Unit 3 (Week 10 Gene Regulation) Flashcards
1
Q
What is the gene function either at the level of traits or at the molecular level?
A
Gene expression
2
Q
What is the ability of cells to control the expression of their genes?
A
Gene regulation
3
Q
What are unregulated genes that has a relatively constant level of expression in all conditions over time?
A
Constitutive genes
4
Q
What are the benefits of gene regulation? (2)
A
- Conserves energy. Proteins that are encoded by genes are produced only when needed.
- In multicellular organisms, gene regulation also ensures that genes are expressed in the appropriate cell types and at the correct stage of development.
5
Q
What does E. coli do within gene regulation that pertains to its ability to uptake lactose?
A
When lactose is not present in the environment, an E. coli cell makes very little of these proteins, lactose permease (transporter) and B-galactosidase (breaks linkage in lactose and galactose). However, when lactose becomes available, the bacterium produces many more of these proteins, enabling it to readily use lactose from its environment.
6
Q
What are one of the most amazing examples of gene regulation in humans?
A
Cell differentiation. The process by which cells become specialized into particular types. Cells may differentiate into muscle cells, neurons, skin cells, or other types.
They have the same genome but a different proteome. Or they may have the same genome and proteome but produce the same proteins at different rates.
7
Q
How does gene regulation underlie the different morphologies of the various types of cells?
A
Gene regulation causes each type of cell to express its own unique set of proteins, which, in turn, are largely responsible for the morphology and function of that type of cell.
8
Q
What is the protein responsible for delivering oxygen to the cell’s of a mammal’s body?
A
Hemoglobin
Genes that encode slightly different globin polypeptides are turned off and on throughout the embryonic stage of development and the fetal stage of development and to include at birth.
The differences between these proteins that are produced is their affinity to oxygen.
9
Q
Where does gene regulation happen most commonly in bacteria?
A
In bacteria, gene regulation most commonly occurs at the level of transcription, which means that bacteria regulate how much mRNA is made from genes. When geneticists say a gene is “turned off,” they mean that very little or no mRNA is made from that gene, whereas a gene that is “turned on” is transcribed into mRNA.
Bacteria can also regulate genes is by controlling mRNA translation, and can be regulated post-translational level in which the protein’s function is controlled after it is synthesized.
10
Q
What protein, in most cases, is needed for the regulation of transcription?
A
REGULATORY TRANSCRIPTION FACTORS which is a protein that binds to DNA, usually in the vicinity of a promoter, and affects the rate of transcription of one or nearby genes. (Repressors and Activators induce negative and positive controls on rate of transcription)
The REGULATORY SEQUENCE in a DNA sequence that functions as a binding site for REGULATORY TRANSCRIPTION FACTOR proteins, which influences the rate of transcription.
11
Q
What is a transcription factor that binds to DNA and inhibits transcription?
A
Repressor
12
Q
What type of control in transcriptional regulation happens by repressor proteins?
A
Negative control
13
Q
What is a transcription factor that binds to DNA and increases the rate of transcription?
A
Activators
14
Q
What type of control in transcriptional regulation happens by activator proteins?
A
Positive control
15
Q
What is a molecule that affects gene transcription by binding to a regulatory transcription factor, causing a conformational change in that protein?
A
Small effector molecule.
These changes can determine whether or not a regulatory protein can bind to the regulatory sequence.
16
Q
What are the two domains (sites) on activators and repressors?
A
One site where it allows them to bind to DNA and another site where small effecter molecules bind.
17
Q
In bacteria, a set of two or more genes may be under the transcriptional control of a single promoter. What is this arrangement called?
A
An operon.
18
Q
What is a group of genes are transcribed as a single unit, resulting in the production of _______ that is capable of encoding more than one protein?
A
Polycistronic mRNA
19
Q
What is the advantage of a bacterium to have an operon?
A
To regulate a group of genes that encode proteins whose functions are used for a common pathway.
20
Q
The genome of E. coli carries an operon, called the lac operon, that contains the genes to metabolize what?
A
Lactose
21
Q
[Focus on lac operon]
What is transcripted from the lac operon?
What does the lac operon genes consist of? Be specific.
A
- A polycistronic mRNA that encodes multiple proteins for the utilization of lactose.
- The lac operon consists of a promoter (lacP), and three protein-encoding genes.
LacZ gene encodes B-galactosidase which is an enzyme that breaks down lactose into glucose and galactose. As a side reaction, it is also responsible for a side reaction of breaking down a small amount of lactose into allolactose. This is a lactose analogue meaning structually differernt but similar function.
LacY gene encodes lactose permease, which is the transmembrane protein needed to transport lactose into the cytoplasm of E. coli.
LacA gene encodes glactoside transacetylase, which covalently modifies lactose and lactose analogues (allolactose) by attaching an acetyl group (-COCH3). This attachment of aceytal groups to nonmetabolizable lactose analogues prevents their toxic buildup.
22
Q
Which genes are under the control of the lac promoter?
A
The lacZ, lacY, and lacA genes are under the control of the lac promoter.
23
Q
What “sandwhiches” the lac promotor or lacP in the lac operon and are condisered regulatory sequences?
Note: Regulatory sequences are the areas that repressors and activators attach to.
