Biochemistry LS2101 Slides 1,2 3,4

BIOCHEMISTRY: LS2101
Dr. Partha P. Datta
IISER Kolkata
1
Syllabus
Introductory biochemistry: biological interactions.
•Protein structure and folding, Enzymology, Enzyme kinetics, and allostery. vitamins
and coenzymes.
•Overview of techniques in protein purification.
•Nucleic acid structure.
•Introduction to intermediary metabolism: Glycolysis, TCA cycle, Electron transport
2
Atom: is the smallest particle of an element that can exist either alone or in combination
Cell: is the smallest unit of a living body that can exist either alone or in combination
Living organisms are special:
A high degree of chemical complexity and microscopic organization.
Systems for extracting, transforming, and using energy from the environment
A capacity for precise self-replication and self-assembly
Mechanisms for sensing and responding to alterations in their surroundings
Defined functions for each of their components and regulated interactions among them
A history of evolutionary change 3

THE FOUNDATIONS OF BIOCHEMISTRY
1. Cellular Foundations
2. Chemical Foundations
3. Physical Foundations
4. Genetic Foundations
5. Evolutionary Foundations
4
Cells Are the Structural and Functional Units of All Living Organisms
5
Ratio of cells Surface Area to Volume
Animal and plant cells are generally between 5 to 100 micro meter in diameter
Bacteria are generally 1 to 5 micro meter in length
Mycoplasma: 300 nm
Ribosome: 20 nm
6
There Are Three Distinct Domains of Life
7
Organisms can be classified according to their source of energy
8
Escherichia coli Is the Most-Studied Prokaryotic Cell
9
Eukaryotic Cells Have a Variety of Membranous Organelles, Which Can Be Isolated for Study
10
Subcellular fractionation of tissue
11
The Cytoplasm Is Organized by the Cytoskeleton and Is Highly Dynamic
12
13
THE FOUNDATIONS OF BIOCHEMISTRY
1. Cellular Foundations
14
15
Cells Build Supramolecular Structures from smaller components of organic molecules
16
18
Carbon: is special and

the 0.154 nm
central element to life
0.134 nm
19
0.134 nm
0.154 nm
20
21
R is an abbreviation
for radical
22
Cells Contain a Universal Set of Small

Molecules: Amino acids, ATP, GTP etc
Secondary metabolites: Caffeine, Nicotine,

Quinine etc
Metabolome: The entire collection of small molecules in a given cell

has been called that cell’s metabolome
23
Macromolecules Are the Major Constituents of Cells
DNA
RNA
Protein
Lipid
Carbohydrates
24
25
26
Three-Dimensional Structure Is Described

by Configuration and Conformation
27
Configuration
28
Stereoisomers
29
Optical Activity
30
Optical Activity
31
Conformations
32
Interactions between Biomolecules

Are Stereospecific
33
34
35
Organisms Transform Energy and Matter from Their Surroundings
System: Every reactants and products are the contained
Universe: System plus surroundings
Isolated system: No exchange of matter, no energy with its surroundings
Closed system: Only exchange energy but no matters
Open system: Both matter and energy are exchanged: Living system
36
Living cells are open systems.
They exchange matter and energy with their surroundings
They extract and channelize energy to maintain themselves in a dynamic steady state.
Ultimately their energy is obtained from sunlight or chemical fuels by converting the energy from electron flow into
the chemical bonds of ATP.
Living Organisms Exist in a Dynamic Steady State, Never at Equilibrium with Their Surroundings
37
The first law of thermodynamics, developed from physics and chemistry but fully valid for
biological systems as well, describes the principle of the conservation of energy:
The first law of thermodynamics : “In any physical or chemical change, the total amount
of energy in the universe remains constant, although the form of the energy may
change.”
38
The Flow of Electrons Provides Energy for Organisms
39
All these reactions involving electron flow are oxidation reduction reactions:
one reactant is oxidized (loses electrons) as another is reduced (gains electrons).
40
Creating and Maintaining Order Requires Work and Energy
The second law of thermodynamics, the tendency in nature is toward ever-greater disorder in the
universe:
The second law of thermodynamics: The total entropy of the universe is continually increasing.
41
42
Entropy: The randomness or disorder of the components of a chemical system is expressed as entropy, S
Free energy content, G,

