Introduction to Biochemistry

• Biochemistry is the study of the chemical substances and vital processes occurring in living organisms.
• It focuses on the structure, function, and interactions of biological macromolecules, such as proteins, nucleic acids, carbohydrates, and lipids.
• Biochemistry aims to explain biological processes at a molecular level using chemical principles.

Key Areas of Biochemistry

• Structure and function of biomolecules (proteins, nucleic acids, carbohydrates, and lipids).
• Enzymes: Their catalytic mechanisms, regulation, and kinetics.
• Metabolic pathways: Catabolism (breakdown) and anabolism (synthesis) of biomolecules.
• Bioenergetics: The study of energy flow in living systems.
• Molecular genetics: The structure, function, and replication of DNA, RNA, and the genetic code.
• Protein synthesis: Transcription, translation, and post-translational modifications of proteins.
• Membrane structure and function: Transport mechanisms and cell signaling.
• Signal transduction: How cells receive and respond to external signals.
• Hormones and other regulatory molecules: Their synthesis, function, and mechanisms of action.

Biomolecules

Proteins

• Polymers of amino acids linked by peptide bonds.
• Amino acids have a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a distinctive side chain (R-group).
• Proteins have four levels of structure: primary (amino acid sequence), secondary (local folding patterns like alpha-helices and beta-sheets), tertiary (three-dimensional structure), and quaternary (arrangement of multiple polypeptide chains).
• Proteins perform diverse functions, including enzymes, structural components, transport, immune defense, and regulation.

Nucleic Acids

• Polymers of nucleotides; two main types are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
• Nucleotides consist of a nitrogenous base (adenine, guanine, cytosine, thymine in DNA; uracil in RNA), a pentose sugar (deoxyribose in DNA; ribose in RNA), and one or more phosphate groups.
• DNA stores genetic information and RNA is involved in gene expression.
• DNA has a double helix structure with complementary base pairing (A with T, G with C).
• RNA is typically single-stranded and can fold into complex structures.

Carbohydrates

• Composed of carbon, hydrogen, and oxygen, typically in the ratio 1:2:1.
• Monosaccharides (e.g., glucose, fructose) are simple sugars.
• Disaccharides (e.g., sucrose, lactose) consist of two monosaccharides joined by a glycosidic bond.
• Polysaccharides (e.g., starch, cellulose, glycogen) are long chains of monosaccharides.
• Carbohydrates serve as energy sources and structural components.

Lipids

• Diverse group of hydrophobic molecules, including fats, oils, phospholipids, and steroids.
• Fats and oils (triglycerides) are composed of glycerol and three fatty acids.
• Fatty acids can be saturated (no double bonds) or unsaturated (one or more double bonds).
• Phospholipids are major components of cell membranes, containing a polar head group and two hydrophobic fatty acid tails.
• Steroids (e.g., cholesterol) have a characteristic four-ring structure and serve as hormones or membrane components.

Enzymes

• Biological catalysts that accelerate chemical reactions by lowering the activation energy.
• Highly specific for their substrates.
• Active site is the region of an enzyme where the substrate binds and catalysis occurs.
• Classified into six major classes based on the type of reaction they catalyze: oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases.
• Enzyme activity can be affected by factors such as temperature, pH, and the presence of inhibitors or activators.
• Cofactors (inorganic ions or coenzymes) may be required for enzyme activity.
• Enzyme kinetics: Michaelis-Menten kinetics describes the relationship between substrate concentration and reaction rate.

Metabolic Pathways

• Series of interconnected biochemical reactions that convert specific substrates into specific products.
• Catabolic pathways break down complex molecules to release energy and smaller molecules.
• Anabolic pathways use energy to synthesize complex molecules from simpler precursors.
• Metabolic pathways are regulated by enzymes, hormones, and other signaling molecules.
• Examples of key metabolic pathways: glycolysis, gluconeogenesis, citric acid cycle (Krebs cycle), oxidative phosphorylation, fatty acid metabolism, and amino acid metabolism.