A
On the left, we have the CAP site, which is a site recognized by the catabolite activator protein (CAP).
On the right of the promotor, we have the operator or lacO, which is a sequence of bases which provides a binding site for a repressor protein.
24
Q
What is adjacent to the lac operon?
A
The lac regulatory gene. This gene, known as lacI, encodes the lac repressor and has its own promoter called an I promoter.
This repressor protein is important for the regulation of the lac operon. The lacI gene, which is constitutively expressed at a fairly low level, has its own promoter called the i promoter. The lacI gene is not considered a part of the lac operon.
25
What did Monod and Jacob do, under the interest of enzyme adaption, which occurs when a particular enzyme appears within a living cell only after the cell has been exposed to the substrate for that enzyme?
They exposed bacteria to lactose, the levels of lactose-utilizing enzymes in the cells increased by 1,000- to 10,000-fold. After lactose was removed, the synthesis of the enzymes abruptly stopped.
26
The first mechanism Jacob and Monod discovered involved the lac repressor, which binds to the sequence of bases found at the lac operator site, which prevented RNA polymerase from what?
Note: The lac repressor is synthesized by the expression of the lac regulatory gene i.e. the lacI segment.
From transcribing the lacZ, lacY, and lacA genes.
27
T/F RNA polymerase can still bind to the lacP (promotor) when the lac repressor is bound to the operator site.
True but the polymerase cannot move past the operator to transcribe lacZ, lacY, and lacA genes.
Note: With the lac repressor bound to the lacO site, and polymerase not able to move past it means that the lacO site or operator site lies after the promoter site, or lacP site.
28
What depends on whether or not the lac repressor binds to the operator site?
Allolactose. This is a product of B-galactosidase enzyme, a side reaction or conversion of lactose when it is present.
This is because allolactose is a small effector molecule and it adheres to the four subunits within the lac repressor which THEN induces a conformational change and prevents the repressor from binding to the operator.
RNA polymerase is free to transcribe the lac operon.
29
What is the importance of E. coli and the regulation of the lac operon?
It conserves energy since the proteins that utilize lactose are made only when lactose is present in the environment.
30
The respressor protein, lacI, is made in small quantities when lactose is not present which prevents the lac operon to express. Since allolactose is created by B-galactosidase when lactose is present, it effectively creates a conformational change in lacI therefore increasing the rate of transcription (without an activator). What is allolactose called?
In this case, what can the lac operon be called because of the effects of the inducer?
An inducer which is a small effector molecule that increases the rate of transcription.
The lac operon is an inducible operon because transcription increases which the presence of a small effector molecule.
31
What is the reality of a repressor and the proteins of the lac operon?
The respressor does not 100% repress the lac operon. The amount of B-galactosidase, lactose permease, and galactoside transaceytalase is very small but is present for when lactose shows up in the environment to jump start the process of metabolism.
The presence of lactose increases the cytoplasmic levels of allolactose gradually and eventually increases the transcription of the lac operon.
32
With regard to regulatory proteins and small effector molecules, explain the meaning of negative control and inducible.
Negative control refers to the action of a repressor protein, which inhibits transcription when it binds to the DNA. Inducible refers to the action of a small effector molecule. When it is present, it promotes transcription.
33
Who were the pioneers who focused on mutated strains of E. coli, specifically the mutation of lacI (repressor DNA), where lactose enzymes were created without the presence of lactose?
The study of merozygotes, bacterial cells containing F' factor, or F prime factors. This study allowed the scientists exchange circular segments of wild type DNA to bacteria (E. coli) that had DNA which was mutated.
Jacob, Monod, and Pardee
When they added normal genes to the cell of mutant genes, the regulation of the mutant gene, meaning its constitutive expression of lacZ, lacY, and lacZ proteins, was shut off as well. This helped them understand the function of the lacI- mutation since the merozygote was able to introduce lacI+ (normal functioning lacI repressor gene) which inhibited the lac operon from creating proteins for both the gene with the mutation and the one without.
34
What were the three genetic terms to come from Jacob, Monod, and Pardee's experiment with mutant lacI genes in E. coli?
Cis-acting element - A DNA segment that must be adjacent to the gene(s) that it regulates. Ex. The operator site (lacO) is a cis-acting element for the lac operon.
Trans-effect - A form of genetic regulation that can occur even though two DNA segments are not physically adjacent. Ex. The action of the lac repressor on the lac operon is a trans-effect.
A cis-effect is mediated by a cis-acting element that binds regulatory proteins, whereas a trans-effect is mediated by genes that encode diffusible regulatory proteins. Diffusible means it can spread through the cytoplasm.
35
[Focus on Activator for lac operon] 1. Even though the lac operon is under negative control by a repressor, it is also positively controlled by what?
2. What is the small effector molecule that controls the CAP?
3. When influenced by CAP and cAMP, what type of control is this?
4. When cAMP binds to CAP, what transpires next?
1. The CAP (catabolite activator protein)
2. The cyclic AMP (cAMP) which is produced from ATP via an enzyme known as adenylyl cyclase.
3. Positive
4. Well, the cAMP-CAP complex then binds to the CAP site near the lac promoter, which causes the DNA to bend that enhances the ability of RNA polymerase to bind to the promoter. Transcription is then increased.
