BIOCHEMISTRY of CYTOSOL

Department of Biochemistry,
Medical Faculty Jenderal Soedirman University
CYTOSOL vs CYTOPLASM ???
CYTOPLASM
• It is the total content within the cell
membrane other than the contents of the
nucleus of the cell.
• It is the jelly-like substance together with the
organelles (mitochondrion, golgi apparatus,
vacuoles, plastids, and the endoplasmic
reticulum)

CYTOSOL
• The cytosol is the intra-cellular fluid that is
present inside the cells, without any organelles
Cells are composed of :
• water : 70-75%
• ions (inorganic)
• carbon-containing
(organic) molecules : 25-
30%

The molecules found in a cell

are a major part of
the language of biochemistry
Water is the predominant chemical component of living organisms.

in adult person: male & female Changes in Water Content with Age
The Body’s Internal Water Is Compartmentalized

• ± 2/3 of total body water : Intracelular

Fluid (ICF)
• 1/3 of total body water : Extracellular
(ECF)
• interstitial fluid
• Exchange with vascular fluid via
lymph system
• Plasma/intravascular
• transcellular fluids
• Present in gastrointestinal fluid,
urine, intraocular fluid,
cerebrospinal fluid/CSF, synovial
(joint)
Intracellular fluid provides the environment for the
cell
1. to make, store, and utilize energy;
2. to repair itself;
3. to replicate; and
4. to perform special functions.
Extracellular fluid is a delivery system
• It brings to the cell nutrients
(glucose,fatty acids, amino
acids), oxygen, various ions trace
minerals, and a variety of
regulatory molecules
(hormones) that coordinate the
functions of widely separated
cells.

• removes CO2, waste products,

and toxic or detoxified materials
from the immediate cellular
environment.
 CYTOSOL
• is made of water Other substances present :
 up to 80%. non-organic ions ( 1%),
nucleic acids,
enzymes,
lipids,
amino acids,
Glucose
Cytosol is the main site for cellular activities :
glycolysis, fatty acid synthesis, activation of amino acids
and other metabolic paths.

fatty acid synthesis glycolysis

The inorganic ions

• In Plasma (extracellular fluid) :

• Sodium chloride is the main ionic
• Glucose and urea also contribute
to plasma osmolality.

• In intracellular fluid:
• Potassium & magnesium are
predominant cation
• the main anions are phosphates
and proteins.

 Ions present in the plasma and in

the intracellular fluids differ greatly
WATER
We begin with water because its properties affect the structure and
function of all other cellular constituents including proteins, nucleic
acids, and lipids

Its because the attractive forces between water molecules and the
slight tendency to ionize
 In water the sharing electron is not equal
Water (H2O) is made up
of 2 hydrogen atoms
and 1 oxygen atom

This gives water an asymmetrical

distribution of charge.
 Water has two very important properties

Physical Properties: Chemical Properties :

• Polar molecule • Ionizes to O and OH
• Hydrophilic substances dissolve • Acids and bases alter pH
• Hydrophobic substances • Buffers resists changes in
aggregate pH
• Osmosis
• Diffusion
A water molecule is formed
when 2 atoms of hydrogen
bond covalently with an atom
of oxygen.

In a covalent bond electrons are

shared between atoms.
Molecules that have ends with partial negative and positive charges
are known as polar molecules

 able to solvate a wide range of

organic and inorganic molecules
A molecule with electrical charge distributed asymmetrically about its
structure is referred to as a dipole.

• Water’s strong dipole is responsible for its high dielectric constant.

Water’s strong dipole and high dielectric constant enable water to
dissolve a wide range of organic and inorganic molecules

water dissolve large quantities of

charged compounds such as salts.
 Water dissolves salts ( such as NaCl )

By :
• replacing solute-solute hydrogen
bonds with solute-water
hydrogen bonds
• hydrating and stabilizing the Na+
and Cl- ions,
• weakening the electrostatic
interactions
Water molecules self-associate via hydrogen bonds

Hidrogen bonds between water molecules provide

the cohesive forces that make water a liquid at room
temperature
Hydrogen bonding profoundly influences the physical properties of water and
accounts for its relatively high viscosity, surface tension, and boiling point.