Glycolysis

• Breakdown of glucose into pyruvate, producing ATP and NADH.
• Occurs in the cytoplasm.
• Consists of ten enzymatic steps.
• Can proceed under aerobic or anaerobic conditions.
• Under anaerobic conditions, pyruvate is converted to lactate (in animals) or ethanol (in yeast).

Gluconeogenesis

• Synthesis of glucose from non-carbohydrate precursors, such as pyruvate, lactate, and glycerol.
• Occurs mainly in the liver and kidneys.
• Important for maintaining blood glucose levels during fasting or starvation.

Citric Acid Cycle

• Also known as the Krebs cycle or tricarboxylic acid (TCA) cycle.
• Oxidizes acetyl-CoA to carbon dioxide, generating ATP, NADH, and FADH2.
• Occurs in the mitochondrial matrix.
• Central pathway in energy metabolism, linking glycolysis, fatty acid metabolism, and amino acid metabolism.

Oxidative Phosphorylation

• Process by which ATP is synthesized using the energy released from the electron transport chain.
• Occurs in the inner mitochondrial membrane.
• Electrons are transferred from NADH and FADH2 to oxygen, generating a proton gradient across the membrane.
• ATP synthase uses the proton gradient to drive the synthesis of ATP.

Fatty Acid Metabolism

• Breakdown and synthesis of fatty acids.
• Beta-oxidation is the process by which fatty acids are broken down into acetyl-CoA, NADH, and FADH2.
• Fatty acid synthesis occurs in the cytoplasm and involves the sequential addition of two-carbon units to a growing fatty acid chain.

Bioenergetics

• Study of energy transformations in living organisms.
• Gibbs free energy (G) is a measure of the energy available to do work.
• Reactions with a negative ΔG are spontaneous (exergonic), while reactions with a positive ΔG require energy input (endergonic).
• ATP (adenosine triphosphate) is the primary energy currency of the cell.
• Hydrolysis of ATP releases energy that can be used to drive endergonic reactions.

Molecular Genetics

• Study of the structure, function, and inheritance of genes.
• DNA replication is the process by which DNA is duplicated.
• Transcription is the process by which RNA is synthesized from a DNA template.
• Translation is the process by which proteins are synthesized from an RNA template.
• The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells.

Protein Synthesis

• Transcription involves RNA polymerase synthesizing mRNA from a DNA template.
• mRNA carries the genetic code from the nucleus to the ribosomes in the cytoplasm.
• Translation occurs on ribosomes, where tRNA molecules bring amino acids to the mRNA template based on the codon sequence.
• Post-translational modifications include phosphorylation, glycosylation, and ubiquitination.

Membrane Structure and Function

• Cell membranes are composed of a lipid bilayer with embedded proteins.
• The lipid bilayer is selectively permeable, allowing small, nonpolar molecules to pass through easily.
• Transport proteins facilitate the movement of larger or charged molecules across the membrane.
• Passive transport: Movement of molecules across the membrane down their concentration gradient (no energy required).
• Active transport: Movement of molecules across the membrane against their concentration gradient (requires energy).

Signal Transduction

• Process by which cells receive and respond to external signals.
• Signaling molecules (ligands) bind to receptor proteins on the cell surface or inside the cell.
• Receptor activation triggers a cascade of intracellular events, such as protein phosphorylation and the generation of second messengers (e.g., cAMP, calcium).
• Signal transduction pathways regulate a wide range of cellular processes, including gene expression, metabolism, and cell growth.

Hormones and Other Regulatory Molecules

• Hormones are signaling molecules produced by endocrine glands and transported through the bloodstream to target cells.
• Hormones can be peptides, steroids, or amino acid derivatives.
• Each hormone binds to a specific receptor in target cells, triggering a cellular response.
• Other regulatory molecules include growth factors, cytokines, and neurotransmitters.