Biochemistry: An Introduction

• Biochemistry is a branch of science exploring the chemical processes within and relating to living organisms.
• It combines biology and chemistry to investigate the composition, reactions, and molecular interactions in biological systems.
• Biochemistry seeks to explain biological processes at the molecular level.

Core Concepts

• Biomolecules: The major classes include carbohydrates, lipids, proteins, and nucleic acids.
• Metabolism: Encompasses all chemical reactions that occur in an organism, including catabolism (breakdown) and anabolism (synthesis).
• Enzymes: Biological catalysts that accelerate chemical reactions in living organisms.
• Bioenergetics: The study of energy flow through living systems.
• Genetics: The study of heredity and the variation of inherited characteristics.

Biomolecules: Carbohydrates

• Carbohydrates are organic compounds containing carbon, hydrogen, and oxygen, generally in a 1:2:1 ratio.
• They serve as a primary source of energy for living organisms.
• Monosaccharides: Simple sugars such as glucose, fructose, and galactose.
• Disaccharides: Formed by the joining of two monosaccharides, e.g., sucrose (glucose + fructose) and lactose (glucose + galactose).
• Polysaccharides: Complex carbohydrates consisting of many monosaccharide units, e.g., starch, glycogen, and cellulose.
• Starch is a storage form of glucose in plants.
• Glycogen is a storage form of glucose in animals.
• Cellulose provides structural support in plant cell walls.

Biomolecules: Lipids

• Lipids are hydrophobic or amphipathic molecules, including fats, oils, phospholipids, and steroids.
• They are essential for energy storage, cell membrane structure, and hormone signaling.
• Triglycerides: Composed of a glycerol molecule esterified with three fatty acids.
• Saturated fatty acids: Contain no carbon-carbon double bonds and are typically solid at room temperature.
• Unsaturated fatty acids: Contain one or more carbon-carbon double bonds and are typically liquid at room temperature.
• Phospholipids: Major components of cell membranes, composed of a glycerol backbone, two fatty acids, and a phosphate group.
• Steroids: Characterized by a four-ring structure, e.g., cholesterol, testosterone, and estrogen.

Biomolecules: Proteins

• Proteins are complex macromolecules composed of amino acids linked by peptide bonds.
• They perform a wide variety of functions, including catalysis, transport, structural support, and immune defense.
• Amino acids: The building blocks of proteins, each containing an amino group, a carboxyl group, and a side chain (R group).
• Primary structure: The linear sequence of amino acids in a protein.
• Secondary structure: Local folding patterns, such as alpha-helices and beta-sheets, stabilized by hydrogen bonds.
• Tertiary structure: The overall three-dimensional structure of a protein, stabilized by various interactions (e.g., hydrophobic interactions, disulfide bonds).
• Quaternary structure: The arrangement of multiple polypeptide chains in a multi-subunit protein.
• Enzymes are proteins that catalyze biochemical reactions by lowering the activation energy.
• Antibodies are proteins that recognize and bind to specific antigens, providing immunity.

Biomolecules: Nucleic Acids

• Nucleic acids are polymers of nucleotides involved in storing and transmitting genetic information.
• DNA (deoxyribonucleic acid): Contains the genetic instructions for the development and function of living organisms.
• RNA (ribonucleic acid): Involved in various cellular processes, including protein synthesis and gene regulation.
• Nucleotides: Composed of a nitrogenous base, a pentose sugar (deoxyribose in DNA, ribose in RNA), and one or more phosphate groups.
• Nitrogenous bases: Adenine (A), guanine (G), cytosine (C), thymine (T) in DNA; uracil (U) replaces thymine in RNA.
• DNA structure: A double helix consisting of two strands held together by hydrogen bonds between complementary base pairs (A-T, G-C).
• RNA structure: Usually single-stranded, but can form complex secondary and tertiary structures.

Metabolism

• Metabolism is the sum of all chemical reactions occurring in an organism.
• Catabolism: The breakdown of complex molecules into simpler ones, releasing energy (e.g., cellular respiration).
• Anabolism: The synthesis of complex molecules from simpler ones, requiring energy (e.g., photosynthesis).
• Metabolic pathways: Sequences of enzyme-catalyzed reactions that convert specific reactants into specific products.
• Glycolysis: The breakdown of glucose into pyruvate, producing ATP and NADH.
• Citric acid cycle (Krebs cycle): A series of reactions that oxidize acetyl-CoA, producing ATP, NADH, and FADH2.
• Oxidative phosphorylation: The process by which ATP is synthesized using the energy from the electron transport chain.
• Photosynthesis: The process by which plants convert light energy into chemical energy in the form of glucose.
• Gluconeogenesis: The synthesis of glucose from non-carbohydrate precursors.

Enzymes

• Enzymes are biological catalysts that accelerate chemical reactions by lowering the activation energy.
• Active site: The region of an enzyme where the substrate binds and the reaction occurs.
• Substrate: The molecule upon which an enzyme acts.
• Cofactors: Non-protein molecules or ions that are required for enzyme activity (e.g., metal ions, coenzymes).
• Coenzymes: Organic cofactors (e.g., vitamins).
• Enzyme specificity: Enzymes are highly specific for their substrates.
• Enzyme kinetics: The study of the rates of enzyme-catalyzed reactions.
• Michaelis-Menten kinetics: A model describing the relationship between enzyme activity and substrate concentration.
• Enzyme inhibition: Molecules that reduce enzyme activity (e.g., competitive inhibitors, non-competitive inhibitors).
• Allosteric regulation: The regulation of enzyme activity by the binding of molecules to sites other than the active site.

Bioenergetics

• Bioenergetics is the study of energy flow through living systems.
• Thermodynamics: The study of energy and its transformations.
• First law of thermodynamics: Energy cannot be created or destroyed, only converted from one form to another.
• Second law of thermodynamics: The entropy (disorder) of an isolated system always increases.
• Gibbs free energy (G): A measure of the energy available to do work in a chemical or physical system.
• Exergonic reactions: Reactions that release energy (negative ΔG).
• Endergonic reactions: Reactions that require energy (positive ΔG).
• ATP (adenosine triphosphate): The primary energy currency of the cell.
• ATP hydrolysis: The breakdown of ATP into ADP and inorganic phosphate, releasing energy.
• Coupled reactions: The use of energy from an exergonic reaction to drive an endergonic reaction.

Genetics

• Genetics is the study of heredity and the variation of inherited characteristics.
• Genes: Units of heredity that contain the instructions for making proteins.
• Genome: The complete set of genetic information in an organism.
• DNA replication: The process by which DNA is copied.
• Transcription: The process by which RNA is synthesized from a DNA template.
• Translation: The process by which proteins are synthesized from RNA.
• Central dogma of molecular biology: DNA -> RNA -> Protein.
• Mutations: Changes in the DNA sequence that can lead to altered protein function.
• Gene regulation: The control of gene expression, determining when and where genes are transcribed and translated.
• Recombinant DNA technology: Techniques for manipulating and combining DNA from different sources.
• Polymerase chain reaction (PCR): A technique for amplifying specific DNA sequences.
• DNA sequencing: Determining the nucleotide sequence of a DNA molecule.