5. Protein structure Flashcards
what determines 3D protein structure
the amino acid sequence (primary structure)
T or F: the function of a protein is dependent on its structure
true
how many conformations do most proteins exist in
1 or 2
what type of forces stabilize protein structures
non-covalent forces
T or F: a proteins shape is different each time it folds
false; each protein has (at most) a few unique and consistent 3D structures
define configuration in regards to protein structure
requires the breaking of bonds (ie switching a protein from cis to trans)
define conformation in regards to protein structure
rotations about bonds don’t require breaking of bonds (ie binding to another molecule)
what does it mean for a protein to be stable
it maintains a functional, folded, native conformation under biological conditions
describe gibbs free energy (G) for a stable protein
a stable conformation has the lowest G compared to other conformations (this comes from many weak interacts)
why does a stable protein conformation have the lowest G value
due to many weak interactions
what features of an unfolded protein promote low G values (this discourages folding btw)
- unfolded state=high entropy
- polar residues in the unfolded state can form lots of hydrogen bonds with water (=many weak interactions)
- charged residues in the unfolded state can interact with salts
how does folding occur (ie what needs to happen)
a hydrogen bond that already existed in the folded state must be broken with water (so enthalpy doesn’t change much)
describe the enthalpy difference between folded and unfolded
since hydrogen bonds needed for folding come from pre-existing hydrogen bonds, the enthalpy (# of bonds) doesn’t change much
what are the weak interactions of a folded protein
- hydrophobic effect on the interior
- Van der Waals in the interior
- stabilizing ionic bonds between residues
- hydrogen bonds between residues
- disulfide bridges if the protein is to be secreted
T or F: the hydrophobic effect plays the biggest role in promoting the folded state
true
how does the hydrophobic effect plays the biggest role in promoting the folded state
it reduces the highly ordered solvation shell of water as residues clump together, which increases the entropy of the folded state. Without the large increase upon folding, the conformational entropy of the folded state wouldn’t be overcome. Proteins usually have a large number of hydrophobic residues because of this
why do proteins have lots of hydrophobic residues
- promotes folding
- entropy is increased as the highly ordered water shell is depleted when residues clump
define salt bridge
an ionic interaction of oppositely fully charged groups
T or F: salt bridges can form in the unfolded state
true; they can form between a polypeptide with salts in the aqueous solution
T or F: salt bridges help drive folding
true
how do salt bridges help drive folding
the strength of a salt bridge is higher as it moves from the aqueous cytoplasm to the protein’s hydrophobic interior
what properties do peptide bonds help with for the polypeptide chain
length, resonance, and rigidity
where is the peptide bond located
between the carboxyl C and the amino N of two residues
compare the peptide C-N bond with a simple amide C-N bond
the peptide C-N bond is a bit shorter than a simple amide C-N bond
what is the result of the peptide C-N bond being shorter than a simple amide C-N bond
it suggests partial sharing (resonance) or two electron pairs between the C and the N, and a formation of a small electric dipole
T or F: the peptide C-N bond can rotate freely
false; there is a slight double bond character, so the bond cannot rotate
what are the two possible positions of an alpha carbon
cis or trans
which position of the alpha carbon is least favorable? why
cis is less favorable because if steric hindrance between the R groups off the alpha carbon
in which position are nearly all peptide bonds in
trans
T or F: besides the C-N peptide bond, rotation occurs around other bonds in the backbone
true
what is a Phi bond?
N-C(a)
what is a Psi bond?
