Protein Metabolism Flashcards
Most pathways and systems of protein biosynthesis are?
highly conserved amongst organisms
How many enzymes and associated proteins are needed to make polypeptides?
300
What percentage of chemical energy in the cell does protein synthesis use?
90%
What percentage of the cell’s dry weight is related to the synthesis of proteins?
35%
Translation
process by which proteins are made
tRNA with amino acid reads mRNA code so rRNA can make a protein
Codon
nucleotide triplet on mRNA that encodes the amino acid
Amino acid sequence is determined by?
the codon sequence
How many codons encode amino acids?
61
Start codon
AUG
Stop Codons
UAA
UAG
UGA
alteration of the 3rd nucleotide
typically has no change for the amino acid it encodes
In a random sequence how many in 20 codons is a stop code?
1
open reading frame
reading frame with more than 50 codons and no stop codon
anti-codon
complementary sequence to codon on mRNA
The first two bases of the codon bind strongly while the third can?
wobble
If the wobble base is C or A
no wobble
If the wobble base is U or G
it can recognize 2
If the wobble base is I
it can recognize 3; A, U or C
missense mutation
most common, single alteration
silent mutation
nucleotide changes but amino acids encoded for remains the same
transition mutation
purine/pyrimidine swapped for a purine/pyrimidine
A change in the first nucleotide results in ?
a similar amino acid
Describe transitional frame shifting
ribosome will skip a stop codon and change reading frame to make a modified protein
How many reading frames are for every gene?
3
gRNA
guide RNA
acts as template for alterations when mRNA is edited before translation
Deamination can lead to?
an early stop codon and shorter peptide
Where does protein synthesis happen?
in the ribosome
Ribosome
supramolecular structure that doesn’t vary across organisms
5 stages of protein synthesis
activation
initiation
elongation
termination
folding and post translational modifications
Where are amino acids activated?
C-terminus
What is the link between the amino acid and mRNA code?
tRNA
How many tRNA synthetases per amino acid
1
tRNA synthetase
attaches amino acid to tRNA and proofreads it
amino acid arm
binds amino acid
anticodon arm
matches mRNA
tells which amino acid to bind
D arm
helps with folding
T Psi C arm
interacts with ribosome
extra arm
variable
Carboxylic acid attaches to ATP to form what?
an adenylyl end amino acid
Class 1 Activation
2’ OH of tRNA binding arm attacks carbonyl, kicks off AMP as a leaving group
transesterification; amino acid moves from 2’ to 3’ OH
Class 2 Activation
3’ OH of tRNA binding arm attacks carbonyl, kicks off AMP as a leaving group
When does proofreading occur?
during amino acid tRNA attachment
How does tRNA Synthetase proofread?
larger amino acid wont fit in active site
smaller amino acid will be hydrolysis off
Which amino acid initiates protein synthesis in eukaryotes? Bacteria?
Met
FMet
Steps of initiation in bacteria
- binding of initiation factors
- binding of FMet tRNA to start codon on mRNA
- assembly of active ribosome
IF 1 binds
in A site
IF3 binds
in E site, blocks large subunit
mRNA binds with start codon near which site?
P site
IF2 brings FMet-tRNA to bind where?
P site
When 50s binds and kicks of the IFs what forms?
the active ribosome
Exit Site
empty tRNA leaves from here
Peptidyl Site
where peptide bond is made
Aminoacyl site
incoming amino acid-tRNA enters
Where is the AUG codon in eukaryotic initiation?
further up the mRNA strand
Peptide bond steps
- binding of incoming amino acid tRNA
- bond formation
- translocation
During elongation the next amino acid is brought by tRNA into the A site with?
EF-Tu
Hydrolysis of GTP and removal alters?
the shape of tRNA so that a bond can be made between amino acid and peptide
Does proofreading occur in elongation?
no
How does EF-Tu dissociate?
slowly
If the tRNA-mRNA interaction is incorrect what happens?
the tRNA-amino acid will leave without adding its amino acid
During elongation what attacks what?
the amino terminus of the incoming amino acid attacks the C terminus of the peptide chain
During elongation what happens to tRNA?
is removed from the P site
changes conformation- empty towards E site, tRNA with peptide towards P site
EF-G
binds to the A site and shoves tRNAs over by 1 site
When the stop codon is released what binds and what does it do?
releasing factor- cleaves the peptide chain from tRNA
Each peptide bond formed requires the hydrolysis of 4 nucleotide triphosphates which are?
1 ATP
3 GTP
What is termination regulated by?
ribosomal recycling factors
Polysome
multiple ribosomes on the same mRNA; allows for rapid and high levels of protein expression in bacteria
How can proteins be post translationally modified?
amino and carboxy terminal modifications
loss of signal sequences
modification of amino acids
attachment of carbohydrates, isoprenyl groups, or prosthetic groups
proteolytic processing
disulfide cross-links
Which amino acids are likely to get phosphorylated?
Tyr
Thr
Ser
Which amino acid is likely to get carboxylated?
Glu
Which amino acids are likely to get methylated?
Lys, Arg
Which amino acids can make O-linked glycoproteins?
Ser, Thr, Tyr
Which amino acids can make N-linked glycoproteins?
Asn, Arg
Isoprenes attach to which amino acid?
Cys
Isoprenylation of Ras is?
oncogenic
What are some examples of prosthetic groups?
heme, biotin
Proteolytic processing
when a larger protein is cut into a smaller one for function
Disulfide cross links
Cys-Cys
help hold protein in folded shape
Puromycin
mimics amino acid attached to tRNA
enters the A site and makes a peptide bond
causes early termination
antibiotic
Tetracyclines
bind in the A site and block tRNA from binding
causes early termination
antibiotic
Cycloheximide
toxin that blocks translation of tRNA
Ricin
Toxin that is a large protein that inactivates the large subunit of the ribosome
Where does posttranslational modification occur?
endoplasmic reticulum
Signal sequence brings the ribosome to the ER using?
signal recognition particles
Where does glycosylation start?
in the endoplasmic reticulum
Where is the protein transported from the endoplasmic reticulum?
the golgi complex
Lysosome
enzyme breaks down proteins
Secretory granules are used for?
extracellular release
Transport vesicles are used for?
intracellular release
Are signal sequences for nuclear transport cleaved?
no
Where do nuclear localization sequences occur?
internal site of the peptide
How can cells import proteins?
endocytosing
Proteosome
enzyme that degrades proteins
The longer a protein is in a cell, the more it collects ?
ubiquitin
The level of ubiquitination is highly influenced by?
the N-terminal amino acid
Stabilizing amino acids
Ala, Gly, Met, Ser, Thr, Val
Destabilizing amino acids
Gln, Ile, Glu, Tyr, Pro, Asp, Leu, Lys, Phe, Arg
