🐇Honors Biology Unit 2 – Biochemistry – The Chemistry of Life

Key Molecules of Life

• Four main categories of biological macromolecules are carbohydrates, lipids, proteins, and nucleic acids
• Monomers are small molecules that serve as building blocks for larger polymers through dehydration synthesis reactions
• Polymers are long chains of monomers linked together by covalent bonds formed during condensation reactions
• Hydrolysis reactions break down polymers into their constituent monomers by adding a water molecule across the bond
• Carbohydrates primarily provide energy for cells and include monosaccharides (glucose), disaccharides (sucrose), and polysaccharides (starch, cellulose)
• Lipids are hydrophobic molecules that include fats, oils, waxes, and steroids which serve as energy storage, cell membrane components, and signaling molecules
• Proteins are composed of amino acids and perform a wide range of functions such as enzymes, structural components, transport molecules, and hormones
• Nucleic acids store and transmit genetic information in the form of DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)

Chemical Bonds and Interactions

• Atoms form chemical bonds by sharing or transferring electrons to achieve a stable electron configuration
• Covalent bonds involve the sharing of electrons between atoms and can be single, double, or triple bonds depending on the number of electron pairs shared
  • Nonpolar covalent bonds occur when electrons are shared equally between atoms (O2, CH4)
  • Polar covalent bonds form when electrons are shared unequally due to differences in electronegativity (H2O, NH3)
• Ionic bonds result from the complete transfer of electrons from one atom to another, creating positively and negatively charged ions that attract each other (NaCl)
• Hydrogen bonds are weak electrostatic attractions between a hydrogen atom bonded to an electronegative atom (oxygen or nitrogen) and another electronegative atom
• Van der Waals forces are weak intermolecular attractions between molecules resulting from temporary dipoles induced by electron movement
• Hydrophobic interactions occur between nonpolar molecules in aqueous solutions, causing them to aggregate and minimize contact with water

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 gives rise to many of its unique properties essential for life
• High specific heat capacity allows water to absorb and release large amounts of heat energy without significant temperature changes, helping to regulate body temperature
• High heat of vaporization requires a large amount of energy to break hydrogen bonds and evaporate water, contributing to evaporative cooling in organisms
• Cohesion is the attraction between water molecules that allows for high surface tension and capillary action in plants
• Adhesion is the attraction between water molecules and other surfaces, enabling water to "climb" up narrow tubes against gravity
• Water is an excellent solvent for polar and ionic compounds due to its polarity, facilitating chemical reactions and transport of substances in living systems
• Ice is less dense than liquid water because hydrogen bonds cause water molecules to arrange in an open lattice structure, allowing life to persist under frozen surfaces

Carbon and Organic Compounds

• Carbon is the backbone of organic compounds due to its ability to form four stable covalent bonds and create diverse molecules
• Hydrocarbons are organic compounds composed entirely of carbon and hydrogen atoms, including alkanes (single bonds), alkenes (double bonds), and alkynes (triple bonds)
• Functional groups are specific arrangements of atoms within organic molecules that give them distinct chemical properties
  • Hydroxyl group (-OH) is characteristic of alcohols and makes molecules more polar and water-soluble
  • Carboxyl group (-COOH) is found in carboxylic acids and contributes to the acidic properties of molecules like amino acids and fatty acids
• Isomers are compounds with the same molecular formula but different structural arrangements, leading to different properties (glucose and fructose)
• Enantiomers are mirror-image isomers that have the same physical properties but may have different biological activities (L-amino acids vs. D-amino acids)
• Polymers are large organic molecules formed by the repetition of smaller monomers, such as proteins (amino acids), nucleic acids (nucleotides), and polysaccharides (monosaccharides)

