ch 9 proteins and their synthesis Flashcards
r group properties
- charged
- hydrophilic
- hydrophobic
- aromatic
primary structure
linear sequence of amino acids
secondary structure
arises from interaction btw neighboring amino acids
- alpha helix or pleated sheet
tertiary structure
interactions btw more distant amino acids or cofactors
- 3d
quaternary structure
interactions btw multiple polypeptides
- dimer, trimer, tetramer
- homo - identical polypeptides
- hetero - different polypeptides
polypeptide
chain of amino acids linked by peptide bonds
3d structure of tertiary structure stabilized by
- hydrophobic interactions
- ionic interactions
- h-bonding
- van de waals forces
2 major protein classes
- structural (myosin, actin, collagen)
- active (PEP carboxylase, endonuclease)
sanger sequencing
determining amino acid sequence
- proteolytic enzymes cut btw specific amino acids to produce specific fragments
- movement through electrophoretic field depends on size and charge of fragments
unambigous
1 codon, 1 amino acid
degernate
1 amino acid, >1 codon
3 features of the genetic code
- each amino acid is specified by a group of three nucleotides, a codon, in the mRNA
- the genetic code is non-overlapping
- of the 64 possible codons, 61 encode individual amino acids. therefore most amino acids are specified by more than one codon
5 components required for translation
mRNA - template for protein synthesis
amino acids - protein building blocks
tRNAs - carry aa to the ribosome, decode mRNA info
ribosome - RNP complex, catalyzes peptide bond formation
protein factors - IF, EF, RF
tRNA
- adapter molecule for protein synthesis
- base-pairing btw tRNA and an mRNA codon specifies the aa to be inserted
- a cell must contain at least 20 different tRNA (one for each aa)
- aa are covalently attached to tRNA = charging
aminoacyl-tRNA synthetase
charging accuracy is crucial for translation
- binds only one amino acid
- binds only the appropriate tRNA
how does the cellular tRNA set relate to degeneracy
- more than one tRNA species can be charged with the same amino acid — isoacceptors - most organisms contain at least 3 different tRNAs that are charged with serine
- a single tRNA species can recognize more than one codon — wobble
wobble
the ability of the 3rd nucleotide of the anticodon (5’ end) to pair imprecisely, allowing the anticodon to align with different codons
G-C or G-U pair
U-A pr U-G pair
ribosome function
brings all components together
catalyzes peptide bond formation
two subunits of ribosomes
small subunit - binds mRNA, decoding site
large subunit - catalyzes peptide bond formation
APE
key site of interaction on the ribosome
A - amino acyl site - incoming tRNA binds
P - peptidyl site - tRNA temporarily carrying the elongating pp chain
E - exit site - empty tRNA leaves
3 steps of translation
- initiation
- elongation
- termination
initiation (prokaryotes)
SSU binds to mRNA - start codon is positioned at P site
fMet-tRNA binds to the start codon - IF1 and IF2 ensure correct positioning
16S aligns with shine-dalgarno sequence to position the start codon at the P site
the large subunit recognizes the 30S initiation complex and binds - IF1 and IF2 are released
shine-dalgarno sequence
ribosome binding site (RBS)
base-paring btw the shine-dalgarno sequence and the 16S rRNA aligns the start codon in the P site
initiation (eukaryotes)
small subunit recognizes the 5’ cap and binds - i-tRNA and IF associated
mRNA is scanned processively for the 1st AUG (start codon)
large subunit binds - IF release, i-tRNA in P site
elongation
continuing cycle of peptide bond catalysis
termination
stop codon recognized by a RF
RF binds in the A site
hydrolysis breaks the bond btw the tRNA (P site and the PP chain
ribosome subunits dissociated from each other and mRNA
nonsense mutation
introduction of a stop codon leading to premature termination of translation
- generally biologically inactive
- may be toxic
3 types of post-translational processing
protein folding
covalent additions of chemical groups or peptides to defined positions/sequences
protein sorting and trageting
post-translational processing
chaperonin complexes aid protein folding
chemical modifications
- addition of chemical groups
- addition of polypeptides
- addition of complex molecules
- cleavage
- amino acid modification
phosphorylation regulates:
enzyme activity
protein-protein interactions
protein-nucleic acid interactions
cellular localization
protein degradation
tagging a protein with ubiquitin targets a protein for destruction
- small peptide attached to lysine side chains
signal sequence
the amino-terminal sequence of a secreted protein which is required for the export of the protein from the cell
nuclear localization sequence (nls)
the sequence of a protein required for its transport from the cytoplasm to the nucleus
