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Most antibiotics target
protein synthesis components
What is the coding ratio? n
number of nucleotides used to make a codon. A coding ratio of 3 will allow for 64 codes
The genetic code is degenerate/redundant. How?
One amino acid can have more than one codons.
How many codons do not represent any AA?
3, all stop codons.
The genetic code is unambiguous. what does that mean?
Each codon specifies only one amino acid
What are the characteristics of the genetic code (5)
4. no punctuation
What is a missense mutation?
One base is replaced by another, changing the amino acid
nonsense mutation is when
a point mutation causes a change from an amino acid to a stop codon
Hemoglovin to methhemoglobin, what kind of mutation?
The amino acid is attached to what end of a tRNA molecule?
What specifically does the amino acid attach to in tRNA at the 3'end?
2 or 3'OH of the last ribos
CCA is the ending code at the 3' end of what molecule?
The 5' cap and 3'poly a tail in eukaryotic mRNA creates what structure when interacting with polyA binding proteins?
a loop. Start AUG is synthesized last?
*ribosomal rna that makes up the subunit.
slippage of the mRNA could alter what?
the reading frame
codon recognition by tRNA: _____________ complementary base pairing
the third nucleotide of the codon interacts with what codon of the anticodon?
synthesis of the peptide bond require GTP/ATP?
Steps involved in protein synthesis (4)
1. amino acid activation
How many specific aminoacyl-tRNA synthetases?
20, only 1 for each amino acid, recognizes all tRNAs that bind for a specific amino acid
If an aa has 6 tRNAs that correspond to its codons, how many aminoacyl-tRNAs does it have?
What is the reaction of aminoacyl-tRNA synthetases
amino acid+tRNA--> aminoacyl-tRNA+AMP+2Pi
a peculiar structure in the 3' UTR allows what to be be made at the stop codon?
selenocysteine is created by attaching serine to a serine trNA synthetase and modified later
aminoacyl tRNA becomes what?
peptidyl tRNA then free tRNA
amino acid chain (polypeptide chain) grows from what terminal?
starts at N terminal and continues adding to COO- terminal
the initiator tRNA is the same as other tRNAs that code for methionine.
in prokaryotes, the methionine bound to the initiator tRNA is _________
initator tRNA is also called
prokaryotes) or tRNA
f (prokaryotes too)
amino acid in front of the tRNA: already attached.
: not attached yet
remember: tRNA pairs with mRNA and look for where the CAA end is.
What sequence positions the first AUG in P site in prokaryotes?
What does the Shine-Dalgarno sequence bind?
The 16S rRNA in the Ribosomal Binding Site
In eukaryotes, where does the mRNA attach to the rRNA?
the 1st AUG, in the Kozak sequence surrounding this first AUG.
dissease where kozak sequence causes reduced synthesis of hemoglobin
mutations in kozak's sequence would affect what in a kinetics equation?
the sequence of tRNA is written 5-3, but when pairing with mRNA, you need to flip it.
pay attention to where amino acid is
IF-1, IF-2, IF-3 are in what? prokaryotes or eukaryotes?
IF-3 and IF-1 bind 30s subunit of prokaryotes rRNA.
IF-2 is brought to the rRNA with GTP. when it is bound together, it brings a tRNA+aa to the site. this complex has a low GTP activity, but when it binds to 50S of ribosome, what happens?
hydrolysis of GTP.
the equivalent of IF-2 in eukaryotes
Multiple proteins bind to the _____ of eukaryotic mRNA
remember EIF4-b and EIF-2
important role in regulation
If proper anticodon/codon pairing happens, (proper tRNA), there will be a confomrational change based on what?
the hydrolysis of GTP which alters the conformation of EF-tu
The peptide chain is transferred from P to what?
partially in A site, but then translocation happens and it all moves to the P site again, leaving the A site open.
What happens to EF-Tu after it disassociates from the tRNA after delivery?
Ef-Tu-GDP + GTP-----> Ef-TU-GTP + GDP via EF-Ts (guanine nucelotide exhange factor)
EF1B or EF-Ts is a guanine nucleotide exchange factor for what?
