INDIAN INSTITUTE OF TECHNOLOGY ROORKEE

Biochemistry

Unit I
Chemical basis of life
Definition and Scope of Biochemistry
• Essentially the study of chemistry of life or molecular basis of life.

• Reveals the working of natural world and covers entire spectrum of all life forms.

• Deals with the study of chemical processes of living organisms and their interactions
with environment.

• Foundation for all biological processes and overlaps with disciplines such as cell
biology, genetics, microbiology, immunology etc.

• Advances in biochemistry has enabled scientist to answer most exciting questions in

biology and find applications in the areas of medicine, nutrition and agriculture.

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Definition and Scope
• The study of biochemistry largely involves:

- Chemical and three-dimensional structures of biological

molecules and their interaction with each other.

- Metabolism which involves synthesis and breakdown of

biomolecules and production of energy, its conservation
and use.

- Mechanisms of organizing biomolecules and coordinating

their activities.

- Expression and transmission of genetic information.

• Biochemistry also deals with physiological aspects, evolutionary history of organisms,

metabolic systems and individual molecules. Biochemistry coves all chemical
processes of all living forms.

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Chemical basis of life
• Analysis of living matter reveals that only a small number of elements are found in
construction of biomolecules. These are (97% of dry weight of humans) C, H, O , N, P,
Ca and S (61.7, 5.7, 9., 11, 3.32, 5, 1% respectively). Other trace amounts of elements
are B, F, Al, Si, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Se, Br, Mo, Cd, and W.

• In prebiotic era or early earth, atmosphere probably was made of small simple
compounds such as H2O, N2, CO2 and to a certain extent CH4 and NH3.

• Evidences suggest chemical basis of life where life evolved from generation of simple
biomolecules from limited number of elements through chemical evolution.

• Which unique properties make carbon central to the structure of biomolecules?

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Origin of life
• The origin of life is still a greatest mystery and there are many scientific theories on
origin of life.

• The water is central to life and must have played important role in origin of life.

• The underlying genetic and biochemical unity of different life forms point to a
common origin of life.

• General biochemical features are common across life forms.

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Common biochemical features
• The basic unit of life is a cell.

• All living organisms contains only a few different types of macromolecules.

• The transfer of hereditary information expressed and encoded is common and there
are common metabolic processes for generation of energy.

• Common molecular patterns and principles underlie the biochemistry of living

organisms

• ATP is the universal carrier of metabolic energy, linking catabolic and anabolic
pathways.

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Miller-Urey experiment

• Alexander Oparin and JBS Haldane, in 1920s, independently suggested that lightening
discharges or UV radiation from sun led to the generation of simple organic
compounds (Carbon containing) from chemicals present in atmosphere of early earth.

• In 1953, Stanley Miller and Harold Urey conducted an experiment where a mixture of
H2O, CH4, NH3 and H2 was subjected to an electric discharge for around a week. They
found that simple water soluble organic compounds (like many amino acids) were
generated.

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Miller-Urey experiment

Apparatus used by
Miller and Urey to
simulate the conditions
on primordial earth.
They provided the first
evidence that organic
molecules needed for
life could be formed
from inorganic
components present on
early earth.

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From simple molecules to complex systems
• In course of chemical evolution, simple molecules combined to form complex
molecules or polymers of repeating units.

• The major biopolymers were polypeptides, polynucleotides and polysaccharides. The

significant quantities of organic compounds such as amino acid may have been
delivered by meteorites on primordial earth.

• Combining of different macromolecules with complementary pairing of functional

groups resulted in complex molecular assemblies with even higher functional
versatility.

• Chemical evolution, therefore, led to transition from simple molecules to complex self-
replicating systems. The natural selection must have favored through competitive
process macromolecular assemblies which adapted well to evolve further.

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Complex self-replicating systems

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 RNA world
• According to one hypothesis, self-replicating RNA preceded DNA in evolutionary time
known as ‘RNA World’. RNA, in certain forms, possessed catalytic activity and
primordial enzymes may have been entirely RNA. The cooperative relationship
between RNA and proteins gave rise to proto-ribosome, a more efficient self-
replicating system.

