CELL:-

A cell is the basic structural and functional unit of life. It is enclosed by a plasma membrane, which
separates the cell's internal environment from its external surroundings. Within the cell, several
components work together to carry out various functions:

Plasma Membrane: Also known as the cell membrane, it regulates the passage of substances into
and out of the cell, maintaining homeostasis.

Cytoplasm: A gel-like substance that fills the cell and contains various organelles. It plays a role in
supporting the organelles and facilitating intracellular transport.

Nucleus: The nucleus houses the cell's genetic material in the form of DNA. It serves as the control
center of the cell, regulating gene expression and coordinating cellular activities.

Organelles: These are specialized structures within the cell that perform specific functions. Examples
include:

Mitochondria: Powerhouses of the cell, responsible for generating energy in the form of ATP
through cellular respiration.

Endoplasmic Reticulum (ER): A network of membranes involved in protein and lipid synthesis.

Golgi Apparatus: Modifies, sorts, and packages proteins and lipids for transport within or outside the
cell.

Lysosomes: Contain enzymes that break down waste materials and cellular debris.

Ribosomes: Sites of protein synthesis, where amino acids are assembled into proteins according to
the instructions encoded in mRNA.

Cytoskeleton: A network of protein filaments that provides structural support, maintains cell shape,
and facilitates cell movement.

Cytosol: The liquid portion of the cytoplasm, where many metabolic reactions take place.

These components work together to carry out the essential functions of the cell, including
metabolism, growth, reproduction, and response to stimuli.

CELL THEORY:- The classical cell theory was proposed by Theodor Schwann in 1839. There are three
parts to this theory. The first part states that all organisms are made of cells. The second part states
that cells are the basic unit of life. These parts were based on a conclusion made by Schwann and
Matthias Schleiden in 1838,after comparing their observations of plant and animal cells. The third
part, which asserts that cells come from preexisting cells that have multiplied, was described by
Rudolf Virchow in 1858, when he stated omnis cellula e cellula (all cells come from cells).Since the
formation of classical cell theory, technology has improved, allowing for more detailed observations
that have led to new discoveries about cells. These findings led to the formation ofthe modern cell
theory, which has three main additions: first, that DNA is passed between cells during cell division;
second, that the cells of all organisms within a similar species are mostly the same, both structurally
and chemically; and finally, that energy flow occurs within cells.
STRUCTURE OF BUILDING BLOCKS:-

Proteins:

 Building Blocks: Proteins are composed of smaller units called amino acids.

 Amino Acids: There are 20 different types of amino acids, each with a unique side chain.

 Structure of Amino Acids: Amino acids have a central carbon atom (alpha carbon) bonded to
four groups: a hydrogen atom, an amino group (NH2), a carboxyl group (COOH), and a side
chain (R group) that varies in size and chemical properties.

 Peptide Bonds: Amino acids are linked together through peptide bonds, formed by a
condensation reaction between the amino group of one amino acid and the carboxyl group
of another.

 Polypeptide Chain: A chain of amino acids linked by peptide bonds forms a polypeptide
chain.

 Folding and Structure: Polypeptide chains can fold and twist into specific three-dimensional
structures, including primary, secondary, tertiary, and quaternary structures, driven by
interactions between amino acid side chains and the surrounding environment.

 Function: The specific structure of a protein determines its function. Proteins can act as
enzymes, structural components, hormones, antibodies, transport molecules, and more,
playing vital roles in the structure and functioning of cells and organisms.

 What are Biomolecules?

 Biomolecules are the most essential organic molecules, which are involved in the maintenance and
metabolic processes of living organisms. These non-living molecules are the actual foot-soldiers of the
battle of sustenance of life. They range from small molecules such as primary and secondary
metabolites and hormones to large macromolecules like proteins, nucleic acids, carbohydrates, lipids
etc.

 Types of Biomolecules

 There are four major classes of Biomolecules – Carbohydrates, Proteins, Nucleic acids and Lipids.
Each of them is discussed below.
 Carbohydrates
 Carbohydrates are chemically defined as polyhydroxy aldehydes or ketones or compounds which
produce them on hydrolysis. In layman’s terms, we acknowledge carbohydrates as sugars or substances
that taste sweet. They are collectively called as saccharides (Greek: sakcharon = sugar). Depending on
the number of constituting sugar units obtained upon hydrolysis, they are classified as monosaccharides
(1 unit), oligosaccharides (2-10 units) and polysaccharides (more than 10 units). They have multiple
functions’ viz. they’re the most abundant dietary source of energy; they are structurally very important
for many living organisms as they form a major structural component, e.g. cellulose is an important
structural fibre for plants.

