Chapter 7 - RNA and the Genetic Code

3 Types of RNA

mRNA, tRNA,rRNA

mRNA

Messenger RNA carries information specifying AA sequence of the protein to the ribosome, transcribed from template DNA by strands of RNA pol

mRNA contains

information that is translated into protein and is read in 3 nucleotide segments called codons

mRNA in euk

monocistronic meaning each RNA molecule translates into only one protein

mRNA in prok

polycistronic

tRNA

responsible for converting the language of nucleic acids to the language of AA and peptides, each contains a folded strand of RNA that includes a anticodona

anticodon

recognizes and pairs with the appropriate codon

term when AA are connected to a tRNA

charged or activated

each type of AA is activated by

a different aminoacyl-tRNA-synthetase that requires 2 high energy bonds form ATP

rRNA

synthesized in the nucleolus and functions as an integral part of ribosomal machinery

rRNA molecules function as

ribozymes that help catalyze the formation of peptide bonds and splice put introns

codons

basic unit of the gene sequence which is translated into an AA

Anticodon

allows the tRNA to pair with the codon on mRNA, orientation is antiparallel

start codon

methionine AUG

stop codons

UAA, UGA, UAG

Degenaracy

the code is degenerate because more than one codon can specify a single AA

Wobble position

the third base on a codon does not really matter

mutations in the wobble position

silent of degenerate meaning there is no effect on expression

point mutations

silent, missense, nonsense

missense

a mutation where one AA substitutes for another

nonsense

mutation where ht codon encodes for a stop codon

frameshift

occur when a number of nucleotides are added or deleted

transcription

creation of mRNA from a DNA template

transcription results in

a single strand of mRNA synthesized from one of the 2 template strands

RNA is synthesized by

DNA-dependent RNA polymerase

RNA pol locates genes by

searching for specialized DNA regions known as promoter regions

in euk what is the main player for trancription

RNA pol 2 transcribed mRNA and its binding site in the promoter known as the TATA box, does not require a primer

transcription factors

help RNA pol locate bind to the promoter

3 types of RNA pol

pol 1, pol 2, pol 3

pol 1

located in nucleolus and synthesizes rRNAl

pol 2

located in the nucleus and synthesizes hnRNA and snRNA

pol 3

located in the nucleus and synthesized tRNA and rRNA

RNA pol travels in the

3’-5’ and transcribed in the 5’-3’

after the stop of RNA pol the transcript formed is

heterogeneous nuclear RNA

mRNA is derived from

hnRNA via post transcriptional modification

maturation of hnRNA includes

splicing of the transcript to remove noncoding introns and ligate coding exons

splicing is done by

spliceosome in which small nuclear RNA couple with small nuclear ribonucleoproteins, the complex then recognizes the 5’ and 3’ splice sites

5’ cap

at the end of the hnRNA a 8-methylguanylate triphosphate cap is added which protects mRNA from degradation

3’ poly A tail

added to the 3’ end and protects against degradation, composed of adenine bases

translation

converting mRNA into a functional protein requiring mRNA, tRNA, ribosomes, AA, and energy (GTP)

ribosome

composed of proteins and rRNA including large and small subunits which bind during protein synthesisf

function of ribosomes

brings the mRNA message together with the charged aminoacyl-tRNA complex

3 binding sites in the ribosome

A(aminoacyl), P(peptidul), E(exit)

3 stages of translation

initiation, elongation, termination

initiation

the small subunit binds to the mRNA, the charged initiator tRNA binds to the start codon through base pairing with its anticodon within the P site, the large subunit then bids to the small forming the initiation complex assisted by initiation factors

initiation in prok

small subunitin binds to the Shine-Dalgarno sequence in the 5’ untranslated region of mRNA

initiation in euk

the small subunit binds to the 5’ cap

initial AA in prok

n-formylmethionine (fMet)

elongation

3-step cycle that repeats for each AA. ribosomes move in the 5’-3’ synthesizing protein from the N-C ter,omis

3 binding sites in the ribosome

A, P, E

A binding site

holds the aminoacyl-tRNA

P site

holds the tRNA that carries the polypeptide chain, also where the AUG binds, a peptide bond is formed as the polypeptide is passed from the tRNA in the P to the tRNA in the At

transfer from P to A requires

peptidyl transferase, GTP is used for energy for bond formation

E site

where the inactivated tRNA pauses before exiting

Elongation factors

assist by locating and recruiting aminoacyl-tRNA along with GTP and help remove GDP

termination

when a stop codon moves into the A site, a release factor binds to the termination codon causing a H2O to be added to the chain, the H2O allows peptidyl transferase and termination factors to hydrolyze the chain

chaperones

proteins that assist in the folding process

biomolecules added to the peptide

phosphorylation, carboxylation, glycosylation, prenylation

phosphorylation

addition of a phosphate by protein kinases to activate or deactivate proteins

carboxylation

addition of carb acid to serve as calcium binding sites

glycosylation

addition of oligosaccharides as proteins pass through the ER and golgi to determine destination

prenylation

addition of lipid groups to certain enzymes

operons

a cluster of genes transcribed as a single mRNA

Jacob-Monod mondel

operons contain structural genes, an operator, promoter, and a regulatory gene

structural gene

codes for protein

operator

upstream of the structural gene, a nontranscribable region of DNA that is capable of binding to a repressor

promoter

upstream of the operator, provides a place for RNA pol to bind

regulator gene

upstream to the promoter, codes for the repressor

2 types of operons

inducible and repressible

inducible

repressor is bonded tightly to the operator and acts a roadblock so that RNA pol is unable to move from the promoter

how do inducible systems work

an inducer must bind the repressor so that RNA pol can move down, as the concentration of the inducer increases more repressors are pulled off

repressible systems

allow constant production of a protein product, the repressor is inactive until it binds to a corepressor which then binds to the operator negative feedback

transcription factors

transcription-activating proteins that search dna looking for specific binding motifs

2 domains of transcription factors

DNA binding and activation

DNA binding domain

binds to a specific nucleotide in the protomer or to a DNA response element to help in the recruitment of transcriptional machinery

activation domain

allows for the binding of several transcription factors and other important regulatory proteins

gene amplification

in response to specific signals, through enhancers or gene duplication, expression is increased e

enhncers

response elements can group together to form an enhancer which allows for the control of one gene’s expression by multiple signals

location of enhancers

very far from the gene they regulate and can be located within an intron

gene duplication

cells can increase expression by duplicating the relevant gene

histone acetylation

transcription factors that bind to the DNA can recruit other activators like histone acetylases which are involved in chromatin remodeling

histone acetylases in chromatin remodeling

acetylate lysine residues found in the amino-terminal tail regions of histone proteins a

acetylation

of histone protein decreases the positive charge on lysine residues and weakens the interaction of the histone with DNA resulting in an open chromatin conformation

histone deacetylases

function to remove acetyl groups from histones which close chromatin

DNA methylaion

DNA methylases add methyl groups to C and A nucleotides, this silences genes