• Rupture of a hydrogen
bond in liquid water
requires only about 4.5
kcal/ mol, less than 5%
of the energy required
to rupture a covalent
O—H bond.
Hydrogen bonding enables water to dissolve many organic biomolecules that
contain functional groups which can participate in hydrogen bonding.
 Additional polar groups participate in hydrogen bonding

Hydrogen bonds formed between :

• alcohol and water,
• two molecules of ethanol,
• the peptide carbonyl oxygen
and the peptide nitrogen
hydrogen of an adjacent amino
acid.
 Covalent and Noncovalent Bonds Stabilize Biologic Molecules

• The covalent bond is the strongest force that

holds molecules together.

• Noncovalent forces, while of lesser

magnitude, make significant contributions to
the structure, stability, and functional
competence of macromolecules in living cells.

Bond Energies for Atoms of Biologic

Significance
Most biomolecules are amphipathic : rich in charged or polar functional
groups (hidrophylic) and regions with hydrophobic character.
Amino acids with charged or polar amino acid side chains generally are
present on the surface in contact with water.

Proteins tend to fold with the R-groups of amino acids with hydrophobic side
chains in the interior.
Amphipathic compounds contain
regions that are polar (or charged)
and nonpolar.

(a)
Long chain fatty acids have very
hydrophobic alkyl chains, each of which is
surrounded by a layer of highly ordered
water molecules

Amphipathic compounds in aqueous solution

When an amphipathic compound is mixed with water:

• polar, hydrophiJic region interacts with the solvent and

tends to dissolve
• nonpolar, hydrophobic region avoid contact with the
water, cluster together to present the smallest hydrophobic
area to the aqueous solvent, and the polar regions are
arranged to maximize their interaction with the solvent

 stable structures of amphipathic compounds in

water :micelles
Hydrophobic interaction : the tendency of nonpolar compounds to
self-associate in an aqueous environment.
Biomolecules Fold to Position Polar & Charged Groups on Their
Surfaces

Hydrophobic interactions
between nonpolar amino
acids also stabilize the
three-dimensional
structures of proteins
A similar pattern to phospholipid bilayer :

charged “head groups” of phosphatidylserine or phosphatidylethanolamine contact water

while their hydrophobic fatty acyl side chains cluster together, excluding water.
 Hydrophobic interactions among lipids, and between lipids and proteins, are the
most important determinants of structure in biological membranes.

in the aqueous environment of the living cell the hydrophobic portions of biopolymers tend to be
buried inside the structure of the molecule, or within a lipid bilayer, minimizing contact with water.
 Electrostatic Interactions :Interactions between charged groups

• Electrostatic interaction often

facilitate the binding of charged
molecules and ions to proteins
and nucleic acids
 van der Waals Forces

• two uncharged atoms are close

together  surrounding electron
influence each other.

• weaker than hydrogen bonds

Hydrogen bonds and ionic,
hydrophobic, and van der Waals
interactions are individually weak

But collectively,
very significant influence on the three-
dimensional structures of proteins,
nucleic acids, polysaccharides, and
membrane lipids.
The DNA double helix illustrates the contribution
of multiple forces to the structure of biomolecules

Multiple Forces Stabilize Biomolecules

• each individual DNA strand is held
together by covalent bonds
• the 2 strands of the helix are held
together by noncovalent interactions :
• hydrogen bonds between nucleotide
bases (Watson-Crick base pairing)
• van der Waals interactions between the
stacked purine and pyrimidine bases.
• the noncovalent binding of an ENZYME to its SUBSTRATS
may involve several hydrogen bonds and one or more ionic
interactions, as well as hydrophobic and van der Waals
interactions.
 Water is not just the solvent in which the chemical reactions of living
cells occur; it is very often a direct participant in those reactions

• Formation of ATP from ADP

and inorganic phosphate is an
example of a condensation
reaction.
 Water are eliminated.

• Hydrolysis reactions are

responsible for enzymatic
depolymerisation of proteins,
carbohydrates and nucleic
acids.
 Addition of elements of water
 Hydrolysis reactions, catalyzed by enzymes hydrolases
• In the cell, enzymes accelerate the
rate of hydrolytic reactions when
needed.
• Proteases catalyze the hydrolysis of
proteins into their component amino
acids
• nucleases catalyse the hydrolysis of the
phosphoester bonds in DNA and RNA.

