavity) or
cisternal space
smooth ER: it lacks ribosomes. It makes lipids and steroids, such as cholesterol and the
reproductive hormones oestrogen and testosterone. Also include detoxification of drugs and
poisons（细胞色素P450）, and storage of calcium ions（Ca2+-ATPase）.
Rough ER
• making secretory proteins
Most secretory proteins are
glycoproteins, proteins with carbohydrates
covalently bonded to them. The
carbohydrates are attached to the proteins
in the ER lumen by enzymes built into the
ER membrane

• a membrane factory for the cell

Golgi apparatus

Golgi apparatus (Golgi body, Golgi complex): an organelle found in

eukaryotic cells; the Golgi apparatus consists of a stack of flattened sacs
called cisternae.

• Sugars are added to proteins to make molecules known as glycoproteins.

• Golgi vesicles are used to make lysosomes.
• Sugars are added to lipids to make glycolipids. Glycoproteins and glycolipids are
important components of membranes
 The Golgi Apparatus: Shipping and Receiving Center

“cisternal maturation model”

• a cis face that receives vesicles
containing ER products and a
trans face that dispatches vesicles
Lysosomes

lysosome: a spherical organelle found in eukaryotic cells; it contains digestive (hydrolytic) enzymes and
has a variety of destructive functions, such as removal of old cell organelles

- the contents of lysosomes are acidic, pH 4–5

- Hydrolytic enzymes and lysosomal membrane are made by rough ER and then transferred to the Golgi
apparatus for further processing.
Lysosomes: Digestive Compartments

• At least some lysosomes probably arise by budding from the trans face of
the Golgi apparatus

• phagocytosis & Autophagy:

Lysosomes also use their hydrolytic enzymes to recycle the cell’s own organic
material, a process called autophagy /ɔː'tɒfədʒɪ/(细胞的)自我吞噬(作用).
autophagosome
 Peroxisomes过氧物酶体: Oxidation
• Peroxisomes are specialized metabolic compartments bounded by a single membrane
• Peroxisomes contain enzymes that remove hydrogen atoms from various substrates and
transfer them to oxygen (O2), producing hydrogen peroxide (H2O2) as a by-product
• The H2O2 formed by peroxisomes is itself toxic, but the organelle also contains an enzyme
that converts H2O2 to water.
• Oxygen is used to break down different types of molecules
• Autophagy

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Peroxisomes: Oxidation
• EXAMPLE:
glyoxysomes 乙醛酸循环体 are
found in the fat-storing tissues of
plant seeds. These organelles
contain enzymes that initiate the
conversion of fatty acids to sugar,
which the emerging seedling uses as
a source of energy and carbon until
it can produce its own sugar by
photosynthesis
endosymbiont theory

- the proposed ancestors of

mitochondria were oxygen-using non-
photosynthetic prokaryotes

- the proposed ancestors of chloroplasts

were photosynthetic prokaryotes.
Mitochondria: Chemical Energy Conversion
• generally in the range of 1–10 µm long.
• The outer membrane is smooth, but the inner membrane is convoluted,
with infoldings called cristae.
• The inner membrane divides the mitochondrion into two internal
compartments
- The first is the intermembrane space, the narrow region between the inner
and outer membranes.
- The second compartment, the mitochondrial matrix, is enclosed by the
inner membrane (The matrix contains many different enzymes as well as
the mitochondrial DNA and ribosomes).
Chloroplasts: Capture of Light Energy
• about 3–6 µm in length
• The membranes of the chloroplast divide the chloroplast space into
three compartments:
- the intermembrane space
- the stroma基质: contains the chloroplast DNA and ribosomes as well as
many enzymes
- the thylakoid space.
Plants: amyloplast

Amyloplast/'æməlo,plæst/造粉体: storage of
starch
Statolith/'stætəʊlɪθ/平衡⽯: gravitropism
Vacuoles: Diverse Maintenance Compartments

• Vacuoles perform a variety of functions in different kinds of cells:

- Food vacuoles, formed by phagocytosis
- contractile vacuoles收缩泡: pump excess water out of the cell, that
maintaining a suitable concentration of ions and molecules inside the cell
eukaryotic cytoskeleton
• organizing the structures and activities of the cell
• composed of three types of molecular structures:
microtubules, microfilaments, and intermediate filaments
Fig. 6-20

Cytoskeleton
Microtubule

0.25 µm Microfilamen
ts
Components of the Cytoskeleton
• Three main types of fibers make up the cytoskeleton:
• Microtubules微管 are the thickest of the three components
of the cytoskeleton, formed by tubulin微管蛋白
• Microfilaments微丝, also called actin filaments, are the
thinnest components
• Intermediate filaments 中间纤维are fibers with diameters in
a middle range

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Microtubules

Function of microtubules:
- cell support and determining cell shape;
- the 'spindle' on which chromatids and chromosomes separate
during nuclear division is made of microtubules

The assembly of microtubules from tubulin molecules is

controlled by special locations in cells called microtubule
organising centres (MTOCs).
microtubules

