Biochem Exam 3 Study Guide

1. Fundamentals of Bonding, Amino Acids, Proteins, and Enzymes

• Review covalent, ionic, hydrogen bonds, and van der Waals forces.

• Amino acids: Know structure, properties, and classifications (polar, nonpolar, charged).

• Proteins: Understand primary, secondary, tertiary, and quaternary structures.

• Enzymes: Study catalysis, kinetics (Michaelis-Menten, Lineweaver-Burk), and inhibition types.

2. Nucleic Acids

• Recognize and name nucleotides (adenine, thymine, cytosine, guanine, uracil).

• Differentiate purines (A, G) from pyrimidines (C, T, U).

• Structure of DNA/RNA: Identify phosphate-sugar backbone, base pairing (A-T, C-G), and directionality (5' → 3').

3. Open Reading Frames (ORFs) in DNA

• Identify ORFs in double-stranded DNA.

• Look for start codon (ATG) and stop codons (TAA, TAG, TGA).

• Read both strands to find potential coding regions.

4. Polymerases & Their Mechanisms

• DNA polymerase: Synthesizes DNA from a template, requires dNTPs and a primer.

• RNA polymerase: Synthesizes RNA from DNA, requires rNTPs and no primer.

• Understand proofreading mechanisms (exonuclease activity) and error rates.

5. Synthetic Biology Applications

• Reading DNA sequencing gels: Recognize bands corresponding to nucleotides in Sanger sequencing.

• Cloning & gene expression in bacteria:

  • Insert DNA into a plasmid vector.

  • Requires promoters, ribosome binding sites, and antibiotic resistance markers.

  • Restriction enzymes recognize palindromic sequences (e.g., EcoRI: GAATTC).

6. Carbohydrates

A. Nomenclature

• Aldoses vs. ketoses: Recognize the carbonyl group location.

• D vs. L configurations: Based on the position of the hydroxyl (-OH) group on the chiral center.

B. Converting Fischer ↔ Haworth Projections

• Fischer: Straight-chain representation.

• Haworth: Cyclic form (pyranose for 6-membered rings, furanose for 5-membered rings).

• Example: Convert D-galactose to β-D-galactopyranose.

C. Glycobiology & Glycoproteins

• Functions of glycoproteins: Cell signaling, immunity (antibodies), and molecular recognition.

7. Membranes

A. Fatty Acids & Lipids

• Recognize saturated vs. unsaturated fatty acids.

• Draw key phospholipids and glycolipids.

B. Hydropathy Plots

• Used to predict membrane-spanning regions of proteins.

• Hydrophobic regions correspond to transmembrane domains.

C. Types of Membrane Proteins

• Integral: Embedded in the membrane (e.g., GPCRs, ion channels).

• Peripheral: Attach to membrane surfaces (e.g., signaling proteins).

• Lipid-anchored: Covalently linked to lipids (e.g., GPI-anchored proteins).

D. Transport Mechanisms

• Passive Transport: No energy required.

  • Simple diffusion: Moves down concentration gradient.

  • Facilitated diffusion: Uses channels or carriers (e.g., GLUT transporters).

• Active Transport: Requires ATP.

  • Na⁺/K⁺ ATPase pumps 3 Na⁺ out and 2 K⁺ in.

  • Proton pumps create electrochemical gradients.

• Channels vs. Pumps:

  • Na⁺ and K⁺ channels help propagate action potentials in neurons.

Final Review Concepts

• Transcription & Translation:

  • -35 and -10 regions in promoters (TTGACA, TATAAT).

  • Start codon (ATG) and ribosome binding site (Shine-Dalgarno sequence: AGGAGG).

• Electrophysiology: Na⁺ and K⁺ channels regulate nerve impulse conduction.