• Careful control of the activities of

these enzymes is required to ensure
that they act only at appropriate
times.
 in liquid water have a bond dissociation energy

• Hydrogen bonds are of about 23 kJ/mol (relatively weak)

• covalent C-C bond 348 kJ/mol.
• the covalent O-H bond 470 kJ/mol

At any given time, most of the molecules in

liquid water are hydrogen bonded

At room temperature, the thermal energy

of an aqueous solution is of the same
magnitude as that required to break
hydrogen bonds.
Solubilities of some gases in water
Nonpolar gases : CO2, O2, and N2 are poorly soluble in water

• So, Some organisms have water-soluble "carrier proteins“

(hemoglobin and myoglobin, for example) that facilitate the
transport of 02
• CO2 forms carbonic acid (H2CO3) in aqueous solution and is
transported as the HCO3 (bicarbonate) ion
• either free-bicarbonate is very soluble in water (-100 glL at 25 oC)-or bound to
hemoglobin.
Polar gases : NH3,NO, and H2S
• dissolve readily in water
• ionize in aqueous solution.
• When two different aqueous solutions are
separated by a semipermeable membrane(
one that allows the passage of water but not
solute molecules),
water molecules diffusing from the
region of higher water concentration to the
region of lower water concentration, produce
osmotic pressure
• Plasma membranes are more permeable to water than to most
other small molecules, ions, and macromolecules.
• This permeability is due largely to protein channels (aquaporins) in
the membrane that selectively permit the passage of water
water movement across a semipermeable membrane driven by
differences in osmotic pressure, is an important factor in the
life of most cells
• Solutions of osmolarity equal to
that of a cell's cytosol are said to
be isotonic relative to that cell.
• In a hypertonic solution, one with
higher osmolarity than that of the
cytosol, the cell shrinks as water
moves out.
• In a hypotonic solution, one with
a lower osmolarity than the
cytosol, the cell swells as water
enters.
Effect of extracellular
osmolarity on water
movement across a plasma
membrane:

 water moves across the

plasma membrane in the
direction that tends to equalize
osmolarity outside and inside
the cell
• In natural environments, cells generally contain higher concentrations
of biomolecules and ions than their surroundings, so osmotic
pressure drive water into cells inward movement of water 
distend the plasma membrane  bursting of the cell (osmotic lysis).

• Several mechanisms to prevent that:

• In bacteria and plants  the plasma membrane is surrounded by a non
expandable cell wall of sufficient rigidity and strength to resist osmotic
pressure and prevent osmotic lysis.
• Certain fresh water protists that live in a highly hypotonic medium have an
organelle (contractile vacuole) that pumps water out of the cell.
• In multicellular animals, blood plasma and interstitial fluid (the extracellular
fluid of tissues) are maintained at an osmolarity close to that of the cytosol.
The high concentration of albumin and other proteins in biood plasma
contributes to its osmolarity.

• Cells actively pump out Na+ and other ios into the interstitial fluid to stay in
osmotic balance with their surroundings
effect of solutes on osmolarity depends on the
number of dissolved particles, not their mass
• macromolecules (proteins, nucleic acids, polysaccharides) have less
effect on the osmolarity of a solution than an equal mass of their
monomeric components.
• For example, a gram of a polysaccharide composed of 1,000 glucose units
has the same effect on osmolarity as a milligram of glucose.

 Storing fuel as polysaccharides (starch or glycogen) rather than as

glucose or other simple sugars avoids an increase in osmotic pressure in
the storage cell.
Cells and organisms maintain a specific and
constant cytosolic pH, usually near pH 7
• keeping biomolecules in their optimal ionic state.
• The pH affects the structure and activity of biological macromolecules
• for example, the catalytic activity of enzymes is strongly dependent on pH.
• ionic interactions stabilize a protein molecule and allow an enzyme to
recognize and bind its substrate.
• In multicellular organisms, the pH of extracellular fluids is also tightly
regulated.

• Constancy of pH is achieved primarily by biological buffers: mixtures

of weak acids and their conjugate bases
The intracellular and extracellular fluids of multicellular organisms
have a characteristic and nearly constant pH.

• The organism's first line of defense against changes in internal pH is

provided by buffer systems.
• The cytoplasm of most cells contains high concentrations of proteins,
which contain many amino acids with functional groups that are
weak acids or weak bases.
reference

• Nelson DL, Cox MM. 2008. Lehlinger Principle of Biochemistry fifth

edition.
• Rodwell VW, Bender DA, Botham KM, Kennelly PJ, Weil PA. 2015.
Harper’s Illustrated Biochemistry 30th Edition. McGraw Hill Lange
TERIMAKASIH