Amino Acids and Macromolecule Monomers

Amino Acid Interactions

• Aspartic acid and lysine can interact via ionic bonds, as aspartic acid has a negatively charged carboxyl group, and lysine has a positively charged amino group.
• Phenylalanine and alanine primarily interact via London dispersion forces, as they are both nonpolar amino acids.
• Serine and lysine can interact via dipole-dipole interactions due to the polar hydroxyl group in serine and the polar amino group in lysine.

Macromolecule Monomers

• Carbohydrates: Monosaccharides (simple sugars), like glucose and fructose. These molecules contain multiple polar hydroxyl groups and ether bonds, making them polar. Monosaccharides form disaccharides through glycosidic bonds (formed through dehydration synthesis), a type of condensation reaction.
• Lipids: Glycerol (a polar molecule with three hydroxyl groups) and fatty acids (long chains of hydrocarbons with a carboxyl group at one end). Fatty acids are nonpolar due to their hydrocarbon chains. These monomers form triglycerides (or fats) through ester bonds.
• Proteins: Amino acids, which contain both a polar amino group and a polar carboxyl group, as well as a variable R-group that can be polar or nonpolar. Amino acids join to form polypeptides through peptide bonds, a type of amide bond.

Importance of Water for Breakdown

• Carbohydrate and protein breakdown requires water because these molecules are broken down through hydrolysis reactions. Hydrolysis involves adding a water molecule to break a bond between monomers, resulting in two smaller units.

Protein Structure and Function

• The 3D shape and conformation of a protein is crucial for its function.
• Primary structure: This is the linear sequence of amino acids in the polypeptide chain, determined by peptide bonds.
• Secondary structure: The folding of the polypeptide chain into alpha-helices or beta-sheets, due to hydrogen bonding between the backbone carbonyl oxygen and the backbone amino hydrogen.
• Tertiary structure: The overall 3D shape of a single polypeptide chain, formed by interactions between the R-groups of the amino acids, including hydrogen bonding, ionic interactions, hydrophobic interactions, and disulfide bridges.
• Quaternary structure: The arrangement of multiple polypeptide chains, each folded into its tertiary structure, also stabilized by interactions between the R-groups, including hydrogen bonding, ionic interactions, hydrophobic interactions, and disulfide bridges.

Enzyme Activity

• Substrate concentration: Increased substrate concentration generally leads to an increased rate of reaction until the enzyme becomes saturated.
• Temperature: Enzymes have an optimal temperature for activity. The rate of reaction increases with temperature until the optimal temperature is reached. Then, the rate of reaction drops significantly due to denaturation of the enzyme.
• pH: Enzymes have an optimal pH for activity. The rate of reaction decreases dramatically at acidic or basic pH due to changes in enzyme structure.
• Feedback regulation: The product of a reaction can act as an allosteric regulator, either promoting or inhibiting further activity of the enzyme.
• Competitive inhibition: An inhibitor molecule competes with the substrate for the active site of the enzyme, decreasing the intended enzyme activity.

Enzyme Regulation

• Allosteric activation: An activator molecule binds to a site other than the active site, causing a conformational change in the enzyme that increases its activity.
• Allosteric inhibition/non-competitive inhibition: An inhibitor molecule binds to a site other than the active site, causing a conformational change in the enzyme that decreases its activity.
• Competitive inhibition: An inhibitor molecule competes with the substrate for the active site of the enzyme, decreasing the intended enzyme activity.

Cofactors, Coenzymes & Prosthetic Groups

• Cofactors: Non-protein components that are required for the activity of some enzymes.
• Coenzymes: Organic cofactors that are loosely bound to enzymes.
• Prosthetic groups: Cofactors that are permanently associated with enzymes.

Enzyme Specificity

• An enzyme that catalyzes the breakdown of a glycosidic bond (in carbohydrates) is unlikely to catalyze the breakdown of a peptide bond (in proteins) because these bonds are structurally different. Enzymes are highly specific for their substrates, requiring specific active binding sites for recognition and catalysis.

Cell Membrane

• The plasma membrane is a selectively permeable barrier that controls the movement of substances into and out of the cell.
• It's composed of a phospholipid bilayer.
• A: Integral membrane protein.
• B: Peripheral membrane protein.
• C: Phosphate head (hydrophilic).
• D: Fatty acid tails (hydrophobic).
• E: Phospholipid.
• F: Cytosol.
• G: Cholesterol.

Starch and Cell Membrane

• Starch cannot pass through the plasma membrane via simple diffusion for two reasons:
  • Size: Starch molecules are too large to fit through the phospholipid bilayer.
  • Polarity: The multiple hydroxyl groups on starch molecules make them polar, making it difficult to pass through the nonpolar interior of the phospholipid bilayer.

Cell Transport

• Hypotonic Environment: A cell placed in a hypotonic environment will swell up. Water will move into the cell (higher solute concentration inside the cell will draw water in) to try to reach equilibrium.
• Primary Active Transport: Energy is directly used (usually from ATP hydrolysis) to move molecules against their concentration gradient.
• Secondary Active Transport: Energy is indirectly utilized by coupling the movement of one molecule against its concentration gradient with the simultaneous movement of another molecule down its concentration gradient.
• Electrochemical gradient: The combination of both a chemical gradient (concentration difference) and an electrical gradient (difference in charge) drives the movement of charged molecules (ions).

Endocytosis and Exocytosis

• Endocytosis and exocytosis are processes that involve the movement of large molecules or particles into or out of the cell via membrane-bound vesicles.

Transporting Ions Against Gradient

• Transporting ions against a gradient requires more energy than transporting neutral molecules against a gradient because of both the chemical gradient (concentration difference) and the electrical gradient (charge difference) that must be overcome.