Biological Chemistry I

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

Biochemistry explores the chemical processes that sustain life. This unit introduces the building blocks of life: carbohydrates, lipids, proteins, and nucleic acids. It covers their structure, function, and how they interact to form complex biological systems. The unit also delves into cellular metabolism, energy transformations, and enzyme catalysis. It examines how cells maintain homeostasis, the role of water in biological systems, and the importance of pH and buffers in biochemical reactions.

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+]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=pKa+log[A][HA]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=Vmax[S]Km+[S]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


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AP® and SAT® are trademarks registered by the College Board, which is not affiliated with, and does not endorse this website.