BCH 102: Introductory Biochemistry II

Prokaryotic and Eukaryotic cells

Cells fall into one of two broad categories: prokaryotic and eukaryotic. The single-celled
organisms of the domains are bacteria and archaea, which are classified as prokaryotes (pro =
before; karyon = nucleus). Animal cells, plant cells, fungi, and protists are eukaryotes (eu = true).

Components of Prokaryotic cells

prokaryotes share four common components: (a) a plasma membrane, an outer covering that
separates the cell’s interior from its surrounding environment; (b) cytoplasm, consisting of a jelly-
like region within the cell in which other cellular components are found; (c) DNA, the genetic
material of the cell; and (d) ribosomes, particles that synthesize proteins.

A generalized structure of a prokaryotic cell.

A prokaryotic cell is a simple, single-celled (unicellular) organism that lacks a nucleus, or any
other membrane-bound organelle. The DNA is found in the central part of the cell: a darkened
region called the nucleoid. Bacteria have a cell wall made of peptidoglycan, comprised of sugars
and amino acids, and many have a polysaccharide capsule. The cell wall acts as an extra layer of
protection, helps the cell maintain its shape, and prevents dehydration. The capsule enables the
cell to attach to surfaces in its environment. Some prokaryotes have flagella, pili, or fimbriae.
Flagella are used for locomotion, while most pili are used to exchange genetic material during a
type of reproduction called conjugation.

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Eukaryotic Cells

A eukaryotic cell is a cell that has a membrane-bound nucleus and other membrane-bound
compartments or sacs, called organelles, which have specialized functions. The word eukaryotic
means “true kernel” or “true nucleus,” referring to the presence of the membrane-bound nucleus
in these cells. The word “organelle” means “little organ,” and they have specialized cellular
functions, just as the organs of the body have specialized functions.

All living cells in multicellular organisms contain an internal cytoplasmic compartment, and a
nucleus within the cytoplasm. Cytosol, the jelly-like substance within the cell, provides the fluid
medium necessary for biochemical reactions. Eukaryotic cells, including all animal cells, also
contain various cellular organelles. An organelle (“little organ”) is one of several different types
of membrane-enclosed bodies in the cell, each performing a unique function. The organelles and
cytosol, taken together, compose the cell’s cytoplasm.

A typical human cell

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 A typical plant cell

Endoplasmic Reticulum

The endoplasmic reticulum (ER) is a system of channels that is continuous with the nuclear
membrane (or “envelope”) covering the nucleus and composed of the same lipid bilayer material.
ER provides passages throughout much of the cell that function in transporting, synthesizing, and
storing materials.

There are two forms of ER: rough ER and smooth ER. These two types of ER perform some very
different functions and can be found in very different amounts depending on the type of cell. Rough
ER (RER) is so-called because its membrane is dotted with embedded granules—organelles called
ribosomes, giving the RER a bumpy appearance. A ribosome is an organelle that serves as the site
of protein synthesis. It is composed of two ribosomal RNA subunits that wrap around mRNA to
start the process of translation, followed by protein synthesis. Smooth ER (SER) lacks these
ribosomes. One of the main functions of the smooth ER is in the synthesis of lipids. The smooth
ER synthesizes phospholipids, the main component of biological membranes, as well as steroid
hormones. For this reason, cells that produce large quantities of such hormones, such as those of
the female ovaries and male testes, contain large amounts of smooth ER. In addition to lipid
synthesis, the smooth ER also sequesters (i.e., stores) and regulates the concentration of cellular
Ca++, a function extremely important in cells of the nervous system where Ca++ is the trigger for
neurotransmitter release. The smooth ER additionally metabolizes some carbohydrates and
performs a detoxification role, breaking down certain toxins.

In contrast with the smooth ER, the primary job of the rough ER is the synthesis and modification
of proteins destined for the cell membrane or for export from the cell. Typically, a protein is
synthesized within the ribosome and released inside the channel of the rough ER, where sugars

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can be added to it (by a process called glycosylation) before it is transported within a vesicle to the
next stage in the packaging and shipping process- the Golgi apparatus.

Golgi apparatus

The Golgi apparatus is responsible for sorting, modifying, and shipping off the products that
come from the rough ER, much like a post-office. The Golgi apparatus looks like stacked flattened
discs, almost like stacks of oddly shaped pancakes. The Golgi apparatus has two distinct sides,
each with a different role. One side of the apparatus receives products in vesicles. These products
are sorted through the apparatus, and then they are released from the opposite side after being
repackaged into new vesicles. If the product is to be exported from the cell, the vesicle migrates to
the cell surface and fuses to the cell membrane and the cargo is secreted.

