UNIT-1

Biology is just as fundamental as Maths, Physics, and Chemistry. While those focus on
matter and energy, biology explores the complex world of living organisms and their
interactions—essential for understanding life and our place in the universe
Science vs. Engineering: Eye and Camera, Bird Flying and Aircraft
Science aims to understand the natural world, while engineering uses that knowledge
to design and build useful systems. This difference is clear in examples like the eye vs.
camera or bird flight vs. aircraft.
* Eye vs. Camera: The eye, shaped by evolution, is a complex organ that senses light
and forms images. Science explores how it works, from light detection to brain
interpretation. A camera, inspired by the eye, is an engineered device built using
scientific principles to capture images.
* Bird Flying vs. Aircraft: Bird flight is a result of evolution, with biology studying how
anatomy and physiology enable it. Aircraft, inspired by birds, use engineered designs
based on physics to achieve flight through lift, thrust, and control.
The Most Exciting Aspect of Biology
Biology is exciting because it explores the very nature of life—its origins, functions,
evolution, and interactions. Its complexity and diversity offer endless discovery, with
fields like genomics and neuroscience constantly revealing new insights.
Why We Need to Study Biology
Studying biology is crucial for several reasons:
To Understand Life: Biology explains how living organisms function, grow, and evolve.
Health & Medicine: It forms the basis for medical science—understanding diseases,
treatments, and the human body.
Environment & Sustainability: Biology helps us understand ecosystems and how to
protect natural resources.
Food & Agriculture: It improves crop production, pest control, and food safety
through genetic and ecological knowledge.

* Discovery of Oxygen and its Role in Respiration: Lavoisier showed that respiration
is similar to combustion—both use oxygen and release carbon dioxide and heat—
laying the foundation for our understanding of metabolism.
* Cell Theory Emergence: 18th-century microscope advancements revealed common
cell structures in plants and animals, covering the way for cell theory and the concept
of the cell as life’s basic unit.
Brownian Motion and the Origin of Thermodynamics: The Importance of
Observation
* Brownian Motion (Brown): In 1827, Robert Brown observed random motion of
pollen grains in water—later known as Brownian motion. Though a biological
observation, it offered key evidence for atoms and molecules, linking biology to
fundamental physics.
* Origin of Thermodynamics (Mayer): Julius Mayer observed that sailors’ blood was
red in warm climates, leading him to propose that less body heat was needed. This
insight helped him formulate the principle of energy conservation, laying the
foundation for thermodynamics.
These examples of Brownian motion and thermodynamics highlight the key role of
observation in science, including biology. Careful observation of biological
phenomena can lead to significant discoveries that enhance our understanding of the
physical world and drive progress across various fields.

UNIT-2
I. Underlying Criteria for Biological Classification:
Classification of life forms isn't arbitrary; it's based on fundamental similarities and
differences.
Morphological: Based on the form and structure of organisms (e.g., presence of a cell
wall, number of limbs, flower structure).
Biochemical: Based on the chemical composition and processes within organisms
(e.g., types of pigments, enzyme pathways, DNA/RNA sequences).
Ecological: Based on the organism's role and interactions within its environment (e.g.,
producer, consumer, decomposer; habitat preference).
A single classification scheme may prioritize one or more of these criteria.
II. Hierarchy of Life Forms at Phenomenological Level:
1. Molecular Level
o Involves biomolecules like DNA, proteins, and enzymes that perform
essential life processes.
2. Cellular Level
o The cell is the basic unit of life; includes unicellular organisms like
bacteria and protozoa.
 3. Tissue Level
o Groups of similar cells working together to perform specific functions
(e.g., muscle, nerve tissue).
4. Organ Level
o Different tissues combine to form organs (e.g., heart, lungs), each with a
specialized role.
5. Organ System Level
o Organs work together as systems (e.g., circulatory, nervous) to maintain
body functions.
6. Organism Level
o A complete individual capable of all life processes (e.g., a human, plant,
or animal).
7. Population Level
o A group of organisms of the same species living in a specific area.
8. Community Level
o Different populations (species) interacting within a shared environment.
9. Ecosystem Level
o Interaction of living organisms with their physical (non-living)
environment.
10.Biosphere Level
• The highest level; includes all ecosystems on Earth — the global sum of all life.

