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Biochemistry > Chapter 4-Three Dimensional Structure of Proteins > Flashcards

Chapter 4-Three Dimensional Structure of Proteins Flashcards

1
Q

native conformations

A

3D shapes of proteins with biological activity

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2
Q

primary structure

A
  • the order in which the amino acids in a protein are linked by peptide bonds
  • the 1D first step in specifying the 3D structure of a protein
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3
Q

secondary structure

A
  • the arrangement in space of the backbone atoms in a polypeptide chain
  • alpha helix and beta pleated sheets
  • contain repetitive interactions resulting from hydrogen bonding between the N-H and the carbonyl group of the peptide
  • contains domains or supersecondary structures
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4
Q

tertiary structure

A

-3D arrangement of all the atoms in the protein (including those in the sedition and in prosthetic groups)

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5
Q

prosthetic groups

A

portions of proteins that do not consist of amino acids

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6
Q

subunits

A

individual parts of the larger molecule

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7
Q

quaternary structure

A

interaction of several polypeptide chains in a multisubunit protein

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8
Q

what does the primary structure of a protein determine?

A

the 3D structure, which determines the properties

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9
Q

hemoglobin is associated with what disease?

A

sickle cell anemia

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10
Q

sickle cell anemia

A
  • RBC can’t bind oxygen efficiently
  • RBC lack sickle shape
  • stem from a change in one amino acid residue
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11
Q

domain

A

aka supersecondary structure

-specific clusters of secondary structural motifs in proteins

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12
Q

what type of bonds in secondary structure?

A

hydrogen

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13
Q

Ramachandran angles

A

used to designate rotations of the C-N (phi) and C-C (psi) bond

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14
Q

alpha and beta pleated sheets are found in what structure

A

secondary

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15
Q

alpha helix

A
  • one of the most frequently encountered folding patterns in the protein backbone
  • rodlike
  • one polypeptide chain
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16
Q

beta pleated sheets

A
  • one of the most important types of secondary structure, in which the protein backbone is almost fully extended with hydrogen bonding between adjacent strands
  • can give 2D array
  • can involve 1+ more polypepetide chains
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17
Q

why are alpha helices and beta sheets considered periodic structures?

A

they feature repeats at regular intervals

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18
Q

Alpha helices are stabilized by

A
  • hydrogen bonds parallel to the helix axis within the backbone of a single polypeptide chain
  • hydrogen bonding is linear
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19
Q

There are ____ residues for each turn of the helix

A

3.6

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20
Q

pitch (linear distance between corresponding points on successive turns) is ____ A

A

5.4A

1A= 10-8cm=10-10m

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21
Q

Disruptive forces in alpha helices

A
  • Proline: creates bend in the backbone b/c of its cyclic structure
  • strong electrostatic repulsion
  • steric replusion: caused by bulky side chains
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22
Q

in alpha helices, where do side chains lie?

A

outside the helix

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23
Q

describe the peptide backbone in the B sheet

A
  • completely extended
  • hydrogen bonds can be formed between different parts of a single chain that is doubled back on itself or between different chains
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24
Q

Hydrogens bonds are ______ to the direction of the protein chain in beta pleated sheets and ______ in the alpha helix

A

perpendicular; parallel

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25
Q

Three10 helix

A

three residues per turn and 10 atoms in the ring formed by making the hydrogen bond

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26
Q

B-Bulge

A
  • common non-repetive irregularity found in antiparallel beta sheets
  • occurs between two normal B structure hydrogen bonds
  • involves 2 residues on one strand and 1 on another
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27
Q

what does a reverse turn often mark?

A

a transition between one secondary structure to another

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28
Q

reverse turn

A

parts of proteins where the polypeptide chain folds back on itself

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29
Q

motif

A

repetitive super secondary structure

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30
Q

what molecule is frequently encountered in reverse turns?

A

glycine: the single hydrogen of the side chain prevents crowding

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31
Q

list the super secondary structure

A
  • beta alpha beta
  • alpha alpha
  • beta meander
  • greek key
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32
Q

beta alpha beta

A

two parallel stands of B sheets are connected by a stretch of alpha helices

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33
Q

alpha alpha unit

A
  • aka helix turn helix
  • consists of two antiparallel alpha helices
  • energetically favorable contacts exist between the side chains in the two stretches of helix
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34
Q

B meander

A

-antiparallel sheet is formed by a series of tight reverse turns connecting stretches of polypeptide chain

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35
Q

greek key

A

-antiparallel sheet doubles back on itself in a pattern

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36
Q

protein sequences that allow for B meander or greek key can often be found arranged into a B-barrel in

A

the tertiary structure of the protein

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37
Q

can motifs predict biological function?