Lysosomes

A lysosome is an organelle that contains enzymes that break down and digest unneeded cellular
components, such as a damaged organelle. Autophagy (“self-eating”) is the process of a cell
digesting its own structures. Lysosomes are also important for breaking down foreign material.
For example, when certain immune defense cells (white blood cells) phagocytize bacteria, the
bacterial cell is transported into a lysosome and digested by the enzymes in the lysosome.

Mitochondria

A mitochondrion (plural = mitochondria) is a membranous, bean-shaped organelle that is the

“energy transformer” of the cell. Mitochondria consist of an outer lipid bilayer membrane as well
as an additional inner lipid bilayer membrane. The inner membrane is highly folded into winding
structures with a great deal of surface area, called cristae. It is along this inner membrane that a
series of proteins, enzymes, and other molecules perform the biochemical reactions of cellular
respiration. These reactions convert energy stored in nutrient molecules (such as glucose) into
adenosine triphosphate (ATP), which provides usable cellular energy to the cell.

Structure of a Mitochondrion

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Peroxisomes

Like lysosomes, a peroxisome is a membrane-bound cellular organelle that contains mostly

enzymes. Peroxisomes perform a couple of different functions, including lipid metabolism and
chemical detoxification. In contrast to the digestive enzymes found in lysosomes, the enzymes
within peroxisomes serve to transfer hydrogen atoms from various molecules to oxygen, producing
hydrogen peroxide (H2O2).

Nucleus

This is usually the most obvious structure in eukaryote. Cell nucleus contains all of the cell's
genome, except for a small fraction of mitochondrial DNA, organized as multiple long linear DNA
molecules in a complex with a large variety of proteins, such as histones, to form chromosomes.
The genes within these chromosomes are structured in such a way to promote cell function. The
nucleus maintains the integrity of genes and controls the activities of the cell by regulating gene
expression—the nucleus is, therefore, the control center of the cell. The main structures making
up the nucleus are the nuclear envelope, a double membrane that surrounds the entire organelle
and isolates its contents from the cellular cytoplasm, and the nuclear matrix (which includes the
nuclear lamina), a network within the nucleus that adds mechanical support, much like the
cytoskeleton, which supports the cell as a whole.

A Nucleus

Chloroplast

Chloroplasts are one of many types of organelles in the plant cell. It is surrounded by double
membrane and have an internal membrane system of thylakoid vesicles. These vesicles contain
chlorophyll that trap sunlight for photosynthesis.

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 Chloroplast

Cell wall

The cell wall is a rigid organelle composed of cellulose and lying just outside the cell
membrane. The cell wall gives the plant cell its box-like shape. It also protects the cell. It contains
pores, which allow materials to pass to and from the cell membrane. Cell wall is one of the
organelles in the plant cell.

Vacuoles

Vacuoles are fluid filled organelles enclosed by a membrane. They can store materials such as
food, water, sugar, minerals and waste products.

The Cytoskeleton

Much like the bony skeleton structurally supports the human body, the cytoskeleton helps the cells
to maintain their structural integrity. The cytoskeleton is a group of fibrous proteins that provide
structural support for cells, but this is only one of the functions of the cytoskeleton. Cytoskeletal
components are also critical for cell motility, cell reproduction, and transportation of substances
within the cell.

The cytoskeleton forms a complex thread-like network throughout the cell consisting of three
different kinds of protein-based filaments: microfilaments, intermediate filaments, and
microtubules. The thickest of the three is the microtubule, a structural filament composed of
subunits of a protein called tubulin. Microtubules maintain cell shape and structure, help resist
compression of the cell, and play a role in positioning the organelles within the cell. Microtubules
also make up two types of cellular appendages important for motion: cilia and flagella. Cilia are
found on many cells of the body, including the epithelial cells that line the airways of the
respiratory system. Cilia move rhythmically; they beat constantly, moving waste materials such as
dust, mucus, and bacteria upward through the airways, away from the lungs and toward the mouth.
Beating cilia on cells in the female fallopian tubes move egg cells from the ovary towards the
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uterus. A flagellum (plural = flagella) is an appendage larger than a cilium and specialized for cell
locomotion. The only flagellated cell in humans is the sperm cell that must propel itself towards
female egg cells.

Microfilament is a thinner type of cytoskeletal filament. Actin, a protein that forms chains, is the
primary component of these microfilaments. Actin fibers, twisted chains of actin filaments,
constitute a large component of muscle tissue and, along with the protein myosin, are responsible
for muscle contraction.

