Chapter 12: The Control of Genetic Information via Gene Regulation

Question 1

Define gene regulation.

12.1

Answer 1

The ability of cells to control the expression of their genes.

Question 2

What is gene expression?

12.1

Answer 2

the process by which the information within a gene is made into a functional product, such as an RNA molecule or a protein

Question 3

Define constitutive genes.

12.1

Answer 3

unregulated gene that has constant levels of expression in all conditions over time

Question 4

How do living organisms benefit from gene regulation?

12.1

Answer 4

1. conserves energy by producing only what is needed
2. ensures that genes are expressed in the appropriate cell types & at correct stage of development (in multicellular organisms)

Question 5

How do proteins regulate gene expression?

12.1

Answer 5

through binding to DNA

Question 6

The different cell types of an individual contain the same ________, meaning they carry the same set of genes. However, their _______, which is the collection of proteins they make, is quite different.

12.1

Answer 6

genome; proteome

Question 7

How does gene regulation play a role in mammals (embryonic and fetus stages)?

12.1

Answer 7

gene regulation plays a role in ensuring that an embryo and fetus get a proper amount of oxygen; offspring can take oxygen from the maternal bloodstream

Question 8

T or F: During mammalian development, all globin genes are expressed during all developmental stages.

12.1

Answer 8

False; DIFFERENT globin genes are expressed at DIFFERENT developmental stages

Question 9

Which process is present in the gene expression of Eukaryotes that Prokaryotes lack?

12.1

Answer 9

RNA modification

Question 10

Gene regulation most commonly occurs at the level of ____________.

12.1

Answer 10

transcription

Question 11

There are 5 different types of gene expression during the developmental stages of a mammal. Determine which ones occur during the embryonic stage, fetal stage, and birth to adult stage.

12.1

Answer 11

Embryonic: epsilon and zeta globin genes
Fetal: alpha and gamma globin genes
Birth: alpha and beta globin genes

Question 12

Define regulatory transcription factors.

12.2

Answer 12

proteins that bind to regulatory sequences in the DNA, usually in the vicinity of a promoter and either increase of decrease the rate of transcription of a gene

Question 13

What type regulatory transcription factors decrease the rate of transcription, and what is this form of regulation called?

12.2

Answer 13

repressors; negative control

Question 14

Try your best to draw what a negative control looks like on a whiteboard or piece of paper! :)

12.2

Answer 14

Question 15

Try your best to draw what a positive control looks like on the whiteboard or a piece of paper! :)

12.2

Answer 15

Question 16

What is the function of a small effector molecule?

12.2

Answer 16

they bind repressors or activators, causing a change in their conformation and function

Question 17

What is an operon? Where can they be found?

12.2

Answer 17

a cluster of genes ( 2+ ) that is under the transcriptional control of one promoter; found in bacterial chromosomes

Question 18

Define the functions of each step in Eukaryotic gene expression (i.e., transcription, RNA modification, translation & post-translation).

12.1

Answer 18

Transcription: control of synthesis of mRNA from a gene
RNA modification: regulation of splicing of mRNA
Translation: regulation of protein synthesis
Post-translation: regulation of the amount or function of a protein that has already been synthesized

Question 19

What is the advantage of operon organization in bacteria?

12.2

Answer 19

bacteria can coordinate the expression of multiple genes in the same biological pathway

Question 20

What are the basic components of the lac operon (lactose operon)?

12.2

Answer 20

promoter (lacP), and three structural genes: lacZ, lacY, and lacA

Question 21

In the lac operon, the ______ is the DNA sequence at which the lac repressor binds.

12.2

Answer 21

operator (lacO site)

Question 22

What is the CAP site for the lac operon?

12.2

Answer 22

a regulatory sequence in the DNA that is recognized by an activator protein

Question 23

How does the presence of lactose in the cell influence the transcription of the lac operon?

12.2

Answer 23

1. when lactose is present, transcription of the lac operon is high
2. when lactose is present, the lac repressor protein does not bind to the operator site and transcription can occur

Question 24

How does allolactose affect the lac repressor protein?

12.2

Answer 24

It binds to the repressor protein and prevents it from binding to the operator site of the lac operon

Question 25

The catabolite activator protein (CAP) is involved in ______ control of the lac operon. ##Footnote 12.2

Answer 25

positive

Question 26

Describe the relationship between the level of cAMP and glucose. ##Footnote 12.2

Answer 26

glucose present ——-> low cAMP glucose absent ———> high cAMP

Question 27

Describe the function of glucose and lactose in the lac operon. ##Footnote 12.2

Answer 27

glucose BLOCKS activation of the lac operon; lactose RELIEVES repression of the lac operon

Question 28

Which relationship between glucose and lactose allows for the transcription rate of the lac operon to be very high? Why? ##Footnote 12.2

Answer 28

When lactose is HIGH and glucose is LOW, the rate is very high because CAP is bound to the CAP site and lac repressor is not bound to the operator; bacteria readily metabolize lactose

Question 29

Which factors help increase transcription levels in eukaryotes? ##Footnote 12.3

Answer 29

1. binding of an activator protein to DNA 2. loosening of chromatin structure

Question 30

How does eukaryotic regulation differ from prokaryotic? ##Footnote 12.3

Answer 30

1. genes are organized individually (not in operons) 2. tends to be more intricate bc they possess complexities not found in prokaryotes

Question 31

What factors INHIBIT transcription in eukaryotes? ##Footnote 12.3

Answer 31

1. repressors inhibit RNA polymerase to initiate transcription 2. DNA methylation inhibits transcription by preventing binding of activator OR by recruiting proteins that inhibit transcription

