Proteins Flashcards
Peptides are…
amino acids linked together by a peptide bond usually through dehydration reactions
Peptide bonds are…
an amide linkage between amino acids
Peptides are always named from the…
N-terminus to the C-terminus
T/F: peptides are not polyamphoteric
F
Polyamphoteric molecule:
polypeptide with one or more amino acids containing an ionizable side chain
- gives multiple pKa values
T/F: shifts in pH can greatly affect protein shape
T
Two possible forms of peptides:
- trans: usually favored due to steric hindrance
- cis: possible but still not favored in proline
Enzymatic cleavage of peptides:
- enzymes required to hydrolyze polypeptide since uncatalyzed hydrolysis is extremely slow at physiological pH
Digestive enzymes or proteases cleave…
peptide bonds at specific locations
Two types of chemical cleavage:
- cyanogen bromide (CNBr)
- Edman degradation
Where does cyanogen bromide cleave?
cleaves after methionine amino acids
How/what does Edman degradation cleave?
amino acids are chemically cleaved from N-terminus one at a time
Rn-1 means that it cuts…
after amino acid listed
Rn means that it cuts…
before amino acid listed
Protease inhibitors function by blocking..
cleavage of specific materials in viral envelope and stops newly formed virus from maturing
Proteins have a defined sequence that dictates…
- specific folding pattern
- structure of the protein
Structure of the protein enables protein to…
perform specific function
Primary structure is the..
amino acid sequence
- dictated by genetic code
Secondary structure is the…
local folding
Tertiary structure is the…
overall fold
Quaternary structure is the…
subunit association
- organization of multiple subunits/domains
Ramachandran Plot:
demonstrates the type of secondary structure that a particular amino acid is likely to form
Secondary structure describes the local fold of a protein and can be predicted from….
Ramachandran Plot
Alpha helix are found where…
amino acid angles psi and phi are about -50 degrees and -60 degrees
- corresponds with the bottom left quadrant of Ramachandran Plot
Alpha helix has _____ residues per turn
3.6
The H bonds between C’=O in the alpha helix have residue of…
n
N-H in alpha helix have residue of…
n+4
- fewer residues per turn compared to H bonds
Alpha helix have a dipole moment w/…
negative at C terminus and positive at N terminus
What makes alpha helix and beta sheet very stable and energetically favorable?
- H bonds
- max separation of amino acid (residue) side chains
beta-pleated sheets are arranged either:
- parallel
- antiparallel
beta-pleated sheets are usually up to _____ residues long w/ psi and phi angles in the _______ quadrant of Ramachandran plot
5-10, upper left
T/F: For beta-pleated sheets, H bonds that form between C’=O groups and the N-H groups are on the same strand
F, each are on their own strand
T/F: beta-pleated sheets are pleated w/ alpha C above and below plane
T
Loop regions (turns) usually connect…
two adjacent antiparallel beta strands
- proline is often found here
Random coil is a term given to…
secondary structure which is neither helical or beta sheet
Globular proteins have a defined…
inside and outside
Beta sheets of globular proteins are…
usually twisted/wrapped into barrel structures
Polypeptide chain of globular proteins can…
turn in a # of ways
Helix-loop-helix motif is called…
EF HAND
Protein stability is affected by:
- pH
- temp
- chemicals
T/F: electrostatic interaction that contributes to enthalpy stabilizes protein and reduces entropy
T
pH can cause a change in _______ and alter _______
protonation state, H bonds
pH will eventually cause ______
protein to denature
Proteins are soluble at _____ pH, but insoluble near their ____
high and low, pl
Proteins can denature due to change in:
- temp (thermal denaturation)
- chem (guanadinium hydrochloride/urea)
- ionic strength
- solvent nature (hydrophobic effect)
Thermal denaturation:
increase in temp = increases unfolding
Protein folding is driven by…
enthalpy
An increase in [urea] leads to…
denaturization of proteins
Ionic strength changes include:
- salting in
- salting out
Salting in:
soluble proteins by increasing ionic strength w/ type of ion that tends to result in solubilizing of proteins
Salting out:
precipitate proteins by increasing ionic strength w/ type of on that tends to form protective ion shells
- repels protein molecules and decreases solubility
Folding proteins will maximize:
- # of H bonds
- buried nonpolar groups
Folding proteins will minimize:
- interstitial cavities or spaces
- # of “bad” contacts
- # of buried charges
- radius of gyration
- covalent and noncovalent E
T/F: all proteins can be renatured by slowly changing conditions back to favorable
F, some but not all
Problems w/ protein drugs:
- denaturation
- aggregation and precipitation
- protein modification
- proteolysis
Classes of protein drugs:
- vaccines
- peptides
- blood products
- recombinant therapeutic proteins
Storage to overcome problems:
- freeze drying
- maintaining pH
- balancing ionic strength
- refrigeration
Delivery systems to overcome problems:
- pH sensitive microspheres
- transdermal patches
Prion diseases are associated w/…
mis-folded proteins
Normal form of PrPc:
- transmembrane glycoprotein found at surface of neural cells
- very soluble
- easily digested by proteases
- c stands for cellular
Normal PrPc is primarily what shape?
alpha helix
Abnormal PrPsc:
- sc stands for scrapie
- identical primary protein structure to PrPc
- insoluble
- resistant to digestion by proteases
Abnormal PrPsc is primarily what shape?
beta sheet
Human prion diseases:
- Creutzfeldt-Jakob Diseases (CJD)
- kuru
% of Creutzfeldt-Jakob Diseases (CJD) that are in sporadic form?
85
% of Creutzfeldt-Jakob Diseases (CJD) that are caused by family genetic mutations?
14
% of Creutzfeldt-Jakob Diseases (CJD) are caused by contamination from brain surgery?
1
Main symptoms of human prion diseases:
- social withdrawal
- insomnia
- dementia
- muscle paralysis
- coma
Kuru is infectious and comes from…
eating brain of deceased humans
Effects of disulfide bonds on protein fold:
oxidizing and reducing disulfide bonds may affect folding
T/F: some proteins require chaperonins to aid in folding
T
Where are charperonins secreted from?
ribosome during translation
Most common and understood charperoins:
Gro-EL
