Cell Bio Test 2

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Gene expression

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•is acomplex process by which cells selectively direct the synthesis of the manythousands of proteins and RNAs encoded in their genome

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Differentiation

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•cellsbecome highly specialized, ultimately producing an array of muscle, nerve, andblood cells, along with the hundreds of other cell types seen

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housekeeping proteins

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•common to all the cells.

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example of housekeeping proteins ?

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–structural proteins of chromosomes,RNA polymerases, DNA repair enzymes, ribosomal proteins, enzymes involved inbasic metabolic processes, and many of the proteins that form the cytoskeleton.

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An example of cells changing their gene expression is ?

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the steroid cortisol (Released by theadrenal gland during periods

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Regulation of gene expression :

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•(1) controlling when and how oftena given gene is transcribed

••(2) controlling how an RNAtranscript is spliced or processed

••(3) selecting which mRNAs areexported from the nucleus to the cytosol

••(4) regulating how quickly certainmRNA molecules are degraded

••(5) selecting which mRNAs aretranslated into protein

••(6) regulating how rapidly specificproteins are destroyed after they have been made

••(7) regulating protein activity.

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gene expression:

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The promoters of both bacterial and eukaryotic genes include ?

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a transcription initiation site, plus asequence that extends upstream from the initiation site (required for the RNApol to recognize the promoter)

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The Promoter region of a gene binds to what enzyme in transcriptional control of gene expression?

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enzyme RNA polymerase

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Sigma factor is only used in?

(Bacteria or eukaryotes)

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Bacteria

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The general transcription factors are used only in ?

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eukaryotes

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Regulatory DNA sequences:

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-used to switch the gene on or off.

-predominate in bacteria.

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Regulatory DNA sequences in prokayotes are as (short or long) ?

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short; 10 nucleotide pairs

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Regulatory DNA sequences in eukaryotes are how long or short?

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-very long (sometimes spanning more than 10,000 nucleotide pairs)

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Regulatory DNA sequences in eukaryotes ?

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integrates information from a variety of signals that dictates how often transcription of the gene is initiated.

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Regulatory DNA sequences are recognized by ?

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transcription regulators.

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The binding of a transcription regulator to a regulatory DNA sequence acts as ?

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the switch to control transcription

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Different DNA-binding proteins recognize different ?

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nucleotide sequences

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E.coli have five genes which code for enzymes that make the ?

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AA tryptophan

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a unit made up of linked genes that is thought to regulate other genes responsible for protein synthesis is called ?

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an operon

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Are Operons found mostly in eukaryotes ?

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No they are rare in eukaryotes

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transcriptional activator proteins:

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•bind near promoters and contact theRNA polymerase to help it initiate transcription

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transcriptional repressor protein:

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in its active form, it switches genesoff, or represses them.

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tryptophan repressor:

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therepressor can bind to DNA only if it has also bound several molecules oftryptophan.

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Thetryptophan repressor is an allosteric meaning ?

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thebinding of tryptophan causes a change in its structure so that the protein canbind to the operator sequence

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In E.coli the Lac operon encodes ?

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proteins required to import and digestlactose

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Lactose is controlled by both ?

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both theLac repressor and the CAP activator

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If Lactose present ........

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no repressor, but if glucose is present cAMP and Cap not made

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If there is no glucose.....

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cAMP made, which activates CAP to switch on genes

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Lac repressor shuts off...

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the operon in the absence of lactose

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The operon is highly expressed onlywhen two conditions are met:

what are they?

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glucose must be absent and lactose must be present

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Transcriptional Regulation inEukaryotes use ?

They also ....

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-activators and repressors

- attract proteins that modify chromatinstructure

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Enhancers:

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DNAsites where gene activators bind

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What happens to the DNA between the enhancer and the promoter?

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loops out to allow eukaryotic activatorproteins to influence directly events that takeplace at the promoter

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Repressorsproteins:

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preventtranscription complex from assembling

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Mediator:

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- linksthe distantly bound transcription regulators to proteins at the promoter

- aidsthe assembly of the general transcription factors and RNA polymerase to form alarge transcriptioncomplex atthe promoter.

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eukaryotic DNA is packed into ?

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nucleosomes

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Nucleosomes can inhibit transcription ifthey are ?

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-positioned over a promoter

-physically block the assembly of thegeneral transcription factors or RNA polymerase

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RNA Polymerase is moving from ?

( what direction ?)

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5 to 3

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If trytophan is low that means the operon is ( on or off) ?

