MODULE 5

1. Nucleotides, Nucleosides, and Nitrogenous Bases

 Nitrogenous Bases: These are the core units of nucleotides, categorized as purines
(adenine and guanine) and pyrimidines (cytosine, thymine, and uracil). They are the
molecules that carry genetic information.
 Nucleosides: A nucleoside is formed when a nitrogenous base binds with a sugar
molecule (ribose in RNA and deoxyribose in DNA). Examples include adenosine,
guanosine, cytidine, thymidine, and uridine.
 Nucleotides: These are nucleosides with one or more phosphate groups attached.
Nucleotides serve as the building blocks of DNA and RNA and play key roles in energy
transfer and cellular signaling (e.g., ATP, GTP).

2. Chemical Structures of DNA and RNA

 DNA: Composed of two strands of nucleotides twisted into a double helix. It contains the
sugar deoxyribose
 and the nitrogenous bases adenine, guanine, cytosine, and thymine.
 RNA: Usually single-stranded, it contains the sugar ribose and the bases adenine,
guanine, cytosine, and uracil (uracil replaces thymine).

3. Double Helical DNA (The Watson-Crick Model)

 The Watson-Crick model of DNA describes it as a right-handed double helix with two
antiparallel strands.
 Each strand has a backbone of alternating phosphate and deoxyribose sugar molecules.
Base pairing occurs between complementary nitrogenous bases, with adenine pairing
with thymine (A-T) and cytosine pairing
 with guanine (C-G), held together by hydrogen bonds.

4. Types of DNA and RNA

 DNA Types:
o B-DNA: The most common form in cells, with a right-handed helix.
o A-DNA: A more compact, right-handed helix found in dehydrated conditions.
o Z-DNA: A left-handed helix, rare in cells, and thought to play a role in gene
expression.
 RNA Types:
o mRNA (messenger RNA): Carries genetic information from DNA to ribosomes.

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 o tRNA (transfer RNA): Brings amino acids to ribosomes for protein synthesis.
o rRNA (ribosomal RNA): Combines with proteins to form ribosomes.
o snRNA (small nuclear RNA): Involved in splicing mRNA.
o siRNA and miRNA (small interfering RNA and microRNA): Regulate gene
expression.

5. Metabolism of Nucleotides
 Synthesis of Purine and Pyrimidine Ribonucleotides:
o Purine Synthesis: Built step-by-step on a ribose phosphate scaffold to form
inosine monophosphate (IMP), which then branches to form AMP and GMP.
o Pyrimidine Synthesis: The pyrimidine ring is synthesized first and then attached
to ribose phosphate to form UMP (which further produces CMP and dTMP).

 De Novo and Salvage Pathway of Purine Nucleotides:

o De Novo Pathway: Nucleotides are synthesized from basic building blocks
o (amino acids, ribose phosphate, CO₂).
o Salvage Pathway: Recycles free purine bases or nucleosides from cellular
breakdown products into nucleotides. Enzymes like HGPRT play a critical role
here, especially in tissues with high energy needs.

 Roles of Folic Acid in Nucleotide Biosynthesis:

o Folic acid (vitamin B9) is essential as a cofactor in purine and pyrimidine
synthesis, aiding in the transfer of one-carbon groups to form important
intermediates like N⁵,N¹⁰-methylene tetrahydrofolate for thymidine synthesis.

6. Catabolism of Purines and Pyrimidines

 Purine Catabolism:
o Purines are broken down into uric acid, which is excreted in urine. Excessive
o uric acid can lead to conditions like gout due to crystal accumulation.

 Fate of Uric Acid:

o In humans, uric acid is the end product of purine catabolism, but some animals
convert it further into allantoin via the enzyme uricase (which humans lack).

 Catabolism of Pyrimidines:
o Pyrimidines are broken down into simpler, water-soluble molecules like beta-
alanine and beta-aminoisobutyrate that can be excreted or used in other
o metabolic pathways.