Microtubules- tubulin
• Alpha and beta tubulin
• dimer
• intracellular transport
system
• In animal cells, microtubules grow out from a centrosome
• Within the centrosome there is a pair of centrioles, each composed of
nine sets of triplet microtubules arranged in a ring
• Spindle microtubules：help determine the locations of the chromosome
Cilia 纤毛and Flagella 鞭毛

cilia: short and often numerous flagella: long and found usually one or two per cell
Cilia and Flagella
dynein:动力蛋白
 Microfilaments

Microfilaments- actin filaments肌动蛋白丝

• A microfilament is a twisted double chain of
actin subunits
• actin, a globular protein
• dimer
Microfilaments
• Bear tension (pulling forces)
• helps support the cell’s shape
• cell motility
 Intermediate Filaments
• larger than the diameter of microfilaments but smaller than that of
microtubules
• more permanent fixtures of cells
• keratin角蛋白
Cell wall
• there are channels between adjacent cells called plasmodesmata
Extracellular matrix (ECM)of animal cells
• The main ingredients of the ECM are glycoproteins and other carbohydrate-
containing molecules secreted by the cells.
• The most abundant glycoprotein in the ECM of most animal cells is collagen, which
forms strong fibers outside the cells
Collagen Proteoglycan
EXTRACELLULAR FLUID
complex
*proteoglycan蛋白聚糖

Fibronectin

Integrins

Plasma
membrane

Micro- CYTOPLASM
filaments
Fig. 6-30a

Collagen Proteoglycan
EXTRACELLULAR FLUID complex

Fibronectin

Integrins

Plasma
membrane

Micro- CYTOPLASM
filaments

• Functions of the ECM: Four types of intercellular junctions

• Support • Plasmodesmata(in plant)
• Adhesion
• Movement • Tight junctions
• Regulation • Desmosomes
• Gap junctions
Cell membrane and transport
• Davson-Danielli model (“sandwich”)
• Singer-Nicolson model (“fluid-mosaic”)
Cell membrane and transport
Freeze-fracture
 Structure of membranes

• Phospholipids bilayer + proteins +cholesterol

• 7nm
• Fluid mosaic model:
• Fluid: phospholipid and protein move freely within their monolayer.
• Mosaic: the scattering of the proteins
 phospholipids
• hydrophilic heads + hydrophobic tails
• Spontaneously form bilayeràmembrane
• Phosphate groups form hydrogen bonds with the water molecules
• Function: form a barrier to most water-soluble molecules (sugar, amino acids and
protein) so they can not be leaked out.
 Cholesterol
• hydrophilic heads + hydrophobic tails
• relatively small
• similar proportion between cholesterol and phospholipids in animal cell,
but much less in plant cell, absent in prokaryotes.
• It combines with the fatty acid tail and holds the fatty acid chain together
• Function:
• at low temperature, increases membrane fluidity, preventing it from becoming too
rigidàsurvive at low temperature
• At high temperature, stablising cell membrane prevents membrane being too fluid.
• mechanical stability of membranes, without it membranes break and cells burst
open
 Proteins
• integral proteins嵌入蛋白-permanently embedded within the plasma
membrane
• peripheral proteins 外周蛋白
• Signaling proteins (receptors)
• Antigens
• Transport proteins: for ions and polar molecules to pass through
• Enzymes
• Cytoskeleton
Glycoproteins and glycolipids

• Carbohydrates chains projects out from proteins or lipids

• Stablising membrane structure by forming hydrogen
bonds with water
• Function
• Cell-cell recognition (antigen)
• Cell-cell adhesion
• Receptor
Cell signaling
• To coordinate the activities of the cells.
• A signaling pathway include: receive stimulus/signals, transmits the message,
making an appropriate response
• Stimulus—receptor–transmission—effector—response
• release of chemicals that combine with cell surface receptors on target cells,
leading to specific responses
• Nervous system vs Endocrine system
• Water-soluble vs Lipid-soluble signaling molecules
 Passive transport

• Simple diffusion – movement of small or

lipophilic molecules (e.g. O2, CO2, etc.)
• Osmosis – movement of water molecules
(dependent on solute concentrations)
• Facilitated diffusion – movement of large or
charged molecules via membrane proteins (e.g.
ions, sucrose, etc.)
 Osmolarity渗透压
• Osmolarity is a measure of solute concentration, as defined by the
number of osmoles of a solute per litre of solution (osmol/L)
• Solutions with a relatively higher osmolarity: hypertonic高渗溶液 (high solute
concentration ⇒ gains water)
• Solutions with a relatively lower osmolarity: hypotonic低渗溶液 (low solute
concentration ⇒ loses water)
• Solutions that have the same osmolarity: isotonic等渗溶液 (same solute
concentration ⇒ no net water flow)
• Tissues or organs to be used in medical procedures must be bathed in
a solution with the same osmolarity as the cytoplasm to prevent
osmosis
 • water pressure
acting against an
inelastic cell wall to
make the cell turgid

Flaccid, vacuole shrinks,

pulling cytoplasm away from
cell wall
HOW DO ANIMAL CELLS PRVENT
THEMSELVES FROM BURSTING
• Multicellular animals: osmoregulation
• Single-celled animals: contractile vacuole—continuously pump out
excess water
Facilitated Diffusion

