Chapter 15, 17, 18, 19 Flashcards
A model proposed by Jacob and Monod whereby a group of genes is regulated and expressed together as a unit.
Operon model
How does lacI gene regulate the transcription of the structural genes?
By producing a repressor molecule, and that the repressor is allosteric, meaning that it reversibly interacts with another molecule, causing both a conformational change in the repressor’s three-dimensional shape and a change in its chemical activity.
Because transcription occurs only when the
repressor fails to bind to the operator region, regulation is said to be under?
negative control
If a regulator gene needs to be located adjacent to the gene it regulates, it is said to be?
cis-acting factor (example: O region in lac operon)
If a regulator gene does not need to be located adjacent to the gene it regulates, it is said to be?
trans-acting factor (example: I gene in lac operon)
A molecule called the catabolite-activating protein (CAP) helps activate expression of the lac operon but is able to inhibit expression when glucose is present. This inhibition is called?
catabolite repression
True or False. For maximal transcription of the structural genes, the repressor must be bound by lactose (so as not to repress lac operon transcription), and CAP must be bound to the CAP-binding site.
True
This enzyme catalyzes the conversion of ATP to cyclic adenosine monophosphate.
adenyl cyclase
What is the role of glucose in catabolite expression?
inhibits the activity of adenyl cyclase
When both RNA polymerase and cAMP-CAP complex are together in the presence of the lac promoter DNA, a tightly bound complex is formed. This is an example of a phenomenon called?
cooperative binding
Tryptophan is referred to as ____ because is participates in the repression of genes coding tryptophan synthesizing enzymes.
corepressor
When tryptophan is present and the trp operon is repressed, initiation of transcription still occurs at a low level but is subsequently terminated at a point
about 140 nucleotides along the transcript. This process is called?
Attenuation
The site involved in attenuation is located 115 to 140 nucleotides into the leader sequence and is referred to as?
Attenuator region
The initial DNA sequence that is transcribed gives rise to an mRNA sequence that has the potential to fold into two mutually exclusive stem-loop structures referred to as?
hairpins
In the presence of excess tryptophan, the mRNA hairpin that is formed behave as a ____ structure, and transcription is almost always terminated prematurely, just beyond the attenuator.
terminator hairpin
If tryptophan is scarce, an alternative mRNA
hairpin referred to as the ______ is formed.
antiterminator hairpin
Biosynthesis of which amino acids uses attenuation as regulatory mechanism?
- tryptophan
- threonine
- histidine
- leucine
- phenylalanine
Are mRNA sequences (or elements) present in the
5’-untranslated region (5’-UTR) upstream from the coding sequences. These elements are capable of binding with small molecule ligands, such as metabolites, whose synthesis or activity is controlled by the genes encoded by the mRNA.
riboswitches
It is the ligand binding site within a riboswitch.
aptamer
It one of the domains of a riboswitch capable of forming the terminator structure.
expression platform
True of False. Eukaryotic gene expression is influenced by chromatin modification.
True
In the interphase nucleus, each chromosome occupies a discrete domain called a _______ and stays separate from other chromosomes.
chromosome territory
Channels between chromosomes contain little or no DNA and are called ____?
interchromosomal domains.
Are nuclear sites at which most RNA polymerase II transcription occurs. These sites also contain the majority of active RNA polymerase and other transcription factors.
transcription factory
True or False. The tight association of DNA with nucleosomes and other chromatin-binding proteins inhibits access of the DNA to the proteins involved in many functions, including transcription.
True
True or False. Acetylation decreases the positive charge on histones, resulting in a reduced affinity of the histone for DNA. In turn, this may assist the formation of open chromatin conformations, which would allow the binding of transcription regulatory proteins to DNA.
True
Histone acetylation is catalyzed by which enzyme? They are recruited to genes by the presence of certain transcription activator proteins that bind to transcription regulatory regions.
histone acetyltransferase enzymes (HATs).
This enzymes reverses the action of HAT by removing acetyl groups from histone tails. They are recruited to genes by the presence of certain repressor proteins on regulatory regions.
histone deacetylases
HDACs
Are large multi-subunit complexes that use the energy of ATP hydrolysis to move and rearrange nucleosomes along the DNA.
Chromatin remodeling complexes
True or False. Repositioned nucleosomes make regions of the chromosome accessible to transcription regulatory proteins, such as transcription activators and RNA polymerase II.
True
Addition or removal of methyl groups to or from bases in DNA. Cytosine is most often involved.
DNA methylation
True or False. A direct relationship exists between the degree of methylation and the degree of expression.
False. Inverse
True or False. Methylation patterns are tissue specific and, once established, are heritable for all cells of that tissue.
True
True or False. Data from in vitro studies suggest that methylation can repress transcription by inhibiting the binding of transcription factors to DNA. Methylated DNA may also recruit repressive chromatin remodeling complexes to gene-regulatory regions.
