I. DNA-Binding Proteins and Transcriptional Regulation

Question 1

What is meant by the phrase ‘constitutive expression’?

Answer 1

Constitutive expression refers to genes that are continuously expressed regardless of environmental conditions.

Question 2

What two major approaches are used by cells to regulate protein function?

Answer 2

Cells regulate protein function through allosteric regulation and covalent modification.

Question 3

What two regions of DNA are often involved in the regulation of gene expression?

Answer 3

The promoter and the operator regions of DNA are often involved in the regulation of gene expression.

Question 4

What are four mechanisms for regulating protein activity after translation occurs?

Answer 4

The four mechanisms are phosphorylation, methylation, acetylation, and ubiquitination.

Question 5

What is the major method of protein regulation used by Bacteria and Archaea?

Answer 5

The major method is through transcriptional regulation.

Question 6

What must happen in order for a gene to be transcribed?

Answer 6

RNA polymerase must bind to the promoter region of the gene.

Question 7

Where do DNA-binding proteins typically bind on a dsDNA molecule?

Answer 7

DNA-binding proteins typically bind in the major groove of the dsDNA molecule.

Question 8

What determines the ‘specificity’ of a DNA-binding protein?

Answer 8

The specificity is determined by the protein’s structure and the sequence of the DNA it binds.

Question 9

What type of DNA sequences interact with most DNA-binding proteins?

Answer 9

Most DNA-binding proteins interact with specific, short sequences of DNA.

Question 10

Most DNA-binding proteins are homodimeric. Why is this significant?

Answer 10

Being homodimeric allows for increased binding affinity and specificity to DNA.

Question 11

What are three common structural ‘motifs’ found in DNA-binding proteins?

Answer 11

The three common motifs are helix-turn-helix, zinc finger, and leucine zipper.

Question 12

What exactly is meant by the phrase ‘negative control’ of transcription?

Answer 12

Negative control refers to mechanisms that inhibit transcription.

Question 13

What is enzyme repression?

Answer 13

Enzyme repression is the process by which the synthesis of an enzyme is decreased.

Question 14

What types of pathways are most often controlled by enzyme repression?

Answer 14

Biosynthetic pathways are most often controlled by enzyme repression.

Question 15

What is enzyme induction?

Answer 15

Enzyme induction is the process by which the synthesis of an enzyme is increased.

Question 16

What types of pathways are most often controlled by enzyme induction?

Answer 16

Catabolic pathways are most often controlled by enzyme induction.

Question 17

What is an inducer?

Answer 17

An inducer is a molecule that increases the expression of a gene.

Question 18

What is a corepressor?

Answer 18

A corepressor is a molecule that decreases the expression of a gene.

Question 19

How do inducers and corepressors affect transcription?

Answer 19

Inducers activate transcription, while corepressors inhibit it.

Question 20

What is a repressor protein?

Answer 20

A repressor protein is a molecule that binds to an operator to inhibit transcription.

Question 21

What does the term ‘allosteric’ mean?

Answer 21

Allosteric refers to the regulation of a protein’s function through the binding of a molecule at a site other than the active site.

Question 22

What exactly is an ‘operator’ region of a gene?

Answer 22

An operator is a segment of DNA that a repressor protein binds to, blocking transcription.

Question 23

What exactly is an operon?

Answer 23

An operon is a cluster of genes under the control of a single promoter.

Question 24

Do inducers activate or inactivate repressor proteins?

Answer 24

Inducers activate repressor proteins.

Question 25

Do corepressors activate or inactivate repressor proteins?

Answer 25

Corepressors inactivate repressor proteins.

Question 26

What exactly is meant by the phrase 'positive control' of transcription?

Answer 26

Positive control refers to mechanisms that promote transcription.

Question 27

What are activator proteins? Are they activated by inducers or corepressors?

Answer 27

Activator proteins are molecules that enhance transcription and are activated by inducers.

Question 28

What is an activator-binding site?

