Midterm 2.4.2 Flashcards
where are peptide bonds in a protein
between the carboxylic acid group of one amino acid and the amino group of the next amino acid
proteins are directional. how do they run?
N terminus (free amino terminus) to C terminus (free carboxylic acid terminus)
the chain of AAs in a proteins is referred to as
1 structure
what’s in secondary structure proteins and how are they formed
⍺-helices & β-sheets
Formed
by hydrogen bonding in peptide backbone (amide H & carbonyl O)
Quaternary structure is made of
multimeric proteins. multiple different polypeptides, protein complexes
individual polypeptide chains in a multimeric protein are _____
____ can be _____ or ______
subunits
subunits, identical (homomeric) or different (heteromeric)
what do ribosomes use to convert the mRNA sequence into a protein sequence?
tRNA
tRNAS contain
modified based (residues that are chemically altered after transcription)
anticodon that binds a particular three base codon
carry specific AA (cognate AA) that correspond to that codon
what are tRNA synthetases
enzymes that
“charge” tRNAs – add the amino
acid to the CCA at the 3’ end.
what is the CAA end of an AA?
acceptor end
same tRNA for 2 different codons occur when there is a single mismatch in
3rd position wobbe
each codon corresponds to
a specific AA
the start codon encodes the first amino acid of a
particular ORF (N terminal amino acid of a protein) - where translation begins
AUG (ATG in DNA sequences (for all three domains of life)
In bacteria, start codon is translated to
N-formylmethionine (fMet) (chemically modified version of methionine) using a special tRNA
AUG encountered during normal translation encodes a standard
methionine. fMet often removed from proteins after translation.
Prokaryotic ribosome is the….made up of two subunits….each subunit comprised of….
70S ribosome
30S (small subunit) and 50S (large subunit)
rRNA and ribosomal proteins.
RNA has many “AUG”s. To locate bona fide start codons, bacterial mRNAs
use a ribosome binding site (RBS)
RBS is an RNA sequence (some variation in exact sequence)that is recognized
by ribosome - must be appropriately spaced from a start codon (e.g. AUG).
16S rRNA component of a free 30S ribosomal subunit (not bound to 50S)
binds to….to initiate translation
then … binds to …..
once bound….
RBS/start codon
Initiator (fMet) tRNA then binds the start codon
Once bound, energy from
GTP is used to recruit 50S subunit & full 70S ribosome forms
the ribosome has 3 tRNA binding sites
A (aminoacyl) site
P (peptidyl) site
E (exit) site:
A (aminoacyl) site
Where new charged tRNAs enter and recognize the
codon being translated. Once in place, the growing peptide from P site is
transferred its amino acid & peptide bond forms.
P (peptidyl) site
After peptide bond formation, translocation occurs –
RNA moves 3 bases (one codon). The tRNA from A site moves to P site.
This tRNA transfers growing amino acid chain to the new charged tRNA
that has entered the A site. P site tRNA now lacks amino acid (uncharged)
E (exit) site
Uncharged tRNAs exit here
during translation, APE repeats until…
once this occurs,
resulting in
then
ribosome encounters a stop codon UAA, UGA & UAG
a protein called a release factor binds
ribosome releasing the mRNA & the completed
polypeptide
30S/50S subunits dissociate. Ribosome is free to begin a new round
of translation
in translation, … is used as an energy source
GTP
chaperones are
functions are:
proteins that help other proteins adopt their properly
folded and fully active state - all 3 domains in life require chaperones.
initial folding, re-folding denatured proteins, helping
subunits in multimeric proteins come together, etc.
what is the sec system
Protein secretion
recognizes a signal sequence in the first ~20
amino acids of protein - translocates unfolded protein before it folds
Tat pathway
secretes pre-folded proteins across membrane
In Sec pathway, proteins are either:
1) Passed across cytoplasmic membrane (SecA pathway)
2) Recognized by RNA/protein complex – signal recognition particle - and
inserted into the cytoplasmic membrane (SRP pathway).
Both pathways: (sec and tat)
1) Pass the unfolded protein through a membrane channel - Sec YEG
translocon
2) Require ATP for energy
3) Signal sequence is cleaved following translocation
