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Biochem Lec > 3 -The 3-Dimensional Structure of Proteins > Flashcards

3 -The 3-Dimensional Structure of Proteins Flashcards

1
Q

What does a protein sturcture adopt what specific conformation?

A

Three-dimensional

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2
Q

spatial arrangement of atoms in a protein

A

Conformation

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3
Q

Most abundant and diverse macromolecule in
the cell

A

Proteins

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4
Q

This three-dimensional structure of a protein is called

A

Native conformation

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5
Q

proteins in any of their functional, folded
conformation.

A

Native proteins

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6
Q

essential for the biological
function of a protein.

A

Native conformation

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7
Q

What happens to the proteins of their is loss of structure?

A

Loss of biological functions

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8
Q

What are the level of protein organization?

A

Primary structure
Secondary structure
Tertiary structure
Quaternary structure

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9
Q

what level of protein organization is amino acids

A

Primary structure

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10
Q

what level of protein organization is a-helix

A

Secondary structure

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11
Q

what level of protein organization is polypeptide chain

A

Tertiary structure

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12
Q

what level of protein organization is Assemble subunits

A

Quaternary structure

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13
Q

It refers to the sequence of amino acids in a polypeptide chain (read from the N- to C-terminal end).

A

PRIMARY STRUCTURE

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14
Q

It determines the native conformation of the peptide/protein.

A

PRIMARY STRUCTURE

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15
Q

What level of organization is the Spike protein

A

Primary structure

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16
Q

full name of SARS-CoV-2

A

Severe acute respiratory syndrome coronavirus 2

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17
Q

It refers to the ordered 3D
arrangements in localized regions of a polypeptide chain (regular folding)

A

SECONDARY STRUCTURE

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18
Q

Spatial arrangement of the atoms in the polypeptide chain

A

SECONDARY STRUCTURE

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19
Q

Formed and stabilized by
hydrogen bond between the
amide proton and carbonyl
oxygen

A

SECONDARY STRUCTURE

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20
Q

Does the primary structure dictates the secondary structure?

A

Yes

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21
Q

In a secondary structure why is H-bonded arrangment of backbone protein is possible due to free rotation of bonds between?

A

*α-C and α-N (phi φ)
*α-C and carboxyl
carbon (psi ψ)

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22
Q

What kinds of structure can be found in a secondary structure

A
  • α-Helix
  • β-sheet
  • Random coil
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23
Q

Spiral structure

A

SECONDARY STRUCTURE: α-HELIX

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24
Q

Stabilized by intramolecular hydrogen bonds

A

SECONDARY STRUCTURE: α-HELIX

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25
Q

C=O of each peptide bond is hydrogen
bonded to the N-H of the fourth amino acid
away; there are 3.6 aa/turn

A

SECONDARY STRUCTURE: α-HELIX

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26
Q

Pitch: 5.4Å

A

SECONDARY STRUCTURE: α-HELIX

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27
Q

H-bonds are parallel to helical axis

A

SECONDARY STRUCTURE: α-HELIX

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28
Q

All R groups point outward from helix

A

SECONDARY STRUCTURE: α-HELIX

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29
Q

Coil of the helix either right-handed (clockwise) or left-handed (counter- clockwise)

A

SECONDARY STRUCTURE: α-HELIX

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30
Q

Enumerate the CONSTRAINTS TO STABILITY OF HELIX

A
  • Presence of helix breakers
  • Electrostatic repulsion (or attraction) between successive charged aa residues.
  • Bulkiness (steric strain) between adjacent R-groups
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31
Q

What are the examples of helix breakers

A

Pro
Gly

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32
Q

(1) the rotation around the N-αC bond is restricted bec it is part of the ring (2)
N has no H to participate in H-bonds

A

Pro

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33
Q

has more conformational flexibility due to its R-group; it supports other
conformations (e.g. coil or bend)

A

Gly

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34
Q

what are strong helix formers

A

Small hydrophic residues like (Ala, Leu)

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35
Q

It is formed when 2 or more polypeptides line up side by side.

A

SECONDARY STRUCTURE: β-PLEATED SHEET

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36
Q

Stabilized by hydrogen bonds (intrachain or
interchain) of adjacent polypeptide chains

A

SECONDARY STRUCTURE: β-PLEATED SHEET

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37
Q

Each β-strand (polypeptide chain in β-sheet)
is extended into a zigzag.

A

SECONDARY STRUCTURE: β-PLEATED SHEET

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38
Q

H-bonds form are adjacent between β-
strands.

A

SECONDARY STRUCTURE: β-PLEATED SHEET

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39
Q

All R groups extend above or below the sheet
in an alternating up and down direction.

A

SECONDARY STRUCTURE: β-PLEATED SHEET

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40
Q

Adjacent β-strands can run in parallel or anti- parallel

A

SECONDARY STRUCTURE: β-PLEATED SHEET

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41
Q

These are non-repetitive
structures.

A

SECONDARY STRUCTURE: RANDOM COILS

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42
Q

An irregular or unique
conformation

A

SECONDARY STRUCTURE: RANDOM COILS

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43
Q

Combinations of α and β-strands

A

SUPERSECONDARY STRUCTURES

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44
Q

What are examples of SUPERSECONDARY STRUCTURES

A

βαβ unit, αα unit, β-meander and Greek key

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45
Q

repetitive supersecondary structures

46
Q

It refers to three-dimensional conformation of the entire polypeptide.

