UBM1302

Fundamentals of Biochemistry
Body response to injury to restore normal
structure and function

BIOMOLECULES AND MOLECULAR

LOGIC OF LIFE

Dr. R. Subashini
Assistant Professor/BME

1
 Session objectives
• To know what is Biochemistry and biomolecules
• To know Distinguishing features of living organisms
• To know the foundations of life (Chemical, cellular, energy,
genetic etc...)

2 v 1.1
 What is
Biochemistry?
Biochemistry is:

• the study of life at the molecular level.

• the application of the principles of chemistry to

explain biology.

• the common sets of reactions and principles that

underlie all living organisms.

• the study of the molecular logic of life.

3 v 1.1
 Unity of Biochemistry/Unity of Life
• In spite of differences in size and complexity, all living organisms are
remarkably uniform at the molecular level.
• All organisms use:
• a common repertoire of building blocks to create common nucleic
acids, proteins, polysaccharides and lipids.
• A common core of essential biochemical processes.

“Anything found to be true of

E. coli must also be true of
elephants.”
-Jacques Monod

4 v 1.1
 Distinguishing Features of Living
Organisms
• High degree of chemical complexity and microscopic organization.

• Systems for extracting, transforming, and using energy from the

environment.

• Defined functions for each of the organism’s components and regulated

interactions among them.

• Mechanism for sensing and responding to alterations in their

surrounding.

• A capacity for precise self-replication and self-assembly.

• A capacity to change over time by gradual evolution.

5 v 1.1
 The Foundations of Life
consider the living state in terms of five foundations:

• Chemical Foundation

• Cellular Foundations

• Energy Foundations

• Genetic Foundations

• Evolutionary Foundations

Philosophers may ask why life exists,

biochemists ask how life exists.
6 v 1.1
 Chemical Foundations

• Three elements (carbon, oxygen,

hydrogen) account for 98% of most
organisms.
• The abundance of these elements in
organisms very different from
Earth’s crust.
• Water accounts for much of the
oxygen and hydrogen in living
things.
• As all known life forms are carbon
based.
• Carbon is the third most common
element in living organisms.

7 v 1.1
 Chemical Foundations
-All Life (as we know it) is Carbon-Based-
• Carbon is extremely versatile in terms of the number and variety of chemical
binds that it can form.

• Silicon is the “next-best” candidate as a chemical foundation for life.

• Also forms four covalent bonds.
• Highly abundant in the Earth’s crust

• Why are we based in carbon rather than silicon?

• Carbon-to-carbon bonds are stronger than silicon-to-silicon bonds
(biomolecules).
• More energy released on combustion of carbon-carbon bonds
(Fuels).
• Combustion products of carbon (carbon dioxide) are soluble and remain
active in biosphere.
8 v 1.1
 Chemical Foundations
-Biomolecules Contain a Variety of Functional Groups-

• Different functional groups have unique properties with respect to

9 v 1.1
size, shape, charge, hydrogen-bonding capacity, etc.
 Chemical Foundations
-Biomolecules Contain a Variety of Functional Groups-

• Functional groups typically exist in the context of higher order

biomolecules.
• The collective properties of the functional groups within a biomolecule
will determine the structure, function and properties of the biomolecule.
10 v 1.1
 Chemical Foundations
-Structure-Function Relationship of Biomolecules-
• For all biomolecules, structure dictates function.

• Molecules “do what they do” because of their structures.

• A central goal of this course is to appreciate the structure-

function relationship of biomolecules.

• Understanding the structure-function relationship allows one to

predict function, under disease pathology and develop molecular
treatments in a rationale fashion.

11 v 1.1
 Chemical Foundations
-Biochemistry is Highly Stereospecific-
• The stereospecificity of biochemistry is apparent in how
biomolecules are constructed and interact with other molecules.
• Building Blocks: Biomolecules are often constructed
exclusively from one building block stereoisomer. For example,
proteins are built entirely from L-Amino acids.
• Interactions: Interactions between biomolecules, as well as between
biomolecules and small molecule ligands, are stereospecific.

12 v 1.1
 Chemical Foundations
-Complex Molecules from Simple Precursors-
• Biomolecules often polymers of simple building blocks.
• The structure and function of the final biomolecules are more complex than
their precursor molecules; the whole is greater than the sum of the parts.
• Advantages of Polymers
1) Simplicity of chemistry: one type of reaction for polymerization, a second
type of reaction for degradation.

2) Recycling: biomolecules can be digested back to

component
building blocks which are reusable for production of other
biomolecules.
3) Incredible diversity of polymer length and sequence.

13 v 1.1
 Chemical Foundations
-Four Major Classes of Biomolecules-
1) Proteins: Linear polymers of amino acids which serve a wide range of
biological functions.
2) Nucleic Acids: Linear polymers of nucleotides that are involved in all aspects
storage and utilization of genetic information.
3) Polysaccharides: Linear or branched polymers of sugars that serve in
structural, energy storage and cellular recognition roles.