 Proteins
 Proteins are another class of indispensable biomolecules, which make up around 50per cent of the
cellular dry weight. Proteins are polymers of amino acids arranged in the form of polypeptide chains.
The structure of proteins is classified as primary, secondary, tertiary and quaternary in some cases.
These structures are based on the level of complexity of the folding of a polypeptide chain. Proteins
play both structural and dynamic roles. Myosin is the protein that allows movement by contraction of
muscles. Most enzymes are proteinaceous in nature.

 Nucleic Acids
 Nucleic acids refer to the genetic material found in the cell that carries all the hereditary information
from parents to progeny. There are two types of nucleic acids namely, deoxyribonucleic acid (DNA)
and ribonucleic acid (RNA). The main function of nucleic acid is the transfer of genetic information
and synthesis of proteins by processes known as translation and transcription. The monomeric unit of
nucleic acids is known as nucleotide and is composed of a nitrogenous base, pentose sugar, and
phosphate. The nucleotides are linked by a 3’ and 5’ phosphodiester bond. The nitrogen base attached
to the pentose sugar makes the nucleotide distinct. There are 4 major nitrogenous bases found in DNA:
adenine, guanine, cytosine, and thymine. In RNA, thymine is replaced by uracil. The DNA structure is
described as a double-helix or double-helical structure which is formed by hydrogen bonding between
the bases of two antiparallel polynucleotide chains. Overall, the DNA structure looks similar to a
twisted ladder.

 Lipids
 Lipids are organic substances that are insoluble in water, soluble in organic solvents, are related to fatty
acids and are utilized by the living cell. They include fats, waxes, sterols, fat-soluble vitamins, mono-,
di- or triglycerides, phospholipids, etc. Unlike carbohydrates, proteins, and nucleic acids, lipids are not
polymeric molecules. Lipids play a great role in the cellular structure and are the chief source of
energy.

 Frequently Asked Questions on Biomolecules

 Q1What are biomolecules? What is its function?
 Biomolecules are biological molecules produced by the cells of the living organism. They are critical for life as it
helps organisms to carry out basic biological processes such as reproduction, growth and sustainence.
 Q2 What are the 4 main classes of biomolecules?
 The 4 main types of biomolecules are – lipids, carbohydrates, proteins and nucleic acids.
 Q3 What are the two most important biomolecules?
 Nucleic acids, amongst biomolecules, precisely DNA and RNA are most important. This is because they have the
important function of storing the unique genetic code of an entity and passing it during reproduction.
 Q4 Describe the structure of biomolecules.
 The structure of Biomolecule is the complex three-dimensional, folded configuration formed by a molecule of
nucleic acid or protein which is vital for its functioning.
 Q5What are the properties of Biomolecules?
 1. Most of the Biomolecules are organic compounds 2. Those molecules that are building blocks have a simpler
configuration 3.They have particular dimensions and shapes 4. The functional group associated determines its
chemical attributes.
 Carbohydrates:
 Building Blocks: Carbohydrates are made up of smaller units called sugars or saccharides.
 Structure: Think of carbohydrates like strings of beads made of different shapes and sizes of sugar molecules.
 Function: Carbohydrates are the body's main source of energy. They also play roles in cell structure, cell
recognition, and as energy storage molecules.
Nucleic Acids:
 Building Blocks: Nucleic acids are made up of smaller units called nucleotides.
 Structure: Picture a ladder twisted into a spiral shape, where each rung represents a pair of nucleotides. This
spiral ladder is known as a double helix.
 Function: Nucleic acids, such as DNA and RNA, store and transmit genetic information. They contain
instructions for building and maintaining living organisms.
Lipids:
 Building Blocks: Lipids are made up of smaller units called fatty acids and glycerol.
 Structure: Imagine a cluster of balls and sticks, where the balls represent fatty acids and the sticks represent
glycerol. Lipids can form structures like membranes or be stored as droplets in cells.
 Function: Lipids have various functions, including providing energy storage, forming cell membranes, and
serving as signaling molecules.