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on

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If glucose is absent but lactose is present that means the operon is ?

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on

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The lac operon is only on when what is present and what is absent ?

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no glucose

only lactose

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What kind of sites are needed to start transcription in E.coli ?

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CAP binding site and RNA polymerase binding site ( promoter)

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To start transcription in eukaryotes you need ?

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GTF, RNA POL II , MEDIATOR,

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Histone deacetylases ( HDACs)

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enzymes that remove acetyl groups from histone tails

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histone acetyltransfarases (HATS)

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promote attachment of acetyl groups to lysines on tail of histones

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Cell memory is required to ?

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Create organized tissues and for maintenance of stably differentiated cells

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combinatorial control :

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the way that groups of transcription regulators work to determine expression of gene

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Cortisol receptor complex binding to a regulatory sequence in DNA of each gene is important in ?

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regulating genes

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When cortisol receptor is inactive then that means that the gene expressed is at a high or low level ?

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low

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When cortisol receptor is active then that means that the gene expressed is at a high or low level ?

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high

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transcription regulators can cause differentiated cells to de-differentiate meaning ?

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it gives cells other options to turn into a cell for another part of the body

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Pluripotent stem (iPS) cells:

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cells that look and behave like the pluripotent ES cells derived from embryos

* can be turned into diff cells

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(iPS) cells are induced into where ?

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the nucleus

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In what type of animals can the Ey gene be expressed ?

In cells that would normally give rise to ? what body part ?

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fruit fly : drosphilia

a leg but instead gives rise to an eye

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How do cells remember what they are supposed to be? ( hint 3 types of ways)

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- feedback loops

-DNA methylation

-histone modifications

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What is the importance of epigentic memory ?

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helps understand how cells operate, how they malfunction in disease, maintain cell identity, record , transmitting patterns of gene expression

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Postive feedback loops is an example of ?

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epigenetic memory

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Describe Postive feedback loops

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“self-sustaining”circuits of gene expression that allow a cell to commit to a particular fateand then to transmit that information to its progeny

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DNA Methylation

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•turns off genes by attractingproteins that bind to methylated cytosines and block gene transcription

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Where does DNA Methylation occur ?

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•on cytosine bases

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Invertebrates, this modification ( DNA Methylation) is confined to ?

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CpGislands

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Histone Modifications:

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Whena cell replicates its DNA, each daughter double helix receives half of itsparent’shistone proteins

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When do Post-transcriptional Controls operate ?

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•after transcription has begun

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Examples of posttranscriptional Controls are ?

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–Splicing

-methylation, acetylation, ubiquitin

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By blocking—or exposing—theribosome-binding sequence, the bacterium can either ?

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•inhibit—orpromote—the translation of an mRNA

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If translation repressor protein is on then that means ?

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no protein can be made

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In eukaryotes repressor proteins can inhibit translation initiation by binding to ?

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specific nucleotide sequences inthe 5’ untranslated region of the mRNA, preventing the ribosome from findingthe first AUGD

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Three major types of regulatory RNAs:

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–microRNAs(miRNAs)

–smallinterfering RNAs (siRNAs)

- long noncoding RNAs (lncRNAs)

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Regulatory mRNAs Play important roles in ?

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•regulating gene expression

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microRNA (miRNAs) :

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•Base-pairwith specific mRNAs••Reducestability of mRNA ••Reducetranslation of mRNA into protein. ••Inhumans, miRNAs are thought to regulate the expression of at least one-third ofall protein- coding genes••miRNAtranscript undergoes a special type of processing to yield the mature,functional miRNA molecule••Onlyabout 22 nucleotides in length���?T��

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Mature miRNA is packaged with proteins toform an?

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•RNA-inducedsilencing complex (RISC)

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Destruction of the mRNA releases ?

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RISC

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a single miRNA can eliminate

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many mRNA

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what two features of miRNAs make themespecially useful regulators of gene expression?

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–a single miRNA can inhibit thetranscription of a whole set of different mRNAs so long as all the mRNAs carrya common sequence

–a gene that encodes an miRNA occupiesrelatively little space in the genome compared with one that encodes atranscription regulator.

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Small interfering RNAs (siRNAs)

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Used to eliminate “foreign” RNAmolecules

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Xist is an example of ?

It is a key player in ?

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Long Noncoding RNAs (lncRNAs)

is a key player in Xinactivation.

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Horizontal gene transfer:

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•A piece of DNA can be transferredfrom the genome of one cell to that of another—even to that of another species.