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 MODULE 4
1. Amino Acids of Proteins: General Properties,
Classification, and Characteristics
 General Properties:
o Amino acids are organic molecules containing an amino group (-NH₂) and a
carboxyl group (-COOH).
o They are the building blocks of proteins, linked by peptide bonds to form
polypeptide chains.
o There are 20 standard amino acids used in protein synthesis in humans.
 Classification:
o By R-Group Polarity:
 Nonpolar, Hydrophobic: e.g., alanine, valine, leucine.
 Polar, Uncharged: e.g., serine, threonine, asparagine.
 Acidic: e.g., aspartic acid, glutamic acid.
 Basic: e.g., lysine, arginine, histidine.
o By Nutritional Requirement:
 Essential Amino Acids: Cannot be synthesized by the body and must be
obtained from diet (e.g., leucine, lysine).
 Non-Essential Amino Acids: Synthesized by the body (e.g., glycine,
alanine).
 Optical Properties:
o Amino acids (except glycine) are chiral and can exist in L and D forms.
o L-amino acids are the ones used in proteins.
o They exhibit optical activity due to the chiral center, rotating polarized light.

2. Peptide Bond: Configuration and Properties

 A peptide bond is a covalent bond formed between the carboxyl group of one amino
acid and the amino group of another, releasing a molecule of water.
 Properties:
o It is planar and generally has a trans configuration to avoid steric clashes
between R groups.

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 o Peptide bonds exhibit partial double-bond character due to resonance, making
them relatively rigid and planar.

3. Protein Structures
 Primary Structure:
o The linear sequence of amino acids in a protein chain, held together by peptide
bonds.
 Secondary Structure:
o Alpha Helices: Right-handed coils stabilized by hydrogen bonds between every
fourth amino acid.
o Beta Pleated Sheets: Parallel or antiparallel strands connected by hydrogen bonds,
creating a sheet-like structure.
 Tertiary Structure:
o The overall 3D folding of a single polypeptide chain, stabilized by hydrophobic
interactions, hydrogen bonds, ionic bonds, and disulfide bridges (covalent
bonds between cysteine residues).
 Quaternary Structure:
o The structure formed by multiple polypeptide subunits (e.g., hemoglobin is made
up of four subunits).

4. Major Bonds/Forces Stabilizing Protein Structures

 Hydrogen Bonds: Occur between polar groups.
 Hydrophobic Interactions: Nonpolar amino acids aggregate to avoid water.
 Ionic Bonds (Salt Bridges): Form between charged R groups.
 Disulfide Bonds: Covalent bonds between cysteine residues in the same or different
chains.
 Van der Waals Forces: Weak interactions that stabilize the close packing of amino
acids.

5. Ramachandran Plot
 The Ramachandran plot displays the allowable angles of phi (φ) and psi (ψ) for each
amino acid in a protein.
 The plot reveals which angle combinations are sterically allowed and are important for
understanding protein structure and predicting secondary structure.

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6. Denaturation and Renaturation of Proteins
 Denaturation: Loss of protein structure (secondary, tertiary, or quaternary) due to heat,
pH changes, or chemicals, leading to loss of function.
 Renaturation: Some proteins can regain their native structure if denaturing conditions
are removed, as demonstrated in the renaturation of ribonuclease A.

7. Amino Acid Metabolism

 Amino Acid De-amination:
o Amino acids are broken down by de-amination, which removes the amino group,
producing ammonia and a keto acid.
 Urea Cycle:
o Converts toxic ammonia to urea for safe excretion in urine. It involves several
steps in the liver, including the formation of carbamoyl phosphate and citrulline.
o Link with TCA Cycle: The fumarate produced in the urea cycle enters the TCA
cycle, linking amino acid catabolism to energy metabolism.
 Ammonia Toxicity:
o High levels of ammonia are toxic, especially to the nervous system, as it can lead
to hepatic encephalopathy.

8. Glycolytic and TCA Cycle Intermediates as

Precursors for Amino Acid Biosynthesis
 Intermediates like pyruvate, alpha-ketoglutarate, oxaloacetate, and 3-
phosphoglycerate serve as precursors for non-essential amino acids.
 For example:
o Pyruvate can lead to alanine.
o Alpha-ketoglutarate can lead to glutamate, glutamine, proline, and arginine.
o Oxaloacetate can lead to aspartate and asparagine.