III. Classification Based On:

• (a) Cellularity:
o Unicellular: Organisms composed of a single cell (e.g., bacteria, yeast,
Amoeba). All life processes occur within that single cell.
o Multicellular: Organisms composed of many cells organized into tissues,
organs, and organ systems (e.g., plants, animals, fungi). Specialization of
cells allows for complex functions.
• (b) Ultrastructure: (Internal structure visible with electron microscopy)
o Prokaryotes: Prokaryotes are unicellular organisms that lack a true
nucleus and membrane-bound organelles. Their genetic material is
found in a single circular DNA molecule located in a region called the
nucleoid.
o Eukaryotes: Eukaryotes are organisms whose cells have a true nucleus
enclosed by a nuclear membrane and contain various membrane-bound
 organelles, such as mitochondria, endoplasmic reticulum, and Golgi
apparatus.
• (c) Energy and Carbon Utilisation:
o Autotrophs: Organisms that can produce their own food using energy
from inorganic sources (light or chemical reactions).
▪ Photoautotrophs: Use light energy (e.g., plants,.
▪ Chemoautotrophs: Use energy from chemical reactions .e.g. some
bacteria.
o Heterotrophs: Organisms that obtain energy and carbon by consuming
organic matter produced by other organisms .e.g. animals, many bacteria.
o Lithotrophs: Organisms that obtain energy from autotrophic or
heterotrophic in terms of carbon source. e.g., some bacteria.
• (d) Ammonia Excretion: (remove Ammonia waste substances)
o Ammoniotelic: Organisms that remove nitrogenous waste primarily as
ammonia (NH₃), which is highly toxic and requires large amounts of
water for dilution .
o Uricotelic: Organisms that remove nitrogenous waste primarily as uric
acid, a relatively non-toxic, semi-solid compound, conserving water .
• (e) Habitat:
o Aquatic: Organisms living primarily in water. e.g. fish, aquatic plants.
o Terrestrial: Organisms living primarily on land e.g., mammals, trees.
• (f) Molecular Taxonomy:
o Classification based on molecular data, primarily the comparison of
nucleic acid (DNA, RNA) and protein sequences.
o Three Major Kingdoms of Life :
▪ Bacteria : Prokaryotic, diverse metabolic strategies.
▪ Archaea : Prokaryotic, often found in extreme environments,
biochemically distinct from Bacteria.
▪ Eukarya: Eukaryotic organisms, encompassing protists, fungi,
plants, and animals.

IV. A Given Organism Can Come Under Different Categories:

• It's crucial to understand that an organism possesses a suite of characteristics
and can be classified in multiple ways depending on the chosen criterion.
• Example: A human is:
o Multicellular (cellularity)
 o Eukaryote (ultrastructure)
o Heterotroph (energy and carbon utilisation)
o Ureotelic (ammonia excretion)
o Terrestrial (habitat)
o Eukarya (molecular taxonomy)

V. Model Organisms for the Study of Biology:

• Certain organisms are extensively studied to understand fundamental biological
processes. They are chosen for their specific advantages (e.g., rapid
reproduction, genetic simplicity, ease of manipulation).
• E. coli (Escherichia coli): A bacterium; model for molecular biology, genetics,
and prokaryotic processes.
• S. cerevisiae (Saccharomyces cerevisiae): Baker's yeast; a unicellular
eukaryote; model for basic eukaryotic cell biology, genetics, and metabolism.
• D. melanogaster (Drosophila melanogaster): Fruit fly; a multicellular
eukaryote (insect); model for genetics, development, and neurobiology.
• C. elegans (Caenorhabditis elegans): A nematode worm; a multicellular
eukaryote; model for development, neurobiology, and aging.
• A. thaliana (Arabidopsis thaliana): A flowering plant; a multicellular
eukaryote; model for plant biology, development, and genetics.
• M. musculus (Mus musculus): House mouse; a multicellular eukaryote
(mammal); model for mammalian genetics, physiology, and disease.
• These model organisms, representing diverse groups, allow scientists to
extrapolate fundamental biological principles across the tree of life.
"Genetics is to biology what Newton’s laws are to Physical Sciences"
• This statement emphasizes the fundamental and unifying role of genetics in
biology. Just as Newton's laws provide the framework for understanding motion
and gravity in physics, genetics provides the framework for understanding
heredity, variation, and the mechanisms of life itself.
• Genetics explains the continuity of life, the diversity within species, and the
evolutionary relationships between organisms. It underpins our understanding of
development, disease, and the very nature of what it means to be alive.
 UNIT-3
I. Mendel's Laws:

Law of Dominance

• Definition: In a pair of alleles, one is dominant and masks the effect of the
other, which is recessive.
• Example: In pea plants, the allele for tallness (T) is dominant over dwarfness
(t). So, Tt results in a tall plant.

