exam 2 biochem practice questions Flashcards
(107 cards)
what is the major themes in chapter 4
primary sequence to 3-D structure
structure = function
each protein has a unique structure (is also not static but dynamic)
non-covalent forces are very important
many structures have common patterns that are given a name (like domain and motif….I think)
what is different about protein compared to other organic polymers
what does the conformation of a protein allow the protein to do
has a specific 3-D conformation
allows the protein to function
what is a native fold
what can be said about its energy
the properly folded, functional conformation of a protein
it has the lowest free energy
what does the native fold have and are examples of it
The native fold has a large number of favorable interactions within the protein for stability
example: ”burying” hydrophobic groups and maximizing H-bonding
how is protein conformation stabilized by
what do these combat
Disulfide bonds
Weak, non-covalent interactions
THESE COMBAT ENTROPY
what are the Favorable Interactions in Protein Folding used to Maintain a Native State (fold)?
hydrophobic effect
hydrogen bonds
van der waals interactions
electrostatic interactions
what does the Hydrophobic Effect do for the native fold
Release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy
Correctly position hydrophobic side chains depending on the environment
what does hydrogen bonding do for the native fold
Interaction of N-H and C=O of the peptide bond leads to local regular structures such as α-helices and β-sheets
- Side chain – side chain interactions. H-bonding between R-groups, H-bonding between backbone and R-groups.
what does van der waals do for the native fold
Weak attraction between all atoms contributes significantly to the stability in the interior of the protein
what do Electrostatic Interactions
dof ro native fold
Long-range strong interactions between permanently charged groups
Salt-bridges, especially buried in the hydrophobic environment strongly stabilize the protein
what does secondary structure start with
starts with primary structure
2 structures
describe the peptide bond
describe carbon-carbon bonds, what is another name for it
describe the carbon-nitrogen bond, what is another name for it
for psi/phi bonds, what can occur but what will be prevented
the peptide bond is rigid and planar, constraining the protein to certain, allowed conformations
Carbon-carbon (psi - Ψ) bonds can rotate
Carbon-nitrogen (peptide) bond (phi - Φ) cannot rotate
In theory, + / - 180° rotation for phi/psi bonds can occur,but…
- Steric Hinderance will prevent some angles from occurring…
what does steric hindrance effect and what is the result
steric hindrance can affect side chains and the backbone reduces possible rotations
what does a Ramachandran plot show
what does steric hindrance prevent
Shows common secondary structural elements and the acceptable range of rotation
Steric hindrance prevents all but a handful of secondarystructures
what is the structure of a peptide bond?
how many atoms does it have
is rigid and planar, constraining the protein to certain conformations
has 6 atoms
what do secondary structures consist of
alpha helix
beta-sheets
parallel beta sheets
antiparallel beta sheets
how is the helical backbone of an alpha helix held together?
what kind of direction is an alpha helix
what stabilizes the alpha helix
where are the side chains for the alpha helix
which residues align on top of each other
The helical backbone is held together by hydrogen bonds between the backbone amide of an “n” and carbonyl group of the “n + 4” amino acid
ann alpha helix is a right-handed helix
the hydrogen bond aligns roughly parallel with the helical axis and this stabilizes it
Side chains point out and are roughly perpendicular to the helical axis
residues 1 and 8 align on top of each other
describe the inner diameter of alpha helix, what can fit innside
describe the outer diameter of alpha helix, what can fit inside
what can amphipathic alpha helices form
what is the relatiionship between proline, glycines and alpha helices
does every polypeptide forrm a alpha helcies
what amino acids are strong helix formers
The inner diameter of the helix is about 4-5ÅToo small for anything to bind inside
The outer diameter of the helix (with side chains)is 10-12 Å. Fits into the major groove of dsDNA
Some amphipathic α-helices can form coiled-coildimers (stay tuned – keratin)
α-helices cannot be formed with Pro kink(disrupts the helix). Gly is a helix breaker too.
Not all polypeptide sequences adopt α-helical structures
Small hydrophobic residues such as Ala and Leu are stronghelix formers.
what is the cause of the sheet-like zig zag structure of beta sheets
what holds together the sheet-like arrangement for beta sheet
where are the side chains in beta sheets
what amino acids are found in beta sheets
what amino acids are not found in beta sheets
The planarity of the peptide bond and tetrahedral geometry of the α-carbon create a pleated sheet-like structure (zigzag)
Sheet-like arrangement of the backbone is held together by hydrogen bonds between the backbone amides and carbonyl groups in different strands
Side chains protrude from the sheet alternating in up and down directions
Found in β-Sheets:
Large, aromatic (Y, F, W)
Branched (T, V, I)
NOT Found in β-Sheets:
G, P
in parallel beta sheet, where do the H-Bonds run and what does it result in
where can the individual strands be in the primary structure
In parallel β-sheets, the H-bonded strands run in the same direction,
Resulting in bent H-bonds (weaker)
Individual strands can be close, or distant, in the primary structure
in anti-parallel beta sheet, where do the H-Bonds run and what does it result in
where can the individual strands be in the primary structure
In antiparallel β-sheets, the H-bonded strands run in opposite directions, Resulting in linear H-bonds (stronger)
Individual strands can be close, or distant, in the primary structure
how are most proteins shaped
what is the reason for this shape
how many A.A residues are in turns or loops
what do the arrows in strands and sometimes in helices indicate
when do beta turns occur
how is the 180* turn accomplished
how are beta turns stabilized
what amino acid is found in beta turn type 1
what amino acid is found in beta turn type 2
Most proteins are globular in shape
the globular shape is due to of frequent turns or loops in the polypeptide chain that connects beta strands and alpha-helices
1/3 of AA residues are in turns or loops
Strands, and sometimes helices, will have arrows to indicate N- and C- termini of the 2° structural element
β turns occur frequently whenever strands in β sheets change direction (so whenever the beta sheets turn to change direction)
The 180° turn is accomplished over 4 amino acids
Turn stabilized by a H-bond
type 1: proline
type 2: glycine
what is the tertiary structure and what does it include
how is it stabilized
what interactions largely make it up
how else can it be stabilized
what Is also possible
what are two major of tertiary structure
Tertiary Structure – overall 3D arrangement of all atoms in a protein
Includes long-range contacts between AA’s in a single polypeptide chain
‘Stabilized by numerous weak interactions between amino acid side chains
Largely hydrophobic and polar interactions
Can be stabilized by disulfide bonds
Side chain with backbone interactions are also possible
Two Major Groups
- Fibrous (elongated; structural)
- Globular (enzymes, etc.)
what do tertiary structures often have and is it solute in water
what does it contain a high proportion of and what are examples of these
are the underlying structures complicated
what does it have a high proportion of
what does it have extensive of
what are examples of fibrous proteins
Often have structural rather than dynamic roles and are water insoluble
Typically contain high proportions of α-helices (keratin) or β-pleated sheets (fibroin)
High proportion of hydrophobic AAs–that is why it is water insoluble!!!!!!!!!
Extensive supramolecular complexes
Fibrous Proteins: α-keratin, collagen, silk fibroin