Reading...
Play button
Play button
Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
76 Cards in this Set
- Front
- Back
|
What is a gene?
|
a segment of DNA including its structure (double helix) and code
|
|
|
How is gene expression regulated?
|
transcription and mRNA splicing
|
|
|
What is the process of gene expression?
|
genes from DNA are transcribed into RNA which is translated into proteins
|
|
|
how is the rate of gene expression altered? (conceptually)
|
gene transcription and/or translation is increased/decreased to alter the rate, so that 1 gene might only produce one RNA or multiple RNA's and those RNA's might produce a single protein or multiple proteins
|
|
|
how does a cell determine what proteins to produce?
|
external stimuli like bacteria, toxins and virals stimulate the cell which triggers DNA to create RNA to create proteins which do things
|
|
|
what are the six levels of control a cell exercises on gene expression?
|
transcriptional conrol, RNA processing control, RNA transport and localization control, translation control, mRNA degradation control, protein activity control
|
|
|
in general, how is gene expression regulated?
|
not all genes are expressed at the same time or in the same tissues or cell types, and many can be regulated
|
|
|
what are receptor mediated signal transduction pathways? Name an example
|
the process by which a cell converts one type of signal or stimulus into another, generally via biochemical reactions in the cell that are rapid and generally evoke a protein formation for response, an example is the immune response of a cell to bacterial LPS where the LPS binds to a receptor on the external cell membrane, triggering a response via proteins in the cytoplasm of the cell which also activates the immune response genes in the nucleus
|
|
|
*How does the shape of DNA (double helix) affect gene regulation?
|
The physical structure makes minor grooves harder to access than major grooves, which are different directionally and chemically, which helps to turn regulation on and off
|
|
|
what is mRNA?
|
a series of nucleic acids (5' to 3') that mimics the structure of DNA (5' to 3') opposing the template strand (3' to 5') via transcription
|
|
|
What is the nucleic acid code?
|
Genes become template strads (3' to 5') that is transcribed into mRNA (5' to 3') which is then read and translated in 3 acid subunits, each of which is called a codon and that codes for a specific amino acid, the order and interaction of creates proteins
|
|
|
how do you use a codon dictionary?
|
identify the first unit of the codon on the left row the second unit in the top column, and find the data cell, in the data cell, identify the third unit of the codon and identify the amino acid associated with that codon
|
|
|
what are the types of DNA mutation?
|
insertion/deletion & single point: changing of a single nucleotide can result in missense (change of an amino acid), nonsense (change to a stop codon), or silent (change that doesn't affect the amino acid)
|
|
|
what does a missense mutation do?
|
cause a change in a single amino acid
|
|
|
what does a nonsense mutation do?
|
change an amino acid to a stop codon, truncating the protein
|
|
|
what does a silent mutation do?
|
nothing, but may be because of polymorphisms where the change occurs at a portion of the DNA that isn't part of the gene or may be a silent change
|
|
|
what does an insertion or deletion mutation do?
|
cause a frameshift; a shift in reading and formation of proteins, which likely will not fold properly and won't function,
|
|
|
what does a codon insertion/deletion mutation do?
|
may or may not affect since the frame shift only affects a particular area, and in general, one amino acid
|
|
|
what is transcription?
|
mRNA's are created from the template strand of DNA by RNApolymerases in the nucleus, then most migrate to the cytoplasm for translation into proteins, in most cases proteins and RNA's are proportional. DNA is not directly involved in protein synthesis
|
|
|
What proteins are necessary for transcription in eukaryotes?
|
Three RNA polymerases (I - rRNA, II - mRNA, snRNA, III - 5s rRNA, tRNA) made up of 2 large subunits and 10-15 smaller subunits
|
|
|
What are the three steps in transcription?
|
initiation, elongation, termination
|
|
|
How does transcription initiate?
|
The DNA template strand (the opposing strand is the partner strand) is transcribed when RNA polymerase binds to the strand and recognizes a promotor sequence and DNA is unwound locally.