4) Lipids: Fats, and aggregates of fats, that serve in energy storage, formation of
14
membrane and signalling. Aggregates rather than defined polymers of building
v 1.1
blocks.
 Cellular Foundations

Cells May be Prokaryotic or Eukaryotic

• Prokaryotes include bacteria & lack a nucleus or membrane-

bound structures called organelles

• Eukaryotes include most other cells & have a nucleus and

membrane-bound organelles (plants, fungi, & animals)

15 v 1.1
 Nucleoid region contains the DNA
•Cell membrane & cell wall
• Contain ribosomes (no membrane)
to make proteins in
their cytoplasm
16
Contain 3 basic cell structures:
• Nucleus
• Cell Membrane
• Cytoplasm with organelles
Prokaryotic Cell
 The organisms made of prokaryotic cells are called prokaryotes e.g. bacteria and
cyanobacteria.
 These cells lack a membrane bound nucleus.
 The hereditary material (DNA) is found in cytoplasm.
 These cells lack membrane bound organelles.
 Ribosome’s are of small size in and freely scattered cytoplasm.
 Cellulose is absent in cell wall, rather it is made up of peptido-glycan or murrain.
 These cells are simple and of smaller size (average diameter 0.5 – 10 nm)

Eukaryotic Cell
 The organisms made of Eukaryotic cells are called Eukaryotes, e.g. animals, plants
fungi and protista.
 These cells have a membrane bound nucleus; and hereditary material is found
inside the nucleus.
 These cells have membrane bound organelles.
 Ribosome’s are of large size and are present in endoplasmic reticulum free in
cytoplasm.
 Cellulose is present in cell wall of plant cells. The cell wall of most of fungi is
composed of chitin.
 These cells are complex and of larger size (Average diameter 10-100nm).

17
 Two Main Types of Eukaryotic Cells

18 v 1.1
 Characteristic Bio-membranes and Organelles

Plasma Membrane
A lipid/protein/carbohydrate complex, providing a barrier and
containing transport and signaling systems.

Nucleus
Double membrane surrounding the chromosomes and the nucleolus.
Pores allow specific communication with the cytoplasm. The
nucleolus is a site for synthesis of RNA making up the ribosome

Mitochondrion
Surrounded by a double membrane with a series of folds
called cristae. Functions in energy production through metabolism.
Contains its own DNA, and is believed to have originated as a
captured bacterium.

Chloroplasts (plastids)
Surrounded by a double membrane, containing stacked thylakoid
membranes. Responsible for photosynthesis, the trapping of light
energy for the synthesis of sugars. Contains DNA, and like
mitochondria is believed to have originated as a captured
bacterium.
19
.

Rough endoplasmic reticulum (RER)

A network of interconnected membranes forming channels within the
cell. Covered with ribosomes (causing the "rough" appearance) which
are in the process of synthesizing proteins for secretion or
localization in membranes.
Ribosomes
Protein and RNA complex responsible for protein synthesis

Smooth endoplasmic reticulum (SER)

A network of interconnected membranes forming channels within the
cell. A site for synthesis and metabolism of lipids. Also contains
enzymes for detoxifying chemicals including drugs and pesticides.

Golgi apparatus
A series of stacked membranes. Vesicles (small membrane
surrounded bags) carry materials from the RER to the Golgi
apparatus. Vesicles move between the stacks while the proteins are
"processed" to a mature form. Vesicles then carry newly formed
membrane and secreted proteins to their final destinations including
secretion or membrane localization.
Lysosymes
A membrane bound organelle that is responsible for degrading
proteins and membranes in the cell, and also helps degrade materials
20 ingested by the cell.
 Vacuoles
Membrane surrounded "bags" that contain water and storage
materials in plants.

Peroxisomes or Microbodies
Produce and degrade hydrogen peroxide, a toxic
compound that can be produced during metabolism.

Cell wall
Plants have a rigid cell wall in addition to their cell membranes

Cytoplasm
enclosed by the plasma membrane, liquid portion called cytosol
and it houses the membranous organelles.

Cytoskeleton
Arrays of protein filaments in the cytosol. Gives the cell its
shape and provides basis for movement.
E.g. microtubules and microfilaments.

21
 Bio-molecules
• Just like cells are building blocks of tissues likewise molecules are building blocks of
cells.

• Animal and plant cells contain approximately 10, 000 kinds of molecules (bio-
molecules)

• Water constitutes 50-95% of cells content by weight.

• Ions like Na+, K+ and Ca+ may account for another 1%

• Almost all other kinds of bio-molecules are organic (C, H, N, O, P, S)

• Infinite variety of molecules contain C.

• Most bio-molecules considered to be derived from hydrocarbons.

• The chemical properties of organic bio-molecules are determined by their functional

groups. Most bio-molecules have more than one.

22 v 1.1
 Major Classes of small Bio-molecules

• Building blocks of proteins.

• 1. Amino acids:
• 20 commonly occurring.
• Contains amino group and carboxyl group
function groups (behavioral properties)
• R Group (side chains) determines the
chemical properties of each amino acids.
• Also determines how the protein folds and
its biological function.
• Individual amino acids in protein connected
by peptide bond.