A

no; they are found in proteins and enzymes with very dissimilar functions

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38
Q

type 1 reverse turn

A

residue 3 the side chain lies outside the loop

any amino acid can be there

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39
Q

type 2 reverse turn

A

side chain of residue 3 has been rotated 180 degrees
residue 3 now on inside of loop
glycine must be residue 3

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40
Q

proline residue normally occupies what residue on the reverse turn

A

2

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41
Q

collagen

A
  • component of bone and connective tissue
  • consists of three polypoetide chains wrapped around eacahother in a triple helix
  • either X-Pro-Gly or X-Hyp-Gly
  • every third position must be Gly (inside the helix)
42
Q

proline and hydroxyproline can constitute up to 30% of the residues in

A

collagen

43
Q

how is hydroxyproline formed?

A

from proline by a specific hydroxylating enzyme after the amino acids are linked together

44
Q

tropocollagen

A
  • triple helical molecule
  • 300nm long and 1.5nm diameter
  • held together by hydrogen bonds
  • each strand contains 800AA residues
45
Q

T/F: amount of cross linking increases with age

A

true

46
Q

collagen is both intramolecularly and intermolecularly linked by covalent bonds formed by

A

reactions of lysine and histidine residues

47
Q

Scurvy

A
  • result of fragile collagen (when proline is not hydroxylated to normal extent)
  • bleeding of gums and skin discoloration
  • deficient in Vitamin C
48
Q

fibrous proteins

A

proteins whose overall shape is that of a long, narrow rod

49
Q

globular proteins

A
  • proteins whose overall shape is more or less spherical
  • water soluble
  • compact structures
  • complex tertiary and quaternary structures
50
Q

characteristics of tertiary structure

A
  • 3D arrangement of all atoms
  • side chains (arrangement of atoms inside and position)
  • position of prosthetic groups
51
Q

secondary and tertiary structure depends on ______ interactions

A

non-covalent

52
Q

information about the location of disulfide links combined with primary structure gives

A

complete covalent structure of a protein

53
Q

what two molecules lack disulfide bonds, but have metal ions? what metal ion?

A

myoglobin and hemoglobin; Fe(II) as part of a prostethic group

54
Q

list the forces that stabilize the tertiary structure of proteins

A
  • metal ion coordination
  • hydrophobic interactions
  • disulfide bond
  • electrostatic interaction
  • side chain hydrogen bonding
55
Q

xray crystallography

A

experimental method for determining the 3D structure of proteins using crystals

56
Q

NMR

A

method for determining the shape of proteins in a solution

depends on H atoms

57
Q

myoglobin

A
  • globular protein
  • 153 AA residues
  • heme group
  • compact structure (interior atoms close together)
  • 8 alpha helices; no beta sheets
  • 2 polar histidine residues on inside that interact with heme group and oxygen
58
Q

heme

A
  • iron-containing cyclic compound found in cytochromes, hemoglobin and myoglobin
  • consists of metal ion Fe(II), protroporhrin ring
59
Q

porphyrin part consists of

A

4 five membered rings based on pyrrole structure

4 rings linked by bridging methane groups

60
Q

Fe(II)

A
  • 6 coordination sites (4 sites occupied by nitrogen of pyrrole; 1 by nitrogen atoms in imidazole side chain of histidine residue F8; 1 by oxygen)
  • forms 6 metal ion complexation bonds
61
Q

the presence of what is required for myoglobin to bind to oxygen

A

heme

62
Q

E7 histidine

A

streakily inhibits oxygen from binding perpendicularly to the heme plane; lies by binding site of oxygen

63
Q

why does oxygen have imperfect binding to the heme group?

A
  • more than 1 molecule can bind to the heme
  • affinity of heme for CO2 is greater than oxygen (but is forced to bind at an angle)
  • too perfect binding would defeat purpose of having the oxygen-carrying proteins
64
Q

combination of both heme and protein is needed to bind

A

O2; without protein the iron of heme can be oxidized to Fe(III) and won’t bind oxygen

65
Q

denaturation

A

unraveling of the 3D structure (3level) of a macromolecules caused by breakdown of noncovalent interactions

66
Q

reduction of disulfide bonds causes

A

extensive unraveling of 3 structure

67
Q

how can proteins be denatured?

