New: RNA Synthesis and Regulation

Question 1

a DNA sequence that is transcribed

Answer 1

gene

Question 2

central dogma

Answer 2

biological information flow from DNA to RNA irreversible except by viral reverse transcriptase; RNA to protein is always irreversible

Question 3

housekeeping genes encode

Answer 3

proteins or RNA essential for normal activities of the cell

Question 4

DNA is transcribed to ____ is translated to _____

Answer 4

RNA; protein

Question 5

Exceptions to the central dogma

Answer 5

RNA–> DNA via reverse transcriptase

protein –> protein (prion protein)

Question 6

Prions-proteinaceous infections particles do what to proteins

Answer 6

like a virus, prions cannot replicate themselves, it enters a cell then it converts normal proteins into prions

Question 7

prion proteins are a

Answer 7

tightly packed beta sheet that is too stable

Question 8

examples of prion-proteinaceous infectious particle diseases

Answer 8

bovine spongifrom encephalopathy; creutzfeldt-jakob; chronic wasting;

Question 9

4 types of RNA

Answer 9

transfer (tRNA)
ribosomal (rRNA)
messenger (mRNA)
small/micro RNA

Question 10

transfer RNA

Answer 10

carries amino acids to translation machinery; very stable

Question 11

ribosomal RNA

Answer 11

makes up much of the ribosome; very stable; majority of cellular RNA

Question 12

messenger RNA

Answer 12

encodes message from DNA to ribosomes
rapidly degraded by nucleases (clicker Q)
small fraction of steady-state RNA, but uses a large percentage of synthetic capacity of cell

Question 13

small/micro RNA

Answer 13

participate in metabolic events; many have catalytic activity and are turned over rapidly

Question 14

Transcription in E. coli RNA polymease catalyzes

Answer 14

DNA-directed RNA synthesis (transcription)

Question 15

RNA pol is core of a larger

Answer 15

transcription complex

Question 16

complex assembles at one end of a gene when transcription is

Answer 16

initiated

Question 17

DNA is continuously unwound as RNA pol catalyzes a

Answer 17

processive elongation of RNA chain

Question 18

transcription complex responds to specific ________ signals and disassembles

Answer 18

termination

Question 19

the synthesis of RNA from DNA template is called

Answer 19

transcription

Question 20

transcription is catalyzed by

Answer 20

RNA polymerase

Question 21

RNA polymerase requires the following 3 things:

Answer 21

1. a template (but uses T instead of U)
2. Activated precursors in the form of the four ribonucleoside triphosphates ATP, GTP, UTP, CTP
3. Divalent metal ions, either Mg2+, or Mn2+

Question 22

How many subunits is RNA polymerase composed of

Answer 22

multiple

Question 23

core enzyme

Answer 23

alpha2betabeta’omega participates in many of the transcription reactions

Question 24

Beta subunit in RNA polymerase assists in

Answer 24

*DNA binding and catalysis

Question 25

a subunits are scaffolding and interact with

Answer 25

other proteins that regulate transcription

Question 26

omega subunit aids in restoring

Answer 26

denatured polymerase

Question 27

sigma subunit is used for

Answer 27

*promoter recognition

Question 28

RNA polymerazation chain elongation reaction

Answer 28

mechanism almost identical to that for DNA polymerase - growing RNA chain is base-paired to DNA template strand

Question 29

Step one of RNA polymerase reaction is incoming ribonucleotide triphosphates (RTPs) form correct H bond to template and

Answer 29

new phosphodiester bond formed and PPi released

Question 30

in RNA polymerase chain elongation reaction it is catalyzed in the 5'-->3' direction, is highly processive and thermodynamically assisted by

Answer 30

PPi hydrolysis

Question 31

transcription is initiated at ______ _____ on the DNA template

Answer 31

promoter sites

Question 32

three stages of RNA synthesis are

Answer 32

initiation, elongation, and termination

Question 33

how does RNA polymerase know where to start?

Answer 33

specific DNA sequences called promoters

Question 34

in E. coli 2 DNA sequences that act as promoter for many genes are the -10 sequence and at the -35 sequence these are the

Answer 34

TATA or Pribow box

Question 35

operon

Answer 35

transcription unit in which several genes are contranscribed from a single promote in prokaryotes

Question 36

in ____ not every gene needs a promoter

Answer 36

E. coli

Question 37

a genes start site is said to be _____ of its stop codon

Answer 37

upstream

Question 38

convention for double stranded DNA: coding and template strands are written in what direction?

