BIO 310 - CH 14 (Regulation of Genes and Proteins)

Describe the zinc finger DNA-binding motif?

"Finger" is an alpha helix that interacts with DNA

What does the tryptophan (trp) operon consist of?

5 structural genes that code for enzymes needed to synthesize tryptophan

A chemoorganotroph and a photoautotroph in the same environment would not compete for? A. Carbon and oxygen B. Oxygen C. Carbon D. Nitrogen

A

Organisms able to live in environments with high sugar concentrations are? A. Osmophiles B. Halotolerant C. Anaerobic fermenting bacteria D. Xerophiles

A

You experimentally change the DNA sequence directly upstream of a start codon of an operon in E. coli to investigate the function of this region of DNA. Analysis reveals that after the change the same amount of mRNA is made from the operon, but there are very few proteins made from the operon. What is the most likely function of the DNA sequence that you changed? A. The DNA sequence likely functions as a ribosome-binding site. B. The DNA sequence likely functions as a termination sequence. C, The DNA sequence likely functions as in transcriptional regulation. D. The DNA sequence likely functions as a promoter.

A

Protein involved in positive regulation?

ACTIVATOR protein

When the allosteric effector is NOT bound to the allosteric site of the allosteric enzyme, inhibition or activity?

ACTIVITY

Inducer for lac I repressor?

ALLOLACTOSE

Common covalent chemical modifications?

AMP; ADP; phosphorylation; acetylation; methylation; glycosylation

Repressor proteins (negative transcriptional control) exist in what forms?

Active; inactive

What binds to the lac repressor and causes it to fall off of the operator region of DNA?

Allolactose (it is the inducer)

What are the major modes used to regulate the activity of biosynthetic enzymes?

Allosteric regulation; covalent chemical modifications

For negative regulation (induction and repression), RNA polymerase is?

Already at the promoter, but transcription is prevented by the repressor bound to operator

GTP provides energy for? A. Protein folding B. Translation C. Transcription D. DNA replication

B

In the absence of lactose, the lac repressor is? A. Inactive and cannot bind to the operator. B. Active and can bind to the operator. C. Inactive and can bind to the operator. D. Active and cannot bind to the operator. E. Inactive and cannot bind to the promoter.

B

Which of the following would be used by a chemoorganotroph for energy? A. H2 B. C2H3O2- C. H+ D. CO2

B

Select all of the answers that apply to catabolite repression and the lac operon: A. CAP is inactive when bound to cAMP. B. CAP is active when bound to cAMP. C. Adenyl cyclase synthesizes cAMP when glucose levels are high. D. Adenyl cyclase synthesizes cAMP when glucose levels are low. E. THe lac operon contains a CAP recognition site. F. Transcription of the lac operon is maximized when both lactose and glucose are present.

B; D; E

What can cause premature termination of transcription? (regulation at transcription level in Bacteria)

Binding of a metabolite to a riboswitch in mRNA

Describe negative transcriptional control.

Binding of a repressor protein to inhibit DNA transcription

Describe positive transcriptional control.

Binding of activating protein to DNA promotes transcription.

How do regulator proteins act to modulate gene expression? Interact?

Binding the major groove of DNA; interact with DNA through a DNA binding motif (sequence of amino acids)

DNA in cells can encode thousands of different proteins. Why do cells require mechanisms to regulate expression of the genes that code for these proteins? A. In order to develop, a cell must be able to make every protein that it possesses a gene for. It must have the ability to turn off the genes that aren't needed as it develops into each different cell type. B. There are unlimited genes available for making proteins, but limited amounts of energy to do so. C. Not all proteins are needed at all times, or in equal amounts. Regulating their expression saves energy and time. D. There are a limited number of genes available for making proteins. Proteins derived from all genes cannot all be made simultaneously.

C

The lac operon is expressed when glucose is? A. High and lactose is present. B. High and lactose is absent. C. Low and lactose is present. D. Low and lactose is absent. E. Glucose is low, regardless of the presence or absence of lactose.

C

The stringent response occurs when bacteria are? A. Overwhelmed by glucose abundance. B. Starved for glucose. C. Starved for amino acids. D. Overwhelmed by amino acid abundance.