9. Pathways of Non-Essential Amino Acid

Degradation
 Asparagine and Aspartic Acid: Converted to oxaloacetate.
 Cysteine: Degraded to pyruvate and sulfate.
 Glutamic Acid and Glutamine: Converted to alpha-ketoglutarate.
 Glycine: Converted to carbon dioxide and ammonia.
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  Proline: Oxidized to glutamate.
 Serine: Converted to pyruvate.
 Tyrosine: Converted to fumarate and acetoacetate.

10. Degradation of Heme to Bilirubin

 Heme from degraded red blood cells is converted to biliverdin by heme oxygenase,
releasing iron and carbon monoxide.
 Biliverdin is then reduced to bilirubin, which is transported to the liver for excretion.
 Bilirubin is conjugated in the liver and excreted in bile, playing a key role in the body's
elimination of heme breakdown products.

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 MODULE 3
1. Lipid Classification
Lipids are a diverse group of biological molecules, primarily hydrophobic, and play various
roles in energy storage, structural support, and signaling.

 Fatty Acids: Carboxylic acids with a hydrocarbon chain. They are classified based on
chain length, saturation, and dietary requirement.
o Saturated Fatty Acids: Contain no double bonds between carbon atoms. They are
solid at room temperature (e.g., palmitic acid, stearic acid).
o Unsaturated Fatty Acids: Contain one or more double bonds, making them
kinked and usually liquid at room temperature.
 Monounsaturated (one double bond, e.g., oleic acid)
 Polyunsaturated (multiple double bonds, e.g., linoleic acid, linolenic acid)
o Essential Fatty Acids: Cannot be synthesized by the body and must be obtained
through diet, including omega-3 and omega-6 fatty acids (e.g., linoleic acid, alpha-
linolenic acid).
o Non-Essential Fatty Acids: Can be synthesized by the body (e.g., palmitic acid).

 Triacylglycerols (Triglycerides): Composed of three fatty acids esterified to a glycerol

backbone. They serve as major energy storage molecules in adipose tissue.
 Glycerophospholipids: Glycerol-based phospholipids, where two fatty acids and one
phosphate group are attached to glycerol. The phosphate group can bind to various polar
groups, forming molecules like phosphatidylcholine and phosphatidylserine. They are
key components of cell membranes.
 Sphingolipids: Contain a sphingosine backbone instead of glycerol. Major classes
include:
o Sphingomyelin: Contains a phosphate group, found in the myelin sheath of nerve
cells.
o Glycosphingolipids: Include cerebrosides and gangliosides, important in cell
recognition and signaling.

 Cholesterol: A sterol with a complex ring structure. It is a precursor to steroid hormones,

vitamin D, and bile acids, and is essential for membrane fluidity and integrity.

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2. Saponification and Iodine Value/Number
 Saponification: A chemical reaction where fats or oils (triglycerides) are hydrolyzed
with a strong base (usually NaOH or KOH) to produce glycerol and soap (the salt of the
fatty acids). This reaction is used to determine the saponification value, which is the
amount of base needed to saponify a specific amount of fat or oil.
 Iodine Value/Number: A measure of the degree of unsaturation in a lipid. It indicates
the amount of iodine (in grams) that reacts with 100 grams of fat or oil. Higher iodine
values correspond to a higher degree of unsaturation, as more iodine is required to break
the double bonds.

3. Glycolipids and Lipoproteins

 Glycolipids: Lipids with one or more carbohydrate groups attached. They are found on
cell surfaces and play roles in cell recognition, adhesion, and signaling. Glycolipids
include cerebrosides and gangliosides and are essential components of nerve cell
membranes.
 Lipoproteins: Complexes of lipids and proteins that transport lipids (such as
triglycerides and cholesterol) through the bloodstream. Types include:
o Chylomicrons: Transport dietary lipids from the intestines to peripheral tissues.
o VLDL (Very Low-Density Lipoprotein): Carries triglycerides from the liver to
tissues.
o LDL (Low-Density Lipoprotein): Known as “bad cholesterol”; delivers
cholesterol to tissues and may lead to plaque formation in arteries.
o HDL (High-Density Lipoprotein): Known as “good cholesterol”; collects excess
cholesterol from tissues and transports it back to the liver.

