DNA transcription and Translation

Question 1

What are the steps of the Central Dogma?

Answer 1

In nucleus: DNA to RNA through RNA synthesis (transcription) which is produced in the nucleus and travels to the cytoplasm

RNA to Protein through protein synthesis (translation) produced in the cytoplasm

Question 2

List the ways to regulate protein conc in a cell

Answer 2

Synthesis of primary RNA transcription
How to process this RNA into mRNA
Post-transcriptional modifications of mRNA
Degradation of mRNA
Protein synthesis
Post-translational modification of protein
Targeting and transport of the protein
Degradation of the protein

Question 3

What are the seven processes that affect the steady state concentration of a protein?

Answer 3

1) Transcription initiation: From gene to primary RNA transcript
2) Post-transcriptional processing: pRNA transcript to mRNA
3) RNA stability
4) translational regulation: mRNA to protein
5) Protein modification: Protein to modified protein
6) Protein transport
7) Protein degradation: Modified protein causes positive feedback by releasing Amino acids back to the previous step

Question 4

The mechanism of posttranscriptional and translation regulation are?

Answer 4

elaborate and interdependent,especially in development

Question 5

Regulation of posttranscriptional and translation regulation relies on?

Answer 5

Precise protein-DNA and protein-protein contacts

Question 6

Define a house keeping gene

Answer 6

under constitutive expression

constantly expressed in approximately all cell

Question 7

Define and give examples of a regulated gene

Answer 7

Levels of the gene product rise and fall with the needs of
the organism.

Such genes are inducible: able to be turned on

Such genes are also repressible: able to be turned off

Question 8

Explain the process of RNA polymerase binding to promoters

Answer 8

RNA polymerases bind to promoter sequences near the starting point of the transcription initiation

The RNA polymerase promoter interaction greatly influences the rate of transcription initiation

Question 9

How is the RNA polymerase binding to promoters a major target of regulation?

Answer 9

Regulatory proteins (transcription factors) work to enhance or inhibit this interaction between RNA polymerase and the promoter DNA

Question 10

What is the consensus sequence found in?

Answer 10

Many E.coli promoters

Question 11

What do most bacterial promoters include?

Answer 11

Conserved -10 and -35 regions

Question 12

What do the conserved -10 and -35 region interact with?

Answer 12

the o factor of RNA polymerase

Question 13

What does substitution in the -10 to -35 region usual reduce?

Answer 13

the affinity of RNA pol for the promoter

Question 14

What does the upstream element interact with?

Answer 14

The Alpha subunit of RNA polymerase

Question 15

What are the uses of o factors

Answer 15

Recognize different classes of promoters

Allows coordinated expression of different sets of genes

Question 16

How does binding other proteins (transcription factors) to promoters regulate transcription in bacteria?

Answer 16

Recognize promoters of specific genes

May bind small signaling molecules

May undergo posttranslational modifications

Protein’s affinity towards DNA is altered by ligand binding or posttranslational modifications

Allows expression of specific genes in response to signals in the environment

Question 17

How does specifity factors such as o subunits of RNA pol help regulation?

Answer 17

Specificity factors alter RNA polymerase’s affinity for certain promoters

Question 18

Give an example of regulation by specifity factors such as o subunits of RNA pol

Answer 18

o subunit of E.coli RNA pol:

Most E.coli promoters recognized by o^70

This subunit can be replaced by one of six additional specificity factors

Heat shock will replace o^70 with o^32 and direct RNA pol to different promoters

Question 19

What does heat shock induce?

Answer 19

Transcription of new products to protect cell

Question 20

When does heat shock occur?

Answer 20

Bacteria are subject to heat stress

Question 21

What does heat shock cause?

Answer 21

RNA pol replaces o^70 with o^32

Causes RNA pol to bind to different set of promoters:

Transcription of new products including chaperones that keep proteins in correct conformation, even in heat

Question 22

What can regulate Activators and repressors?

Answer 22

Small-molecule Effectors

Question 23

What is the role of repressors?

Answer 23

Reduce RNA pol-promoters interactions or block the polymerase

Bind to operator sequences of DNA:
Usually near a promoter in bacteria but further away in many Eu

Question 24

What is the role of Effectors?

Answer 24

Can bind to repressor and induce a conformation change

Change may increase or decrease repressor’s affinity for the operator and thus may increase or decrease transcription

Question 25

What do Activators improve?

Answer 25

Contacts between RNA polymerase and the promoter

Question 26

What are the binding sites in DNA for activators called?

Answer 26

Enhancers

Question 27

What are enhancers usually adjacent too?

Answer 27

Promoters

Often adjacent to promoters that are weak (bind RNA polymerase weakly) so the activator is necessary

In Eu, enhancers may be very distant from the promoter

Question 28

How are repressors involved in Negative regulation?

Answer 28

Repressors binds to DNA and shuts down transcription

Or alternatively signal causes repressor to dissociate from DNA transcription induced

Question 29

What are the two types of Negative regulation?

Answer 29

Molecular signal causes dissociate of repressor from DNA, inducing transcription

Molecular signal causes binding of respressor to DNA inhibiting transcription

Question 30

How does Positive regulation involve activators?

Answer 30

Enhance activity of RNA polymerase

Activator binding sites are near promoters that weakly bind RNA pol or do not bind at all

it may remain bound until molecule signals dissociation

Alternatively the activator may only bind when signaled

Question 31

What are two types of positive regulation

Answer 31

Molecular signal causes dissociate of activator from DNA, inhibiting transcription

Molecular signal causes binding of activator to inducing transcription

Question 32

DNA looping allows?

Answer 32

Eukaryotic enhancers to be far from promoters

Activators can influence transcription at promoters thousands of bp away.

Question 33

Looping can be facilitated by?

Answer 33

Architectural regulator proteins

Question 34

Co-activators may mediate binding by?

Answer 34

Binding to both activator and RNA polymerase

Question 35

Define an Operon

Answer 35

A cluster of genes sharing a promoter and regulatory sequences.

Genes are transcribed together, so mRNA’s are several genes represented on one mRNA (polycistronic).

Question 36

What did the Iac operon discovery reveal?

Answer 36

many principles of gene regulation

Question 37

Three genes for metabolism of lactose are regulated together as a operon:

What is the job of Beta-galactosidase(lacZ)?

Answer 37

Cleaves the lactose to yield glucose and galactose

Question 38

Three genes for metabolism of lactose are regulated together as a operon:

What is the job of Lactose permease (galactoside permease lacY)?

Answer 38

Transport lactose into cell

Question 39

Three genes for metabolism of lactose are regulated together as a operon:

What is the job of Thiogalactoside transacetylase (LacA)?

Answer 39

They rely on negative regulation via a repressor

Question 40

What happens when glucose is abundant and lactose is lacking?

Answer 40

Cells make only very low levels of enzymes for lactose metabolism

Transcription is repressed

Question 41

What happens when glucose is scarce and cells are fed lactose?

Answer 41

The cells can use it as their energy source

The cells suddenly express the genes for the enzymes for lactose metabolism

Transcription is no longer repressed

Question 42

A gene called lacl encodes a repressor called?

Answer 42

The lac repressor