bio 2 gene regulation

34- all transciprtions factors are________(noun)

all transcirption factors are proteins

promoters, where are they located and what do they do

(In genetics, a promoter is a region of DNA that initiates transcription of a particular gene. Promoters are located near the genes they transcribe, on the same strand and upstream on the DNA )Promoters are DNA sequences that act like switches that turn genes on/off Promoters are located upstream of the structural gene. DNA bases (nucleotides) that indicate the presence of a promoter TATAATT box Termination sequences tell the enzyme where to stop transcription of a gene....when we say promoter is up stream(our oritnetaion always starts with the strctural gene, so upstream is to 5 prime and downstream is 3rd prime...the promoter is where the RNA polymerase is where mRNA is makes/transcribes

lactose(which is a prokaryote)

(disaccharide )gal+glc, glucose breaks down easily once cleaved by the lactose enzymes...Lactose is a disaccharide derived from the condensation of galactose and glucose(monosaccharides)...The lactose operon of E. coli consists of three structural genes under coordinate control (Figure 26.17). Transcription commences at a promoter (lacP) to the left of lacZ and transcribes a 5,200 nucleotide messenger RNA molecule (mRNA), ending at a terminator beyond lacA. The three genes on the polygenic (polycistronic) messenger are separately translated and the products are beta-galactosidase (which cleaves lactose into galactose and glucose)

39-40 gene accesibility

....

slide 29, 30, 3 featyres found in most promoters of eukaryotes

3 features found in most promoters of eukaryotes Transcriptional start site Where transcription begins With TATA box forms core promoter By itself results in low level basal transcription TATA box 5' - TATAAAA - 3' 25 base pairs upstream from transcriptional start site Determines precise starting point for transcription Response elements Recognized by regulatory proteins that control initiation of transcription Enhancers and silencers

effector molecules, transcription factors, slide 14..whats a domain

=chemical, =proteins...In biochemistry, an effector molecule is usually a small molecule that selectively binds to a protein and regulates its biological activity. In this manner, effector molecules act as ligands that can increase or decrease enzyme activity, gene expression, or cell signalling...regulatory transcription factors have two domains one to attached to DNA other to have an effector bind to it

35- regulatory sequiences, activators and repressors bind to what,what do they do, and do they bind directly to RNA polymerase 2...THINK genes are silences and enhancers while activators and repressors are things that bind to genes aka proteins

Activators bind to enhancers Repressors bind to silencers Regulate rate of transcription of a nearby gene Most do not bind directly to RNA polymerase II

what does the repessor protein prevent?

By binding to the operator, the repressor protein prevents the RNA polymerase from creating messenger RNA.

Gene regulation

Gene regulation refers to the ability of cells to control their level of gene expression Structural genes are regulated so proteins are only produced at certain times and in specific amount Constitutive genes are unregulated and have essentially constant levels of expression

slide 32

RNA polymerase 2 cant work on its own needs these five GTFs and in addition to this there is a large mediator protein complex(called sumply the mediator)

what is allolactose?

The operon is under the control of the adjacent lacI gene, encoding the lactose repressor. The repressor is a regulatory gene. In the absence of allolactose, the inducer of the lac operon, the repressor tetramer binds to the lac operator (lacO) and prevents RNA polymerase from transcribing the operon. However, when allolactose is present it binds to the repressor this prevents repressor from binding to lacO and permits RNA polymerase to bind to lacP and to initiate transcription.

situation lactose high and glucosehigh, situation 2- glucose low lactose high...operon on or off, CAP? how baout if lactose is low

When both lactose and glucose are high, the lac operon is shut off Glucose uptake causes cAMP levels to drop CAP does not activate transcription Bacterium uses one sugar at a time, glucose When lactose is high and glucose is low, the lac operon is turned on Allolactose levels rise and prevent lac repressor from binding to operator CAP is bound to the CAP site Bacterium uses lactose...When lactose is low and glucose is high or low, the lac operon is shut off Under low lactose conditions, lac repressor prevents transcription of lac operon

negative control(one way of negative control is repressor inhibit transcription and one of positive control is activators slide 15, positive control

activator proteins and repressor proteins learn them, would would make it go faster and one will stop transcription

allactose is an intermediate step she showed on board slide 23

allolactose is a small effecotr molecule...lac repressor protein is usually sitting on the operator(regulatory sequenc) but when allolactose is around and cell needs to metabolize lactose so it binds to..blahblahblah...Technically, allolactose is the inducer. e. coli converts a small amount of lactose to allolactose and this then binds to the repressor....When the lac repressor protein is bound to the promotor on the lacZYA operator, transcription of the three lac genes is inhibited. Active transcription requires the presence of an inducer molecule such as the lactose derivative allolactose. (Allolactose is made from lactose by an enzyme.) Only when an inducer is bound to the repressor molecule does a conformational change occur, and the DNA is released from the repressor molecule. This permits RNA polymerase to bind and transcribe the lac genes. The repressor protein therefore has two binding sites, one for the lac operator (a sequence overlapping the promoter) and another for the inducer molecule (allolactose). The presence of allolactose signals the cell that lactose is available to be metabolized. As the lactose is metabolized, both lactose and allolactose eventually are used up and no longer induce the operon....the allolactose binds to the repressor in 4 spots and this causes a conformational change making the lac repressor inactive

gene vs protein (how do you know the difference in print)

gene always italicized and small letter, a protein it will be capital letters and not italicized

wikipedia take on repressors related to lactose and lactase

gene is essentially turned off. There is no lactose to inhibit the repressor, so the repressor binds to the operator, which obstructs the RNA polymerase from binding to the promoter and making lactase. Bottom: The gene is turned on. Lactose is inhibiting the repressor, allowing the RNA polymerase to bind with the promoter, and express the genes, which synthesize lactase. Eventually, the lactase will digest all of the lactose, until there is none to bind to the repressor. The repressor will then bind to the operator, stopping the manufacture of lactase.