C

When in a complex with ______, the CAP protein binds to the CAP site and ________ the expression of the lac operon. A. glucose; switches off B. Lactose; switches on C. cAMP; switches on D. cAMP; switches off E. glucose; switches on

C

Polycistronic mRNA code for?

Code for MORE THAN ONE polypeptide (operon)

Covalent modifications result in?

Conformational changes that change enzyme activity

What ACTIVATES an inactive repressor protein in negative transcriptional control? (thus NO transcription occurs)

Corepressor

What types of changes in proteins can alter the structure and function of the proteins? (general) (regulation at posttranslation level in Bacteria)

Covalent changes

In the absence of tryptophan, the trp repressor is? A. Inactive and can bind to the operator. B. Active and cannot bind to the operator. C. Inactive and cannot bind to the promoter. D. Inactive and cannot bind to the operator. E. Active and can bind to the operator.

D

If tryptophan is present in the cell's environment, tryptophan will bind to the? A. Operator B. Promoter C. RNA polymerase D. trp genes E. trp repressor

E

Examples of helix-turn-helix DNA-binding motif?

E. coli lac and trp repressors

What happens in allosteric regulation? (specific name for molecule?)

Effector molecules bind to non-catalytic sites of the enzyme (the allosteric site) which changes enzyme conformation and changes activity

T/F: In fast-growing E. coli cells, multiple replication forks of genomic DNA allows binary fission to occur before the genome has been fully duplicated.

FALSE (have to finish 1 replication fork before binary fission)

T/F: While both transcriptional and translational riboswitches are regions fo the 5' leader mRNA that can bind an effector molecule, translational riboswitches occlude the Shine-Dalgarno sequence preventing ribosome binding when an effector molecule is absent.

FALSE (should be when an effector molecule is PRESENT)

What do the two helixes do in HTH (helix-turn-helix) do as part of the DNA-binding protein motif?

First helix is site specific for recognition; second helix stabilizes binding (hydrophobic interaction with the first helix)

Do bacteria prefer glucose or lactose?

GLUCOSE

Ribosomes use GTP or ATP in translation?

GTP

What are inducible genes? Example?

Genes that code for inducible enzymes needed only in certain environments; beta-Galactosidase

What are the 3 main DNA-binding protein motifs? (that allow regulator proteins to interact with DNA)

Helix-turn helix; zinc finger; leucine zipper

Regulator proteins that modulate gene expression are often?

Homodimeric and bind specific DNA sequences

What are constitutive genes?

Housekeeping genes expressed continuously by the cell (involved in replacing worn out parts?)

Interaction between first helix and second helix of helix-turn-helix DNA-binding motif?

Hydrophobic interaction

What INACTIVATES an active repressor protein in negative transcriptional control? (thus turning transcription ON)

INDUCER

When the allosteric effector is bound to the allosteric site of the allosteric enzyme, inhibition or activity?

INHIBITION

Negative control of regulatory proteins: inhibits or promotes transcription?

INHIBITS

When does the trp operon function, the absence or presence of tryptophan?

In the ABSENCE of tryptophan

What ACTIVATES an inactive activator protein in positive transcriptional control?

Inducer

What alters the activity of a repressor protein (negative transcriptional control)?

Inducers and corepressors

Lac operon contains what type of genes?

Inducible genes

What INACTIVATES an active activator protein in positive transcriptional control?

Inhibitor

Regulatory proteins often detect?

Inverted repeats

Describe the leucine zipper DNA-binding motif?

Leu every 7 amino acids forms the teeth of the zipper; zipper doesn't directly interact with DNA

What are regulator proteins involved in?

Modulating gene expression

Charge of a phosphate group?

NEGATIVE

What type of transcriptional control is the lac operon under? So what type of protein is involved?

NEGATIVE control; REPRESSOR protein

What control is the tryptophan (trp) operon under?

NEGATIVE transcriptional control by trp repressor

Are enzymes of the lac operon normally produced when lactose is absent?

NO

Does the "zipper" of the leucine zipper DNA-binding motif interact directly with DNA?

NO

Is it possible for a eukaryote to have a polycistronic operon?

NO

Is the removal of amino acid residues a reversible modification to proteins? (regulation at posttranslation level in Bacteria)

NO

Are activator binding sites the same as operator sites?

NO (positive control)

Catabolic enzymes: if a bacterial cell's preferred carbon and energy source is present, will the gene/operon be "on" and enzymes synthesized?

