Module 8

Question 1

Gene Regulation

Answer 1

The ability to alter the expression of genes

Question 2

Gene regulation can occur at three distinct points in bacteria:

Answer 2

1. Transcription
2. Translation
3. Posttranslation

Question 3

Regulatory Proteins

Answer 3

Utilized in transcriptional regulation, includes repressors (bind to DNA and inhibit transcription) and activators (bind to DNA and increase transcription) and influenced by small effector molecules

Question 4

Small Effector Molecules

Answer 4

Bind to regulatory proteins, influence whether or not they can bind (inducers and corepressors)

Question 5

Inducers

Answer 5

Increase transcription by either binding to activators or binding to repressors and preventing them from binding

Genes regulated by these small effector molecules are “inducible”

Question 6

Corepressors

Answer 6

Decrease transcription by either binding to repressors or binding to activators and preventing them from binding

Genes regulated by these small effector molecules are “repressible”

Question 7

Enzyme Adaptation

Answer 7

A particular enzyme appears in the cell only after the cell has been exposed to the enzyme substrate

Question 8

Operon

Answer 8

Regulatory unit consisting of a few protein-encoding genes under the control of a single promoter, encodes a polycystronic mRNA sequence

Question 9

DNA elements that control lac operon transcription:

Answer 9

• Promoter (binds to RNA polymerase)
• Operator (binds to lac repressor)
• CAP site (binds the Catabolite Activator Protein)

Question 10

lac Operon Structure

Answer 10

i promoter > lacI regulatory gene > CAP site > lac promoter > operator site > lacZ > lacY > lacA > lac terminator

Question 11

lacZ Gene

Answer 11

Encodes B-galactosidase which enzymatically cleaves lactose, converting into allolactose

Question 12

lacY Gene

Answer 12

Encodes lactose permease, allows for transport of lactose across cell membrane

Question 13

lacA Gene

Answer 13

Encodes galactoside transacetylase which acetylates lactose to prevent buildup of toxins

Question 14

After B-galactosidase breaks down lactose into allolactose, it acts as an ____ and binds to ____, preventing it from binding to the DNA

Answer 14

inducer, lac repressor

increases transcription

Question 15

lacI Gene

Answer 15

Encodes the lac repressor, which binds to the operator when no lactose is present

Question 16

Jacob, Monod, and Pardee Experiment Results

Answer 16

Determined that merozygote (lacI⁺ on chromosomal, lacI^- on F’ factor) will remain inactive when lactose is absent and activate in presence of lactose

Due to presence of active repressor protein in chromosomal gene

Question 17

Loss of function in lacI vs lacO

Answer 17

When negative with no lactose, both are at 100% expression. With lacI⁺ on F’ factor both will express 200% when lactose is present, when it is not present lacI will then cut its expression to 0% while lacO will still produce 100%

Question 18

Catabolite Activator Protein (CAP)

Answer 18

In the presence of two sugars (diauxic growth), bacteria use glucose before lactose. Glucose inhibits cAMP production and leads to lack of small effector molecules needed to start lac operon

Question 19

Results of lac operator research

Answer 19

Discovery that lac operon has three separate activators (O₁ next to promoter, O₂ downstream within lacZ gene, and O₃ slightly upstream of promoter)

Found that DNA loops form from binding of lac repressors; if not all bound, O₁ must bind to either O₂ (stronger repression) or O₃ (weaker repression)

Question 20

Binding of lac operators (O₁ to O₂ or O₁ to O₃) forms a ____ since operators are far apart

Answer 20

loop

Question 21

Riboswitches can regulate transcription and translation via the formation of a ____

Answer 21

stem loop (terminator/anti-terminator in RNA for transcription, inhibits translation of Shine-Dalgarno RNA sequence in translation)

Question 22

Gene Regulation in Eukaryotes

Answer 22

Can occur at any point in the transcription, RNA processing, translation, posttranslational modification process

Question 23

Combinatorial Control

Answer 23

Most eukaryotic genes regulated by many factors, such as activators and repressors

