Lecture 5

Question 1

Transcription

Answer 1

1. RNA Polymerase binds to promoter region
2. Transcription factors recognise the promoter sequence (on RNA polymerase) then leave
3. Little bits of DNA are unwound via transcription bubble, reads and copies it
4. Termination site (C and G rich) is transcribed causing hair-pin loop which pause/stops transcription or, Rho protein binds and uses helicase activity to travel up an dissociate the DNA/RNA hybrid complex

Question 2

Protein synthesis

Answer 2

2 amino acids use condensation polymerisation to form a dipeptide which is thermodynamically unfavourable due to presence of water. Hydrolysis is always favoured in an aqueous environment

Question 3

tRNA

Answer 3

brings correct aa works with aa-tRNA synthetases. Has anticodon

Question 4

rRNA

Answer 4

Ribosomal RNA combines with proteins to form the machinery for protein synthesis and catalyses peptide bond formation.

Question 5

aa-tRNA

Answer 5

Amino acyl tRNA attach the amino acid to the tRNA. They are proteins/enzymes that recognise the amino acid, the anticodon and the other parts of the tRNA therefore, different aa-tRNA for each aa combination. Catalyse the activation of aa. Use ATP hydrolysis to get the energy to make a high energy bond.

Question 6

Ribosome

Answer 6

enzymes and riboproteins. Growing protein sits in P-sites while tRNA diffuses into A-sites and used tRNA leaves E-site

Question 7

translation Steps

Answer 7

1. start codon is read by ribosome and MET begins chain
2. aa-tRNA is guided by codon/anticodon matching. Activated aa are positioned next to each other.
3. Peptidyl transferace in ribosome catalyse peptide bond formation using energy stored in the aa-tRNA bond; first MET bound to aa.
4. First tRNA released; ribosome moves along to next codon on mRNA
5. When stop codon is reached, no tRNA matches; release factor binds
6. Peptidyl transferase adds H2O instead of aa releasing in the polypeptide
7. The machinery disassembles and the parts can be released.

Question 8

Prokaryotic vs eukaryotic translation

Answer 8

less regulation in prokaryotes, special tRNA but regular MET as 1st aa, eukaryotes have 1 release whereas prokaryotes have 2-3

Question 9

Protein structure

Answer 9

Primary: aa sequence
Secondary: alpha/beta sheets
tertiary: Overall 3D arrangement of p.p chain
quartinary: multiple proteins joined to form subunits

Question 10

alpha and beta sheets

Answer 10

alpha: helical where H bonds join once part of helix to the other. side chains point outwards

Beta: pleated where H bonds occur across the sheet, point above and below.

Question 11

tertiary structure

Answer 11

held together by ionic/electrostatic and polar interactions. H bonds, hydrophobic interactions. A driving force for protein folding is the hydrophobic effect. pH, solvents and temp. are really important to maintain tertiary structure

Question 12

Protein folding

Answer 12

info encoded in the aa sequence. Burial of hydrophobic surfaces/side chains in aqueous solvent. Collapse of protein chain/formation of secondary structure. Firming up tertiary structure by interactions between different parts of the protein.