Enzymes:
 Structure: Enzymes are special proteins with specific shapes that allow them to bind to other molecules.
 Function: Enzymes act as catalysts in biochemical reactions, speeding up the rate of these reactions without being
consumed in the process. They help break down larger molecules into smaller ones or build larger molecules from
smaller ones.
 1. Enzyme:
 Definition: Enzymes are biological catalysts, typically proteins, that speed up chemical reactions by lowering the
activation energy required for the reaction to occur.
 How Enzymes Work: Enzymes bind to specific molecules called substrates at their active sites, forming enzyme-
substrate complexes. This binding facilitates the conversion of substrates into products. Enzymes are not
consumed in the reaction and can be reused multiple times.
 2. Holoenzyme:
 Definition: A holoenzyme is the complete, active form of an enzyme, consisting of both the protein portion
(apoenzyme) and non-protein portion (cofactor or coenzyme).
 Example: An example of a holoenzyme is lactate dehydrogenase, which consists of the protein portion
(apoenzyme) and the coenzyme NAD+.
 3. Monomeric Enzyme:
 Definition: Monomeric enzymes are enzymes composed of a single polypeptide chain.
 Example: Hexokinase, an enzyme involved in glycolysis, is a monomeric enzyme.
  4. Coenzyme:
 Definition: Coenzymes are organic molecules that assist enzymes in catalyzing biochemical reactions. They often
act as carriers of functional groups or electrons.
 Examples: Coenzymes include vitamins such as NAD+ (nicotinamide adenine dinucleotide) and coenzyme A
(CoA).
How Enzymes Work:
 Enzymes work by lowering the activation energy required for a chemical reaction to occur. They facilitate this
process by binding to substrates at their active sites and stabilizing transition states, allowing reactions to proceed
more rapidly.
 Enzymes do not alter the overall energy change of a reaction (ΔG), but they lower the energy barrier (activation
energy) required for the reaction to occur.
 6. Types of Inhibition:
Competitive Inhibition: Competitive inhibitors bind to the active site of an enzyme, preventing substrate binding
and reducing enzyme activity.
Non-competitive Inhibition: Non-competitive inhibitors bind to a site on the enzyme other than the active site,
altering the enzyme's shape and reducing its activity.
Uncompetitive Inhibition: Uncompetitive inhibitors bind only to the enzyme-substrate complex, preventing the
release of products and reducing enzyme activity.
Factors Affecting Enzyme Activity:
 pH: Enzymes have an optimal pH at which they function most effectively. Deviations from this pH can alter the
enzyme's structure and reduce its activity.
 Temperature: Enzyme activity increases with temperature up to a certain point (optimal temperature). Beyond
this temperature, enzymes can denature and lose their activity.
 Substrate Concentration: Enzyme activity typically increases with increasing substrate concentration, up to a
point where all enzyme active sites are saturated with substrate (Vmax).

 How do enzymes work? Enzymes work by binding to specific molecules called substrates and facilitating the
conversion of substrates into products. They lower the activation energy required for a reaction to occur, making
the reaction proceed more quickly.
 Enzyme-substrate complex: Enzymes bind to substrates at specific regions called active sites, forming enzyme-
substrate complexes. This binding allows the enzyme to catalyze the conversion of substrates into products.
 Lock-and-key model: The interaction between enzymes and substrates is often described using the lock-and-key
model, where the enzyme's active site is the lock and the substrate is the key that fits into the lock.

Significance of Glycolysis:

 Energy Production: Glycolysis is a vital metabolic pathway that breaks down glucose into pyruvate, generating
ATP molecules to provide energy for cellular activities.

 Universal Process: It is found in nearly all living organisms, from bacteria to humans, highlighting its
fundamental role in cellular metabolism.

 Anaerobic Respiration: Glycolysis can occur in the absence of oxygen, making it crucial for energy production in
anaerobic conditions, such as during intense exercise or in oxygen-deprived environments.

ATP Generated:
  Glycolysis generates a net of 2 ATP molecules per glucose molecule through substrate-level phosphorylation.

Start and End Products:

 Start Product: Glucose is the initial substrate for glycolysis.

