Class 4 E1 Flashcards
ubiquitination
targets proteins for destruction, original protein cannot be recovered; not reversible.
What is the name of this enzyme?
ADP + Pi -> ATP
ATP synthase.
Roles of AA’s in biochemistry?
- nitrogen disposal (urea cycle)
- lipid metabolism
- neurotransmitters (GABA, glutamate
- source of E when sugar fats are low
What are the 4 levels of protein structure?
- Primary
- Secondary
- Tertiary
- Quaternary
What does ATP kinase do?
phosphorylates ADP (adds a phosphate).
What does ADP phosphorylase do?
Removes a phosphate.
primary structure
linear sequence of AA’s made by ribosome, crucial to protein function.
What are the 2 ends of a primary structure?
- Amino / N-terminus
2. Carboxy / C-terminus
What does a deletion mutation in the CFTR gene produce?
cystic fibrosis, stops exporting chloride ions.
Which would explain the defect in the chloride channel function in humans with CFTR mutations?
A. missing Phe important for stabilizing alpha helices in CFTR protein.
B. missing Phe important for CFTR recognition by protein folding chaperones.
C. missing Phe part of beta sheet - no longer has correct structure w/o it.
D. missing F shifted neighboring amino acids out of frame - no longer contribute to folding.
E. all of the above.
E. all of the above.
What do ribosomes do?
translates mRNA into proteins, adds one AA at a time, makes peptide bond btw AA’s.
Which way do we read primary structures?
Amino / N-terminus to Carboxy / C-terminus.
Cysteine is in its oxidized form when?
its sulfhydryl group loses its Hs and forms a single bond btw 2 sulfurs.
2 sulfhydryl groups are in:
reduced form when they lose e-‘s to H
oxidized form when they share e-‘s w/ H.
What do disulfide bonds do?
stabilize protein structures using cysteines.
secondary structure
held together by H bonding
What are the 2 major structural components of secondary structures?
- alpha helix
2. beta sheet
What are some other structural components of secondary structures?
coiled coil, zinc finger, hairpin loops.
alpha helix
predicted from primary AA seq, part of secondary structure, R groups play a role.
beta sheets
parallel or antiparallel, form pleated sheets, R groups play a role.
What is a parallel beta sheet?
C-terminus and N-terminus on same sides.
What is an antiparallel beta sheet?
C-terminus and N-terminus on each side.
tertiary structure
gives overall 3-D shape of protein, combines elements of secondary structure, beta sheet and alpha helix.
motifs
combinations of secondary structures, determined by appearance not function.
domains
portion of protein that retains structure / function in absence of rest of protein, discretely folding 3D structure.
helix-turn-helix is an example of a?
motif
DNA-binding domain is an example of a?
domain
There is a physical and conceptual overlap btw?
motifs and domains.
What types of alpha helices are found in motifs?
helix-turn-helix, four-helix bundle, goblin fold (8 helices)
beta mofifs
include beta barrel, Greek key motif, and beta propeller.
What are the stabilizing forces involved in protein structure?
van der Waals forces, H-bonds, disulfide bridges, salt bridges.
Where is a G-protein coupled receptor located?
embedded in plasma membrane (typically).
Function of G-protein coupled receptors?
huge family of proteins: changes in receptor lead to activation and recruitment of other proteins on intracellular surface of receptors and transmit signals.
What are transmembrane domains?
span membrane, have many hydrophobic residues.
Hydrophobic effects help?
proteins bind, fold, embed into membranes.
hydrophobic effect
phenomenon where hydrophobic groups cluster together.
What are the 3 integral proteins?
- alpha-helix
- helical bundle
- beta-barrel
What are peripheral proteins?
enzymes, anchorage, transporters (carriers).
alpha helices are used for and by?
recognition, receptors.
Helical bundles are used for and by?
enzymes, transporters, receptors.
beta-barrels are used for and by?
transporters, channel proteins.
quaternary structure
complex structure, incorporates multiple subunits / diff proteins.
Multimers are made of?
monomers
monomers
single chains of AA’s folded into active protein.
multimers
several subunits, each is its own protein monomer (polypeptide chain) and are labeled based on function (catalytic / regulatory / etc.), not usually covalently linked.
What are the 3 types of multimers?
- dimers
- trimers
- tetramers
DNA helicase
unwinds DNA
What is the diff btw integral and peripheral proteins?
integral proteins span the cell membrane while peripheral proteins are on one side of the cell membrane.
