Question 1

types of secondary structures

Accepted Answer

α-helix
β-pleated sheet
β-turn

Question 2

secondary structures are held together by

Accepted Answer

hydrogen bonds

Question 3

linear primary structures are held together by

Accepted Answer

peptide bonds

Question 4

quaternary structure is

Accepted Answer

3D shape of multiple interacting polypeptides

Question 5

tertiary structure is

Accepted Answer

3D shape of polypeptides

Question 6

secondary structure is

Accepted Answer

folded 2D structure of primary structures

Question 7

primary structure is

Accepted Answer

linear sequence of amino acid held by peptide bonds

Question 8

R groups location in α-helix

Accepted Answer

point outward away from the seemingly hollow core

Question 9

how many aa's per turn in α-helix

Accepted Answer

3.6 amino acids

Question 10

why is proline rarely found in helices?

Accepted Answer

because it has cyclic structure, amine group is rigid and can't form H bonds with carbonyl oxygen

Question 11

what causes the transition or stops an α helix?

Accepted Answer

proline

Question 12

in α helices, the carbonyl oxygen h bonds to the ________ amide hydrogen down the line

Accepted Answer

4th

Question 13

in α helices, hydrophobic and hydrophilic amino acids are ___________

Accepted Answer

on opposite sides, due to amphipathic nature of αhelices

Question 14

β strands can

Accepted Answer

parallel or antiparallel

Question 15

in antiparallel  β strands, atoms involved in H bonding are _____________ of eachother and in parallel atoms are __________________

Accepted Answer

directly opposite, slightly skewered

Question 16

antiparallel strands have ________________ while parallel tend to have ___________________

Accepted Answer

hydrophobic side and hydrophilic side, hydrophobic residues on both sides

Question 17

function of β turns

Accepted Answer

connects 2 β strands in an antiparallel β sheet

Question 18

β turns vs loop

Accepted Answer

tight changes in direction- turn
slow, gradual change in direction- loop

Question 19

why do we see a lot of glycine and proline when making β turns?

Accepted Answer

because they have small R groups that can turn more easily than a big group

Question 20

silk is composed of

Accepted Answer

antiparallel β-pleated sheet

Question 21

keratin is composed of

Accepted Answer

two αhelical polypeptides covalently linked by disulfide bridges

Question 22

collagen consists of

Accepted Answer

three intertwined αhelices

Question 23

what secondary structure provides tough, insoluble protective structures of varying hardness and flexibility? example?

Accepted Answer

α helices cross linked by disulfide bonds
ex: keratin of hair, feathers, nails

Question 24

what secondary structure provides soft, flexible filaments? example?

Accepted Answer

β conformation
ex: silk fibroin

Question 25

what secondary structure provides high tensile strength without stretch? example?

Accepted Answer

collagen triple helix 
ex: collagen of tendons, bone matrix

Question 26

what allows collagen to twist the way it does? or what gives it its elastic properties?

Accepted Answer

high percentage of proline and glycine (small side groups) 
almost 2/3 glycine+proline

Question 27

define motif give example

Accepted Answer

combinations of αhelices, βstrands, and loops (secondary structures) found in multiple proteins, can have different functions in different proteins
ex: helix-loop-helix

Question 28

leucine zipper function
where is it found?

Accepted Answer

mediates transcription factor dimerization
found straddling DNA at major groove

Question 29

zinc finger domains have similar structure but differ in ______________

Accepted Answer

amino acid sequence

Question 30

define domains

Accepted Answer

conserved, discrete parts of a protein sequence that are folded, compact combination of motifs (sometimes tertiary structures).

Question 31

features of domains

Accepted Answer

- predict a specific protein function
- exist independently of the protein chain

Question 32

most proteins consists of several __________ (motifs/domains)

Accepted Answer

domains

Question 33

immunoglobulin domains can be seen in ______________

Accepted Answer

antibodies

Question 34

function of PDZ domain

Accepted Answer

anchors receptor proteins in the membrane to cytoskeletal components

Question 35

what bonds do tertiary structures require to tell protein how to fold in 3D space?

Accepted Answer

all noncovalent (hydrophobic forces, salt bridges, h bonds, van der waals) and disulfide bonds

Question 36

what maintains the secondary structure of a protein?

Accepted Answer

hydrogen bonds

Question 37

which of the following does not influence protein shape? disulfide,peptide,hydrogen bonds,ionic bonds, none of the above

Accepted Answer

peptide bonds (interaction of R groups influences shape)

Question 38

heme group in myoglobin is a

Accepted Answer

prosthetic group

Question 39

heme is tucked into an area to protect it from environment called

Accepted Answer

hydrophobic cleft

Question 40

similarity between tertiary and quaternary? difference?

Accepted Answer

use same bonds
difference is quaternary is composed of multiple polypeptides

Question 41

T/F polypeptides that form quaternary structures have to be similar

Accepted Answer

FALSE, they can be similar or different

Question 42

in what protein quaternary structures are disulfide bonds found

Accepted Answer

fibrous/structural proteins. rarely in globular

Question 43

hemoglobin is a ____________

Accepted Answer

tetramer  (has 4 monomers)

Question 44

hemoglobin can carry ______ oxygens, one per _____________

Accepted Answer

4, heme group

Question 45

amino acid R groups are most important for stabilizing what level(s) of protein structure?

Accepted Answer

tertiary and quaternary

Lecture 4

Protein structure

Question	Answer
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

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