Proteins 2 - folding 09/05 Traish Flashcards
what is protein primary structure
order of aa’s
by convention, an aa polypeptide sequence is written from __-terminus to __-terminus
N-terminus to C-terminus
secondary structure consists of…
locally folded structures (a-helices, b-sheets, turns, random coils [loops]) dependent on H-bonding between a-N and a-C groups
T/F secondary structure depends upon H-bonding between R groups
False
depends upon H-bonding between primary amino and carbonyl
by convention, the __-terminus is left and the __-terminus is right in an aa polypeptide sequence
N-terminus left
C-terminus right
tertiary structure consists of…
3-D structure from interactions between domains in a single pp sequence
tertiary structure is dependent upon what kinds of intermolecular interactions
H-bonds, hydrophobic interactions, electrostatic interactions, van der Waal’s forces, disulfide bonds
quaternary structure is dependent upon what kinds of intermolecular interactions
H-bonds, hydrophobic interactions, electrostatic interactions, van der Waal’s forces, disulfide bonds (same as tertiary) BUT globular protein monomers are RARELY held together by disulfide bonds and never by other covalent linkages
do the same intermolecular interactions stabilize tertiary and quaternary structure?
yes they can
is hemoglobin a homo-oligomer or hetero-oligomer?
hetero-oligomer – 2 alpha subunits, 2 beta subunits
what is a homo-oligomer?
an oligomer composed of identical subunit monomers
what is a hetero-oligomer?
an oligomer composed of non-identical subunit monomers
a tetramer is__
an oligomer with 4 monomeric subunits
the bond between a-amino and a-carboxyl aa groups is called
a peptide bond
can a peptide bond twist/rotate? why?
very little – partial double bond character (delocalization of pi electrons)
quaternary structure consists of
the oligomerization of multiple monomeric subunits from separate pp sequences
how are the C=O and N-H bonds of a peptide bond oriented to one another?
parallel – usually antiparallel
T/F the O, C, N, and H of a peptide bond are nearly coplanar
true
what does it mean that a peptide bond is “metastable?”
proteins hydrolyze in an aqueous environment when a catalyst is present
T/F a peptide bond can rotate
false (double bond character)
T/F the N-C alpha and C-C alpha bonds can rotate?
true
the aa N-C alpha bond is called __
phi (O with |
the aa C-C alpha bond is called __
psi (pitchfork)
common secondary structures include
a helices, b sheets, turns, loops / coils (as yet unclassified)
what is a crystallographic repeat?
a periodically repeating pattern of atoms in 3D
what does a crystallographic repeat measurement (c) refer to?
distance parallel to the axis of a-helix over which the structure exactly repeats itself
a-helix pitch (p) refers to…
distance parallel to a-helix axis in one turn
a-helix rise (h) refers to
distance parallel to a-helix axis from one residue to next
a-helix (n) refers to
the number of residues… per turn, or repeat, or what have you
do R groups exist on exterior or interior of an a-helix?
exterior
2 aa’s that are likely to disrupt an a-helix include:
G, P
a “dihedral” angle is…
the angle between two planes
T/F the dihedral angle pairs, phi and psi, can differ from one residue from the next in an a-helix
false – dihedral angle pairs are the same for each residue
T/F a-helices are classified as “repetitive secondary structure”
true – their backbone phi and psi angles repeat
what are the phi and psi angles in an ideal, right-handed a-helix?
phi = -57.8
psi = -47.0
(- signifies counter clockwise)
what do + and - rotation angles in phi and psi refer to?
\+ = clockwise rotation - = ccw rotation
T/F a-helices are the most abundant helical conformation found in globular proteins
true
a-helices account for __ to __ percent of all globular protein residues
32-38%
average n in an a-helix is…
10 residues
H-bonds in an a-helix are between…
each backbone C=O and the backbone N-H 4 residues ahead (i+4)
T/F H-bonds in an a-helix are between each backbone N-H and the backbone C=O 4 residues ahead
false. between each backbone C=O and the backbone N-H 4 residues ahead (i+4)
X-ray data suggest that an a-helix repeats itself after __ residues
18
how many turns are there in an alpha helix repeat?
5
how many residues per a-helix turn?
3.6
a-helix pitch (p) is __ nm
.54 nm per turn
a-helix rise (h) is __ nm, or __ angstroms
.15 nm per residue
- or-
1. 5 A per residue
how many angstroms in a nanometer?