2️ Law of Segregation

• Definition: This law states that during the formation of gametes (sex cells), the
two alleles for each gene separate (segregate) from each other so that each
gamete carries only one allele for each gene.
• Example: A Tt plant produces two types of gametes — one with T and one with
t.

3 Law of Independent Assortment

• Definition: Genes for different traits are passed down from parents to offspring
independently of each other, if they are not linked.
• Example: A plant's height and seed colour are passed on separately, so a tall
plant can have green or yellow seeds.

II. Key Genetic Concepts:

• Allele: Different versions of a gene at a specific locus (position) on a

chromosome. For example, a gene for flower color in peas might have alleles for
purple or white flowers.
• Gene Mapping: Determining the relative positions of genes on a chromosome
based on the frequency of recombination (crossing over) during meiosis.
o Genes located closer together on a chromosome tend to be inherited
together (linked) more often.
o The higher the recombination frequency between two genes, the farther
apart they are likely to be.
• Gene Interaction: When the expression of one gene influences the expression
of another gene.
• Epistasis: A specific type of gene interaction where the alleles of one gene
mask or modify the phenotypic expression of the alleles of a different gene.
o Example: In Labrador retrievers, one gene determines pigment
production (black or brown), while another gene determines whether the
pigment is deposited in the fur at all (resulting in a yellow lab regardless
of the pigment allele).

III. Meiosis and Mitosis: Genetic Material Passing from Parent to Offspring:
 • Mitosis:
• Mitosis is a type of cell division that occurs in body cells and is essential for
growth, repair, and asexual reproduction. During mitosis, a single parent cell
divides once to produce two genetically identical daughter cells, each with the
same number of chromosomes as the parent cell. Mitosis plays a vital role in
replacing old or damaged cells and allows organisms to grow and maintain their
tissues. It ensures that genetic information is passed on accurately, maintaining
stability across cells.
• Meiosis:
• Meiosis, on the other hand, is a cell division process that occurs in reproductive
(germ) cells and is necessary for sexual reproduction. Meiosis involves two
rounds of division, resulting in four non-identical daughter cells, each with half
the number of chromosomes of the parent cell . These cells become gametes.
Meiosis introduces genetic variation.
IV. Concepts of Recessiveness and Dominance:
• Dominance: When one allele (the dominant allele) masks the phenotypic
expression of another allele (the recessive allele) for the same trait in a
heterozygote (an individual with two different alleles).
• Recessiveness: The allele whose phenotypic expression is masked by the
dominant allele in a heterozygote. The recessive phenotype is only expressed in
individuals who are homozygous for the recessive allele (have two copies of the
recessive allele).
• Relationship to Mendel's Laws: Dominance and recessiveness explain the
phenotypic ratios observed in Mendel's experiments (e.g., the 3:1 ratio in the F2
generation of a monohybrid cross).
V. Concept of Mapping of Phenotype to Genes:
o The mapping of phenotype to genes is the process of identifying which
specific genes or genetic regions are responsible for observable
characteristics in an organism. Phenotypes include characteristics like
height, eye color, or disease resistance. This mapping is done using
techniques such as linkage analysis or genome-wide association studies
(GWAS). It helps scientists understand how genetic variation leads to
differences in traits, and is useful in fields like medicine, agriculture, and
evolutionary biology. Genetic studies help to identify the genes involved
in specific phenotypes.
VI. Single Gene Disorders in Humans:
• Single gene disorders are diseases caused by mutations in a single gene. These
mutations can be inherited in different patterns such as dominant, recessive, or
sex-linked
 • Examples:
o Dominant: Affected individuals usually have at least one affected parent.
o Recessive: Affected individuals usually have unaffected parents who are
carriers.
o X-linked Recessive: More common in males as they only have one X
chromosome .
o X-linked Dominant: Affected males pass the trait to all their daughters
and none of their sons .
VII. Concept of Complementation Using Human Genetics:
• Complementation: Complementation is a genetic concept used to determine
whether two mutations causing a similar phenotype (like a genetic disorder) are
in the same gene or in different genes. In human genetics, complementation is
often studied using cell fusion or molecular techniques.
• Explanation: Each parent carries a mutation in a different gene required for the
same pathway or function. Their offspring inherit one normal copy of each gene,
thus "complementing" for the missing function.