 End Products: The end products of glycolysis are two molecules of pyruvate, along with a net gain of 2 ATP
molecules. Pyruvate can then enter further metabolic pathways, such as the citric acid cycle or fermentation,
depending on cellular conditions.

KREB CYCLE:-
The Krebs cycle is vital for cellular energy production:
 It generates high-energy molecules like NADH and FADH2, which fuel the production of ATP in the electron
transport chain.
 Acetyl-CoA starts the cycle, combining with oxaloacetate to produce citrate. Carbon dioxide, ATP, NADH, and
FADH2 are end products, contributing to energy production and metabolic processes.
THE ATP COUNT:-
the Krebs cycle (also known as the citric acid cycle or TCA cycle), the production of NADH and FADH2 is essential for subsequent ATP generation
through oxidative phosphorylation in the electron transport chain (ETC). Here's a simplified calculation of the NADH and FADH2 produced in one turn of
the Krebs cycle and their contribution to ATP production:
1. NADH Production:
 For each turn of the Krebs cycle, 3 molecules of NADH are produced.

 Each NADH molecule can generate approximately 2.5 to 3 ATP molecules during oxidative phosphorylation in the ETC.
So, for one turn of the Krebs cycle:
 3 NADH * 2.5 ATP/NADH = 7.5 ATP (minimum estimate)

 3 NADH * 3 ATP/NADH = 9 ATP (maximum estimate)

Therefore, the total ATP yield from NADH in one turn of the Krebs cycle ranges from approximately 7.5 to 9 ATP.
2. FADH2 Production:
 For each turn of the Krebs cycle, 1 molecule of FADH2 is produced.

 Each FADH2 molecule can generate approximately 1.5 to 2 ATP molecules during oxidative phosphorylation in the ETC.
So, for one turn of the Krebs cycle:
 1 FADH2 * 1.5 ATP/FADH2 = 1.5 ATP (minimum estimate)

 1 FADH2 * 2 ATP/FADH2 = 2 ATP (maximum estimate)

Therefore, the total ATP yield from FADH2 in one turn of the Krebs cycle ranges from approximately 1.5 to 2 ATP.
In summary, the Krebs cycle produces NADH and FADH2, which are essential for ATP generation through oxidative phosphorylation in the electron
transport chain. The total ATP yield from NADH and FADH2 in one turn of the Krebs cycle ranges from approximately 9.5 to 11 ATP.

Start Product:
 The start product of the Krebs cycle is Acetyl-CoA.

 Acetyl-CoA enters the Krebs cycle by combining with a molecule called oxaloacetate to form citrate, which initiates the cycle.
End Product:
 The end products of the Krebs cycle are:
1. ATP: Though ATP is not directly produced in the Krebs cycle, the high-energy molecules NADH and FADH2, generated during the cycle, proceed to the
electron transport chain where they contribute to ATP synthesis through oxidative phosphorylation.
2. Carbon Dioxide (CO2): Carbon dioxide is released as a waste product during several steps of the Krebs cycle.
3. Reduced Coenzymes (NADH and FADH2): NADH and FADH2 carry high-energy electrons to the electron transport chain for ATP production.

the Krebs cycle starts with Acetyl-CoA and ends with the production of ATP, carbon dioxide, and reduced coenzymes (NADH and FADH2). These end
products play essential roles in cellular energy production and metabolism.

Glycogenesis:
1. Significance of Glycogenesis:
 Glycogenesis is the process by which glucose is converted into glycogen for storage in the liver and muscles.

 It serves as a way to store excess glucose efficiently for later use, helping to maintain blood glucose levels and provide a readily available energy source
during times of need.
2. ATP Generated:
 Glycogenesis itself does not directly generate ATP; instead, it consumes ATP as an energy source.

 However, by storing glucose as glycogen, glycogenesis indirectly contributes to ATP production during glycogenolysis (the breakdown of glycogen) when
energy is required.
3. Start and End Products:
 Start Product: The start product of glycogenesis is glucose, which is derived from the breakdown of carbohydrates in the diet or from gluconeogenesis (the
synthesis of glucose from non-carbohydrate sources).
 End Product: The end product of glycogenesis is glycogen, a branched polymer of glucose molecules.

