Module 4 Practice Exam and Review Flashcards
What role does RNA stability play in gene regulation?
List 3 types of RNA structural elements that can affect the stability of an RNA molecule in eukaryotic cells.
Explain how these elements act to influence RNA stability.
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The stability of mRNA influences gene expression by affecting the amount of mRNA available to be translated. The stability of mRNA is affected by the 5′ cap, the poly(A) tail, the 5′ UTR, the coding section, and sequences in 3′ UTR.
- if RNA is unstable, it will be degraded and unable to use for translation –> amt of protein synthesized depends on amt of available mRNA
- stability controlled by 5’ cap, polyA tail, 5’ UTR, 3’ UTR, and coding region
List 4 levels at which gene control can take place in eukaryotes.
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Alteration of structure, transcription, mRNA processing, RNA stability, translation, Post-translational modification
Define RNA silencing (or interference). Explain how siRNAs arise and how they potentially affect gene expression. How are siRNAs different from the antisense RNA mechanism?
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defn: when siRNA binds to mRNA, stimulating mRNA degradation
- arise from cleavage of dsRNA to make small fragments of ss siRNA
- block gene expression by degrading mRNA before it can be translated
- antisense RNA binds to mRNA too, but physically prevents translation
Process in which cleavage of double-stranded RNA produces small interfering RNAs (siRNAs) that bind to mRNAs containing complementary sequences and bring about their cleavage and degradation.
siRNAs are produced by the cleavage and processing of double-stranded RNA. antisense RNA are small RNA molecule that base pairs with a complementary DNA or RNA sequence and affects its functioning.
RNA silencing is a form of posttranscriptional regulation of mRNA that involves a small interfering RNA molecule formed from the cleavage of double-stranded RNA.
siRNA’s can affect gene expression by binding to complementary sites in mRNA and marking the mRNA for deletion. Antisense RNA binds to the complementary mRNA sequence, keeping it from being transcribed.
RNAi is the formation of 21-25 nucleotide-long siRNAs by Dicer cleavage of double stranded mRNA molecules. These form the RNA-induced silencing complex. The RISC can affect gene expression by inhibiting translation of mRNAs that code for a specific target gene. Antisense RNA mechanism is when a small single strand of RNA binds to the complementary mRNA, physically blocking translation from occurring; RNAi literally chops up the mRNA to prevent translation.
siRNAs arise from transposons, mRNA, and viruses. They are first recognized by a dicer which cleaves the double stranded RNA into short interfering RNA molecules which bind to the RNA induced silencing complex (RISC) which unwinds the RNA. These RNA strands can then bind to complementry strands of RNA and slow their translation down significantly as well as target them for degredation.
antisense RNA:
An RNA molecule (synthesized in vivo or in vitro) with a ribonucleotide sequence that is complementary to part of an mRNA molecule.
Frameshift mutations are caused by the ____ or ____ of one or more nucleotides in DNA.
insertion or removal
b,d
a) No lactose present, no glucose present
b) Lactose present, no glucose present
c) No lactose present, glucose present
d) Lactose present, glucose present
off, high, off, off
______ are complexes where, among other activities, a great deal of RNA degradation takes place.
P bodies
Recent discoveries on causes of fragile-X syndrome, myotonic dystrophy, and Huntington disease indicate what type of genetic alteration?
!!??
not “trinucleotide repeats”
changes in trinucleotide repeats?
When regions around genes become sensitive to the enzyme ______________ this is an indication that those regions are becoming ______________ active.
DNase I, transcriptionally
The __________ stabilizes the 5’ cap, which must be removed before the mRNA molecule can be degraded from the 5’ end.
!!???
NOT Poly(A) tail
Mutations which arise in nature, from no particular artificial agent are called
spontaneous mutations
Which of the following is TRUE for both prokaryotic and eukaryotic gene expression?
RNA polymerase binds to the promoter region to begin transcription.
In what part of the mRNA does degradation generally begin?
at the 5’ end with the removal of the methyl cap
The lac repressor binds to:
lactose and DNA.
__________ mutations produce new traits and are usually dominant.
Gain-of-function
Riboswitches were first discovered in 2002 and have been found in…
In all of the listed organisms:
bacteria
archaea
plants
fungi
Which of the following clusters of terms applies when addressing enhancers as elements associated with eukaryotic genetic regulation?
cis-acting, variable orientation, variable position
Two formal terms used to describe categories of mutational nucleotide substitutions in DNA are called
transversions and transitions
What is the difference between a missense mutation and a nonsense mutation?
missense mutation:
A mutation that changes a codon to that of another amino acid and thus results in an amino acid substitution in the translated protein.
nonsense mutation:
A mutation that changes a codon specifying an amino acid into a Termination codon, leading to premature termination during translation of mRNA.