36
What is the key functional role of CAP and what does it cause?
Allows E. coli to choose between different sugars as an energy source.
It causes catabolite repression, meaning the prescense of a preferred energy source inhibits the use of other energy sources.
EXAMPLE
In the case of transcription, the presence of glucose (which is a catabolite; it is broken down-catabolized-inside the cell) causes catabolite repression and decreases rate of transcription by inhibiting the production of cAMP, thereby preventing the binding of CAP to the DNA.
Glucose blocks activation of the lac operon.
Sounds wierd? CAP and its relationship with increasing synthesis of operon proteins? Name was chosen before understanding that CAP actually increases the rate of anabolic properties.
37
What is the function of cAMP in eukaryotic cells?
In eukaryotic cells, cAMP acts as a second messenger in signal transduction pathways.
38
[Four possible environmental conditions that E. coli might experience with two sugars]
1. High lactose, high glucose - What happens?
2. High lactose, low glucose - What happens?
3. Low lactose, high glucose - What happens?
4. Low lactose, low glucose - What happens?
1. CAP does NOT bind, but low level of transcription does occur. Repressor protein is inactive, and E. coli uses glucose.
2. CAP does bind (no catabolite repression) to CAP site, lac repressor is inactive due to allolactose, meaning lac operon very high transcription.
3. CAP does NOT bind, lac repressor binds as well blocking RNA polymerase. Very low rate of transcription.
4. Regardless, when lactose is low, the lacI gene is expressed without allolactose meaning the lac repressor gene represses transcription of the lac operon even if glucose is low.
39
What are the advantages of having both an activator and a repressor protein?
In the case of bacterial metabolism of sugars, the repressor keeps the lac operon turned off unless lactose is present in the environment. The activator allows the bacterium to choose between glucose and lactose.
40
[Focus on operon that does biosynthesis in E. coli]
1. What is an example of an operon in E. coli that involves the encoding of enzymes involved in biosynthesis and not the breakdown of a molecule?
2. What does this operon make?
3. What genes does this polycistronic mRNA express specifically? (5) These enzymes are involved in the pathway where its end product is tryptophan.
4. What is the gene that regulates the trp operon via a repressor protein?
5. Guess where the trpR binds to for regulation?
6. How is the trpR controlled?
7. With the answer to 6, what do you know about this whole process?
1. The trp operon
2. It encodes the enzymes needed to make the amino acid, tryptophan, a building block of proteins
3. trpE, trpD, trpC, trpB, and trpA.
4. trpR
5. The trp operon operator site.
6. It is controlled by the presence of tryptophan, which is the product of the metabolic pathway.
7. When tryptophan presence is low, trpR does not bind to the operator site, therefore allowing the cell to express trp operon which then readily makes tryptophan. When tryptophan levels are high, tryptophan acts as a small effector molecule and binds to the trpR repressor protein. This repressor undergoes a conformational change that then binds to the trpO or operator site inhibiting transcription of the trp operon.
42
So with the lac operon, the small effector molecule is allolactose increases the rate of transcription when lactose is present and it is known as an inducer. However, in the case of the trp operon, the small effector molecule is the product of trp operon transcription, which reduces transcription of the trp operon which sufficient levels of tryptophan exist. What do you call this small effector molecule in this case? And since this is NOT an inducible operon, what type of operon is it?
Tryptophan, as a small effector molecule, is called an co-repressor. The trp operon is a repressible operon.
The lac operon is categorized as an inducible operon because allolactose, its small effector molecule, induces transcription. By comparison, the trp operon is considered to be a repressible operon because its small effector molecule, namely tryptophan, represses transcription.
43
[Start transcription within Eukaryotes]
1. What are the similarities with bacteria in transcription?
2. What are the differences with bacteria in transcription?
1. Activator and repressor proteins are used affecting the ability of RNA polymerase. Many eukaryotic genes are influenced by small effector molecules.
2. Many genes are almost always organized individually, not as operons. Eukaryotic gene regulation is much more intricate, because of eukaryotic complexity.
44
What is the phenomenon wherehy a combination of many factors determines the expression of any given gene in eukaryotes?
Combinatorial control
45
For initial transcription in eukaryotic protein-encoding genes, what are the three features common among most promoters?
Regulatory elements, a TATA box, and a transcriptional start site.
45
[Focus factors that contribute to combinatorial control in transcription]
1. The stimulation and inhibition of RNA polymerase is affected by what?
2. What refers to the binding of small effector molecules, protein-protein interactions, and covalent bonds?
3. What is necessary for the change in chromatin for RNA polymerase to easily identify a gene to be recognized and transcribed?
4. What inhibits transcription, either by preventing the binding of an activator or by recruiting proteins that inhibit transcription?
All of these can play a part simultaneously, or maybe just two of them. Most cases, transcriptional regulation in eukaryotes involves the initiation at the promoter.
