Biochem

Question 1

Differences between DNA and RNA

Answer 1

DNA: -Longer (3x10^6 bp)
- H at 2’ carbon
- Thymine
- Few base modifications
- Base has methyl group (thymine)

RNA: - shorter (few thousand bp)
- OH at 2’ carbon
- Uracil
- Lots of base modifications
- Base doesn’t have methyl group (uracil)

Question 2

2 forces that stabilize alpha helices

Answer 2

Base stacking: Hydrophobic bases stack on top of each other
Base pairing: H-Bonds between bases (3 between G-C)

Question 3

What factors affect Tm (at least 5)

Answer 3

Increase:
- Increase in length of DNA
- Increase in % GC regions (base stacking)
- Increase in bp complementation
- Increase in [salt] (makes environment more hydrophilic therefore increase hydrophobic base stacking affect in helix)
Decrease:
- [organic solvent], [urea], [formamide]
- Extremes in pH

Question 4

What do the major and minor groove do + example

Answer 4

directly provide sequencing information to DNA-binding proteins
- Protein alpha helix sits in major groove; Way for protein to get a direct read of the information in DNA w/o having to unwind it; Protein side chains make contact with the DNA bases; DNA-Protein interaction; recognize promoter for example

Question 5

DNA dimensions and bp

Answer 5

tall: 10 cm/3.4 nm (bp is 0.34 nm)
Width: 2 nm (20 A)

Question 6

What makes up a nucleosome and how many bp

Answer 6

Nucleosome core particle (150bp)
- 150 bp of DNA wrapped around a histone core octamer; 2 of each histone protein (H2A, H2B, H3, H4)
+Linker DNA (50 bp)

Question 7

Whats 30nm chromatin fibre

Answer 7

Nucleosome core particles stacked tightly together
Requires H1 histone

Question 7

What are histones

Answer 7

Proteins that package DNA; Mostly made up of Arg and Lys (both + charge to complement DNA - charge)
- Highly conserved throughout diff organisms

Question 8

Describe the steps of replication

Answer 8

1) Uncoiling: Done by helicase; strands held apart by ssb proteins
2) Primer synthesis: Primase will make short RNA primer (10-20nt)