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Chapter 11: Control of Transcription
Chapter 11: Control of Transcription Notecards
84
Biology
Undergraduate 3
12/15/2012
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Term
__________ __________ is the regulation at the level of transcription.
 Definition
1) Transcriptional regulation
Term
In microbial systems (__________ and __________) gene activity is often regulated at __________ level.
 Definition
1) Bacteria
2) Phages
3) Transcription
Term
A regulatory protein that shuts off genes is a __________ (negative control).
 Definition
1) Repressor
Term
A regulatory protein which turns on genes is an __________ (positive control).
 Definition
1) Activator
Term
__________ __________ occurs when the binding of a small compound (inducer) prevents the shut-off of genes.
 Definition
1) Inducible transcription
Term
When the repressor alone cannot shut off transcription and requires a small compound (__________) to do so, it is called __________ __________.
 Definition
1) Co-repressor
2) Repressible transcription
Term
Genes under __________ control are almost always off; those under __________ control are almost always on.
 Definition
1) Inducible
2) Repressible
Term
__________ is a set of genes that map in a cluster and are regulated together (co-ordinate regulaiton).
 Definition
1) Operon
Term
Lactose is composed of __________ and __________.
 Definition
1) Glucose
2) Galactose
Term
__________ gene mutations generally affect only one protein.
 Definition
1) Structural
Term
__________ gene mutations affect all the genes of an operon.
 Definition
1) Regulatory
Term
The operator gene (__________ __________) napped very close to the promoter (__________ __________) while the regulator (__________ __________) mapped upstream of the promoter.
 Definition
1) "O" site
2) "P" site
3) "I" gene
Term
In the absence of lactose (the __________), the "z-y-a" genes are nearly __________ (__________ state); when lactose is present, the levels of "Z-Y-A" increase greatly (__________ state)
 Definition
1) Inducer
2) Silent
3) Uninduced
4) Induced
Term
Induction increases __________ synthesis.
 Definition
1) mRNA
Term
__________ __________ are fully induced even in the absence of an inducer while the __________ __________ are off even when the inducer is present.
 Definition
1) Constitutive mutants
2) Uninducible mutants
Term
__________ __________ affect the function of the mutant gene and all genes downstream (Z- polar, y- polar, etc; causes 1 1, for all genes downstream).
 Definition
1) Polar mutations
Term
Constitutive mutations map to two different genes (__________ and __________; they cause 100 100 for all genes downstream without other dominant mutations).
 Definition
1) i (specifically i-)
2) o (specifically oc)
Term
A mutation in a structural gene is __________ to the wild type gene (z+/z-, y+/y-, etc.)
 Definition
1) Recessive
Term
The wild type gene __________ is dominant over the mutant __________ (constitutive) gene
 Definition
1) i+
2) i-
Term
The wild type i+ gene is __________ to the mutant is (uninducible) gene (i+/is is unducible, or 1 1, 1 1)
 Definition
1) Recessive
Term
The wild type o+ gene is __________ to the mutant oc (__________) gene (o+/oc is constitutive, or 100 100, 100 100).
 Definition
1) Recessive
2) Constitutive
Term
The uninducible is mutation is __________ to the oc mutation (is/oc double mutant is constitutive, so 100 100)
 Definition
1) Recessive
Term
What is the dominance relationship between genes for the lac operon?
 Definition
1) i- < i+ < is < oc < Z- polar
Term
If E. coli cells are given __________, the lac operon is silent; if given __________, the lac operon was turned on.
If the two were added together, the lac operon remains off and only __________ is used.
 Definition
1) Glucose
2) Lactose
3) Glucose
Term
In E. coli, levels of __________ are inversely related to the presence of glucose.
 Definition
1) cAMP
Term
The __________ protein can only stimulate transcription of the lac operon when cAMP is bound to it
 Definition
1) Catabolite activator protein (CAP
Term
__________ is a cofactor for the CAP protein.
 Definition
1) cAMP
Term
High level transcription of the lac operon requires the __________-__________ complex.
 Definition
1) CAP-cAMP
Term
When the function of a regulatory protein is to turn on a gene (or cluster of genes), it is called __________ control.
Mutations in the regulatory gene result in a silent (__________) operon.
The __________ protein action in the lac operon is an example of positive control.
 Definition
1) Positive
2) Uninducible
3) CAP
Term
When a regulatory protein acts to shut down a gene (or cluster of genes) it is called __________ control.
Mutations in the regulatory gene result in a fully-induced (__________) operon.