1. One or more activators and repressors.
2. The function of activators and repressors are modulated and changed.
3. Activators
4. DNA methylation
46
[Focus promoter of a eukaryotic gene]
1. What does the TATA box and transcriptional site form?
2. Where does transcription actually begin in DNA?
3. What is the sequence, to include its primes, of the TATA box which is 25 bp before the transcriptional start site?
4. What does the TATA box determine?
5. What type of transcription happens when the core promoter acts alone?
1. The core promoter.
2. The transcriptional start site
3. 5'-TATAAA-3' sequence
4. The precise starting point for transcription
5. Basal transcription
47
The regulatory elements or sequences are DNA segments that regulate eukaryotic genes and are recognized by regulatory transcription factors that affect RNA polymerase to transcript at the core promoter. What are the two elements that either enhance the rate of transcription or prevent transcription of a given gene when its expression is not needed?
Bonus: How far can regulatory elements locations be found?
Enhancers & Silencers
Between 50-100 bp before the transcriptional site or core promoter. In some cases, over 10,000 bps away!!!
48
What RNA is responsible for transcribing protein-encoding genes?
RNA polymerase II
49
What are the three types of proteins that play a role in initiating transcription at the core promoter of protein-encoding genes?
-------------------------------------------------------------------------------------------------------------
Which two of these types of proteins must come together at the TATA box fo the core promoter so transcription can be initiated?
What does the two types of proteins form when they come together at the TATA box?
1. RNA polymerase II
2. 5 different proteins called general transcription factors (GTFs)
3. A large protein complex called mediator
---------------------------------------------------------------------------------
RNA polymerase II and the GTFs
Preinitiation Complex
49
What is the protein complex that partially wraps around the RNA polymerase II and the GTFs?
The mediator
Mediator derives its name from the observation that it mediates interactions between the preinitiation complex and regulatory transcription factors such as activators or repressors that bind to enhancers or silencers. The function of mediator is to control the rate at which RNA polymerase begins to transcribe RNA at the transcriptional start site.
52
In eukaryotes, what do the activators and repressors bind to?
The enhancers and silencers, respectively, and regulate the rate of transcription of genes.
They can regulate the function of RNA polyermerase by binding to GTFs or mediator (assuming that the enhancers and silencers are located there).
53
The binding of activators to an enhancers or repressors binding to silencers has what effect on the ability for GTFs and RNA polymerase to create the preinitiation complex?
The GTF known as transcription factor II D (TFIID) which functions to recognize the TATAbox and begin the assembly process. Comparatively the activators and repressors either enhance or reduce the effectiveness for TFIID to recognize the TATA box and therefore effects the binding of RNA polymerase II and other GTFs at the core promoter (if acting alone).
54
[Focus of the Mediator and regulatory transcription factors]
1. What is something an activator interacts with that is a protein that increases the rate of transcription but does not directly bind to the DNA itself?
2. What does the activator-coactivator complex stimulate the function of which causes RNA polymerase II to proceed to the elongation phase of transcription more quickly?
3. What about a repressor?
4. We have talked about two ways that regulatory transcription factors influence transcription. What is the third way?
1. The coactivator
2. The function of the mediator
3. The repressor does the opposite and prevents RNA polymerase II from progressing to the elongation phase.
4. Recruiting proteins that affect chromatin structure in the promoter region.
55
[Focus in Chromatin Structure and DNA Methylation]
1. What is DNA associated with like proteins to create a structure called and what does it make up?
2. For GTFs and RNA polymerase II to be able to transcript chromatin, what must happen?
3. What involves the attachment of methyl groups to cytosine bases which also affects the chromatin conformation and gene expression?
1. Chromatin and it makes up eukaryotic chromosomes.
2. Chromatin must be in open conformation and not closed conformation which makes transcription difficult or impossible.
3. DNA methylation
56
What is one way that change chromatin structure which involve complexes of proteins that alter said structure?
Where does this structure get energy from?
ATP-dependent chromatin-remodeling complexes
ATP hydrolysis
57
What are the three effects possible on how ATP-dependent chromatin-remodeling complexes change chromatin structure?
1. Binding to chromatin and change the locations of nucleosomes. Shifting of positions or change in spacing between nucleosomes.
2. Eviction of histone octamers from DNA, thereby creating gaps.
3. Change the composition of histone proteins with a histone variant. These histone variants can promote or inhibit gene transcription.
58
What enzyme attaches acetyl groups (-COCH3) to the amino terminal tails of histone proteins and how does it affect the histone?
Histone acetyltransferase and when acetyled, the histone proteins do not bind tightly to the DNA, which aids in transcription.
The histone proteins in the histone can actually be modified by methyl and phosphate groups as well.
59
What are the effects of covalent modifications of histones?
1. Modifications may directly influence interactions between DNA and histone proteins, and between adjacent nucleosomes. As mentioned, the acetylation of histones loosens their binding to DNA and aids in transcription.
2. Histone modifications provide binding sites that are recognized by other proteins. According to the histone code hypothesis, proposed by American biologists Brian Strahl and David Allis in 2000, the pattern of histone modification is recognized by proteins much like a language or code. One pattern of histone modification may attract proteins that inhibit transcription. Alternatively, a different combination of histone modifications may attract proteins, such as ATP-dependent chromatin-remodeling complexes, that promote gene transcription.
60
For active genes in the chromatin, where is the core promoter found which is a site in the chromatin that is missing nucleosomes?