A
  • heat
  • change in pH
  • binding of detergents
  • urea & guanidine hydrochloride
  • B mercaptoethanol
68
Q

describe how heat causes denaturation

A

increase in temp, favors vibrations, energy of these vibrations disrupt the structure

69
Q

describe how change in pH causes denaturation

A

at either extreme, charges are missing and so the electrostatic interactions that normally stabilize the protein are reduced

70
Q

describe how binding of detergents causes denaturation

A

ex) SDS
- disrupt hydrophobic interactions
- if charged can disrupt electrostatic interactions

71
Q

describe how urea & guanidine hydrochloride causes denaturation

A
  • they form hydrogen bonds with the protein that are stronger than those within the protein
  • disrupt hydrophobic interactions
72
Q

describe how B mercaptoethanol causes denaturation

A

-reduces disulfide bridges to two sulfhydryl groups

73
Q

dimers

A

molecules with two subuntis

74
Q

oligomer

A

aggregate of several smaller units; bonding can be covalent or non

75
Q

allosteric

A

property of a multisubunit proteins such that a conformational change in one subunit induces a change in another

76
Q

how to chains of quaternary structure interact with eachother

A

electrostatic interactions, hydrogen bonds and hydrophobic interactions

77
Q

hemoglobin

A
  • allosteric protein
  • tetramer (4 polypeptide chains, 2alpha/2beta that are identical)
  • alpha chain: 141 residues
  • beta chain: 153 residues
  • heme
  • four molecules of oxygen bind to 1 hemoglobin
78
Q

binding of oxygen to hemoglobin exhibits

A

positive cooperativity

79
Q

postive cooperativity

A

cooperative effect where by binding the first ligand to an enzyme or protein causes the affinity for the next to be higher (i.e.: once one O is bound it is easier for the next to bind)

80
Q

oxygen binding curve of myoglobin

A

hyperbolic (rises quickly then levels off)

81
Q

oxygen binding curve of hemoglobin

A

sigmodial (S shaped curve); characteristic of cooperative interactions

82
Q

myoglobin has a higher percentage of _______ that hemoglobin at any level

A

saturation

83
Q

function of myoglobin

A

oxygen storage

84
Q

function of hemoglobin

A

oxygen transport; must be able to bind and release oxygen easily

85
Q

alveoli of lungs

A

where hemoglobin must bind oxygen for transport, O2 pressure 100torr
so hemoglobin is 100% saturated with oxygen

86
Q

capillaries of active muscle

A

O2 pressure 20torr; less than 50% saturation

aka hemoglobin gives up oxygen here easily because need is great

87
Q

in the bound (oxygenated) form of hemoglobin the B chains are

A

much closer to each other than that of the deoxygenated

88
Q

What other molecules affect the affinity of hemoglobin for oxygen by alterating the proteins 3D shape?

A

H+ and C02 (bind to hemoglobin)

89
Q

Bohr effect

A
  • the effect of H+
  • in actively metabolizing tissue (lower pH), hemoglobin releases oxygen and binds both CO2 and H+
  • in the lungs (higher pH), hemoglobin hemoglobin releases CO2 and H+ and binds to oxygen
  • in the presence of H+ and CO2, the oxygen binding capacity of hemoglobin decreases
90
Q

2,3-bisphosphoglycerate (2,3-BPG)

A
  • binds to hemoglobin in blood
  • binding to hemoglobin is electrostatic
  • lowers oxygen binding capacity when bound to hemoglobin
91
Q

fetal hemoglobin

A
  • fetus obtains oxygen from bloodstream of mom via placenta

- has high affinity for oxygen

92
Q

why does fetal hemoglobin have a higher oxygen binding capacity?

A
  • presence of two polypeptide chains (HbF & HbA)

- HbF binds less strongly to BPG than HbA

93
Q

role of hydrophobic interactions

A

-protein folding into 3D shape `

94
Q

what makes hydrophobic interactions favorable?

A
  • spontaneous

- entropy (S) increases when reactions occur

95
Q

what diseases are caused by acculmulation of protein deposits from incorrect folding of hydrophobic regions?

A

Alzheimers
Parkinsons
Huntingtons

96
Q

chaperones

A

prevents a protein from associating with another protein which it shouldn’t or itself in negative ways

97
Q

AHSP

A

globin chaperone that binds to alpha global (excess) and keeps it from aggravating with itself and delivers it to the B-globin

98
Q

thalassemia

A

damaged red blood cells from excessive alpha chain aggravates

99
Q

Prion diseases

A
  • cause of mad cow
  • cause of creutzfeldt jakobs
  • comes about when normal form of PrP folds into PrPsc
100
Q

what are prions

A

natural glycoproteins found in cell membrane of nerve tissue

101
Q

abnormal prions have

A

more beta sheets

Biochemistry (7 decks)

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