organic compounds AP

Organic Compounds in AP Biology

Proteins

  • Proteins are polymers made up of amino acids.

  • Basic structure involves:

    • Central carbon atom (C)

    • Amino group (NH2)

    • Carboxyl group (COOH)

    • Hydrogen atom (H)

    • Variable R group (side chain) specific to each amino acid.

Dipeptide Formation

  • A dipeptide consists of two amino acids linked by a peptide bond with the elimination of water (H2O).

  • Example: Glycine + Glycine = Dipeptide.

Polypeptide Structure

  • Polypeptides are long chains of amino acids (e.g., glycine + cysteine structures).

Structure of Proteins

What Are Proteins?

  • Proteins are composed of different sequences of amino acids. Examples of amino acids:

    • Phenylalanine (Phe)

    • Glycine (Gly)

    • Glutamic acid (Glu)

    • Asparagine (Asn)

    • Glutamine (Gln)

    • Alanine (Ala)

    • Arginine (Arg)

    • Proline (Pro)

    • Tyrosine (Tyr)

    • Tryptophan (Trp)

    • Serine (Ser)

    • Aspartic acid (Asp)

    • Isoleucine (Ile)

    • Methionine (Met)

    • Cysteine (Cys)

    • Leucine (Leu)

Types of Protein Structures

  1. Primary Structure

    • Determined by the amino acid sequence.

  2. Secondary Structure

    • Involves hydrogen bonding between amino acids, forming:

      • Alpha helices

      • Pleated sheets

  3. Tertiary Structure

    • The three-dimensional shape of a single polypeptide chain, influenced by various interactions (S–S bonds, ionic, hydrophobic interactions).

    • Types:

      • Globular proteins (e.g., enzymes) are water-soluble.

      • Fibrous proteins (structural) are rod-like and less soluble.

  4. Quaternary Structure

    • Composed of multiple polypeptide chains.

Functional Aspects of Proteins

  • Some proteins, like chaperonins, assist in folding.

  • Misfolding can lead to diseases (e.g., Parkinson's, Alzheimer's, prion disease).

Enzymes

  • Catalysts that lower activation energy, allowing reactions at lower temperatures.

Understanding Activation Energy

  • Activation energy is the energy required to initiate a reaction.

  • Enzymes facilitate the reaction by lowering this energy barrier.

Types of Reactions

  1. Endergonic Reactions

    • Non-spontaneous (ΔG > 0).

    • Energy is absorbed.

  2. Exergonic Reactions

    • Spontaneous (ΔG < 0).

    • Energy is released.

Properties of Enzymes

  • Proteins with high specificity.

  • Enzyme + substrate form an enzyme-substrate complex, which then releases product.

  • Specificity emerges from complementary structures of substrate and enzyme.

Enzyme Activity Influencers

  1. Temperature

    • High temperatures may denature enzymes.

    • Low temperatures render enzymes inactive.

  2. pH Levels

    • Each enzyme has an optimal pH for activity.

Concentration Effects

  • Activity can be influenced by substrate and enzyme concentrations.

Inhibition of Enzymes

  1. Competitive Inhibition

    • Inhibitor competes with substrate for the active site.

  2. Non-Competitive Inhibition

    • Inhibitor binds to an allosteric site, changing the active site's shape.

Lipids

  • Composed mainly of carbon, hydrogen, and less oxygen compared to carbohydrates.

Types of Lipids

  1. Phospholipids

    • Comprise hydrophilic heads and hydrophobic tails.

  2. Steroids

    • Include cholesterol and hormones.

  3. Waxes

    • Provide waterproofing functions.

Importance of Lipids

  1. Energy storage.

  2. Composing vital hormones.

  3. Insulating heat.

  4. Assisting nerve impulse transmission.

  5. Providing buoyancy.

Nucleic Acids

  • Polymers formed from nucleotides, consisting of nitrogenous bases, sugar, and phosphate groups.

  • Key nitrogenous bases include:

    • Adenine

    • Thymine

    • Guanine

    • Cytosine

  • Structure of nucleic acids supports information storage and transfer in biological contexts.