C(a)-C
what are phi and psi bonds often referred to as
dihedral angles
how do you determine the angle of a phi or psi bond
the atoms around the bond of interest are labelled 2 and 3. Place 1 at the bottom and 4 can then rotate with respect to 1. Look down atom 2, then look where 4 is and we can determine the angle
what are the angles of the cis and trans positions
cis=0
trans=+/- 180
T or F: even with the free rotation of phi/psi bonds, a rigid peptide bond greatly restricts the possible number of conformations that a polypeptide chain can adapt
true
how might phi and psi angles be limited
steric hindrance of the groups
what does a Ramachadran plot show
the likeliness of different conformations with respect to the phi and psi angles
what does each color represent on a ramachandran plot
dark blue=no steric hindrance (fully allowed)
light blue=conformations with slight clashes
white=non-permitted conformations
on a ramachandran plot, what does each dot represent
1 amino acid
which axis shows the phi bond
x axis
which axis shows the psi bond
y axis
how might glycine look on a ramachadran plot
it’s R group is only H, so there’s many options available (small R group=less steric hindrance). Glycine will have many dots in the white areas
how might proline look on a ramachadran plot
it’s R group is cyclic and very rigid, so it will be very limited in the types of angles it can make. It will only be in dark blue areas, but will be more constricted
which region of a ramachandran plot shows beta sheets
upper left quadrant
which region of a ramachandran plot shows alpha helixes
bottom left quadrant
what is the secondary structure of a polypeptide
can refer to any chosen segment of a polypeptide and describes the local spatial arrangement of its main-chain atoms (not side chains)
how might a secondary structure become regular
if the phi and psi angles remain very similar across the entire segment
what are the common regular secondary structures
alpha helix, beta conformation, beta turn
describe the shape of an alpha helix
the backbone is tightly wound around an imaginary longitudinal axis through the center
T or F: the alpha helix maximizes the number of hydrogen bonds for the segment
true
T or F: the alpha helix is hollow
false
describe the direction of the R groups of an alpha helix
they protrude outwards from the helical backbone
what are the two directions of alpha helices, and how do you determine this
left and right. Put your thumb in the direction of the helix, then see how your hand curls
are most alpha helices right or left
right
what is the length of one turn of the helix
5.4 Å
what is the length of one residue of the helix
1.5Å
how many amino acids are there per one helical turn
3.6
what is the degree of rotation per amino acid R group
100 degrees
what are the phi angles of the helix
-57
what are the psi angles of the helix
-47
how many residues apart do hydrogen bonds form (between carbonyl C and amide N)
4
T or F: each amino acid in a polypeptide has an intrinsic propensity to form an alpha helix
true
which amino acids have the greatest tendency to form alpha helices
those with numbers close to zero (ie alanine)
T or F: the neighbors of a residue influence its propensity to form an alpha helix
true
describe how dipole moments relate to alpha helices
each peptide bond has a small dipole, so these dipoles are aligned in the helix, resulting in a net dipole for the entire helix
how does the net dipole of an alpha helix relate to the length of the helix
the longer the helix=the longer the dipole
T or F: the ends of a helix have hydrogen bonding pairs
false
how might the unsatisfied ends of a helix find a hydrogen bonding pair
the partial charges may bond with the R groups to form caps of the helix
what percentage of alpha helices do proteins contain on average
26%
what is the average length of a helix
12 amino acids in length (3-4 turns)
describe the structure of an amphipathic alpha helix
hydrophobic amino acids on one face, hydrophilic on the other
describe amphipathic helices on the surface of proteins
the hydrophilic surface faces the aqueous solvent, and the hydrophobic surface faces the protein interior
what are the 3 types of beta conformations
strands, sheets, and turns
describe beta strands
single segment of backbone atoms into a zigzag pattern. The R groups alternate extending above and below the backbone
describe beta sheets
several beta strands side by side: zigzag causes a pleated appearance
describe beta turns
instances in globular proteins where the polypeptide chain reverses direction by 180 degrees
what are the two types of beta sheets
antiparallel and parallel
describe antiparallel beta sheets
stands have opposing amino-to-carboxyl orientations (more strength due to straight hydrogen bonds)
describe parallel beta sheets
strands have the same amino-to-carboxyl orientations (weaker due to angled hydrogen bonds)
which type of beta sheet is stronger + why
antiparallel, hydrogen bonds are straight
T or F: it’s common for beta sheets to have a hydrophobic side and a hydrophilic side
true
what is the purpose of beta turns
they tend to connect the ends of two adjacent antiparallel beta sheets
how many amino acids does a beta turn require
4
T or F: hydrogen bonds form in beta turns
true
where do beta turns form hydrogen bonds
the carbonyl oxygen of residue 1 forms a hydrogen bond with the amino group hydrogen of residue 4
how many types of beta turns are there? why
2, they have different phi and psi angles
which type of beta turn is more common
type 1 (the hydrogen bond is more straight)
which residues are common in beta turns
glycine and proline
why do beta turns commonly involve gly and pro residues
gly: extra flexibility due to smallest R group
pro: can uniquely form cis peptide bonds 6% of the time, which works great for a tight turn
what is the purpose of circular dichroism
it’s often used to determine the secondary structures present in a protein, and to monitor conformational changes or denaturation in proteins
what does circular dichroism show
shows the percentage of alpha helices and beta sheets in a protein
how do you interpret circular dichroism
on the graph, there’s light absorbance depending on the structure of the protein
what is tertiary structure
overall 3D arrangement of all the atoms in a polypeptide. Residues far apart may interact
how are tertiary structures held together
via several types of non-covalent interactions (ie disulfide bonds, hydrogen bonds, ionic bonds)
what is quaternary structure
the arrangement of multiple polypeptides into a 3D shape to form a functional protein
can monomers have quaternary structure
no
define homodimer
when the polypeptide chains of quaternary structure are identical
define heterodimer
when the polypeptide chains of quaternary structure are not identical