• RNA is hereditary material of many viruses. The nucleic acids with improved efficiency
and accuracy of their own replication evolved. How nucleic acid directed protein
synthesis occurred before ribosomes remain unknown.

• Further refinements may have given way from RNA world to DNA and protein as best
adapted system in course of evolution.

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Development of cellular architecture
• Complex self-replicating systems evolved to sequester and protect
themselves by certain boundaries.

• The advantage of compartmentalization included protection from adverse

environmental conditions, maintain high local concentration of various
components important for enhancing efficiency of polymerization and other
chemical reactions.

• A membrane bound entity or a cell with its contents and composition is

quite different from surrounding. They maintain a high concentration of ions
and small & large molecules. For example, E.coli contains millions of
components with 3000 to 6000 types. Animal cell may contain 100000
different types of components.

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Development of metabolic pathways
• As cells evolved, they developed metabolic pathways and then energy
generating metabolic pathways.

• The process of photosynthesis evolved to take advantage of abundant energy

supply from Sun. It led to accumulation of oxygen in atmosphere and evolved
metabolic pathways to overcome oxidative damages (aerobic metabolism).

• Development of various metabolic strategies to conserve and utilize energy and

adaptation of early cells to different environmental conditions led to diversity of
species. Further, working together of differentiating cells with various
specialization led to multicellular organisms.

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Two major type of cells evolved
• Prokaryotic cell (Greek: Pro, before + karyon, kernel or nut) lacks a
membrane-bound nucleus, are unicellular (forms filaments or colonies of
independent cells. For example, E.coli is rod like with dimensions of 2µm by
1 µm).

• Eukaryotic cell (Greek: eu, true) have membrane-bound nucleus, are uni- or
multicellular, dimension of 10 to 100 µm, contains membrane-bound
organelles organized by cytoskeletons .

• Three evolutionary domains are Archaea, Eubacteria and Eukarya.

• The natural selection continues to direct evolution of life forms..

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Tree of life

Phylogenetic or evolutionary tree showing three domains of life having common origin

Time line for evolutionary path indicating key events from a common ancestor to present life forms

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Thermodynamics

• Thermodynamics (Greek: therme, heat and dynamics, power) refers to the

study of energy and its effect on matter.

• The biological systems are governed by the laws of thermodynamics.

• The understanding of thermodynamics is important not only for quantifying

a process in terms of energy but also to know if the process is spontaneous.

• Life achieves homeostasis while obeying the laws of thermodynamics

through open system in non-equilibrium steady state.

• The matter within a defined region is referred to as system and matter in the
rest of the universe is known as surroundings.
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Laws of thermodynamics
• First law states that total energy of a system and its surroundings is conserved.

∆E = EB – EA = Q – W [Q, Heat absorbed & W, Work done by system]

• The second law states that a process can occur spontaneously only if the sum of the
entropies of system and its surroundings increases.

(∆SSystem + ∆SSurrounding) > 0 for spontaneous process

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Gibbs free energy
• In 1878, Josiah Willard Gibbs combined first & second law of
thermodynamics to give free energy function.

∆G = ∆H – T∆S [∆G, change in free energy of a system undergoing

transformation at constant temperature and pressure]

- The ∆G of a reaction is independent of path (or mechanism) of transformation.

It depends only on free energy of product minus that of reactants (Final – initial
states). The free energy term takes into account the entropy of both the system and
surroundings.

- The ∆G must be negative for a process to occur spontaneously. The free energy
change will be negative only when the overall entropy of the universe increases.

- It provides no information about rate of reaction.

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Composition of living matter

Organic Compounds

• Carbohydrates
• Lipids
• Proteins
• Nucleic acids

Inorganic Compounds

• Water
• Salts
• Acids
• Bases

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Non-covalent Interactions

• Electrostatic, or charge-charge interactions

• Hydrogen bonds

• Van der Waals interactions

• Hydrophobic interactions

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Electrostatic or charge-charge interactions

• The force (F) of such an electrostatic attraction is given by Coulomb’s law:

F=kq1q2/Dr2 (F=force between two electric charges; r= distance
between two charges; D=Dielectric constant of the
medium and k= proportionality constant)

• The attraction is strongest in a vacuum (D=1) and weakest in a medium such

as water (D=80).

