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54 Cards in this Set

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  • Back
Is the alpha helix right or left handed?
right handed
How many residues does the alpha helix have per turn?
3.6
What is a pitch?
The distance the alpha helix rises per turn
What is the average length of the alpha helix?
12 residues, which corresponds to three helical turns and a length of 18 A
How are the backbone hydrogens of the alpha helix arranged?
they are arranged such that the peptide C=O bond of the nth residue points along the helix toward the peptide N-H group of the (n + 4)th residue.
Which way do amino acid side chains point in the alpha helix?
amino acid side chains project outward and downward from the helix... consequently they avoid steric interference with the polypeptide backbone and with each other
How close are the atoms in the inner of the alpha helix?
the core of the alpha helix is tightly packed, so the atoms are in van der Waals contact
What type of bonding do alpha helices and beta sheets rely on?
Hydrogen bonding of the polypeptide backbone
Where does the hydrogen bonding take place in beta sheets?
Hydrogen bonding takes place between neighboring polypeptide chains rather than within one as in an alpha helix
antiparallel beta sheet
neighboring hydrogen-bonded polypeptide chains run in opposite directions

N-C
C-N
parallel beta sheet
hydrogen bonded chains extend in the same direction

N-C
N-C
What type of appearance do beta sheets have?
rippled or pleated
Is parallel or antiparallel more stable, and why?
Parallel beta sheets are less stable than antiparallel beta possibly because the H bonds of parallel sheets are distorted compared to those of antiparallel sheets.
Can mixtures of parallel and antiparallel sheets occur?
yes
What does topology refer to?
connectivity
How does the appearace of a beta sheet come about?
it is a compromise between optimizing the conformational energies of the polypeptide bonds and preserving the hydrogen bonding
Historically proteins have been classified as what?
fibrous or globular
Does keratin occur in all higher vertibrates?
yes
Name two characteristics of keratin?
mechanically durable, chemically unreactive
What type of keratin occurs in mammals?
alpha keratin
What type of keratin occurs in birds and reptiles?
beta keratin
What is the normal pitch of the alpha helix?
5.4
What type of structure is alpha keratin said to possess?
coiled coil
What is a coiled coil?
an arrangement of polypeptide chains in which two alpha helices wind around each other as in alpha keratin
What type of residues is alpha keratin rich in?
Cys- form disulfide bonds that crosslink adjacent polypeptide chains
What determines whether an alpha keratin is hard or soft?
sulfur content
Hard keratin is found in what?
hair, horns and nail
Soft keratin is found in what?
skin and callus
What can cleave disulfide bonds?
mercaptans
Why are hair and wool fibers springy?
since the coiled coil of alpha keratin likes to recover its original conformation
What is the most abundant vertebrate protein?
collagen
How many polypeptide chains is a single collagen molecule made of?
three
What does scurvy result from?
not enough vitamin C
What keeps collagen from forming an alpha helix?
Pro residues
What type of conformation does collagen like to assume?
left-handed helical conformation with about three residues per turn-three parallel chains wind around each other with a gentle, right-handed, ropelike twist to form the triple-helical structure it so loves!
What residue exists at every third position of a collagen polypeptide chain?
Gly
Lathyrism is caused by what?
regular ingestion of the seeds from the sweet pea (which contains a compound that inactivates lysyl oxidase)
Osteogenesis imperfecta (brittle bone disease) can be caused by what?
mutations of Type I collagen
Why can the twist in helix not be pulled out under tension?
its component polypeptide chains run in opposite directions
As what are collagen molecules in fibrils organized?
staggered arrays stabilized by hydrophobic interactions that result form the close packing of the triple-helical units
Why does collagen have a poor solubility?
because it is covalently crosslinked
Does collagen have Cys residues?
no, unlike keratin it is almost devoid of them
From what are the crosslinks in collagen derived?
Lys and His side chains
What does lysyl oxidase do?
converts Lys residues to those of the aldehyde allysine
Where do the cross links tend to be?
near the N- and C-termini of the collagen molecules
How does cross-linking compare to age?
increases with age- meat from older animals is tougher
The majority of proteins are...?
globular
random coil
the totally disordered and rapidly fluctuating conformations assumed by denatured proteins
denatured protein
fully unfolded
coils
segments of polypeptide chains whose successive residues do not have similar phi and theta values
native protein
folded proteins-nonrepetitive structures that are no less ordered than helices or beta sheets- only damn hard to describe
beta bulge
distortion in a beta sheet caused by an extra residue that is not hydrogen bonded to a neighboring strand
helix capping
a protein structural element in which the side chain of a residue preceding or succeeding a helix folds back to form a hydrogen bond with the backbong of one of the helix's four terminal residues
reverse turns, beta bends
a polypeptide conformation in which the chain makes an abrupt reversal in direction, usually consisting of 4 successive reversals