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Biochemistry Translation and Mutations
KYCOM Block 1
69
Biochemistry
Graduate
08/23/2012

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Cards

Term
how many codons are there?
Definition
4 bases 3 nucleotides=64 codons
Term
in which direction is a protein synthesized
Definition
N terimus to C terminus
Term
in which direction are nucleotides read
Definition
5' to 3'
Term
stop codons
Definition

do not encode an aa

UGA, UAA, UAG

u go away, u are away, u are gone

Term
start codons
Definition

AUG (methionine) only

starts all protein synthesis

DOES code for the amino acid. AUG is the ONLY codon for methionine.

there could be an AUG down stream but it wont start anything

Term
how many codons code for an amino acid
Definition
63 codons - 3 stop codons = 61 codons
Term
what if there is another stop codon down stream?
Definition
too bad you already stopped at the first one
Term
what are the 4 words that describe the genetic code
Definition
specific (a codon specifies one aa), universial (across most orgnanisms), redundant aka commaless (each aa may have >1 codon), non overlaping (every third base is a codon)
Term
what is different about non coding region codons
Definition
not grouped into triplets
Term
what types of mutations can occur in DNA
Definition
single nucleotide, silent, missense, conservitive, nonsense, insertions, deletions, frameshift, splice site, trinucleotide repeat extension
Term
single nucleotide mutation
Definition
point mutation
Term
silent mutation
Definition
no effect on final protein, codon changes but codes for the same aa
Term
missense mutation
Definition
different codon leads to a different aa
Term
conservitive mutation
Definition
missense mutation but new aa has the same properities as the original
Term
insertion / deletion mutation
Definition

adding / subtracting nucleotides from a coding region

can cause a frameshift mutation

if it is a multiple of three added / subtracted and amino acid is completely deleted or added and the frame isnt shifted, no trunkation

Term
frameshift mutation
Definition
insertion / deletion mutation that is not a multiple of three. the closer to the begining of the sequence the worse it is. a stop codon is usually introduced pretty soon leading to a trunkated protein
Term
nonense mutation
Definition
codon becomes a stop codon when mutated
Term
splice site mutation
Definition
splice site sequences are specific, changes lead to deletion of nucleotides from the exon, leaving nucleotides from an intron, deleting an exon, can be point mutations
Term
trinucleotide repeat expansion
Definition
sequences of bases, in coding or non coding regions, tend to get expanded by DNA polymerase. if it gets too big it causes problems
Term
what happens if the nucleotide repeat in a coding region is expanded too much
Definition

trinucleotide repeat expansion mutation

it expands the protein

Term
what happens if the nucleotide repeat in a non coding region is expanded too much
Definition
if it is a small change it is ok, if it is big it interferes with the translation because the 5' and 3' untranslated regions interact. the protein is normal but less protein is made and a cellular feedback loop methlyates the gene to stop production of the mRNA making the protein
Term
what effect does a missense mutation have on a protein
Definition
decrease in function, variable other effects
Term
what effects does a nonsense mutation have on a protein
Definition
shorter than normal, usually non functional
Term
what effects does a frameshift mutation have on a protein
Definition
usually non functional, shorter than normal
Term
what effect does a large segment deletion mutation have on a protein
Definition
loss of function, shorter than normal or entirly missing
Term
what effect does a splice site mutation have on a protein
Definition
addition or deletion of a few aa to deletion of an entire exon
Term
what effect does a triplet repeat expansion mutation have on a protein
Definition

in coding region: cause protein product to be longer than normal and unstable

disease often shows anticipation in pedigree

Term
what mutation is sickle cell anemia? what does it effect?
Definition

point mutation

effects betas-globin gene (s for sickle cell effected)

normal code: GAG --> glatamic acid (-)

mutant code: GTG --> valine (neutral)

Term
what mutation is PKU? what does it effect? what is the result? what is a symptom? what is a treatment?
Definition

nonsense and frame shift mutation

phenylalanine hydroxylase gene: converts phenylalanine to tyrosine

>400 mutations possible

phenylalanine metabolites accumulate

retardation

 oral phenylalanine and tyrosine

Term
what mutation is cystic fibrosis? what does it effect? what is the result?
Definition

deletion mutation

70% of the time it is 3 base pairs in the coding region of the cystic fibrosis transfer gene

phenylalanine is missing

protein is functional in the membrane but it does not get put on the membrane right so it does not function

Term
what mutation is alpha or beta-thalasemic? what does it effect?
Definition

splice site mutation

deficiency in alpha or beta-globin of Hb

Term
what is the most common single gene disorder in humans
Definition
alpha or beta thalassemia
Term
what mutation is fragile X syndrome? what does it effect? what are some symptoms? what is the result?
Definition

trinucleotide repeat in a 5' non coding region

FMR-1 gene

retardation, long face, everted ears, large mandible, macro-orchidism (large testicles)

less protein is made, feedback methlyates the gene and stops its mRNA production

 