|
|
|
mRNA is what direction?
|
5' to 3'
|
|
|
DNA template strand is what direction?
|
3' to 5'
|
|
|
DNA partner strand is what direction?
|
5' to 3'
|
|
|
What happens with template binding?
|
RNA polymerase recognizes a promotor sequence of the DNA template strands and initiates transcription
|
|
|
What happens with the promotor during mRNA transcription initiation?
|
It acts as a docking station for RNA polymerase, but is not transcribed itself.
|
|
|
Which direction does transcription occur on the DNA strand?
|
Either direction (there are 5' to 3' directions on both strands) but the directionality will net different end products (mRNA's) since the codes will be opposing
|
|
|
RNA polymerase reads which direction?
|
3' to 5'
|
|
|
mRNA is formed which direction?
|
5' to 3'
|
|
|
what starts mRNA elongation?
|
sigma unit dissassociates
|
|
|
how much DNA does RNA polymerase cover and unwind?
|
It covers ~ 30bp and unwinds 12-13bp at a time
|
|
|
what part of DNA does mRNA look like?
|
partner strand
|
|
|
what kind of mRNA's do eukaryotes and prokaryotes have?
|
eukaryotes = monocistronic and prokaryotes = polycistronic
|
|
|
what does polycistronic mean?
|
having multiple genes clustered onto one long RNA, as seen in bacteria
|
|
|
How does termination of mRNA transcription occur?
|
RNA polymerase recognizes a specific nucleotide sequence that is ~40nt long which signals termination
|
|
|
What happens with exons?
|
they are encoded!
|
|
|
what are the RNA modifications (name in order of occurrence)?
|
5' cap, polyA tail, splicing
|
|
|
what occurs during splicing?
|
exons are encoded and expressed while introns (located between exons within gDNA and pre-mRNA) are intervening and cut out of the mRNA (not expressed)
|
|
|
what is a 5' cap?
|
a guanosine nucleotide that is methylated on the 7 position by methyl transferase in vitro post capping and provides stability by resisting 5' exonucleases
|
|
|
what is a polyA tail?
|
a series of adenosines that add stability to mRNA by being shortened by enzymatic degradation rather than the degradation occuring to the RNA and it is added after the AAUAAA consensus is cleaved off the 3' end of the mRNA
|
|
|
what is the consensus sequence?
|
AAUAAA
|
|
|
what occurs with the introns removed during splicing?
|
degraded
|
|
|
what are introns?
|
parts of pre-mRNA that are intervening (not expressed) that may be up to 20k bp long, often begin with GU and end with AG, and are recognized by the splicesome
|
|
|
what does the splicesome do?
|
recognizes and removes introns from pre-mRNA
|
|
|
Do all pre-mRNA's have introns?
|
not necessarily
|
|
|
what is a splicesome?
|
a large structure with man subunitis including protein and sall nuclear RNA's (snRNA's) which are 100-200 nt or less and complexed with proteins to from 'small nuclear ribonucleoproteins' (snRNPs or snurps) and are only in the nucleus and rich in uracil (and named for uracil as U1, U2, etc)
|
|
|
how does spicing occur?
|
a splicesome recognizes an intron donor site and an exon acceptor site and attaches an A-OH to the 3' end of the intron, which causes a lariat to form, which is degraded while the remaining exons bind to each other due to a nucleophilic band (the A-OH remain with the lariat)
|
|
|
what happens if alternative mRNA splicing occurs?
|
different proteins are created.
|
|
|
why would an mRNA have alternative splicing?
|
one gene = potentially multiple proteins, with a greater number of exons resulting in a greater number of possibilities, but mutant versions may also be caused by disease
|
|
|
how is a genome defined?
|
the individual genes transcribed in one direction but both strands are transcribed
|
|
|
how is gene expression regulated?