UNIT-4
I. Molecules of Life: Monomers and Polymers
• Monomers: Small, repeating units that serve as the basic building blocks of
larger biological molecules.
• Polymers: Large molecules formed by the covalent linkage of many similar or
identical monomers. This process is often called polymerization or dehydration
synthesis (water is removed).
• Depolymerization: The breakdown of polymers into monomers, often through
hydrolysis (water is added).
II. Key Classes of Biomolecules:
• A. Sugars, Starch, and Cellulose (Carbohydrates):
o Simple Sugars
▪ Examples: Glucose (primary energy source), Fructose (fruit sugar),
Galactose (part of milk sugar).
▪ General formula: (CH₂O)n
▪ Can exist as linear chains or ring structures in aqueous solutions.
o Starch:
▪ Storage polysaccharide in plants.
▪ Composed of glucose monomers linked in α(1→4) and
α(1→6) glycosidic bonds (branched structure - amylopectin,
unbranched - amylose).
 ▪ Easily digestible by animals, serving as a readily available
energy source.
o Cellulose:
▪ Structural polysaccharide in plant cell walls.
▪ Composed of glucose monomers linked in β(1→4)
glycosidic bonds.
▪ Forms linear, unbranched chains that pack tightly, providing
rigidity and strength.
▪ Difficult for most animals to digest due to the β linkages
(herbivores have specialized enzymes or symbiotic
microorganisms).
Amino Acids (Monomers):
• Organic molecules with a central carbon bonded to:
o Amino group (-NH₂)
o Hydrogen atom (-H)
• 20 common types used in protein synthesis.
• Linked by peptide bonds (covalent bond between the carboxyl of one and the
amino of another, with water loss).
Proteins (Polymers):
• Polymers of amino acids (polypeptides) folded into specific 3D structures.
• Structure dictates function:
o Primary: Linear sequence of amino acids.
o Secondary: Localized folding (alpha-helices, beta-pleated sheets) via
hydrogen bonds.
o Tertiary: Overall 3D shape due to R-group interactions.
o Quaternary: Arrangement of multiple polypeptide subunits.
C. Nucleotides and DNA/RNA (Nucleic Acids):
• Monomeric Units: Nucleotides
o Composed of three parts:
▪ A nitrogenous base (Adenine, Guanine, Cytosine, Thymine in
DNA; Uracil replaces Thymine in RNA).
▪ A pentose sugar (Deoxyribose in DNA; Ribose in RNA).
▪ One or more phosphate groups.
• Polymeric Structures: Nucleic Acids (DNA and RNA)
 • Formed by the linkage of nucleotides through phosphodiester bonds between
the sugar of one nucleotide and the phosphate group of the next.
• Deoxyribonucleic Acid (DNA):
o Double-stranded helix structure.
o Contains the genetic information of the cell, encoding the instructions for
building and maintaining an organism.
o Bases pair specifically: Adenine (A) with Thymine (T), and Guanine (G)
with Cytosine (C) through hydrogen bonds.
• Ribonucleic Acid (RNA):
o Typically single-stranded.
o Various types with different roles in protein synthesis and gene regulation
(e.g., mRNA, tRNA, rRNA).
o Bases pair specifically: Adenine (A) with Uracil (U), and Guanine (G)
with Cytosine (C).
D. Two Carbon Units and Lipids:
• "Two Carbon Units": Primarily refers to Acetyl-CoA (though lipids are
more diverse):
o Acetyl-CoA: A crucial molecule in metabolism, formed from the
breakdown of carbohydrates, fats, and proteins. Consists of a two-carbon
acetyl group attached to Coenzyme A. Enters the citric acid cycle (Krebs
cycle) for energy production. Also a precursor for the synthesis of fatty
acids and other lipids.
• Lipids (Fats, Oils, Phospholipids, Steroids):
o Diverse group of hydrophobic molecules.
o Fats and Oils (Triglycerides):
▪ Composed of a glycerol molecule linked to three fatty acid
molecules through ester bonds.
▪ Fatty acids are long hydrocarbon chains with a carboxyl group at
one end (saturated - no double bonds, unsaturated - one or more
double bonds).
▪ Primary function: Energy storage.

