L 17

Question 1

DNA binding proteins have specific what that allows them to interact with DNA

Answer 1

specific motifs

Question 2

Proteins that bind to DNA via interactions with sugar phosphate backbone of DNA function are…

Answer 2

replication and maintenance

i.e histones helicases, DNA polymerases

Question 3

Proteins that bind to DNA via sequence spec interactions functions are

Answer 3

site spec cleavage, RNA transcription

i.e transcription factors, restriction endocnucleases

Question 4

Sequence specific DNA binding protein discriminate between what?

Answer 4

base pairs

Question 5

Major groove of DNA allows for more contacts because

Answer 5

it is more exposed

Question 6

How do sequence spec DNA binding proteins bind?

Answer 6

via H-bond, VDW and ionic interactions

binds loosely to DNA to scan until spec DNA sequence is found then tight binding

Question 7

Prokaryotes transcripe by

Answer 7

Type II restriction endonuclease

motif ex: helix turn helix motif with two alpha helices, about 120 degree from ea ch other

Question 8

Transcription for eukaryotes

Answer 8

motif examples: zinc finger or leucine zipper or basic helix loop helix

endonuclease cleaves a nucleic acid with poly nucleotide strand

exonuclease cleaves a nucleic acid by removing one of the terminal residues

Question 9

What are three major types of RNA

Answer 9

rRNA
tRNA
mRNA

and noncoding RNA

Question 10

All cellular RNAs are transcribed from what?

Answer 10

DNA templates

Question 11

RNAPs are

Answer 11

RNA polymerases

Question 12

DNA dependent DNA polymerases can only add nucleotides to free what?

Answer 12

free 3OH

so even the leading strand during DNA replication , a RNA primer is needed, but no need RNA polymerase

Question 13

Why is only one strand of DNA copied in the bubble?

Answer 13

steric hindrance

Question 14

What are promoters?

Answer 14

RNA polymerases are large multi subunit complexes that bind DNA at spec sites

Question 15

The DNA strand copied during transcription is what?

Answer 15

antisense (noncoding strand) and complementary to RNA

Question 16

What does the coding DNA strand have?

Answer 16

The same sequence as transcribed RNA, except for U vs T

Question 17

Torsional tension is what?

Answer 17

driver of transcription versus falling off

Question 18

RNA polymerases is processive and rapid

Answer 18

at 20-50 nt/sec

Question 19

Transcription of ribosomal genes?

Answer 19

1. gene regulation dicates rate of transcription
2. initiate spec sites in DNA
3. multiple RNAPs can successively bind to promoter
4. constitutive enzymes vs inducible enzymes
5. transcripts vary in their stability
6. Termination at specific site

Question 20

genetic units in bacteria (operons) have promoters that are recognized by what factors?

Answer 20

sigma factors that help initiation factors

Question 21

sigma factor proteins direct what to the promoter?

Answer 21

RNAP

dif bonding sites have dif sigma factors that help find initiation site

Question 22

What are three eukaryotic DNA dependent RNA polymerases?

Answer 22

RNAP I, RNAP II, RNAP III

Question 23

What does RNAP I synthesize?

Answer 23

most rRNA that resides in nucleolus

Question 24

What does RNAP II synthesizes what?

Answer 24

mRNA: resides in nucleoplasm

Question 25

What does RNAP III synthesize ?

Answer 25

5s rRNA, tRNA, and many other RNA types: resides in nucleoplasm

Question 26

Where are other dedicated RNAPs in?

Answer 26

mitochondria and choloroplasts

Question 27

how is transcription in eukaryotes different from prokaryotes?

Answer 27

different promoters allows dynamic range for mRNA production not found in prokaryotes

Question 28

What is PIC

Answer 28

pre initiation complex

Question 29

What is GTFs

Answer 29

general Transcription Factors

Question 30

RNAP II and GTFs form what

Answer 30

PIC

Question 31

What is TBP?

Answer 31

TATA binding protein. Key to subunit of TFIID

Question 32

What does TBP do to untwist the DNA?

Answer 32

into a 45 degree bend into double helix

Question 33

TBP is a universal GTF that requires what for initiation

Answer 33

RNAP I, RNAP II, RNAP III

Question 34

Unphosphorylated RNAP II initiates what?

Answer 34

transcription

Question 35

Phosphorylated RNAP II can do what?

Answer 35

elongate

Question 36

Inhibitors of transcription are also known as

Answer 36

antibiotics

Question 37

What does Rifampicin do (antibiotic)?

Answer 37

inhibits prokaryotic, not eukaryotic by preventing elongation of RNAP

Question 38

What does Actinomycin D (antibiotic) do?

Answer 38

binds to duplex DNA and blocks transcription and replication

Question 39

What does the Death Cap mushroom derived alpha amanitan antibiotic do?

Answer 39

binds to RNAP II and RNAP III blocks elongation steps (not prokaryotic)

Question 40

What does DNA polymerases do that the RNA polymerases don't?

Answer 40

DNA polymerases require an initiating primer made from either DNA or RNA

Question 41

Most eukaryotic mRNA transcripts are spliced, what does this mean?

Answer 41

introns are removed and exons remain.