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Biochem Final > Gene Expression > Flashcards

Gene Expression Flashcards

1
Q

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.

A
  • functional protein
  • transcription
  • processing
  • translation
  • mRNA
  • protein
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2
Q

Tissue-specific gene expression is essential for:

A

multicellular, differentiated organisms.

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3
Q

Transcription factors, as noted previously, are ___ that bind to ___ and affect the ___ of genes located ___ where they bind.

A
  • proteins
  • DNA
  • transcription
  • near
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4
Q

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.

A
  • respond
  • environments
  • glucose
  • lactose
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5
Q

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 ___.

A
  • operon
  • same
  • control
  • mRNA
  • polycistronic
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6
Q

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.

A
  • three
  • utilization
  • regulatory
  • z, y, and a
  • beta-galactosidase
  • beta-galactose permease
  • thioglactoside transacetylase
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7
Q

Transcription of the lac operon commences at a promoter (___) before ___ and transcribes a ___ nucleotide mRNA molecule, ending at a terminator beyond ___.

A
  • lacP
  • lacZ
  • 5200
  • lacA
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8
Q

___ 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.

A
  • X-Gal
  • lac operon
  • X-Gal
  • blue
  • beta-galactosidase
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9
Q

___ transcriptional regulation of the lac operon is accomplished by a protein known as the ___ ___. It binds the operon’s ___ ___ and ___ transcription.

A
  • Negative
  • lac repressor
  • operator region
  • inhibits
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10
Q

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.

A
  • inducer molecules
  • tightly binds
  • inhibits
  • lac repressor
  • reduce
  • RNA polymerase
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11
Q

The promoter sequence of the lac operon differs somewhat from the ___ ___ ___ of an E. coli promoter.

A

-ideal consensus sequence

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12
Q

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 ___-___ ___ ___).

A
  • absence
  • lac promoter
  • not
  • CAP (CRP-cAMP receptor protein)
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13
Q

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 ___ ___ ___ .

A
  • strong

- amino acid metabolism

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14
Q

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 ___.

A
  • tryptophan
  • tryptophan
  • tryptophan
  • tryptophan
  • quickly
  • protein
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15
Q

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.

A
  • tryptophan
  • limiting
  • terminates
  • early
  • transcriptional
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16
Q

The trp operon accomplishes being a “sensor” by a “___” sequence that contains coding for a ___ ___. It includes within it coding for two ___ ___ ___ ___.

A
  • leader
  • short polypeptide
  • consecutive trptophan amino acids
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17
Q

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.

A
  • trp-tRNA
  • anti-terminator sequence
  • continue
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18
Q

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

A
  • anti-terminator
  • terminator
  • terminator
  • stop
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19
Q

Common DNA-binding structures are found in the diverse set of transcription factors that are known. They include motifs (structural features) for ___-___-___, ___, ___ ___, and ___ ___.

A
  • helix-turn-helix
  • homeodomains
  • leucine zippers
  • zinc fingers
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20
Q

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.

A
  • alpha helices
  • leucine residues
  • 7
  • interact
  • DNA
21
Q

Zinc fingers are structures with ___ residues that hold ___ ___ and create a ___-like structure that can stick into the ___ ___.

A
  • cysteine
  • zinc ions
  • finger
  • DNA helix
22
Q

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.

A
  • read
  • major groove
  • checking
  • hydrogen bonding molecules
23
Q

Since different base pairs have unique hydrogen bonding orientations, the proteins that find and bind to ___ ___ ___.

A

-specific base sequences

24
Q

In eukaryotic cells, DNA is wrapped up (coiled up) with basic proteins called ___. ___ sequences are strongly conserved from ___ to ___.

A
  • histones
  • histones
  • yeast
  • humans
25
Q

Four histones form a ___ around which DNA is wrapped. This ___ contains ___ copies each of histones ___, ___, ___, and ___. This core of proteins is called an ___.

A
  • core
  • core
  • two
  • H2A, H2B, H3, H4
  • octamer
26
Q

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.

A
  • octamer
  • H1
  • H5
  • string
27
Q

Histones of the octamer have strong ___ ___ to each other.

A

-structural similarity

28
Q

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.

A
  • partial compression
  • coiling
  • octamer
29
Q

Enhancer sequences are bound by ___ ___ and are found only in ___. Multiple enhance sequences may be present before the ___ ___ of a particular gene.

A
  • enhancer proteins
  • eukaryotes
  • start site
30
Q

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.

A
  • tissue specific expression
  • clear
  • histones
  • transcription
31
Q

___ ___ ___, 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.

A
  • Nuclear hormone receptors
  • estrogen
  • ligand
  • estradiol
  • conformational
  • binding
32
Q

Binding of the estradiol DOES appear to ___ the protein and thus ___ transcription of the genes that the receptor binds to the ___ of.

A
  • activate
  • activate
  • promoter
33
Q

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 ___.

A
  • favors
  • co-activator proteins
  • turn on
  • genes
34
Q

Binding of co-activator proteins by transcriptional factors, such as the estrogen receptor is called ___.

A

-recruitment

35
Q

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.

A
  • tamoxifen
  • Antagonists
  • acting
  • tamoxifen
  • activating
36
Q

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 ___.

A
  • extending

- co-activators

37
Q

Thus, tamoxifen acts by stopping ___ by the receptor of ___. Tamoxifen is used to treat ___ that are stimulated by the binding of ___ to the receptor.

A
  • recruitment
  • co-activators
  • tumors
  • estrogens
38
Q

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 ___.

A
  • activation
  • eukaryotes
  • catalyzing
  • acetylation
  • lysine
  • histones
39
Q

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.

A
  • neutralizes
  • positive
  • affinity
  • DNA
  • gain access
  • acetylation
40
Q

Bromodomains are regions of proteins that ___ ___ ___. Proteins involved in ___ ___ often have bromodomains. These regions of protein recognize and bind to acetylated ___ ___ in histones.

A
  • recognize acetylated lysines
  • transcriptional control
  • lysine residues
41
Q

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.

A
  • remodeling
  • transcription factor
  • recruitment
  • lysines
  • remodeling engine
  • exposing
  • RNA Polymerase II
42
Q

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 ___.

A
  • ferritin
  • iron response element
  • IRE-BP (iron- response binding protein)
  • iron response element
  • absent
43
Q

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.

A
  • ferritin
  • block
  • mRNA
  • high
  • ferritin
44
Q

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 ___ ___.

A
  • not made
  • not made
  • ferritin
  • translational control
45
Q

The transferrin receptor has ___ ___ ___ ___ at the ___ end of its mRNA. When IRE-BP binds to it, the 3’ end is ___ and ___ ___ is made.

A
  • multiple iron response elements
  • 3’
  • protected
  • transferrin receptor
46
Q

Thus, when iron is low, the ___ binds the mRNA, ___ it, and the transferrin receptor is ___ to bring ___ into the cells.

A
  • IRE-BP
  • protecting
  • made
  • iron
47
Q

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 ___.

A
  • leaves
  • 3’
  • degradation
  • transferrin receptor
  • mRNA
48
Q

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.

A
  • ferritin

- transferrin

Biochem Final (5 decks)

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