2. protein structure

cumamiwu's version from 2016-03-09 20:36

basics of protein structure

Question Answer
define primary structuresequence of amino acids, from N to C
local stcture of small segment of protienlocal structures of small segment of protein
define tertiary structureorientations of secondary structures of a single polypeptide – one molecule
define quaternary structureorientations of polypeptide subunits
there is hindered rotation about the _____ bonds in a peptide chainC-N
what generally prevents the cis configuration of peptide bond?steric hindrance
what is psi?trident-looking, represents angle between Calpha & carbonyl C
what is phi?sideways theta, represents angle between N & Calpha
when phi & psi both = 0 there is a steric clash between _______ of one and ______ of othercarboxyl O amino H
when phi = _____ & psi = _____, backbone is fully extended180

fibrous proteins & secondary structure

Question Answer
how are alpha helices stabilized?hydrogen bonds
each amino acid turns about ____ degrees in an alpha helix100
each turn of an alpha helix is how long (what is the pitch)?5.4 Angstroms
how many residues per turn of an alpha helix ?3.6
who first imagined the alpha helix?linus pauling, later verified by xray
R-groups, in an alpha helix,project away from the helix core, if mutually attracted can help hold helix together
what is the numerical representation of an alpha helix? why?3.6 sub13, because 13 atoms form ring closed by H-bond
in an alpha helix, phi =-60
in an alpha helix, psi =-45 - -50
most alpha helices found in proteins are ____-handedright
what’s the handedness rule for helices?point thumb towards C-terminus
negative residues are often found at the ___ terminus of an alpha helixN
positive residues are often found at the ___ terminus of an alpha helixC
residues _________ do not participate fully in hydrogen bonds4 residues at end of alpha helix
the dipole nature of the alpha helix is in what direction (- to +)?C to N
side-chains that contain _________ in close proximity to the main chain destabilize the alpha helixH-bond donor & acceptor – compete with main chain H bonds
R with H-bond donor & acceptor?e.g. Asp
putting _____ in an alpha helix is entropically expensiveGly
Proline phi = _____ because of ring structure-65 degrees
2 reasons proline isn’t likely in an alpha helix1) ring structure, rigid angles, poor backbone packing (2) no amide H… no H-bonds
Beta sheets are held together byhydrogen bonds
Beta sheets are pleated at which atom? alpha C
antiparallel beta sheets have a (smaller/larger) repeat distance and (smaller/larger) phi & psi angleslarger, larger
(anti/parallel) is held together by more linear H-bondsantiparallel
parallel beta sheets have a (smaller/larger) repeat distance and (smaller/larger) phi & psi anglessmaller, smaller
which type of beta turn is more common?type I
which type of beta turn uses glycine as the #_________ residue?type II, 3
how many residues are in a beta turn?4
in cis-proline, phi is locked at-65 degrees
cis proline is useful forbeta turns
3 most common residues in alpha helixglu(E), met(M), ala(A)
3 least common resides in alpha helixgly(G), pro(P), Tyr(Y)
in a Ramachandran plot, phi is on the ___ axisx
in a Ramachandran plot, psi is on the ___ axisy
most bond angles lie where on the Ramachandran plot?second quadrant, (-180 phi, +180 psi)
left-handed alpha helices lie where on the Ramachandran plot?first quadrant (+60 phi, +60 psi)
right-handed alpha helices lie where on the Ramachandran plot?third quadrant (-60 phi, -60 psi)
beta sheets lie where on the Ramachandran plot?second quadrant, (~ -120 phi, +120 psi)
collagen triple helix lies where on the Ramachandran plot?second quadrant
why isn’t glycine included in most Ramachandran plots?too many angles
Ramachandran plots can give us an idea about a protein’s ______ary structuretertiary

protein folding

Question Answer
there are on the order of _____ supersecondary structures (folds/motifs)100
compare the alpha helix to beta sheet ratio for lysozyme, myoglobin, & ribonucleasemost alpha sheet: myoglobin, lysozyme, ribonuclease
what can we infer from the relatively few supersecondary structures, given that many are theoretically possible?folds come together to form domains, sorta independent regions (still single polypeptide) – can have independent functions
these two proteins are L-handed superhelices of 2 R-handed helicesmyosin & keratin
in coiled coils, helices are packed against each other in a(n) (anti/parallel) orientationparallel
define leucine zipperin L(R,R) supercoils, hydrophobic leucine points towards the interface
collagen is a _________-handed superhelix of ___ _________-handed helicesR(L,L,L)
in collagen, how many residues per turn? more or less than alpha helix?3.3, less than alpha helix
near the center of the triple helix, what residues make up the strand?P, P, G, P, P, G…
collagen constitutes ___% of protein in your body25%
what is the function of the post-translationally modified residues in collagenadding OH to increase H-bonding to stabilize protein
what is the pre-modified collagen called?pro-collagen
modifications to pro-collagen are catalyzed by a family of ______ enzymesdioxygenase
the catalysis of pro-collagen  collagen requiresascorbate (vitamin C)
which two residues comprise 30% of collagen? what do they do for it?Pro & Hyp

