Control of Gene Expression Flashcards
Controlling gene expression can often be achieved by controlling _______ _______
transcription initiation
_______ _______ bind to DNA, modulating the binding of RNA polymerase to the promoter
Regulatory proteins
_______ organisms regulate gene expression in responds to their environment
Prokaryotic
_______ cells regulate gene expression to maintain a constant internal environment (_______ ) in the organism
Eukaryotic, homeostasis
Regulatory proteins gain access to the bases of DNA at the _______ _______
major groove
Regulatory proteins possess DNA-binding _______
motifs
Regulatory proteins either block transcription by preventing _______ _______ to bind, or stimulate transcription by facilitating it to bind to the _______
RNA polymerase, promoter
Within the major groove, nucleotides’ _______ _______ donors and acceptors are accessible. There is a unique pattern of accessibility for each base pair combination which enables _______ to read the sequence without _______ DNA
hydrogen bond, proteins, unwinding
DNA-binding _______ are regions of _______ proteins which bind to DNA
motifs, regulatory
The _______-_______-_______ motif is two α-helical segments linked by a nonhelical segment. The _______ is a special class of this and is critical in Eukaryotic development
Helix-turn-helix, Homeodomain
The _______ _______ motif has several forms, and uses zinc atoms to coordinate DNA binding
Zinc finger
The _______ _______ motif is a dimerization motif in which a region in one subunit interacts with a similar region on another subunit forming a zipper-like connection
Leucine zipper
In Prokaryotic regulation, Transcription inititiation can be _______ or _______ controlled
positively, negatively
_______ control of prokaryotic transcription initiation increases frequency. _______ enhance binding of RNA polymerase to the _______
Positive, Activators, promoter
_______ control of Prokaryotic transcription initiation decreases frequency. _______ bind to regulatory sites on DNA called _______ that prevent or decrease initiation frequency
Negative, Repressors, operators
_______ molecules can act on both repressors and activators
Effector
Prokaryotic cells often respond to their _______ by changes in gene expression. Genes involved in the same metabolic pathway are organized in _______.
environment, operons
_______ occurs when the presence of a substrate (a specific substance) triggers the production of enzymes needed to produce it
Induction
_______ means the cell is capable of making an enzyme but doesn’t
Repression
The _______ _______ encodes proteins necessary for the use of lactose as an energy source
lac operon
β-galactosidase is known as _______, permease as _______, and transacetylase as _______. The gene for the lac repressor (_______) is linked to the rest of the lac operon
lacZ, lacY, lacA, lacl
The lac operon is _______ regulated by a _______ protein.
negatively, repressor
The lac repressor binds to the _______ to block transcription. In the presence of lactose, an inducer molecule (_______) binds to the repressor protein. The repressor can no longer bind to the _______ and transcription proceeds
operator, allolactose, operator
_______ _______ is a mechanism for the preferential use of glucose in the presence of other sugars.
Glucose repression
_______ _______ _______ (CAP) is an allosteric protein with cAMP as effector
Catabolic activator protein
The level of _______ in cells is reduced in the presence of glucose so that no stimulation of transcription from _______-responsive operons takes place.
cAMP, CAP
_______ _______ - The presence of glucose inhibits the transport of lactose into the cell, EVEN IF there is lactose present
Inducer exclusion
The _______ _______ encodes genes for the biosynthesis of tryptophan
trp operon
The trp operon is not expressed when the cell contains sufficient amounts of _______
tryptophan
The trp _______ is a helix-turn-helix protein that binds to the operator site adjacent to the trp _______
repressor, promoter
The trp operon is negatively regulated by the trp _______ protein. This protein binds to the _______ to block transcription. This binding process requires a _______ which is tryptophan.
repressor, operator, corepressor
When tryptophan levels fall, the repressor can’t bind to the operator, so the operon is _______ (versus being induced).
derepressed
Tryptophan binding increases the _______ between the two recognition helices, allowing the repressor to fit into two adjacent portions of the _______ _______ in DNA
distance, major groove
In Eukaryotic regulation, the control of _______ is more complex. The major differences from prokaryotes is that Eukaryotes have DNA organized into _______ which complicates the protein-DNA interaction. Also, Eukaryotic transcription occurs in the _______ while translation occurs in the _______.
transcription, chromatin, nucleus, cytoplasm
_______ transcription factors are named TF + roman numeral + letter. The roman numeral indicates which _______ _______ the TF interacts with.
