Rafferty - DNA, RNA, ribozymes Flashcards
key features of purines?
larger,
2 ring structure,
5C and 6C rings,
adenine and guanine
key features of pyrimidines?
smaller, 1 ring structure, 6C ring, cytosine and thymine and uracil U/T can form 3 H bonds but A can only form 2
6 most common p53 mutations?
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
3 types of drugs that interact with dna?
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
3 similarities in nucleic acid and protein structure?
Both have h.phobic groups on the inside
Both have h.philic groups on the outside
Both have internal H-bonds to form structure
what is the structure of the ribosome (in Svedberg units)
70S ribosome
50S large subunit (23s and 5s)
30S small subunit (16S)
name 4 antibiotics, which part of the ribosome they affect and how they affect it
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
What does the large subunit do in the ribosome? Also describe it’s structure
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
What is a riboswitch?
Segments of mRNA that bind that bind small target molecules to effect mRNA transcription
describe the structure and key catalytic groups in the AS of protein synthesis within the ribosome
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)
Describe the structure and function of the small subunit in the ribosome
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
why are base modifications so present in tRNA ?
allows flexibility - moderates rigidity of tRNA transcripts
may suit tRNA to thermophilic bacteria
what is the base triplet found in tRNA?
A=U=U - planar
what is the major stabilising force for tRNA assembly?
base stacking interactions
which enzyme attaches a/a’s to tRNA?
tRNA synthetase - recognises structures within the tRNA
describe ribozyme structure
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
describe the 4 main structural features of group II introns
binds Mg2+ via catalytic triad of bases and structurally important K+
has clear defined cleft
how do ribozymes catalyse reactions?
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
what is the driving force of protein folding?
the increase in entropy of water
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?
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