10
how many meters in an angstrom?
10^-10
how many angstroms in a meter?
10^10
a stretched a-helix will have a (higher or lower) rise and a (higher or lower) n per turn
a stretched a-helix will have a higher rise and a lower number of residues per turn
prolyl residues, adjacent bulky residues, adjacent branched residues ,and adjacent charged residues can all do what to an a-helix?
interrupt it
how many polypeptide stretches are involved in an a-helix vs a b-sheet?
a-helix – single stretch
b-sheet – multiple stretch
beta stretches consist of at least __ to __ aa’s
5-10
a key difference between the H-bonds in a-helices vs b-sheets is…
b-sheets H-bond between different pp stretches
a-helices H-bond along the same strand
why are b-sheets “pleated” ?
the alpha carbons alternate above and below the plane of the sheet
T/F b-sheets can be parallel, antiparallel, or mixed
true
what is a parallel b-sheet
adjacent stretches’ N-termini and C-termini run in same directions
what is an anti-parallel b-sheet
adjacent stretches’ N-termini and C-termini run in opposite directions
golubular proteins cointain __ to __ percent b-sheets
20-28%
what is the basic unit of a b-sheet
b-strand (n=2 residues/turn)
a b-strand can be thought of one turn of a helix with n = __ residues per turn
n=2 residues per turn
the backbone dihedral angels, phi and psi, in a b-strand, are:
phi = -120 psi = +120
translational “rise” (h) in a beta sheet is __ for antiparallel strands
3.2 nm per residue
translational “rise” (h) in a beta sheet is __ for parallel strands
3.4 nm per residue
is translational “rise” (h) in a beta sheet greater for parallel strands or antiparallel strands?
h is greater in parallel strands (3.4 nm vs 3.2 nm)
are there any intrasegment H-bonds or van der Waal’s forces in a b-sheet?
no – only intersegment forces – due to the extended nature of the chain
what is the average length of a b-pleated sheet?
6 residues
most b-pleated sheets contain fewer than __ strands
fewer than 6 strands
do side chains from adjacent residues in a b-sheet interact with each other?
no – because they exist on alternating sides of the sheet
can b-sheets exhibit amphiphilicity with one face polar and one face nonpolar? can a-helices?
yes in both cases
can a-helices be formed from strands from distant portions of the pp chain? can b-sheets?
a-helices - no
b-sheets - yes
which is thought to be more intrinsically stable, antiparallel b-sheets or parallel b-sheets? why?
antiparallel
- more optimal orientation of hydrogen bonds
- peptide dipoles cancel
are side chains closer / interacting more strongly in parallel or antiparallel b-sheets?
same in both. side chains can match up above and below the plane of the sheet either way
the most stretched “helix”, with n=2 residues per turn, is also known as…
a beta sheet
what kind of secondary structure is pervasive in silk versus wool?
silk = b-sheets (strong & inextensible because already maximally stretched, flexible because only H-bonding) wool = a-helices (stretchy because coiled and H-bonds along axis of fiber, not perpendicular)
what is the typical secondary structure of an immunoglobulin fold (hypervariable domain / antigen binding site) ?
two antiparallel b-sheets in a barrel structure
what is the primary function of a “turn” in protein secondary structure?
reverse the direction of the polypeptide chain
where are turns primarily located?
on the protein surface
are residues on a turn mostly hydrophobic or hydrophilic?
polar and charged because they exist usually at surface where protein must be turned back in
T/F antibody recognition, phosphorylation, glycosylation, and hydroxilation sites are frequently found at or adjacent to “turns”
True – turns mostly located at surface with polar and charged residues as it turns the pp sequence back toward protein
approximately what proportion of globular protein residues are “turns” ?
