Lecture 35 Rna Synthesis And Regulation

Front 1

True or false: biological information flow from DNA to RNA is always irreversible.

Back 1

false, viral reverse transcriptase

Front 2

True or false: biological information flow from RNA to protein is always irreversible.

Back 2

true

Front 3

DNA sequence that is transcribed

Back 3

gene

Front 4

encode proteins or RNA essential for normal activities of the cell

Back 4

housekeeping genes

Front 5

What are three examples of housekeeping genes?

Back 5

enzymes in basic metabolic pathways

tRNA

rRNA

Front 6

What is the second exception to the "Central Dogma"?

Back 6

protein -> protein

Front 7

What are three diseases caused by prions?

Back 7

BSE (bovine spongiform encephalopathy)

CJD (Creutzfeldt-Jakob)

CWD (chronic wasting disease)

Front 8

True or false: prion diseases are universally fatal.

Back 8

true

Front 9

How is a prion like a virus?

Back 9

cannot replicate by itself

Front 10

What happens once a prion enters a cell?

Back 10

It converts normal proteins into prions.

Front 11

tightly packed Beta-sheet that is too stable to be turned over

Back 11

prion

Front 12

What are three other diseases that may be attributed to prions?

Back 12

Alzheimer's

FTD (fronto-temporal dementias)

Parkinson's

Front 13

True or false: tRNA is very stable.

Back 13

true

Front 14

carries amino acids to translation machinery

Back 14

tRNA

Front 15

True or false: rRNA is very stable.

Back 15

true

Front 16

What makes up the majority of cellular RNA?

Back 16

rRNA

Front 17

True or false: mRNA is very stable.

Back 17

false, rapidly degraded by nucleases

Front 18

encodes message from DNA to ribosomes

Back 18

mRNA

Front 19

uses a large percentage of synthetic capacity of cell

Back 19

mRNA

Front 20

many have catalytic activity and are turned over rapidly

Back 20

small/micro RNA

Front 21

DNA-directed RNA synthesis

Back 21

transcription

Front 22

What catalyzes transcription?

Back 22

RNA polymerase

Front 23

core of a larger transcription complex

Back 23

RNA polymerase

Front 24

True or false: elongation of RNA chain is processive.

Back 24

true

Front 25

Which type(s) of RNA is/are generally rapidly degraded by nucleases?

Back 25

small RNA and mRNA

Front 26

Which strand is complementary to mRNA?

Back 26

template strand

Front 27

What strand matches mRNA?

Back 27

coding strand

Front 28

antisense strand of DNA

Back 28

template

Front 29

sense strand of DNA

Back 29

coding

Front 30

What three things are required for RNA polymerase?

Back 30

template

ribonucleoside triphosphates

divalent metal ions, either Mg2+ or Mn2+

Front 31

What are the subunits of RNA polymerase core enzyme?

Back 31

2alpha

Beta

Beta'

omega

Front 32

Which subunit(s) of RNA polymerase assist(s) in DNA binding and catalysis?

Back 32

Beta and Beta'

Front 33

Which subunit(s) of RNA polymerase is/are scaffolding and interact(s) with other proteins that regulate transcription?

Back 33

alpha

Front 34

Which subunit(s) of RNA polymerase aid(s) in restoring denatured polymerase?

Back 34

omega

Front 35

Which subunit(s) of RNA polymerase recognize(s) promoter?

Back 35

sigma

Front 36

important in contacting proteins that assists with processivity of RNA polymerase

Back 36

two alpha subunits in the back

Front 37

What is the rate of RNA transcription compared to DNA replication?

Back 37

1/10th

Front 38

What is the error rate of RNA transcription and how does it compare to DNA replication?

Back 38

10^-6, which is higher than DNA replication because there's not proofreading and mistake isn't passed on to daughter cells so it's okay

Front 39

What are the three stages of RNA synthesis?

