Gene Regulation I

Front 1

Genes that are expressed in what manner are at a constant level and are typically genes that are critical for survival of the cell or organism?

Back 1

constitutively

Front 2

Other genes that are non-critical are subject to regulation and are transcribed how often?

Cell efficiency and cell-specific functions are important traits allowed by what?

Back 2

As needed; Gene regulation

Front 3

One type of regulation in gene expression of bacteria is by influencing the initiation of what?
(I.e. controls the rate of RNA synthesis increasing or decreasing)

Back 3

the initiation of transcription

Front 4

These bind to regulatory proteins but NOT to DNA directly and affect transcription regulation?

Presence of a small effector molecule that may increase transcription are termed what?

Back 4

Small effector molecules; inducers

Front 5

(INFO) a) In the absence of the inducer, the repressor protein blocks transcription (repressor protein is dependent on corepressor).

b) The presence of the inducer causes a conformational change that inhibits the ability of the repressor protein to bind to the DNA. Transcription proceeds

Back 5

(INFO) c) This activator protein cannot bind
to the DNA unless an inducer is
present. When the inducer is bound
to the activator protein, this enables
the activator protein to bind to the
DNA and activate transcription.

Front 6

(INFO) d) In the absence of a corepressor,
the repressor protein will not bind to the DNA. Therefore, transcription can occur.

e) When the corepressor is
bound to the repressor protein, this
causes a conformational change that
allows the protein to bind to the DNA
and inhibit transcription.

Back 6

(INFO) f) This activator protein will bind to
the DNA without the aid of an effector
molecule. The presence of an inhibitor
causes a conformational change that
releases the activator protein from the
DNA. This inhibits transcription.

Front 7

These regulatory proteins have two binding sites: one for the DNA and the other site for what?

Back 7

One for a small effector molecule

Front 8

A particular enzyme appears in the cell only after the cell has been exposed to the enzyme’s substrate. This observation became known as?

Back 8

enzyme adaptation (this led to the study of lactose metabolism)

Front 9

Having a polycistronic mRNA allows a bacterium to coordinately regulate a group of genes that encode proteins with a common functional goal, T or F?

Back 9

True

Front 10

The _______ operon regulates transport and metabolism of lactose in E. coli? The lac operon contains 4 important DNA sequences, what are these called?

Back 10

Lac; Promoter, terminator, structural genes, and operator

Front 11

In the lac operon, RNA polymerase binds to what DNA region? Lac repressor protein binds to which region? Catabolite Activator Protein binds to which region?

Back 11

Promoter(lacP); operator(lacO); CAP site

Front 12

The structural gene lacZ encodes what enzyme? lacY encodes? lacA encodes? This membrane protein/enzyme required for transport of lactose and analogues?

Back 12

b-galactosidase; lactose permease; galactoside transacetylase; lactose permease

Front 13

**This protein enzymatically cleaves lactose and lactose analogues and also converts lactose to allolactose (an isomer)? This protein covalently modifies lactose and analogues and Its functional necessity remains unclear?

Back 13

b-galactosidase; galactoside transacetylase

Front 14

This regulatory structural gene that is NOT considered part of the lac operon, has its own promoter = the i promoter and is CONSTITUTIVELY expressed at fairly low levels and encodes the lac repressor?

Back 14

The lacI gene

Front 15

The lac repressor protein functions as a what? Only a small amount of protein is needed to repress the lac operon, T or F?

Back 15

tetramer; True

Front 16

Galactosidase as a side reaction produces allolactose and as a final product produces what two sugars? RNA polymerase can transcribe the structural genes, lacZ, lacY, and lacA if the lac operon is repressed, T or F?

Back 16

Galactose and glucose; True

Front 17

If not lactose is in the environment lacL transcribes a mRNA to produce the lac repressor to bind to the operator and inhibit transcription leaving the lac operon repressed and what important protein is missing because of no lactose?

Back 17

allolactose

Front 18

When lactose is present, allolactose is also present(due to B-galactosidase being transcribed) and the binding of allolactose causes a conformational change that prevents the lac repressor from binding to where on the lac operon?

Back 18

operator site

Front 19

Repressor does not completely inhibit transcription, ie. small amounts of protein of the lac operon are still made, T or F?

Back 19

True

Front 20

The lac Operon Is Also regulated By an Activator Protein, transcriptionally regulated in a second way, this is known as? This sugar transport signals for cAMP levels in the cell to decrease? CAP is an activator protein binding to the CAP site when this protein is bound?