What is catabolite repression? How does it allow a bacterial cell to use glucose in preference to other sugars?
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catabolite repression =
The selective inactivation of an operon by a metabolic product of the enzymes encoded by the operon.
In catabolite repression, the presence of glucose inhibits (represses) the transcription of genes involved in the metabolism of other sugars.
Because the gene expression necessary for utilizing other sugars is turned off, only enzymes involved in the metabolism of glucose will be synthesized.
Operons that exhibit catabolite repression are under the positive control of catabolic activator protein (CAP).
For CAP to be active, it must form a complex with cAMP.
Glucose affects the level of cAMP.
The levels of glucose and cAMP are inversely proportional—as glucose levels increase, the level of cAMP decreases. Thus, CAP is not activated.
Name 6 different levels at which gene expression might be controlled.
- Regulation of Transcription
- Regulation of Splicing and Processing.
- Regulation of Transport
- Degradation of mRNA
- Regulation of Translation
- Modification and Activity of Protein
(1) Alteration or modification of the gene structure at the DNA level.
(2) Transcriptional regulation.
(3) Regulation at the level of mRNA processing.
(4) Regulation of mRNA stability.
(5) Regulation of translation.
(6) Regulation by post-translational modification of the synthesized protein.
Degradation of a eukaryotic mRNA is generally preceded by shortening of the _____________.
Poly(A) tail
Mutations in the promoter region of the b-globin gene indicate that some areas are more sensitive than others. When mutations occur in consensus sequences (modular elements such as GC box, CAAT box, TATA box), transcription ________________.
decreases
telomeres
highly repetitive DNA
The __________ is a type of _________ protein that binds to a region of DNA in the promoter of a gene called the _________ and prevents transcription from taking place.
??!!
The REPRESSOR is a type of REGULATOR protein that binds to a region of DNA in the promoter of a gene called the OPERATOR and prevents transcription from taking place.
A constitutive gene is _______ regulated and is expressed ____________.
A constitutive gene is NOT regulated and is expressed CONTINUALLY.
A highly-methylated region of a chromosome that has become largely deactivated and can be seen as dense-regions when viewed using electron microscopy.
Heterochromatin
The following may be caused by mobile genetic elements except ________________
undergo mutation
An operon is controlled by a repressor. When the repressor binds to a small molecule, it binds to DNA near the operon. The operon is constitutively expressed if a mutation prevents the repressor from binding to the small molecule.
negative repressible
Nutritional mutations can be defined as
those mutations which do not allow an organism to grow on minimal medium, but do allow the organism to grow on complete medium.
I = lac repressor gene;
Z, Y, A = lac operon structural genes;
P = lac promoter;
O = lac operator
I—–P-O–Z—Y——–A—
Which parts of the DNA region shown in the diagram encode proteins?
I, Z, Y, A
Insulators can block the effects of enhancers only when….
they lie between an enhancer and a promoter.
What is a mutation?
A change in the DNA sequence.
A _________ mutation changes a codon that specifies an amino acid into one that terminates translation.
nonsense
An example of a gene product encoded by a regulatory gene is
repressor protein
The following may be caused by mobile genetic elements:
activate a gene in which they reside
cause chromosome breaks
disrupt a gene
Fill in the blanks in the “level of transcription” column of this table with: + for high levels of transcription, and – for minimal levels of transcription of the lac operon.
Consider regulation by both the lac repressor and CAP (catabolite activator protein). The strain is wild type, with no partial diploidy.
????
- high glucose, no lactose: -
- no glucose, high lactose: +
- high glucose, high lactose: -
- no glucose, no lactose: -
Over the past decade, the most significant finding in biology has been the identification of miRNAs and siRNAs and their role in regulating the development of many multicellular organisms. Briefly describe the 4 different ways these small RNAs influence gene expression.