Back 39

initiation

elongation

termination

Front 40

How does the RNA polymerase know where to start?

Back 40

promoter

Front 41

specific DNA sequences that direct RNA polymerase to the proper initiation site

Back 41

promoters

Front 42

What is the promoter in E. coli?

Back 42

TATA box and -35 sequence

Front 43

Where does transcription complex assemble?

Back 43

at initiation site (DNA promoter region)

Front 44

transcription unit in which several genes are cotranscribed from a single promoter

Back 44

operon

Front 45

True or false: operons are found in eukaryotes.

Back 45

false, prokaryotes

Front 46

True or false: eukaryotic genes generally have their own promoter.

Back 46

true

Front 47

What is frequency of transcription initiation related to?

Back 47

need for gene product

Front 48

What is the directionality of copying the template strand of DNA in transcription?

Back 48

3' to 5'

Front 49

A gene's start site is said to be what of its stop codon?

Back 49

upstream

Front 50

Where are consensus sequences found?

Back 50

upstream from transcription start sites

Front 51

match consensus sequence closely

Back 51

strong promoters

Front 52

match consensus sequences poorly

Back 52

weak promoters

Front 53

bind to promoter sequences (prokaryotes and eukaryotes) and direct RNA polymerase to the promoter site

Back 53

DNA-binding proteins

Front 54

What is required for promoter recognition and formation of the complex in prokaryotes?

Back 54

sigma subunit

Front 55

Would housekeeping genes have a strong or weak promoter?

Back 55

strong, need a lot

Front 56

Does the sigma subunit increase or decrease the affinity of the core polymerase for specific promoter sequences?

Back 56

increases

Front 57

Does the sigma subunit increase or decrease the affinity of the core polymerase for nonpromoter regions?

Back 57

decreases

Front 58

What happens if a core polymerase lacks a sigma factor?

Back 58

It will bind DNA non-specifically.

Front 59

How does the sigma factor act catalytically?

Back 59

one can aid many polymerases in finding promoters

Front 60

True or false: E. coli has many different sigma factors.

Back 60

true, they recognize different consensus sequences at the promoter

Front 61

What is the rate limiting step of transcription?

Back 61

unwinding of DNA at the initiation site, which requires a conformational change

Front 62

True or false: it takes awhile for RNA polymerase to find and bind promoter.

Back 62

false, rapid

Front 63

What is RPc?

Back 63

closed complex of RNA polymerase and promoter

Front 64

What is RPo?

Back 64

open complex of RNA polymerase and promoter, 18 bp of DNA is unwound to form a transcription bubble

Front 65

region containing RNA polymerase, DNA, and RNA product

Back 65

transcription bubble

Front 66

True or false: RNA polymerase can start RNA synthesis de novo.

Back 66

true

Front 67

Why is DNA polymerase faster than RNA polymerase?

Back 67

RNA polymerase unwinds DNA itself, while DNA polymerase has helicase and gyrase to help.

Front 68

How is transcription initiated in E. coli? (first four steps)

Back 68

RNA polymerase binds non-specifically to DNA

Holoenzyme searches for promoter

Holoenzyme and promoter form a closed complex

Conformational change to open complex, forming transcription bubble and making a short stretch of DNA

Front 69

What is the final step in transcription initiation? (3)

Back 69

Sigma subunit dissociates from core

Other accessory proteins such as NusA bind to polymerase

Promoter is cleared and elongation begins

Front 70

True or false: all DNA is transcribed.

Back 70

false, only certain regions

Front 71

What are the two types of termination sequences?

Back 71

unstable elongation complex

Rho-dependent termination

Front 72

What termination sequence uses ATP?

Back 72

Rho-dependent termination

Front 73

regions of the gene where the rate of elongation slows down (10 to 100-fold) or stops temporarily

Back 73

pause sites

Front 74

Why do pause sites tend to be GC-rich?

Back 74

more difficult to separate

Front 75

When are pause sites exaggerated?