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Exon shuffling:

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Two or more existing genes can be brokenand rejoined to make a hybrid gene

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Mobile genetic elements:

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-Specialized DNA sequences that can movefrom one chromosomal location to another can alter the activity or regulationof a gene;

- they can also promote geneduplication, exon shuffling, and other genome rearrangements.

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Horizontal gene transfer:

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-A piece of DNA can be transferredfrom the genome of one cell to that of another—even to that of another species.

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germ-line cells:

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•(eggsand sperm)—contain half the number of chromosomes•

•Whentwo germ cells come together during fertilization, they form a fertilized eggor zygote -contains a full set of chromosomes

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•somatic cell:

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—effect the individual but will not be transmitted to the organism’s offspring.

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Changesthat affect a single nucleotide pair are called ?

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point mutations

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•Atmany sites in the genome, a point mutation has no effect on the ?

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organism

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A small number of people are resistant tomalaria because of ?

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point mutation

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Plasmodium vivax :

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malaria parasite

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People who retain the ability to digestmilk as adults contain?

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a point mutation in the regulatory DNA ofthe lactase gene

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Misalignment during recombination causes ?

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unequal exchange of genetic information}

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Subsequent unequal crossovers causes ?

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crossovers can readily add extra copiesto the duplicated set by the same mechanism.

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the blood of adult mammals and most othervertebrates is composed of four globin chains of two distinct types ?

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α globin and β globin.

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The frog genusXenopus is an example of ?

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Whole Genome Duplication

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•conjugation :

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exchange DNA with a sex pilus.

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An extreme example of genome compressionis the ?

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pufferfishFugu rubripes,whose genome is one-tenth the size of mammalian genomes, largely because of thesmall size of introns

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One particular gene that is conserved inall living species is ?

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thegene that codes for the ribosomal RNA (rRNA) of the small ribosomal subunit

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Two families of transposons ?

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•DNA transposons •

•Retrotransposons

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transposons

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- rearrange the DNA sequences of the genome

-•Transposase can integrate new exoninto regions of a new location or chromosome

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How do transposons move?

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DNA mobile genetic elements

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DNA mobile genetic elements

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•typicallyencodes a specialized enzyme, called a transposase,that mediates its movement.

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Threetypes of bacterial DNA-only transposons :

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IS3, Tn3, Tn10

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Inbacteria, the most common mobile genetic elements are the ?

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DNA-onlytransposons

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• Retroviruses are thought to have derivedfrom a ______________ thatacquired additional genes encoding the coat proteins and other proteinsrequired to make a virus particle.

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retrotransposon

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plasma membrane :

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aprotein-studded, thin fatty film.

-Involved in cell communication,import and export of molecules and cell growth and motility

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nutrientsmust pass _________ across the plasma membrane, and waste products must pass _____ .

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inward; out

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Lipid Bilayer

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serves as a permeability barrier to mostwater-soluble molecules.

- are composed of lipids and proteins

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each lipid has a hydrophilic (“water-loving”) ______ ?

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head

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hydrophobic(“water-fearing”) ____ ?

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tail

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The most abundant lipids in cellmembranes are the ?

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phospholipids,

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Amphipathic:

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both hydrophilic and hydrophobic parts

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Hydrophilic molecules:

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readily dissolve in water

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Hydrophobic Molecules

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insoluble in water

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•The hydrophilic heads face water onboth surfaces of the bilayer; but the hydrophobic tails are all shielded fromwater, as they lie next to one another in the interior ? (true or false)

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true

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the only way a amphipathic sheetcan avoid having free edges is to

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bend and seal

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how fluid a lipid bilayer is depends onits ?

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phospholipid composition and nature ofthe hydrocarbon tails

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the closer and more regular the packing of the tails, the ( more or less) fluid the bilayer will be ?

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less

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shorter chain lengthcauses ?

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increases the fluidity of the bilayer.

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The hydrocarbon tail with no double bondshas a full complement of hydrogen atoms and is said to be ?

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•saturated.

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hydrocarbon tail that harbors a doublebond does not contain the maximum number of hydrogen atoms is said to be ?

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unsaturated

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•lipidbilayers that contain a large proportion of unsaturated hydrocarbon tails are ( less or more) fluid than those with lower proportions

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more

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Each double bond in an unsaturated tailcreates a small ?

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kink in the tail

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tails are ? ( polar or non-polar )

heads are ?

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non-polar

polar

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What does cholesterol do to the cell membrane ?

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stiffen the bilayer, makes it less fluid