Are they alone, enough for transcription? And what are they typically surrounded by and what do they indicate?
Nucleosome-free region (NFR)
Although the NFR may be required for transcription, it is not, by itself, sufficient for gene activation. The NFR is flanked by two nucleosomes that are termed the –1 and +1 nucleosomes. These nucleosomes often contain histone variants that promote transcription. The end of many eukaryotic genes is followed by another NFR. This arrangement at the end of genes may be important for transcriptional termination.
61
[Review of Histones and Nucleosome locations] [No Answer]
In the scenario shown in Figure 14.20, an activator binds to an enhancer in the NFR. The activator then recruits chromatin-remodeling complexes and histone-modifying enzymes to this region. A chromatin-remodeling complex may shift nucleosomes or temporarily evict nucleosomes from the promoter region. Nucleosomes containing certain histone variants are thought to be more easily removed from the DNA than those containing the standard histones. Histone-modifying enzymes, such as histone acetyltransferase, covalently modify histone proteins and may affect nucleosome contact with the DNA.
Further changes in chromatin structure are necessary for elongation to occur. RNA polymerase II cannot transcribe DNA that is tightly wrapped in nucleosomes. For transcription to occur, histones are evicted, partially displaced, or destabilized so RNA polymerase II can pass. Evicted histones are then reassembled by chaperone proteins and placed back on the DNA behind the moving RNA polymerase II. These histones may be deacetylated—have their acetyl groups removed—so that they bind more tightly to the DNA.
No Answer
62
What is a mechanism that usually silences gene expression where a DNA structure can be modified covalently with the attachment of methyl groups (-CH3) usually by an enzyme called DNA methyltransferase?
DNA methylation
63
T/F Yeast and Drosophila have litte or no detectable methylation of their DNA, whereas DNA methylation in vertebraes and plants is relatively abundant.
True. In mammals, approaxiamtely 5% of the DNA is methyalted.
64
[Focus DNA Methylation]
1. At what base in eukaryotic DNA does methylation happen?
2. What is a cluster of CpG sites, C and G refer to the bases cytosine and guanine in DNA, and p refers to a phosphodiester linkage between the nucleotides containing those bases?
3. What is typically correclated to active and repressed genes in the context of methylation?
4. How does methylation inhibit transcription? (2)
1. Cytosine bases.
2. CpG islands
3. Active genes are unmethylated while repressed genes are methylated.
4. Prevents an activator from binding to an enhancer which inhibits the initiation of transcription. Additionally, methylation alters chromatin structure. Proteins known as methyl-CpG-binding proteins bind methyalted sequences which then recriuts proteins that inhibit transcription.
65
[Focus of Regulation of RNA modification and translation]
1. What is the benefits of regulatiing RNA modification?
2. What must be accomplished for regulation to happen at the transcription level which takes time? (4)
1. Eukaryotes can produce more than one mRNA transcript from a single gene thus encoding two or more polypeptides. Timing at transcription takes a fair amount of time before effects are observed at the cellular level. One way to achieve faster regulation is after the RNA transcript is made which is a faster way to regulate levels of gene products, namely, proteins.
2. Chromatin must be converted to open conformation, the gene must be transcribed, RNA must be modified and exported from the nucleus, and protein made via translation.
66
[Focus Alternative Splicing]
1. What happens to pre-mRNA because it becomes mature mRNA?
2. What can happen if pre-mRNA has mutiple exons and introns?
3. What is a form of gene regulation that allows an organism to use the same gene to make different proteins at different stages of development, in different cell types, and/or in response to a change in environmental conditions?
4. [BONUS] How many protein-encoding genes do humans have compared to the amount of different proteins that are created?
1. It is modified.
2. It can be spliced in multiple ways resulting in the production of two or more polypeptides.
3. Alternative splicing. This increases the size of the proteome by keeping the genome the same size.
4. 22,000 different protein-encoding genes yet they make over 100,000 different proteins! Alternative splicing increases the level of information contained within the human genome.
67
Although iron is a vital cofactor for many cellular enzymes, it is toxic at high levels. To prevent toxicity, how does mammalian cells store excess iron?
What protein controls the encoding of ferritin?
Where does this controlling protein bind to on the mRNA containing the code for ferritin?
By synthesizing a protein called ferritin, which forms a hollow, spherical complex that stores the iron.
Iron regulatory protein (IRP)
The iron regulatory element (IRE)
68
Poisoning may occur if a young child finds a bottle of vitamins, such as those that taste like candy, and eats a large number of them. One of the toxic effects involves the ingestion of too much iron. How does the IRP protect people from the toxic effects of too much iron?
When iron levels rise in the cell, the iron binds to IRP and removes it from the mRNA that encodes ferritin. This results in the rapid translation of ferritin protein, which can store excess iron. Unfortunately, ferritin storage does have limits, so iron poisoning can still occur if too much is ingested.
69
The functional product of genes arises from what process?
Multiple choice question.
Genomic stability
Gene silencing
DNA methylation
RNA interference
Gene expression
Gene expression
70
How does gene regulation help conserve energy for an organism?
Multiple choice question.
By only making small amounts of a gene product.
By always expressing a gene product, so that it will be available when needed by the cell.