Question 24

Activators and repressors in eukaryotes can be modulated by ____

Answer 24

small effector molecules, protein-protein interactions, covalent modifications, also via regulatory proteins, DNA methylation, and formation of heterochromatin

Question 25

Activators and repressors bind ____ of the primary promoter

Answer 25

upstream

Question 26

Regulatory transcription factors control ____ either directly or through coactivators to enhance transcription or silence it

Answer 26

TFIID

Question 27

Glucocorticoid Pathway

Answer 27

1. Glucocorticoid molecules enter cell via glucocorticoid receptor 2. Receptors binds to Glucocorticoid Response Element (GRE) inside cell 3. GRE then positions itself on the chromatin and functions as an enhancer for many genes

Question 28

CREB Protein Pathway

Answer 28

1. cAMP increases in response to extracellular signaling 2. CREB binds to two adjacent sites (cAMP response elements - CRE) 3. CREB then binds to specific binding protein, CBP, which also serves as a coactivator and causes transcription to dramatically increase

Question 29

ATP-Dependent Chromatin Remodeling

Answer 29

Dynamic changes in chromatin structure which repositions and restructures nucleosomes, goal is to make DNA **more** or **less** open for transcription

Question 30

Histone Variant

Answer 30

Histones that have been altered through accumulated mutations, specialized to certain cell types or genome regions

Question 31

Histone Code

Answer 31

Modifications of amino terminal tails of histones can affect transcription by influencing interactions between DNA and histone proteins and by occurring in patterns recognized by proteins

Question 32

ChIP-Seq Technique

Answer 32

Technique used to map locations of specific nucleosomes within genome, allows for the determination of nucleosome/histone variant locations and where histone modifications occur. 1. After breaking DNA into segments, Abs specific to histones and attached to heavy bead bind to them 2. Centrifuged which produces pellet with core histones and cross-linked proteins 3. Exposed to agent to separate histones from DNA before sequencing to determine where sequence originates from Nucleosome-free regions are found at the beginning and end of most genes

Question 33

When a gene is transcriptionally activated, chromatin remodeling and histone modification occurs via ____

Answer 33

remodeling complex, histones are evicted and acetylation occurs

Question 34

DNA Methylation

Answer 34

A covalent attachment of methyl groups carried out by DNA methyltransferase, often inhibits transcription

Question 35

Methylated DNA sequences are inherited during cell division (genomic imprinting). Specific methylated genes from mother and father via ____, and maintained in offspring via ____

Answer 35

de novo methylation, maintenance methylation

Question 36

A small effector molecule induces transcription. Which combination below is consistent with this idea? A. Repressor and inducer B. Activator and inhibitor C. Repressor and corepressor D. None of the above

Answer 36

A. Repressor and inducer The inducer prevents the repressor from binding, allowing transcription to move ahead

Question 37

Let's suppose that mediator has interacted with an activator protein. What would you expect to happen next? A. TFIID would bind to the core promoter B. RNA polymerase would bind to the core promoter C. Histones would be displaced from the core promoter D. RNA polymerase would switch to the elongation phase of transcription

Answer 37

D. RNA polymerase would switch to the elongation phase of transcription RNA polymerase is already bound to the core promoter, however mediator lies in its path along the operon preventing transcription

Question 38

If histones were not removed during eukaryotic gene transcription, which processes would be inhibited? A. The formation of the pre-initiation complex B. Transcriptional elongation C. Phosphorylation of CTD D. Both A and B

Answer 38

D. Both A (The formation of the pre-initiation complex) and B (Transcriptional elongation)

Question 39

Which of the following phenomena could you study using ChIp-Seq? A. To see if a regulatory transcription factor binds to mediator and/or TFIID B. To measure the level of transcription of a given gene in real time C. To analyze the binding of protein(s) to DNA on a genome-wide scale D. To determine if a mutation at a regulatory site alters the transcription level of a given gene

Answer 39

C. To analyze the binding of protein(s) to DNA on a genome-wide scale