genetics test 2 (thursday?)

constitutive expression

the small set of an organism’s genes that are expressed at the same rate all the time

what does “need-based” transcription entail for prokaryotes?

prokaryotes maintain their efficiency by only transcribing the needed genes that code for a peptide; genes that aren’t currently needed are transcribed

operon

prokaryotic on/off switch for controlling gene expression

what makes up the operon?

several functionally related genes + the controlling elements that influence when those genes get expressed

inducible operons

operons that have their default state as off; certain events turn them on

what kind of enzymes do inducible operons produce?

inducible operons produce catabolic enzymes

what is the purpose of the Lac operon of E.coli?

the Lac operon of E.coli produces the enzymes needed to degrade the sugar lactose and only activates WHEN lactose is present

repressible operons

operons that are on by default; certain events turn them off

what kind of enzymes do repressible operons produce?

repressible operons produce anabolic enzymes

what is the purpose of the Trp operon?

Trp operon produces the enzymes that synthesize the amino acid tryptophan and deactivate ONLY when tryptophan excess is detected

which letter labels the regulatory gene?

letter i labels the regulatory gene

which region represents the promoter region?

LETTER P LMFAOOOOOOO

which region represents operator region?

letter O LMFAOOOOOOOOO

what is the function of B-galactosidase?

enzyme that breaks own lactose

what is the function of permease?

transports lactose from outside environment → inside of the cell

what is the purpose of transacetylase?

detoxifies non-metabolizable sugars and keeps them out of the cell (not strictly required, but helpful)

catabolite repression

mechanism by which glucose influences Lac operon & function

what is lactose composed of?

glucose & galactose

what does a lack of glucose promote?

promote further production of B-galactosidase

what does an excess of glucose cause?

production of B-galactosidase to stop

what begins the process of B-galactosidase production?

the presence of lactose

how does the creation of B-galactosidase lead to the creation of glucose?

B-galactosidase cleaves lactose in to galactose and glucose

what enzyme do high glucose enzymes inactivate?

adenylate cyclase

what happens as a result of adenylate cyclase inactivation?

cells do not produce cAMP (cyclic adenosine monophosphate), which is an ATp-derived messenger that’s essential for many cellular processes

how does cAMP function in the lac operon?

it’s a positive regulator in the Lac operon: it attaches to CAP (catabolite activator protein) to create the cAMP - CAP complex

what happens with the cAMP-Cap complex attaches to the promoter region of the Lac operon?

transcription of the three structural genes (z,y,a) get enhanced

do cells with a large glucose supply break down glucose?

YES

what determines gene expression in cells with both glucose & lactose?

glucose

does absence of glucose lead to maximum or minimum gene expression?

maximum: the lack of glucose enables adenyl cyclase creation, allowing the creation of the CAP c-AMP complex that binds to the promoter region and enables maximum DNA expression

does presence of glucose lead to maximum or minimum gene expression?

minimum/low-level: the presence of glucose prevents adenyl cyclase creation: no adenyl cyclase is able to bind with ATP and create the CAP- cAMP complex; thus leading to low level expression

what does the regulatory gene in repressible operons create?

inactive/immature repressor molecule

what does tryptophan serve as?

co-repressor: which attaches to apo-repressor and helps create the repressor-tryptophan complex

where does the repressor-tryptophan complex attach to block structural gene transcription?

it attaches to the operator

leader sequence

segment of 162 bases, located between the operator and the first structural genes

attenuator region

region found within the leader, extending from approx. base 130-150

what determines the sensitivity of tryptophan presence/absence?

leader sequence & the attenuator region found within

what did yanofsky & bertrand discover?

even in high levels of tryptophan, transcription is initiated, yet not always completed

leader peptide

a short region within the leader peptide from base 25-70

in the operon for tryptophan, where and when does the ribosome attach?

it attaches at the 5’ end as soon as RNA transcribes the 5’ end of the leader region; translation and transcription are coupled?

when does ribosome stall in cells with low Trp?

when it reaches two consecutive Trp codons within the leader peptide

which loops form in cells with low Trp levels?

Loop #1 doesn’t form (ribosome stalls in the region that should form it), Loop #2 forms; Loop #3, containing the attenuator/termination region, is impossible to form

when does ribosome stall in cells with high Trp levels?

as tryptophan is readily available; no stalling at the consecutive Trp codons occurs

which loops form in cells with high Trp levels?