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- Cleavage of mRNA: mRNA is cleaved in the middle of the siRNA, then mRNA degrades
- Inhibition of translation: base pairs to mRNA inhibiting translation (complementary)
- Transcriptional silencing: alter the chromatin structure, for RITS, causes methylation of histones binding DNA more tightly
- Degradation of mRNA - degrades but does not require slicer (as in cleavage)
degrading mRNA: through slicer activity
inhibiting transcription: transcriptional silencing due to methylation of either histone proteins or DNA sequences
inhibiting translation: binding of complementary regions with the mRNA molecule by miRNAs to prevent translation (premature termination)
silence genes:slicer-independent mRNA degradation stimulated by miRNA binding to complementary regions in the 3’ UTR of the mRNA
What are 3 ways in which gene regulation is accomplished by modifying the structure of chromatin?
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(1) the modification of histone proteins
(2) chromatin remodeling
(3) DNA methylation.
A promoter that affects only genes that are on the same piece of DNA is ____-acting.
cis
Since the binding of the ______ to the ______ prevents it from binding to DNA by causing a conformational change in its structure, it is called an _______ protein.
inducer, repressor, allosteric
An insulator is also known as a ____________ .
boundary element
This term describes genetic elements that affect other elements only when they are located adjacent to them. For example, the operator has this effect on its structural genes.
Cis-acting
This process moves a nucleosome from the TATA box of a gene’s promoter so that transcription can occur.
Chromatin remodeling
The _________ consists of modifications to histone proteins that affect the expression of DNA sequences.
histone code
The type of control illustrated by GAL4 in the control of genes for yeast galactose-metabolizing enzymes.
positive inducible
The lac repressor protein controls expression of the lac operon via _________ .
binding to the lac operator site to repress expression
Ultraviolet light causes pyrimidine dimers to form in DNA. Some individuals are genetically incapable of repairing some dimers at “normal” rates. Such individuals are likely to suffer from ______ .
xeroderma pigmentosum
A mutant E. coli strain, grown under conditions that normally induce the lac operon, does NOT produce ß-galactosidase. What is a possible genotype of the cells?
lacI+ lacP– lacO+ lacZ+ lacY+ lacA+
It is estimated that transposable elements compose approximately what percent of the human genome?
50
When referring to attenuation in regulation of the tryptophan operon, it would be safe to say that when there are high levels of tryptophan available to the organism
transcriptional termination is likely.
Which of the following is NOT true regarding the differences in mRNA between prokaryotic cells and eukaryotic cells?
In eukaryotic cells, the transcription to mRNA and the translation from mRNA are coupled, while in prokaryotic cells transcription and translation are not coupled.
In the above diagram, if there is a mutation in P and I, which of the following is true?
These are mutations that are, respectively, cis and trans acting on lac operon expression.
Define gene regulation.
What are 3 ways gene regulation can be controlled in a cell?
Verified Correct Answer:
Gene regulation is defined as the control of a gene’s transcript and its protein product.
It can be achieved by altering either the transcription of the gene, RNA level, the translation of the protein from that transcript, or by altering the structure of DNA such that transcription cannot occur.
What are the basic regulatory elements in a strand of DNA that allow for genes to be regulated?
Are these different in eukaryotes and prokaryotes?
If so, how?
Verified Correct Answer:
Promoters, Operators in prokaryotes.
Promoters, proximal promoter elements, enhancers, and silencers in eukaryotes.
Eukaryotic transcription is different in a few ways, most notable in that prokaryotic genes are transcribed as operons, while eukaryotic genes are not.
In addition, the Role of the Nucleosome is different in eukaryotic Transcription.
Why do extra copies of genes sometimes cause drastic phenotypic effects?
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the expression of some genes is balanced with the expression of other genes;
the ratios of their gene products, usually proteins, must be maintained within a narrow range for proper cell function.
Extra copies of one of these genes cause that gene to be expressed at proportionately higher levels, thereby upsetting the balance of gene products.
___________act as intermediaries between _____________ and specific _____ sequences to modify chromatin structure and activate transcription.
transcriptional activators, chromatin remodeling complexes, DNA
The region of a protein that is capable of holding on to a particular nucleotide sequence in order to affect proper gene regulation.
DNA binding domain
A condition in which a gene or group of genes is expressed all the time.
constitutive
This is the region of a gene where RNA polymerase binds to initiate transcription.
promoter
The molecular nature of transposable elements was first understood in E. coli due to the simplicity of the E. coli genome.
Which of the following types of DNA contribute significantly to the genome complexity of other organisms?
LINES (long interspersed elements),
SINES (short interspersed elements),
LTR (long terminal repeat)
retrotransposons…
The process by which excessive numbers of a sex chromosome are corrected, often by methylating the X chromosome to form a Barr body.
Dosage compensation
