genetics ch 12 Transcription and RNA Modification

gene

a segment if DNA that is used to make a functional product: either an RNA molecule or a polypeptide

structural genes

encode the amino acid sequence of a polypeptide

mRNA

the first produce when a structural gene is transcribed. The sequence of nucleotides within mRNA determines amino acid sequence in a polypeptide

gene expression

the overall process by which the information within a gene is used to produce a functional product, such as a polypeptide

promoter

In DNA, the site for RNA polymerase binding; signals the beginning of transcription. Usually located upstream from where transcription begins

terminator

in DNA, signals the end of transcription

template strand

the sequence that is complimentary to the RNA binding strand

nontemplate/coding strand

the opposite of template strand; the transcribed mRNA has the same sequence

transcription factors

proteins that recognize base sequences in DNA and control transcription. Some bind directly to the promoter and facilitate transcription, others recognize regulatory sequences

regulatory sequences/elements

short sequences of DNA involved in the regulation of transcription, some increase the rate of transcription and some inhibit

ribosome-binding site

in bacteria, a short sequence within the mRNA the provides a location for the ribosomes to bind and begin translation

RNA polymerase

the enzyme that synthesized RNA

open complex

a bubble like structure that forms in the catalytic site of RNA polymerase

transcriptional start site

The first base used as a template for RNA transcription, denoted +1

sequence elements (2)

short sequences of bases necessary to create a functional promoter, located at -35 and -10:

consensus sequence

the most commonly occurring bases within a sequence element (although sequence elements vary slightly, the consensus sequence is used). for many bacterial genes, a maximal rate or transcription relates to the degree to which the -35 and -10 regions agree with their consensus sequence

RNA polymerase core enzyme and functions of each subunit

5 subunits of RNA polymerase: alpha(2), beta, beta', and omega.

RNA polymerase holoenzyme

the core enzyme (5 subunits) +a 6th subunit: the sigma factor

sigma factor

part of the RNA polymerase holoenzyme that recognizes the bases at both the -35 and -10 regions. Sigma factor releases at the beginning of the elongation phase

helix-turn motif

a structure within the sigma factor of RNA polymerase that can bind tightly to the -35 and -10 regions

p (rho)

an RNA binding protein that is responsible for terminating transcription in a mechanism called rho-dependent termination. functions as a helicase that can separate hybrid regions between DNA and RNA

p (rho) dependent termination

Termination of translation without the p protien. requires two components:

rut site

(rna transcription) a sequence upstream from the promoter. tho utilization site. acts as a recognition site for the p protein.

p-independent termination

the terminator is composed of two adjacent nucleotide sequences that function within the RNA. One is a U rich sequence that promotes the formation of a stem loop. The stem loop causes transcription to pause and the polymerase eventually destabilizes and dissociates.

Eukaryotic RNA Polymerases and functions

RNA Polymerase:

Clamp of RNA polymerase

thought to control the movement of DNA through RNA polymerase

core promoter

a relatively short DNA sequence that is necessary for transcription to take place. Consists of a TATAAA sequence called a TATA box, and the transcriptional start site where transcription begins

TATA box

usually about 25bp upstream from the transcriptional start site, is important in determining the precise start point for transcription.

basal transcription

a low level of transcription produced by the core promoter by itself

enhancers

one category of regulatory elements: activating sequences that are needed to stimulate transcription

silencers

one category of regulatory elements: DNA sequences that are recognized by transcription factors that inhibit transcription

cis-acting elements

regulatory elemets that exert their effects only over a particular gene. though possibly far away from the core promoter, are always found within the same chromosome as the genes they regulate

trans-acting elements

regulatory transcription factors that bind to cis-acting elements that control gene expression

5 general transcription factors in eukaryotes

always needed for RNA polymerase II to initiate transcription; TFIID, TFIIB, TFIIF, TFIIE, TFIIH