Loop #2 doesn’t form as the pairing of region 2&3 are blocked by the ribosome; Loop #3 forms the termination/attenuator loop

what happens when Loop #3 is created?

structural gene transcription is halted

gene expression

transcription of a gene followed by the translation of resulting RNA: leading to polypeptide & phenotype

what regulates the levels of gene expression?

the cell’s perception of how much the associated polypeptide is needed

general transcription factors

assist with core polymerase attachment to the promoter and with progressing from initiation to elongation

regulatory transcription factors

monitor the rate that transcription occurs

activators

transcription factors that increase transcription rates

repressors

transcription factors that decrease transcription rates

control elements

DNA sequences that flank eukaryotic genes; operate similarly to operators found in bacterial operons

enhancer elements

binding site for activators

silencer elements

binding site for repressors

where do activator proteins bind?

they bind to an enhancer region in the DNA

DNA-bending protein

brings the bound activator closer to the promoter

transcription initiation complex

forms as a result of activators binding to transcription factors and mediator proteins; enhances gene expression

small effector molecules

mechanism that regulates the function of transcription factors: promotes the ability of the transcription factor to attach to DNA; steroid hormone fill this role and up-regulate certain genes

protein

mechanism that regulates the function of transcription factors: homodimer / heterodimer formation can affect sequences of transcription events

covalent mods

mechanism that regulates the function of transcription factors: adding a phosphate group to an activator for example can stimulate transcription

DNA Methylation

inhibits gene expression through the addition of methyl groups

how common is DNA methylation?

relatively common; human genomes include up to 7% methylated nucleotides

DNA methlytransferase

attaches a methyl group to cytosine: part of CpG island formation

CpG Island

forms when the methylated C is connected to a G on the same strand by a phosphodiester bond; inhibit promoter function when near promoters

what does the protruding methyl group thought to do?

interfere with normal enhancer-activator attachment

alternative splicing

post transcription regulation method: works through constitutive and alternative exons; allows a single gene to code for multiple different proteins

constitutive exons

always included in mRNA transcripts, forming the core backbone of messenger NRA and maintaining essential structures

alternative exons

segments that can be alternative and excluded at times to promote protein diversity

RNAi interference

post transcription regulation method: “sense” and “anti-sense” RNA forming double stranded RNA fragments due to base complementary that cant be translated

siRNA

Small interfering RNA that silences specific genes that breaks down complementary messenger RNA

miRNA

micro RNA, bind to complementary sequences on target RNA molecules to regulate their gene expression through mRNA cleavage or blocking protein production

RISC

RNA-inducing silencing complex; targets mRNA transcripts in the cytoplasm and not permanent DNA instruction

genome

an organism’s complete set of inheritance information (cumulative collection of DNA)

gene

subset of organism’s genome that directs the inheritance and production of a polypeptide

locus

the physical position a gene occupies within a genome

allele

one of multiple variations of expressing a gene

chromosome

organized package of DNA found in the nucleus of a cell

chromatin

the DNA and associated packaging proteins found in the nucleus of a cell, prior to the organization into compacted chromosomes

are chromosomes contained in the nuclear membrane when they are visible?

NOOOOOOOOOO

is the nuclear membrane in place when chromatin transforms into chromosomes?

NOOOOOOOOOOOOOOOOOOOOO it is not in place

somatic cells

cells of all body tissues in a sexually reproducing organism, except those used to produce new organisms (contains both chromosomes from the mother & father)

gametes

cells of a sexually reproducing organism that directly contribute to the production of a new organism (contain only 1 of each type of chromosome)

ploidity

count of the number of chromosomes in a cell

haploid

word used to describe a cell that has one of each type of chromosome for the species (haploid gametes)

diploid

word used to describe a cell that has two of each type of chromosomes (diploid somatic cells)

G1

growth, active metabolism, chromatin expanded, intact nucleus

S

replication of DNA, chromatin expaned, intact nucleus

G2

growth, active metabolism, chromatin expanded, intact nucleus

M

cell division, visible chromosomes

replicated chromosome

twin chromatids

unreplicated chromosome

single chromatid

critical checkpoints

checkpoints that lead up to the next stage that can only be activated by the correct combination of cyclins, CdK (cyclin-dependent kinases), and target molecules (for phosphorylation)

sexual reproduction

combines genetic mateiral from 2 parents to produce a new organism

species identity

done through maintaining a standard chromosome # from generation to generation

prophase

chromatin condenses into chromosomes + nuclear membrane breaks & metabolism slows down

metaphase

chromosomes (replicated) align on spindle

kinetochore

protein disk that connects that centromere of a replicated chromosome to the mitotic spindle (during metaphase)

cohesin proteins

play a role in attachment to the spindle in metaphase

anaphase

centromeres break + each replicated chromosome becomes 2 unreplicated chromosomes

telophase

unreplicated chromosomes move towards opposite poles to form new nuclei

cytokinesis

separation of cytoplasm into two cells (follows telophase)