GENETICS EXAM 4, GENETICS EXAM 3, GENETICS EXAM 2, GENETICS EXAM 1

activator

A protein that binds to DNA and stimulates transcription of a specific gene. aka Positive regulator

centromeres

Region around ____is constitutive heterochromatin

lacIs

Special partial loss of function mutation in lacI creates superrepressor b/c binds DNa but cannot bind inducer

Poly A binding protein

The circularization of mRNAs through the association of initiation factors at the 5′ cap &_____________ at the 3′ poly-A tail is basis of a mechanism for regulating translational initiation through control of poly-A tail length. -------Longer tails attract PABP more efficiently than shorter tails do, and thus the longer the poly-A tail, the more translation

Lac permease

involved in the transport of lactose into cell

TATA box

A DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex. --, consisting of roughly seven nucleotides of the sequence T-A-T-A-(A or T)-A-(A or T), located just upstream of the transcription initiation site. ----attracts RNA polymerase only weakly on its own (without an enhancer), the TATA box allows a low, so-called basal level of transcription.

dominant negative mutation

A heterozygote produces a nonfunctional altered protein that also prevents the normal gene product from functioning ---Examples: 1. A mutation in a transcription factor that removes the activation domain, but still contains the DNA binding domain. This product can then block the wild-type transcription factor from binding the DNA site leading to reduced levels of gene activation

Repressor

A protein that binds to an operator and physically blocks RNA polymerase from binding to a promoter site -aka negative regulator

allosteric protein

A protein that undergoes a reversible change in conformation when bound to another molecule allolactose in lac operon

enhancer

A segment of eukaryotic DNA containing multiple control elements, usually located far from the gene whose transcription it regulates. --Binding of proteins to enhancers can augment or repress basal levels of transcription ------ may be located either 5′ or 3′ to the transcription start site --may have multiple binding sites for different transcription factors.

plasmid

A small ring of DNA that carries accessory genes separate from those of the bacterial chromosome --some bacteria carry genes not needed under normal conditions in smaller circles of double- stranded DNA known as__________

siRNA small-interfering RNA

A type of small double-stranded regulatory RNA that becomes part of a complex able to cleave and destroy single-stranded RNA with a complementary sequence.

Chromatin (nucleosome) remodeling proteins

Able to add or remove histones from DNA

Epigenetic

B/c DNA methylation affects gene transcription, & b/c methylation patterns are copied during DNA replication, DNA methylation can alter gene expression heritably without changing the base sequence of DNA—and thus causes a __________ phenomenon.

loops

B/c enhancers may be far away from promoters, the DNA btw enhancer & promoter _______ as a consequence of interactions between basal factors, Mediator, and activators (or repressors) -----Long stretches of DNA can be quite flexible explaining why enhancer sequences can function if moved to different positions relative to the promoter.

negative regulation

Binding of repressor inhibits transcription ---inhibition of RNA polymerase activity

DNA methylation

Biochemical modification of DNA in which a methyl (CH3) group is added to the fifth carbon of the cytosine base in a 5′ CpG 3′ dinucleotide pair on one strand of the double helix

piRNAs small Piwi-interacting RNAs

Block both the transcription of Transposable Elements in the genome and the translation of the TE mRNAs that do get transcribed. --Without the synthesis of enzymes like transposase (for DNA transposons) or reverse tran- scriptase (for retrotransposons), the TEs cannot move.

opens, closes

C residues in CpG islands are usually unmethylated. When the CpG islands in the vicinity of a gene's promoter are unmethylated, the chromatin is _______ and the gene is transcriptionally active. Methylation of the CpG islands _________ the chromatin and represses transcription

eukaryotic

Control of _______ gene expression occurs at many levels; these include transcription initiation, transcript processing, mRNA stability, mRNA translation, protein modifications, and protein stability.

Gene regulation

Control of the amount, time, & place of gene expression

Constituitive gene expression

Corresponding mRNA is made all the time w/o positive or negative regulators

insulators

DNA elements located between a promoter and an enhancer that block the enhancer from activating transcription from that promoter. ---act as barrier to changes in chromatin structure/limit effect of enhancers to correct genes

CpG islands

DNA regions rich in C residues adjacent to G residues. Especially abundant in promoters, these regions are where methylation of cytosine usually occurs.

prototrophic

E. coli normally encodes all the enzymes it needs for amino acid and nucleotide biosynthesis. It is therefore a ________ organism that can grow in minimal media, which contain a single carbon and energy source, such as glucose, and inorganic salts to supply the other elements that compose bacterial cells

expressed

Euchromatic regions have __________ genes & heterochromatic regions are silences (not expressed) ----Consituitive heterochromatin is always heterochromatic while facultative can switch btw heterochromatic & euchromatic