Back 75

when newly transcribed RNA can form a hairpin

Front 76

may destabilize RNA-DNA hybrid in elongation complex and cause a pause that can last 10s to 30 min

Back 76

hairpin

Front 77

triggers disassembly of the transcription complex at some pause sites by binding RNA and destabilizing RNA-DNA hybrid

Back 77

Rho

Front 78

How does Rho terminate transcription?

Back 78

binds to ssRNA chain, destabilizing the RNA-DNA hybrid

Front 79

When does Rho bind ssRNA?

Back 79

when RNA polymerase is stalled at pause site

Front 80

True or false: mRNA is modified after synthesis in bacteria.

Back 80

false, modified little to none

Front 81

True or false: tRNA is modified after synthesis in bacteria.

Back 81

true

Front 82

True or false: rRNA is modified after synthesis in bacteria.

Back 82

true

Front 83

Which final mature RNAs are cleaved from a larger precursor?

Back 83

tRNA and rRNA

Front 84

What do many tRNA transcripts lack and how do they make up for this?

Back 84

CCA sequence at the 3' end of the strand

Nucleotides are added post-transcriptionally.

Front 85

How can the bases and riboses of tRNA and rRNA be modified?

Back 85

attachment of methyl groups

Front 86

What are two antibiotics that inhibit transcription?

Back 86

rifampicin

actinomycin

Front 87

antibiotic inhibits initiation by binding to the polymerase and blocking the exit of the nascent RNA

Back 87

rifampicin

Front 88

antibiotic inserts between the bases of the DNA double helix, preventing the DNA from being used as a template

Back 88

actinomycin

Front 89

What can E. coli use as a carbon source when glucose is absent?

Back 89

lactose and other Beta-galactosides

Front 90

What three genes must be translated for uptake and catabolism of Beta-galactosides?

Back 90

lacZ

lacY

lacA

Front 91

What is lacY?

Back 91

lactose permease

Front 92

transporter for uptake of Beta-galactosides

Back 92

lacY

Front 93

What is lacZ?

Back 93

Beta-galactosidase

Front 94

hydrolyzes Beta-galactosides to hexoses

Back 94

lacZ

Front 95

What is lacA?

Back 95

thiogalactoside transacetylase

Front 96

acetylates nonmetabolizable Beta-galactosides

Back 96

lacA

Front 97

What amount of lac proteins are synthesized when glucose is present?

Back 97

low

Front 98

What increases the amount of lac proteins synthesized?

Back 98

low glucose and high lactose

Front 99

What does the lac repressor bind to?

Back 99

operator

Front 100

What blocks initiation of transcription of the lac operon?

Back 100

repressor binding operator

Front 101

act as inducers to cause the repressor to dissociate from the lac operon allowing transcription to continue

Back 101

Beta-galactosides

Front 102

What is the inducer for the lac operon in the presence of lactose?

Back 102

allolactose

Front 103

True or false: several Beta-galactosides can act as inducers to start gene transcription.

Back 103

true

Front 104

How does allolactose induce the lac operon?

Back 104

binds tightly to lac repressor and causes a conformational change that decreases affinity of lac repressor for operator

Front 105

What converts lactose to allolactose?

Back 105

Beta-galactosidase

Front 106

Under what conditions would the lac operon have neither a repressor nor an activator bound to it?

Back 106

high glucose, high Beta-galactosides

Front 107

Under what conditions would the lac operon have both a repressor and an activator bound to it?

Back 107

low glucose, no Beta-galactosides

Front 108

What can some bacterial mRNA do in addition to coding for proteins?

Back 108

sense environmental signals

Front 109

special structures that bind small molecules that cause a structural change that terminates the synthesis of mRNA

Back 109

riboswitches

Front 110

What three important characteristics influence gene expression in eukaryotes?

Back 110

complex transcription regulation

RNA processing

nuclear membrane that separates the site of RNA synthesis from that of protein synthesis