• Functions as transport proteins, structural

proteins, enzymes, antibodies, cell
receptors.

23 v 1.1
 Sugars
• Carbohydrates most abundant organic molecule
found in nature.

• Initially synthesized in plants from a complex series

of reactions involving photosynthesis.

• Basic unit is monosaccharides.

• Monosaccharides can form larger molecules e.g. glycogen, plant starch or

cellulose.

Functions
• Store energy in the form of starch (photosynthesis in plants) or glycogen (in
animals and humans).

• Provide energy through metabolism pathways and cycles.

• Supply carbon for synthesis of other compounds.

• Form structural components in cells and tissues.

• Intercellular communications

24 v 1.1
 Fatty acids

• Are monocarboxylic acid contains even number C atoms

• Two types: saturated (C-C sb) and unsaturated (C-C db)

• Fatty acids are components of several lipid molecules.

• E,g. of lipids are triacylglycerol, streiods (cholestrol, sex

hormones), fat soluble vitamins.

Functions
• Storage of energy in the form of fat
• Membrane structures
• Insulation (thermal blanket)
• Synthesis of hormones

25 v 1.1
 Cellular Foundations
-In vitro vs In vivo-
• Within the cell biomolecules undergo complex, organized interactions.
• Understanding these molecules and their interactions is a central challenge
of biochemistry.
• While a reductionist approach of studying molecules in isolation simplifies
experiments, it may be at the expense of biological significance.
• In general there are two experimental approaches:
• In vitro (in glass) studies the behaviour of molecules outside the context
of the cell and organism.
• In vivo (in the living) studies occur within the context and complexity of
the cell or organism.
• Experiments which are successful in vitro often fail in vivo because of the
greater complexity of the system.

26 v 1.1
 Energy Foundations
• Living cells and organisms must perform work to stay alive and
reproduce themselves.
• This requires considerable amounts of energy, energy that must be
obtained from the environment.
• Goal is to understand, in quantitative and chemical terms, the
means by which energy is extracted, channeled, and consumed in
living cells.
• Cellular energy conversion -like all other energy conversion- can be
considered in the context of the laws of thermodynamics.

27 v 1.1
 Energy Foundations
-Energy Coupling Links Reactions in Biology-
• By coupling energy requiring (endergonic) reactions to reactions that
liberate free energy (exergonic reactions), cells can drive
thermodynamically unfavorable reactions.
• The sum of the free energy changes is negative such that the overall
process is exergonic.

28 v 1.1
 Energy Foundations
-The Central Role of ATP in Metabolism-
• Use energy from the environment (either chemical
or light) to perform cellular work.
• Energy extracted to the form of adenosine
triphosphate (ATP) which serves as a common
energy currency.
• ATP serves as the link between catabolic
reactions and anabolic reactions.

29 ATP v 1.1
 Genetic Foundations
• The perpetuation of biology requires that genetic information be:
• stored in a stable form.
• expressed accurately in the form of gene products.
• reproduced with minimal errors.

• For most organisms, deoxyribonucleic acid (DNA) provides:

• the instructions for forming all other cellular components.
• a template for production of identical DNA molecules to be distributed
to the progeny when a cell divides.

Central Dogma of Biochemistry

30 v 1.1
 Genetic Foundations
-Structure of DNA Allows For Replication and Repair-

• The basic unit of DNA is two complimentary

strands.
• Each strand is a linear polymer of four different
types of building blocks.
• It is the linear sequence of the strands that
encodes information.

"It has not escaped our notice that the specific pairing we
have postulated immediately suggests a possible copying
mechanism for the genetic material.“
Watson & Crick: Nature 171: 737-738 (1953)

31 v 1.1
 Genetic Foundations
-Linear Sequence in DNA Encodes Three-Dimensional
Protein Structures-

• The nucleotide sequence within

genes dictates the sequence of amino
a c id s i n c o r p o r a t e d i n t o the
corresponding protein.
• The amino acid sequence of the
protein, in turn, dictates the structure
of the protein.
• The structure of the protein which, in
turn, dictates the biological activity
of the protein.

32 v 1.1
 Genetic Foundations
-Changes in the Hereditary Instructions Allow Evolution-
• Random changes in genotype
(genetic information) can result in a
change in phenotype (observable
characteristics).
• If this change offers a survival
advantage it will be selected for over
time, if it disadvantages the organism it
will be selected against.

“Nothing in biology makes sense except

in the light of evolution.”
- Theodosius Dobzhansky

33 v 1.1
 Questions
• What are biomolecules in biochemistry?
• What are the 4 main elements in biomolecules?
• What are the important of biomolecules?
• What are 3 characteristics of biomolecules?
• What are the basic principles of biochemistry?
• How biomolecules are formed?
• Which biomolecule is most important?
• What is biochemistry of cell?
• What is the relationship between biochemistry and
medicine?

34 v 1.1