• The distance between oppositely charged atoms in an optimal electrostatic

attraction is about 2.8 Å.

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 Hydrogen Bonds

• Hydrogen bonds can be formed between uncharged as well as

charged molecules. The hydrogen atom in hydrogen bond is partly
shared between two electronegative atoms.

• Hydrogen bonds are highly directional. The strongest hydrogen

bonds those in which the donor, hydrogen and acceptor atoms are
collinear.

• Hydrogen bonds are crucial for biological macromolecules such as

DNA and proteins and are also responsible for many of the
properties of water that makes it special solvent.

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 Van der Waals interactions
• A nonspecific attractive force.

• The transient asymmetry in the electronic charge around an

atom encourages a similar asymmetry in electron
distribution around the neighboring atoms. The resulting
attraction between two atoms increases as they come closer
to each other, until separated by the van der Waals contact
distance.

• At a shorter distance, very strong repulsive forces become

dominant as the outer electron clouds overlap. Contact
distance ranges from 2.8 to 4.1 Å, so forces are weak.
However, in a folded protein, thousands of individual
interactions occur, thus providing a significant cumulative
stabilizing force.
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 Hydrophobic interactions
• Nonpolar groups have a tendency to aggregate
in water. This phenomenon is termed as
hydrophobic interactions or hydrophobic
effect.

• Interactions between hydrophobic amino acids

is likely the largest noncovalent force
responsible for most protein folding. This
drives formation of hydrophobic regions of
protein chains to come together, the water
shell is disrupted and entropy increases.

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Non-covalent Interactions

Covalent Bond
(kJ/mol)

C-C = 350

C-H = 410

O-H = 460

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 Water
• Essential for life. Structure of water and hydration of ions

• Universal solvent. Very polar.

• Dipolar nature (partial negative charge on

oxygen, partial positive charge on hydrogen)
leads to formation of low energy hydrogen
bonds. H-bonding in ice

• Can form four H-bonds with other water

molecules. Hydrogen bonding is cooperative.

• Why ice floats on water?

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 Water
• High Dielectric constant.

• Density of water is greater than ice (at 0 °C, liquid water has density of 1.00 g/mL, whereas ice has
density of 0.92 g/mL).

• High boiling point, melting point, heat of vaporization and surface tension.

• Ionizes to H+ (H3O+) & OH-. High ionic

mobility of both H3O+ and OH- ions (due to
rapidity of proton jump mechanism).

• H+ is expressed as pH (pH<7, acidic; pH>7,

basic and pH=7, neutral).

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Acids and Bases
Svante Arrhenius (1880) defined acids and bases as substances capable of donating
protons and hydroxide ions respectively

Acid : HCl  H+ + Cl-

Base : NaOH  Na+ + OH-

Johannes Brønsted & Thomas Lowry (1923)

Brønsted-Lowry theory

Acid : Proton donor

Base : Proton acceptor

Acid-Base reaction:

HA + H2 O  H3O+ + A-
Acid Base Conjugate Acid Conjugate Base
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Dissociation Constant
Dissociation constant is a measure of strength of an acid
K = [H3O+] [A-] / [HA] [H2O]

(Dissociation constant is a quantity that is a measure of the relative proton affinities of the HA/A- and H3O+/H2O
conjugate acid base pairs)

Ka = K [H2O] = [H+] [A-]/[HA] (in dilute solutions water concentration is essentially

constant, [H2O] = 1000 g.L-1/18.015 g.mol-1 = 55.5 M)

Dissociation constant of H3O+ is unity in aqueous solution

Weak Acid ( K < 1); Strong Acid (K > 1)