Answer 28

An activator-binding site is a region of DNA where an activator protein binds to promote transcription.

Question 29

What is a major characteristic of promoters found in positively controlled operons?

Answer 29

They have a strong affinity for RNA polymerase.

Question 30

What are two ways that activator proteins can increase the binding of RNA polymerase to the gene promoter?

Answer 30

Activator proteins can increase binding by altering DNA structure and recruiting RNA polymerase.

Question 31

What is a regulon?

Answer 31

A regulon is a group of genes or operons controlled by the same regulatory protein.

Question 32

What are global control systems?

Answer 32

Global control systems are regulatory mechanisms that coordinate the expression of multiple genes in response to environmental changes.

Question 33

What is catabolite repression?

Answer 33

Catabolite repression is the inhibition of the expression of certain genes in the presence of a preferred carbon source.

Question 34

What is the ultimate goal of catabolite repression?

Answer 34

The goal is to prioritize the use of more efficient energy sources.

Question 35

Why would genes for flagella synthesis be controlled by catabolite repression?

Answer 35

Flagella synthesis is not essential when a preferred carbon source is available.

Question 36

What is diauxic growth?

Answer 36

Diauxic growth is a pattern of growth where two different carbon sources are used sequentially.

Question 37

Why is catabolite repression a type of positive control?

Answer 37

It is considered positive control because it enhances the expression of genes when preferred substrates are present.

Question 38

What are the roles of cyclic AMP (cAMP) and cyclic AMP receptor protein (CRP) in catabolite repression?

Answer 38

cAMP and CRP work together to promote the transcription of genes when glucose levels are low.

Question 39

What are regulatory nucleotides? What are some examples?

Answer 39

Regulatory nucleotides are molecules that influence gene expression; examples include cAMP and ppGpp.

Question 40

How is cAMP synthesized?

Answer 40

cAMP is synthesized from ATP by the enzyme adenylate cyclase.

Question 41

In what two ways does the presence of glucose cause the level of cAMP to decrease?

Answer 41

Glucose inhibits adenylate cyclase and promotes the activity of phosphodiesterase.

Question 42

What two requirements must be met in order for the lac operon genes to be transcribed?

Answer 42

The absence of glucose and the presence of lactose must be met.

Question 43

How do archaeal repressor proteins work?

Answer 43

Archaeal repressor proteins bind to operator regions to inhibit transcription.

Question 44

How do archaeal activator proteins work?

Answer 44

Archaeal activator proteins bind to specific DNA sites to enhance transcription.

Question 45

What two nitrogen assimilation functions are suppressed by the NrpR protein?

Answer 45

The functions are the assimilation of ammonium and nitrate.

Question 46

How is α-ketoglutarate involved in nitrogen assimilation?

Answer 46

α-ketoglutarate serves as a carbon skeleton for amino acid synthesis.

Question 47

Is α-ketoglutarate an inducer or a corepressor of NrpR?

Answer 47

α-ketoglutarate is an inducer of NrpR.

Question 48

What are dual-acting transcriptional regulators?

Answer 48

Dual-acting transcriptional regulators can function as both activators and repressors.

Question 49

In P. furiosus, what process is repressed by TrmBL1? What process is activated?

Answer 49

TrmBL1 represses sugar uptake and activates gluconeogenesis.

Question 50

What three molecules can function as 'effector molecules' for TrmBL1?

Answer 50

The three molecules are glucose, fructose, and mannose.

Question 51

What is the effect of TrmBL1 binding 'downstream' of the BRE/TATA box in the promoter region of the 'sugar uptake' operon?

Answer 51

It inhibits transcription of the operon.

Question 52

What is the effect of TrmBL1 binding 'upstream' of the BRE/TATA box in the promoter region of the gluconeogenesis operon?

Answer 52

It enhances transcription of the operon.

Question 53

Are the TrmBL1 effector molecules inducers, corepressors, both, or neither? Explain your answer.

Answer 53

They are inducers because they promote the expression of genes involved in gluconeogenesis.