4. Lipids and Biomembranes

 Lipids, primarily phospholipids, cholesterol, and sphingolipids, form the lipid bilayer of
biological membranes. This bilayer is semi-permeable and provides structural integrity,
compartmentalization, and fluidity.
 Membrane Fluidity: Regulated by cholesterol and the degree of saturation of fatty acids;
unsaturated fatty acids increase fluidity, while saturated fatty acids and cholesterol reduce
it.

5. Metabolism of Lipids
 Fatty Acid Oxidation (Beta-Oxidation):
o Fatty acids are broken down in the mitochondria through beta-oxidation, producing
acetyl-CoA, NADH, and FADH₂.
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 o Even-Chain Fatty Acid Oxidation: Sequentially produces acetyl-CoA units,
which enter the TCA cycle.
o Odd-Chain Fatty Acid Oxidation: Ends with one molecule of acetyl-CoA and
one of propionyl-CoA, which is converted to succinyl-CoA and enters the TCA
cycle.

 ATP Formation from Complete Oxidation of Fatty Acids:

o The complete oxidation of a fatty acid yields a large amount of ATP. For
o instance, the oxidation of palmitic acid (16 carbons) produces 106 molecules of
ATP through beta-oxidation and subsequent entry of acetyl-CoA into the TCA
cycle.

 Formation of Ketone Bodies and Utilization:

o In conditions of low carbohydrate availability (e.g., fasting, starvation,
uncontrolled diabetes), excess acetyl-CoA is converted into ketone bodies
(acetoacetate, beta-hydroxybutyrate, and acetone) in the liver.
o Ketone bodies are used as an alternative energy source, especially by the brain
o and muscles, during prolonged fasting.

 Biosynthesis of Fatty Acids in Eukaryotes:

o Fatty acid synthesis occurs in the cytoplasm and involves the sequential addition
o of two-carbon units from malonyl-CoA to form a growing fatty acid chain.
o The process is catalyzed by fatty acid synthase and requires NADPH as a
reducing agent.
o Acetyl-CoA (originating from carbohydrates and amino acids) is transported
o out of the mitochondria in the form of citrate, which is then converted back to
acetyl-CoA in the cytoplasm for fatty acid synthesis.

 Cholesterol Metabolism:
o Cholesterol is synthesized primarily in the liver from acetyl-CoA via the
mevalonate pathway, which includes the formation of HMG-CoA and
mevalonate (rate-limiting step catalyzed by HMG-CoA reductase).
o Cholesterol is then used for the synthesis of steroid hormones, vitamin D, bile
acids, and is also incorporated into cell membranes.

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 MODULE 2
1. Monosaccharides

 Aldoses and Ketoses:

o Monosaccharides are simple sugars, classified as aldoses or ketoses based on the
functional group present.
o Aldoses contain an aldehyde group (-CHO) at the first carbon (e.g., glucose,
galactose).
o Ketoses contain a ketone group (C=O) typically at the second carbon (e.g.,
fructose).

 Configuration and Conformation:

o Configuration refers to the fixed spatial arrangement of atoms in a molecule,
especially regarding the chiral centers (e.g., D- or L- configurations, where D-
sugars are the most common in nature).
o Conformation refers to the spatial orientation of the molecule that can change
without breaking bonds. For example, glucose can adopt chair and boat
conformations in the ring form.

 Reducing and Non-Reducing Sugars:

o Reducing Sugars: Contain a free aldehyde or ketone group capable of reducing
agents (like Benedict's or Fehling’s solution), allowing the sugar to donate
electrons (e.g., glucose, maltose).
o Non-Reducing Sugars: Do not have a free aldehyde or ketone group; they do not
reduce other compounds (e.g., sucrose).

 Stereoisomerism:

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 o Monosaccharides with the same molecular formula but different spatial
arrangements are stereoisomers. Enantiomers (D- and L- forms) are mirror
images, while diastereomers are not (e.g., glucose and galactose).
o Epimers are a type of diastereomer differing at just one chiral center (e.g., glucose
and mannose).