Question 32

The lac operon is turned off/on in the presence of lactose. ##Footnote 12.2

Answer 32

on

Question 33

How does the cell recognize that lactose needs to be metabolized? ##Footnote 12.2

Answer 33

lactose is converted into allolactose, which inhibits the lac repressor

Question 34

How do CAP and cAMP increase transcription of the lac operon? ##Footnote 12.2

Answer 34

when CAP and cAMP bind to the CAP site, this enhances binding of RNA polymerase to the promoter site

Question 35

What are the two components of the core promoter in eukaryotes? ##Footnote 12.3

Answer 35

TATA box and transcriptional start site

Question 36

Under what conditions does the lac repressor bind to the operator of the lac operon and prevent transcription? ##Footnote 12.2

Answer 36

when the concentration of lactose is LOW in the cell

Question 37

How does allolactose affect the lac repressor protein? ##Footnote 12.2

Answer 37

it binds to the repressor protein and prevents it from binding to the operator site of the lac operon

Question 38

What determines the precise starting point for transcription? ##Footnote 12.3

Answer 38

the TATA box

Question 39

What are enhancers? What about silencers? ##Footnote 12.3

Answer 39

Enhancers: DNA sequences that increase transcription Silencers: DNA sequences that prevent transcription

Question 40

Bacteria requires once transcription factor (called sigma factor) to initiate transcription. How many do eukaryotes need? What are they called? ##Footnote 12.3

Answer 40

RNA polymerase II requires 5 different proteins called general transcription factors (GTFs) in eukaryotes

Question 41

What is the function of general transcription factors (GTFs) in the initiation of transcription? ##Footnote 12.3

Answer 41

GTFs and RNA polymerase come together at the core promoter for the initiation of transcription

Question 42

A sequence upstream of the transcriptional start site. Determines the precise starting point for transcription. These factors describe what? ##Footnote 12.3

Answer 42

the TATA box

Question 43

Try to draw an illustration of how an activator can regulate the function of RNA polymerase by affecting the function of GTFs. Make sure to include the following: activator, coactivator, enhancer, TATA box, TFIID, and the pre-initiation complex! :) ##Footnote 12.3

Answer 43

Question 44

Identify the two ways that a repressor can interact with a GTF to inhibit transcription. ##Footnote 12.3

Answer 44

1. a repressor can prevent binding of TFIID to the TATA box 2. a repressor can inhibit assembly of the pre-initiation complex

Question 45

Suppose a mutation in the lacl gene prevented lac repressor from being made. How would this mutation affect the expression of the lac operon? ##Footnote 12.2

Answer 45

it would be expressed in the presence or absence of lactose in the environment

Question 46

What serves as a target for activators or repressors to either promote or inhibit translation? ##Footnote 12.3

Answer 46

TFIID (transcription factor IID)

Question 47

Depending on the locations and arrangements of ___________, regions of DNA may or may not be accessible for transcription. ##Footnote 12.4

Answer 47

nucleosomes

Question 48

What is the difference between a region in a closed and open conformation? ##Footnote 12.4

Answer 48

Closed: transcription is difficult/impossible Open: accessible to GTFs and RNA polymerase, thus, can be transcribed

Question 49

What are the 3 different ways that chromatin-remodeling complexes can change chromatic structure? ##Footnote 12.4

Answer 49

1. binding to a chromatic and changing the positions of nucleosomes 2. removing histones from DNA 3. replacing standard histones with histone variants

Question 50

T or F: Acetylated histone proteins do not bind as tightly to the DNA, which promotes transcription.

Answer 50

true

Question 51

Many eukaryotic genes are flanked by a nucleosome- ______ ________, which is a site that is missing nucleosomes. ##Footnote 12.4

Answer 51

free region

Question 52

Briefly describe the sequence that occurs during the recruitment of chromatin-remodeling complexes and histone-modifying enzymes to the promoter region. ##Footnote 12.4

Answer 52

1. activator binds to an enhancer in the nucleosome-free region (NFR) 2. activator recruits chromatin-remodeling complex and histone modifying enzymes 3. biding of GTFs and RNA polymerase II to the core promoter is facilitated; preinitiation complex forms 4. histones are evicted/shifted from promoter region, or destabilized so RNA polymerase II can pass 5. transcription occurs

Question 53

DNA _______ usually inhibits the transcription of eukaryotic genes, particularly when it occurs in the vicinity of the __________. ##Footnote 12.4

Answer 53

methylation; promoter

Question 54

How does methylation inhibit transcription? ##Footnote 12.4

Answer 54

by preventing the binding of an activator OR by facilitating the binding of proteins that inhibit transcription

Question 55

The formation of what, is a way to silence genes in a tissue specific manner? ##Footnote 12.4

Answer 55

facultative heterochromatin

Question 56

When a pre-mRNA has multiple introns and exons, the coding sequences can be put together in more than one way. This process, which results in the production of two or more different polypeptides, is termed __________ ____________. ##Footnote 12.5

Answer 56

alternative splicing

Question 57

When iron levels are low, the iron regulatory protein: ##Footnote 12.5

Answer 57

binds to the iron regulatory element (IRE) and blocks translation of ferritin

Question 58

The mRNA encoding ferritin is controlled by an RNA-binding protein called the _______. ##Footnote 12.5

Answer 58

iron regulatory protein

Question 59

Another way to regulate mRNAs involves _______________, that directly affect the initiation of translation. ##Footnote 12.5

Answer 59

RNA-binding proteins

Question 60

T or F: Alternative splicing of pre-mRNAs decreases protein diversity. ##Footnote 12.5

Answer 60

false; it INCREASES protein diversity

Question 61

When the iron regulatory protein (IRP) is bound to ______, translation is blocked. When the IRP is bound to _____, translation proceeds. ##Footnote 12.5

Answer 61

IRE; iron