MODULE 2

BIOCHEMISTRY

Definition of Biochemistry

  • Biochemistry: Deals with the structures and functions of biomolecules/macromolecules, including:

    • Proteins

    • Nucleic acids

    • Carbohydrates

    • Lipids

The Cell

Basic Units of the Cell

  • Mitochondria: Powerhouse of the cell responsible for ATP synthesis through oxidative phosphorylation (ETC).

  • Nucleus: Control center of the cell containing genetic material.

  • Vesicles/ Vacuoles: Storage sites within the cell.

  • Smooth Endoplasmic Reticulum: Fatty acid synthesis.

  • Rough Endoplasmic Reticulum: Protein synthesis with ribosomes.

  • Ribosomes: Complexes of ribosomal RNA and proteins facilitating protein synthesis.

  • Chloroplasts (in plants): Site of photosynthesis.

  • Golgi Apparatus: Modifies, sorts, and packages proteins and lipids for secretion or delivery to other organelles.

  • Cell Wall (in plant cells): Provides structural support and protection.

  • Cell Membrane: Barrier and protective layer surrounding the cell.

  • Cytoplasm/Cytosol: Liquid portion of the cell where cellular processes occur.

  • Lysosomes: Known as suicide sacs, involved in the breakdown of waste materials.

Types of Cells

  • Prokaryotes: Non-membrane-bound organelles (e.g., bacteria).

  • Eukaryotes: Membrane-bound organelles, including a true nucleus (e.g., plants, animals).

Cell Division Processes

  • Mitosis: Division of somatic/body cells.

  • Meiosis: Division of sex cells/gametes (diploids to haploids).

Chromosome Information

  • Humans: Have 46 chromosomes (23 pairs); 22 pairs of somatic chromosomes and one pair of sex chromosomes (XX for females, XY for males).

  • Aneuploidy: Any abnormality in the number of chromosomes (e.g., Trisomy 21, Down syndrome).

Types of Chromosomal Abnormalities

  • Fluid Mosaic Model: Explanation of the cell membrane structure with lipid bilayer and associated proteins.

    • Integral Proteins: Embedded in the membrane, function as ion channels.

    • Peripheral Proteins: Located on the surface of the membrane, often serving as receptors.

Chromosome Number Disorders

  • Aneuploidy Examples:

    • Trisomy 21 (Down syndrome): Three copies of chromosome 21 (47 total).

    • Klinefelter's Syndrome (XXY): Male with extra X chromosome, may show female traits.

    • Turner Syndrome (X0): Female with one X chromosome missing, causing sterility.

PROTEINS

Classification of Proteins

  • Polymers of Amino Acids: Linked by peptide bonds, varying in function and structure.

Dynamic Functions of Proteins

  1. Storage:

    • Ferritin: Iron storage.

    • Myoglobin: Oxygen carrier in muscles.

    • Hemoglobin: Oxygen carrier in blood.

  2. Transport:

    • Transferrin: Transports iron.

    • Albumins: Plasma proteins involved in transportation and osmotic balance.

  3. Functional Categories:

    • Globular Proteins: Water-soluble, involved in metabolic processes.

    • Fibrous Proteins: Insoluble, providing structural support (e.g., collagen, keratin).

    • Conjugated Proteins: Proteins complexed with other macromolecules, including:

      • Glycoproteins (carbohydrates).

      • Nucleoproteins (nucleic acids).

  4. Biological Functions:

    • Enzymes: Catalysts in metabolic reactions.

    • Hormones: Signaling molecules.

Protein Structure Levels

  1. Primary Structure: Linear sequence of amino acids.

  2. Secondary Structure:

    • Alpha helices: Coiled structure stabilized by hydrogen bonds.

    • Beta sheets: Sheets formed by hydrogen bonding between amino acids.

  3. Tertiary Structure: 3D conformation.

  4. Quaternary Structure: Complex of multiple polypeptide chains.

Denaturation and Hydrolysis

  • Denaturation: Destruction of 3D structure due to factors like temperature, pH, and organic solvents.