EF-Tu, adds GTP and gets rid of GDP
GTP mainly changes conformation of proteins, resulting changes in structure of ribosome, moving the ribosome forward (translocation) or termination
--------- through hydrolysis to GDP
only the peptide from the peptidyl-tRNA from P site to A site happens. true or false?
ORF includes stop codon. true or false?
Phosphorylation of what in the alpha subunit of eIF2 interferes with exhange of GDP with GTP?
of serine in the alpha subunit of eIF2
reduced heme= activation of GRI (reduces heme deficiency oxidative stress)= activation of.....?
eIF2alpha via phosphorylation
heme can regulate protein synthesis. true or false
what are some ways that phosphorylation of the alpha unit of the eIF2 happens?
-lack of heme
-hypoxia, unfolded protein response
-amino acid starvation, UV
eIF4E binds where?
to the cap of eukaryotes' mrna
what is eIF4E inhibited by?
What happens when 4E-BP is hyperphosphorylated?
it removes it from eIF-4E, and eIF 4E can bind 5' cap
viral proteases target what?
eIF3, ??? (look up)
ADP ribosylation attaches the group to eEF2. What happens?
Protein inactivated, this is performed by diphtheria toxin
question on degradation is on exam
cytoplasmic proteins get degradation by
where does ubiquitin get attached?
Lys in target protein
protein unfolding in the proteasome complex is catalyzed by what?
What are the 5 major histones?
H1, H2A, H2B, H3, H4
epigenetic modification happens on what in terms of eukaryotic DNA-bound proteins?
epigenetic marks happen on histones, and are passed onto daughters.
What are the 7 components required for protein synthesis?
1. amino acids
5. aminoacyl-tRNA synthetases
6. protein factors
polysome/ polyribosome is
a cluster of ribosomes translating a SINGLE mRNA.
What is the 70S prokaryotic ribosome's two major components?
What are the two major components of 80S eukaryotic ribosomes
40S and 60S
what is the small subunit of the ribosome's main function?
to bind the mRNA and tRNA
what is the large subunit of a ribosome's main duty?
catalyze peptide bond formation
What sub-part of the small ribosome enables initiation in prokaryotes?
Which RNA subunit of the small unit proofreads correct codon-anticodon base pairing?
16s and 18s rRNA
What part of the large subunit of the ribosome catalyzes peptide bonds?
23s rRNA in prokaryotes and 28S rRNA in eukaryotes
31 types of tRNA thanks to wobble base pairing. true or false
Does it take ATP to attach an amino acid to a tRNA?
What is ATP eventually synthesized to in the reaction binding an aa to a tRNA?
AMP and 2Pi, ATP used to catalyze peptide bond through aminoacyl-AMP+tRNA
What is the tRNA that brings in the first methionine for eukaryotes?
What is the N-terminal AA is prokaryotes?
Shine-Dalgarno region base pairs with what?
3' end of 16s rRNA and positions it in the P site
Shine Dalgarno sequence is a leader sequence, true or false
true, a polypurine stretch
True or false: each cistron (coding region) is a polycistronic mRNA will have its own shine-dalgarno sequence
What are the prokaryotic initiation factors called?
IF-1, IF-2, IF-3
What does IF-3 do?
Prevents the 30S subunit in prokaryotes from associating with the large one too early, and If-1 assists it.
What does IF-2 bind in initiation?
First, IF-2 binds GTP. Then, it binds the small ribosomal subunit, 30S. Then it binds the initiator f-Met tRNA
to help it dock in the small ribosomal subunit.
After IF-2-GTP helps settle the f-Met-tRNA
into the small ribosomal subunit, what happens?
IF-3 positions the complex into the P site of the ribosome so it interacts with the AUG.
After IF-3 places the f-met tRNA
in the P site, what happens?
The large ribosomal subunit attaches and GTP of the IF-2 is hydrolyzed, leading to disassociation of IF-2-GDP and IF-1 and IF-3
Does a full initiation complex have any association protein factors like IF, GTP, or GDP?
Where does the pre-initation complex for eukaryotes occur?
at 5'cap and scans until initation codon is reach.
eIF4A is involved in the initiation of eukaryotes' translation. how?
It scans the mRNA from 5' to 3' until it finds the initiation codon.
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