The final cytoskeletal filament is the intermediate filament (thickness is in between the
microtubules and microfilaments). Intermediate filaments are made up of long fibrous subunits of
a protein called keratin that are coiled together like the threads that compose a rope. This filament
in concert with the microtubules, are important for maintaining cell shape and structure.

Summary

The internal environmental of a living cell is made up of a fluid, jelly-like substance called
cytosol, which consists mainly of water, but also contains various dissolved nutrients and
other molecules. The cell contains an array of cellular organelles, each one performing a
specific function and helping to maintain the health and activity of the cell. The cytosol and
organelles together compose the cell’s cytoplasm. Most organelles are surrounded by a
lipid membrane similar to the cell membrane of the cell. The endoplasmic reticulum (ER),
Golgi apparatus, and lysosomes share a functional connectivity and are collectively called
endomembrane system. There are two types of ER: smooth and rough. While the smooth
ER performs various functions, including lipid synthesis and ion storage, the rough ER is
mainly responsible for protein synthesis using its associated ribosomes. The rough ER sends
newly made proteins to the Golgi apparatus where they are modified and packaged for
delivery to various locations within or outside of the cell. Some of these protein products
are enzymes destined to break down unwanted material and are packaged as lysosomes for
use inside the cell. Nucleus is the control center of the cell and is a site for replication and
transcription of DNA. Chloroplast is the site for photosynthesis in plant cell.

Cells also contain mitochondria and peroxisomes, which are the organelles responsible for
producing the cell’s energy supply and detoxifying certain chemicals, respectively.
Biochemical reactions within mitochondria transform energy-carrying molecules into the
usable form of cellular energy known as ATP. Peroxisomes contain enzymes that transform
harmful substances such as free radicals into oxygen and water. Cells also contain a
miniaturized “skeleton” of protein filaments that extend throughout its interior. Three
different kinds of filaments compose this cytoskeleton (in order of increasing thickness):
microfilaments, intermediate filaments, and microtubules. Each cytoskeletal component
performs unique functions as well as provides a supportive framework for the cell.

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Fluid Compartments

The major body-fluid compartments include: intracellular fluid and extracellular fluid (plasma,
interstitial fluid, and transcellular fluid).

 The intracellular fluid of the cytosol or intracellular fluid (or cytoplasmic matrix) is the
liquid found inside cells.
 The cytosol is a complex mixture of substances that include proteins, ions, and organelles
dissolved in water.
 Extracellular fluid (ECF) or extracellular fluid volume (ECFV) usually denotes all body
fluid outside of cells, and consists of plasma, interstitial, and transcellular fluid.
 An extracellular matrix is an extracellular fluid space containing cell-excreted molecules,
and they vary in their type and function.
 Plasma also serves as extracellular matrices (ECM) for the cells and molecules of the blood.
 Interstitial fluid (or tissue fluid) is a solution that bathes and surrounds the cells of
multicellular animals.
 Transcellular fluid is the portion of total body water contained within epithelial -lined
spaces.

Key Terminologies

 Intracellular fluid: The liquid found inside cells, between the endomembrane and the
membrane-bound organelles.
 Interstitial fluid: A solution that bathes and surrounds the cells of multicellular animals;
also called tissue fluid.
 Plasma: The straw-colored/pale-yellow, liquid component of blood that normally holds
the blood cells of whole blood in suspension.

Fluid Compartments

The fluids of the various tissues of the human body are divided into fluid compartments, which
can be used to compare the position and characteristics of fluid in relation to the fluid within other
compartments.

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 Fluid Compartments in the Human Body

Intracellular Fluid

The intracellular fluid of the cytosol or intracellular fluid (or cytoplasm) is the fluid found inside
cells. It is separated into compartments by membranes that encircle the various organelles of the
cell. For example, the mitochondrial matrix separates the mitochondrion into compartments. The
contents of a eukaryotic cell within the cell membrane, excluding the cell nucleus and other
membrane-bound organelles (e.g., mitochondria, lumen of endoplasmic reticulum, etc.), is referred
to as the cytoplasm.

Cytosol:

The cytosol is the fluid within the plasma membrane of a cell and contains the organelles. The
cytosol includes dissolved molecules and water. The latter forms the large majority of the cytosol,
it mainly functions as a fluid medium for intracellular signaling (signal transduction) within the
cell, and plays a role in determining cell size and shape.

The concentrations of ions, such as sodium and potassium, are generally lower in the cytosol
compared to the extracellular fluid; these differences in ion levels are important in processes such
as osmoregulation and signal transduction. The cytosol also contains large amounts of
macromolecules that can alter how molecules behave, through macromolecular crowding.

