Lecture 33 Flashcards
prokaryotic vs eukaryotic translation (location, subunits, how does it initiate, first aa, shape)
Describe mRNA transport
mRNA must leave the nucleus to be translate
must pass nuclear pore complex
Selection at NPC (naked RNA can’t pass, cap and tail binding proteins are required, unspliced pre-mRNA is blocked)
Once in the cytoplasm, chaperones can be recycled and the mRNA associates with the ribosomes
Start and stop codon
Start: AUG (methionine)
Stop: UAA, UAG, UGA
Are there individual tRNA for every codon
no, modified anticodon bases allow a single tRNA to pair with multiple codons
tRNAs contain modified nucleotides at several positions, including the anticodon
The wobble position is the 5’base of the anticodon
What do codon biases help with
Each organism has more of some tRNA and less of others, because some codons are rarer so it is best to have more tRNA for the over-represented codons
Codon bias affect protein expression
What do truncated proteins create
Many truncated proteins may create dominant negative proteins
* Enzymes which can not be turned off
* Proteins which permanently bind their DNA, RNA or protein partners
* Proteins which form non-functional dimers with good subunit
4 methods of proofreading that are utilized during translation
nonsense mediated decay
nonsense associated alternative splicing
non-stop mediated decay
no-go decay
What are decay pathways initiated by
mRNA decay pathways are initiated by deadenylation catalyzed by pol(A) 3’exoribonuclease
Longer tail = longer halflife
Deadenylated mRNA can be ________ by 3’–>5’ exonucleases of the exosome, or have the cap removed by _____ _______ and 5′–>3′ exonuclease digestion by ____
recycled
decapping enzyme
Xrn1
nonsense mediated decay
almost all genes contain the stop codon with the last exon of the mRNA
– Splicing leaves behind Exon Junction Complexes (EJC’s) at exon-exon boundaries
– If mutation or aberrant splicing produces a stop codon 5’ of a EJC (not in the last exon) this causes the mRNA to be rapidly degraded by translational proofreading
Checking occurs in the first round of translation as ribosomes normally displace EJC’s
Upf’s are activated if EJC’s remain, and decapping enzyme is activated
mRNA is decapped and mRNA is rapidly degraded
NMD allows for many mutations to produce no proteins
When are up-shift frameshift proteins activated? What do they do
Checking occurs in the first round of translation as ribosomes normally displace EJC’s
If any EJC’s remain, they activate Frameshift proteins (Upf)
Upf’s activate the decapping enzyme to remove the 5’ cap
Decapped mRNA is rapidly degraded in the cytoplasm by 5’–>3’ exonucleases
NMD example
Beta Thalassemia
what is Beta thalassemia? Hetero vs homzygotes
Thalassemia is a mutation caused by the mutation affecting 1 of the subunits of hemoglobin
Recessive and homozygotes have severe anemia from lack of Beta-hemoglobin
In heterozygous, they have a premature stop codon but no protein is made as NMD quickly destroys the mRNA
If homozygous, stop codon near the last exon causes a dominant disease because mRNA is stable as EJC’s are removed. So no NMD, all premature stop codons produce truncated proteins and usually die
How is NMD beneficial
Many diseases which cause mutations are masked to create a recessive disease through NMD
NMD can also remove semi-functional mutated mRNAs encoding useful proteins as in DMD
Nonsense-associated alternate splicing (NAS)
Uses a premature stop codon and detect by EJC’s
Poorly understood
Evidence from T-cells and B-cells that premature codons cause exon skipping to produce functional pathogen recognizing proteins
