Genetics Chapter 15
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111 Terms
What do the mechanisms of gene regulation determine?
1) Where a gene is expressed 2) When a gene is expressed 3) How much a gene is expressed
What is every gene in regard to RNA
an RNA-coding region (a transcribed region) of DNA
3 multiple choice options
What regions are not transcribed
regulatory regions
What are transcription factors
DNA-binding proteins that recognize specific sequences within the regulatory region(s) near the gene
Transcription factors bind to DNA?
YES!!!
1 multiple choice option
What do transcription factors recognize at regulatory regions?
specific sequences
What do transcription factor do at regulatory region(s)
activate or repress transcription
What regulates genes in prokaryotes?
the operon
What is the operon? (Sotero definition)
a cluster of structural genes with related functions under the control of a common regulatory system
What is an operon? (Simple definition)
cluster of genes controlled by one promoter
What are operons key to in prokaryotes
helping control protein production
What do operons respond to?
Changes in the environment
Do prokaryotes prefer lactose or glucose?
glucose
What do the structural genes under lac operon control
What does lactose isomerize into
allolactose
2 multiple choice options
The operon inducer is
allolactose
What happens to the lac operon if glucose and lactose are present?
allolactose will bind to lac repressor inhibiting it from binding to the operator, no cAMP, RNA polymerase performs insignificant transcription
Lactose and glucose are present; lac operon is ...
OFF
2 multiple choice options
Lactose is absent, glucose is present; lac operon is ...
OFF
3 multiple choice options
Lactose and glucose are absent; lac operon is
OFF
3 multiple choice options
Lactose is present, glucose is absent; lac operon is
ON
3 multiple choice options
What happens to the lac operon if only lactose is present?
allolactose will bind to lac repressor inhibiting it from binding to the operator, high cAMP, RNA polymerase can perform transcription
2 multiple choice options
What is the relationship between cAMP and glucose?
Inverse relationship; the absence of glucose induces the activity of the enzyme adenylate cyclase which catalyzes the hydrolysis of ATP into cAMP + PP
2 multiple choice options
What catalyzes the hydrolysis of ATP into cAMP + PP
adenylate cyclase
3 multiple choice options
In the presence of glucose are the lac structural genes on or off?
off
2 multiple choice options
In the lac operon, ___ polymerase binds to the promoter when ___ is ___
RNA, glucose, absent
3 multiple choice options
What is CAP and its function?
catabolite activator protein; binds to a site next to the lac promoter (lacP) and facilitates the binding of RNA polymerase to it
2 multiple choice options
What are the products of the trp operon involved in?
the biosynthesis of the amino acid tryptophan
What happens to the structural genes when Trp is absent
the structural genes are expressed
What happens to the structural genes when Trp is present
the structural genes are turned off
What are the structural genes turned off by by Trp is present
Trp
What is the biding site for RNA polymerase on the trp operon
promoter (trpP)
3 multiple choice options
What is the binding site for the repressor protein on the trp operon
operator (trpO)
3 multiple choice options
What is the status of the repressor protein when Trp is absent?
the repressor protein is inactive
Why is the repressor protein inactive when Trp is absent?
Trp presence is needed to bind to the repressor protein and activate it
What does RNA polymerase do when Trp is absent?
RNA polymerase binds to the promoter and initiates the transcription of structural genes
What is the status of the repressor protein when Trp is present?
the repressor protein is active
What does RNA polymerase do when Trp is present?
it's unable to bind and no transcription occurs
2 multiple choice options
EMSA stands for ...
electrophoretic mobility shift assay
What is EMSA used for?
Detecting specific DNA-protein interactions
What kind of DNA-protein interactions can EMSA detect?
specific binding of transcription factors and other regulatory proteins to regulatory
In EMSA, why would cAMP cause a mobility shift if added to a test tube with E. coli cell extract (containing all cellular proteins) with a CAP binding site, while being fed glucose.
cAMP allows CAP to bind to DNA
You are conducting five experiments using EMSA to establish the specific binding of the trp repressor protein to the trp operator (trpO) in the presence of tryptophan.
If vial one contains a fragment of DNA containing trpO, what would its migration distance be on a 1-3 scale (1 = minimal migration, 3 = maximal migration)?
3
2 multiple choice options
You are conducting five experiments using EMSA to establish the specific binding of the trp repressor protein to the trp operator (trpO) in the presence of tryptophan.
If vial two contains a fragment of DNA containing trpO + cell extract (no Trp, contains all cellular proteins), what would its migration distance be on a 1-3 scale (1 = minimal migration, 3 = maximal migration)?
What is the mobility shift?
3; no mobility shift
3 multiple choice options
You are conducting five experiments using EMSA to establish the specific binding of the trp repressor protein to the trp operator (trpO) in the presence of tryptophan.
If vial three contains a fragment of DNA containing trpO + cell extract (contains all cellular proteins) + Trp, what would its migration distance be on a 1-3 scale (1 = minimal migration, 3 = maximal migration)?
What is the mobility shift?
2; first mobility shift
3 multiple choice options
You are conducting five experiments using EMSA to establish the specific binding of the trp repressor protein to the trp operator (trpO) in the presence of tryptophan.
If vial four contains a fragment of DNA containing trpO + cell extract (contains all cellular proteins) + Trp + anti-lac repressor, what would its migration distance be on a 1-3 scale (1 = minimal migration, 3 = maximal migration)?
What is the mobility shift?