A

TERTIARY STRUCTURE

47
Q

Stabilized by numerous interactions
between amino acid side chains.

A

TERTIARY STRUCTURE

48
Q

What does a Tertiary Structure contain?

A
  • Covalent bonds (e.g. disulfide bond
    between 2 cys)
  • H-bonds
  • Salt bridges (electrostatic)
  • Hydrophobic interaction
49
Q

polypeptide chain arranged in long strands or sheets

A

Fibrous proteins

50
Q

What is Fibrous proteins consist largely of one type of structure?

A

Secondary structure

51
Q

What is the function of fibrous proteins?

A

Strucutral (strength and support)

52
Q

What are examples of fibrous proteins

A

Collagen and Keratin

53
Q

Most are water insoluble

A

Fibrous proteins

54
Q

polypeptide chain
folded into compact, spherical structure

A

Globular proteins

58
Q

What does globular proteins consist of many types of?

A

seconday structures

58
Q

They are largely water soluble.

A

Globular proteins

59
Q

what is the functions of globular proteins?

A

Metabolic (catalyctic, transport)

59
Q

what are some examples of globular proteins

A

Enzymes and Hemoglobin

60
Q

It refers to spatial arrangement of
polypeptide subunits.

A

QUATERNARY STRUCTURE

61
Q

subunit

62
Q

It is formed by the assembly of
individual polypeptides
(subunit/monomer) into a larger
functional cluster.

A

QUATERNARY STRUCTURE

63
Q

how is subunits stabilized?

A

noncovalent interactions

64
Q

dimer

A

2 subunits

65
Q

trimer

A

3 subunits

66
Q

tetramer

A

4 subunits

67
Q

Glucose Homeostatic Proteins

A

INSULIN AND GLUCAGON

68
Q

Control carbohydrate metabolism by binding on specific receptors

A

INSULIN AND GLUCAGON

69
Q

Synthesized at the pancreas

A

INSULIN AND GLUCAGON

70
Q

what does the pancreas produce?

A

Insulin
Glucagon

71
Q

β-cells

72
Q

α-cells

73
Q

Hormone of nutrient abundance

74
Q

A protein hormone consisting of two
amino acid chains linked by disulfide
bonds

75
Q

86 AA

A

proinsulin

76
Q

function insulin

77
Q

29 AA

78
Q

What are major targets for insulin are?

A
  • liver
  • Skeletal muscle
  • adipose tissue
79
Q

The net result is fuel storage

80
Q

A 29-amino-acid polypeptide hormone
that is a potent hyperglycemic agent

81
Q

Its major target is the liver

82
Q

Glucagons major target is the liver, where it
promotes:

A
  • Breakdown of glycogen to glucose
    (glycogenolysis)
  • Synthesis of glucose from lactic acid
    and noncarbohydrates
    (gluconeogenesis)
  • Release of glucose to the blood from
    liver cells
83
Q

Fed state: insulin dominates causes?

A

Glucose oxidation
Glycogen synthesis
Fat syntheis
Protein synthesis

84
Q

Fasted stat: glucagon dominates

A

Glycogenolysis
Gluconeogenesis

85
Q

Hemeproteins

A

HEMOGLOBIN & MYOGLOBIN

86
Q

What is major or role HEMOGLOBIN & MYOGLOBIN

A
  • Hemoglobin: O2

transport

  • Myoglobin: O2

storage

87
Q

O2 transport

A

Hemoglobin

88
Q

O2 storage

89
Q

it is a Tetramer

A

Hemoglobin

90
Q

what is the primary structure of hemoglibin

A
  • α = 141 aa
  • β = 146 aa
91
Q

the is secondary structure of hemoglobin

92
Q

what is secondary structure of hemoglobin

93
Q

What is tertiary structure of hemoglobin

94
Q

What is the 4th structure of hemoglobin

A

4 folded chain in tetrahedral arrangement

95
Q

aka as antibodies

A

IMMUNOGLOBULIN

96
Q

Y-shaped molecule produced by
B-cells during adaptive immune
response

A

Immunoglobulin

97
Q

what is immunoglobulin composed of how many sub-units and what are those?

A

Composed of 4 sub-units
* 2 heavy chains
* 2 light chains

98
Q

what is immunoglobulin comprised of? (CVH)

A
  • Constant regions
  • Variable regions
  • Hinge
99
Q

Antibody that is commonly found in human secretions like tears, mucous and saliva

100
Q

Cell attached antibody which functuon is still under study

101
Q

Antibody responsible for allergic reactions

102
Q

Most dominant antibody in humans. This antibody is responsible for secondary immune response

103
Q

The antibody whichh serves as protection for primary infections

104
Q

It refers to disruption of the protein
conformation as well as its function

A

DENATURATION

105
Q

Alteration in the environment causing
disruption in the bonds and forces of
interaction that stabilized protein
structure

A

DENATURATION

106
Q

Enumerate the PROTEIN DENATURATION

A
  1. Physical Denaturants (heat)
  2. Chaotropic Agents (urea, detergents, salts, acids, bases, alcohols)
  3. Reducing agents (mercaptoethanol)
  4. Heavy metals
107
Q

what are urea, detergents, salts, acids, based, alcohols

A

Chaotropic agents

108
Q

What does altered protein sequence contain two categories

A

Normal protein function
Altered protein function

Biochem Lec (10 decks)

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