2. Disaccharides

 Maltose: Consists of two glucose molecules linked by an alpha(1→4) glycosidic bond.

It is a reducing sugar.
 Lactose: Composed of glucose and galactose, connected by a beta(1→4) glycosidic
bond. It is found in milk and is also a reducing sugar.

 Sucrose: Made of glucose and fructose linked by an alpha(1→2) glycosidic bond.

It is a non-reducing sugar since both anomeric carbons are involved in the linkage.

3. Polysaccharides

 Storage Polysaccharides:
o Starch: The primary storage carbohydrate in plants, consisting of amylose
(unbranched, alpha(1→4) linkages) and amylopectin (branched, with alpha(1→6)
linkages at branch points).
o Glycogen: The storage form of glucose in animals. It is similar to amylopectin but
more highly branched, allowing faster mobilization of glucose during high energy
demands.

 Structural Polysaccharides:
o Cellulose: Composed of glucose units linked by beta(1→4) glycosidic bonds. It
provides rigidity to plant cell walls and cannot be digested by humans due to the
beta linkages.
o Chitin: Found in the exoskeletons of arthropods and cell walls of fungi. It consists
of N-acetylglucosamine units linked by beta(1→4) glycosidic bonds, contributing
to structural strength.

4. Important Sugar Derivatives and Glycosaminoglycans

 Sugar Derivatives:
o Amino Sugars: Sugars where a hydroxyl group is replaced by an amino group
(e.g., glucosamine, galactosamine).

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 o Sugar Alcohols: Formed by reducing the aldehyde or ketone group to an alcohol
(e.g., sorbitol, mannitol).
o Sugar Acids: Produced by oxidation of sugars, e.g., glucuronic acid (involved in
detoxification in the liver).

 Glycosaminoglycans (GAGs):
o Long unbranched polysaccharides with repeating disaccharide units. GAGs include
hyaluronic acid, chondroitin sulfate, and heparin. They play crucial roles in
connective tissue structure, lubrication, and cellular signaling.

5. Importance of Carbohydrates

 Carbohydrates are the primary energy source, form structural components (e.g., cellulose
in plants, chitin in insects), and serve as molecular recognition sites on cell surfaces.
They are also involved in immune response, fertilization, and blood clotting.

6. Carbohydrate Metabolism

 Glycolysis:
o Occurs in the cytoplasm, breaking down glucose into two molecules of pyruvate
while generating 2 ATP and 2 NADH molecules per glucose.
o Glycolysis has ten steps, divided into energy-investing and energy-generating
phases.

 Formation of Acetyl Co-A from Pyruvate:

o In the mitochondria, pyruvate is converted into acetyl Co-A by the pyruvate
dehydrogenase complex. This process produces one molecule of NADH per
pyruvate and releases CO₂.

 Citric Acid (TCA) Cycle:

o Occurs in the mitochondrial matrix, where acetyl Co-A is oxidized, producing 3
NADH, 1 FADH₂, and 1 GTP (or ATP) per cycle turn. It releases two CO₂
molecules and serves as a hub for various metabolic pathways.

 Substrate-Level and Oxidative Phosphorylation:

o Substrate-Level Phosphorylation: Direct generation of ATP/GTP by transferring
a phosphate group from a substrate to ADP/GDP (e.g., in glycolysis and TCA
cycle).
o Oxidative Phosphorylation: ATP production driven by the electron transport
chain in mitochondria, where electrons from NADH and FADH₂ move through
protein complexes, creating a proton gradient that drives ATP synthesis by ATP
synthase.

 Total ATP Formation during Glycolysis and TCA Cycle:

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 o Glycolysis: Net gain of 2 ATP and 2 NADH (producing ~5 ATP in the electron
transport chain).
o Pyruvate to Acetyl Co-A: 2 NADH (~5 ATP).
o TCA Cycle: For two acetyl Co-A, 6 NADH, 2 FADH₂, and 2 GTP are produced,
generating approximately 20 ATP.
o Total ATP Yield per Glucose: Around 30-32 ATP.

