Transcription, Translation, and Gene Regulation

transcription

the synthesis of a strand of mRNA (and other RNA); proceeds in same direction as replication (5' --> 3'); forms complementary strand of mRNA

promoter

DNA sequence 20-30 base pairs upstream from the beginning of a gene (translational start site) that is recognized by transcription factors and RNA polymerase

polycistronic

mRNA that codes for more than one protein; no splicing (prokaryotes)

monocystronic

mRNA that codes for one protein; splicing and RNA processing occur (eukaryotes)

ATG

start codon

TAA, TAG, TGA

stop codon

TATA box

exact sequence where transcription factors and RNA polymerase bind in eukaryotes; almost all specialized genes that encode cell-type specific proteins have this

TATA-less

types of genes with ________________ promoters are either:

1) constitutively expressed (housekeeping genes)

2) developmentally regulated genes

RNA polymerase I

synthesizes rRNA

RNA polymerase II

synthesizes hnRNA (pre-mRNA) and snRNA

RNA polymerase III

synthesizes some 5S-rRNA (small ribosomal RNA) and tRNA

template strand

3' --> 5' strand; strand that enzymes act on and synthesize mRNA; often the leading strand

antisense (-)

the template strand of DNA is the _________________ strand

coding strand

5' --> 3' strand; strand that does not interact with polymerizing proteins; is almost exactly the same (has U instead of T) as the newly synthesized mRNA; often the lagging strand

sense (+)

coding strand of DNA is the ______________ strand

initiation

beginning of transcription in which RNA polymerase causes unwinding of DNA double helix and RNA polymerase joins the first nucleotides via phosphodiester bonds in RNA

elongation

RNA polymerase grows the RNA chain in 5' to 3' direction (reads DNA 3' to 5'); assembles ribonucleotide triphosphates into strand of RNA

termination

newly formed RNA dissociates from RNA polymerase and transcription stops with pre-mRNA as the finished product

ribosomes

site of protein synthesis; composed of two subunits in eukaryotes: 60S (large) and 40S (small); has binding sites for mRNA and tRNA

80S

eukaryotic ribosome

A (activation)

tRNA binding site on the ribosome where the tRNA first binds

P (polymerization)

tRNA binding site on the ribosome where the peptide bond forms between the amino acids on adjacent tRNA molecules

E (exit)

tRNA binding site on the ribosome where the empty tRNA molecule leaves the ribosome

codons

sequences of three nucleic acids coding for a specific amino acid

first

_____ base in the codon is defining and always important

second

_____ base in the codon is important about 30% of the time

third

_____ base in the codon is almost never important because of the wobble effect

wobble effect

third nitrogenous base in a codon can vary and still code for the same amino acid

release factor protein

contains the anticodon for the stop codon on mRNA, terminating translation

nucleus

transcriptional control and RNA processing regulate gene expression in the _______________

cytosol

RNA transport control, translation control, and protein activity control regulate gene expression in the ______________

transcriptional control

most important form of gene regulation; controls which genes are turned on or off - modification of whether or not RNA polymerase can bind to promotor and transcribe a gene

alternative splicing

gene regulation at the RNA processing level involves __________________________

degredation

gene regulation at the RNA transport level involves the _____________ of mRNA

DNA methylation

chromatin modification that decreases gene expression

histone acetylation

chromatin modification that increases gene expression

transcription factors

can activate or repress the transcription of adjacent genes; have DNA binding domains - activating domain binds to RNA polymerase and several proteins such as coactivators, enhancers, etc.

constitutive

genes that are always expressed and essential for cell function

inducible

genes in which the protein isn't always needed; certain proteins or chemicals can turn the gene on

activators

proteins that recognize specific short DNA sequences inducing the efficiency of the promoters

co-activators

proteins that are required for more efficient transcription - do NOT bind to DNA

nuclear receptors

function as a ligand-activated transcription factor that regulates gene expression involved in reproduction, development, and general metabolism; only accept lipophilic molecules because they have to pass through the nuclear envelope

CYP3A

enzyme involved in the metabolism of many drugs; certain drugs may increase the expression of this enzyme and cause drugs like estradiol to be metabolized faster (this would prevent birth control from being effective for 24 hours)

DNA methylation

the addition of a methyl group to cytosine, making it look like a thymine residue; decreases RNA polymerase binding and therefore decreases gene expression

HATs (histone acetyltransferases)

transfer acetyl groups to lysine side chains or histone proteins; addition of the acetyl increases gene expression

HDACs (Histone deactyletrasferases)

remove acetyl groups from a histone to decrease transcription of a gene

DNMT

DNA methyltransferase; add methyl groups to cytosines

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.

occur less often in than expected in mammalian genomes, probably due to mutation into TpG dinucleotides over evolution

posttranscriptional

_______________ regulation can control gene expression with siRNA, miRNA, alternative splicing, RNA editing, and mRNA degredation

miRNA (microRNA)

repress genes different from their origin; produced in the nucleus and end in the cytoplasm as a ~22 nucleotide RNA that functions to decrease gene expression; loaded into RNA induced silencing complexes (RISC)

RISC (RNA-induced silencing complex)

targeted to decrease expression of genes based on sequence complementary to the miRNA it is associated with

siRNA (small interfering RNA)

repress genes they were derrived from; target mRNA is degraded