Carbohydrates: Structure and Function

• Carbohydrates are organic compounds composed of carbon, hydrogen, and oxygen atoms in a 1:2:1 ratio (CH2O)n
• Monosaccharides are simple sugars that serve as the building blocks of more complex carbohydrates (glucose, fructose, galactose)
  • Glucose is the primary energy source for cells and is oxidized during cellular respiration to produce ATP
  • Fructose is found in fruits and honey and is often used as a sweetener in processed foods
• Disaccharides are formed when two monosaccharides are joined together by a glycosidic bond (sucrose, lactose, maltose)
  • Sucrose (table sugar) is composed of glucose and fructose and is commonly found in plants
  • Lactose (milk sugar) consists of glucose and galactose and is found in mammalian milk
• Polysaccharides are long chains of monosaccharides linked by glycosidic bonds and serve various functions in living organisms
  • Starch is a storage polysaccharide in plants composed of amylose (unbranched) and amylopectin (branched) glucose polymers
  • Glycogen is the primary storage polysaccharide in animals, consisting of highly branched glucose polymers
  • Cellulose is a structural polysaccharide in plant cell walls made up of long, unbranched chains of glucose molecules linked by β-1,4 glycosidic bonds
  • Chitin is a structural polysaccharide found in the exoskeletons of arthropods and cell walls of fungi, composed of N-acetylglucosamine monomers

Lipids: Types and Roles

• Lipids are a diverse group of hydrophobic organic molecules that include fats, oils, waxes, steroids, and phospholipids
• Triglycerides (fats and oils) are composed of a glycerol molecule and three fatty acids connected by ester bonds
  • Saturated fatty acids have single bonds between carbon atoms and are solid at room temperature (animal fats)
  • Unsaturated fatty acids contain one or more double bonds between carbon atoms and are liquid at room temperature (plant oils)
• Phospholipids are the main components of cell membranes and consist of a glycerol molecule, two fatty acids, and a phosphate group
  • The hydrophilic phosphate head and hydrophobic fatty acid tails give phospholipids their amphipathic nature
  • Phospholipids form bilayers in aqueous solutions, with the hydrophilic heads facing the water and the hydrophobic tails facing each other
• Steroids are lipids with a characteristic four-ring structure and include hormones (testosterone, estrogen), vitamin D, and cholesterol
  • Cholesterol is an essential component of animal cell membranes, regulating membrane fluidity and permeability
  • Cholesterol also serves as a precursor for the synthesis of steroid hormones and bile acids
• Waxes are esters of long-chain fatty acids and long-chain alcohols, providing protective coatings on plant leaves, insect exoskeletons, and animal fur

Proteins: Building Blocks and Functions

• Proteins are polymers of amino acids linked together by peptide bonds formed through dehydration synthesis reactions
• There are 20 different amino acids used to build proteins, each with a unique side chain (R group) that determines its chemical properties
• The sequence of amino acids in a protein is determined by the genetic code and ultimately dictates the protein's structure and function
• Protein structure is organized into four levels: primary, secondary, tertiary, and quaternary
  • Primary structure is the linear sequence of amino acids in a polypeptide chain
  • Secondary structure refers to the local folding of the polypeptide chain into α-helices and β-sheets stabilized by hydrogen bonds
  • Tertiary structure is the three-dimensional shape of a single polypeptide chain resulting from interactions between side chains (disulfide bridges, hydrophobic interactions, ionic bonds)
  • Quaternary structure is the arrangement of multiple polypeptide subunits into a functional protein complex (hemoglobin, DNA polymerase)
• Proteins perform a wide variety of functions in living organisms, including:
  • Enzymes that catalyze biochemical reactions by lowering activation energy
  • Structural proteins that provide support and shape to cells and tissues (collagen, keratin)
  • Transport proteins that move molecules across membranes or throughout the body (hemoglobin, ion channels)
  • Signaling proteins that transmit messages between cells (hormones, receptors)
  • Defensive proteins that protect organisms from pathogens (antibodies, complement proteins)