|
promoters, enhancers, chromatin
|
|
|
what are bacterial promoters?
|
TATAAT (-10 position), and TTGACA (-35 position)
|
|
|
what are eukaryotic promoters?
|
TATA box (-30 position)
|
|
|
what do differences in promoter sequences cause?
|
differences in transcription levels (generally more promotores result in more expression)
|
|
|
how does E Coli use sigma subunits?
|
different subunits recognize different promoters
|
|
|
in simplified eukarytoic transcription, what are trans factors?
|
trans means across from; proteins that are transcription factors that facilitate the initial binding of RNA polymerase II, but are not necessarily produced on the same gene
|
|
|
how are trans factors named?
|
TF = transcription factor, II = RNA polymerase II, and A,B, C = order discovered in
|
|
|
what does TFIID do?
|
Binds to the TATA Box, also known as TBP (TATA binding protein)
|
|
|
what is TBP?
|
TATA binding protein, also known at TFIID, a 10 subunit transcription factor that binds to the TATA box promotor sequence to promote transcription
|
|
|
in simplified eukaryotic transciption, what are cis factors?
|
cis means next to: the DNA sequences that proteins act on to regulate gene expression through the influence of transcription from specific genes and include the TATA box (-30, nonspecific promotor), CAAT box (-80, common promotor sequence, GGCCAATCT), and others, including enhancers
|
|
|
what are TATA boxes?
|
nonspecific promoters at -30nt
|
|
|
what are CAAT boxes?
|
common promoter at -80 with the sequence GGCCAATCT
|
|
|
what are enhancers?
|
parts of the DNA that are 'distant' to the gene, they are not fixed near the transcriptional start site, can be 5' or 3' or even within the gene, but are usually long distance from the gene (50kb), they are bound by transcription factors that alter the chromatin structure (bending or looping) and can be inverted and still function (DNA bends and twists to moung promoters into RNA polymerase II
|
|
|
what do combinations of cis factors do?
|
define transcriptions, with CAAT maximizing transcription
|
|
|
how many promoters to genes have?
|
most have more than one
|
|
|
what is a repressor?
|
DNA binding protein regulates expression of one or more genes by decreasing the rate of transcription
|
|
|
what do transcription factors do?
|
control where, when and at what rate genese are expressed (not part of the RNA polymerase which initiates and executes transcription) and usually possess a DNA binding domain and a trans-activating domain that usually binds other proteins (other transcription factors or RNA polymerase)
|
|
|
what are the structures of transcription factors?
|
large families of proteins that may be tissue specific (enabling tissues specific gene regulation) and include the chemical structures of proteins: helix-turn-helix, zinc fingers, basic leucine zipper
|
|
|
are promoters additive?
|
not necessarily
|
|
|
how do repressors work?
|
by competitive DNA binding, or masking the activation surface, and direct interaction with the general transcription factors
|
|
|
what is chromatin?
|
a genomic DNA complexed with proteins and formed of nucleosomes (which consis to an octamer of 4 different histone proteins complexes with ~150bp of DNA), it is considered condensed and inaccessible for transcription, so histones must be acetylated to disrupt the chromatin structure and make it accessible for transcription
|
|
|
what are steroid hormones?
|
proteins that enter a cell through the plama membrane, bind cytoplasmic hormone receptor proteins (bind to hormone responsive elements: HREs, which can be 100s of bp upstream, or 5', of the gene or within, overlapping promotors/enhancers) creating complexes that translocate into the nucleus and activate transcription of specific genes
|
|
|
what do hormones do (conceptually)?
|
hormones trigger gene expression
|
|
|
what else influences gene expression?
|
environment
|
|
|
what is the future clinical relevance for gene expression?
|
novel gene expression profiles defines for a variety of human tumor types and infection models, PCR or protein based assays (ELISAs) are likely to be developed for diagnosing specific infections or disease states, understand how genes are regulated will greatly help you understand the signficance of these assays
|