genome vs proteomes

genomes is our 46 chromosomes, the proteome is proteins expressed in different cells, conundurom of gene regulation :if we have same 46 chromomes why do we have differentiation between cells and the answer is gene regulation(some only used durign development and then never again)(liver and intestinal cells will have more enzymes released like liver enzymes and so on all genes being transcribed)...The proteome is the entire set of proteins expressed by a genome, cell, tissue or organism at a certain time. More specifically, it is the set of expressed proteins in a given type of cells or an organism at a given time under defined conditions.

differnt ways and components for eukarytoes, eukaryotic gene expression is levels and levels above that....what is the major difference?

how gene is arranged, there are exons and...one gene with several exons and introns, and these are the things that provide cell with ability to produce different kinds of proteins(discovery within past ten years)

operon, also how about the CAP site and operator, and how about the lacI gene?

in this operon example slide 18 we have the three genes and they are all one long sequence so that when transcription happens we never just transcribe one of them, instea transcription happens to operons makes sense...7 genes that are metabolically related to each other...WIKI-The lac operon consists of three structural genes, and a promoter, a terminator, regulator, and an operator. The three structural genes are: lacZ, lacY, and lacA......lacO - operator - provides binding site for repressor protein CAP site - activator protein binding site...lacI gene - codes for lac repressor Considered a regulatory gene since its sole function is to regulate other gene's expression Has its own promoter (not part of lac operon) The lac repressor results in negative control of the lac operon.

inducible

inducible operon or inducible promoter called this because in the presence of the metabolites(lactose) the operon gets turned on or the promoter gets turned on(the promoter is allowed to transcribe the gene for the cell to metabolize lactose)..inducible is usally in off position until metabolite(big word that can mean many things, and it is lactose itself is the metabolite

regulator protein binds to an operon, explain what type of control it may be and the condition of the operon

negative control- lac repressor, if bound operon is off if not operon is on...positive control- CRP protein, if bound operon is on if not operon is off

genes are regulated by what kinds of control, also what are these(also genes?)

negative, positive(inducible )...Gene regulatory proteins are proteins that recognize and bind to specific short stretches of double-helical DNA and thereby determine which of the thousands of genes in a cell will be transcribed. The mode of control may be negative or positive. By definition, negative control occurs when a repressor protein is involved, that is when a regulator protein is active, DNA-binding repressor prevents RNA polymerase from binding and turning the genes off. Positive control is the exact opposite of negative control: instead of interfering with the initiation of transcription, it enhances transcription. Positive control occurs when an active, DNA-binding regulatory protein binds to DNA and assists the binding of RNA polymerase and therefore facilitates transcription. Such regulator proteins are called transcriptional activators.

cyclic aMP and CAP protein use these two to describe a situation of positive control(catabolite, proteins etc)

once get together allows polymerase to be a promoter...(i believe)...An example of positive control When cAMP binds to CAP, complex binds to CAP site near lac promoter Resulting bend in DNA enhances RNA polymerase binding which increases transcription...Catabolite repression - glucose, a catabolite, represses lac operon Small effector molecule, cAMP, binds to activator protein called catabolite activator protein (CAP) or cAMP receptor protein (CRP) Operon is turned off when CAP is not bound Glucose inhibits production of cAMP and so prevents binding of CAP to DNA

allactose

repressor always on and being made but the allalactose binds to repressor

Eukaryotes gene regulation occurs where?

slide 12 Chromatin(relaxed DNA form which means the genes are accesible for transcription) Transcriptional regulation common RNA processing Translation Post-translation

talking about cap sites and lacO and then lacI, promoters, ...normally the repressor is always on making the protein which will bind to cap...when environment is deficient of glucose then lactose becomes available,allolactose binds to represor protein and now repressor can no longer bind at lacO and now they are makign more beta-gal and more of

so you see everything required for lactose metabolism is on one row of genes including repressors and activators

constitutive gene

structural genes that are always on but dont seem to be regulated at all and they are usually called housekeeping genes like ribosomal, and tubulin genes...so no matter the environment this gene is continued to be transcribed constantly

when lactose is present it both is no expression is inducible and there is positive control cuz CAP protein binds and allows RNA polymerase crank out genes, crank of conscription

this is a positive component know the negative ones as well

slide 45

this thing can produce one of two proteins(one may be in nervous system while oteher is in muscle) this is what we call alternative splicing(this phenom is extremely new not until 2003 when sequence of human genome publish and completed and we have 25,000 genes, same number of genes in rats....1 gene has several polypeptides

transciption factros have how many sites? know slide 16 and 17

two, one needs to bind dna and sometimes have a domain that can combin an effector molecule

slide 47

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three major classes of gene

Structural genes code for proteins Regulatory genes are responsible for the expression of structural genes Promoters Terminators Variable Sequences (do not code for proteins nor have a role in gene regulation, they just seem to be sequences in genome that do not have a function that we know of, so they can accumulate diseases and not affect us)...I think she said structural and regulatory genes are all the same for us all. Short Tandem Repeats (STR's)

transciption factorsslide 42 name four different motifs

Transcription factor proteins contain domains with specific functions Motif - domains or portions of domains with similar structures in different proteins α helix important in recognition of DNA double helix Zinc fingers can recognize DNA sequences within the major groove ....helix turned helix means they neatly fit to either repress or activate....zinc fingers(her favorite) works with some of transcription factors

shold be on earlier slide

transcription, post transciptional, translation and post translation