UNIT-5
Why without catalysis life would not have existed on earth.
Enzymes are biological catalysts essential for life as we know it. Without their ability
to dramatically accelerate biochemical reactions, the complex processes necessary for
life would occur too slowly to sustain it.
Enzymology: Monitoring Enzyme Reactions
Enzymology involves studying how enzymes speed up biochemical reactions by
measuring their activity. This is done by monitoring the rate at which substrate is
converted to product, or vice versa, over time.
Factors that significantly affect enzyme activity and are thus considered in monitoring
include:
• Substrate Concentration: Reaction rate changes with available substrate.
• Enzyme Concentration: More enzyme generally leads to a faster rate.
• Environmental Conditions: Temperature and pH have optimal ranges for
enzyme function.
• Presence of Modulators: Inhibitors decrease activity, while activators increase
it.
How Do Enzymes Catalyze Reactions?
Enzymes accelerate reactions by lowering the activation energy. They achieve this
by:
1. Binding Substrates: Enzymes bind specific reactant molecules (substrates) at
their active site, forming an enzyme-substrate complex.
2. Stabilizing the Transition State: The enzyme's active site is shaped to
optimally bind and stabilize the high-energy transition state of the reaction,
thus reducing the energy needed to reach it.
3. Providing a Favorable Environment: The active site can create a specific
microenvironment (e.g., optimal pH, exclusion of water, correct orientation) that
facilitates the reaction.
4. Weakening Substrate Bonds: Enzyme binding can strain or distort substrate
bonds, making them easier to break and promoting product formation.
Enzyme Classification
Enzymes are systematically categorized into six main classes based on the type of
chemical reaction they catalyze. Each class has a corresponding Enzyme Commission
(EC) number starting with the respective class number (EC 1-6). These classes are:
1. Oxidoreductases (EC 1): Catalyze oxidation-reduction reactions (transfer of
electrons or hydrogen atoms).
2. Transferases (EC 2️): Catalyze the transfer of a functional group (e.g.,
methyl, phosphate) from one molecule to another.
3. Hydrolases (EC 3): Catalyze the cleavage of bonds by the addition of water
(hydrolysis).
4. Lyases (EC 4): Catalyze the breaking of bonds without hydrolysis or
oxidation, often forming double bonds.
 5. Isomerases (EC 5): Catalyze the rearrangement of atoms within a molecule
(isomerization).
6. Ligases (EC 6): Catalyze the formation of new covalent bonds, often coupled
with ATP hydrolysis.
Mechanism of Enzyme Action (Examples):
• 1. Lysozyme (Hydrolase):
o Catalyzes the hydrolysis of the β(1→4) glycosidic bond in
peptidoglycans, a component of bacterial cell walls.
o Mechanism:
▪ Binds to the polysaccharide substrate in its active site.
▪ Strains the bond between two sugar residues, making it more
susceptible to hydrolysis.
▪ Provides a specific acidic environment (via amino acid residues in
the active site) that facilitates bond breakage by water.
• 2️. Hexokinase (Transferase):
o Catalyzes the phosphorylation of glucose to glucose-6-phosphate by
transferring a phosphate group from ATP. This is the first step in
glycolysis.
o Mechanism:
▪ Binding of glucose induces a conformational change in hexokinase
that brings the ATP binding site close to the glucose.
▪ This proximity facilitates the transfer of the phosphate group.
▪ The enzyme also helps to shield the reaction from water, preventing
unwanted ATP hydrolysis.
Enzyme Kinetics and Kinetic Parameters
Enzyme kinetics studies the rates of enzyme-catalyzed reactions and how they are
affected by various factors, particularly substrate concentration. The Michaelis-
Menten model describes this relationship for many enzymes.
Key kinetic parameters derived from this model are:
1. Michaelis Constant (Km): Represents the substrate concentration at which the
reaction rate is half of the maximum velocity (Vmax). Km is an approximate
measure of the enzyme's affinity for its substrate; a lower Km indicates higher
affinity.
2. Maximum Velocity (Vmax): The theoretical maximum rate of the reaction
when the enzyme is saturated with substrate. Vmax reflects the turnover
number (kcat, the number of substrate molecules converted per enzyme
molecule per unit time) and the total enzyme concentration.
Why Should We Know These Parameters to Understand Biology?
 1. Metabolic Regulation: Km and Vmax values help predict how enzymes will
behave under varying substrate concentrations within cells, revealing how
metabolic pathways are controlled and adjusted.
2. Enzyme Efficiency and Comparison: These parameters allow us to compare
the catalytic efficiency of different enzymes or different forms of the same
enzyme, highlighting which enzymes are most effective under specific
conditions.
3. Drug Development: Many drugs target enzymes. Knowing their kinetic
parameters is essential for designing effective inhibitors that can specifically
bind to and reduce enzyme activity, treating diseases.
4. Disease Diagnosis: Alterations in enzyme kinetics or the presence of abnormal
enzyme forms can serve as diagnostic markers for various diseases
Biology Exam Notes: Enzymes - The Catalysts of Life
Central Theme: Enzymes are biological catalysts essential for life as we know it.
Without their ability to dramatically accelerate biochemical reactions, the complex
processes necessary for life would occur too slowly to sustain it.
I. Enzymology: Monitoring Enzyme-Catalyzed Reactions
• Enzyme Assay: A laboratory technique used to measure the activity of an
enzyme. This typically involves monitoring the rate of formation of product or
the rate of disappearance of substrate over time.
• Factors Influencing Enzyme Activity (and thus monitored):
o Substrate Concentration: Reaction rate increases with substrate
concentration up to a point (saturation).
o Enzyme Concentration: Reaction rate is directly proportional to enzyme
concentration (if substrate is in excess).
o Temperature: Enzyme activity increases with temperature up to an
optimum, beyond which it decreases due to denaturation.
o pH: Enzymes have an optimal pH range for activity; deviations can alter
enzyme structure and function.
o Inhibitors: Molecules that reduce enzyme activity.
o Activators: Molecules that increase enzyme activity.
• Measuring Reaction Rate: Typically expressed as the change in concentration
of substrate or product per unit time (e.g., µmol/min).
II. How Do Enzymes Catalyze Reactions?
