Lecture 5

Question 1

What are the two steps of gene expression?

Answer 1

transcription and translation

Question 2

What is transcription?

Answer 2

Reading a DNA template to make an RNA copy

Question 3

What is translation?

Answer 3

Decoding RNA to assemble a protein.

Question 4

True or False: transcription and translation are coupled in prokaryotes.

Answer 4

True

Question 5

What is RNA polymerase?

Answer 5

A complex enzyme that carries out transcription by making RNA copies (called transcripts) of a DNA template strand

Question 6

What is a sigma factor?

Answer 6

Guides the core RNA polymerase to the promoter.

Question 7

How many RNA polymerases do prokaryotes have?

Answer 7

One

Question 8

How many RNA polymerases do eukaryotes have?

Answer 8

Multiple (Pol I- Pol V)

Question 9

Archaeal RNA polymerases and transcription factors are more similar to _______________.

Answer 9

eukaryotes

Question 10

True or False: Every cell has a ‘housekeeping’ sigma factor.

Answer 10

True

Question 11

What is the sigma factor in E.coli?

Answer 11

sigma^70

Question 12

Which consensus sequences does the sigma factor recognize?

Answer 12

-10 & -35 regions relative to the start site of transcription (start site= +1)

Question 13

True or false: A single bacterial species can make several different sigma factors.

Answer 13

True

Question 14

What is the function of the ‘housekeeping’ sigma factor?

Answer 14

It serves routine transcription duties

Question 15

What is the function of ‘alternative’ sigma factors?

Answer 15

Genes that serve a specialized function

Question 16

True or False: Mutations in the consensus sequence can affect the strength of the promoter.

Answer 16

True

Question 17

What are the three phases of transcription?

Answer 17

1. Initiation
2. Elongation
3. Termination

Question 18

What is the initiation phase of transcription?

Answer 18

RNA Pol holoenzyme binds to the promoter

Question 19

What is the elongation phase of transcription?

Answer 19

Sequential addition of ribonucleotides from nucleoside triphosphates

Question 20

What is the termination phase of transcription?

Answer 20

RNA Pol detaches from DNA, after the transcript is made.

Question 21

RNA holoenzyme forms a loosely bound, _______________ with DNA during initiation.

Answer 21

closed complex

Question 22

The closed complex must become a ______________ through the unwinding of one helical turn.

Answer 22

open complex

Question 23

RNA polymerase becomes _______________ to DNA, and so begins transcription.

Answer 23

tightly bound

Question 24

What is typically the first ribonucleoside triphosphate of the new RNA chain?

Answer 24

A purine (A or G)

Question 25

True or False: The sigma factor leaves the complex after transcription is initiated?

Answer 25

True

Question 26

How fast does RNA polymerase move along the template?

Answer 26

45 bases/sec

Question 27

What complex is formed when the DNA is unwound further ahead of the complex?

Answer 27

17-bp transcription bubble

Question 28

Positive supercoils are removed by what?

Answer 28

DNA topoisomerases

Question 29

What are the two known termination signals/mechanisms in bacteria?

Answer 29

Rho-Dependent & Rho-Independet

Question 30

In Rho-dependent termination:

Answer 30

1. Rho binds to C-rich regions 2. RNA is threaded through Rho hexamer, pulling Rho towards RNA polymerase 3. Contact between Rho and RNA polymerase leads to termination

Question 31

In Rho-independent termination:

Answer 31

contact between hairpin NusA protein and RNA pol causes termination

Question 32

What two fundamental criteria must antibiotics meet?

Answer 32

- They must grow or retard the growth of a pathogen - Must not harm the host (its selective)

Question 33

What is Rifamycin B?

Answer 33

- Selectively binds to the bacterial RNA pol - Inhibits transcription initiation

Question 34

What is Actinomycin D?

Answer 34

- Nonselectively binds to DNA - Inhibits transcription elongation

Question 35

What does Rifamycin B bind to?

Answer 35

Beta subunit of RNA Pol

Question 36

What is Rifamycin B effective against?

Answer 36

Mycobacterium

Question 37

True or False: Rifamycin B is naturally produced by amacolatopsis rifamycinia.

Answer 37

True

Question 38

How does actinomycin D inhibit transcription elongation?

Answer 38

Phenoxazone rings nonspecifically intercalate into DNA between base stacks

Question 39

Do the side chains of actinomycin D wrap around the major or minor groove?

Answer 39

minor groove

Question 40

True or False: Actinomycin D has been used to treat cancer.

Answer 40

True

Question 41

What are the consensus sequences of sigma^70?

Answer 41

TTGACAT (-35), TATAAT(-10)

Question 42

In archea, is translation initiation similar to that of bacteria or eukaryotes?

Answer 42

Similar to bacteria

Question 43

In bacteria, is the size of the ribosome similar to that of archea or eukaryotes?

Answer 43

Similar to archea

Question 44

In archea, is the chemical sensitivity of ribosomes similar to that of bacteria or eukaryotes?

Answer 44

Similar to eukaryotes

Question 45

True or False: Even though the ribosomes found in archea are similar to eukaryotes, the eukaryotic cells have larger and more complex ribosomes.

Answer 45

True

Question 46

True or False: Bacteria use a complex set of transcription factors.

Answer 46

False

Question 47

True or False: Bacteria is sensitive to chemical inhibitors.

Answer 47

True

Question 48

True or False: The sigma factor, RpoD^70 is recognized in most genes.

Answer 48

True

Question 49

How is RpoD^32 recognized?

Answer 49

In heat-shocked genes

Question 50

Where is RopF^28 recognized?

Answer 50

Recognized in genes for chemotaxis/motility

Question 51

Where is RopS^38 recognized?

Answer 51

In stationary and response genes

Question 52

Where is RpoN^54 recognized?

Answer 52

In genes responsible for nitrogen metabolism