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Lecture 4

Protein structure

types of secondary structures α-helix β-pleated sheet β-turn
secondary structures are held together by hydrogen bonds
linear primary structures are held together by peptide bonds
quaternary structure is 3D shape of multiple interacting polypeptides
tertiary structure is 3D shape of polypeptides
secondary structure is folded 2D structure of primary structures
primary structure is linear sequence of amino acid held by peptide bonds
R groups location in α-helix point outward away from the seemingly hollow core
how many aa's per turn in α-helix 3.6 amino acids
why is proline rarely found in helices? because it has cyclic structure, amine group is rigid and can't form H bonds with carbonyl oxygen
what causes the transition or stops an α helix? proline
in α helices, the carbonyl oxygen h bonds to the ________ amide hydrogen down the line 4th
in α helices, hydrophobic and hydrophilic amino acids are ___________ on opposite sides, due to amphipathic nature of αhelices
β strands can parallel or antiparallel
in antiparallel β strands, atoms involved in H bonding are _____________ of eachother and in parallel atoms are __________________ directly opposite, slightly skewered
antiparallel strands have ________________ while parallel tend to have ___________________ hydrophobic side and hydrophilic side, hydrophobic residues on both sides
function of β turns connects 2 β strands in an antiparallel β sheet
β turns vs loop tight changes in direction- turn slow, gradual change in direction- loop
why do we see a lot of glycine and proline when making β turns? because they have small R groups that can turn more easily than a big group
silk is composed of antiparallel β-pleated sheet
keratin is composed of two αhelical polypeptides covalently linked by disulfide bridges
collagen consists of three intertwined αhelices
what secondary structure provides tough, insoluble protective structures of varying hardness and flexibility? example? α helices cross linked by disulfide bonds ex: keratin of hair, feathers, nails
what secondary structure provides soft, flexible filaments? example? β conformation ex: silk fibroin
what secondary structure provides high tensile strength without stretch? example? collagen triple helix ex: collagen of tendons, bone matrix
what allows collagen to twist the way it does? or what gives it its elastic properties? high percentage of proline and glycine (small side groups) almost 2/3 glycine+proline
define motif give example combinations of αhelices, βstrands, and loops (secondary structures) found in multiple proteins, can have different functions in different proteins ex: helix-loop-helix
leucine zipper function where is it found? mediates transcription factor dimerization found straddling DNA at major groove
zinc finger domains have similar structure but differ in ______________ amino acid sequence
define domains conserved, discrete parts of a protein sequence that are folded, compact combination of motifs (sometimes tertiary structures).
features of domains - predict a specific protein function - exist independently of the protein chain
most proteins consists of several __________ (motifs/domains) domains
immunoglobulin domains can be seen in ______________ antibodies
function of PDZ domain anchors receptor proteins in the membrane to cytoskeletal components
what bonds do tertiary structures require to tell protein how to fold in 3D space? all noncovalent (hydrophobic forces, salt bridges, h bonds, van der waals) and disulfide bonds
what maintains the secondary structure of a protein? hydrogen bonds
which of the following does not influence protein shape? disulfide,peptide,hydrogen bonds,ionic bonds, none of the above peptide bonds (interaction of R groups influences shape)
heme group in myoglobin is a prosthetic group
heme is tucked into an area to protect it from environment called hydrophobic cleft
similarity between tertiary and quaternary? difference? use same bonds difference is quaternary is composed of multiple polypeptides
T/F polypeptides that form quaternary structures have to be similar FALSE, they can be similar or different
in what protein quaternary structures are disulfide bonds found fibrous/structural proteins. rarely in globular
hemoglobin is a ____________ tetramer (has 4 monomers)
hemoglobin can carry ______ oxygens, one per _____________ 4, heme group
amino acid R groups are most important for stabilizing what level(s) of protein structure? tertiary and quaternary
Created by: rusulali97



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