Module 10: V9 - V13

Question 1

What is the major groove?

Answer 1

an important binding site for sequence specific protein binding

Question 2

How is information encoded in the DNA helix (apart from base pairing)?

Answer 2

H-bond acceptor / H-bond donor / other H / methyl group patterns provided by the presence of particular base pairs in the major and minor groove

Question 3

What is the significance of H-bond acceptor / H-bond donor / other H / methyl group patterns?

Answer 3

recognised by DNA binding proteins as they interact with these features

Question 4

What are characteristics of eukaryotic transcription factors?

Answer 4

transcription factors are usually made up of several domains, there is only a small number of possible DNA binding domains, most transcription factors exist in large gene families

Question 5

What is an example of a DNA binding domain?

Answer 5

a helix-loop-helix

Question 6

What is the Max subfamily?

Answer 6

subfamily of helix-loop-helix binding domains which is involved in regulating the genes for cell growth and division

Question 7

Since helix-loop-helices are able to form dimers, what is able to occur?

Answer 7

they can form both homodimers and heterodimers meaning that even more variations of transcription factors can be formed

Question 8

What happens when MYC-MAX is bound to the gene?

Answer 8

acetylation occurs resulting in activation of the gene

Question 9

What happens when MAD-MAX is bound to the gene?

Answer 9

deacetylation occurs resulting in repression of the gene

Question 10

What allows several different proteins to be produced from one gene?

Answer 10

alternative splicing in which some exons are kept in some proteins while some exons are spliced out in others

Question 11

How does one cell produce on type of mRNA and a different cell produce a different type of mRNA?

Answer 11

splicing repressors and activators which can bind to the pre-mRNA and alter how the spliceosome interacts with it
different cells have different combinations of splicing activators and repressors which allows them to produce different mRNAs and proteins from the same gene

Question 12

At which levels is eukaryotic gene expression regulated?

Answer 12

1. transcription initiation 2. posttranscriptional processing 3. RNA stability 4. transcriptional regulation 5. protein modification 6. protein transport 7. protein degradation

Question 13

What is the role of miRNAs?

Answer 13

controls the expression of genes
miRNA is the reverse complement of the targeted mRNA and it will bind to that mRNA
near-perfect complementarity = degradation of mRNA
partial complementarity = translational repression

Question 14

What may a researcher ask about a gene?

Answer 14

Is the expression high or low?

How much does it change under different conditions?

Question 15

How is quantitative reverse transcriptase PCR carried out?

Answer 15

sample taken -> RNA extracted -> exposed to DNase I to destroy the DNA -> RT reaction -> added into a quantitative RT-PCR machine (measures what cycle number it takes to acquire a certain number of copies)

Question 16

Which reagent is added to the qRT-PCR?

Answer 16

fluorescent probes which consist of a fluorophore and quenching molecule
when the fluorophore is next to the quenching molecule (unbound) there is no fluorescence and when the fluorophore is not next to the quenching molecule (bound) there is fluorescence allowing for number of copies to be detected