Gene Expression Flashcards
Gene expression refers to the processes that result in the production of ___ ___. Gene expression can be controlled at the levels of ___, ___ (splicing in eukaryotes), ___, ___mRNA stability, and ___ stability.
- functional protein
- transcription
- processing
- translation
- mRNA
- protein
Tissue-specific gene expression is essential for:
multicellular, differentiated organisms.
Transcription factors, as noted previously, are ___ that bind to ___ and affect the ___ of genes located ___ where they bind.
- proteins
- DNA
- transcription
- near
Control of gene expression is also essential for organisms to be able to ___ properly to their ___. For example, E. coli prefers ___ for energy, but must be able to use other sugars, like ___, when they are available.
- respond
- environments
- glucose
- lactose
An ___ is a prokaryotic system for organizing genes all under the ___ transcriptional ___. Genes on the same operon in prokaryotes are all synthesized on the same ___. mRNAs containing multiple gene coding sequences are referred to as ___.
- operon
- same
- control
- mRNA
- polycistronic
The lactose operon consists of ___ linked structural genes that encode enzymes of lactose ___, plus adjacent ___ sites. The three enzymes –_, _, and _–encode ___-______, ___-___ ___ (a transport protein), and ___ ___ (an enzyme of still unknown metabolic function), respectively.
- three
- utilization
- regulatory
- z, y, and a
- beta-galactosidase
- beta-galactose permease
- thioglactoside transacetylase
Transcription of the lac operon commences at a promoter (___) before ___ and transcribes a ___ nucleotide mRNA molecule, ending at a terminator beyond ___.
- lacP
- lacZ
- 5200
- lacA
___ is a synthetic substance used to study ___ ___ expression. ___ has the useful property that it turns ___ when acted on by ___-______, giving a measure of how much the operon has been induced by the amount of blue color produced.
- X-Gal
- lac operon
- X-Gal
- blue
- beta-galactosidase
___ transcriptional regulation of the lac operon is accomplished by a protein known as the ___ ___. It binds the operon’s ___ ___ and ___ transcription.
- Negative
- lac repressor
- operator region
- inhibits
In the absence of ___ ___, the lac repressor ___ ___ to the operator and ___ transcription of the operon. When inducer molecules are present, they bind to the ___ ___ and change its shape and ___ its ability to bind the operator, thus allowing the ___ ___ to bind the promoter and start transcription.
- inducer molecules
- tightly binds
- inhibits
- lac repressor
- reduce
- RNA polymerase
The promoter sequence of the lac operon differs somewhat from the ___ ___ ___ of an E. coli promoter.
-ideal consensus sequence
In the ___ of positive acting elements, the ___ ___ does ___ function well on its own. A protein that acts positively to help activate the lac operon is the ___ (also called ___-___ ___ ___).
- absence
- lac promoter
- not
- CAP (CRP-cAMP receptor protein)
CAP is important because the lac promoter by itself is not a ___ one.
Attenuation is a regulatory mechanism for several E. coli operons involved in ___ ___ ___ .
- strong
- amino acid metabolism
The ___ operon of E. coli (trp operon) acts as a “sensor” for ___ in the cell and controls the expression of genes necessary to make ___. When ___ is abundant in E. coli, the ribosome moves ___ along the trp operon mRNA, making ___.
- tryptophan
- tryptophan
- tryptophan
- tryptophan
- quickly
- protein
Control of the ___ operon is set up so that transcription of the entire operon only occurs when tryptophan is ___ in the cells. When tryptophan is abundant, transcription ___ very ___. The system is set up such that translation of the operon plays a role in the early ___ termination.
- tryptophan
- limiting
- terminates
- early
- transcriptional
The trp operon accomplishes being a “sensor” by a “___” sequence that contains coding for a ___ ___. It includes within it coding for two ___ ___ ___ ___.
- leader
- short polypeptide
- consecutive trptophan amino acids
If tryptophan is in short supply in the cell, the ribosome pauses to wait for ___-___ to come. This pause allows an ___-___ ___ to form in the mRNA. The anti-terminator causes the RNA polymerase to ___ synthesizing the rest of the operon.
- trp-tRNA
- anti-terminator sequence
- continue
If tryptophan is abundant in the cell, the ribosome covers up the ___-___ sequence and a ___ sequence instead forms in the mRNA. The ___ sequence causes the RNA polymerase to ___ synthesizing the operon
- anti-terminator
- terminator
- terminator
- stop
Common DNA-binding structures are found in the diverse set of transcription factors that are known. They include motifs (structural features) for ___-___-___, ___, ___ ___, and ___ ___.
- helix-turn-helix
- homeodomains
- leucine zippers
- zinc fingers
Leucine zipper structures are found in adjacent ___ ___ and contain regions with ___ ___ appearing about every _ amino acids. The leucine ___ with each other to hold the strands together and in doing so allow other portions of the helix to bind ___ properly.
- alpha helices
- leucine residues
- 7
- interact
- DNA
Zinc fingers are structures with ___ residues that hold ___ ___ and create a ___-like structure that can stick into the ___ ___.
- cysteine
- zinc ions
- finger
- DNA helix
Proteins that bind to specific DNA sequences must “___” the sequence of bases inside the helix, usually by inserting a region into the ___ ___ of the DNA and “___” the ___ ___ ___ inside.
- read
- major groove
- checking
- hydrogen bonding molecules
Since different base pairs have unique hydrogen bonding orientations, the proteins that find and bind to ___ ___ ___.
-specific base sequences
In eukaryotic cells, DNA is wrapped up (coiled up) with basic proteins called ___. ___ sequences are strongly conserved from ___ to ___.