 Glycogenesis, Glycogenolysis, and Gluconeogenesis:

o Glycogenesis: The formation of glycogen from glucose, primarily in the liver and
muscle, for energy storage.
o Glycogenolysis: The breakdown of glycogen into glucose-1-phosphate, which can
be converted to glucose-6-phosphate and enter glycolysis or blood glucose levels.
o Gluconeogenesis: The synthesis of glucose from non-carbohydrate precursors
(e.g., lactate, amino acids, glycerol) during fasting or intense exercise, primarily in
the liver.

 Pentose Phosphate Pathway (PPP):

o Occurs in the cytoplasm and serves two main purposes:
 NADPH Production: NADPH is used in anabolic reactions (e.g., fatty acid
synthesis) and in maintaining the redox balance by regenerating glutathione.
 Ribose-5-Phosphate Production: A precursor for nucleotide synthesis.
o Significance: PPP is important for cells with high oxidative stress (e.g., red blood
cells) and for anabolic tissues (e.g., liver, adipose tissue).

MODULE 1
1. Covalent, Non-Covalent, Hydrophilic, and Hydrophobic
Interactions and Their Influence on the Structure of Biomolecules

 Covalent Interactions:
o Covalent bonds involve the sharing of electrons between atoms, creating
very stable bonds. They are the primary type of bond holding atoms
together in biomolecules (e.g., in proteins, nucleic acids, and lipids).
o Examples include peptide bonds in proteins, glycosidic bonds in
carbohydrates, and phosphodiester bonds in nucleic acids. The strength
and stability of covalent bonds provide the backbone for the structure of
these biomolecules.

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  Non-Covalent Interactions:
o Non-covalent interactions are weaker than covalent bonds but crucial for
the 3D structure, function, and flexibility of biomolecules. They include:
 Hydrogen Bonds: Formed between a hydrogen atom covalently
bonded to an electronegative atom (like oxygen or nitrogen) and
another electronegative atom. Hydrogen bonds are important for
stabilizing structures like DNA double helices and protein
secondary structures.
 Ionic (Electrostatic) Interactions: Occur between oppositely
charged groups (e.g., between acidic and basic side chains in
proteins). They play a role in the folding of proteins and the
binding of substrates to enzymes.
 Van der Waals Interactions: Weak attractions due to transient
dipoles in molecules. They contribute to the stability of
biomolecular structures by creating a collective effect when
numerous.
 Hydrophobic Interactions: Nonpolar molecules or groups cluster
together in an aqueous environment to minimize their exposure to
water. This interaction drives the folding of proteins, with
nonpolar (hydrophobic) side chains often positioned internally,
away from water.

 Hydrophilic and Hydrophobic Interactions:

o Hydrophilic (Water-Loving): Molecules or groups that interact
favorably with water (often polar or charged).
o Hydrophobic (Water-Fearing): Molecules or groups that do not
interact well with water and tend to aggregate with other nonpolar
molecules.
o These interactions influence how biomolecules, such as proteins and
lipids, fold and arrange themselves. For example, lipid bilayers form in
cell membranes because hydrophobic tails face inward, while
hydrophilic heads face the aqueous environment.

2. Acids, Bases, pH, pK, and Ionization of Water

 Acids and Bases:

o Acids are substances that donate protons (H⁺ ions) and increase the
concentration of H⁺ in a solution.
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 o Bases accept protons, reducing the concentration of H⁺ in solution.
o Strong acids and bases ionize completely in water, while weak acids
and bases only partially ionize.

 pH:
o pH is a measure of the concentration of hydrogen ions in a solution. It is
calculated as: pH=−log⁡[H+]\text{pH} = -\log[H⁺]pH=−log[H+]
o A low pH indicates a high concentration of H⁺ ions (acidic), while a
high pH indicates a low concentration of H⁺ ions (basic or alkaline).

 pK:
o pK is the pH at which half of a given acid is dissociated (50% ionized),
and it is an intrinsic property of weak acids.
o It is a key value in determining the strength of an acid, with lower pK
values corresponding to stronger acids.

