Chapter 3: Protein Structure and Function

Amino Acid Structure

Proteins are polymers made of amino acid monomers, each consisting of a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable R group.

• N & C Terminus: The amino (N) terminus is the start of a polypeptide, and the carboxyl (C) terminus is the end.

• Hydrophilic & Hydrophobic Amino Acids: Amino acids are classified based on the properties of their R groups; hydrophilic (polar/charged) and hydrophobic (nonpolar).

• Monomer, Polymer, Polymerization: Amino acids (monomers) join via dehydration synthesis to form polypeptides (polymers).

Peptide Bonding

Peptide bonds form between the carboxyl group of one amino acid and the amino group of another, releasing water.

• Formula:

Protein Structure (Primary, Secondary, Tertiary, Quaternary)

Proteins have four levels of structure that determine their function.

• Primary Structure: Sequence of amino acids.

• Secondary Structure: Local folding (α-helix, β-sheet) stabilized by hydrogen bonds.

• Tertiary Structure: Overall 3D shape due to interactions among R groups.

• Quaternary Structure: Association of multiple polypeptide chains.

Protein Folding

Proper folding is essential for protein function; misfolding can lead to diseases.

Enzymes

Enzymes are biological catalysts that speed up chemical reactions by lowering activation energy.

• Energy of Activation: The minimum energy required for a reaction to occur.

• Substrates and Active Sites: Substrates bind to the enzyme's active site, where the reaction occurs.

• Competitive & Non-Competitive Enzyme Inhibitors: Competitive inhibitors bind to the active site; non-competitive inhibitors bind elsewhere, altering enzyme activity.

Chapter 4: Nucleic Acids

Nucleotide Structure

Nucleic acids (DNA and RNA) are polymers of nucleotides, each composed of a phosphate group, a five-carbon sugar, and a nitrogenous base.

• Ribose & Deoxyribose Nucleotides: RNA contains ribose; DNA contains deoxyribose.

• Purines and Pyrimidines: Purines (adenine, guanine) have two rings; pyrimidines (cytosine, thymine, uracil) have one ring.

• Complementary Base Pairing: A-T (DNA), A-U (RNA), G-C.

Phosphodiester Bonding

Nucleotides are linked by phosphodiester bonds between the 3' hydroxyl and 5' phosphate groups.

• Formula:

Primary and Secondary Structure of Nucleic Acids

• Primary Structure: Linear sequence of nucleotides.

• Secondary Structure: Double helix (DNA), stem-loop (RNA).

DNA and RNA Function

• DNA: Stores genetic information.

• RNA: Involved in protein synthesis and gene regulation.

Chapter 5: Carbohydrates

Structure and Function

Carbohydrates are energy sources and structural components, composed of monosaccharide monomers.

• Monosaccharide Monomers: Simple sugars like glucose, fructose.

• Glycosidic Linkages: Covalent bonds joining monosaccharides to form disaccharides and polysaccharides.

Chapter 6: Lipids

Structure and Physical Properties of Lipids

Lipids are hydrophobic molecules including fats, phospholipids, and steroids.

• Hydrocarbons: Chains or rings of carbon and hydrogen.

• Saturated, Unsaturated, and Trans Fats: Saturated fats have no double bonds; unsaturated have one or more; trans fats are artificially altered.

• Phospholipid Structure & Function: Phospholipids have hydrophilic heads and hydrophobic tails, forming bilayers in membranes.

• Amphipathic: Molecules with both hydrophilic and hydrophobic regions.

Selectively Permeable Membranes

• Influence of Structure on Permeability: Membrane composition affects what can pass through.

• Diffusion and Osmosis: Movement of molecules from high to low concentration; osmosis is diffusion of water.

• Passive and Active Transport: Passive transport does not require energy; active transport does.

• Tonicity: Isotonic (equal solute), Hypertonic (higher solute outside), Hypotonic (lower solute outside).

Chapter 7: Inside the Cell

Features of All Cells

All cells share certain features, but prokaryotic and eukaryotic cells differ in complexity.

• Prokaryotes vs. Eukaryotes: Prokaryotes lack a nucleus and membrane-bound organelles; eukaryotes have both.

• Cytoplasm & Organelles: Organelles perform specialized functions within eukaryotic cells.

• DNA, Ribosomes, Smooth & Rough Endoplasmic Reticulum, Golgi Apparatus, Peroxisomes, Lysosomes, Mitochondria, Vacuoles, Chloroplasts, Cell Wall: Each organelle has a specific role in cell function.

• Compartmentalization: Separation of cellular processes into different organelles increases efficiency.

Chapter 8: Energy and Enzymes

Enzymes and Activation Energy

Enzymes lower the activation energy required for biochemical reactions, increasing reaction rates.

• Formula:

• Competitive vs. Allosteric Enzyme Regulation: Competitive inhibitors block the active site; allosteric regulators bind elsewhere, changing enzyme shape and activity.

Chapter 11: Cell-Cell Interactions

Extracellular Layers

Cells interact with their environment and each other through specialized structures.

• Cell Walls & Extracellular Matrix: Provide structural support and mediate cell signaling.

• Lamella: Middle lamella glues plant cells together.

• Tight Junctions: Seal cells together to prevent leakage.

• Desmosomes: Anchor cells together, providing mechanical strength.

• Plasmodesmata: Channels between plant cells for communication.

• Gap Junctions: Channels between animal cells for communication.