Midterm 2.4.1

Question 1

is DNA inert?

Answer 1

yes. it must be converted to RNA via transcription to carry out functions (encode genes)

Question 2

3 phases of transcription

Answer 2

initiation, transcription/elongation, termination

Question 3

what is the name of the DNA sequence that guides transcriptional initiation?

Answer 3

promotors

Question 4

where do promotors reside?

Answer 4

upstream of (before) genes (left)

Question 5

what determines whether or not a sequence acts as a promotor & if the promoter is active?

Answer 5

binding of sigma factors and regulatory factors

Question 6

what enzyme is involved in transcription? what is on it that is essential in initiating transcription?

Answer 6

RNA polymerase. a special subunit on RNA polymerase is the sigma factor which binds to DNA

Question 7

what is sigma factor recognized as? how many sequences does it recognize?

Answer 7

σ70 or RpoD

Question 8

sequences are ___

Answer 8

degenerate (don’t usually match exactly)

Question 9

what is special about RpoD and RpoS?

Answer 9

they are sigma factors that are general, and affect many genes. the other sigma factors are specialized

Question 10

how many bp’s uptream of the transcriptional start site (+1) does RpoD recognize a sequence? (2)

Answer 10

~35 and ~10 (Pribnow box, TATAAT), upstream from the mRNA start site

Question 11

going upstream goes to which end of the DNA?

Answer 11

5’

Question 12

what direction would gene x go?

Answer 12

5’ to 3’

Question 13

what does RNA polymerase do?

Answer 13

it binds to DNA template and makes an RNA copy of one of two strands

it binds to the promoter, signaling the start of a gene

it builds RNA 5’ to 3’ because transcription only goes in one direction

Question 14

what is RNA polymerase core enzyme made of? (5 subunits)

Answer 14

2 copies of ⍺
β
β’
ω

Question 15

what does holoenzyme have?

Answer 15

sigma subunit

Question 16

what does RNA polymerase core enzyme and sigma factor make?

Answer 16

a functional enzyme, holoenzyme

Question 17

what does core enzyme do>

Answer 17

unwinds DNA to expose template, forms the transcription bubble

Question 18

what does the RNA chain use as a substrate and guide to build one nucleotide at a time?

Answer 18

NTPs (ATP, CTP, GTP, UTP) as substrates

template strand as a guide

Question 19

what happens when RNA polymerase encounters a transcriptional terminator?

Answer 19

RNA polymerase will dissociate from the template and release the RNA

Question 20

when does transcription stop?

Answer 20

when RNAP encounters a transcriptional terminator

RNAP dissociates from DNA stops making RNA and releases transcript

Question 21

what forms when RNA hairpin structures form, followed by a string of U residues? what do U residues act as? what does the formation of the hairpin do?

Answer 21

intrinsic (rho-independent) terminators

U residues act as a pause signal for RNAP

the formation of the hairpin forces RNAP off the template

Question 22

central dogma:

Answer 22

DNA is replicated
DNA is transcribed to RNA
RNA is translated to protein

Question 23

what are rho dependent terminators

Answer 23

protein called Rho binds RNA as it is being transcribed and causes RNA polymerase to dissociate after it encounters certain sequences

Question 24

3 majors classes of RNA

Answer 24

mRNA - converted to protein via translation
tRNA - functional RNA, used in translation process
rRNA - functional RNAs, used in translation process

Question 25

mRNAs contain:

Answer 25

ORF and UTR

ORFs are translated to protein

UTRs are part of the mRNA transcript that are not translated int protein

Question 26

mRNAs that encode multiple ORFs are…
such genes are arranged in an…

Answer 26

polycistronic
operon. genes in an operon are cotranscribed

Question 27

organization of bacterial mRNA: in a simple mRNA encoding a single open reading frame (ORF):

Answer 27

5’UTR: everything from first transcribed residue (+1) through the start codon of the gene. contains RBS

ORF: start codon through stop codon

3’UTR: everything from the stop codon of the gene through the final transcribed residue. often contains transcriptional terminator sequences