Enthalpy, H, number and kinds of bonds
Absolute Temperature T (in degrees Kelvin).
The definition of free energy of a closed system is G = H - TS.
Free Energy Change:
The tendency for a chemical reaction to proceed toward equilibrium can be expressed
as the free-energy change,
It has two components:
Enthalpy change, and Entropy change,
These variables are related by the equation

How to know which way a reaction might proceed?
If of a reaction is negative, the reaction is exergonic and tends to go toward completion
If is positive, the reaction is endergonic and tends to go in the reverse direction.
When two reactions can be summed to yield a third reaction, the for this overall reaction is the
sum of the of the two separate reactions.
This provides a way to couple reactions.
44
45
46
47
When a reaction has reached equilibrium, no driving

The equilibrium constant, Keq force remains and it can do no work: =0
Standard free-energy change,
48
The standard free-energy change for a reaction,
It is a physical constant that is related to the equilibrium constant by
the equation
49
50
51
52
Metabolism Is Regulated to Achieve Balance and Economy
Feedback inhibition
53
What is the best genetic material for the living organisms?
54
55
DNA
56
57
58
59
60
Biochemistry
61
Nothing in biology makes sense except in the light of evolution.
—Theodosius Dobzhansky, The American Biology Teacher,

March 1973
62
63
Biomolecules First Arose by Chemical Evolution
64
Biological Evolution Began More
Than Three and a Half Billion Years Ago
65
The First Cell Was Probably a

Biological Evolution Began More Chemoheterotroph
Than Three and a Half Billion Years Ago
Eukaryotic Cells Evolved from Prokaryotes

in Several Stages
66
Eukaryotic Cells Evolved from Prokaryotes
in Several Stages
67
68
69
70

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BIOCHEMISTRY: LS2101

Dr. Partha P. Datta

Introductory biochemistry: biological interactions.

•Overview of techniques in protein purification.

•Nucleic acid structure.

•Introduction to intermediary metabolism: Glycolysis, TCA cycle, Electron transport

Living organisms are special:

A high degree of chemical complexity and microscopic organization.

A capacity for precise self-replication and self-assembly

Mechanisms for sensing and responding to alterations in their surroundings

A history of evolutionary change 3

Bacteria are generally 1 to 5 micro meter in length

Carbon: is special and

central element to life

Cells Contain a Universal Set of Small

Secondary metabolites: Caffeine, Nicotine,

Metabolome: The entire collection of small molecules in a given cell

Macromolecules Are the Major Constituents of Cells

Three-Dimensional Structure Is Described

Interactions between Biomolecules

Organisms Transform Energy and Matter from Their Surroundings

System: Every reactants and products are the contained

Universe: System plus surroundings

Isolated system: No exchange of matter, no energy with its surroundings

Closed system: Only exchange energy but no matters

Living cells are open systems.

They exchange matter and energy with their surroundings

The Flow of Electrons Provides Energy for Organisms

one reactant is oxidized (loses electrons) as another is reduced (gains electrons).

Creating and Maintaining Order Requires Work and Energy

Free energy content, G,

The definition of free energy of a closed system is G = H - TS.

Free Energy Change:

It has two components:

Enthalpy change, and Entropy change,

These variables are related by the equation

If of a reaction is negative, the reaction is exergonic and tends to go toward completion

If is positive, the reaction is endergonic and tends to go in the reverse direction.

This provides a way to couple reactions.

When a reaction has reached equilibrium, no driving

Standard free-energy change,

The standard free-energy change for a reaction,

It is a physical constant that is related to the equilibrium constant by

What is the best genetic material for the living organisms?

Nothing in biology makes sense except in the light of evolution.

—Theodosius Dobzhansky, The American Biology Teacher,

Biological Evolution Began More

Than Three and a Half Billion Years Ago

The First Cell Was Probably a

Than Three and a Half Billion Years Ago

Eukaryotic Cells Evolved from Prokaryotes

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