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Extracellular Fluid

Extracellular fluid (ECF) or extracellular fluid volume (ECFV) usually denotes all the body fluid
that is outside of the cells. ECF can be divided into two major subcompartments:

i. interstitial fluid and

ii. blood plasma.

The extracellular fluid also includes the transcellular fluid; this makes up only about 2.5% of the
ECF. In humans, the normal glucose concentration of extracellular fluid that is regulated by
homeostasis is approximately 5 mm. The pH of extracellular fluid is tightly regulated by buffers
and is maintained around pH of 7.4. The volume of ECF is typically 15L (of which 12L is
interstitial fluid and 3L is plasma). The ECF contains extracellular matrices (ECMs) that act as
fluids of suspension for cells and molecules inside the ECF. Extracellular matrix is a spatial
relationship between the blood vessels, basement membranes, and interstitial space between
structures.

Blood Plasma

Blood plasma is the straw-colored/pale-yellow, liquid component of blood that normally holds the
blood cells in whole blood in suspension, making it a type of ECM for blood cells and a diverse
group of molecules. It makes up about 55% of total blood volume. It is the intravascular fluid part
of the extracellular fluid. It is mostly water (93% by volume) and contains dissolved proteins (the
major proteins are fibrinogens, globulins, and albumins), glucose, clotting factors, mineral ions
(Na+, Ca++, Mg++, HCO3- Cl-, etc.), hormones, and carbon dioxide (plasma is the main medium
for excretory product transportation). It plays a vital role in intravascular osmotic effects that keep
electrolyte levels balanced and protects the body from infection and other blood disorders.

Interstitial Fluid

Interstitial fluid (also knownas tissue fluid) is a solution that bathes and surrounds the cells of
multicellular animals. The interstitial fluid is found in the interstitial spaces, also known as the
tissue spaces.

On average, a person has about 11 liters of interstitial fluid that provide the cells of the body with
nutrients and a way of waste removal. The majority of the interstitial space functions as an ECM,
a fluid space consisting of cell-excreted molecules that lies between the basement membranes of
the interstitial spaces. The interstitial ECM contains a great deal of connective tissue and proteins
(such as collagen) that are involved in blood clotting and wound healing.

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Transcellular Fluid

Transcellular fluid is the portion of total body water contained within the epithelial-lined spaces.
It is the smallest component of extracellular fluid, which also includes interstitial fluid and plasma.
It is about 2.5% of the total body water. Examples are cerebrospinal fluid, ocular fluid and joint
fluid. The function of transcellular fluid is mainly lubrication of these cavities, and sometimes
electrolyte transport.

Body Fluid Composition

 The cytosol or intracellular fluid consists mostly of water, dissolved ions, small molecules,
and large, water-soluble molecules (such as proteins).
 Enzymes in the cytosol are important for cellular metabolism.
 The extracellular fluid is mainly cations and anions.
 Plasma is mostly water and dissolved proteins, but also contains metabolic blood gasses,
hormones, and glucose.
 The composition of transcellular fluid varies, but some of its main electrolytes include
sodium ions, chloride ions, and bicarbonate ions.

Key Terminologies

 electrolyte: Any of the various ions (such as sodium or chloride) that regulate the electric
charge on cells and the flow of water across their membranes.
 transcellular fluid: The portion of total body water contained within epithelial-lined
spaces, such as the cerebrospinal fluid, and the fluid of the eyes and joints.
 ion: An atom or molecule in which the total number of electrons is not equal to the total
number of protons, giving it a net positive or negative electrical charge.

Body Fluid Composition

The composition of tissue fluid depends upon the exchanges between the cells in the biological
tissue and the blood, suggesting fluid composition varies between body compartments.

Intracellular Fluid Composition

The cytosol/intracellular fluid containss mostly of water, dissolved ions, small molecules, and
large, water-soluble molecules (such as proteins). This mixture of small molecules is
extraordinarily complex, as the variety of enzymes that are involved in cellular metabolism is
immense.

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 Ions in solution.

These enzymes are involved in the biochemical processes that sustain cells and activate or
deactivate toxins. Most of the cytosol is water, which makes up about 70% of the total volume of
a typical cell. The pH of the intracellular fluid is 7.4. The cell membrane separates cytosol from
extracellular fluid, but can pass through the membrane via specialized channels and pumps during
passive and active transport.

The concentrations of the other ions in cytosol or intracellular fluid are quite different from those
in extracellular fluid. The cytosol also contains much higher amounts of charged macromolecules,
such as proteins and nucleic acids, than the outside of the cell. In contrast to extracellular fluid,
cytosol has a high concentration of potassium ions and a low concentration of sodium ions. The
reason for these specific sodium and potassium ion concentrations are Na+/K ATPase pumps that
facilitate the active transport of these ions. These pumps transport ions against their concentration
gradients to maintain the cytosol fluid composition of the ions.