Answer 38

``` Coding strand (top) is written 5' --> 3' (also called 'sense') template strand (bottom) is written 3'-->5' ```

Question 39

gene is transcribed from the

Answer 39

5'-->3' end

Question 40

template strand of DNA is copied from

Answer 40

3' --> 5'

Question 41

transcription complex assembles at a

Answer 41

promoter

Question 42

consensus sequences are found

Answer 42

upstream from transcription start sites

Question 43

strong promoters

Answer 43

match consensus sequence closely

Question 44

weak promoters

Answer 44

match consensus sequences poorly

Question 45

DNA-binding proteins bind to promoter sequences and direct RNA pol to the

Answer 45

promoter site

Question 46

the sigma subunit of prokaryotic RNA polymerases is required for promoter recognition and formation of the

Answer 46

complex

Question 47

what subunit recognizes the promoter

Answer 47

sigma subunit

Question 48

sigma subunit ___ the affinity of the core polymerase for specific promoter sequences

Answer 48

increases

Question 49

sigma subunit _____ the affinity of the core polymerase for nonpromoter regions

Answer 49

decreases

Question 50

**if a core polymerase lacks a sigma factore then it will bind to DNA

Answer 50

nonspecifically

Question 51

the sigma factor acts catalytically - one sigma can aid many polymeraes in finding

Answer 51

promoters

Question 52

e. coli has many different sigma factors that recongnize different consensus sequences at the

Answer 52

promoter

Question 53

RNA polymerase changes

Answer 53

conformation

Question 54

RNA polymerase rapidly searches for and bind promoter but initiation is

Answer 54

slow

Question 55

unwinding of DNA at the initiation site requires a conformational change with is often the

Answer 55

rate limiting step

Question 56

RNA pol (R) and promoter (P) shift from

Answer 56

closed complex (DNA ds) to open complex (18 bp DNA unwound - forms transcription bubble)

Question 57

RNA polymerase lacks a

Answer 57

helicase

Question 58

RNA polymerase can start RNA synthesis de novo which means

Answer 58

no primer needed

Question 59

transcription bubble is the

Answer 59

region containing RNA polymerase, DNA, and RNA product

Question 60

steps of initiation of transcription in E. coli

Answer 60

* 1. RNA polymerase binds non-specifically to DNA 2. holoenzyme conducts a 1-D search for promoter 3. holoenzyme and promoter form a closed complex 4. conformational change to open complex - transcription bubble form, short stretch of RNA made 5. sigma subunit dissociates from core, other accessory proteins (NusA) bind to polymerase - promoter clearance, shift to elongation stage

Question 61

transcription termination

Answer 61

only certain regions of DNA are transcribed; transcription compexes assemble a promoters and disassemble at the 3' end of genes at specific termination sequences

Question 62

two types of termination sequences

Answer 62

1. unstable elongation complex | 2. rho-dependent termination

Question 63

regions of the gene where the rate of elongation slows down or stops temporarily

Answer 63

pause sites

Question 64

pause is exaggerated when newly transcribed RNA can form what type of structure

Answer 64

hairpin

Question 65

hairpin may ________ RNA-DNA hybrid in elongation complex

Answer 65

destabilize

Question 66

Rho-dependant termination sites; rho triggers disassembly of the transcription complex at some pause sites by

Answer 66

binding RNA and destabilizing RNA-DNA hybrid

Question 67

Rho binds to ssRNA chain, destabilizing the RNA-DNA hybrid and

Answer 67

terminating transcription

Question 68

precursors of tRNA and rRNA are cleaved and chemically modified after

Answer 68

transcription

Question 69

the final mature RNA is cleaved from a larger

Answer 69

precursor

Question 70

many tRNA transcripts lack CCA sequence at the 3' end of the strand, these nucleotides are added

Answer 70

post- transcriptionally

Question 71

the bases and riboses of tRNA and rRNA are modified for instance by the attachment of

Answer 71

methyl groups

Question 72

some antibiotics inhibit

Answer 72

bacterial transcription

Question 73

rifampicin inhibits initiation by binding to the polymerase and blocking the exit of the

Answer 73

nascent RNA

Question 74

actinomycin intercalates between the bases of the DNA double helix, preventing the DNA from

Answer 74

being used as a template

Question 75

example of an operon

Answer 75

lactose operon

Question 76

some mRNAs directly sense and respond to

Answer 76

metabolites

Question 77

riboswitches

Answer 77

bind small molecules that cause as structural change in the riboswitch that terminates the synthesis of the mRNA

Question 78

transcription and translation occur at the same time in prokaryotes which ______ in eukaryotes

Answer 78

can not happen

Question 79

gene expression in eukaryotes is influences by 3 important characteristics

Answer 79

1. complex transcription regulation 2. RNA processing, including extensive processing of mRNA precursors 3. the nuclear membrane that separates the site of RNA synthesis from that of protein synthesis

Question 80

RNA synthesis is catalyzed by 3 RNA polymerases that differ in

Answer 80

DNA substrate specificity and location

Question 81

in eukaryotes, each type of polymerase has a distinct

Answer 81

promoter element

Question 82

in eukaryotes, the promoters bind to proteins, called trans-acting elements or transcription factors, that

Answer 82

regulate polymerase activity

Question 83

RNA pol 2 requires

Answer 83

complex regulation

Question 84

most genes transcribed by RNA pol 2have an A/T rich sequence called

Answer 84

TATA box

Question 85

TATA box is located

Answer 85

-24 to -32

Question 86

initiator element (Inr) is at the transcriptional

Answer 86

start site

Question 87

The TFIID complex initiates assembly of the

Answer 87

active transcription complex

Question 88

transcription factors for RNA polymerase 2 =

Answer 88

TFII

Question 89

in genes with a TATA box, the _____, a component of TFIID, binds to the TATA bos

Answer 89

TATA box binding protein (TBP)* key player

Question 90

TFIIH binds to the complex and phosphorylates the carboxyl-terminal domain (CTD) of the polymerase, facilitating the transition from

Answer 90

initiation phase to the elongation phase.

Question 91

multiple transcription factors interact with eukaryotic promoters and

Answer 91

enhancers

Question 92

a large complex called ______ acts as a bridge between enhancer-bound activators and proteins, including the polymerase, at the promoter

Answer 92

mediator