• Lowering Activation Energy: Enzymes work by providing an alternative
reaction pathway with a lower activation energy (the energy required for a
reaction to start).
• Transition State Stabilization: Enzymes bind to the substrate(s) and stabilize
the transition state, a high-energy intermediate in the reaction. This
 stabilization reduces the energy difference between the reactants and the
transition state, thus lowering the activation energy.
• Providing a Favorable Microenvironment: The active site of an enzyme can
create a specific microenvironment (e.g., altered pH, exclusion of water) that is
more conducive to the reaction.
• Bringing Substrates Together: For reactions involving multiple substrates,
enzymes can bind them in the correct orientation and proximity to facilitate their
interaction.
• Straining Substrate Bonds: Enzyme binding can induce strain on the substrate
bonds, making them easier to break.
III. Enzyme Classification:
Enzymes are classified into six main classes based on the type of reaction they
catalyze, with each class further divided into subclasses and sub-subclasses, each with
a specific Enzyme Commission (EC) number:
1. Oxidoreductases: Catalyze oxidation-reduction reactions (transfer of electrons
or hydrogen atoms). (e.g., Dehydrogenases, Oxidases)
2. Transferases: Catalyze the transfer of a functional group (e.g., methyl,
phosphate) from one molecule to another. (e.g., Kinases, Aminotransferases)
3. Hydrolases: Catalyze the cleavage of bonds by the addition of water
(hydrolysis). (e.g., Lipases, Proteases, Amylases)
4. Lyases: Catalyze the breaking of bonds without hydrolysis or oxidation, often
forming double bonds. (e.g., Decarboxylases, Aldolases)
5. Isomerases: Catalyze the rearrangement of atoms within a molecule
(isomerization). (e.g., Isomerases, Mutases)
6. Ligases: Catalyze the formation of new covalent bonds, often coupled with ATP
hydrolysis. (e.g., Synthetases, Carboxylases)
IV. Mechanism of Enzyme Action (Examples):
• 1. Lysozyme (Hydrolase):
o Catalyzes the hydrolysis of the β(1→4) glycosidic bond in
peptidoglycans, a component of bacterial cell walls.
o Mechanism:
▪ Binds to the polysaccharide substrate in its active site.
▪ Strains the bond between two sugar residues, making it more
susceptible to hydrolysis.
▪ Provides a specific acidic environment (via amino acid residues in
the active site) that facilitates bond breakage by water.
• 2️. Hexokinase (Transferase):
 o Catalyzes the phosphorylation of glucose to glucose-6-phosphate by
transferring a phosphate group from ATP. This is the first step in
glycolysis.
o Mechanism:
▪ Binding of glucose induces a conformational change in hexokinase
that brings the ATP binding site close to the glucose.
▪ This proximity facilitates the transfer of the phosphate group.
▪ The enzyme also helps to shield the reaction from water, preventing
unwanted ATP hydrolysis.
V. Enzyme Kinetics and Kinetic Parameters:
• Enzyme Kinetics: The study of the rates of enzyme-catalyzed reactions and
how these rates are affected by various factors.
• Michaelis-Menten Kinetics: A common model describing the relationship
between the initial reaction velocity (v₀) and the substrate concentration ([S]) for
many enzymes:
o Michaelis Constant (Km): The substrate concentration at which the
reaction velocity is half of the maximum velocity (Vmax).
▪ Km is an approximate measure of the affinity of the enzyme for its
substrate. A lower Km indicates higher affinity.
o Maximum Velocity (Vmax): The theoretical maximum rate of the
reaction when the enzyme is saturated with substrate.
▪ Vmax reflects the turnover number (kcat) of the enzyme (the
number of substrate molecules converted to product per enzyme
molecule per unit time) and the total enzyme concentration ([E]t):
Vmax = kcat[E]t.
• Lineweaver-Burk Plot: A double reciprocal plot (1/v₀ vs. 1/[S]) that linearizes
the Michaelis-Menten equation, allowing for easier determination of Km and
Vmax.
VI. Why Should We Know These Parameters to Understand Biology?
• Understanding Metabolic Pathways: Km and Vmax values help predict how
enzymes will behave under different substrate concentrations within cells and
how metabolic pathways are regulated.
• Drug Design: Many drugs act as enzyme inhibitors. Knowing the kinetic
parameters of target enzymes is crucial for designing effective and specific
inhibitors.
• Diagnosing Diseases: Altered enzyme activity or the presence of specific
enzyme isoforms can be diagnostic indicators of certain diseases. Understanding
normal and pathological enzyme kinetics is essential.
 • Engineering Enzymes: In biotechnology, knowledge of enzyme kinetics allows
for the optimization of enzyme activity for industrial processes.
• Predicting Cellular Responses: Changes in substrate or enzyme concentrations
can have significant effects on reaction rates and downstream cellular processes.
Kinetic parameters help predict these responses.
• Comparing Enzyme Efficiencies: Km and kcat (related to Vmax) allow for the
comparison of the catalytic efficiency of different enzymes or different forms of
the same enzyme.
VII. RNA Catalysis (Ribozymes):
• Ribozymes: RNA molecules that possess catalytic activity, acting like
enzymes.
• Examples:
o Ribonuclease P: Involved in processing tRNA precursors.
o Peptidyl transferase: The catalytic center of the ribosome responsible for
peptide bond formation during protein synthesis (considered a
ribozyme).
• Mechanism: Similar to protein enzymes, ribozymes can stabilize transition
states, provide specific binding sites for substrates, and facilitate chemical
reactions through their three-dimensional structure and the chemical properties
of their nucleotide bases.
UNIT-6
Information Transfer - The Language of Life.
Central Theme: The flow of genetic information, from DNA to RNA to protein, is a
fundamental and remarkably conserved process across all forms of life. This molecular
basis of coding and decoding ensures the continuity and expression of hereditary traits.
Molecular Basis of Information Transfer:
• Central Dogma of Molecular Biology: Describes the primary flow of genetic
information:
o DNA → RNA (Transcription): The information encoded in DNA is
copied into a messenger RNA (mRNA) molecule.
o RNA → Protein (Translation): The sequence of nucleotides in mRNA is
used to direct the synthesis of a polypeptide chain (protein) with a specific
amino acid sequence.
o DNA → DNA (Replication): The process by which DNA makes copies
of itself, ensuring the faithful transmission of genetic information to
daughter cells during cell division.