Chromatin immunoprecipitation-sequencing

Find target genes of a transcription factor within the genome of a particular type of cell ----- first isolate chromatin from nuclei of cells, chemically cross-link DNA and protein components of chromatin and fragment DNA in chromatin -----add microscopic beads coated w/ an antibody that binds specifically to transcription factor of interest. ----The only protein− DNA complexes that will stick to the beads are those containing the transcription factor cross-linked to the enhancers with which it interacts

Screen

Grow cells on medium so everything can grow ----Transfer onto medium with & without methionine --Screen for Met+

select

Grow cells on medium without methionine but all other nutrients ---Only Met+ cells can grow ---Select for Met+

Minimal media

Growth media containing the bare essentials (inorganic salts, carbon and water), only wild type cells can grow.

Steroid hormone receptor transcription factors

Hormone binding causes a shape change in the receptor protein that greatly increases the affinity of its DNA-binding domain for its target enhancer

3-4 stem loop

If mRNA makes terminator structure:_____, TRP operon transcription & translation stops ----2 stem loop structure of 1-2 & 3-4 is favored when tryptophan levels are high in the cell

methyl-CpG-binding proteins

If the activators are absent, the CpG island becomes methylated. The gene cannot be transcribed because repressors called____________ (MeCPs) bind to methylated CpG islands and close the chromatin structure ---DNA Methylation at CpG Islands Silences Gene Expression

RNA Polymerase

Lac repressor prevents _____from binding to promoter

promoter

Promoters and Enhancers Are the Major cis-Acting Regulatory Elements --always very close to the gene's protein-coding region --binds RNa poly, typically adjacent to the start of transcription.

translation initiation complex

Regulating assembly of ________ Small ribosomal subunit recognizes the mRNA 5′ cap in the context of an RNA/protein complex. In the complex are eIF4A (4A), eIF4E (4E), eIF4G (4G), and poly-A binding protein

Green Fluroescent Protein

Reporter to identify enhancers in eukaryotes ---Construct recombinant DNA molecule where regulatory sequence of interest is fused to GFP gene coding sequence ---- recombinant DNA then used to generate a transgenic organism whose genome harbors fusion. ----If DNA fragment contains enhancer that directs transcription in particular type of tissue, then reporter will express detectable levels of GFP in that tissue.

operator

Repression In the absence of lactose, the repressor protein binds to the DNA of the ________ and this binding prevents transcription. The repressor thus serves as a negative regulatory element.

silencing

Repression of genes by DNA methylation is often long-term because the methylation pattern is maintained through numerous cell divisions; long-term repression through DNA methylation is called ________

repressible regulation

Required for anabolic pathway: pathway should be turned on only when the cell doesn't have enough of needed end product ex: specific amino acid. If end product is present in sufficient quantities, pathway should be turned off— repressed—so cell does not waste resources trying to make molecules that it already has.

inducible regulation

Required for catabolic pathway: pathway should only be turned on when the complex molecules to be broken down (catabolites) are present in the cell's environment. -Cell would waste resources synthesizing enzymes needed to break down sugar if sugar not available

Riboswitches

Small molecules bind RNA to generate alternative regulatory structures: regulate initiation of translation ex: in guanine biosynthesis: no guanine, mRNa made but in presence of guanine, terminator structure formed that blocks transcription ---In adenine biosynthesis: presence of adenine: mRNA binds adenine to make stem loop that blocks ribosome binding site (translation)

Gene regulation

Some genes constiuitively expressed (little/no regulation) ---Constant level of expression in all conditions over time (housekeeping genes) ---Many genes regulated, Gene is expressed & active product produced only at certain times/places

eIF4E binding protein 1 (4E-BP1)

This protein can bind to the initiation factor eIF4E, and this binding blocks the assembly of the remainder of the initiation complex on the 5′ cap -----When 4E-BP1 becomes phosphorylated, it can no longer bind to eIF-4E, so the initiation complex can assemble at the 5′ caps of mRNAs

Phosphorylations

Transcription factor proteins can be modified after they are synthesized by the covalent addition of phosphate by kinase: can either activate or deactivate a TF: by influencing movement of the factor into the nucleus, the factor's DNA-binding properties, its ability to multimerize, or its ability to interact with other proteins, including coactivators or corepressors.