True
It is a region of DNA that binds one or more proteins that regulate transcription initiation. It is located immediately adjacent to the genes they regulate.
Promoter
Are short nucleotide sequences located within promoters that bind specific regulatory factors.
Promoter elements
A eukaryotic promoter element that determines the accurate initiation of transcription by RNA polymerase II.
core promoter
A eukaryotic promoter element that modulates
the efficiency of basal levels of transcription.
proximal promoter elements
Type of core promoter that specifies transcription initiation at a single specific nucleotide (the transcription start site).
Focused promoters
Type of core promoter that direct initiation from
a number of weak transcription start sites located over a 50- to 100-nucleotide region.
dispersed promoters
True or False. Focused promoters are usually associated with genes whose transcription levels are highly regulated, whereas dispersed promoters are associated with genes that are transcribed constitutively.
True
True or False. Focused promoters are usually found within CG-rich regions, suggesting that chromatin modifications may influence initiation from these promoters.
False. Dispersed promoters
What are the components of focused promoters?
- BRE (TFIIB recognition site)
- TATA (TATA Box)
- Inr (initiator element)
- MTE (motif ten element)
- DPE (downstream promoter element)
True or False. Core-promoter elements are usually located between -40 and +40 nucleotides, relative to the transcription start site, indicated as +1. None of these elements is universal, and a core promoter may contain only one, or several, of these elements.
True
This core promoter element encompasses the transcription start site, from approximately nucleotides -2 to +4, relative to the start site.
Inr element
What is the Inr consensus sequence?
YYANA/TYY where Y is any pyrimidine and N indicates any nucleotide.
Located at approximately -30 relative to the transcription start site and has the consensus sequence TATAA/TAAR (where R indicates any purine nucleotide).
TATA box
Core promoter element usually found in some core promoters at positions either immediately upstream or downstream from the TATA box.
BRE
Is a common proximal-promoter element located about 70 to 80 base pairs upstream from the start site. Mutations on either side of this element have no effect on transcription, whereas mutations within the CAAT sequence dramatically lower the rate of transcription.
CAAT box (consensus sequence: CAAT or CCAAT)
A proximal-promoter element often found in proximal promoter regions and has the consensus sequence GGGCGG. It is located, in one or more copies, at about position -110.
GC Box
A type of cis-acting transcription regulatory element that acts upon eukaryotic genes to repress the level of transcription initiation. They are short DNA sequence elements that affect the rate of transcription initiated from an associated promoter. They often act in tissue- or temporal-specific ways to control gene expression.
silencers
Transcription factors that increase the levels of transcription initiation and are known as?
Activators
Transcription factors that reduce the levels of transcription initiation and are known as?
Repressors
The product of this gene is a protein that binds
to heavy metals such as zinc and cadmium, thereby protecting cells from the toxic effects of high levels of these metals.
The human metallothionein IIA gene (hMTIIA)
General transcription factors assemble at the promoter region in a specific order, forming a structure called?
transcriptional pre initiation complex (PIC); provides a platform for RNA polymerase to recognize and bind to the promoter.
The first step in the formation of a pre-initiation complex is the binding of ____ to the TATA box of the core promoter. It is a multi-subunit complex that contains TBP (TATA Binding Protein) and approximately 13 proteins called TAFs (TBP Associated Factors).
Transcription Factor II D (TFIID)
In this model on how transcription activators and repressors bring about changes to RNA polymerase II transcription, enhancer and silencer elements act as donors that increase the concentrations of important regulatory proteins at gene promoters. By enhancing the rate of PIC assembly or stability, or by accelerating the release of RNA polymerase II from a promoter, transcription activators bound at enhancers may stimulate the rate of transcription initiation.
Recruitment model
In recruitment model, to make contact with promoter-bound factors, activators are thought to interact with other proteins called coactivators to form a complex known as an ______.
Enhanceosomes
This model of transcription activation and repression states that enhancer or repressor looping may relocate a target gene to a nuclear region that is favorable or inhibitory to transcription.
Nuclear relocation model
Modifications of eukaryotic nuclear RNA transcripts prior to translation are called?
posttranscriptional regulation
Regulatory modifications of eukaryotic nuclear RNA transcripts prior to translation are called?
posttranscriptional regulation
Posttranscriptional regulation includes what processes?
- removal of noncoding introns
- precise splicing together of the remaining exons
- the addition of a cap at the mRNA’s 5’ end and a poly-A tail at its 3’-end.
This splicing mechanism can generate different forms of mRNA from identical pre-mRNA molecules, so that expression of one gene can give rise to a number of proteins with similar or different functions.
Alternative splicing
True or Fasle. In thyroid cells, the calcitonin/calcitonin gene-related peptide (CT/CGRP) gene primary transcript is spliced in such a way that the mature mRNA contains the first four exons
only.
