Lecture 8 - Gene expression

Question 1

7 ways to regulate protein production

Answer 1

transcription, posttranscriptional processing, mRNA degradation, Translation, Posttranslational processing, Protein degradation, and Protein targeting and transport

Question 2

Method of posttranscriptional processing in terms of protein synthesis.

Answer 2

Length of poly A tail determines the RNA lifespan (mRNA degradation). Alternative splicing

Question 3

Translation in terms of protein synthesis and inhibition

Answer 3

will determine how many proteins are made. If poorly translated, then not a lot of proteins being made.

Question 4

Apoprotein vs holoprotein

Answer 4

Apoprotein: not active protein since missing its coenzyme
Holoprotein: functional protein

Question 5

DNA sequences involved in regulation of gene expression

Answer 5

Promoter region (-35 and -10) and UP elements. Sigma and alpha subunits bind respectively.

Question 6

Ligand binding and post-translational modifications and affinity

Answer 6

Kd can either go up or down.
Ligand - could bind to an enhancer
Post-translational - phosphorylation could cause a signal casade, often resulting in regulation.

Question 7

Ribo switches

Answer 7

transcripts at the 5’ end that form a 3D structure which has affinity for a specific ligand (product of protein). If this ligand binds to the structure, it can turn off the production of the ligand. Feedback regulation process.

Question 8

Activator vs repressor

Answer 8

Activator - facilitates transcription (often binds to the UP element)
Repressor - inhibits transcription

Question 9

Derepression by signal causing dissociation

Answer 9

a signal molecule which has an affinity for the repressor will bind causing a conformational change (Kd goes up) causing the repressor to dissociate

Question 10

Two types of derepression (negative regulation)

Answer 10

Molecule signal causes dissociation of regulatory protein or molecular signal causes binding of regulatory protein

Question 11

Derepression by signal causing binding of regulatory protein

Answer 11

When level of signal drops, transcription will then take place.

Question 12

Where will the repressor bind?

Answer 12

binds to the promoter to prevent the RNA polymerase from binding

Question 13

Two types of positive regulation (Enhancers)

Answer 13

Molecular signal causes dissociation of regulatory protein from DNA or molecular signal causes binding of regulatory protein to DNA

Question 14

Promoter’s affect on polycistronic mRNA in an operon

Answer 14

the promoter controls the gene expression of all the genes

Question 15

E. Coli’s ideal situation with glucose and lactose

Answer 15

Glucose is preferred but if glucose is low, then it will use lactose to produce glucose.

Question 16

If glucose is high, what happens with permease and B-galactosidase?

Answer 16

Still present in the cell since if gone, then function would be lost.

Question 17

Lactose when split will make?

Answer 17

Glucose and galactose

Question 18

How does lactose come into the cell?

Answer 18

Permease to help with the polar groups on the sugar

Question 19

What cleaves lactose?

Answer 19

B-galactosidase via hydrolysis.

Question 20

Allolactose production and function

Answer 20

when B-galactosidase will do a transglycosylation. Can cause derepression

Question 21

How many sites does the lac Operon have for binding the lac repressor?

Answer 21

3 - a primary site and two secondary sites

Question 22

LacI

Answer 22

repressor gene and is always on and making the gene.

Question 23

What happens to DNA when the Lac repressor is bound?

Answer 23

the DNA will wrap around the repressor

Question 24

4 methods of DNA sequence recognition

Answer 24

base specific in major groove, helical part that sticks into the major groove, interactions with the phosphate backbone, and fingers into the minor groove for enhanced specificity

Question 25

Common motif in DNA-binding proteins

Answer 25

helix-turn-helix. Helix will slip into the major groove.

Question 26

What causes the conformational change in represssor for the lac operon?

Answer 26

Allolactose or other lactose analogs (IPTG in lab). When bound, the repressor dissociates from DNA. (Legs being hidden when bound)

Question 27

cAMP receptor protein (CRP) and lac operon

Answer 27

positive regulator of the lac operon. and will bind in the absence of glucose, stimulating expression

Question 28

Where is the CRP site found?

Answer 28

in the UP element because it is an activator

Question 29

Lac promoter and E.Coli promoter region and RNA polymerase afinity

Answer 29

There is a difference between the two promoters, thus the RNA polymerase will bind much poorer on the lac promoter (sigma binding)

Question 30

cAMP when glucose is high

Answer 30

There is little cAMP. Thus CRP will not bind and lac operon is less likely to be transcribed

Question 31

cAMP when glucose is low

Answer 31

cAMP is high. CRP binding to occur and thus binding of RNA polymerase. But will need repressor to be removed if present.

Question 32

Lactose is low, repressor bound

Answer 32

inhibition

Question 33

Lactose is high, lots of allolactose

Answer 33

Allolactose causes the repressor to dissociate. Thus allowing for transcription

Question 34

Glucose is high

Answer 34

low cAMP, CRP is not bound and transcription is dampened.

Question 35

Glucose is low

Answer 35

high is cAMP, CRP is bound, and transcription occurs.

Question 36

Regulation of transcription in eukaryotes

Answer 36

TATA binding protein, transcription factors, homeodomain proteins, leucine zippers, and zinc fingers

Question 37

Homeodomain proteins

Answer 37

share similarities with helix-turn-helix bacterial counterparts. their alpha helix interacts with the primary DNA

Question 38

Leucine zippers

Answer 38

made of two amphipathic polypeptides. one side of each peptide is hydrophobic, facilitating dimerization. Lysines and arg interact with the negative charges of DNA. Leucine occurs every 7 residues

Question 39

Zinc fingers

Answer 39

form elongated loops held together by one or more Zn ions. cysteine and histidine residues help. B- turn - helix motif

Question 40

Eukaryotic is primarily positive regulation because

Answer 40

DNA is stored in chromatin

Question 41

Binding of eukaryotic Polymerase II needs

Answer 41

Transcription factors (ABFEH), transcription activators (specific or global), coactivators, and chromatin modification and remodeling proteins

Question 42

Global transcription activators vs specific

Answer 42

Global - facilitate transcription at hundreds of genes.

Question 43

Heterochromatin vs euchromatin and transcription

Answer 43

Heterochromatin is condensed and transcriptionally inactive. Euchromatin is uncondensed and thus transcriptionally active.

Question 44

Coactivators or mediators

Answer 44

Bridge between the enhancers and the RNA polymerase to facilitate binding thus 20-30 proteins in length usually

Question 45

carbohydrate response element binding protein (ChREBP)

Answer 45

transcription factor that regulates expression of genes in carbohydrate metabolism (ChoRE).

Question 46

Hexokinase IV or glucokinase

Answer 46

adds a phosphate onto glucose at the 6 position.

Question 47

PP2A

Answer 47

protein phosphatase 2A, influenced by xylulose 5-phosphate. desphosphorylates ChREBP once.

Question 48

Once ChREBP has been dephosphorylated once

Answer 48

It will enter into the nucleus. Where it is dephosphorylated again by PP2A.

Question 49

Dephosphorylated ChREBP

Answer 49

is active now and will bind to Mlx and associate with the promoter of the gene of ChoRE.

Question 50

FOXO1

Answer 50

stimulates synthesis of gluconeogenic enzymes and suppresses synthesis of glycolytic and PPP enzymes

Question 51

FOXO1 is found where and insulin's impact

Answer 51

Unphosphorylated in nucleus. Insulin causes it to move to the cytosol, where it is phosphorylated, ubiquinated, and then degraded.