AP Biology Notes: Water and Biological Molecules

Water Properties

• Living systems depend on properties of water that arise from polarity and hydrogen bonding.
• Four emergent properties of water that contribute to life on Earth:
  1) Cohesive behavior
  2) Ability to moderate temperature
  3) Expansion upon freezing
  4) Versatility as a solvent
• Key definitions:
  • Polarity: an uneven charge distribution
  • Hydrogen bond: a weak chemical bond between a slightly positive hydrogen atom on one molecule and a slightly negative atom on another molecule

1. COHESIVE BEHAVIOR

• Cohesion: joining together of like molecules by hydrogen bonding
• Surface tension: a measure of how difficult it is to break the surface of a liquid
• At the interface between water and air there is an ordered arrangement of water molecules
• Adhesion: joining together of different molecules by hydrogen bonds

2. ABILITY TO MODERATE TEMPERATURE

• Water has a high specific heat: it can absorb or release a large amount of heat with only a small change in its own temperature
• Specific heat: the amount of heat that must be absorbed or lost for 1 g of a substance to change its temperature by 1°C; numerically, for water, this is unusually high
• Water moderates air temperature by absorbing heat from warmer air and releasing stored heat to cooler air
• Water’s high specific heat is due to hydrogen bonding:
  • heat must be absorbed to break hydrogen bonds
  • heat is released when hydrogen bonds form
• Mathematical note: the relationship between heat, mass, specific heat, and temperature change is expressed as
  $\Delta q = m c \Delta T$
  where $\Delta q$ is heat, $m$ is mass, $c$ is specific heat, and $\Delta T$ is the temperature change

3. EXPANSION UPON FREEZING

• Ice floats in liquid water because hydrogen bonds in ice are more ordered, making ice less dense than liquid water
• If ice sank, all bodies of water could freeze solid, making life impossible on Earth
• Floating ice insulates the liquid water below, helping to maintain liquid water habitats

4. VERSATILITY AS A SOLVENT

• Water is a versatile solvent because of its polarity
• Water can dissolve a variety of polar substances
• A solution is a completely homogeneous mixture of two or more substances
  • solvent: a substance (usually a liquid) that dissolves other substances
  • solute: the dissolved substance

Biological Molecules

CARBON: THE BACKBONE OF LIFE

• Carbon atoms can be assembled and remodeled into many organic compounds
• Carbon exhibits versatile bonding behavior:
  • can form up to 4 covalent bonds with other atoms
  • can form polar or nonpolar bonds
  • can form chains or rings

Functional groups

• A functional group is a cluster of atoms covalently bonded to a carbon atom of an organic molecule and determines chemical properties (polarity, acidity, etc.). Common groups include:
• Hydroxyl group (–OH): found in sugars; glycerol; amino acids
• Methyl group (–CH3): found in fatty acids; some amino acids
• Carbonyl group (–C=O): found in sugars; amino acids; nucleotides
• Carboxyl group (–COOH): found in amino acids; fatty acids; sugars
• Amine group (–NH2): found in amino acids; some nucleotides
• Phosphate group (–OPO3^2−): found in nucleotides; phospholipids
• Sulfhydryl group (–SH): found in amino acid cysteine
• Location and structure of groups influence molecule polarity and reactivity

BIOLOGICAL MOLECULES

• Monomer: a subunit that makes up larger molecules
• Polymer: chains of monomers
• Macromolecule: a large biological molecule
• Four classes of biological molecules:
  1) Carbohydrates
  2) Lipids
  3) Proteins
  4) Nucleic Acids
• Biological molecules consist primarily of carbon and hydrogen (hydrocarbons)

SYNTHESIS AND BREAKDOWN OF POLYMERS

• All four classes use similar reactions to build and break down polymers, with enzyme help:
• Dehydration synthesis (condensation): synthesizing a polymer by removing a water molecule and forming a new bond (energy absorbed)
• Hydrolysis: breaking down a molecule by adding a water molecule and breaking a bond (energy released)

1. CARBOHYDRATES

• Composition: $ext{C}, ext{H}, ext{O}$ in a 1:2:1 ratio
  • often written as empirical formula $ext{CH}_2 ext{O}$ for simple sugars
• Monomer: monosaccharides
• Bond: glycosidic linkage
• Function: energy and structural roles
• Types:
  • monosaccharides
  • disaccharides
  • polysaccharides

MONOSACCHARIDES

• Monosaccharides: one sugar unit (simplest carbohydrates)
• Classified by number of carbons and location of the carbonyl group
• 5C and 6C sugars form rings in aqueous solutions
• Glucose is the most common monosaccharide
• Two forms of glucose differ only in the orientation of H and OH on the first carbon (epimers); small changes can dramatically alter properties

DISACCHARIDES

• Disaccharide: two monosaccharides joined by a glycosidic linkage
• Sucrose is the most common disaccharide; monomers are glucose and fructose

POLYSACCHARIDES

• Polysaccharides are straight or branched chains of many sugar monomers
• All major polysaccharides consist of glucose monomers, but different linkage patterns yield different properties
• The three most common polysaccharides:
  1. Starch — storage polysaccharide in plants; α-glucose
  2. Glycogen — storage polysaccharide in animals; α-glucose
  3. Cellulose — structural polysaccharide (plant cell wall); β-glucose