NO (see diagram in notes)

When allolactose is present, is transcription of lac operon blocked?

NO (so transcription proceeds)

When a corepressor binds to a repressor protein, does transcription occur?

NO (the corepressor binds to the repressor protein thus allowing the repressor protein to bind to DNA, thus preventing RNAP access to the gene)

Are enzymes of catabolic pathway synthesized when substrate is absent? Why or why not?

NO; to promote an efficient use of energy and materials

Where do activators bind in positive control of transcription?

Near the promoter OR several hundred bp away

What do regulatory proteins do?

Negative control (inhibit transcription); positive control (promote transcription)

What types of proteins can regulate gene activity in bacteria in transcription? (regulation at transcription level in Bacteria)

Nucleoid-associated proteins

When there are low amounts of lactose, is transcription of the lac operon on or off?

OFF (b/c there is no allolactose to bind to the repressor protein and inactivate it)

When there are high amounts of lactose, is transcription of the lac operon on or off?

ON (b/c the allolactose binds to the repressor and induces a conformation change, so lac I repressor falls of the DNA)

When are enzymes of the catabolite pathway needed?

ONLY when substrate is available

Positive control of regulatory proteins: inhibits or promotes transcription?

PROMOTES

How to alter activity of enzymes and proteins? (at what step)

Post-translational modifications

What are the three approaches to regulation?

Posttranslational modifications; transcription; translation

Where are polycistronic mRNA's found?

Prokaryotes

What destroys protein activity? (regulation at posttranslation level in Bacteria)

Protein degradation - via proteases (in actinobacteria - proteasomes)

In positive control of transcription, why is the activator needed for RNAP activity?

RNAP weakly binds to promoter and can't start transcription even if it binds to the promoter

What happens in covalent chemical modifications that regulate biosynthetic enzymes?

Regulation involves a small molecule attached to or removed from the protein; results in conformational change that changes enzymatic activity

Induction and repression of gene expression occur due to? WITH?

Regulatory proteins with DNA binding domains

Why is gene regulation needed?

Replacement of worn out parts; making more or less protein if conditions change

What prevents degradation of mRNA?

Secondary structure in 3' end

What is a DNA binding motif?

Sequence of amino acids

What can bind (NONCOVALENTLY) to proteins to affect its function? (regulation at posttranslation level in Bacteria)

Small molecules

Of the major sites of regulation (transcription, translation, and posttranslational), which is the best method in terms of energy?

TRANSCRIPTION (preventing mRNA from even being made)

T/F: When a cell is starved of one or more amino acids, synthesis of the biosynthetic machinery (rRNA and tRNA) is halted while mRNAs coding for specific amino acid synthesis are upregulated mediated by RelA, which produces ppGpp.

TRUE

Structure of lac operon?

Three structural genes coding for lactose uptake and metabolism

What is attenuation? (regulation at transcription level in Bacteria)

Transcription can terminate very early after it has begun due to the formation of a transcriptional terminator (termination within leader region)

What proteins bind to the DNA and control whether transcription begins or not? (regulation at transcription level in Bacteria)

Transcription regulatory proteins

WHERE in the process of central dogma are the major sites of regulation?

Transcription; Translation; Post-translational modification

How to regulate gene expression? (at what steps)

Transcription; translation

What can prevent translation from starting by binding to the mRNA strand? (regulation at translation level in Bacteria)

Translational repressor proteins; small RNA; metabolite to a riboswitch

Are enzymes of the lac operon normally produced when lactose is present?

YES

Is methylation/demethylation a reversible modification to proteins? (regulation at posttranslation level in Bacteria)

YES

Is phosphorylation/dephosphorylation a reversible modification to proteins? (regulation at posttranslation level in Bacteria)

YES

When an inducer binds to a repressor protein, does transcription occur?

YES (inducer binding to repressor protein causes the repressor protein to fall off of the DNA, allowing for RNAP to have access to the DNA and thus transcribing it)

When allolactose is absent, is transcription of lac operon blocked?

YES (so NO transcription)

What are the effector molecules for an activator protein? (positive control of transcription)

inhibitor; inducer

Type of protein involved in regulation of lac operon?

lac repressor (from lacI) binds to operator to inhibit transcription

lac repressor comes from?

lacI