transcription

Question 1

give 3 similarities between DNA replication and transcription

Answer 1

1. Both processes use DNA as the template.
2. Both synthesis directions are from 5´ to 3´.
3. Phosphodiester bonds are formed in both cases

Question 2

give 5 differences between DNA replication and protein synthesis

Answer 2

1. double/single strands
2. substrates- dNTP/NTP
3. DNA polymerase/RNA polymerase
4. product- dsDNA/ssRNA
5. thymine/uracil

Question 3

what are structural genes

Answer 3

DNA regions that can be transcribed into RNA

Question 4

what is the antisense strand

Answer 4

template strand

Question 5

what is the sense strand

Answer 5

coding strand i.e. the strand whose base sequence specifies the amino acid sequence of the encoded protein

Question 6

what is it called when transcription direction on different strands is opposite

Answer 6

asymmetric transcription

Question 7

what is the function of the α, β, β’, and σ subunits in bacterial RNA polymerase

Answer 7

α- Determine the DNA to be transcribed
β- Catalyze polymerization
β’- Bind & open DNA template
σ- Bind & open DNA template

Question 8

what does Rifampicin do

Answer 8

therapeutic drug for tuberculosis treatment, can bind specifically to the beta subunit of RNA-pol, and inhibit the RNA synthesis

Question 9

what does one operon include

Answer 9

several structural genes and upstream regulatory sequences (or regulatory regions)

Question 10

what is the -35 region of TTGACA sequence

Answer 10

recognition site and the binding site of RNA-pol

Question 11

what is -10 region of TATAAT (pribnow box)

Answer 11

region at which a stable complex of DNA and RNA-pol is formed

Question 12

what is the consensus sequence

Answer 12

a sequence of DNA having similar structure and function in different organisms

Question 13

what do the RNA polymerase holoenzyme and promoter form

Answer 13

closed promoter complex

Question 14

how does the open promoter complex form

Answer 14

when polymerase unwinds about 17 pairs

Question 15

what is a holoenzyme

Answer 15

the core enzyme saturated with sigma factor

Question 16

in bacteria what sequence does the RNA pol recognize and then after slides to

Answer 16

TTGACA region and TATAAT region

Question 17

what is the first nucleotide on RNA transcript

Answer 17

purine triphosphate

Question 18

when does the sigma subunit fall of from the RNA pol

Answer 18

once the first 3 prime,5 prime phosphodiester bond is formed

Question 19

where are the free NTPs added in bacteria

Answer 19

sequentially to the 3 prime -OH of the nascent RNA strand

Question 20

what forms the transcription bubble in bacteria

Answer 20

RNA-pol, DNA segment (~40nt) and the nascent RNA

Question 21

what
a) hybridizes with the DNA template
b) extends out the transcription bubble as the synthesis is processing
(in bacteria)

Answer 21

a) 3 prime segment

b) 5 prime segment

Question 22

what do RNA polymerases I, II and III transcribe respectively

Answer 22

rRNA, mRNA and tRNA genes, respectively

Question 23

what transcribes other RNAs as well

Answer 23

RNA polymerase III

Question 24

what are cis and trans regulatory products

Answer 24

• cis-regulatory elements are present on the same molecule of DNA as the gene they regulate (often binding sites for one or more transacting factors)
• trans-regulatory elements can regulate genes distant from the gene from which they were transcribed

Question 25

what are the cis- acting elements

Answer 25

* Promotor | * Enhancer

Question 26

what is a region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur

Answer 26

enhancer

Question 27

enhancers are only in eukaryotes, true or false

Answer 27

false, they are in both eukaryotes and prokaryotes

Question 28

what are the three cis acting elements that help | polymerase II initiate transcription in eukaryotes

Answer 28

TATA box (determine the starting point of transcription by facilitating the unwinding of the helix) CAAT box GC box

Question 29

what are the functions of the transacting elements

Answer 29

1) interact with cisacting elements to control transcription initiation 2) facilitate binding to the DNA template

Question 30

what do most transcription factors do during elongation

Answer 30

Most of the TFs fall off from from the pre-initiation complex

Question 31

what is the termination sequence in eukaryotes

Answer 31

AATAAA followed by GT repeats

Question 32

what is the primary transcript also called

Answer 32

heteronuclear RNA

Question 33

what are the postmodifications that occur on RNA

Answer 33

* Capping at the 5- end * Tailing at the 3- end * mRNA splicing * RNA edition

Question 34

what is the 5 prime cap

Answer 34

7-methylguanosine cap which is a modified guanine (G) | nucleotide

Question 35

what enzyme catalyzes the additions of 200 A nucleotides to the 3′ end of the just cleaved pre-mRNA

Answer 35

Poly (A) Polymerase (PAP)

Question 36

when cleaving, what does the endonuclease-containing protein complex bind to

Answer 36

AAUAAA sequence upstream of the cleavage site and to a GU-rich sequence downstream of the cut site

Question 37

what does the spliceosome do

Answer 37

spliceosome removes introns from a transcribed pre-mRNA

Question 38

what is RNA editing

Answer 38

may include the insertion, deletion, and base substitution of nucleotides within the RNA molecule (rare)

Question 39

what are the four rRNAs in eukaryotes first transcribed as

Answer 39

two long precursor molecules

Question 40

why are some of the bases of pre-rRNAs methylated

Answer 40

for added stability

Question 41

all of ribosome's RNA is structural, true or false

Answer 41

False. Some of a ribosome’s RNA molecules are purely structural, whereas others have catalytic or binding activities

Question 42

what is the first step in processing tRNA

Answer 42

digestion of the RNA to release individual pre-tRNAs

Question 43

what are the five steps in converting the pre-tRNA to a mature tRNA

Answer 43

(1) The 5′ end of the pre-tRNA, called the 5′ leader sequence, is cleaved off (2) The 3′ end of the pre-tRNA is cleaved off (3) a CCA sequence of nucleotides is added to the 3′end of the pre-tRNA (4) Multiple nucleotides in the pre-tRNA are chemically modified, altering their nitrogen bases (5) introns that have to be spliced out

Question 44

what are the most common modifications of tRNA nucleotides

Answer 44

conversion of adenine (A) to pseudouridine (ψ), the conversion of adenine to inosine (I), and the conversion of uridine to dihydrouridine (D)