By only expressing the gene product when it is needed in the cell.
By only expressing the gene product when it is needed in the cell.
71
What are two major benefits of gene regulation?
Multiple select question.
Expression of genes at appropriate times
Production of all proteins simultaneously
The conservation of energy
Production of ATP
Expression of genes at appropriate times
The conservation of energy
72
True or false: In multicellular organisms, genes are regulated in the same way to ensure that gene expression levels are constant regardless of cell type or developmental stage.
True false question.
True
False
False
73
When are the genes involved in lactose metabolism in E. coli expressed and when are they turned off?
Multiple choice question.
The genes for lactose metabolism are expressed when lactose is present and when it is absent.
The genes for lactose metabolism are expressed when lactose is absent but not when it is present.
The genes for lactose metabolism are expressed when lactose is present but not when it is absent.
The genes for lactose metabolism are turned off when lactose is present and when it is absent.
The genes for lactose metabolism are expressed when lactose is present but not when it is absent.
74
The process in which the information in a gene is made into a functional gene product, such as an RNA molecule or a protein, is termed gene \_\_\_\_\_\_.
expression
75
Cell ______ is the process by which cells become specialized into particular types.
Multiple choice question.
adhesion
interference
migration
differentiation
differentiation
76
Some proteins are produced only when needed. This is an example of gene regulation that conserves \_\_\_\_\_\_\_\_\_
energy or ATP
76
In mammals, the protein which delivers oxygen to body cells is \_\_\_\_\_\_
Hemoglobin
77
Most _______ in multicellular organisms are regulated so the proteins they specify are produced at appropriate times and in appropriate cell types
genes
77
In E. coli, the genes required to metabolize lactose are expressed \_\_\_\_\_\_.
Multiple choice question.
independently of lactose
only when lactose is present
only when lactose is absent
only when lactose is present
78
At what levels does gene regulation occur in prokaryotes?
Multiple select question.
Replication
Post-translation
mRNA processing
Translation
Transcription
Post-translation
Translation
Transcription
79
How can gene regulation be specific?
Multiple select question.
Specific gene sequences are present in the DNA of different cell types.
Specific genes are expressed at different developmental stages.
Specific genes are expressed only in certain cells.
Specific genes differ in expression levels from cell to cell.
Specific genes are expressed at different developmental stages.
Specific genes are expressed only in certain cells.
Specific genes differ in expression levels from cell to cell.
80
What are regulatory transcription factors?
Multiple choice question.
Proteins that bind to DNA and affect the transcription of one or more genes
Small molecules that regulate the synthesis of proteins from mRNA
Small molecules that influence the ability of repressor proteins to bind to DNA
Proteins that synthesize RNA from a DNA template
Proteins that bind to DNA and affect the transcription of one or more genes
82
A(n) _________ is a cluster of genes that are part of a single transcription unit that is under the control of a single promoter.
operon
82
Regulation of prokaryotic gene expression typically involves all of the following mechanisms EXCEPT:
Multiple choice question.
regulation of RNA processing
modifications to proteins after translation
regulation of transcription
regulation of translation
regulation of RNA processing
83
What is cell differentiation?
Multiple choice question.
The process by which cells acquire different DNA sequences as they develop
The process by which cells can attach together to form a multicellular organism
The process by which cells become specialized in different types
The process by which cells express specific genes only when needed
The process by which cells become specialized in different types
84
Polycistronic mRNA \_\_\_\_\_\_.
Multiple choice question.
is only found in eukaryotes
encodes more than one RNA
encodes more than one protein
is only produced in times of stress
encodes more than one protein
85
\_\_\_\_\_\_ is the main protein that delivers oxygen to cells of a mammal's body.
Multiple choice question.
Actin
Hemoglobin
Calmodulin
Ferritin
Myosin
Hemoglobin
86
What are the basic components of the lac operon?
Multiple select question.
RNA polymerase
lacY
lacZ
lacR
Promoter
lacA
lacY
lacZ
Promoter
lacA
88
An mRNA that encodes more than one protein is called \_\_\_\_\_\_\_\_\_\_
mRNA.
polycistronic, poly-cistronic, or poly cistronic
89
Regulatory transcription factors influence the expression of genes by affecting the rate of transcription. They do so by binding directly to DNA at or near the \_\_\_\_\_\_\_\_
site.
promoter
90
What is an operon?
Multiple choice question.
A region of DNA that is responsible of regulation of transcription of a cluster of genes
A small molecule that binds to a transcription factor to regulate its activity
A transcription factor that binds to DNA to control the expression of a cluster of genes
A cluster of genes under the transcriptional control of a single promoter
A cluster of genes under the transcriptional control of a single promoter
91
In the lac operon, the _______ is the DNA sequence at which the lac repressor binds.
Multiple choice question.
operator
silencer
promoter
enhancer
operator
92
What is the CAP site for the lac operon?
Multiple choice question.
The sequence of nucleotides that provides a binding site for the repressor protein
The domain on the repressor protein where allolactose binds
The sequence of nucleotides that is recognized by an activator protein
The domain on the RNA polymerase that allows it to bind to the promoter
The sequence of nucleotides that is recognized by an activator protein
92
The lacO of the lac operon is the site where the repressor protein binds. It is referred to as the \_\_\_\_\_\_\_\_
operator
93
What does the lac operon region contain?