Extracellular Fluid Composition

The extracellular fluid is mainly cations and anions.

Cations

Sodium (Na+ = 136-145 mEq/L), potassium (K+ = 3.5-5.5 mEq/L) and calcium (Ca2+ = 8.4-10.5
mEq/L).

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Anions

Chloride (96- 106 mEq/L) and hydrogen carbonate (HCO3- 22-26 mM). These ions are important
for water transport throughout the body.

Plasma is mostly water (93% by volume) and contains dissolved proteins (the major proteins are
fibrinogens, globulins, and albumins), glucose, mineral ions (Na+, Ca++, Mg++, HCO3-, Cl- etc.),
hormones and carbon IV oxide (plasma being the main medium for excretory product
transportation). These dissolved substances are involved in many different physiological
processes, which include gas exchange, immune system function, and drug distribution throughout
the body.

Transcellular Fluid Composition

The composition of transcellular fluid vividly changes due to the varying locations. Electrolytes
present in this compartment include sodium ions, chloride ions, and bicarbonate ions.

Cerebrospinal fluid is similar in composition to blood plasma, but lacks most proteins, such as
albumins, because they are too large to pass through the blood–brain barrier. Ocular fluid in the
eyes differs from cerebrospinal fluid because it contains high concentrations of proteins, including
antibodies.

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ATP

Adenosine triphosphate (ATP) is the main source of energy for most cellular processes. ATP is
referred to as currency because it can be spent to make chemical reactions occur. The building
blocks of ATP are carbon, nitrogen, hydrogen, oxygen, and phosphorus. Because of the presence
of unstable, high-energy bonds in ATP, it is readily hydrolyzed in reactions to release a large
amount of energy. It is composed of adenine (a purine base), ribose (a 5- carbon sugar ring) and
triphosphate (3 phosphorus group).

The enzymatic removal of a phosphate group from ATP to form ADP releases a huge amount of
energy, which is used by the cell in several metabolic processes as well as in the synthesis of
macromolecules such as proteins. The removal of a second phosphate group from ATP results in
further energy release and the formation of adenosine monophosphate (AMP). When energy is not
required by the organism, the phosphate group is added back to AMP and ADP to form ATP.
Hence, ATP functions as a reliable energy source for cellular pathways. At standard state, the
hydrolysis of ATP to adenosine diphosphate (ADP) would cleaved the anhydride bond to release
approximately 30.5 kJ/mol.

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Functions of ATP in cells

Some important functions of ATP in the cell are briefly discussed below:

Active Transport

ATP plays a critical role in the transport of macromolecules such as proteins and lipids into and
out of the cell. The hydrolysis of ATP provides the required energy for active transport
mechanisms to carry such molecules across a concentration gradient.

Cell Signaling

ATP has key roles both in intracellular and extracellular signaling. It is easily recognized by
purinergic receptors in mammalian tissues - its release from synapses and axons activates
purinergic receptors that regulate calcium and cyclic AMP levels inside the cell. In the central
nervous system, adenosine modulates neural development, the control of immune systems, and of
neuron/glial signaling. It is also involved in signal transduction - its phosphate groups are used up
by kinases in phosphate transfer reactions that activate a cascade of protein kinase reactions.

Structural Maintenance

ATP plays a very significant role in preserving the structure of the cell by helping the assembly of
the cytoskeletal elements. ATP supplies energy to the flagella and chromosomes to maintain their
appropriate functioning.

Muscle contraction

ATP is critical for the contraction of muscles; it binds to myosin to provide energy and facilitate
its binding to actin to form a cross-bridge. ADP and phosphate are then released and a new ATP
molecule binds to myosin. This breaks the cross-bridge between myosin and actin filaments,
thereby releasing myosin for the next contraction.

Synthesis of DNA and RNA

During DNA synthesis, ribonucleotide reductase (RNR) reduces the sugar residue from
ribonucleoside diphosphates to form deoxyribonucleoside diphosphates such as dADP. Thus, RNR
regulation helps keep the balance of deoxynucleotides (dNTPs) in the cell. Low concentrations of
dNTPs inhibit DNA synthesis and repair, whereas high levels are shown to be mutagenic because
DNA polymerase tends to add the wrong dNTP during DNA synthesis.

The adenosine from ATP is a building block of RNA and is directly added to RNA molecules
during RNA synthesis by RNA polymerases.

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