Biology 111B

Study Questions 16: Gene Regulation
Answers

 

1. A brain cell differs from a liver cell because: (circle ALL correct answers)

a. they contain different genes

b. they express different genes

c. they use a different genetic code

d. they have different ribosomes

 

2. In eukaryotes, most of the genes in each cell are active. ____True____ False

 

3. Regulation of _____________ is the most common form of control of gene expression.

a. genetic content

b. transcription

c. translation

d. enzyme activity

 

4. Define the following terms:

operon	a unit of coordinated control in a prokaryote including a promoter with its regulatory sequences, one or more genes, and the termination sequence
operator	a downstream regulatory sequence in the DNA to which a repressor protein binds in negative control
effector	the molecule that binds to a regulatory protein to change the state of the system
activator	a protein that binds to DNA at a control element upstream from the promotor in positive control
positive control	the situation in which transcription is stimulated by the binding of a protein at an upstream control element
negative control	the situation in which transcription is impeded by the binding of a protein at a downstream operator site
repressible operon	an operon that is normally "on" but can be turned off under the right circumstances. Repressible operons generally make proteins that produce compounds the cell continually needs like amino acids or glycolysis enzymes
inducible operon	an operon that is normall "off" but can be turned on under the right circumstances. Inducible operons generally make proteins that are required only intermittantly, such as the enzymes that break down alternative energy sources

5. How can you recognize whether a system is under positive or negative control?

 If a system uses a protein bound downstream from the promoter, or has a protein-binding site downstream from the promoter, then it is under negative control. If it has a protein bound upstream or has a protein-binding site upstream from the promoter, then it is under positive control.

6. What is typically the function of genes that are in repressible operons? In inducible operons?

 Genes in repressible operons are generally those whose products are required pretty constantly (amino acid biosynthesis enzymes, glycolysis and Krebs cycle enzymes, for example), but can be turned off when there is a sufficient concentration of these enzymes in the cell. Inducible operons generally control genes whose products are required only under unusual circumstances (lactose breakdown genes in bacteria, for example).

7. What molecule typically serves as the effector in repressible operons? In inducible operons?

 Generally, the effector in a repressible operon is the product of the biochemical pathway. In inducible operons, it is generally the compound that will be broken down.

8. Describe how each of the following control systems would work.

a. an inducible operon under positive control
The operon is normally "off" and it gets turned on by the regulatory (activator) protein binding at the upstream control element. That happens only in the presence of an effector, which could be an alternative sugar to be broken down or a chemical signal from the environment (or in the case of eukaryotes, a signal from another cell).

b. a repressible operon under positive control
The operon is normally "on" and it gets turned off by the regulatory (activator) protein releasing the DNA at the upstream control element. That happens only in the presence of an effector, which is often the product of the pathway enzymes the operon controls.

c. an inducible operon under negative control
The operon is normally "off" and it gets turned on by the regulatory (repressor) protein releasing the DNA at the downstream operator site. That happens only in the presence of an effector, which could be an alternative sugar to be broken down or a chemical signal from the environment.

d. a repressible operon under negative control
The operon is normally "on" and it gets turned off by the regulatory (repressor) protein binding at the downstream operator site. That happens only in the presence of an effector, which is often the product of the pathway enzymes the operon controls.

9. Can an operon have more than one control system? Describe how both positive and negative control works in the lac operon (see Campbell et al. pp. 337-341)
Yes, an operon can be under both positive and negative control as is the lac operon. A cell wants to turn on the lactose breakdown genes in the presence of lactose, but also only if glucose is limited. This is because glucose is a more efficient fuel. So the negative control depends on the presence or absence of lactose (or more precisely, a derivative of lactose), which is the effector for removing the repressor from the operator site. But positive control depends on the cell being low on energy, in which case cyclic AMP (a low-energy signalling molecule we've run into before) acts as an effector (a "co-repressor" in this case) that allows the binding of an activator protein to a control element upstream from the promoter. Only a limited amount of transcription happens without both elements being favorable.