- histones
- histones
- yeast
- humans
Four histones form a ___ around which DNA is wrapped. This ___ contains ___ copies each of histones ___, ___, ___, and ___. This core of proteins is called an ___.
- core
- core
- two
- H2A, H2B, H3, H4
- octamer
The appearance of chromatin DNA is that of beads on a string, with the ___ wrapped with DNA composing the beads and the DNA strand coated with histone __ (and __) composing the string.
- octamer
- H1
- H5
- string
Histones of the octamer have strong ___ ___ to each other.
-structural similarity
Wrapping of DNA around the histone octamer provides only ___ ___ of the length of a DNA molecule. Additional compression occurs as a result of ___ of ___/DNA complexes as well, forming higher order structures.
- partial compression
- coiling
- octamer
Enhancer sequences are bound by ___ ___ and are found only in ___. Multiple enhance sequences may be present before the ___ ___ of a particular gene.
- enhancer proteins
- eukaryotes
- start site
Binding of enhancer proteins to enhancer sequences allows for ___ ___ ___ of genes if the enhancer proteins themselves are expressed tissue specifically. Enhancer proteins help to “___” out the ___ from a region of a chromosome to allow ___ to occur.
- tissue specific expression
- clear
- histones
- transcription
___ ___ ___, such as the ___ receptor, have DNA binding domains and ___ binding domains. The binding of the ___ (and estrogen) ligand to the estrogen receptor causes a ___ change in the protein, but does not change the ___ of the protein to DNA.
- Nuclear hormone receptors
- estrogen
- ligand
- estradiol
- conformational
- binding
Binding of the estradiol DOES appear to ___ the protein and thus ___ transcription of the genes that the receptor binds to the ___ of.
- activate
- activate
- promoter
The key to action of the nuclear hormone receptor that binds estradiol is that binding of estradiol ___ binding of the receptor to ___ ___. These help to ___ ___ transcription of the relevant ___.
- favors
- co-activator proteins
- turn on
- genes
Binding of co-activator proteins by transcriptional factors, such as the estrogen receptor is called ___.
-recruitment
An antagonist of the estrogen receptor is the drug ___. ___ bind proteins and prevent them from ___. Binding of ___ by the estrogen receptor stops the receptor from ___ transcription of genes that it normally activates.
- tamoxifen
- Antagonists
- acting
- tamoxifen
- activating
Tamoxifen appears to act by binding the estrogen receptor (estrogen receptor and nuclear hormone receptor here are the same thing), with a part of the molecule ___ into the region of the protein that normally binds to ___.
- extending
- co-activators
Thus, tamoxifen acts by stopping ___ by the receptor of ___. Tamoxifen is used to treat ___ that are stimulated by the binding of ___ to the receptor.
- recruitment
- co-activators
- tumors
- estrogens
Altering chromatin structure is an essential function for transcriptional ___ in ___. Co-activator proteins appear to play a role in this process by ___ the ___ of ___ residues in ___.
- activation
- eukaryotes
- catalyzing
- acetylation
- lysine
- histones
Acetylation of histone lysines ___ their ___ charge, changing the ___ of histones for ___ and changing the nature of their interaction with DNA, thus allowing more proteins to be able to ___ ___ to the DNA where the ___ has occurred.
- neutralizes
- positive
- affinity
- DNA
- gain access
- acetylation
Bromodomains are regions of proteins that ___ ___ ___. Proteins involved in ___ ___ often have bromodomains. These regions of protein recognize and bind to acetylated ___ ___ in histones.
- recognize acetylated lysines
- transcriptional control
- lysine residues
Altering chromatin structure involves a process called ___. Steps in this process include 1) binding of a ___ ___ to a promoter sequence; 2) ___ of co-activators; 3) acetylation of histone ___ by co-activators; 4) binding of the ‘___ ___’ at the acetylation site; 5) ___ of DNA by the remodeling engine; and 6) binding of ___ ___ ___ to the exposed DNA.
- remodeling
- transcription factor
- recruitment
- lysines
- remodeling engine
- exposing
- RNA Polymerase II
In eukaryotic cells, the ___ mRNA has a region of it called an ___ ___ ___ that can be bound by a protein called ___ (___ ___ ___ ___). IRE-BP binds the ___ ___ ___ when iron is ___.
- ferritin
- iron response element
- IRE-BP (iron- response binding protein)
- iron response element
- absent
When IRE-BP is NOT bound to the iron response element (high iron conditions), ___ is made because the IRE-BP does not ___ the ribosome from translating the ___. Thus, when iron concentration is high, ___ is synthesized to hold it.
- ferritin
- block
- mRNA
- high
- ferritin
When IRE-BP is bound to the iron response element (low iron conditions), ferritin is ___ ___. Thus when iron is not available, ferritin is ___ ___. Gene expression of ferritin is therefore a function of ___ ___.
- not made
- not made
- ferritin
- translational control
The transferrin receptor has ___ ___ ___ ___ at the ___ end of its mRNA. When IRE-BP binds to it, the 3’ end is ___ and ___ ___ is made.
- multiple iron response elements
- 3’
- protected
- transferrin receptor
Thus, when iron is low, the ___ binds the mRNA, ___ it, and the transferrin receptor is ___ to bring ___ into the cells.
- IRE-BP
- protecting
- made
- iron
When iron is high, the IRE-BP ___ the mRNA’s ___ end, leaving it susceptible to ___. Gene expression of the ___ ___is therefore a function of stability of the gene’s ___.
- leaves
- 3’
- degradation
- transferrin receptor
- mRNA
Thus when iron inside the cell is high, ___ is made to hold onto it and when iron is low inside the cell, ___ receptor is made to bring more iron in.
- ferritin
- transferrin
