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57 Cards in this Set

  • Front
  • Back
Two functions of AUG codon
1. only codons that encodes for Methionine.
2. intitiation signal for translation
What are unique/necessary features of tRNA?
1. Nucleosides are highly modified
2. 3'-CCA acceptor arm for aminoacylation
Wobble hypothesis
The 3rd anticodon is oftentimes modified with the formation of non-WC base pairs possible.
1 tRNA can recognize several degenerate codons. What hypothesis says this?
Wobble
Mis-sense mutation
Change of AA code. Usually if 1st or 2nd position is changed.
Non-sense mutation
Stop codon
silent mutation
AA code unchanged most likely to happenn if AA in 3rd position is changed.
An AA insertion or deleation causes
Frameshift mutation
How do organisms ensure the correct reading frame is used?
reading frame is sequential and non-overlapping. This ensures that translation will occur in only one reading frame (to prevent "frame shift" outcomes).
How do Prok start to use the reading frame?
shine dalgarno sequence 10 neuleotides upstream from the AUG recognize the start codon.
How do Euk start to use the reading frame?
Use intitation factor EIF-4 to scan the mRNA for the first AUG
What enzyme aminoacylates tRNA and how is AA specificty and tRNA specificty ensured?
Aminoacyl tRNA synthetase. tRNA specificity is ensured by recognition of the correct AA.
What is a ribosome
complex riboneucleoprotein particles made up of 2 dissimilar subunits, each of which contain RNA and proteins.
Steps in protein synthesis
Initiation, enlongation, termination, and post-translational modification.
What is the function of the shine-dalgarno sequence (AGGAGGU)
it's the signal for initiation of protein biosynthesis in bacterial mRNA. Purine rich located 10nt after start sequence.
Protein initiation factors in EUK protein synth
eIF1
eIF1a
eIF4a,b,f,
eIF5
eIF5b
eIF2a,b
Initiation factors for prok
IF1
IF2
IF3
Elongation factors for EUK
EF-1alpha
EF-2
Elongation factors for Prok
EF-tu and EF-G
Termination factor for EUK
eRF
termination factor for prok
RF-1,2,3
3 steps of ribosomal enlongation
1. EF-1 alpha bind tRNA into the sequence behind the Meth. EF-1alpha exits withour tRNA and GDP instead of GTP
2. Transpeptidation
3.Translocation
Transpeptidation
RNA catalyzed transferase reaction. The 2nd AA attracts the carboxyl group on the adjacent preceding AA and enlongating the chain, leaving the 1st t-RNA as an uncharges tRNA and changing the new aminoacyl-trna as the new peptidyl-tRNA.
Translocation
EF-2 with GTP converts to EF-2 with GDP which, moves the ribosome down the mRNA, moving the peptidyl-tRNA chain into the center slow for further enlongation. This will free the A-binding site.
What is the structural basis for the mode of action of the antibiotic puromycin?
Puromycin resembles the 3' of tyr-tRNA so it binds at the large subunit A site and acts as an acceptor of the nascent peptide in the peptidyl transferase rxn.
which release factors recognize mRNA codons?
RF-1- UAA and UAG
RF-2- UAA and UGA
How do release factors differ from tRNAs
They are proteins not RNA.
What are chaperones?
Proteins that reversibily bind to hydrophobic regions of the nascent proteins. They stabilze intermediates and maintain proteins in an unfloded state to allow for passage thru membranes. Also help prevent aggregation and inappropriate interactions with other proteins.
How is targeting to specific organelles ensured?
sorting of proteins for their ultimate destination occurs in the process of glycosylation and proteolytic trimming. As they pass through the cis, medial 7 trans elements of the golgi apparatus. Families of receptor proteins provide specificty for membrane targetting and fusion.
three kinds of posttranslational modification
phosphorylation, glycosylation, and disulfide formation.
posttranslational modification- phosphorylation
Kinase activity is a property of many growth factor receptors. Regulates singalling to transcription factors.
Posttranslational modification- Glycosylation
forms glycoproteins. Alters the properties of proteins, changing their stability, solubility, and bulk. The carb moieties act as recognition signals that can direct protein targeting and influence cell-cell interaction and development of the organism.
posttranslational modification- disulfide formation
prevents unfolding of proteins and their passage acros membranes. Also becomes a means of localization.
Posttranslational modification- acetylation
occurs in histones and modulates interations with DNA.
What characteristics of a peptide would suggest a non-ribosmal biosynth?
D-AA, N-methylated modified units, or unusual AAs
Operator
segment of DNA which regulates the activity of the structural genes of the operon by interacting with a specific receptor/activator
Repressor
DNA-binding protein that regulates the expression of one or more genes by dec the rate of transcription.
Features of an operon
an operon contains it's own regulatory gene with it's own promoter, control elements, and structural genes. Control elements are promoters and operators.
Coordinate expression of a biosynthetic pathway
Important because you want all genes for a specific pathway are transcribed at once. So all genes in the cluster are either express or not.
meaning of CIS
signifies the co-location of two or more genes on the same chromosome of a homologous pair and refers to internal factors for example, a specific promoter sequence. Only has effect on gene downstream.
Meaning of Trans
external factors which act on a molecule. Trans refers to the ability to diffuse to the site of action.
Major diff between repressor of the lac operon and repressor of trytophan operon?
Lac repressor binds it's repressor in the abcense of it's inducer while trp repressor must be complexed to the inducer (2 try molecules) so it can bind to the operator.
How is it ensured that transcription occurs in one direction?
through the attenuator region which provides RNA polymerase with a 2nd chance to regulate transcription of the tryp operator.
Feed back inhibition
regulation of the 1st step in a pathway by the path's end product.
Regulation of ribosomal protein biosynth is based on affiinity to various RNA types. How do the affinities compare?
See notes!
In EUK what two factors determine whether regions are transcriptionally active and what is the physical basis for each?
1.acetylation of e-lysine residue: reduces net charge so there is less electrostatic interaction between DNA and histones.
2.DNA methylation- methylation of 5-CpG-3', proteins recognise and bind methylated DNA, which prevents binding of transcription factors.
how tetracyclin works
inhibits binding of aminoacyl-tRNA to 30s subunit in proK
How streptomycin works
causes mRNA reading errors and inhibits initiation ProK. Interfers with base pairing.
Fusidic Acid
inhibits enlongation in proK by preventing ef-G and GDP dissociation from 50s subunits
chloramphenicol
inhibits peptidyl-transferase in prok
Cycloheximid
inhibits peptidyl-transferase EUK
erthyromycin
inhibits translocation PROK
aminoacyl-tRNA synthase
proofreading
Ubiquitin
intracellular protein degradation
Shine-D sequence
responsible for proper alignment so that translation can begin in PROK
CCA arm
is where AA will attach in amincoacylation reaction
S7
regulate it's own level by binding to it's mRNA