Gene expression

Transfer of information from DNA to final, active product (RNA or protein)

miRNA (microRNA)

Usually negative regulators of target mRNAs, resulting in the destruction of these mRNAs or prevention of their translation.

transcriptional activators

When bound to an enhancer element____________ increase transcription(RNA synthesis) above the basal levels that occur by action of the promoter alone. ---recruit RNA Pol II & basal factors -----can interact directly or indirectly with basal factors at the promoter in a 3D protein/DNA complex to cause an increase in transcriptional activity.

move quickly

When trp is abundant, cell contains many tRNA charged w/ trp ------This causes ribosome to _________ to end of leader ----Frees repeat 1 to pair w/ 2 & 3 pairs w/ 4 to make terminator Result: When terminator structure formed, ribosome gets kicked off, translation stops

charged tRNAs

When tryptophan levels low, cell has few ________that encode trp ------This causes ribosome to stall when it gets to the Trp codon, ribosome is covering repeat 1, creates formation of loop 2-3 & prevent formation of terminator hairpin 3-4 ----Result: RNA poly not terminated & continue w/ rest of mRNA

C

Which operon will produce b-galactosidase even if lactose absent? A) lacI+ P+ Oc lacZ- B) lacI+ P+ O+ lacZ+ C) lacI- P+ Oc lacZ+ D) lacI- P- Oc lacZ+ Oc = loss of function operator

transcription factors

____________ sequence-specific DNA-binding proteins that influence transcription ----. Once the transcription factors bind to the DNA, they recruit additional proteins to the gene that can also influence transcription --Proteins Act in trans to Control Transcription Initiation ---Different types of proteins bind to each of the cis-acting regulatory regions: basal factors _bind to the promoter, while activators and repressors bind to the enhancers.

Transcriptional activators

_____________bind to enhancers to incr. transcription thru: 1) Activators recruit RNA Pol II to basal promoter 2) Activators recruit coactivator to displace nucleosome

upstream open reading frames (uORFs)

____________begin with decoy AUGs and encode small peptides that have no function. If ribosomes translate a uORF, translation of the major ORF in the mRNA is in- hibited

ribosome binding site

region on prokaryotic mRNAs containing both an initiation codon and a Shine-Dalgarno box; ribosomes bind to these elements to start translation of protein-coding sequences on the mRNAs.

sRNA

Act in trans to regulate gene expression by regulating mRNA translation Base pairing of ___w/ leader sequence can inhibit translation of an mRNA by hiding ribosome binding site ---can also facilitate mRNa translation thru base pairing interaction w/ leader that prevent formation of a stem loop that blocks ribosome binding site

Histone modification proteins

Add or remove chemical groups for the histones to weaken their attachment to DNA or generate specific sites on histones so other proteins can bind them ----act as positive activators of eukaryotic transcription

Anabolic pathway

Allow cells to construct end product molecules they need, such as amino acids and nucleotides, from simpler constituents.

Antiterminator

Alternative stem loop structure:_______loop 2-3 is favored when tryptophan levels are low ----Ribosome becomes stalled at the leader TRp codons, allowing the 2-3 loop to form, preventing formation of 3-4 terminator loop

basal factors

Assist the binding of RNA polymerase II to promoter. ----- key component of basal factor complex that forms on most promoters is TATA box-binding protein, or TBP. This protein recruits other proteins called TBP- associated factors, or TAFs, to the promoter in an ordered pathway of assembly ---Once basal factor complex has formed, RNA polymerase can initiate a low level of transcription (basal transcription).

ribosome profiling

B/c gene expression can be regulated at level of translation, amount of a gene's protein product does not always correlate directly w/ amount of mRNA ---identifies the locations on mRNAs where ribosomes are bound because the ribosomes protect these RNA sequences from RNase digestion

prokaryotes

In __________ there is no nuclear membrane & RNA made by RNa Poly needs no processing, ribosomes can start making protein as soon as RNa clears polymerase ----Transcription & translation coupled

screen, selection

In a __________ individual colonies are tested for a particular phenotype. In a____________, only bacteria with the phenotype in question are recovered as colonies, enabling the identification of extremely rare mutants.

histone

In eukaryotes, chromatin keeps DNA inactive by default ---chromatin = DNA covered by protein: ________ ---When bound to histone, DNA inaccessible to proteins

general transcription factors

In eukaryotes, similar to sigma in prokaryotes ---involved in getting RNA Polymerase to bind to promoter, needed for transcription at all promoters

upstream activating sequences

In yeast, genes are are regulated by simple elements similar to enhancers called_________, binds multiple copies of 1 transcription factor

repressor

Induction When lactose is present, inducer allolactose binds to the _________. changes the shape of the re- pressor, making it unable to bind to the operator. --With/ release of repressor from operator, RNA polymerase gains access to the lac operon promoter and initiates transcription of the three lactose-utilization genes into a single polycistronic mRNA.

constituitive expression

Loss of function mutations in lacI (repressor) and lacO (operator) cause ______expression of lac operon

