Bio Chemistry

- Pooja Uday Parulekar

Bio molecules
• Body is made up of Biomolecules
• Types of Biomolecules:
• Proteins, Lipids, Nucleic Acid and Carbohydrates
• These are compiling units of Polymers
• Made out of Monomers
• Amino acids are present in monomers
Amino Acids
• There are 20 standard amino acids, which are the building blocks of
proteins.
• Each amino acid has a central carbon (α-carbon)
• attached to an amino group (-NH₂)
• a carboxyl group (-COOH)
• a hydrogen atom
• a variable side chain (R-group)
• Are classified into Polar, Non polar,
Acidic and Basic
• GAVLIMP PT says that cats take all
Good land after hope.
Essential and non Essential Amino acids
Peptide Bond
• Peptide Greek word for Digest
• Amino acids are linked together by peptide bonds
• which form through a condensation reaction between the amino
group of one amino acid and the carboxyl group of another.
• This bond is a type of covalent bond and the resulting chain of amino
acids is called a polypeptide.
• Peptide bonds can be broken down with 2 methods
• 1. Heat + Acid Hydrolysis (non-specific)
• 2. Proteolysis (specific Proteases) eg: tripsin: Arg and Lys
Protein Structures
• Protein synthesis in
Ribosomes
• Modification of proteins in
necessary for proteins to
be functional
• Shape and Function:
• A. Cell signalling: Protein
receptors signal molecules
to bind together to signal a
response.
• B. Enzyme and Substrate
• Gene determines the
number and order of
Amino acids
Primary structure
• Definition: The linear sequence of amino acids in a polypeptide chain
• Importance: Determines the protein’s ultimate shape and function
• as the sequence of amino acids
• dictates how the protein will fold and interact with other molecules
Secondary structure
• Definition: The local folding of the
polypeptide chain into specific
structures such as α-helices and β-
sheets
• Stabilization: Maintained by
hydrogen bonds between the
backbone atoms in the
polypeptide chain
• α-Helix: A right-handed coil where
each amino acid forms a hydrogen
bond with the amino acid four
residues ahead
• β-Sheet: Strands of the
polypeptide chain run alongside
each other, forming hydrogen
bonds between the backbone
atoms in different strands. These
can be parallel or antiparallel.
 Tertiary structure
• Definition: The overall three-dimensional
structure of a single polypeptide chain.
• Stabilization: Stabilized by interactions
between the side chains (R-groups) of the
amino acids, including:
• Hydrophobic Interactions: Nonpolar side
chains tend to cluster together inside the
protein, away from water
• Hydrophilic Bonds: Form between polar
side chains or between side chains and
backbone atoms
• Ionic Bonds: Occur between positively
and negatively charged side chains
• Disulfide Bridges: Covalent bonds
between the sulfur atoms of two cysteine
residues, providing additional stability
Quaternary Structure
• Definition: The structure formed
by the assembly of multiple
polypeptide chains (subunits) into
a functional protein.
• Stabilization: Similar interactions
as in the tertiary structure
(hydrophobic, ionic, hydrogen
bonds and disulfide bridges)
occur between subunits
• Examples: Hemoglobin is a classic
example, composed of four
polypeptide subunits, two α and
two β chains
Basic concepts of Metabolism
• Every single bio chemical reaction going on in the body is known as
metabolism
• 64% water
• 16% protein
• 16% fat
• 4% minerals
• 1% carbohydrates
Catabolism Anabolism
• Definition: The metabolic process • Definition: The metabolic process
that breaks down complex that builds complex molecules
molecules into simpler ones, from simpler ones, requiring an
releasing energy in the process. input of energy
• Example: Glycolysis, where glucose • Example: Protein synthesis, where
is broken down into pyruvate, amino acids are assembled into
releasing energy stored in the form proteins, consuming ATP in the
of ATP (adenosine triphosphate) process
and NADH. • Role in the Body: Supports growth,
• Role in the Body: Provides the repair, and maintenance of cells
energy needed for various cellular and tissues by synthesizing
processes and generates the essential macromolecules.
building blocks for other
molecules.
Energetics
• Definition: The study of energy flow and transformation within biological
systems, focusing on how energy is produced, stored, and utilized in
metabolic processes.
• Key Concepts:
• ATP Production: ATP is the primary energy currency in cells, generated
during catabolic processes like cellular respiration and used in anabolic
processes.
• Energy Coupling: The process by which energy from catabolic reactions is
used to drive anabolic reactions, typically through the hydrolysis of ATP
• Thermodynamics in Metabolism: Understanding how the laws of
thermodynamics apply to biochemical reactions, including the concepts of
free energy, enthalpy, and entropy, to predict whether a reaction is
spontaneous or requires energy input.
 Enzymes: classification
• Most of enzymes are proteins
• Enzymes lower the activation energy of a reaction, allowing
it to proceed faster.
• They have a active site for the substrate to bind, Causing
induced fit
• Thus forming an enzyme-substrate complex and then
catalyze the conversion of substrates into products
• Enzymes can build or break down a substrate resulting on in
product
• Enzymes speed up any chemical reaction
• Generally end with ase and sugars end with ose (
disaccharide)
• Eg: glucose and galatose/ Lactose
• Lipase( lipids), Amylayse (carbs) and Protease( pepsin &
tripsin), Nuclease (Nucleic acid)
• Enzymes when exposed to unfavourable conditions tend to
get denatured
• Classification: Enzymes are classified into six major classes
based on the reactions they catalyse: Oxidoreductases,
Transferases, Hydrolases, Lyases, Isomerases and Ligases
Enzyme regulation
• Enzyme activity can be regulated by allosteric modulators, covalent
modification, feedback inhibition and changes in enzyme synthesis.
Enzyme-inhibition
• Enzyme activity can be regulated by inhibitors.
• Competitive inhibitors bind to the active site, while non-competitive
inhibitors bind to another part of the enzyme, altering its function.
Cofactors Coenzymes