__________ __________ is an example of an inducible operon.
 Definition
1) Negative
2) Constitutive
3) Lac operon
Term
__________ operon consists of a set of five genes involved in the synthesis of the essential amino acid __________.
As a result, it is usually on, making it a __________ operon.
 Definition
1) Tryptophan
2) Tryotophan
3) Repressible
Term
The __________ __________ differs from the lac repressor in that it is incapable of binding to the tryptophan operator by itself.
 Definition
1) Trytophan repressor
Term
An __________-__________ needs a co-repressor to function properly.
 Definition
1) Apo-repressor
Term
__________ involves the premature termination of transcription when the end product of the operon is present in the medium.
 Definition
1) Attenuation
Term
Attenuation supplements __________ as a mechanism for shutting down the tryptophan operon.
 Definition
1) Repression
Term
Attenuation involves a short __________ __________ located between the operator and the first structural gene which is capable of coding for a short __________.
 Definition
1) Leader sequence
2) Peptide
Term
In __________, there is coupled transcription and translation.
When the medium is __________ in tryptophan, the ribosome following on the tail of the RNA polymerase gets hung up at the two tryptophan codons in the leader RNA due to shortage of charged tyrptophan tRNA, resulting in a full size __________.
When the medium is __________ in tryptophan, the ribosome does not stall at the two typtophan codons and creates the leader peptide; this results in prematurely terminated __________.
 Definition
1) Bacteria
2) Low
3) mRNA
4) High
5) mRNA
Term
Premature termination of transcription can also occur due to binding of small molecules such as __________-__________-__________.
 Definition
1) S-adenosyl-methionine
Term
A leader RNA that can adopt alternative anti-terminator and terminator conformations is called a __________.
 Definition
1) Riboswitch
Term
Eukaryotic cells have two types of genes:
__________ genes are needed in all cells and do not have to be regulated.
__________ genes are expressed in tissue, physiology, or development.
 Definition
1) Housekeeping
2) Regulated
Term
There are __________ short stretches critical to the formation of the hairpins.
 Definition
1) Four
Term
When region 1 is unable to pair with region 2, regions __________ and __________ form a hairpin which creates the full-sized mRNA.
When the RNA polymerase is not hung up at the two tryptophan codons regions __________ and __________ can bond together, creating a smaller hairpin and smaller size mRNA.
 Definition
1) 1 + 2
2) 3 + 4
Term
One of the best understood eukaryotic transcription regulation system is that of the genes involved in galactose sugar utilization in the yeast, __________.
There are three __________ genes and three separate __________ which are made only when the sugar galactose is present.
 Definition
1) Saccharomyces
2) Structural
3) mRNAs
Term
__________ gene codes for a transcriptional activator.
 Definition
1) GAL4
Term
__________ is an inhibitor protein which can bind to GAL4 and prevent it from turning on transcription.
 Definition
1) GAL80
Term
In the presence of galactose, the inhibitor __________ protein binds to galactose and becomes incapable of blocking the __________ activator, resulting in the synthesis of mRNAs for galactose utilization proteins (GAL1, GAL7, and GAL10)
 Definition
1) GAL80
2) GAL4
Term
The GAL4 protein can be thought of as a __________ regulator similar to the CAP protein in E. coli __________ __________.
 Definition
1) Positive
2) Lac operon
Term
__________ is an inhibitor of transcription but does not bind to DNA.
 Definition
1) GAL80
Term
A __________ __________ is a protein where six cysteine residues bind to two zinc atoms to create a stable loop which binds to a specific DNA sequence.
 Definition
1) Zinc-finger
Term
Provide examples of the helix-turn-helix DNA binding domain.
 Definition
1) Lac i-gene product
2) Ci and Cro repressors of Lambda
3) Tryptophan operon repressor
4) CAP activator protein
5) Genes which regulate steps in the development in animals
Term
The DNA sequences to which regulatory proteins bind in eukaryotic cells are called __________ if activator proteins bind there and __________ if repressor proteins bind there.
 Definition
1) Enhancers
2) Silencers
Term
Most transcriptional regulation is achieved through __________, not silencers.
 Definition
1) Enhancers
Term
Many __________-binding proteins are inactive unless a small __________-__________ is also bound.
 Definition
1) Enhancer
2) Co-activator
Term
In bacteria, only the __________ factor is needed for proper initiation of transcription.
 Definition
1) Sigma
Term
In eukaryotic cells RNA polymerases require __________ __________ __________ to initiate transcription at an unregulated housekeeping gene.