Antisense RNas

Made on the DNA strand complementary to the template strand for mRNA, can intercept and bind to the protein-coding mRNA strand and prevent it from being translated into protein ----Can act in cis or trans to reg. gene expression: ---base pair to mRNA & degrade: trans Base pair mRNA & block ribosome binding site: trans Antisense transcription prevents sense transcription: cis

histone methyltransferase

Methylation of certain lysines (or arginines) in his-tone tails by_____________ ----these help either to activate or to repress transcription, depending on the proteins that the methylated site recruits to the nucleosome. ex: some methylated amino acids bind factors that open chromatin at specific genes, others bind proteins that close chromatin regionally. Thus, some HMTases are coactivators and others are corepressors.

affinity

Mutation of base pair difference in enhancer is likely within a recognition site for a transcription factor and affects the _______________ of the transcription factor for the site

auxotroph

Mutations that create _______ unable to grow and reproduce on minimal medium. Auxotrophs cannot synthesize crucial complex compounds from simple materials.

ribosome binding site

No membrane encloses the bacterial chromosome, so translation of the RNA message into a polypeptide can begin while mRNA is still being transcribed. Ribosomes bind to special initiation sites at the 5′ end of the reading frame __________ while transcription of downstream regions of the RNA is still in progress

alternative splicing

One of the ways cells can generate more than one type of protein from a single gene is through ___________ that is, the splicing of primary transcripts into distinct mRNAs that produce different proteins

Mediator

Special coactivator that interacts with proteins for transcription initiation: Serves as a bridge between the RNA pol II complex at the promoter and activator or repressor proteins bound at the enhancer --required for eukaryotic transcription

Induction

Specific molecules stimulates synthesis of a given protein, molecule = inducer

more complex

The mechanisms of gene regulation in eukaryotes are __________ than those in prokaryotes because eukaryotes have chromatin, eukaryotic transcripts require more processing, and transcripts are exported from the nucleus to the cytoplasm for translation. In multicellular eukaryotes, complex gene regulation directs the development of numerous cell types.

Transcriptional repressors

_______bind to enhancers to decr transcription thru: 1) Repressors can recruit corepressors that directly prevent RNA Pol II complex from binding promoter 2) Repressors can recruit corepressors that close chromatin

repressible regulation

a mechanism of gene control where transcription occurs only in the absence of an effector that binds a repressor, thereby altering repressor conformation so that it can bind DNA. Repressible regulation is particularly important for the regulation of anabolic pathways

inducible regulation

a mechanism of gene control where transcription occurs only in the presence of a molecule called an inducer. An inducer is a small molecule that binds to a positive regulator, altering the positive regulator's conformation so that it can bind DNA. Inducible regulation is particularly important for the regulation of catabolic pathways

attenuation

a type of generegulation that responds to translation of an ORF in the RNA leader; the RNA leader is called the attenuator. When this ORF is translated efficiently, transcription of a gene or operon terminates in the RNA leader sequence before a complete mRNA transcript is made.

operon

group of genes operating together --single signal can simultaneously regulate the expression of several genes that are clustered together on a chromosome and are involved in the same process. ---- can be transcribed together into a single mRNA, anything that regulates transcription of this mRNA will affect all the genes in the cluster

translation

in eukaryotes, __________ begins when the small subunit of the ribosome binds the cap at the 5′ end of the mRNA. The ribosome then scans the mRNA in the 5′-to-3′ direction to find the first AUG, which serves as the initiation codon that specifies Met at the N-terminus of the protein product.

allolactose

inducer in LAC operon --lactose modified to a derivative known as ___________ is the inducer of the genes for lactose utilization.

karyotype

A display of the chromosome pairs of a cell arranged by size and shape. ---fully compacted homologous chromosomes

positive regulation

Binding of activator stimulates transcription ---enhancement of RNA polymerase activity

catabolic pathways

Complicated molecules are broken down for the use of the cell, inducible reg. ex: break down sugars to provide cells with energy and carbon atoms

low

Lac permease & beta-galactosidase are at very __levels in lac opeon in absence of lactose

Inducer

Molecule responsible for stimulating production of the protein

induction

Process by which a specific molecule stimulates synthesis of a given protein

Leader peptide

The product that would result from translation of a short coding sequence used to regulate transcription of an operon by controlling ribosome movement

RNA Polymerase

_____________ is the crucial enzyme for prokaryotic transcription. Sigma (σ) factor allows the enzyme to recognize promoters, while Rho (ρ) protein terminates the transcription of some genes.

bacterial chromosome

a single molecule of double- helical DNA arranged in a circle

DNA methyl transferases (DNMTs)

catalyze the methylation of cytosines in CpG dinucleotides.

β-galactosidase

enzyme that hydrolyzes lactose to form glucose and galactose --catabolic pathway that breaks down lactose into simpler subcomponents

lactose

glucose + galactose

RNA Polymerase II

transcribes primary transcripts that become mRNA in eukaryote --transcribes genes that encode all proteins

Enhancer can be far from promoter

when CaP/cAMP binds DNA, bend induced in DNA & interactions w/ RNA Poly assist in initiation of transcription