Multiple choice question.
Activator, repressor, and three structural genes
Activator, operator, and two structural genes
Promoter, operator, and three structural genes
Promoter, enhancer, and two structural genes
Promoter, operator, and three structural genes
94
Select all that apply
At what levels does gene regulation occur in prokaryotes?
Multiple select question.
mRNA processing
Post-translation
Translation
Transcription
Replication
Post-translation
Translation
Transcription
95
The transcription of the lac operon genes is inhibited when the lac repressor protein binds to \_\_\_\_\_\_.
Multiple choice question.
lactose
β-galactosidase
the lac operator
RNA polymerase
the lac operator
97
An activator protein recognizes the ______ of the lac operon.
Multiple choice question.
CAP site
lacZ gene
operator
promoter
CAP site
98
An operon that can be turned on in the presence of a small effector molecule is said to be a(n) _________ operon.
inducible
99
Under what conditions does the lac repressor bind to the operator of the lac operon and prevent transcription?
Multiple choice question.
When the concentration of lactose is high in the cell
When lactose binds to the repressor
When lactose binds to the activator
When the concentration of lactose is low in the cell
When the concentration of lactose is low in the cell
100
The catabolite activator protein (CAP) is involved in ______ control of the lac operon.
Multiple choice question.
negative
positive
constitutive
repressible
positive
101
Which of the following enzymes catalyzes the formation of cAMP?
Multiple choice question.
AMP kinase
Cyclic phosphodiesterase
Adenylyl cyclase
ATPase
Adenylyl cyclase
102
The lac operon is an example of what type of operon?
Multiple choice question.
Repressible operon
Inducible operon
Constitutive operon
Inducible operon
103
How does the presence of lactose in the cell influence the transcription of the lac operon?
Multiple select question.
When lactose is present, transcription of the lac operon is high.
When lactose is present, the lac repressor protein binds to the operator site and transcription does not occur.
When lactose is present, transcription of the lac operon is low.
When lactose is present, the lac repressor protein does not bind to the operator site and transcription can occur.
When lactose is present, transcription of the lac operon is high.
When lactose is present, the lac repressor protein does not bind to the operator site and transcription can occur.
104
The lac operon is also under positive control by an activator protein called what?
Multiple choice question.
Lac repressor
Allolactose
cAMP
CAP
CAP
105
How do CAP and cAMP increase the transcription of the lac operon?
Multiple choice question.
When CAP and cAMP bind to the CAP site, this enhances binding of RNA polymerase to the promoter site.
CAP and cAMP are both activator molecules that bind to RNA polymerase and increase transcription.
CAP and cAMP both bind to glucose, which allows RNA polymerase to bind to the promoter site and enhances transcription.
When CAP and cAMP bind to the CAP site, this enhances binding of RNA polymerase to the promoter site.
106
The transcription of the lac operon genes is inhibited when the lac repressor protein binds to \_\_\_\_\_\_.
Multiple choice question.
lactose
β-galactosidase
RNA polymerase
the lac operator
the lac operator
107
The effector molecule cyclic AMP (cAMP) is produced from ATP via an enzyme known as _________ \_\_\_\_\_\_\_.
adenylyl cyclase
108
The genes in the trp operon encode enzymes that make the amino acid \_\_\_\_\_\_\_\_\_\_\_
tryptophan
109
An operon that can be turned on in the presence of a small effector molecule is said to be a(n) __________ operon.
inducible
110
Under what conditions does the *lac* repressor bind to the operator of the *lac* operon and prevent transcription?
Multiple choice question.
When the concentration of lactose is high in the cell
When the concentration of lactose is low in the cell
When lactose binds to the activator
When lactose binds to the repressor
When the concentration of lactose is low in the cell
111
In order for transcription of protein coding genes in eukaryotes to begin, the promoter must have several key features. What are they?
Multiple choice question.
RNA polymerase, TATA box, enhancers
TATA box, regulatory elements, transcriptional start site
Core promoter, RNA polymerase, TATA box
Promoter, operator, CAP site
TATA box, regulatory elements, transcriptional start site
112
When ___________ binds to CAP, the resulting complex binds to the CAP site near the *lac* \_\_\_\_\_\_\_\_\_\_. This causes a bend in the DNA that enhances the ability of RNA polymerase to bind, and so the transcription rate is increased.
cAMP; promoter
113
Why are interactions between RNA polymerase II and GTFs important for transcription in eukaryotes?
Multiple choice question.
RNA polymerase II and GTFs must interact for the polymerase to bind properly at the core promoter site of the DNA.
RNA polymerase II must bind to GTFs in order for the elongation step of transcription.
Interactions between RNA polymerase and GTFs increase the rate of transcription because GTFs act as enhancers.
RNA polymerase II and GTFs must interact for the polymerase to bind properly at the core promoter site of the DNA.
114
Select all that apply
Which of the following are proteins involved in regulating the rate of transcription in eukaryotes?
Multiple select question.
Repressors
Silencers
Enhancers
RNA polymerase II
Activators
Repressors
Activators
115
What is the function of the genes encoded by the *trp* operon?
