Chapter 16: Control of Gene Expression Flashcards
Controlling gene expression is often accomplished by controlling ______ _______
transcription initation
_______ ________ bind to DNA, modulate binding of RNA polymerase to promoter
regulatory proteins
___________ organisms regulate gene expression in response to their environment
prokaryotic
________ cells regulate gene expression to maintain a constant internal environment in the organism
eukaryotic
What type of regulation is this
- chromatin remodeling to make genes accessible for transcription
-regulatory events at a gene’s promoter and regulatory sequences
transcriptional regulation
What type of transcription is this
- variations in pre-mRNA processing
-removal of making proteins
-variations in rate of mRNA breakdown
-RNA interference
posttranscriptional regulation
What type of regulation is this
- variations in rate of initiation of protein synthesis
translational regulation
What type of regulation is this
- variations in rate of protein processing
-removal of making segments
-variations in rate of protein breakdown
posttranslational regulation
What type of regulation determines which genes are transcribed?
transcriptional
What type of regulation determines types and availability of mRNAs to ribosomes?
posttranscriptional
What type of regulation determines the rate at which proteins are made?
translational
What type of regulation determines the availability of finished proteins?
posttranslational
Gene expression is often controlled by _____ _____ binding to specific DNA sequences
regulatory proteins
______ ______ gain access to the bases of DNA at the major groove
regulatory proteins
Regulatory proteins possess ____-_____ motifs
DNA-binding
What are the two things regulatory proteins can do?
- block transcription by preventing RNA polymerase to bind
- stimulate transcription by facilitating RNA polymerase binding to promoter
Within the ____ groove, nucleotides’ hydrogen bond donors and acceptors are accessible
major
T or F: The unique pattern of accessibility for each base pair combination enables proteins to read the sequence without unwinding DNA
True
What are the regions of regulatory proteins that bind to DNA called?
DNA-binding motifs
What is the two a-helical segments linked by a nonhelical segment called?
Helix-turn-helix motif
What is a special class of helix-turn-helix and is critical in eukaryotic development?
Homeodomain
What type of motif uses zinc atoms to coordinate DNA binding?
Zinc finger
What type of motif has one subunit that interacts with a similar region on another subunit forming a zipper-like connection
Leucine zipper motif
(prokaryotic regulation) ______ _____ can be positively or negatively controlled
transcription initiation`
What type of control increases freqeuncy?
positive
In positive control _______ enhance binding of RNA polymerase to promoter?
activators
What type of control decreases frequency?
negative control
In negative control ____ bind to regulatory sites on DNA called operators that prevent or decrease initiation frequency
repressors
_____ molecules can act on both repressors and activators
effector
______ cells often respond to their environment by changes in gene expression
prokaryotic
genes involved in the same metabolic pathway are organized in ______
operons
In _______ enzymes for a certain pathway are produced in response to a substrate
induction
______ is capable of making an enzyme by does not
repression
____ ______ encodes proteins necessary for the use of lactose as an energy source
lac operon
What are the three genes in the lac operon?
LacZ, lacY, lacA
What gene is linked to the rest of the lac operon?
the lac repressor (lacl)
The promoter for the gene, the gene repressor protein, CAP-binding site, the promoter for the operon, and the operator are all in the _____ region
regulatory
if lactose is absent the lac operon is _____
repressed
if lactose is absent the lac operon is ______
induced
What is the mechanisms for the preferential use of glucose in the presence of other sugars?
glucose repression
What is the catabolic activator protein (CAP)?
an allosteric protein with cAMP as effector
The presence of glucose inhibits the transport of lactose into the cell which is ____ exclusion
inducer
If glucose is low the inducer is present so _____ activated
Promoter
If glucose is high, the inducer is ____
absent
____ operon encodes genes for the biosynthesis of tryptophan
trp
T or F: the trp operon is not expressed when the cell contains sufficient amounts of tryptophan
True
The trp repressor is a helix-turn- helix protein that binds to the operator site located _____ to the trp promoter
adjacent
The trp operon is ____ regulated by the trp repressor
negatively
When trytophan levels fall, the ____ cannot bind to the operator
repressor
When the tryptophan is absent the operon is ______
derepressed
If the tryptophan is present then the operon is ____
repressed
tryptophan binding _____ the distance between the two recognition helices
increases
Since the distance is increased between the recognition helices by tryptophan, the repressor can then fit snugly into two adjacent portions of the ______ groove in DNA
major
What are the major differences from prokaryotic control of transcription and eukaryotic control of transcription?
