🔬Biological Chemistry I Unit 1 – Intro to Biochemistry: Chemistry of Life

Key Concepts and Definitions

• Biochemistry studies the chemical processes and reactions that occur within living organisms
• Macromolecules are large, complex molecules essential for life and include carbohydrates, lipids, proteins, and nucleic acids
• Monomers are smaller subunits that combine to form polymers through dehydration synthesis reactions
• Hydrolysis breaks down polymers into their constituent monomers by adding water molecules
• Metabolism encompasses all chemical reactions involved in maintaining the living state of cells and organisms
  • Anabolism constructs complex molecules from simpler ones and requires energy input
  • Catabolism breaks down complex molecules into simpler ones and releases energy
• Homeostasis maintains a stable internal environment within an organism despite external changes
• Bioenergetics studies energy flow through living systems, including energy transformations and heat exchange

Building Blocks of Life

• Carbohydrates, composed of carbon, hydrogen, and oxygen atoms, serve as energy sources and structural components
  • Monosaccharides are simple sugars (glucose, fructose, galactose) that form the building blocks of complex carbohydrates
  • Disaccharides (sucrose, lactose, maltose) consist of two monosaccharides linked by a glycosidic bond
  • Polysaccharides (starch, glycogen, cellulose) are long chains of monosaccharides
• Lipids are hydrophobic molecules that include fats, oils, waxes, and steroids
  • Triglycerides consist of three fatty acids attached to a glycerol backbone and serve as energy storage molecules
  • Phospholipids form cell membranes due to their amphipathic nature, with hydrophilic heads and hydrophobic tails
• Proteins are polymers of amino acids linked by peptide bonds and perform various functions (enzymes, transport, structure)
  • Amino acids contain an amino group, a carboxyl group, and a variable side chain that determines their properties
  • Primary structure is the linear sequence of amino acids in a protein
  • Secondary structure (α-helices and β-sheets) results from hydrogen bonding between the amino acid backbone
  • Tertiary structure is the three-dimensional folding of a protein due to interactions between side chains
  • Quaternary structure involves the assembly of multiple polypeptide subunits
• Nucleic acids store and transmit genetic information
  • DNA (deoxyribonucleic acid) is a double-stranded helix composed of nucleotide monomers (deoxyribose sugar, phosphate group, nitrogenous base)
  • RNA (ribonucleic acid) is single-stranded and contains ribose sugar instead of deoxyribose
  • Nitrogenous bases in DNA include adenine (A), thymine (T), guanine (G), and cytosine (C), while RNA contains uracil (U) instead of thymine

Chemical Bonds and Interactions

• Chemical bonds hold atoms together to form molecules and include covalent, ionic, and hydrogen bonds
• Covalent bonds involve the sharing of electrons between atoms
  • Nonpolar covalent bonds occur when electrons are shared equally (C-C, C-H)
  • Polar covalent bonds form when electrons are shared unequally due to differences in electronegativity (O-H, N-H)
• Ionic bonds result from the electrostatic attraction between oppositely charged ions (Na⁺Cl⁻)
• Hydrogen bonds are weak electrostatic interactions between a hydrogen atom bonded to an electronegative atom (N, O, F) and another electronegative atom
• Van der Waals forces are weak, short-range attractive forces between molecules
• Hydrophobic interactions occur between nonpolar molecules in aqueous solutions, causing them to aggregate and minimize contact with water
• Dipole-dipole interactions are attractive forces between the positive end of one polar molecule and the negative end of another

Water and Its Properties

• Water is a polar molecule with a bent geometry due to the unequal sharing of electrons between oxygen and hydrogen atoms
• Hydrogen bonding between water molecules leads to cohesion (attraction between water molecules) and adhesion (attraction between water and other surfaces)
• High specific heat capacity of water allows it to absorb and release large amounts of heat energy without significant temperature changes, providing a stable environment for biochemical reactions
• Water is an excellent solvent for polar and ionic compounds due to its polarity
• Hydrophilic substances readily dissolve in water, while hydrophobic substances do not
• Surface tension results from the cohesive forces between water molecules at the air-water interface
• Capillary action is the ability of water to rise in narrow spaces against gravity due to adhesive forces between water and the surface
• Ice is less dense than liquid water because of the open, hexagonal arrangement of water molecules in the solid state

pH and Buffers

• pH is a measure of the concentration of hydrogen ions (H⁺) in a solution
  • pH scale ranges from 0 to 14, with 7 being neutral, values below 7 acidic, and values above 7 basic
  • pH is calculated as the negative logarithm of the hydrogen ion concentration: $pH = -log[H⁺]$
• Acids are proton donors that increase the concentration of H⁺ in a solution
• Bases are proton acceptors that decrease the concentration of H⁺ in a solution
• Buffers are solutions that resist changes in pH when small amounts of acid or base are added
  • Buffers typically consist of a weak acid and its conjugate base or a weak base and its conjugate acid
  • Henderson-Hasselbalch equation relates the pH of a buffer system to the concentration of its components: $pH = pK_a + log\frac{[A⁻]}{[HA]}$
• Biological systems rely on buffers to maintain a stable pH for optimal function of proteins and enzymes
  • Bicarbonate buffer system (H₂CO₃/HCO₃⁻) maintains blood pH around 7.4
  • Phosphate buffer system (H₂PO₄⁻/HPO₄²⁻) maintains intracellular pH around 7.2

