Chapter 20: The Regulation of Gene Expression
Benefits to selective gene expression?
It allows cells to be efficient, synthesizing only what it necessary
_____ is a general term, referring to induced expression of any regulated gene. Gene activation has an effect on downstream ____ ____ and ____ ___
activation, protein synthesis, protein activity
There are many similarities between bacteria and eukaryotes. One similarity is that they both have ___/___ and ___/___ elements. Eukaryotes require a diversity of genetic ____ ____, some of which are quite different from those of bacteria.
activation, repression, cis, trans, control mechanisms
General transcription factors usually initiate transcription at _____ (low) rates. Most protein-coding genes have short DNA sequences farther_____ to which additional transcription factors bind, improving the efficiency of the ____ ____. ____ ___ ____ (upstream) are sequences about 100-200 bases upstream of the core promoter.
basal, upstream, core promoter, proximal control elements
____ _____ are specific DNA sequences that exert effects on expression of a nearby gene. ____ _____ are not; they are regulatory proteins that bind to cis-acting elements. An example is the _____ ____ that bind to cis elements like ____ ____.
cis-regulatory elements, trans-regulatory elements, transcription factors, core promoters
_____ mediate the interaction between regulatory transcription factors and the RNA polymerase complex. They include _____ ____ ____ and enzymes that modify histones. A multiprotein complex called a ____ acts as a bridge that binds to activator proteins associated with enhancers and to RNA polymerase; it links ____ to components involved in transcription initiation.
coactivators, chromatin remodeling proteins, mediator, enhancers
Both silencers and enhancers can function ____ from the genes they regulate. Complications can exist if genes with different expression patterns reside near each other. DNA sequences called _____ are sometimes employed to prevent an enhancer or silencer from affecting the wrong genes.
far, insulators
Translation rates can be controlled by ____ ___ and ____ ____.
initiation factors (start), translational repressors (end)
In bacterial regulation of lactose transcription, the ___ ____ is a cis-regulator. The operon is repressed when ____ is absent; repressor binds to operator. ____ ____ is therefore prevented from moving down the ___ ____ and transcribing its genes.
lac operon, lactose, RNA polymerase, lac operon
Chromatin Decondensation: Except when a gene is being transcribed, its ____ ___ is embedded within a highly folded and ordered chromatin superstructure. This must be ____/____ to allow gene expression
promoter region, unfolded, decondensed
_____ ____ is the second main level for controlling and regulating gene expression; it is the regulation of RNA levels (high vs. low)
transcriptional control
DNA binding domains are specific for ____ ___ ____
primary DNA sequences
The number, exact location, and identities of proximal control elements varies with each gene, but three types are common:...
CAAT box, GC box, octamer
1) ____ plus ___ bind to a target protein 2) Ubiquitin molecules are attached to ____ residues in target protein , and then ___ and ___ detach. 3) The marked protein is degraded by a _____.
E2, E3, lysine, E2, E3, proteasome
Histone Modifications/Chromatin Remodeling Factors: Histone _____ and _____ favor compacted, inaccessible chromatin. Histone _____ and ______ favor accessibility of chromatin to the transcriptional machinery.
deacetylation, methylation, acetylation, demethylation
Different sets of genes are transcribed in different cell types. Different proteins produced by two cell types in the same individual result from ___ ____ ____. Different cell types transcribe different sets of ____ as well as differing _______ of the same gene. FOR EXAMPLE: Different SETS Lymphocytes produce ____. Epithelial cells express ____ ____. Different AMOUNTS In ___ cells, there is low actin/myosin, whereas in ___ cells, there is high actin/myosin.
differential gene transcription, genes, amounts, antibodies, junction proteins, epithelial, muscle
In the case of multicellular eukaryotes, a single organism consists of a mixture of specialized or ______ cell types. They are distinguished from each other based on difference in ____ and ____ ___. Such differences indicate that differential____ ____ plays a central role in creating differentiated cells.
differentiated, appearance, protein products, gene expression
Multiple ____ ___ ___ and ___ ___ act in combination to establish patterns of gene expression in different cell types. Gene regulation is ______. Different cell types possess different sets of ___ ___.