- Eukaryotes have DNA organized into chromatin
2.Eukaryotic transcription occurs in nucleus while translation occurs in cytoplasm
General transcription factors are necessary for the assembly of a ______ ______ and recruitment of RNA polymerase II to a promoter
transcription apparatus
What sequence does TFIID recognize?
The TATA box
After TFIID binds what other transcription factors bind?
TFIIE< TFIIF, TFIIA, TFIIB, TFIIH
General transcription factors can initiate synthesis at a _____ level
basal
Specific transcription factors act in a tissue- or time-dependent manner to stimulate _____ levels of transcription than the basal level
higher
Each specific transcription factor consists of a ____-____ domain and a _____ _____ domain that interacts with the transcription apparatus
DNA-binding, separate activating
T or F: in specific transcription factors, the domains are independent in the protein
True
______ form the binding sites for general transcription factors
promoters
_______ are the binding site of the specific transcription factors
enhancers
_______ can act over large distances by bending DNA to form loop to position enhancer closer to promoter
enhancers`
______ and ______ are also required for the function of transcription factors
coactivators, mediators
_______ and _____ bind to transcription factors and bind to other parts of the transcription apparatus
coactivators and mediators
_______ are essential to some but not all transcription factors
mediators
_______ can be used with multiple TF (transcription factors)
coactivators
______ structure is selectively modulated to allow transcription
chromatin
alternations in chromatin structure are thought to be the basis for _______
epigenetics
T or F: heritable changes in phenotype not due to changes in DNA sequence
true
_______ alternations must persist in the absence of the initating stimulus, and must be inherited through cell division
epigenetic
High levels of _____ _______ correlate with inactive genes
DNA methylation
_____-_____ gene expression seen in genomic imprinting is at least partially due to DNA methylation
Allele-specific
T or F: Mammalian females inactivate one X chromosome as a form of dosage compensation
True
How many possible histones can be modified
four
What are the possible modifications to histones?
acetylation, methylation, phosphorylation,
In general _____ is correlated iwth active sites of transcription
acetylation
Some transcription coactivators have been shown to be _____ _____
histone acetylases
Transcription is increased by removing higher order _____ structure that would prevent transcription
chromatin
_______ _______ remove acetyl groups from histones
histone deacetylases
Control of gene expression usually involves the control of _____ initation
transcription
What are posttranscriptional regulation mechanisms?
- small RNAs
2.Alternative splicing - RNA editing
4.mRNA degradation
lin-4 mutant alters developmental timing in ______
C. elegans
_____ does not encode a protein product, instead, it encodes two small RNA molecules
lin-4
_____ RNA acts as a transcriptional repressor of an mRNA
lin-4
_____ production begins with RNA pol II producing a transcript called the pri-mRNA
miRNA
miRNA folds back on itself to form a stem-and loop-structure which is cleaved by _____ to form pre-miRNA
drosha
pre-miRNA exported from the nucleus and cleaved by ____ to produce a short double stranded RNA containing the miRNA
dicer
miRNA loaded into a protein complex called an ____
RISC (RNA induced silencing complex)
RISC includes the _____-____ protein Ago, which interacts with the miRNA
RNA-binding
_____ is targeted to repress the expression of genes based on sequence complementarity to the miRNA
RISC
RNA _______ refers to small RNA gene silencing
interference
siRNA arise from long _____-_______ RNA
double-stranded DNA
with siRNA production, the ______ cuts yield multiple siRNA which are loaded into RISC
Dicer
Biogenesis of both miRNA and siRNA involves cleavage by _____ and incorporation into a _____ complex
Dicer, RISC
target mRNA is cleaved by _______ containing RISC
siRNA
RNA silencing pathways have been implicated in the formation of _______ in different organisms
heterochromatin
_____ repress genes different from their origin
miRNA
endogenous _____ tend to repress genes they were derived from
siRNAs
The editing of mature _____ transcripts can produce an altered mRNA that is not truly encoded in the genome
mRNA
In ______, RNA editing involves chemical modification of base to change its base-pairing properties
mammals