forces that drive protein folding

Question Answer
dG(folding) =(dH – TdS)chain + (dH – TdS)solvent
the enthalpic contribution from the polypeptide makes the folding _____ spontaneousless, because peptide residues have stronger interactions with water molecules than with each other
the enthalpic contribution from the solvent makes the folding _____ spontaneousmore, because water molecules have stronger interactions with each other than with polypeptides
the entropic contribution from the polypeptide makes the folding _____ spontaneousless, because the structure is more constrained
the entropic contribution from the solvent makes the folding _____ spontaneousmore, because water molecules are “caged” around a smaller surface area
two steps of Christian Anfinsen experiment?1) add urea & mercapto-ethanol to protein  reduce disulfide cross-links, (2) remove urea & mercapto-ethanol  reformed native protein
conclusion & significance of Christian Anfinsen experiment?primary structure determines native conformation, can predict native conformation from primary structure
Levinthal paradoxnot enough time for a protein to find the native state through randomly going through possible conformations
why might the native state not have the lowest free energy possible?it needs to catalyze reactions – jiggling is necessary for function, LOCAL MINIMUM - speed of formation might make a difference
1st folding pathwaylocal 2ndary structure formation & hydrophobic collapse
2nd folding pathwaycondensation of supersecondary structures
3rd folding pathwaycompaction – molten globule formation
4th folding pathwayconformational adjustment – e.g. proline isomerization, disulfide bond formation
5th folding pathwaysubunit assembly
in thermodynamic control of protein folding, the outcome is determined by ________, & N is at the ______ energy minimumfree energies of unfolded, intermediates, & native forms. not at all dependent on how folding happens, GLOBAL min
in kinetic control of protein folding, the outcome is determined by ________, & N is at the ________ energy minimumpathway through which protein folds, LOCAL min
major complication of protein folding within a cellular environment?macromolecular crowding  aggregation if not folded
what is the protein concentration inside a cell?300g/L
role of molecular chaperones?encapsulate new proteins in hydrophobic environment – conducive to folding
3 examples of molecular chaperones?chaperonin, PPI & PDI
what is PDI? function?protein disulfide isomerase, a molecular chaperone that rapidly shuffles disulfide bonds, to find native conformation
what is PPI? function?peptidyl prolyl cis-trans isomerase, a molecular chaperone that converts trans proline  cis proline
5 examples of protein misfolding diseasescystic fibrosis, cataracts, scurvy, prions, amyloid diseases (Alz, Hunt, Park)

experimental techniques


Question Answer
4 ways to denature a protein1) extreme pH, (2) detergents, (3) high temp, (4) chaoatropic agents
how does extreme pH denature a protein?alters ionization state of side chains, changes H-bonding
how do detergents denature proteins?associate with nonpolar residues & disrupt hydrophobic interactions
how does heat denature proteins?increases vibrational & rotational energy
how do chaotropic agents denature proteins?make more favorable interactions with all residues than water does
what can be said about free energy in protein-denaturing conditions?unfolded has lower free energy than native
2 chaotropic agentsurea & guanidinium chloride
graph of [GdnHCl], percent unfolded is what shape?sigmoid… cooperative!
separating proteins based on size is called _______, & ______ proteins filter faster.gel-filtration chromatography, larger
medium of gel-filtration chromatography?cross-linked polymer
separating proteins based on charge is called ________ion exchange chromatography
cation exchangers are ______-charged beads which slow down ___-charged proteins(-), (+)
anion exchangers are ___-charged beads which slow down ____-charged proteins(+), (-)
the first fractions of a cation exchanger are ____--charged proteinsnegatively
the first fractions of an anion exchanger are ____-charged proteinspositively
in SDS gel electrophoresis, movement in the gel is a function ofmolecular weight of protein monomers
in SDS gel electrophoresis, denatured proteins are move toward a ______cathode
what agent, other than SDS, is used in SDS gel electrophoresis? function?beta-mercaptoethanol, breaks S-S bonds
medium of SDS gel electrophoresis?polyacrylamide gel


exam 1