Significance of Lipid Biosynthesis: Significance of Lipid Biosynthesis: Lipid biosynthesis is vital for storing energy, maintaining
cell structure, and producing hormones and signaling molecules crucial for various physiological functions.
ATP Generated: While lipid biosynthesis consumes ATP as energy, stored lipids can later be oxidized to produce ATP, serving as an
energy source when needed.
Start and End Products: The process starts with Acetyl-CoA and ends with the production of diverse lipids, including fatty acids,
triglycerides, and phospholipids, essential for energy storage, cellular structure, and signaling.
FATTY ACID CATABOLISM:-
Fatty acid catabolism is vital for energy production, where fats are broken down to generate ATP. The process starts with fatty acid oxidation, yielding
acetyl-CoA, which enters the citric acid cycle. This cycle produces NADH and FADH2, which fuel the electron transport chain, generating ATP. The end
products are carbon dioxide, water, and ATP, providing energy for cellular functions.
BIOSYNTHESIS:-
The biosynthesis of amino acids, oxidation reactions, and nucleotide synthesis are fundamental processes in cellular metabolism. Here's a brief overview of
each process:
1. Biosynthesis of Amino Acids:
 Amino acids are the building blocks of proteins and play crucial roles in various physiological processes.

 Amino acids can be synthesized de novo from simple precursor molecules or obtained from the diet.

 The biosynthesis of amino acids involves a series of enzymatic reactions that convert precursor molecules into specific amino acids.

 There are two main pathways for amino acid biosynthesis: the gluconeogenic pathway (for non-essential amino acids) and the ketogenic pathway (for essential amino
acids).
 Some amino acids are synthesized from intermediates of glycolysis and the citric acid cycle, while others are derived from nitrogen sources such as ammonia or glutamine.
2. Oxidation Reactions:
 Oxidation reactions involve the loss of electrons or hydrogen atoms from molecules.

 These reactions are crucial for energy production and the metabolism of various biomolecules.

 Oxidation reactions occur in pathways such as glycolysis, the citric acid cycle, and oxidative phosphorylation, where energy is harvested from the oxidation of substrates
like glucose and fatty acids.
 NAD+ and FAD are important cofactors involved in oxidation-reduction reactions, acting as electron carriers that shuttle electrons to the electron transport chain for ATP
production.
3. Nucleotide Synthesis:
 Nucleotides are the building blocks of nucleic acids (DNA and RNA) and serve as carriers of chemical energy (ATP, GTP) and signaling molecules (cyclic AMP).

 Nucleotide synthesis involves the assembly of nucleotides from simpler precursors such as ribose-5-phosphate, amino acids, and nitrogenous bases (purines and
pyrimidines).
 Purine nucleotides (adenine and guanine) are synthesized from precursor molecules through a series of enzymatic reactions, while pyrimidine nucleotides (cytosine,
thymine, and uracil) are synthesized via distinct pathways.
 The de novo synthesis of nucleotides requires energy in the form of ATP and utilizes various enzymes and cofactors to catalyze the sequential assembly of nucleotide
monomers.
 Nucleotide synthesis is tightly regulated to maintain cellular nucleotide pools and ensure accurate DNA replication and RNA transcription.
In summary, the biosynthesis of amino acids, oxidation reactions, and nucleotide synthesis are essential processes in cellular metabolism, providing the
building blocks and energy required for cell growth, maintenance, and function. These processes are intricately regulated and interconnected, reflecting the
complexity of cellular metabolism.

AMINO ACID OXIDATION AND UREA PRODUCTION:-

Amino acid oxidation and urea production are essential processes in nitrogen metabolism, responsible for removing excess nitrogen from the body. Here's a
brief explanation of each:
1. Amino Acid Oxidation:
 Amino acid oxidation refers to the breakdown of amino acids into their constituent parts, which typically involves removing the amino group (-NH2).

 This process occurs primarily in the liver and involves transamination and oxidative deamination reactions.

 During transamination, the amino group of an amino acid is transferred to an α-keto acid, forming a new amino acid and a new α-keto acid.

 Oxidative deamination involves the removal of the amino group from an amino acid, resulting in the formation of ammonia (NH3) and a keto acid.

 The ammonia generated from amino acid oxidation is toxic to cells and must be quickly removed from the body to prevent damage.
2. Urea Production:
 Urea production is the primary mechanism for eliminating excess nitrogen in the form of urea, a non-toxic compound.