• Typically metal ions • Typically Organic Molecules

• Eg: Iron • Eg: Vitamins
• Inorganice • Organic
• Non-protein molecules that • Non-protein molecules that
assist enzymes assist enzymes
Vitamins: Types deficiencies.
• Vitamins are organic compounds essential for normal growth,
metabolism and overall health.
• They cannot be synthesized in sufficient quantities by the human
body (with a few exceptions) so they must be obtained from the diet.
• Vitamins are categorized based on their solubility either water-soluble
or fat-soluble, which affects how they are absorbed, stored and
eliminated by the body.
Metabolic strategies
• Rate-Limiting Step: The slowest step in a metabolic pathway, often
subject to regulation to control the pathway's overall rate.
• Modulators: Molecules that influence enzyme activity, including
activators and inhibitors that can increase or decrease the rate of
enzyme-catalyzed reactions
 Rate limiting step
A rate-limiting step is the slowest, or most tightly regulated, step in a biochemical pathway that determines the overall rate at which
the pathway proceeds. It acts as a bottleneck, controlling the speed of the entire process. Because this step is slow or limited in its
activity compared to other steps in the pathway, it essentially sets the pace for how fast the final product of the pathway can be
synthesized.
Characteristics of Rate-Limiting Steps:
1. Highly Regulated: The rate-limiting step is often under tight regulatory control through feedback inhibition, hormonal signals, or
allosteric regulation.
2. Low Activity: The enzyme catalyzing the rate-limiting step usually works more slowly than other enzymes in the pathway.
3. Irreversible: These steps are often irreversible under physiological conditions, meaning the reaction cannot easily go backward.
4. Target for Control: Modulating the rate-limiting enzyme (through hormones, cofactors, or drugs) is an effective way to control the
overall pathway.
Examples of Rate-Limiting Steps:
1. Glycolysis: The rate-limiting step is catalyzed by the enzyme phosphofructokinase-1 (PFK-1). It converts fructose-6-phosphate
to fructose-1,6-bisphosphate and is regulated by ATP levels (high ATP inhibits the enzyme, slowing down glycolysis).
2. 2. Cholesterol Synthesis: The enzyme HMG-CoA reductase catalyzes the rate-limiting step in the synthesis of cholesterol. It is a
target for statin drugs, which inhibit the enzyme to lower cholesterol levels.
3. 3. Fatty Acid Synthesis: The rate-limiting step is catalyzed by acetyl-CoA carboxylase, which converts acetyl-CoA into malonyl-
CoA. This step is tightly regulated by hormonal signals like insulin.
4. 4. Citric Acid Cycle (Krebs Cycle): The conversion of isocitrate to alpha-ketoglutarate by isocitrate dehydrogenase is a rate-
limiting step in the cycle
Modulators.
• Modulators are molecules that influence the activity of enzymes, particularly those involved in rate-limiting steps
of metabolic pathways.
• By interacting with these enzymes, modulators can either increase or decrease the enzyme’s activity, effectively
controlling the speed of the metabolic process.
• Modulation is a critical mechanism in the regulation of metabolic pathways, ensuring that the right amount of
product is made in response to the body’s needs.
• Types of Modulators:
1. Allosteric Modulators: These molecules bind to a site on the enzyme that is different from the active site (called
an allosteric site). Allosteric modulators can either enhance (activators) or inhibit (inhibitors) enzyme activity.
2. Cofactors and Coenzymes
3. Hormonal Modulators: Hormones can regulate enzyme activity by triggering signaling cascades that either
activate or inhibit key enzymes in metabolic pathways.
4. Substrate Availability: The availability of the substrate for the enzyme can act as a modulator. When substrate
levels are low, enzyme activity decreases and when substrate levels are high the enzyme can work faster (up to
a point).
5. Feedback Inhibition: In many pathways, the final product acts as a modulator by inhibiting an enzyme early in
the pathway, preventing the overproduction of that product. This is a common form of negative feedback
regulation
6. Post-Translational Modifications: Enzyme activity can be modulated by the addition or removal of chemical
groups such as phosphate, acetyl, or methyl groups.