Nucleic Acids: DNA and RNA

• Nucleic acids are polymers of nucleotides that store and transmit genetic information in living organisms
• DNA (deoxyribonucleic acid) is the primary genetic material in all cellular life forms and many viruses
  • DNA is composed of four nucleotide monomers: adenine (A), thymine (T), guanine (G), and cytosine (C)
  • The sugar in DNA nucleotides is deoxyribose, which lacks a hydroxyl group on the 2' carbon compared to ribose
• RNA (ribonucleic acid) is a single-stranded nucleic acid that plays various roles in gene expression and protein synthesis
  • RNA nucleotides contain ribose sugar and the base uracil (U) instead of thymine (T)
  • Messenger RNA (mRNA) carries genetic information from DNA to ribosomes for protein synthesis
  • Transfer RNA (tRNA) molecules transport amino acids to ribosomes and recognize codons in mRNA through anticodon base pairing
  • Ribosomal RNA (rRNA) is a structural and catalytic component of ribosomes, the sites of protein synthesis
• The structure of DNA is a double helix composed of two antiparallel polynucleotide strands held together by hydrogen bonds between complementary base pairs (A-T and G-C)
• The base pairing rules (A with T, G with C) and the complementary nature of the double helix enable accurate DNA replication and transcription

Enzymes and Biochemical Reactions

• Enzymes are biological catalysts that speed up chemical reactions in living organisms without being consumed in the process
• Most enzymes are proteins with specific three-dimensional shapes that determine their function and substrate specificity
• The active site is the region of an enzyme where the substrate binds and the catalytic reaction occurs
  • Substrates bind to the active site through a combination of weak interactions (hydrogen bonds, hydrophobic interactions, ionic bonds)
  • The induced fit model suggests that the active site undergoes conformational changes upon substrate binding to optimize catalysis
• Enzymes lower the activation energy of reactions by stabilizing transition states, bringing substrates together, or providing alternative reaction pathways
• Cofactors are non-protein molecules that assist enzymes in catalysis and can be either inorganic ions (Fe2+, Mg2+) or organic molecules (coenzymes)
  • Coenzymes are often derived from vitamins (NAD+ from niacin, FAD from riboflavin, coenzyme A from pantothenic acid)
• Enzyme activity is regulated by various factors, including:
  • Substrate concentration: increasing substrate concentration increases reaction rate until the enzyme is saturated
  • Temperature: increasing temperature increases reaction rate until the enzyme denatures
  • pH: each enzyme has an optimal pH range where it functions most efficiently
  • Inhibitors: molecules that decrease enzyme activity by binding to the active site (competitive inhibition) or allosteric sites (noncompetitive inhibition)
  • Activators: molecules that increase enzyme activity by binding to allosteric sites and inducing conformational changes

Energy in Biological Systems

• Energy is the capacity to do work or cause change and is essential for all life processes
• The first law of thermodynamics states that energy cannot be created or destroyed, only converted from one form to another
• The second law of thermodynamics states that entropy (disorder) in a closed system always increases over time
• Gibbs free energy (G) is a measure of the energy available to do work in a system and is determined by the enthalpy (H) and entropy (S) of the system: ΔG = ΔH - TΔS
  • Exergonic reactions have a negative ΔG and release energy, occurring spontaneously (ATP hydrolysis, glucose oxidation)
  • Endergonic reactions have a positive ΔG and require an input of energy, occurring non-spontaneously (photosynthesis, protein synthesis)
• ATP (adenosine triphosphate) is the primary energy currency in living organisms, storing and transferring energy for cellular processes
  • ATP consists of an adenosine molecule (adenine base, ribose sugar) and three phosphate groups
  • The hydrolysis of ATP to ADP (adenosine diphosphate) and inorganic phosphate (Pi) releases energy that can be coupled to endergonic reactions
• Photosynthesis is the process by which plants and other autotrophs convert light energy into chemical energy stored in glucose
  • Light-dependent reactions occur in the thylakoid membranes of chloroplasts and use light energy to generate ATP and NADPH
  • Light-independent reactions (Calvin cycle) occur in the stroma of chloroplasts and use ATP and NADPH to fix CO2 into glucose
• Cellular respiration is the process by which cells break down glucose to generate ATP in the presence of oxygen
  • Glycolysis occurs in the cytoplasm and converts glucose into two molecules of pyruvate, generating a net of 2 ATP and 2 NADH
  • The citric acid cycle occurs in the mitochondrial matrix and oxidizes acetyl-CoA (derived from pyruvate) to generate 2 ATP, 6 NADH, and 2 FADH2
  • Oxidative phosphorylation occurs in the inner mitochondrial membrane and uses the electron transport chain to create a proton gradient that drives ATP synthesis, generating up to 34 ATP per glucose molecule