Gene Regulation in Prokaryotes CP 36-42

Question 1

when will RNA polymerase stop transcribing DNA?

Answer 1

RNA polymerase will keep transcribing DNA util it reaches a termination signal.

Question 2

Rho-independent terminator (prokaryotic)

Answer 2

DEF: Transcriptional terminator that does not need Rho protein

TO KNOW: region of DNA with 2 inverted repeats six bases apart, followed by a stretch of A’s (forms a secondary structure) - Causes RNA polymerase to stutter and pause.

Question 3

Rho- dependent terminator (prokaryotic)

Answer 3

DEF: Transcriptional terminator that depends on Rho protein

TO KNOW: region of DNA with 2 inverted repeats six bases apart, NOT followed by a string of As. Rho will unwind the DNA/RNA helix to stop the transcription process and release the RNA.

Question 4

Rho protein (prokaryotic)

Answer 4

DEF: Protein factor needed for successful termination at certain transcriptional terminators

TO KNOW: a special helicase that unwinds the DNA/ RNA hybrid double helices

Question 5

what are two difference in how prokaryotic and eukaryotic chromosomes are organized?

Answer 5

1) distance between prokaryotic genes is smaller -> eukaryotic genes are often deparated by large stretches of DNA that do not encode any protein
2) prokaryotic genes associated with one metabolic pathway are found next to each other

Question 6

operon

Answer 6

DEF: A cluster of prokaryotic genes that are transcribed together to give a single mRNA
(i.e., polycistronic mRNA)

TO KNOW: clusters of genes that share the same promoter and are transcribed as a single large mRNA that contains multiple structural genes or cistrons

Question 7

polycistronic mRNA

Answer 7

mRNA carrying multiple coding sequences (cistrons) that may be translated to give several different protein molecules; only found in prokaryotic (bacterial) cells

Question 8

Phosphorelay system

Answer 8

Transfers one phosphate from one location to another to activate different proteins, ultimately regulating transcription of the genes

Question 9

monocistronic mRNA (eukaryotes)

Answer 9

mRNA carrying the information of a single cistron that is a coding sequence for only a single protein

Question 10

Two-component regulatory systems

Answer 10

A regulatory system consisting of two proteins: a sensor kinase and a DNA-binding regulator

Question 11

how many open reading frames and metabolic pathways do bacterial mRNA transcripts have?

Answer 11

multiple open reading frames for the same metabolic pathways

Question 12

how many open reading frames do eukaryotic mRNA transcripts have?

Answer 12

one open reading frame

Question 13

is eukaryotic or prokaryotic transcription more complex?

Answer 13

eukaryotic
- occurs in the nucleus
- 3 different RNA polymerases
- more complex promoter sequence

Question 14

Sensor kinase

Answer 14

A protein that phosphorylates itself when it senses a specific signal (often an environmental stimulus, but sometimes an internal signal)

Question 15

RNA polymerase I

Answer 15

Eukaryotic RNA polymerase that transcribes the genes for the large
ribosomal RNAs - one long strand that becomes 18s and 28s rRNA

Question 16

RNA polymerase II

Answer 16

Eukaryotic RNA polymerase that transcribes the genes encoding proteins

Question 17

RNA polymerase III

Answer 17

Eukaryotic RNA polymerase that transcribes the genes for 5S ribosomal RNA and transfer RNA

Question 18

autogenous regulation

Answer 18

When a DNA-binding protein regulates the expression of its own gene

Question 19

what three regions does RNA polymerase II need?

Answer 19

1) initiator box
2) TATA box
3) upstream elements to bind transcription factors

Question 20

initiator box

Answer 20

Sequence at the start of transcription of a eukaryotic gene

Question 21

TATA box

Answer 21

Binding site for a transcription factor that guides RNA polymerase II to the promoter in eukaryotes

Question 22

co-repressor

Answer 22

In prokaryotes: a small signal molecule is needed for some repressor proteins to bind to DNA

In eukaryotes: an accessory protein, often a histone deacetylase, involved in gene repression

Some repressors or activators rely on activation by these small molecules

Question 23

general transcription factors

Answer 23

DEF: Proteins that work to enhance or repress gene expression for all genes

TO KNOW: required by RNA polymerase II to initiate transcription at all promoters

Question 24

specific transcription factors

Answer 24

Regulatory proteins that exert their effect on a single gene or operon or on a very small number of related genes

Question 25

Two forms of specific regulator proteins to activate RNA polymerase binding and transcription

Answer 25

1. active (bind to DNA in promoter region)
   2.nonactive (nonbinding)

Question 26

TATA binding protein/TATA box protein (TBP)

Answer 26

DEF: Transcription factor that recognizes the TATA box

TO KNOW: TBP is found in protein complex TFIID for RNA polymerase II

aka TBP binds to the TATA box and is part of TFIID

Question 27

inducer/signal molecules

Answer 27

Molecules that exert a regulatory effect by binding to a regulatory protein

Question 28

What are the three structural genes the promoter region for the lac operation controls?

Answer 28

lacZ, lacY, lacA

Question 29

does bacterial RNA polymerase need a promoter to have upstream elements/transcription factors?

Answer 29

NO!! only eukaryotic needs them.

Question 30

how do activator and repressor proteins work in prokaryotes?

Answer 30

they bind to DNA in the promoter region and stimulate or block the action of bacterial RNA polymerase.

Question 31

repressor proteins

Answer 31

Regulatory protein that prevents a gene from being transcribed

Question 32

operator

Answer 32

binding site for the repressor protein

Question 33

positive regulation

Answer 33

Control by an activator that promotes gene expression when it binds

AKA gene is expressed only when activator gives a positive signal - how activator proteins work

Question 34

negative regulation

Answer 34

the gene is only expressed when the repressor is removed - how repressor proteins works

Question 35

anti terminator protein

Answer 35

Protein that allows transcription to continue through a transcription terminator

Question 36

CAP (catabolite activator protein)

Answer 36

activates the transcription of many different operons by using alternate sugar sources

Question 37

what does the sigma subunit of prokaryotic RNA polymerase do?

Answer 37

recognizes the promoter and then binds the catalytic portion of the enzyme (core enzyme)

Question 38

gratuitous inducer

Answer 38

A molecule (usually artificial) that induces a gene but is not metabolized
like the natural substrate

-the best known example: the induction of the lac operon by IPTG

Question 39

chaperonins

Answer 39

Protein that mediates the refolding of misfolded or unfolded proteins

Question 40

protease

Answer 40

An enzyme that degrades polypeptides by hydrolysis

Question 41

what are the elements of an operon?

Answer 41

1) promoter
2) operator (repressor protein binding site)
3) regulatory gene (encodes repressor protein)
4) structural genes (encodes enzymes)