• Facilitated diffusion is the passive movement of molecules from high concentration

area to low concentration area via membrane proteins
• large, polar molecules and ions
• Carrier Proteins
• conformational change to translocate the solute across the membrane
• Also involved in active transport
• Slower
• Channel Proteins
• Hydrophilic region (internal pore) + Hydrophobic region (adjacent to phospholipid)
• not used in active transport
• Faster
Aquaporins (AQP) are integral membrane proteins that serve as
channels in the transfer of water, and in some cases, small solutes
across the membrane
Why is aquaporins necessary?
• Water molecules are polar
• Few water can diffuse through phospholipid because core of
phospholipid bilayer is hydrophobic
• Aquaporin channel is hydrophilic
• Which increase permeability of membranes to water
 Active transport
• Movement of molecules from low
concentration area to high concentration area
• Against concentration gradient
• Through carrier protein
• Using ATP
 Sodium-Potassium Pump
• A specific solute will bind to the protein pump on one side of the
membrane
• The hydrolysis of ATP (to ADP + Pi) causes a conformational change in
the protein pump
• pump three sodium ions out of the cell at the same time as allowing two
potassium ions into the cell
• The solute molecule is consequently translocated across the membrane
(against the gradient) and released
 Bulk Transport

• Bulk transport allows larger materials to enter or leave the cell without having to
cross the membrane (this is an active process and requires ATP hydrolysis)
• Endocytosis
• Phagocytosis: solid
• Pinocytosis: liquid
• Exocytosis
Endocytosis
• Infolding of membrane
• Fusion of membrane
• Form a vesicle
end
Biological molecules
Enzymes
Cell membrane and transport
Mitosis
Fig. 12-17
M G1 S G2 M G1 S G2 M G1

MPF activity
Cyclin
concentration

Time
(a) Fluctuation of MPF activity and cyclin concentration during
the cell cycle

Cyclin accumulation
G1

Cdk

M
Degraded G2
cyclin
G2 Cdk
Cyclin is checkpoint
degraded

Cyclin
MPF

(b) Molecular mechanisms that help regulate the cell cycle

Cyclin D triggers cells to move from G0 to G1 and from G1
into S phase.
Cyclin E prepares the cell for DNA replication in S phase.
Cyclin A activates DNA replication inside the nucleus in S
phase.
Cyclin B promotes the assembly of the mitotic spindle and
other tasks in the cytoplasm to prepare for mitosis.
Mitosis
Bacteria: binary fission
DNA replication
Figure 16.17

Overview
Leading Origin of
replication Lagging
strand strand

Leading
Lagging strand
strand Overall directions
Leading strand of replication

5¢ DNA pol III

3¢ Primer
Primase
3¢ 5¢
3¢ 1
Parental Lagging strand
DNA 5¢ 2 DNA pol III
DNA pol I DNA ligase 4
3¢5¢ 3
3¢

5¢
Helicase unwinds and separates the double-stranded DNA by breaking the hydrogen bonds
between base pairs
DNA Gyrase reduces the torsional strain created by the unwinding of DNA by helicase
Single Stranded Binding bind to the DNA strands after they have been separated and prevent the strands
(SSB) Proteins from re-annealing
DNA Primase generates a short RNA primer (~10–15 nucleotides) on each of the template
strands
DNA Polymerase III attaches to the 3’-end of the primer and covalently joins the free nucleotides
together in a 5’ → 3’ direction
DNA Polymerase I removes the RNA primers from the lagging strand and replaces them with DNA
nucleotides
DNA Ligase joins the Okazaki fragments together to form a continuous strand
DNA polymerase III: 5’→3’
*Proof reading
Protein synthesis
Transcription
• Initiation: RNA polymerase attaches and initiates transcription at
promoter
• Elongation
• Termination:
• in bacteria: terminator
• In eukaryotes: polyadenylation signal sequence
 Transcription

• Initiation: RNA polymerase attaches and initiates transcription at

promoter
• In eukaryotes:
• Also with a collection of proteins called transcription factors
• At certain start point: TATA box
• RNA polymerase II
Transcription
Transcription

• Elongation: attaches to the 3’-end of the primer and

covalently joins the free nucleotides together in a
5’ → 3’ direction
• A-U pairs
Transcription

• Termination: end the process at certain location, release transcription

complex
• In bacteria: terminator
• In eukaryotes: polyadenylation signal sequence (on DNA)
• Transcribed AAUAA in pre-mRNA
Transcription

• polyadenylation signal sequence (on DNA)

• Transcribed AAUAA in pre-mRNA
Post-transcription modification

• Only in eukaryotes
• Alteration of mRNA Ends
• 5’-cap
• Poly-A tail
• Alteration of mRNA Ends
• Remove of introns
Post-transcription modification

• small nuclear
ribonucleoproteins (snRNPs)
• *ribozyme
• Spliceosome
Translation
Translation
Translation

Ribosome: ribosomal RNAs

(rRNAs) + protein
Translation
The central dogma