Dissociation of strong electrolyte

[H+] in solution = [HCl] added to solution; 1.0 M solution of HCl has pH= 0 and 1.0 mM = 3; 1.0
M NaOH solution has pH = 14 and 0.1 M = 13. ([OH-] = 0.1 M & [H+] = 10-13 M]

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Water can act either as an acid or a base
CH3COOH + H 2O  H3O+ + CH3COO-
H2O + NH3  NH4+ + OH-
acid base acid base

Ionization of Water
Water molecules react with each other to form ions
H2O + H2O  H3O+ (10-7 M) + OH-(10-7 M)
Keq = [H3O+ ] [OH-]/ [H2O]
Kw = [H3O+ ] [OH-]
= 1x 10-14 at 25 °C
(At 25 °C, [H2O] = 55.5 M is included in Kw and essentially constant in relation to very low
concentration of H3O+ and OH-, 1x 10-7 M)

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Water and pH relationship

• Very low dissociation of H2O to H+ or OH-

• The ion product of H2O, Keq X 55.5 M, leads to this: [H+] = [OH-] = 1 X 10-7 M
for pure H2O which is a constant in biological systems.

• Therefore, if [H+] > 10-7 M, then [OH-] must be less than 10-7 M, and vice
versa.

• Thus, if the negative logarithm of [H+] is derived ( pH = -log [H+] ), pure water
would be pH = 7, acids pH < 7, and bases pH > 7

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Henderson-Hasselbalch Equation

pH = pKa when exactly half of the acid undergoes dissociation i.e. [A-]/HA equals 1.

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Buffers
• A weak acid plus its conjugate base that cause a solution to resist changes in
pH when an acid or base are added.

• Effectiveness of a buffer is determined by:

- pH of the solution, buffers work best within one pH unit their
pKa.
- concentration of the buffer; the more present, the greater the
buffering capacity.

Physiological Buffers
• Carbon Dioxide-Bicarbonate System; a major regulator of blood pH.

• Phosphate System; major regulator of cytosolic pH.

• [CO2] and [HCO3] are much higher than [PO4] in blood; the reverse is true in
the cytosol, [PO4] >>> [HCO3]

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 pH titration curves
Buffers are most effective in resisting pH change when the pH = pKa, there are equal
amounts of protonated and deprotonated forms of the acid.

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Maintenance of blood pH
• The bicarbonate is the main buffering component of human blood and
maintains the blood pH at about 7.4. The buffering of blood depends on
equilibrium between carbonic acid and bicarbonate (H2CO3 ↔ H+ + HCO3-)
which depends on equilibrium between dissolved CO2 and carbonic acid
formed.

• When blood pH drops, the equilibrium shifts toward more carbonic acid. The
CO2 from carbonic acid is expired from lungs.

• When blood pH rises, more HCO3- is formed. The CO2 in lungs is reintroduced
into the blood for conversion to carbonic acid.

• Kidneys also play role in maintaining blood pH by regenerating depleted blood

buffers excreting excess H+ (also in form of NH4+).

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pH of some biological fluids
pH
Blood plasma 7.4

Intracellular fluid
Lysosomal matrix 5.5-6.5
Cytosol (liver) 6.9

Gastric juice 1.5-3.0

Interstitial fluid 7.4

Pancreatic juice 7.8-8.0

Saliva 6.4-7.0

Urine 5.0-8.0
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Biological Macromolecules

Proteins Nucleic acids Polysaccharides Lipids (Greek:

(Greek:Proteios, of (Greek: sakcharon, lipos, fat)
first importance) sugar)
 
Polymers of nucleotides 

Polymers of sugar
Polymers of amino  soluble in
acids  organic
~8 commonly solvents. Fats,
 oils certain
4 nucleotide each in DNA occurring types of
and RNA sugars vitamins &
  hormones &
20 amino acids most
polyhydroxy nonprotein
genetic information is aldehydes and membran
 componets are
encoded in the linear ketones (CH2O)n that
sequence of amino sequence of 4 kinds of are essential lipids.
acids specify their 3-d subunits of DNA components of
structure biological system
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