Amino Acids and Protein Structure

Amino Acids

• Amino acids are monomers that make up proteins.
• There are 20 different amino acids used by cells.
• Each amino acid has a common structure with a central α-carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R group).
• Side chains exhibit different properties like polarity, charge, and size.
• Non-polar side chains are hydrophobic.
• Polar side chains are hydrophilic.
• Charged side chains, known as acidic and basic, are also hydrophilic.

Proteins

• Proteins are polymers of amino acids called polypeptides.
• The sequence of amino acids determines the unique three-dimensional shape of a protein.
• Proteins have various levels of structure: primary, secondary, tertiary, and quaternary.
• Primary structure is the linear sequence of amino acids.
• Secondary structures include alpha-helices and beta-sheets, stabilized by hydrogen bonds.
• Tertiary structure is the overall three-dimensional folding of the polypeptide chain.
• Quaternary structure describes the arrangement of multiple polypeptide chains in a protein.
• Proteins have diverse functions, including support, storage, transport, cellular communication, movement, and defense against disease.

Enzymes

• Enzymes are biological catalysts that speed up chemical reactions in cells.
• They bind specific substrates at their active sites.
• Enzymes lower the activation energy required for a reaction to occur.
• Enzymes are not consumed or permanently changed by the reactions they catalyze.
• Enzyme activity can be affected by factors like temperature, pH, and substrate concentration.
• Enzymes are crucial for a wide variety of metabolic processes to occur in a timely manner.

Carbohydrates

• Carbohydrates are essential biomolecules for energy storage and structural support.
• Monosaccharides are the simplest form of carbohydrates, with the formula Cx(H₂O)x.
• Examples include glucose, fructose, and ribose.
• Monosaccharides often exist in cyclic forms (like pyranose or furanose), with variations in the position of hydroxyl groups (α or β isomers).
• Disaccharides are formed by the condensation of two monosaccharides.
• Examples include sucrose, lactose, and maltose.
• Polysaccharides are long chains of monosaccharides.
• Examples include starch, glycogen, and cellulose.

Glycolysis

• Glycolysis is a metabolic pathway breaking down glucose into pyruvate.
• It takes place in the cytoplasm.
• It produces 2 ATP molecules per glucose molecule through substrate-level phosphorylation.
• It yields 2 NADH molecules, which can be used for energy production.

TCA Cycle

• Tricarboxylic acid (TCA) cycle, also known as the citric acid cycle, is a central metabolic pathway for energy production in aerobic organisms.
• It takes place in the mitochondrial matrix.
• It is a cyclic process that oxidizes acetyl-CoA to CO2.
• It produces reduced electron carriers (NADH and FADH2), which are crucial for ATP production in oxidative phosphorylation.
• It also generates some GTP or ATP directly.
• It generates intermediates used in biosynthesis.

Oxidative Phosphorylation

• Oxidative phosphorylation is the process using the energy stored in NADH and FADH2 to produce ATP.
• It takes place in the inner mitochondrial membrane.
• The electron transport chain (ETC) moves electrons to oxygen.
• The energy released pumps protons to create a gradient, driving ATP synthesis by ATP synthase.
• This process significantly increases ATP production compared to glycolysis.

Glycogen Metabolism

• Glycogen is the storage form of glucose in animals.
• Glycogenesis is the synthesis of glycogen from glucose.
• Glycogenolysis is the breakdown of glycogen to glucose when needed.
• These processes involve enzymes like glycogen synthase and glycogen phosphorylase.
• Glycogen is stored primarily in the liver and muscles.

Gluconeogenesis

• Gluconeogenesis is the synthesis of glucose from non-carbohydrate sources (like lactate or amino acids).
• It bypasses the irreversible steps of glycolysis, requiring different enzymes.
• Gluconeogenesis is essential for maintaining blood glucose levels between meals or during periods of fasting.

Lipid Metabolism

• Lipids comprise fatty acids, triacylglycerols, phospholipids, and steroids.
• Fatty acids are long hydrocarbon chains with a carboxyl group.
• Saturated fatty acids have no double bonds, whereas unsaturated fatty acids have one or more double bonds.
• Triacylglycerols are the primary storage form of lipids.