2. LIPIDS

• Composition: mostly carbon and hydrogen; some oxygen; sometimes phosphorus
• Monomer: glycerol and fatty acids
• Bond: ester linkage
• Function: energy reservoir and as the structural foundation of cell membranes
• Lipids are fatty, oily, or waxy compounds insoluble in water
• Key structural details:
  • Glycerol: a three-carbon alcohol with an attached hydroxyl group on each carbon
  • Fatty acids: carboxyl group attached to a long carbon skeleton
  • Saturated fatty acids: only single covalent bonds; pack tightly; solid at room temperature
  • Unsaturated fatty acids: one or more double bonds; kinked; liquid at room temperature

TYPES OF LIPIDS

1) Triglycerides: a lipid with 3 fatty acid chains linked to glycerol
2) Phospholipids: lipids with a polar/hydrophilic head (glycerol + phosphate group) and 2 nonpolar/hydrophobic tails; main component of cell membranes
3) Steroids: lipids with a rigid backbone of four carbon rings and no fatty acid tails (e.g., cholesterol – component of cell membranes)

3. PROTEINS

• Composition: carbon, hydrogen, oxygen, nitrogen, and some sulfur
• Monomer: amino acids
• Bond: peptide bonds
• Function: the most diverse biological molecule; catalysis, structure, transport, signaling, defense, etc.

TABLE OVERVIEW (Protein Functions)

• Enzymatic proteins: selective acceleration of chemical reactions (e.g., digestive enzymes)
• Structural proteins: support (e.g., collagen, keratin)
• Storage proteins: storage of amino acids (e.g., seeds)
• Transport proteins: transport of substances (e.g., hemoglobin)
• Hormonal proteins: signaling (e.g., insulin)
• Receptor proteins: cell response to signals
• Contractile and motor proteins: movement (e.g., actin, myosin)
• Defensive proteins: protection against disease (e.g., antibodies)

AMINO ACIDS

• Cells use 20 different amino acids to build proteins
• Each amino acid consists of:
  • Central carbon (α-carbon)
  • Amine group (–NH2 or –NH3+ in solution)
  • Carboxyl group (–COOH)
  • Hydrogen atom
  • R group (side chain) – confers unique chemical properties

SIDE CHAIN CLASSIFICATION (R groups)

• Nonpolar (hydrophobic) side chains: Glycine (G), Gly; Alanine (A), Ala; Valine (V), Val; Leucine (L), Leu; Isoleucine (I), Ile; Methionine (M), Met; Phenylalanine (F), Phe; Tryptophan (W), Trp; Proline (P), Pro
• Polar (uncharged) side chains: Serine (S), Ser; Threonine (T), Thr; Cysteine (C), Cys; Tyrosine (Y), Tyr; Asparagine (N), Asn; Glutamine (Q), Gln
• Acidic (negatively charged) side chains: Aspartate (D), Asp; Glutamate (E), Glu
• Basic (positively charged) side chains: Lysine (K), Lys; Arginine (R), Arg; Histidine (H), His
• These properties affect protein folding, function, and interactions

POLYPEPTIDE

• Polypeptide: a chain of amino acids bonded together by peptide bonds between the amine group of one amino acid and the carboxyl group of another

LEVELS OF PROTEIN STRUCTURE

1) Primary (1°) structure: unique sequence of amino acids; formed by peptide bonds; sequence determined by DNA; small changes can affect structure and function
2) Secondary (2°) structure: coils (α helices) and folds (β pleated sheets) formed by hydrogen bonds between amino acid residues along the polypeptide backbone
3) Tertiary (3°) structure: 3‑D compact shape of a protein; result of interactions among R groups (side chains):

• Ionic bonds
• Disulfide bonds
• Hydrophobic interactions
• Hydrogen bonds
• Denaturation: changes in temperature or pH can disrupt these bonds, causing loss of function
  4) Quaternary (4°) structure: arrangement of two or more polypeptides in a multi-subunit complex; not all proteins have a quaternary structure

NUCLEIC ACIDS

• Composition: carbon, hydrogen, oxygen, nitrogen, and phosphorus
• Monomer: nucleotides
• Bond: phosphodiester linkage
• Function: store and transmit genetic information
• Types: DNA and RNA

NUCLEOTIDES

• Components of a nucleotide: 1) A pentose sugar (five-carbon): deoxyribose (DNA) or ribose (RNA) 2) A nitrogenous base: pyrimidines or purines
  • Pyrimidines: cytosine (C), thymine (T), uracil (U)
  • Purines: adenine (A), guanine (G)
    3) One or more phosphate groups

POLYNUCLEOTIDES (DNA & RNA)

• Adjacent nucleotides joined by a phosphodiester linkage; phosphate connects the sugars of two nucleotides; forms the sugar-phosphate backbone
• The two free ends of a polynucleotide are distinct:
  • 5′ end: phosphate group attached to a 5′ carbon
  • 3′ end: hydroxyl group on a 3′ carbon

DNA – DEOXYRIBONUCLEIC ACID

• Nucleotides: A, G, C, T
• Structure: two polynucleotide strands form a double helix
• Antiparallel: the two sugar-phosphate backbones run in opposite 5′→3′ directions
• Backbone on the outside; bases paired inside via hydrogen bonds:
  • A pairs with T (2 hydrogen bonds)
  • C pairs with G (3 hydrogen bonds)

RNA – RIBONUCLEIC ACID

• Nucleotides: A, G, C, U
• Usually a single polynucleotide strand

ATP

• Adenosine triphosphate (ATP) is a modified adenine nucleotide that releases free energy when its phosphate bonds are hydrolyzed
• Used to drive endergonic reactions in cells
• Simplified hydrolysis reaction:
  $\mathrm{ATP + H<em>2O \rightarrow ADP + P</em>i + \Delta E}$
  where $P_i$ is inorganic phosphate and $\Delta E$ is energy released