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54 Cards in this Set
- Front
- Back
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Is the alpha helix right or left handed?
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right handed
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How many residues does the alpha helix have per turn?
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3.6
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What is a pitch?
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The distance the alpha helix rises per turn
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What is the average length of the alpha helix?
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12 residues, which corresponds to three helical turns and a length of 18 A
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How are the backbone hydrogens of the alpha helix arranged?
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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.
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Which way do amino acid side chains point in the alpha helix?
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amino acid side chains project outward and downward from the helix... consequently they avoid steric interference with the polypeptide backbone and with each other
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How close are the atoms in the inner of the alpha helix?
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the core of the alpha helix is tightly packed, so the atoms are in van der Waals contact
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What type of bonding do alpha helices and beta sheets rely on?
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Hydrogen bonding of the polypeptide backbone
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Where does the hydrogen bonding take place in beta sheets?
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Hydrogen bonding takes place between neighboring polypeptide chains rather than within one as in an alpha helix
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antiparallel beta sheet
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neighboring hydrogen-bonded polypeptide chains run in opposite directions
N-C C-N |
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parallel beta sheet
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hydrogen bonded chains extend in the same direction
N-C N-C |
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What type of appearance do beta sheets have?
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rippled or pleated
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Is parallel or antiparallel more stable, and why?
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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.
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Can mixtures of parallel and antiparallel sheets occur?
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yes
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What does topology refer to?
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connectivity
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How does the appearace of a beta sheet come about?
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it is a compromise between optimizing the conformational energies of the polypeptide bonds and preserving the hydrogen bonding
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Historically proteins have been classified as what?
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fibrous or globular
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Does keratin occur in all higher vertibrates?
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yes
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Name two characteristics of keratin?
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mechanically durable, chemically unreactive
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What type of keratin occurs in mammals?
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alpha keratin
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What type of keratin occurs in birds and reptiles?
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beta keratin
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What is the normal pitch of the alpha helix?
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5.4
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What type of structure is alpha keratin said to possess?
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coiled coil
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What is a coiled coil?
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an arrangement of polypeptide chains in which two alpha helices wind around each other as in alpha keratin
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What type of residues is alpha keratin rich in?
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Cys- form disulfide bonds that crosslink adjacent polypeptide chains
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What determines whether an alpha keratin is hard or soft?
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sulfur content
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Hard keratin is found in what?
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hair, horns and nail
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Soft keratin is found in what?
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skin and callus
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What can cleave disulfide bonds?
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mercaptans
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Why are hair and wool fibers springy?
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since the coiled coil of alpha keratin likes to recover its original conformation
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What is the most abundant vertebrate protein?
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collagen
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How many polypeptide chains is a single collagen molecule made of?
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three
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What does scurvy result from?
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not enough vitamin C
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What keeps collagen from forming an alpha helix?
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Pro residues
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What type of conformation does collagen like to assume?
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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!
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What residue exists at every third position of a collagen polypeptide chain?
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Gly
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Lathyrism is caused by what?
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regular ingestion of the seeds from the sweet pea (which contains a compound that inactivates lysyl oxidase)
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Osteogenesis imperfecta (brittle bone disease) can be caused by what?
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mutations of Type I collagen
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Why can the twist in helix not be pulled out under tension?
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its component polypeptide chains run in opposite directions
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As what are collagen molecules in fibrils organized?
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staggered arrays stabilized by hydrophobic interactions that result form the close packing of the triple-helical units
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Why does collagen have a poor solubility?
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because it is covalently crosslinked
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Does collagen have Cys residues?
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no, unlike keratin it is almost devoid of them
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From what are the crosslinks in collagen derived?
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Lys and His side chains
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What does lysyl oxidase do?
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converts Lys residues to those of the aldehyde allysine
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Where do the cross links tend to be?
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near the N- and C-termini of the collagen molecules
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How does cross-linking compare to age?
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increases with age- meat from older animals is tougher
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The majority of proteins are...?
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globular
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random coil
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the totally disordered and rapidly fluctuating conformations assumed by denatured proteins
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denatured protein
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fully unfolded
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coils
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segments of polypeptide chains whose successive residues do not have similar phi and theta values
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native protein
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folded proteins-nonrepetitive structures that are no less ordered than helices or beta sheets- only damn hard to describe
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beta bulge
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distortion in a beta sheet caused by an extra residue that is not hydrogen bonded to a neighboring strand
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helix capping
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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
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reverse turns, beta bends
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a polypeptide conformation in which the chain makes an abrupt reversal in direction, usually consisting of 4 successive reversals
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