True
Refers to the proteins that an organism can make.
proteome
It is caused by the expansion of the trinucleotide
repeat CTG in the 3’-untranslated region of the DMPK gene. In unaffected individuals, the DMPK gene contains between 5 and 35 copies of the CTG repeat sequence, whereas in individuals affected by this disease, the gene contains between 150 and 2000 copies. The severity of the symptoms is directly related to the number of copies of the repeat sequence.
myotonic dystrophy 1
It is caused by an expansion of the repeat sequence CCTG within the first intron of the ZNF9 gene. Affected individuals may have up to 11,000 copies of the repeat sequence in the ZNF9 intron. The
severity of symptoms is not related to the number of repeats.
myotonic dystrophy 2
Defects in the regulation of RNA splicing.
spliceopathies
The ______ of an mRNA is its amount in the cell as determined by a combination of the rate at which the gene is transcribed and the rate at which the mRNA is degraded.
steady-state level
True or False. Most mRNA molecules become unstable in cells that are treated with translation inhibitors.
False. stable
The presence of premature stop codons in the body of an mRNA, as well as premature translation termination, causes rapid degradation of mRNAs.
True
True or False. Many of the ribonucleases and mRNA-binding proteins that affect mRNA stability associate with ribosomes.
True
Are a stretch of ribonucleotides that consist of A and U ribonucleotides. These are usually located in the 3’-untranslated regions of mRNAs that have short, regulated half-lives.
Adenosine-uracil rich elements
True or False. In cells that are not growing or require low levels of gene expression, specific complexes bind to the ARE elements of these mRNA molecules, bringing about shortening of the poly-A tail and rapid mRNA degradation.
True
True or False. Under normal conditions, the levels of p53 protein are extremely high in cells, and the p53 that is present is inactive. When cells suffer DNA damage or metabolic stress, the amount of p53 protein increases dramatically, and p53 becomes an active transcription factor.
False. In normal circumstances levels of p53 protein are extremely low.
Are small protein that tags other proteins for degradation by proteolytic enzymes.
Ubiquitin
In unstressed cells, p53 is bound by another protein called ____.
Mdm2
True of False. When cells are stressed, Mdm2 and p53 become modified by phosphorylation and acetylation, resulting in the release of Mdm2 from p53. As a consequence, p53 proteins become stable, the levels of p53 increase, and the protein is able to act as a transcription factor.
True
First discovered in plants, they are now known to regulate gene expression in the cytoplasm of plants, animals, and fungi by repressing translation and triggering the degradation of mRNAs.
small noncoding RNA (sncRNAs)
First discovered in plants, sncRNAs are now known to regulate gene expression in the cytoplasm of plants, animals, and fungi by repressing translation and triggering the degradation of mRNAs. This form of sequence-specific posttranscriptional regulation is known as _____.
RNA interference (RNAi)
The sncRNAs have been shown to act in the nucleus to alter chromatin structure and bring about repression of transcription. This phenomenon is known as
RNA-induced gene silencing
Methods used to copy or clone DNA are called ____ and often known as “gene splicing”.
Recombinant DNA technology
Are produced by bacteria as a defense mechanism against infection by bacteriophage. They restrict or prevent viral infection by degrading the DNA of invading viruses.
Restriction enzyme
A restriction enzyme recognizes and binds to DNA at a specific nucleotide sequence called a?
recognition sequence or restriction site
A form of symmetry where the nucleotide sequence reads the same on both strands of the DNA when read in the 5’ to 3’ direction.
Palindrome
Enzymes such as EcoRI and HindIII make offset cuts in the DNA strands, thus producing fragments with single-stranded overhanging ends called?
cohesive ends (or “sticky” ends)
AluI and BalI cut both strands at the same nucleotide pair, producing DNA fragments with double-stranded ends called?
blunt-end fragments
It is a DNA molecules that accept DNA fragments and replicate these fragments when vectors are introduced into host cells.
Cloning vectors
To distinguish host cells that have taken up vectors from host cells that have not, the vector contains a _____ (usually an antibiotic resistance gene or a gene that encodes a protein which produces a visible product, such as color or fluorescent light).
selectable marker gene
It is the process by which plasmid cloning vector are introduced to the host cell.
transformation
This transformation technique uses a brief, but high-intensity, pulse of electricity to move DNA into bacterial cells.
electroporation
Plasmid vectors have also been genetically engineered to contain a number of restriction sites for commonly used restriction enzymes
in a region called?
multiple cloning sites
Process of selecting and identifying bacteria containing recombinant plasmids.
“blue-white” screening
Phage vectors are recombinant versions of what bacteriophage?
bacteriophage lambda
These vectors are designed to ensure mRNA expression of a cloned gene with the purpose of producing many copies of the gene’s encoded protein in a host cell.
expression vectors
This bacterium is commonly utilized to introduce genes into plant cells. It infects plant cells and produces tumors called crown galls.
Rhizobium radiobacter
Represent a collection of cloned DNA.
DNA libraries
Consists of many overlapping fragments of the genome, with at least one copy of every DNA sequence in an organism’s genome, which in summary span the entire genome.
Genomic libraries