General, RNA Polymerase
General TF’s are necessary for the assembly of a transcription _______ and the recruitment of RNA Pol II to a _______
apparatus, promoter
TFIID recognizes _______ _______ sequences
TATA box
The initiation complex formed by _______ _______ _______ can initiate synthesis at a _______ level
General transcription factors, basal
_______ _______ _______ act in a tissue- or time- dependent manner to stimulate higher levels of transcription than the basal level
Specific transcription factors
Each specific TF consists of a _______-_______ domain and a separate _______ domain that interacts with the transcription apparatus. These domains are _______ in the protein
DNA-binding, activating, independent
_______ form the binding sites for general TFs.
Promoters
General TFs mediate the binding of RNA polymerase II to the _______
promoter
_______ are the binding site of the specific TFs
Enhancers
Specific TF’s act over large distances by bending DNA to form a loop to position the _______ closer to the _______
Enhancer, promoter
Coactivators and mediators are required for the function of _______ _______
transcription factors
The number of _______ is small compared to the number of TFs because one can be used with multiple TFs
coactivators
The _______ is essential to some but not all TFs.
mediator
Virtually all genes transcribed by _______ _______ _______ need the same suite of general TFs to assemble an _______ _______
initiation complex
The ultimate level of transcription depends on the _______ _______ _______ that together make up the _______ _______
specific transcription factors, transcription complex
In the Eukaryotic _______ structure, DNA is wound around histone proteins to form nucleosomes.
chromatin
DNA is wound around _______ proteins to form _______ in the Eukaryotic chromatin structure
histone, nucleosomes
_______ and _______ complicate the process of transcription by restricting the access of the transcription machinery to the DNA
Nucleosomes, histones
Alterations in _______ structure are though to be the basis for epigenetics.
chromatin
_______ alterations must persist in the absence of the initiating stimulus, and must be inherited through _______ _______.
Epigenetic, cell division
_______ _______: High levels of it is correlated with inactive genes, and allele-specific gene expression in genomic imprinting is at least partially due to it.
DNA methylation
Mammalian females inactivate one _______ _______ as a form of dosage compensation.
X chromosome
There are four possible _______ that can be modified
histones
_______, _______, and _______ are all possible histone modifications
Acetylation, methylation, phosphorylation
In general, the histone modification _______ is correlated with active sites of transcription.
acetylation
Some transcription coactivators have been shown to be _______ _______ (HATs). Transcription is increased by removing higher order _______ structure that would prevent transcription
Histone acetylases, chromatin
Gene expressions can be controlled after transcription with: _______ RNA’s (miRNA and siRNA), _______ splicing, RNA _______, or _______ degredation
Small, alternative, editing, mRNA
_______-_______ mutant alters developmental timing in C. elegans
lin-4
lin-4 does not encode a protein product, instead it encodes two _______ _______ molecules
small RNA
lin-4 RNA acts as a transcriptional _______ of an mRNA
repressor
miRNA production begins with RNA pol II producing a transcript called the _______-_______
pri-miRNA
miRNA folds back on itself to form a _______-and-_______ structure which is cleaved by _______ to form pre-miRNA
stem, loop, Drosha
pre-miRNA is exported from the nucleus and cleaved by _______ to produce a short double stranded RNA containing the miRNA
Dicer
miRNA is loaded into a protein complex called an _______ _______ _______ _______ (RISC)
RNA induced silencing complex
RISC includes the RNA-binding protein _______, which interacts with the miRNA
Ago
RISC is targeted to repress the expression of genes based on the sequence complementary to the _______. This complementary region is usually in the ___ untranslated region of genes
miRNA, 3’
_______ _______ refers to small RNA gene silencing, and involves the production of _______
RNA interference, siRNAs
Production of siRNA is similar to miRNAs, but siRNAs arise from a _______ double-stranded RNA. _______ cuts yield of multiple siRNAs which are loaded into _______. The target _______ is then cleaved by the siRNA
long, Dicer, RISC, mRNA
_______ represses genes different from its origin
miRNA
_______ tends to repress genes they were derived from
siRNA
The editing of mature _______ transcripts can produce altered versions that are not truly encoded in the genome
mRNA
In mammals, RNA editing involves the chemical modification of a base to change its _______-_______ properties
base-pairing