dna control elements, transcription factors, combinatorial, transcription factors
Main Levels of Controlled Gene Expression: Elaborate on these controls (give examples): Genome --> ... (3) Transcription --> ...(1) RNA Processing & Nuclear Export --> ... (2) Translation --> ... (2) Posttranslation --> ...(4)
dna methylation, chromatin decondensation/condensation, histone modifications transcription (controlled by transcription factors) Rna splicing, transport of mRNA to cytoplasm polypeptide synthesis (controlled by initiation factors & translational repressors) protein folding & assembly, polypeptide cleavage, modification, import
A typical ____ contains several different control elements within it, each a short DNA sequence that is a binding site for a different regulatory factor (activator/repressor). Some of these sequences may be identical to ___ ___ __. The regulatory factors that bind enhancers are called ____ _____.
enhancer, proximal control elements, transcriptional activators
____ and ____ are DNA elements that bind transcription factors to regulate genes downstream or upstream, and are located at variable distances from the _____. _____ inhibit transcription and ____ stimulate gene transcription.
enhancers, silencers, promoter, silencers, enhancers
Eukaryotic Gene Expression: Control is exerted at 5 levels: ... Which categories represent levels of posttranscriptional control?
genome, transcription (activation/repression), RNA processing and nuclear export (nuclear half life), translation (protein half life), posttranslational events, RNA processing and export, translation, posttranslational events
Genome: Though each specialized cell type uses only a fraction of the genes in the genome, almost all cells retain the same complete set of genes. This is known as ____ ____
genomic equivalence
Rates of protein degradation are often expressed as the ___ ___ of a protein. Enzymes with ____ half lives change more dramatically in response to alterations in rate of synthesis than proteins with ____ half lives. Enzymes important in metabolic regulation tend to have ____ half-lives.
half life, shorter, longer, short
regulation is often _____
hierarchical
______ genes, genes that encode proteins called transcription factors that direct cells to form various parts of the body, are master regulators.
homeotic
When an activator binds to an enhancer element, what results is a ____ in transcription. When a repressor binds to a silencer element, what results is a ____ in transcription. An _____ prevents activation of transcription of an adjacent gene.
increase, decrease, insulator
Other Means of Degrading Proteins: ______ take up and degrade proteins by an infolding of the lysosomal membrane. Small vesicles are created that are internalized inside the lysosome and broken down there. This is ______ and the result is a slow continual recycling of amino acids.
lysosomes, microautophagy
DNA ____ is associated with inactive regions of the genome. It regards the ____ of ____ groups to certain cytosine bases in DNA that reduce gene activity. Methylation of _____ regions can block access of proteins needed for transcription, the net effect being _____ ____.
methylation, addition, methyl, promoter, transcriptional repression
Regulatory Transcription Factors are ____ ____ that can bind to a specific DNA sequence and regulate transcription. These activities reside in separate protein domains: ____ ___ ____ and the ____ __ ___ (activation domain)
modular proteins, dna binding domain, transcription regulation domain
Stability of mRNA varies widely. mRNAs with longer poly(A) tails are ____ ___ than those with shorter tails. Short-lived mRNAs have ___-____ ____ in the 3' untranslated region; these trigger removal of the poly(A) tail.
more stable, AU-rich elements
When lactose is present, the repressor is not bound/bound to the operator? The operon is _____ because in the presence of lactose, the repressor is converted to its ____ form, which doesn't bind to the operator. The repressor is ____-regulated and in this case is ____. ____ ____ can therefore move past the operator and transcribe ____ , ____ , and ____ genes into a single mRNA, helping genes in the lac operon specify proteins that help the cell utilize _____.
not bound, derepressed (activated), inactive, trans, repressed, rna polymerase, lacZ, lacY, lacA, lactose
When tryptophan is absent, is the repressor bound/not bound to the operator? The operon is ______ and the repressor is ____ ____. In the absence of tryptophan, the free ___ _____ cannot bind to the operator site. RNA polymerase therefore can move past the ____ and transcribe the ___ ____ genes, giving the cell the capability to synthesize tryptophan.