  • Hydrolysis: Breakdown of the peptide bond leading to loss of protein function.

AMINO ACIDS

Classification of Amino Acids

  • Non-polar Amino Acids: Hydrophobic R groups.

  • Polar Amino Acids: Hydrophilic R groups.

  • Charged Amino Acids: Acidic or basic R groups.

Properties of Amino Acids

  • Amphoteric: Amino acids can act as acids or bases.

  • Zwitterions: Neutral molecules with both positive and negative charges.

  • Optical Activity: All amino acids (except glycine) are chiral.

Test for Amino Acids

  • Various tests to diagnose protein misfolding diseases (e.g., Alzheimer's, Prion diseases).

Enzymes

Classification of Enzymes

  • Oxidoreductases: Catalyze oxidation-reduction reactions.

  • Transferases: Transfer functional groups between molecules.

  • Hydrolases: Catalyze hydrolysis reactions (e.g., proteases).

  • Lyases: Break bonds by means other than hydrolysis or oxidation.

  • Isomerases: Catalyze geometric or structural changes within a molecule.

  • Ligases: Join two molecules together with the help of ATP or another energy source.

Enzyme Kinetics

  • Michaelis-Menten Equation: Used to describe the rate of enzyme-catalyzed reactions.

  • Factors Affecting Enzyme Activity:

    • Temperature

    • pH

    • Enzyme concentration

  • Types of Inhibition:

    • Competitive: Inhibitor competes with substrate for active site.

    • Non-competitive: Inhibitor binds to an alternative site affecting activity.

    • Uncompetitive: Inhibitor binds only to the enzyme-substrate complex.

Diagnostic Enzymes

  • Enzymes used in clinical diagnostics (e.g., Lactate Dehydrogenase, Alanine Aminotransferase).

VITAMINS

General Information

  • Vitamins: Organic compounds required in small quantities for normal metabolism, not synthesised in the body.

Classification

  • Fat-Soluble Vitamins: A, D, E, K

    • Essential for membrane transport and various metabolic functions.

  • Water-Soluble Vitamins: B-complex, C

    • Involve direct metabolic pathways or coenzymes.

Nucleic Acids

Structure

  • Nucleic Acids: Polymers of nucleotides held together by phosphodiester bonds.

  • DNA: Double-helix structure composed of deoxyribonucleotides. Serves as a genetic blueprint.

  • RNA: Single-stranded, functions in protein synthesis as mRNA, tRNA, and rRNA.

Genetic Information Flow

  • Central Dogma: DNA → RNA → Protein.

  • Transcription: DNA is transcribed into mRNA.

  • Translation: mRNA is translated into protein (amino acid chain).

Left-handed and Right-handed DNA Forms

  • Distinction between B-DNA (right-handed) and Z-DNA (left-handed).

CARBOHYDRATES

Definition

  • Carbohydrates: Polyhydroxy aldehydes or ketones; primary energy source for organisms.

Classification

  1. Monosaccharides: Single sugar molecules (e.g., glucose, fructose).

  2. Disaccharides: Two monosaccharides joined (e.g., sucrose, lactose).

  3. Polysaccharides: Long chains of monosaccharides (e.g., glycogen, cellulose).

Functions

  • Energy storage: Glycogen in animals, starch in plants.

  • Structural components: Cellulose in plant cell walls, chitin in exoskeletons.

  • Cell recognition and signaling: Glycoproteins and glycolipids on cell surfaces.

LIPIDS

Definition

  • Lipids: Insoluble in water, soluble in nonpolar solvents; includes fats, oils, waxes, and phospholipids.

Classification

  • Simple Lipids: Fats/oils composed of glycerol and fatty acids.

  • Complex Lipids: Contain additional elements such as phosphate or nitrogen (e.g., phospholipids).

Functions

  • Energy storage: Triglycerides store energy.

  • Structural components: Phospholipids form cellular membranes.

  • Signaling molecules: Steroid hormones derived from cholesterol.