Back 20

catabolite repression; Glucose; cAMP

Front 21

When exposed to both lactose and glucose which one does E. coli utilize first? Catabolite repression allows the use of lactose, T or F? When glucose is depleted, catabolite repression is alleviated, and the lac operon is expressed, T or F?

Back 21

glucose; False = prevents; True

Front 22

When lactose is present but no glucose, allolactose represses repressor, cAMP is high and CAP w/cAMP are bound at the CAP site inducing the rate of transcription, T or F?

Back 22

True

Front 23

When there is neither glucose or lactose, repressor now binds to the operator and cAMP is still high level with CAP protein bound to CAP site, is transcription completely stopped?

Back 23

No, transcription is a low rate

Front 24

What 2 molecules are present/not present when allolactose is present to inhibit repressor to inactive and CAP protein is inactive because there is low cAMP and transcription rate is low due to the lacking of CAP binding?

Back 24

Both glucose and lactose are present

Front 25

Another scenario occurs where CAP protein has no cAMP bound (low cAMP concentration) rendering it inactive and no presence of allolactose and the repressor protein binds to operator and so the transcription is very low because CAP is repressed and operator is inhibited by repressor protein, what molecule(s) is present/ unpresent?

Back 25

Glucose is present and lactose isn't present

Front 26

When there is no allolactose, this means there is no _______ made? What does the allolactose bind to and repress? What does cAMP bind to and activate? Where does this activated molecule bind to?

Back 26

No lactose; repressor protein; CAP protein; CAP site

Front 27

If glucose is present regardless of lactose being present or not what happens to the CAP protein and cAMP levels?

Back 27

CAP protein is inactive because cAMP levels are low

Front 28

What sugar lactose or glucose is preferred in the lac operon? Gene regulation in eukaryotes is necessary to ensure what two events to happen?

Back 28

Glucose; accuracy of gene expression during developmental stages of the life cycle and distinctions among cell types (I.e Some genes are only expressed during embryonic stages, whereas others are only expressed in the adult. Nerve and immune cells look so different because of gene regulation rather than differences in DNA content)

Front 29

In Eukaryotes, transcription is regulated by a complex of what? T or F, transcription factors may function as activators (or repressors) near the promoter?

Back 29

transcription factors in addition to the general transcriptional machinery' both activators and repressors

Front 30

What are the proteins that influence the ability of RNA polymerase to transcribe a given gene? There are 2 types of TF, which one is required for the binding of the RNA pol to the core promoter and its progression to the elongation stage and are necessary for basal transcription?

Back 30

Transcription factors (AKA TF); General transcription factors

Front 31

These TF serve to regulate the rate of transcription of target genes and influence the ability of RNA pol to begin transcription of a particular gene?

Back 31

Regulatory transcription factors

Front 32

What important area can TF recognize and makes contact with on a base sequence along the major groove of DNA?

Back 32

recognition helix (I.e. Hydrogen bonding between an a-helix and nucleotide bases is one way a transcription factor can bind to DNA)

Front 33

What important DNA motifs can also mediate protein dimerization (includes Zinc finger and Leucine zipper motif)? These dimers are formed by two identical transcription factors? Two different TF?

Back 33

Helix-loop-helix; homodimer; heterodimer

Front 34

This motif is composed of one a-helix and two b-sheets held together by a zinc (Zn++) metal ion? This motif has alternating leucine residues in both proteins that interact (“zip up”), resulting in protein dimerization?

Back 34

Zinc finger; Leucine zipper motif

Front 35

Combinatorial regulation consists of TF binding sites in the promoter region of human matrix metalloproteinase (MMP) genes, T or F

Back 35

True

Front 36

Activator and Repressor Transcription Factors can also function from a distance at what 2 regions? What are the three common ways that the function of regulatory transcription factors can be modulated?

Back 36

enhancer and silencer regions; Binding of a small effector molecule, Protein-protein interactions and covalent modification

Front 37

TF's Protein-protein interactions is also called what?What regulatory sequence is used to identify where proteins are binding across the entire genome?

Back 37

Dimerization; ChIP-seq

Front 38

Levels and localization of RNA pol II binding: ChIP-seq to determine whether they're are expressed or not expressed, T or F? DNA-protein interaction sites can be isolated by what to affect gene expression?

Back 38

True; CHIP-sequence(chromatin immunoprecipitation)