not bound, derepressed (activated), not activated, trp repressor, trp operon, trp operon
After transcription has taken place, the flow of genetic information involves a complex series of _____ ____. This regulation is useful in rapidly fine-tuning patterns of gene expression. It includes ____ and __ ___ ____ ____: regulation allows cells to create a variety of different mRNAs from the same pre-MRNA. ____ ____ permits some splice sites to be skipped and others to be activated. ___ ___ into the cytoplasm can be controlled - RNAs with defects in capping or splicing are not readily exported from the nucleus; even with normal mRNAs, certain molecules are retained until their export is triggered by a stimulus
posttranscriptional events, splicing, nuclear export, RNA splicing, alternative splicing
______ are large protein-degrading structures and the predominant proteases of the cytosol; they bind ____ ____ ____ and remove the ____. The proteins are then fed into the central channel of the proteasome and their peptide bonds are ____ in an ATP-dependent manner.
proteasomes, ubiquitin-labeled proteins, ubiquitin, hydrolyzed
cyclic AMP stimulates _____
protein kinase A
Posttranslational Control involves modification of ___ ___, ___, and ____. Posttranslational control mechanisms include structural alterations that influence protein function, such as _____ , ____ ____, _____, and/or ____. They also include guiding of ____ ____, targeting to ____ ____, interaction with ____ ____.
protein structure, function, degradation, phosphorylation, lipid addition, sugars, cleavage, protein folding, specific locations, regulatory molecules
Transcription factors that bind one of the proximal control elements are called ___ or ____ ____ ___
repressing, activating transcription factors
_____ is a general term, referring to reduced expression of any regulated gene. Genetic repression has an effect on _____ ____ and _____ ____.
repression, protein synthesis, protein activity
_____ share many features of enhancers, but inhibit transcription rather than activate it. Regulatory transcription factors that bind to silencers are called _____ ____
silencers, transcriptional repressors
All cells of the body are derived from a ___ cell that divides to make all other cell types. Making cells with different functions is a process called ___ ____. ___ ____ are in a low differentiation state and therefore can be differentiated into other cells through gene correction.
single, cell differentiation, stem cells
Transcriptional Control: _____ ____ are proteins that determine the specificity of transcription; they are ___ elements. ____ ____ ___ are essential for transcription of all the genes transcribed by a given type of RNA polymerase. General transcription factors assemble with RNA polymerase at the ___ ____ (a ____ element) very close to the transcription startpoint.
transcription factors, trans, general transcription factors, core promoter, cis
Once mRNAs reach the cytoplasm, several _____ _____ mechanisms regulate their rate of translation. Some work by altering _____ or _____ ____ ___. Others work by regulating the activity/stability of the _____ itself. Translation can also be controlled by regulation of ___ _____. Translation rates are subject to control by alterations in ____ ____. Degradation rates of mRNA can be measured by ____-____ _____
translational control, ribosomes, protein synthesis factors, mRNA, mRNA degradation, mRNA stability, pulse-chase experiments
In bacterial regulation of tryptophan transcription , the ___ ___ is cis regulated. When tryptophan is ______, the repressor is bound to the repressor. The operon is _____. When complexed with tryptophan, the _____ ____ produced by the trpR gene binds tightly to the ____ operator, thereby preventing ____ _____ from transcribing the operon genes.
trp operan, present, repressed, repressor protein, trp, rna polymerase
_______, a small protein containing 76 amino acids, targets proteins for degradation by proteasomes. It is joined to target proteins by a process involving three components: ...
ubiquitin, ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2), substrate recognition protein/ ubiquitin ligase (E3)
In ___ ___, the DNA of one X is extensively methylated, and the chromatin condenses into a tight mass of heterochromatin, making the X chromosome ______. The inactivated X chromosome is visible as a dark spot called a ___ ____. Once a certain X is inactivated in a cell, all the daughter cells produced by the original have the same X inactivated. What is the result of x-inactivation? Female placental mammals are a ___ of groups of cells in which one or the other X chromosome was initially inactivated, and can be seen in animals in which hair color is controlled by __ ___ ____.
x-inactivation, inactive, barr body, females and males each have one active X chromosome per adult cell, mosaic, X linked genes