 Definition
1) Basal transcription factors
Term
RNA polymerase II needs close to __________ other polypeptide chains for initiating transcription.
 Definition
1) 40
Term
An initiation complex involving one or more enhancer is called an __________.
 Definition
1) Enhanceosome
Term
DNA that has been tightly packed into __________ by complexing with histones to form nucleosomes is incapable of __________.
 Definition
1) Chromatin
2) Transcription
Term
The most common mechanisms by which the histone-DNA attraction is reduced and nucleosomes disrupted is by putting acidic groups on the histones (either __________ or __________) as the negative charges on the histone surface repel those on the phosphate.
 Definition
1) Acetate
2) Phosphate
Term
The __________ __________ __________ in Drosophila have two different promoters.
 Definition
1) Alcohol dehydrogenase gene
Term
__________ mechanisms involve heritable changes that are not due to DNA sequence change but something else that stably changes gene expression; an example is __________ of __________.
 Definition
1) Epigenetic
2) Methylation of cytosines
Term
__________ __________ is the process in which different genes are silenced in males than females (and vice-versa) and involves __________ __________.
 Definition
1) Genomic imprinting
2) Cytosine methylation
Term
A single gene very often produces multiple proteins through alternative __________.
The total number of possible proteins is 2^n, where n = the number of __________.
 Definition
1) Splicing
2) Introns
Term
__________ are short hairpin RNAs which are processed to be inhibitors of gene expression.
 Definition
1) MicroRNAs
Term
MicroRNAs pairing with the coding region of mRNA will lead to __________ of the mRNA.
 Definition
1) Degradation
Term
An alternative mechanism of gene silencing involves pairing of microRNA to the __________-untranslated region of mRNA which leads to blockage of __________ of the mRNA.
 Definition
1) 3'
2) Translated
Term
Regulation of a gene is usually at the __________ step.
 Definition
1) Transcription
Term
During the formation of very large frog eggs, protein synthesis exceeds __________ rRNA genes leading to the regulation of an __________-__________ rolling circle to replicate copies of the rRNA genes.
 Definition
1) 600
2) Extra-chromosomal
Term
Genes that code for antibody polypeptides are produced by __________ __________.
 Definition
1) Genetic rearrangement
Term
Substances that elicit an immune response are called __________.
 Definition
1) Antigens
Term
What cells are responsible for the immune response?
 Definition
1) B and T cells
Term
Where are B cells produced? How do they operate?
 Definition
1) Bone marrow
2) When activated by an antigen, a B cell becomes a plasma cell and makes antibodies, which are embedded in the membrane of the cell as well as secreted into blood and lymph. Antibodies specifically bind to the antigen that stimulated them
Term
What is immune memory?
 Definition
1) When exposed to an antigen a second time, the response is much more rapid
Term
Each B cell can only make __________ kind of antibody which binds to that specific antigen.
 Definition
1) One
Term
Antibodies are called __________.
 Definition
1) Immunoglobulins
Term
There are __________ shorter (or __________) chains and __________ longer (or __________) chains per IgG molecule.
The chains are held together by __________ bonds.
 Definition
1) Shorter
2) Light
3) Longer
4) Heavier
Term
What are the five types of Ig molecules?
 Definition
1) IgA
2) IgD
3) IgE
4) IgG
5) IgM
Term
__________ is the most prevalent immunoglobulin in the body.
 Definition
1) IgG
Term
__________ __________ is the great variety of antibodies generated by rearrangements of parts of the gene during development.
 Definition
1) Somatic recombination
Term
What are the three types of segments for light chains?
 Definition
1) V (variable
2) J (joining)
3) C (constant)
Term
In light chains, there are about __________ different V segments, __________ C sequence, and only __________ J sequences (each about __________ bp long).
As a result, there can be __________ different kappa-light chains.
 Definition
1) 250
2) 1
3) 4
4) 30
5) 1000
Term
Heavy chains have the same segments as light chains; however, they also have __________ D (__________) chains that add to the mix, producing (when combined with light chains) 1000 x 48,000 = __________ million different IgG molecules.
 Definition
1) 12
2) Diversity
3) 48
Term
What are the two sexes of yeast?
 Definition
1) a
2) alpha
Term
The information for producing either sex of yeast is present in every cell of a homothallic strain of yeast in silent form (__________-alpha and __________-a mating type cassettes) on the same chromosome; in addition, there is a third site called __________ at which one of the two mating type cassettes can be put by a special recombination event.
 Definition
1) HML
2) HMR
3) MAT
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