 In the liver, ammonia produced from amino acid oxidation is combined with carbon dioxide (CO2) to form urea in a series of enzymatic reactions known as the urea cycle
or ornithine cycle.
 The urea cycle involves several steps, including the formation of carbamoyl phosphate, which combines with ornithine to form citrulline. Citrulline is then converted into
argininosuccinate and eventually into urea and arginine.
 Urea is transported via the bloodstream to the kidneys, where it is filtered out of the blood and excreted in the urine.

 The urea cycle is essential for maintaining nitrogen balance in the body and preventing the buildup of toxic ammonia.
In summary, amino acid oxidation and urea production are interconnected processes involved in removing excess nitrogen from the body. Amino acid
oxidation breaks down amino acids, producing ammonia, while urea production converts ammonia into urea, which is excreted in the urine. This process
helps maintain nitrogen balance and prevent toxicity in the body.

DNA replication is a process in which the genetic material of a cell, in this case, the DNA makes an exact copy of itself and the process is controlled by the
enzyme DNA polymerase. In mammals, the rate of replication is around 50 nucleotides per second whereas, in bacteria, the rate is around 500 nucleotides
per second.
 In general, the hydrogen bonds between two complementary bases between two DNA strands break which helps the strand to unwind. Each strand acts as a
template for synthesis of a new strand which is complementary to itself.

The entire process continues till all the nucleotides on the template have joined with the free nucleotides and two identical DNA strands are formed. This
model of replication is known as the semiconservative model of replication.

In this topic, we will have a brief overview of both eukaryotic and prokaryotic replication and what their differences are.

DNA Replication in Prokaryotes

Centring on the general principle of DNA replication, the prokaryotic DNA replication in prokaryotic cells takes place just before a cell divides in an
organism and ensures both daughter cells receive an exact copy of the parent’s genetic material. The process uses the semiconservative model of replication
which results in a double-stranded DNA with one parental and one daughter strand.
The Steps of Prokaryotic DNA Replication are as follows:
 The DNA replication process is bi-directional begins at a spot on the DNA molecule called the origin of replication.

 At this spot, enzymes unwind the double helix structure of the DNA which makes its components accessible for replication.

 The helix is unwound by the helicase enzyme to form a pair of replication forks, and the unwound helix is stabilised by SSB proteins and DNA isomerases.

 Primase forms 10 base RNA primers which initiate the synthesis of the leading and the lagging strand.

 The leading continues to synthesise in the 5’ to 3’ direction by DNAP III (DNA Polymerase III)

 The lagging strand is also synthesised in the 5’ to 3’ direction but it is discontinued through the formation of Okazaki fragments.

 DNA polymerase I removes the 10 base RNA primers and replaces the gap with deoxynucleotides.

 Then DNA ligase seals the breaks between Okazaki fragments as well as around the primers to form continuous strands.

 The entire process of replication takes place in the cell cytoplasm.

DNA Replication in Eukaryotes

The eukaryotic DNA replication takes place in the cell nucleus and only occurs in the S phase at many chromosomal origins. Similar to prokaryotic DNA
replication, eukaryotic cells also use the semi-conservative process of replication but there are multiple origins of replication.
The Steps of the Eukaryotic DNA Replication are as follow:
 The replication process starts in a chromosome at multiple origins, with one origin being at 30-300 kb of DNA depending on the tissue and species.

 A replication bubble of two forks forms at each origin. The DNA replicated under the control of a single origin is called a replicon. The synthesis proceeds until all bubbles
merge together.
 The process starts with the unwinding of DNA with the help of enzymes, which makes its components accessible for replication.

 The unwound helix forms a pair of replication forks and is stabilised by DNA topoisomerases and SSB proteins.

 The RNA primers required for the process are made by DNA polymerases α which initiates the synthesis of the lagging strand and makes the first primer. It then extends it
with a short region of DNA.
 The Okazaki fragments and the leading strand are synthesised by DNA polymerase δ.

 The leading strand is synthesised continuously whilst the lagging strand is synthesised discontinuously. Both strands are synthesised in the 5′to 3′ direction.

 At completion, DNA ligase seals the breaks around the primers and between the Okazaki fragments.