Rafferty - DNA, RNA, ribozymes

Question 1

key features of purines?

Answer 1

larger,
2 ring structure,
5C and 6C rings,
adenine and guanine

Question 2

key features of pyrimidines?

Answer 2

smaller, 
1 ring structure, 
6C ring, 
cytosine and thymine and uracil
U/T can form 3 H bonds but A can only form 2

Question 3

6 most common p53 mutations?

Answer 3

2 Arg for interacting with sugar-phosphate backbone
3 Arg which H-bond within protein structure and stabilise conformation
Gly245 stabilises structure of loop in minor groove

Question 4

3 types of drugs that interact with dna?

Answer 4

Intercalating drugs – stack between bases – disrupt DNA structure
Major groove binding drugs – binding proteins can’t bind and begin transcription
Minor groove binding drugs - binding proteins can’t bind and begin transcription and possible structural changes

Question 5

3 similarities in nucleic acid and protein structure?

Answer 5

Both have h.phobic groups on the inside
Both have h.philic groups on the outside
Both have internal H-bonds to form structure

Question 6

what is the structure of the ribosome (in Svedberg units)

Answer 6

70S ribosome
50S large subunit (23s and 5s)
30S small subunit (16S)

Question 7

name 4 antibiotics, which part of the ribosome they affect and how they affect it

Answer 7

Small subunit + tetracycline - Binds to tRNA A site
Small subunit + streptomycin - Interferes with mRNA/tRNA recognitions (error prone)
Large subunit + chloramphenicol - Blocks tRNA associated with A site
Large subunit + erythromycin - Blocks entrance to tunnel

Question 8

What does the large subunit do in the ribosome? Also describe it’s structure

Answer 8

Catalyses peptide bond formation
2 pieces of RNA - complicated organisation into helices
Contains proteins - none near AS or ribosome
Core subunit within large subunit is a packed mass of RNA helices

Question 9

What is a riboswitch?

Answer 9

Segments of mRNA that bind that bind small target molecules to effect mRNA transcription

Question 10

describe the structure and key catalytic groups in the AS of protein synthesis within the ribosome

Answer 10

AS is definitely RNA catalysed not protein catalysed

Catalysis involves adenine in unusual environment which increases its pKa, making it (+) charged at pH 7 (not neutral)

Question 11

Describe the structure and function of the small subunit in the ribosome

Answer 11

Proteins on ribosome exterior stabilise structure
Interior proteins link domains
Small subunit decodes genetic information in translation
Binds mRNA and tRNA
Can rotate about large subunit maybe how ribosome moves along mRNA, as tRNAs enter and leave

Question 12

why are base modifications so present in tRNA ?

Answer 12

allows flexibility - moderates rigidity of tRNA transcripts

may suit tRNA to thermophilic bacteria

Question 13

what is the base triplet found in tRNA?

Answer 13

A=U=U - planar

Question 14

what is the major stabilising force for tRNA assembly?

Answer 14

base stacking interactions

Question 15

which enzyme attaches a/a’s to tRNA?

Answer 15

tRNA synthetase - recognises structures within the tRNA

Question 16

describe ribozyme structure

Answer 16

WC pairing between bases - same stacking interactions
majority is a-form helix
structures linked via metal ions and base triplets
h. phobic interactions are driving force of formation

Question 17

describe the 4 main structural features of group II introns

Answer 17

binds Mg2+ via catalytic triad of bases and structurally important K+
has clear defined cleft

Question 18

how do ribozymes catalyse reactions?

Answer 18

they have unpaired bases in unusual environments

this allows the bases to have a variety of catalytic abilities - similar to that of a/a’s in proteins

Question 19

what is the driving force of protein folding?

Answer 19

the increase in entropy of water

Question 20

brief summary of RNase A

• what does it do?
• what are the key catalytic units
• briefly describe its structure
• how was the structure determined (3 steps)
• what is its medical importance?

Answer 20

cleaves the phosphodiester bond between a U/C and the next RNA base
uses acid-base catalysis with His119 and His12
has specificity pocket of Ser/Thr (U/C determination) and Phe (base interactions)
made of 3beta antiparallel sheets and 3 alpha helices -(his12 on one alpha helix) contains 4 disulphide bonds
found out structure via solution studies, kinetic studies and chemical modification
medically important for angiogenin inhibitors - cancer