DNA as a Genetic Material

DNA (Deoxyribonucleic Acid) serves as the primary genetic material for almost
all living organisms. This means it carries the hereditary information that is passed
from parents to offspring, directing the development, functioning, growth, and
reproduction of an organism.

Several key pieces of evidence support this role:

• Transformation Experiments: Demonstrated that genetic information could be

transferred between bacteria via DNA.
• Bacteriophage Experiments: Showed that viruses inject DNA, not protein, into
bacteria to direct the synthesis of new viruses.
• Quantitative Studies: The amount of DNA is consistent in somatic cells of an
organism and double that in its gametes.
• Direct Correlation: DNA is located in the chromosomes, which are known to
carry hereditary information.

Hierarchy of DNA Structure.

DNA's structure is organized in a hierarchical manner to efficiently package the long
molecule within the cell:

1. Double Helix: The fundamental level is the double helix, with two antiparallel
strands of nucleotides held together by hydrogen bonds between complementary
bases (A-T, G-C).
2. Nucleosomes: In eukaryotes, DNA wraps around histone protein cores, forming
bead-like structures called nucleosomes. This is the first level of DNA
compaction.
3. Chromatin Fibers: Nucleosomes further coil and fold into more condensed
chromatin fibers (e.g., the 30-nm fiber), leading to greater packaging.
4. Chromosomes: During cell division, chromatin fibers undergo even more
extensive coiling and folding to form compact, visible chromosomes, allowing
for organized segregation of genetic material. The level of compaction can also
influence gene expression.

