FPT Biochemistry Study Notes

Biochemistry Study Notes

Water and Its Importance

• Life and Water: Life cannot exist without water.

• Unique Properties of Water:

  1. Universal Solvent: Water dissolves more substances than any other liquid.

  2. High Heat Capacity: This property ensures temperature moderation and homeostasis in organisms.

  3. Cohesion and Adhesion:

  • Adhesion: Water's attraction to polar or charged surfaces, demonstrated by the behavior of water in capillary action.

  • Cohesion: Water molecules stick to each other, contributing to surface tension.

  1. Density Variation: Water is less dense as a solid (ice) than as a liquid, allowing ice to float and insulate bodies of water.

Biological Molecules

• Atoms Found in Biological Molecules:

  • Hydrogen (H): Atomic Number 1, 1 electron in outer shell, forms 1 bond.

  • Oxygen (O): Atomic Number 8, 6 electrons in outer shell, forms 2 bonds.

  • Carbon (C): Atomic Number 6, 4 electrons in outer shell, forms 4 bonds.

  • Nitrogen (N): Atomic Number 7, 5 electrons in outer shell, forms 3 bonds.

Organic vs. Inorganic Molecules

• Organic Molecules:

  • Contains Carbon, Hydrogen, Oxygen, Nitrogen.

  • Large and complex structures (rings and long chains).

• Inorganic Molecules:

  • Omit carbon atoms.

  • Generally small and simple structures.

Functional Groups and Their Roles

• Functional Groups: Reactive sites that impart specific physical and chemical properties to molecules.

  • Examples:

  • Hydroxyl (–OH): Found in alcohols and sugars.

  • Carboxyl (–COOH): Found in fatty acids.

  • Amino (–NH2): Characteristic of amino acids.

  • Phosphate (–PO4): Found in DNA and ATP.

Macromolecules

• Definitions:

  • Monomer: Small building blocks (e.g., amino acids, nucleotides).

  • Polymer: Large molecules made up of repeating monomers (e.g., proteins, nucleic acids).

  • Macromolecule: Large complex molecules formed from monomers.

Reactions

• Dehydration Synthesis: A reaction that joins monomers by removing a water molecule, forming new bonds. An example can be seen in the formation of a polymer from monomers.

• Hydrolysis: A reaction that breaks down polymers into monomers by adding a water molecule, breaking bonds.

Carbohydrates

• Functions:

  • Serve as energy sources (e.g., glucose).

  • Structural components (e.g., cellulose).

  • Involved in cell identification and communication.

• Food Sources: Bread, pasta, fruit, vegetables.

• Monosaccharides: Simple sugars (e.g., glucose, fructose).

• Disaccharides: Two monosaccharides joined by dehydration synthesis (e.g., maltose, sucrose, lactose).

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

Energy Storage in Carbohydrates

• Starch (in plants): Energy stored as granules.

• Glycogen (in animals): Energy storage in liver and muscle tissues.

• Cellulose: A structural component of plant cell walls, and is not digestible in the human digestive system.

Lipids

• Functions:

  • Long-term energy storage (e.g., triglycerides).

  • Form cell membranes (phospholipids).

  • Produce hormones (steroids).

  • Create waterproof coatings (waxes).

• Structure: Composed of glycerol and fatty acids; saturated and unsaturated types differ by the presence of double bonds.

• Phospholipids are crucial for cell membrane structure, having hydrophilic heads and hydrophobic tails, allowing for bilayer formation in aqueous environments.

Proteins

• Functions:

  • Structural roles in cells.

  • Enzymatic activity (catalysts for biochemical reactions).

  • Regulatory roles (hormones).

  • Defense (e.g., antibodies).

• Monomer: Amino acid (20 different kinds involved in protein synthesis).

• Protein Structure Levels:

  • Primary: The sequence of amino acids.

  • Secondary: Local folds like alpha-helix and beta-pleated sheets.

  • Tertiary: Overall 3D structure of a single polypeptide.

  • Quaternary: Assemblage of multiple polypeptides.

Nucleic Acids

• Function: Storage of genetic information (DNA), involved in protein synthesis (RNA), and energy currency of the cell (ATP).

• Monomer: Nucleotide (consists of sugar, phosphate group, nitrogenous base).

• DNA Structure: Consists of deoxyribose sugar, phosphate group, and nitrogenous bases (adenine, thymine, guanine, cytosine).

Cellular Respiration

• Overview: Converts energy stored in glucose into ATP, utilizing processes like glycolysis, Krebs cycle, and electron transport chain.

• Glycolysis: Occurs in the cytoplasm, breaks down glucose into two pyruvate molecules, resulting in a net production of 2 ATP.

• Krebs Cycle: Occurs in the mitochondrial matrix, involves oxidation of acetyl-CoA to produce electron carriers (NADH and FADH2), and produces ATP directly.

• Electron Transport Chain: Uses electrons from NADH and FADH2 to create a proton gradient across the mitochondrial membrane, ultimately synthesizing ATP from ADP and inorganic phosphate through oxidative phosphorylation.

Summary of ATP Yield

• Glycolysis produces 2 ATP & 2 NADH.

• Pyruvate oxidation converts pyruvate into acetyl-CoA and produces 2 more NADH.

• Krebs Cycle results in 2 ATP, 6 NADH, and 2 FADH2 from each glucose.

• Total theoretical ATP yield from one glucose molecule ranges between 36-38 ATP molecules, depending on the shuttle system used to transport electrons into mitochondria.

Fermentation

• Occurs in the absence of oxygen, allows for continued glycolysis by regenerating NAD+ through conversion of pyruvate into lactate or ethanol, depending on the organism and circumstances.

• Ethanol Fermentation: Occurs in yeast and some bacteria.

• Lactic Acid Fermentation: Occurs in animal muscle cells and certain microorganisms during anaerobic respiration.