Energy in Biochemical Systems

• Energy is the capacity to do work or cause change
• Thermodynamics is the study of energy transformations
  • First law of thermodynamics states that energy cannot be created or destroyed, only converted from one form to another
  • Second law of thermodynamics states that entropy (disorder) of the universe always increases in spontaneous processes
• Gibbs free energy (ΔG) predicts the spontaneity of a reaction
  • ΔG < 0: reaction is spontaneous and releases energy
  • ΔG > 0: reaction is non-spontaneous and requires energy input
  • ΔG = 0: system is at equilibrium
• ATP (adenosine triphosphate) is the primary energy currency in biological systems
  • ATP consists of adenosine (adenine base + ribose sugar) and three phosphate groups
  • Hydrolysis of ATP to ADP (adenosine diphosphate) and inorganic phosphate (P_i) releases energy for cellular processes
• Coupled reactions link energetically unfavorable reactions (ΔG > 0) with favorable ones (ΔG < 0) to drive biochemical processes
• Redox reactions involve the transfer of electrons between molecules
  • Oxidation is the loss of electrons, while reduction is the gain of electrons
  • NAD⁺/NADH and FAD/FADH₂ are important electron carriers in cellular metabolism

Enzymes and Catalysis

• Enzymes are biological catalysts that accelerate chemical reactions without being consumed
• Enzymes lower the activation energy (E_a) of a reaction, allowing it to proceed more quickly
• Active site is the region of an enzyme where the substrate binds and the reaction occurs
• Substrate specificity results from the unique three-dimensional structure of the active site
• Enzyme-substrate binding involves interactions such as hydrogen bonds, ionic bonds, and van der Waals forces
• Michaelis-Menten kinetics describes the relationship between substrate concentration and reaction rate
  • $v = \frac{V_{max}[S]}{K_m + [S]}$, where v is the reaction rate, V_max is the maximum rate, [S] is the substrate concentration, and K_m is the Michaelis constant
• Factors affecting enzyme activity include temperature, pH, substrate concentration, and the presence of inhibitors or activators
• Enzyme inhibition can be competitive (inhibitor binds to the active site) or non-competitive (inhibitor binds elsewhere on the enzyme)
• Allosteric regulation involves the binding of effectors at sites other than the active site, causing conformational changes that alter enzyme activity
• Cofactors are non-protein molecules required for enzyme function
  • Coenzymes are organic cofactors (e.g., NAD⁺, FAD, coenzyme A)
  • Inorganic cofactors include metal ions (e.g., Fe²⁺, Mg²⁺, Zn²⁺)

Cellular Metabolism Overview

• Cellular respiration is the process by which cells break down organic molecules to release energy
  • Glycolysis breaks down glucose into two pyruvate molecules in the cytoplasm
  • Pyruvate oxidation converts pyruvate to acetyl-CoA, which enters the citric acid cycle
  • Citric acid cycle (Krebs cycle) oxidizes acetyl-CoA to CO₂, releasing high-energy electrons carried by NADH and FADH₂
  • Electron transport chain transfers electrons from NADH and FADH₂ to oxygen, creating a proton gradient across the inner mitochondrial membrane
  • Chemiosmosis uses the proton gradient to drive ATP synthesis through ATP synthase
• Fermentation is an anaerobic process that regenerates NAD⁺ in the absence of oxygen
  • Lactic acid fermentation converts pyruvate to lactate (muscle cells during intense exercise)
  • Alcohol fermentation converts pyruvate to ethanol and CO₂ (yeast in beer and wine production)
• Photosynthesis is the process by which plants and other autotrophs convert light energy into chemical energy
  • Light-dependent reactions occur in the thylakoid membranes of chloroplasts, where light energy is used to split water and generate ATP and NADPH
  • Calvin cycle (light-independent reactions) in the stroma uses ATP and NADPH to fix CO₂ into organic compounds (glucose)
• Gluconeogenesis is the synthesis of new glucose molecules from non-carbohydrate precursors (amino acids, lactate, glycerol)
• Glycogenesis is the formation of glycogen (storage polysaccharide) from glucose, while glycogenolysis is the breakdown of glycogen into glucose
• Lipogenesis is the synthesis of fatty acids and triglycerides, while lipolysis is the breakdown of triglycerides into fatty acids and glycerol
• Amino acid metabolism involves the synthesis and degradation of amino acids
  • Transamination transfers an amino group from an amino acid to an α-ketoacid
  • Deamination removes the amino group from an amino acid, releasing ammonia