Chapter 7 - RNA and the Genetic Code

wobble position

refers to the third position in codons that when altered by an aa residue likely will still code for the same aa, the genetic code is degenerate

mutations in the wobble position

silent or degenerate

point mutation

mutation of one nucleotide within a codon

expressed mutations

those at effect the primary sequence of a protein

missense mutation

mutation where one aa substitutes for another

nonsense mutation

mutation where codon now encodes for premature stop codon, aka truncation mutation

frameshift mutation

insertion or deletion of nucleotide(s) that cause a shift in the reading frame and causes changes to aa added to the sequence or premature truncation

transcription

DNA template is used to create a strand of mRNA

template strand in relation to mRNA

complentary and anti parallel

coding strand in relation to mRNA

identical aside from U vs T

enzyme responsible for conducting transcription

RNA polymerase II, binds to promoter region to begin transcription
- promoter region in eukaryotes, TATA Box; shine delgarno sequence in prokaryotes

transcription factors

help RNA poly II find promoter region
two regions 1) DNA binding domain 2) activation domain

RNA poly vs DNA poly

RNA polymerase does not proofread its own work

herteogeneous nuclear DNA (hnRNA)

RNA that is synthesized directly from RNA poly that must undergo post transcriptional modifaitions to become mature mRNA

post transcriptional modifiations to hnRNA

1. splicing introns and exons
2. 5' Cap
3. 3' Poly A tail

introns

non coding sequences

exon

coding regions

spliceosomes

conducts splicing of introns and exons
- small nuclear RNA (snRNA) bind proteins known as small nuclear ribonucleoproteins (snRPs)
- snRNA/snRPs recognize 5' and 3' splice sites of introns

5' cap

7-methylguanylate triphosphate cap
added during transcription and recognized by ribosome as binding site
helots protein mRNA in cytoplasm

3' poly A tail

adenine bases
protects against rapid degradation

alternative splicing

hnRNA is spliced at different regions to produce different proteins from the same strand

ribosomes

composed of proteins + rRNA

eukaryote ribosome

80S
60S (large), 40 (small)
4 strand of rRNA

prokaryotes ribsomes

70S
50S (large), 30S (small)
3 strands of rRNA

mechanism of translation

1. initation
2. elongation
3. termination

initiation

small subunit binds start codon (Shin-dalgarno sequence, prokaryotes)
large subunit then binds to create completed initiation complex
initiation factors help, not permanently associated w ribosome

elongation

ribosome moves in 5' to 3' direction across mRNA
aminoacyl-tRNA in A site is the "next" aa to be added
P site hold tRNA with growing polypeptide chain
as polypeptide is passed from tRNA in P to A site, peptide bond formed
- needs peptidyl transferase to help coordinate this

A șite

tRNA with amino acid residue that will be added next to the polypeptide chain

P site

holds tRNA strand that has growing polypeptide chain
where small subunit of ribosome binds for initiation

E site

where uncharged, inactivated tRNA paused before exiting ribosome

elongation factors

help recruiting aminoacyl-tRNA along with GTP, help remove GDP

termination

stop codon enters the A site
release factor binds to termination code and cause water molecule to be added to the polypeptide chain
termination factors hydrolysis polypeptide chain from tRNA in P site through this

glycosylation

adding of oligosaccahardies as proteins pass through ER and Golgi

prenylation

addition of lipid groups to certain membrane bound enzymes

phosphorylation

addition to phosphate group to activate/deactivate protein

carboxylation

addition of carboxylic acid to proteins, typically serve as calcium-binding site

operon

cluster of genes transcribed as a single mRNA
- structural genes
- operator site
- promoter site
- regulator site
*prokaryotes

operator site

upstream from structural gene
nontranscribable region
repression protein can bind

promoter site

place for RNA poly to bind

regulator gene

furthest upstream
codes for a protein known as repressor

indictable systems

repressor is bound to operator system, acting as a roadblock
inducer must bind repressor to allow RNA poly to transcribe (similar to competitive inhibition)

repressible system

repressor made by regulator gene is inactive till bound by a corepressor
this complex can then bind operator site to stop
negative feedback

DNA binding domain, transcription factors

binds to a specific sequence in the promoter region or to DNA response elements

activation domain, transcription factors

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

enhancers

allows for the control of gene expression by mutlope signals
large distance between enhancer and promoter regions explain why DNA needs to form hairpin configuration

gene duplication

opening gene with helices and duplicating only that gene

acylation

decreases postive charge of lysine residues and weakens interaction with histone and DNA resulting in coiled form

histone deacylases

remove acetyl groups from histones to allow for closed chromatin conformation

histone acylated, genes

free for transcription and translation

histones deacyalted, genes

closed off and decreased in gene expression

dna mehtylases

add methyl group to cytosine and adenine nucleotides, methylation is linked with silencing of genes

why DNA double stranded vs RNA single stranded

DNA must carry genetic material, needs more protection

RNA is used for protein then degreased, temporary use

splice donor sites

located near the 5’ end of the intron next to the exon

splice acceptor site

located near the 3’ end of the intron next to the exon

slice donor/acceptor sites

splicosome removes intron region between the donor an acceptor sites

RNA Polymerase I

functions primarily to transcribe rRNA

ribosome assembly

occurs in the nucleolus, ribosome proteins are synthesized in the cytoplasm and transported back into nucleolus for subunit assembly

net charge of histone proteins

positive, to interact with negatively charged backbone of DNA

telomeres and centromeres both composed of

heterochromatin

characteristics of heterchromain

silenced genes, typically highly repetitive in sequence, gene-poor

origin of replication

eukaryotes have multiple

prokaryotes have one singular

formation of cloning DNA, cDNA

1. mRNA of intrest introduced complementary primers (rich in T)
2. these primers bind poly A tail of mRNA
3. Reverse transcriptase binds mRNA at polyA tail and begins transcribing single strand cDNA


1. mRNA strand is degraded, resulting single stranded cDNA is amplified using DNA polymerase and PCR

cDNA insertion

cDNA can be transfected via a vector


1. circular DNA (from bacteria and viruses) as well as cDNA are acted on by restriction enzymes
2. DNA ligase joins cDNA nd circular DNA together at sticky ends generated by restriction enzyme


1. vector can then be transfected into cells

evolutionary related

genes with similar sequences

unequal crossing over

some portion of the chromosome can be duplicated overtime due to this mechanism

alternative splicing

refers to multiple protein products resulting from the SAM DNA sequence

transposable elements

can be moved or copied at to other locations in the genome at any time

retrotransponsons

reverse transcriptase acts on mRNA to produce a single stranded DNA

DNA is then inserted into the genome at different locations

\
\*\*some nearby genes are also copied which could be cause for the amplification of other genes in the genome

siRNA

RNA interferences

binds complentary mRNA and signals its degradation

miRNA

binds complimentary sequence on mRNA to scilence gene expression

oncogene

mutated or overexposed gene that promotes cell proliferation and growth/inhibit apoptosis

tumor suppressor gene

regulate DNA repair by repressing or stalling cells from progressing through the cell cycel

quantitive reverse transcriptase PCR

reverse transcriptase coverts mRNA into cDNA

cDNA amplified

cDNA denatured and primers/reverse primers anneal to stands heat stable polymerase can elongate DNA

rna polymerase I

rRNA

rna polymerase II

mRNA

snRNA

miRNA

rna polymerase III

tRNA

rRNA

snRNA

miRNA