Term
what mutation is myotonic dystrophy? what does it effect? what are the symptoms? what is the physological result?
Definition

trinucleotide repeat in the 3' non coding region

protein kinase gene effected (signal transduction)

muscles contract but do not relax

shuts off the gene

Term
what is the most common inherited cause of mental retardation
Definition
fragile x syndrome
Term
what is the most common known cause of autism
Definition
fragile x syndrome
Term
what is the most common adult muscular dystrophy
Definition
mytonic dystrophy
Term

what mutation is huntingtons disease? what does it effect?

when is ir diagnosed?

Definition

trinucleotide repeat in the coding region

repeat of glutamine codon causes the huntington protein to be unstable and aggergate

nerve cells die, proressive neuro degeneration

diagnosed between age 30-50

Term
what happens if there are not enough amino acids to make the protein
Definition
translation will stop at the codon for the missing aa
Term
essential amino acids
Definition
you body cannot make them and you need them in your diet
Term
where is an amino acid attached to a tRNA
Definition
to the CCA 3' attachment site
Term
charged tRNA
Definition
has amino acid
Term
anticodon
Definition
three nucleotide sequence on the tRNA that base pairs with the mRNA
Term
aminoacul tRNA synthetase
Definition
enzymes that attach aa to the corresponding tRNA, each one regognises an aa and all the rRNA that pair to it, 20 kinds in humans, can proofread and edit
Term
explain the reaction where an amino acid is linked to the tRNA
Definition

aa carboxyl group is covalently bonded to the hydroxyl on the 3' teminus of the tRNA (ester bond)

pyrophosphate is cleaved to two molecules of inorganic phosphate cleaving two high energy bonds

Term
what happens to RNA subunits just befoe translation
Definition
seperated subunits come together
Term
ribosome a site
Definition
binds incoming aminoacyl tRNA
Term
ribosome p site
Definition
binds peptidyl tRNA that carries the chain of aa that have already been synthesized
Term
ribosome e site
Definition
exit site, contains empty tRNA as it is about to leave the ribosome, only in eukaryotes
Term
what is special about proteins made in ribosomes in the RER
Definition
they are destined for post translation modifications or subcellular compartmentalization
Term
protein factors
Definition
accessory proteins involved in stages of synthesis. include initiation, elongation, and termination factors
Term
energy required for translation
Definition

charging tRNA: 2 high energy bonds from ATP

binding aminoacyl-tRNA to A site: 1 GTP

movement of the ribosome to the next codon: 1 GTP

total 4

Term
translocation
Definition
moving ribosome to the next codon
Term
wobble hypothesis
Definition

tRNA can recognise more than one codon for a specific amino acid

the third nucleotide of a codon and the 4th nucleotide of an anticodon can bindin non traditional ways allowing a tRNA to recognise more than one codon

Term
polycistronic
Definition
prokaryotes have multiple coding regions on the same genes
Term
monocistronic
Definition
eukaryotes have one coding region per gene leading to one protein
Term
prokaryote translation initiation
Definition
shine-dalgarno sequence. rRNA in small subunit has a complimentary sequence to the shine-dalgarno sequence allowing correct alignment with the subunit to the start codon
Term
eukaryote translation initiation
Definition
small ribosome subunit recognises 5' cap and scans along the ribosome until the first AUG is found, this makes them monocystonic
Term
prokaryotic binding of the initiator
Definition
initiator is bound to a formylated methionine at the p site of the ribosome
Term
eukaryotic binding of the initiator
Definition
initiator tRNA binds to first methionine at the p site of the ribosome
Term
what energy requirements are there for the initiating sequence to bind
Definition
1 GTP
Term
elongation during translation
Definition
delivery of aminoacyl-tRNA after the initiating sequence is to the a site on the ribosome
Term
what is the energy requirement for each step of an elongation?
Definition
1 GTP
Term
what does phosphotransferase do? where is it located? how does it get the energy to do its job?
Definition
it forms peptide bonds, it is part of the large subunit, it uses the energy from the charged tRNA
Term
translocation process
Definition
uncharged tRNA moves to the e site, prptidyl tRNA moves to the p site, aminoacyl tRNA moves to the a site
Term
termination of translation
Definition
when a stop codon appears in the a site release factors releases the polypeptide from the peptidyl-tRNA and uncharged-tRNA from ribosome, ribosome seperates, requires a GTP
Term
how many release factors are there in parkaryotes
Definition
3
Term
how many release factors are there in eukaryotes
Definition
1
Term
polysome
Definition

aka polyribosome

multiple ribosomes can be on one mRNA to speed things up and protect the mRNA

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