~1/3
approximately __ to __ percent of residues in globular proteins can be calssified as participating in a-helices, b-sheets, or reverse turns
80-90%
this secondary structure is compact and globular in structure
loop
loops contain between __ and __ residues
6 and 16
T/F like turns, loops generally contain polar residues and are predominantly found at the protein surface
true
between a-helices, b-sheets, turns, and loops, this is the order of frequence in globular proteins
a-helices & turns (most common)
loops & b-sheets (less common)
T/F in globular proteins, a-helices and turns are more common than loops and b-sheets
true
describe the hydrophobic effect in protein folding
non polar side chains tend to be buried in the center of proteins with polar chains on outside
T/F hemoglobin exists as a single polypeptide chain
false – it is a tetramer
T/F myoglobin exists as a single polypeptide chain
true – it is a monomer
what is the name of the “O2 warehouse” protein that stores oxygen in muscle tissue?
myoglobin
T/F fibrous proteins are elongated molecules with well-defined secondary structures that play structural roles in cells (skin, connective tissue, hair, silk)
true
T/F alpha-keratin, fibroin, and collagen are examples of globular proteins
false – they are fibrous proteins
T/F a “domain” is a compact, locally folded region of tertiary structure
true
T/F a protein domain can be classified as predominantly a-helix, predominantly b-sheet, or mixed
true
T/F beta sheets can be twisted
true – they are usually twisted or wrapped into barrel structures
T/F “random coil” secondary structures are sometimes referred to as “turns”
false – they are sometimes referred to as “loops”
is the conformational entropy change of protein folding + or -, favorable or unfavorable?
-, unfavorable
is the enthalpy change arising from protein folding + or -, favorable or unfavorable?
-, favorable
is the entropy change of burying hydrophobic groups in protein folding + or -, favorable or unfavorable?
+, favorable
how does the hydrophobic effect in protein folding increase entropy?
it eliminates the orderly formation of “hydration shells” along hydrophobic surfaces. adjacent to hydrophilic surfaces, H2O is not restricted in orientation or mobility
what two thermodynamic factors does Gibbs free energy combine?
enthalpy and entropy
what is the equation for Gibbs free energy of a system
dG = dH - TdS "G = HoTS"
T/F when calculating Gibbs free energy of protein folding, you must remember to account for dH, dS, and T of both protein and solvent
true.
dH = dHp + dHs
dS = dSp + dSs
is protein folding spontaneous when dG is + or - ?
negative dG is spontaneous
what scientist performed the experiment to demonstrate that protein folding depended on primary structure?
Nobel laureate Christian Anfinsen
what protein did C. Anfinsen denature in his experiment with protein folding?
ribonuclease
what is the normal function of ribonuclease?
hydrolyze RNA into single nucleotides
what organic solvent did C. Anfinsen use to denature ribonuclease in his experiment with protein folding?
urea
(disrupts hydrogen bonds in protein by replacing them with hydrogen bonds with itself
what substance did C. Anfinsen use to reduce the disulfide bonds in ribonuclease in his experiment with protein folding?
beta-mercaptoethanol
why were small amounts of beta-mercaptoethanol needed to ensure appropriate renaturation of ribonuclease in c. Anfinsen’s experiments with protein folding?
2ME (b-mercaptoethanol) was needed to allow inappropriate disulfide bonds to break and find the most stable conformation
how many disulfide bonds are involved in the tertiary structure of ribonuclease?
4
how many cysteine residues are involved in the tertiary structure of ribonuclease?
8
what are the odds of approprate renaturation of ribonuclease if determined randomly (not by primary pp sequence?)
1/71/51/3*1/1 = 1/105 = <1%
what was the rate of ribonuclease function restoration (appropriate renaturation) achieved by C. Anfinsen in his experiments with protein folding?
97%
how does beta-mercaptoethanol disrupt disulfide bonds?
it is a thiol agent that reduces disulfide bonds as it is oxidized into dimers joined by disulfide bonds itself
T/F a molecule containing -S-S- bridges has a larger number of conformations available in the unfolded form than does a comparable protein without the bridges
False
-S-S- bridges reduce the number of conformations available to an unfolded protein
what degree of protein structure is involved in allosteric regulation?
quaternary structure (requires interactions with other proteins / molecules -- e.g. hemoglobin)
this amino acid, found in milk, eggs, and lime but not in corn or dry cereal, is a pre-courser of vitamin B3 and a lack may cause dermatitis
W
e.g. southern corn diet vs mexican lime+corn diet
T/F the Linus Pauling postulates re polypeptide conformations include:
- bond length and angles should be distorted as little as possible
- no two atoms should violate each other’s van der Waal’s radii
- amide group remains planar and trans config (phi & psi rotation only)
- non-covalent usually H-bonds between N and C groups stabilize folding
true