 Ionization of Water:
o Water self-ionizes slightly to form H⁺ (or H₃O⁺) and OH⁻ ions. The
product of their concentrations at 25°C is a constant: [H+]
[OH−]=1×10−14[H⁺][OH⁻] = 1 \times 10^{-14}[H+][OH−]=1×10−14
o This relationship underlies the pH scale and affects acid-base balance in
biological systems.

3. Buffers and the Henderson-Hasselbalch Equation

 Buffers:
o Buffers are solutions of weak acids and their conjugate bases that resist
changes in pH when small amounts of acid or base are added.
o They are crucial in biological systems for maintaining a stable pH,
which is necessary for enzyme activity and cellular function (e.g., the
bicarbonate buffer system in blood).

 Henderson-Hasselbalch Equation:
o This equation relates the pH of a buffer solution to the concentration of
the acid and its conjugate base: pH=pKa+log⁡([A−][HA])\text{pH} = \
text{pK}_a + \log\left(\frac{[\text{A}^-]}{[\text{HA}]}\right)pH=pKa
+log([HA][A−])

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 o It is used to calculate the pH of a solution given the concentrations of
the acid (HA) and its conjugate base (A⁻), allowing control over pH in
experimental and physiological settings.

4. Biomolecules: Classification and Functions

 Carbohydrates:
o Provide energy, serve as structural materials (e.g., cellulose), and are
involved in cell recognition and signaling.

 Proteins:
o Perform a wide range of functions, including catalysis (enzymes),
transport (hemoglobin), structural support (collagen), and signaling
(hormones).

 Lipids:
o Serve as energy storage molecules, components of cell membranes
(phospholipids), and signaling molecules (e.g., steroid hormones).

 Nucleic Acids (DNA and RNA):

o DNA stores genetic information, while RNA is involved in protein
synthesis and gene regulation.

5. Concepts of Bioenergetics

 First and Second Laws of Thermodynamics:

o First Law: Energy cannot be created or destroyed, only transformed
from one form to another.
o Second Law: In any energy transfer, the entropy (disorder) of the
universe tends to increase. Biological systems maintain order by
consuming energy, often in the form of ATP.

 Gibb’s Free Energy (ΔG):

o ΔG indicates the spontaneity of a reaction. A negative ΔG implies a
spontaneous reaction, while a positive ΔG indicates a non-spontaneous
reaction.
o ΔG is calculated using the equation: ΔG=ΔH−TΔS\Delta G = \Delta H -
T\Delta SΔG=ΔH−TΔS where ΔH is the change in enthalpy, T is the
temperature in Kelvin, and ΔS is the change in entropy.
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 Calculations of Standard Free Energy (ΔG°'):
o ΔG°' is the free energy change under standard conditions (25°C, 1 atm, 1
M concentration).
o It can be calculated as: ΔG°′=−RTln⁡Keq\Delta G°' = -RT \ln
K_{eq}ΔG°′=−RTlnKeq where RRR is the gas constant, T is the
temperature, and KeqK_{eq}Keq is the equilibrium constant.

 Biological Oxidation-Reduction Reactions:

o Redox reactions involve the transfer of electrons between molecules,
releasing energy that is harnessed for biological processes (e.g., the
electron transport chain).
o Oxidizing agents accept electrons, while reducing agents donate
electrons.

 Redox Potential (E₀'):

o Redox potential measures the tendency of a substance to gain or lose
electrons. A positive E₀' indicates a high affinity for electrons (good
oxidizing agent), while a negative E₀' indicates a good reducing agent.
o Redox potential is significant in cellular respiration, as electrons are
transferred through complexes in the electron transport chain to
ultimately produce ATP.

 High Energy Compounds:

o High-energy molecules, like ATP, GTP, and creatine phosphate, store
and transfer energy for various biological processes.
o ATP (Adenosine Triphosphate): Known as the cell’s energy currency,
ATP provides energy by hydrolysis of its phosphate bonds.
o GTP (Guanosine Triphosphate): Functions similarly to ATP,
particularly in protein synthesis and signal transduction.
o Creatine Phosphate: Acts as a rapid energy reservoir in muscle tissues
by donating phosphate to ADP to regenerate ATP during intense
activity.

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