Week 7

Question 1

euchromatin

Answer 1

permissive chromatin environment; need HATs (acetylate histones) and ATP-dependent chromatin remodeling enzymes (slide nucleosomes around, allowing access to specific sequences in the DNA); opening chromatin is necessary but not sufficient for transcription, must have RNA polymerase recruited to the promoter as well

Question 2

transcription stimulated by activators

Answer 2

1. activator proteins bind to enhancers
2. activator proteins interact with general transcription factors, mediator proteins, or RNAP2
3. so activator proteins recruit RNAP2

Question 3

modular interactions

Answer 3

allow different transcription factors to recruit the same proteins to different DNA sequences

Question 4

introns

Answer 4

noncoding regions, must be removed by RNA splicing by the spliceosome from the DNA sequence during RNA processing

Question 5

alternative splicing

Answer 5

a certain exon being included or not, making two different proteins

Question 6

amplifying RNA

Answer 6

make a cDNA copy by reverse transcription, then amplify by PCR (RT-PCR)

Question 7

RT-PCR

Answer 7

1. degrade DNA with DNase, prime reverse transcription
2. synthesize cDNA
3. regrade RNA with RNase
4. PCR. first cycle generates double-stranded DNA. second cycle similar to first cycle of a normal PCR reaction

Question 8

adding DNA to a plasmid

Answer 8

1. cut plasmid with restriction enzymes
2. cut DNA to be inserted to generate compatible ends
3. use DNA ligase to seal up the plasmid, which now contains the insert DNA

Question 9

affinity tags

Answer 9

purifies proteins, gets protein of interest away from the other molecules

Question 10

repair by NHEJ

Answer 10

fixes the site, occasionally an inaccurate repair because it does insertions and deletions, causing frameshift mutations and inactivation of the gene

Question 11

repair by homologous recombination

Answer 11

allows you to replace the sequence with a new sequence, changes sequence of gene