3 categories of proteins needed for basal transcription at the core promoter

RNA polymerase II, general transcription factors, and a mediator

TFIID

Composed of TATA binding protein (TBP) and other TBP associated factors (TAFs). Recognizes the TATA box of eukaryotic structural gene promoters

TFIIB

Binds to TFIID and then enables RNA polymerase II to bind to the core promoter. Also promotes TFIIF binding

TFIIF

Binds to RNA polymerase II and plays a role in it's ability to bind to TFIIB and the core promoter. Also plays a role in the ability of TFIIE and H to bond to RNA polymerase II

TFIIE

Plays a role in the formation or the maintenance of the open complex. It may exert it's effects by facilitating the binding of TFIIH to RNA polymerase and regulating the activity of TFIIH

TFIIH

A multisubunit protein with multiple roles. Some subunits act as helicases and promote the formation of the open complex. Some phosphorylate the carboxyl terminal domain (CTD) of RNA polymerase II, which releases it's interaction with TFIIB,thereby allowing RNA polymerase II to procede with elongation

basal transcription apparatus

TFIID, TFIIB, TFIIF, TFIIE, TFIIH, RNA polymerase II, and a DNA sequence containing a TATA box and a transcriptional start site

Mediator

A multisubunit complex that mediates the effects of regulatory transcription factors on the function of RNA polymerase II

allosteric vs torpedo model of transcriptional termination

allosteric: RNA poly II becomes destabilized and eventually dissociates

colinearity of gene expression

the one-to-one correspondence between sequence of codons in DNA coding strand and the amino acid sequence of the polypeptide. Euk structural genes are not always colinear.

exons

regions that are contained within mature mRNA; contain coding sequences

introns

regions that are found within the exons

RNA splicing

introns are removed and exons are connected

exonuclease

a type of enzyme that cleaved covalent bond between two nucleotides at one end of a strand

endonuclease

cleaves bonds between two adjacent nucleotides within a strand of RNA

self splicing

splicing among group 1 and group two introns that does not require the aid of other catalysts. The rna functions as it's own ribozyme

differences in group I and group II intron splicing

the 2'-OH group in ribose found in an adenine nucleotide already within the intron strand begins the catalytic process.

maturases

proteins that often enchance the rate of splicing in group 1 and group II introns

pre-mRNA

a long transcript that is eventually altered by splicing by a spliceosome

spliceosome

a large complex that splices pre-mRNA in eukaryotes. composed of several subunits known as snRNPs

snRNPs

subunits of a spliceosome: contains a small nuclear DNA and a set of proteins. They bind to an intron sequence and precisely recognize the intron-exon boundaries. It also must hold the pre-mRNA in the correct configuration. Lastly, catalized chemical reactions to remove introns and link exons

how introns are recognized (3 sites)

5' splice site, branch site, and 3' splice site

specific snRNPs and their functions

U1 binds to the 5' splice site, U2 binds to the branch site, then a U4/U6 dimer and U5 bind to the branch site.

alternative splicing

when a pre-mRNA has multiple introns, variations mar occur in the pattern of splicing.

capping

at the 5' end, most mature mRNAs have a 7-methylguanosine covalently attached. occurs while the pre-mRNA is being made by RNA polymerase II

cap binding proteins

recognize the 7-methylguanosine cap and perform certain functions. required for the proper exit of most mRNAs from the nucleus, and is recognized by initation factors important for translation. Lastly, it may be important in intron splicing

polyA tail

most mature mRNA's have a polyA tail attached which is important for mRNA stability and the synthesis of polypeptides.

polyadenylation

the enzymatic addition of a polyA tail after the pre-mRNA has been completely transcribed.

polyadenylation signal sequence

facilitates the addition of a polyA tail; AAUAAA in mammals.

RNA editing

a change in the nucleotide sequence of the nucleotide sequence that involves additions or deletions of particular bases, or conversion of one type of base to another. Can have various effects, such as generating start or stop codons, and changing the coding sequence of polypeptides