2; no mobility shift
2 multiple choice options
You are conducting five experiments using EMSA to establish the specific binding of the trp repressor protein to the trp operator (trpO) in the presence of tryptophan.
If vial five contains a fragment of DNA containing trpO + cell extract (contains all cellular proteins) + Trp + anti-trp repressor, what would its migration distance be on a 1-3 scale (1 = minimal migration, 3 = maximal migration)?
What is the mobility shift?
1; second mobility shift
1 multiple choice option
Why do mobility shifts occur?
the different sizes that complexes form
Larger complexes have ___ migration in EMSA because they are __
minimal; heavier
3 multiple choice options
Which RNA polymerase transcribes larger rRNA genes?
RNA polymerase I
3 multiple choice options
Which RNA polymerase transcribes small rRNA (5s) gene and all tRNA genes
RNA polymerase III
2 multiple choice options
Which RNA polymerase transcribes all protein-coding genes (mRNA genes)
RNA polymerase II
3 multiple choice options
What are nucleosomes
DNA wrapped in histones
What are heterochromatins?
compact/condensed nucleosomes
How are the nucleosomes in heterochromatins so compact?
The positive charges on the histones have strong affinity for DNA's negatively charged phosphate groups
What are euchromatins? (Not mentioned in lecture)
widely-spaced nucleosomes, loose
What effects do heterochromatins have on DNA
DNA is inaccessible and transcriptionally repressed, no gene expression
How can the cell alter the state of the nucleosomes from heterochromatin to euchromatin?
histone acetylation
What is the process of histone acetylation
1) Transcription activators recruit histone acetyl transferases (HATs) 2) As a coactivator, the enzyme acetylates lysine residues on the histone tails, neutralizing their positive charge. 3) The interaction between histones and DNA is looser; chromatin loosens
T or F: Histone acetyl transferases (HATs) bind to DNA
False
1 multiple choice option
What does histone acetylation cause?
Chromatin decondensation
Once the histones are acetylated what happens to DNA?
RNA polymerase II can bind to DNA
How can the cell go from euchromatin (decondensed) to a heterochromatin?
Transcription repressors recruit histone deacetylases (HDACs) as a corepressor, which cause chromatin condensation.
HATS ___, HDACS ___
relax, compact
Flowering locus C (FLC) codes for ...
a transcription flower that represses flowering
FLC is only expressed if the ___ on the locus are ___
histone; acetylated
Flowering locus D (FLD) is a ...
histone deacetylase that inactivates the FLC locus
The process of FLD
Chromatin is condensed and no transcription can take place
The result of FLD
No repression of flowering
In summary; for flowering to happen __ needs to be___ by a ___ encoded by ___
FLC, deacetylated, deacetylase enzyme, FLD
3 multiple choice options
Acetylation of chromatin =
loose chromatin + transcription
Deacetylation of chromatin
condensed chromatin + no transcription
Transcription factor
any transcription regulator protein that binds to a specific DNA sequence
Cis-acting elements
DNA sequences that are necessary for the control of transcription
What are some examples of cis-acting elements
promoters, enhancers, and silencers
Trans-acting factors
proteins necessary for the control of transcription
What do trans-acting factors do
bind to cis-acting elements
Trans-acting factors are the ___ that bind to the cis-acting elements (the ___)
proteins, DNA
1 multiple choice option
Which is true about promoters?
1) Promoters are always found before its binding gene 2) Promoters are the binding sites for RNA polymerase II transcription initiation complex 3) Many eukaryotic promoters have a TATA Box
Which is true about enhancers?
1) Enhancers are the binding sites for transcriptional activator 2) Enhancers DNA sequences vary widely 3) Enhancers are recognized by a large variety of transcription activators 4) Enhancers are required for stimulated transcription
What is the RNA polymerase II transcription imitation complex called?
basal transcription apparatus
What does the RNA polymerase II transcription imitation complex contain?
TFIID, other TFIIs, RNA polymerase II
What is the purpose of the RNA polymerase II transcription imitation complex?
direct RNA polymerase II to the correct place on the promoter behind the gene transcription initiation site.
Why does RNA polymerase II need direction from RNA polymerase II transcription imitation complex
it does not recognize any specific DNA sequences
TFIIs are
transcription factors of RNA polymerase II
TFIID is
transcription factor D of RNA polymerase II; recognizes TATA Box and binds to it
When does only the basal transcription apparatus form
Only promoter is present
What can DNA do to bring transcriptional activator bound to enhancers closer to the basal transcription apparatus?
Loops
Transcription is ___ when the promoter is present and enhancers are absent
very low/undetectable
1 multiple choice option
Transcription is ___ when the promoter is present and enhancers are present
stimulated/biologically significant
1 multiple choice option
Where is the best position for enhancers on the chromosome
all of the above
3 multiple choice options
T or F: An enhancer before the promoter and gene will stimulate transcription
True
1 multiple choice option
T or F: An enhancer far before the promoter and gene will stimulate transcription
True
T or F: An enhancer after the promoter and gene will stimulate transcription
True
T or F: An enhancer upside down and before the promoter and gene will stimulate transcription
True
T or F: An enhancer upside down and between the promoter and gene will stimulate transcription
True
What does a chromosome have to prevent an enhancer from stimulating transcription of the wrong gene?
insulator
What are insulators?
boundary elements
How are insulators activated?
insulator-binding proteins
When are GAL's structural genes repressed
1) galactose is absent 2) GAL80 blocks GAL4 from activating transcription