Multiple choice question.
The synthesis of the amino acid tryptophan
The breakdown of the amino acid tryptophan
The incorporation of the amino acid tryptophan into cellular proteins
The transport of the amino acid tryptophan into the cell
The synthesis of the amino acid tryptophan
116
What is chromatin?
Multiple choice question.
The type of DNA found in prokaryotic cells
A complex consisting of RNA polymerase, GTFs, and other regulatory proteins
The complex formed by DNA and its associated proteins
Double-stranded DNA without any associated proteins
The complex formed by DNA and its associated proteins
117
Both prokaryotes and eukaryotes use _______ proteins to regulate the process of transcription.
Multiple choice question.
activator and repressor
inducer and repressor
activator and terminator
inducer and terminator
activator and repressor
118
Proteins that use energy from ATP hydrolysis to change the locations and compositions of nucleosomes are called ATP-dependent _______ - _______ complexes.
chromatin-remodeling
119
What are the three features common to most promoters that are needed for the initiation of transcription of protein coding genes in eukaryotes?
Multiple select question.
Pre-initiation complex
Transcriptional start site
TATA box
Regulatory elements
AUG start codon
Transcriptional start site
TATA box
Regulatory elements
120
Histone modifications primarily affect \_\_\_\_\_\_.
Multiple choice question.
the distance between enhancers and promoters
the sequence of DNA
the methylation of DNA
the degree of chromatin compaction
the degree of chromatin compaction
121
In eukaryotes, the rate of transcription of genes is influenced by regulatory transcription factors called ______ and \_\_\_\_\_\_\_\_\_\_\_. These proteins bind to regulatory elements and control the gene expression rate.
activators and repressors
122
DNA and its associated proteins form a compact structure called \_\_\_\_\_\_.
Multiple choice question.
chromatin
histone
promoter
ribosome
Chromatin
123
A nucleosome-free region (NFR) is \_\_\_\_\_\_.
Multiple choice question.
a region in the nucleus which has no chromosomes, and consequently no nucleosomes
a site on a chromosome that is missing nucleosomes
a region in the nucleus which has chromosomes lacking any nucleosomes
a site on a chromosome that has nucleosomes which are free to bind to each other
a site on a chromosome that is missing nucleosomes
124
What is the function of ATP-dependent chromatin-remodeling complexes?
Multiple choice question.
They directly control the ability of RNA polymerase to bind to the promoter site.
They attach acetyl groups to histones, which prevents them from binding well to the DNA.
They cause a change in the locations and/or compositions of nucleosomes.
They bind to activators and repressors and influence their ability to bind to the DNA.
They cause a change in the locations and/or compositions of nucleosomes.
125
Histone modifications can result in which of the following?
Multiple select question.
Activation of transcription
New mutations in DNA
Binding of nucleosomes to enhancers
Loosening of chromatin
Inhibition of the function of ribosomes
Activation of transcription
Loosening of chromatin
126
Sequence the steps that activator proteins take to promote the unraveling of compact chromatin at the site of gene transcription. Start with the first step at the top of the list.
Transcriptional activator binds to an open enhancer site
Activators recruit chromatin remodeling proteins
Compacted chromatin is loosened
Transcription occurs
127
The enzyme responsible for covalently attaching methyl groups to DNA is _________ \_\_\_\_\_\_\_\_\_.
DNA methyltransferase
128
Many eukaryotic genes are flanked by a site that is missing nucleosomes. This site is known as a nucleosome-\_\_\_\_\_\_\_\_\_ \_\_\_\_\_\_\_\_\_.
free region
129
How do activator proteins diminish the level of chromatin compaction at the site of the gene that is to be transcribed?
Multiple choice question.
Activators bind to an enhancer site and then recruit other proteins to unravel and loosen the packed chromatin.
Activators are directly involved in loosening the packed chromatin at the site of the gene.
Activators are also known as ATP-dependent remodeling proteins that loosen packed chromatin so that transcription can take place.
Activators bind to an enhancer site and then recruit other proteins to unravel and loosen the packed chromatin.
130
Which of the following is a common modification that affects the structure of DNA?
Multiple choice question.
Hydroxylation
Methylation
Acetylation
Phosphorylation
Methylation
131
Which of the following is a form of gene regulation in which a eukaryotic pre-mRNA can be processed to produce more than one mature RNA?
Multiple choice question.
Alternative splicing
DNA splicing
Genetic recombination
Exon splicing
Alternative genetic code
Alternative splicing
132
In mammals, iron toxicity is prevented by regulating the ______ of ferritin.
Multiple choice question.
replication
translation
transcription
iron content
splicing
translation
133
Bacteria and eukaryotes can regulate genes at the level of transcription. In eukaryotes, gene expression is also commonly regulated at the levels of RNA ______ and translation.
processing or modification
134
The process whereby different transcripts are made from a single gene is called ________ \_\_\_\_\_\_\_.
alternative splicing
135
In mammals, when iron levels are high, iron binds to the iron regulatory protein. This results in \_\_\_\_\_\_.
decreased translation of ferritin
increased transcription of ferritin
increased translation of ferritin
decreased transcription of ferritin
increased translation of ferritin