10. For both inducible and repressible sequences, think about the effects of mutations in the following sites. Assume the mutations prevent binding of what would normally bind. Would each mutation cause the genes to be constantly turned on or constantly turned off?

Mutation	Constantly ON or OFF?
DNA-binding domain of a repressor protein	ON
control element	OFF
promoter	OFF
effector in an inducible system	OFF
effector in a repressible system	ON
operator	ON
DNA-binding domain of an activator protein	OFF

11. What is the effect in inducible and repressible sequences of a molecule that binds to the effector binding site but does not change the shape of the DNA binding site the way the effector does?
That molecule would not be a switch for the system. In inducible systems, the system would stay off; in repressible systems, the system would stay on.

12. In a particular system, a mutation in the regulator-binding site on the DNA (such that the regulator protein cannot bind to the DNA) causes transcription to be always on. Is this system under positive or negative control? How do you know?
Negative control because without protein binding, the system is on. Therefore, binding of the protein turns the system off, which is the definition of negative control.

What would be the answer if the same kind of mutation caused transcription to be always off?
Positive control, again because in this case, binding of the protein to DNA causes the system to be turned on, and that is the definition of positive control.

13. In an inducible operon under positive control, what effect on transcription would the following scenarios have?

a. A compound that binds to the effector site on the regulatory protein in place of the effector and causes the regulatory protein to be unable to bind to the DNA.
This would cause the system to be always OFF. In an inducible system under positive control, the effictor binds to the activator to allow it to bind to the DNA and turn the system on. With the pseudo-effector in place, the activator cannot bind to the control element and turn on the system.

b. A compound that binds to the effector site on the regulatory protein in place of the effector and causes the regulatory protein to be permanently atttached to the DNA.
This would cause the system to be always ON. In an inducible system under positive control, the effictor binds to the activator to allow it to bind to the DNA and turn the system on. With the pseudo-effector in place, the activator will be constantly bound to the control element and allowing transcription.

14. What are two chemical modifications that more or less permanently "turn off" transcription in regions of DNA?
Permanent condensation of the DNA, as in the second X chromosome in female mammals, and methylation of the cytosines along a region of DNA.

15. The amount of protein made from a given mRNA molecule depends mostly on

a. the degree of DNA methylation

b. the rate at which the mRNA is degraded

c. the presence of certain transcription factors

d. the number of introns present in the mRNA

e. the types of ribosomes present in the cytoplasm

 

16. What is an enhancer and how does it work?
An enhancer is a DNA sequence to which a transcription factor binds to enhance transcription of a gene that might be rather distant from the enhancer site. Enhancers work at a distance because the DNA can bend and fold to bring distant parts of itself into proximity.

17. What is meant by the "DNA-binding domain" of a protein?
The DNA-binding domain is that region of a protein that actually interacts with the DNA. There are several versions that have been described, including the "helix-turn-helix" motif, the "zinc-finger" motif, and the "leucine zipper" motif.

18. In what ways can the amount of protein product be regulated after transcription has occurred?
As we saw in the genetics of development lecture, proteins can be added to mRNA to prevent their translation until the protein is removed. In addition, all mRNAs have a limited lifespan (generally only a few hours, but occasionally days or weeks) during which they can be translated. mRNA degredation apparently begins with shortening of the polyA tail. Different mRNAs can be built with longer or shorter lifespans, which seems to be dictated by a nucleotide sequence in the non-coding trailer region (that includes the termination sequence) of the mRNA.

19. Prokaryotes have operons that coordinate the control of related genes. How do eukaryotes accomplish coordinated control of related genes that might be scattered over many chromosomes?
Because most eukaryotic genes need transcription factors to stimulate transcription, coordinated control can occur if all the related genes have the same control element sequences. Then copies of the same activated transcription factor can bind to the control elements of all the related genes and turn them all on at once.