Concept of Genetic Code:

• Definition: The set of rules used by living cells to translate the sequence of
nucleotide triplets (codons) in mRNA into the sequence of amino acids in a
polypeptide chain during protein synthesis.
• Codon: A sequence of three consecutive nucleotides in mRNA that specifies a
particular amino acid or a stop signal.

Universality and Degeneracy of Genetic Code:

• Universality: The genetic code is nearly universal across all living organisms,
from bacteria to humans. This suggests a common evolutionary origin of life.
• Degeneracy (Redundancy): Most amino acids are encoded by more than one
codon. This redundancy often occurs at the third nucleotide position of the
codon.

Defining a Gene (Complementation & Recombination)

A gene can be defined in two key ways using genetic analysis:

1. By Complementation: A gene represents a functional unit. If two recessive

mutations with the same phenotype fail to produce a wild-type phenotype when
combined in a heterozygote (in trans configuration), they are likely in the same gene
(they fail to complement). If they do produce a wild-type phenotype, they are likely in
different genes (they complement each other), indicating each gene provides the
missing function of the other.

2. By Recombination: A gene is also a physical unit on a chromosome.

Recombination frequency (the percentage of offspring with recombinant phenotypes)
can be used to map genes. Genes located closer together have lower recombination
frequencies. A gene, in this context, is a segment of DNA that is less likely to be
disrupted by recombination within its coding sequence, maintaining its functional
integrity as a heritable unit.

UNIT-7
Macromolecular Analysis - Proteins: Structure and Function
Central Theme: Understanding biological processes at a reductionist level often
involves analyzing the structure and function of macromolecules, particularly proteins,
which play diverse and crucial roles in all aspects of life.

Analyzing Biological Processes at the Reductionist Level:

• Reductionism: A scientific approach that breaks down complex biological
systems into their simpler components to understand their individual roles and
interactions.
• Macromolecular Analysis: A key aspect of reductionism involves studying the
structure and function of large biological molecules (macromolecules) like
proteins, nucleic acids, carbohydrates, and lipids.
• Proteins as Central Players: Proteins are particularly important due to their
diverse structures and functions, acting as the workhorses of the cell. Analyzing
their structure is fundamental to understanding their mechanisms of action in
various biological processes.

Protein Structure and Function:

• Structure Dictates Function: The intricate three-dimensional structure of a
protein is directly responsible for its specific biological activity. Even subtle
changes in structure can drastically alter or abolish function.
• Building Blocks: Proteins are polymers of amino acids linked by peptide bonds.
The sequence of amino acids (primary structure) determines the higher levels of
structural organization.

Hierarchy in Protein Structure

Proteins exhibit four levels of structural organization:
 1. Primary Structure: The linear sequence of amino acids in a polypeptide chain,
linked by peptide bonds. This sequence is genetically determined and dictates
subsequent folding.
2. Secondary Structure: Localized, repetitive folding patterns within the
polypeptide backbone, stabilized by hydrogen bonds. Common types include
alpha-helices (coils) and beta-pleated sheets (extended strands).
3. Tertiary Structure: The overall three-dimensional shape of a single
polypeptide chain, determined by interactions between amino acid side chains
(R-groups). These interactions include hydrogen bonds, ionic bonds,
hydrophobic interactions, and disulfide bridges.
4. Quaternary Structure: The 1 arrangement of multiple polypeptide subunits
(each with its own primary, secondary, and tertiary structure) into a functional
protein complex. Subunits are held together by non-covalent interactions. Not
all proteins have quaternary structure.

Proteins as Functional Elements:

Proteins perform a vast array of essential functions in living organisms, categorized

broadly as:

• A. Enzymes (Biological Catalysts):

o Accelerate biochemical reactions by lowering the activation energy.
Highly specific for their substrates.
o Examples: Lysozyme, Hexokinase.
• B. Transporters:
o Facilitate the movement of molecules across cell membranes or within the
body.
o Examples: Glucose transporters, oxygen transport.
• C. Receptors:
o Bind to specific signaling molecules (ligands) and initiate cellular
responses. Located on the cell surface or within the cell.
o Examples: Hormone receptors, Neurotransmitter receptors.
• D. Structural Elements:
o Provide physical support and shape to cells and tissues.
o Examples: Keratin (hair, nails), (muscle fibers).