CJ 8 paul

Question 1

Positive Regulation

Answer 1

enzyme’s activity is stimulated by a regulatory molecule v.s. being shut down.

As well as getting rid of the inhibitor, an activator must also attach to the DNA to turn on the Lac operon; this is the CAP (Catabolite Activator Protein) that must also be bound in the absence of glucose; if glucose is present, CAP will not be bound to the Lac operon

Question 2

an example of a negative regulation by a metabolite like tryptophan in bacteria?

Answer 2

for the tryptophan operon, when tryptophan levels build up, tryptophan actually binds the tryptophan repressor and then it binds to the tryptophan operator and helps shut down synthesis of tryptophan synthetic enzymes (like when you eat a protein rich meal-lots of tryptophan);

tryptophan operon has an additional level of regulation on top of tryptophan binding the tryptophan repressor

Question 3

an example of positive and negative regulation by a metabolite like lactose in bacteria?

Answer 3

when lactose is absent, lac repressor plugs the lac operon so it stops it from producing the enzyme that breaks down lactose. When lactose is present, allolactose binds the lac repressor so genes that encode for enzymes that help breaks down lactose, so it doesn’t cover the operator and RNA polymerase ca make the mRNA for the tryptophan enzymes

Question 4

genome

Answer 4

the total genetic information carried by a gene on a cell (or an organism)

Question 5

Do all cells have a complete genome? (except mature red blood cells

Answer 5

all cells have a complete genome germ cells however only have a haploid genome

Question 6

How many genes on average will a typical cell express?

Answer 6

a typical human cell expresses ~5000-15,000 genes from a total of 25,000.

Question 7

Can cells change the expression of their genes based upon changing circumstances like receiving an external signal like a hormone?

Answer 7

yes

Question 8

Can small metabolites like lactose or tryptophan affect gene expression?

Answer 8

Yes can provide both positive feedback and negative feedback

Question 9

Can small metabolites positively or negatively affect gene expression?

Answer 9

yes

Question 10

Gene regulatory proteins usually bind to which groove in the DNA double helix?

Answer 10

To the major groove

Question 11

Can gene regulatory proteins form contacts with the bases?

Answer 11

yes, hydrogen bonds, ionic binds, hydrophobic interactions, van der waals interactions

Question 12

do gene regulatory proteins ever bind as dimers?

Answer 12

Yes, DNA binding proteins bind in pairs; doubles the area of contact with the DNA, increasing the strength and specificity of the protein-DNA interaction

Question 13

Can gene regulatory proteins form contacts With the deoxyribose sugar?

Answer 13

yes

Question 14

Can gene regulatory proteins form contacts With the phosphate backbone?

Answer 14

yes

Question 15

What is the initiation site in a gene?

Answer 15

Where RNA polymerase initiates transcription; in bacteria it is specified by the Shine Delgarno -35 and -10 DNA promoter sequences; in eukaryotes, after TBP and other tTBP-associated factors bind to the promoter and assemble a functional transcription initiation complex, then RNA polymerase is recruited and then can itself initiate transcription at a specific nucleotide

Question 16

What is the definition of an operon?

Answer 16

a set of genes that are transcribed into a single mRNA

Question 17

Is it a set of genes found in bacteria transcribed into a single mRNA?

Answer 17

Yes, not eukaryotes tho

Question 18

f lactose is present but not glucose, what is happening with the lac operon?

Answer 18

The operon is on, lactose is bound to the lac inhibitor and removes it from operator and the CAP (Catabolite Activator Protein) is bound to the Lac promoter , and RNA polymerase can produce mRNA

Question 19

If glucose is present and lactose is present, what is happening with the Lac operon?

Answer 19

The operon is not on because the CAP is not on even though lac repressor is not bound to operator (because lactose is present)

Question 20

How does the lactose operon work and how is it regulated?

Answer 20

lac operon codes for enzymes to break lactose into glucose and galactose. Will only transcribe the enzyme if there is lactose to be broken down and no glucose

Question 21

What is the preferred carbon energy source in bacteria like E.coli: glucose or lactose?

Answer 21

glucose

Question 22

In eukaryote where do transcription regulators bind?

Answer 22

They can bind in the proximal promoter, distal promoter or even in the introns or downstream of the gene

Question 23

Do Gene regulatory proteins disrupt the hydrogen bonding between basepairs when they bind to the major groove?

Answer 23

No they do not disrupt normal hydrogen binding pattern of nitrogenous bases

Question 24

What is an operator

Answer 24

short 15 nucleotide DNA sequence within the promoter that is recognized by the transcription regulator such as the Lac represoor or the tryptophan repressor

Question 25

How is eucaryotic gene expression “combinatorial”?

Answer 25

transcription regulators work together as a “committee” to control the expression of a eucaryotic gene. Unit of genes are switched on and off depending on what is attached to the mediator

Question 26

Are combinations of transcription factors turned on in specific cells believed to orchestrate the particular fate of that cell?

Answer 26

Yes, cells pick and choose what they want to express.

Question 27

Can a single transcription factor, if expressed in the appropriate precursor cell, trigger the formation of a specialized cell type or even an entire organ ?

Answer 27

ya dude

Question 28

Is it the precise amino acid sequence in the DNA binding domain that determines the particular DNA sequence that is recognized?

Answer 28

Yes because they attach to specific base pairs to regulate transcription (control the gene expression).

Question 29

acetylation

Answer 29

histone acetylase enzymes add an acetyl group to a charged amino group on the amino acid lysine in histone tails, causing removal of the charge and thus decreases affinity of histone for DNA (makes association looser, not tighter);

generally is associated with increased gene expression