Biology 311 Human Genetics Fall 2006Chap. 1 Outline and Study QuestionsBased on Strachan and Read (2005) Human Molecular Genetics, third editionChap. 1 Outline:1. DNA and RNA- Structure of bases, nomenclature2. Proteins- Structure of amino acids- Chemical nature of side chains3. DNA double helix- Features: complementary, antiparallel, hydrogen bonding4. DNA replication- Semi-conservative model- Okazaki fragments- Enzymes5. Gene expression- Transcription- Translation- Colinearity of gene and protein6. Eukaryotic transcription- Promoters- Enhancers/Silencers- Transcription factors7. RNA processing- GT-AG rule- Branch site- Splicesome- Capping - Polyadenylation8. Translation- Ribosomes- Genetic code- Wobble hypothesis9. Post-translational modifications- Carbohydrate groups- Lipid groups- Proteolytic cleavage- Secretion/export10. Protein secondary and tertiary structureStudy Questions: Review of molecular biology (20 points) 1Please print out your brief, but complete, answers to these questions on separate pages and hand in Monday Aug. 28 in class1. How are the purine bases chemically different from pyrimidine bases?2. Distinguish between the following terms: base, nucleoside, nucleotide, and give an example of each. You may use chemical structures to illustrate your answer.3. Compare the chemical structures of a basic amino acid (such as lysine) and an acidic amino acid (such as glutamic acid). Show the charges on the side chains at pH 7.4. Compare the chemical structure of a small non-polar amino acid (such as alanine) to one with a bulky hydrocarbon side chain (such as isoleucine). What kind of chemical interactions are non-polar side chains involved in?5. Which amino acids contain sulfur? Which contain hydroxyl (-OH) groups? Which contain amide groups?6. For each of the following weak bonds: hydrogen, ionic, Van der Waals, hydrophobic forces, briefly indicate what sort of interaction is involved and illustrate how they may contribute to the secondary or tertiary structure of a protein.7. Distinguish between A-DNA, B-DNA and Z-DNA? Which structure did Watson and Crick devise a model for? Which structures did Rosalind Franklin provide X-ray evidence for?8. Briefly explain how the following terms pertain to the structure of DNA: antiparallel, 5’ end, 3’ end, complementary, major groove, minor groove.9. How do the following terms pertain to DNA replication: semi-conservative model, Okazaki fragments, leading strand, lagging strand?10. What are the roles of the following proteins in DNA replication: Topoisomerase, helicase, DNA polymerases, primase, ligase, single-stranded binding protein?11. How do the following terms relate to the process of transcription: initiator nucleotide, template strand, sense strand, antisense strand, upstream sequences, downstream sequences, transcription factors, promoter?12. What critical information is required in a eukaryotic gene to enable splicing to occur? Distinguish between splicing, capping, and polyadenylation in eukaryotic gene expression.213. How was the genetic code deduced? What is meant by the following terms: triplet code, codon, anticodon, degenerate, wobble pairing, reading frame, 5’ UTR, 3’ UTR?14. What is meant by each of the following protein modifications: phosphorylation, acetylation, N-glycosylation, myristoylation, cleavage of signal sequence?15. Distinguish between the following features of protein structure: α-helix, β-pleated sheet, disulfide bridges, hydrogen bonds, protein