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-10 and -35 regions

prokaryotic sequences of DNA found in promoters

3’ poly A tail

tail at the end of eukaryotic mRNAs

5’ cap

nucleotide on the 5’ end of primary transcripts

7-methylguanosine

forms the 5’ cap

activators

increase transcription of a gene, positive control over gene expression

alternative splicing

exons from the same gene are joined in different combinations

branch point

sequence that assists in removal of introns and joins exons

cAMP receptor protein (CRP)

regulates gene expression in response to cAMP, binds to DNA sequences and activates or represses their transcription

cap binding complex

attaches to 5’ cap of mRNA and incorporates a cap binding protein to promote protein synthesis

catabolite repression

regulatory mechanism, controls which genes are turned on and off based on availability of energy sources

closed complex

initial stage of transcription, DNA is double helical

coactivators

type of transcriptional co-regulator that binds to an activator to increase the rate of transcription

coding strand

3’ - 5’, complimentary nucleotide sequence, does not base pair with rna

combinatorial control

when a small amount of transcription factors can control the expression of a larger number of genes

consensus sequence

most common nucleotides or amino acids in each position within a sequence alignment

constitutive gene expression

continuous or unchanging level of gene expression under normal conditions

core promoter

DNA segment where transcription initiates, immediately upstraem of the transcription start site

corepressors

regulatory proteins that function in gene expression by repressing transcription

cAMP

molecule that serves as a messenger in biological processes

DNA-binding transcription activators

proteins that regulate gene expression by binding to specific DNA sequences and activating their transcription

downstream promoter element

conserved DNA sequence motif, located downstream of transcription start site, contributes to initiation of transcription of RNA polymerase II

effector

molecule that can bind to a protein and modulate its activity or function

elongation

process of synthesizing a complementary RNA or DNA strand, step by step addition of nucleotides to the growing chain

enhancer

dna sequence element that can regulate transcription of genes located at varying distances from the enhancer itself, controls gene expression in eukaryotic cells

exon junction complex

multiprotein complex that forms on mRNA molecules during splicing

exons

sections of eukaryotic dna that are transcribed into mRNA

exportins

class of proteins involved in transport of molecules across the nuclear membrane in eukaryotic cells, mediate export of molecules from nucleus to cytoplasm

GAL genes

a group of genes involved in the metabolism of galactose and glucose

Gal3p

enzyme involved in metabolism of galactose, catalyzes phosphorylation of galactose which is the first step in the pathway.

Gal4p

transcriptional activator, activates genes involved in metabolism of galactose

Gal80p

regulatory protein, inhibits gal4p, binds to gal3p

basal transcription factors

group of proteins that are essential for initiation of transcription at core promoter of genes

housekeeping genes

constitutively expressed in cell types under normal physiological conditions, expression is essential for maintaining basic cellular functions

importins

class of proteins involved in nuclear import process

inducer

molecule that triggers or enhances the expression of specific genes or activity of certain proteins, involved in regulatory processes that allow organisms to respond to changes in their enviornment

inducible

when certain genes or proteins are activated in response to specific signals

initiation

when rna polymerase binds to promoter region of a gene and begins transcribing DNA into RNA

initiator sequence

start site of transcription, located between -3 to +5 in eukaryotes

insulators

DNA-protein complexes defined by their ability to block enhancer-promoter interactions

introns

noncoding sequences of RNA that are spliced out before translation into a protein

karyopherins

importins and exportins, facilitate translocation of proteins, RNAs and ribonuclear particles

lac genes: LacZ, LacY, LacA

lac operon, acts to cleave lactose into galactose and glucose

Lac operator

short DNA sequence adjacent to promoter of lac operon, serves as regulatory element that controls transcription of structural genes

lac repressor

prevents transcription of genes involved in lactose utilization, utilizes multiple operators to increase the efficiency of repression

mediator complex

multi-subunit assembly that is required for regulating expression of RNA transcripts

mRNA

molecule, carries portion of DNA code to other parts of cell for processing

Mig1

protein that mediates glucose repression in yeast

negative regulation

regulating gene expression by inhibiting the expression of that gene

non-template strand

“coding strand”, does not get copied by RNA

nuclear pore complex

mediates transport of all macromolecules between nucleus and cytoplasm

open compex

second stage of transcription, unwound DNA

operator

segment of DNA to which a repressor binds

operon

cluster of genes that are transcribed together, encodes multiple proteins

polyA binding protein

RNA-binding protein that triggers the binding of initiation factors to the polyA tail of an mRNA

polyA polyermase

enzyme, adds a chain of adenine nucleotides to the RNA

polyadenylation signal sequence

highly conserved AAUAAA signal, recognized by RNA cleavage complex

polycistronic mRNA

mRNA corresponding to multiple genes whose expression is controlled by a single promoter and terminator, “operons”

positive regulation

activator binds to the operator on mRNA, permits RNA polymerase binding and allows transcript to occur

primary transcript

single strand RNA synthesized by DNA transcription

promoter

signals where transcription process begins on a strand of DNA

promoter clearance

breaks contact with transcription factors involved in initiation phase

proximal regulatory sequences

located close to a promoter and binds a protein that modulates transcription

regulated gene expression

how a cell controls which genes are turned on

regulatory sites

binding sites for transcription factor proteins

regulon

a group of several genes or operons that are turned on or off in response to the same signal by the same regulatory protein

repression

mechanism used to decrease or inhibit expression of a gene

repressors

proteins that turn off or reduce gene expression

ribosomal RNA

type of RNA that is a major constituent of ribosomes

RNA pol I

produces rRNA

RNA pol II

transcribes all protein coding genes and non coding RNAs

C-terminal domain

located on RNA pol II; does capping, splicing and 3’ processing of mRNA

RNA pol III

transcribes DNA to synthesize 5S ribosomal RNA, tRNA and other small RNAs

RNA polymerase

enzyme responsible for copying DNA sequence into an RNA sequence

RNA polymerase core

enzyme responsible for RNA synthesis using DNA as a template

RNA polymerase holoenzyme

result of RNA pol and sigma factor interactions, capable of RNA synthesis and promoter recognition

RNA splicing

when newly made pre-mRNA transcript is turned into mRNA

sigma 70

acts in transcription initiation and elongation, transcribes housekeeping genes

sigma factor

subunits of bacterial RNA polymerase, play roles in transcription initiation

small nuclear ribonucleoproteins

snRNPs, protein complexes that combine with pre-mRNA to form a spliceosome

small nuclear RNA

snRNAs, critical components of the spliceosome that catalyze the splicing of pre-mRNAs

splice sites

where introns are removed from primary transcripts, found at 5’ and 3’ ends of introns

spliceosome

large RNA-protein complex that catalyses the removal of introns from pre-mRNA

TATA binding protein

general transcription factor that binds to TATA box,

TATA box

DNA promoter sequence that indicates where a genetic sequence can be read and decoded

template strand

DNA sequence that can duplicate itself during mRNA synthesis, runs 3 - 5

termination

ending of transcription, occurs when RNA polymerase crosses a stop sequence

TFIIB recognition element

recognizes DNA sequence-specific motifs that can flank the TATA elements of the promoters

transcription

process where the information in a DNA strand is copied into a new molecule of mRNA

transfer RNA

small RNA molecule that plays a key role in protein synthesis

Tup1

transcriptional corepressor, plays a role in regulating gene expression by repressing the transcription of specific genes

UAS-gal

two part system, responsible for directing expression of a gene

upstream activating sequence

cis-acting regulatory sequence, located upstream of core promoter, serves as a binding site for specific transcriptional activators