3 -The 3-Dimensional Structure of Proteins

Question 1

What does a protein sturcture adopt what specific conformation?

Answer 1

Three-dimensional

Question 2

spatial arrangement of atoms in a protein

Answer 2

Conformation

Question 3

Most abundant and diverse macromolecule in
the cell

Answer 3

Proteins

Question 4

This three-dimensional structure of a protein is called

Answer 4

Native conformation

Question 5

proteins in any of their functional, folded
conformation.

Answer 5

Native proteins

Question 6

essential for the biological
function of a protein.

Answer 6

Native conformation

Question 7

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

Answer 7

Loss of biological functions

Question 8

What are the level of protein organization?

Answer 8

Primary structure
Secondary structure
Tertiary structure
Quaternary structure

Question 9

what level of protein organization is amino acids

Answer 9

Primary structure

Question 10

what level of protein organization is a-helix

Answer 10

Secondary structure

Question 11

what level of protein organization is polypeptide chain

Answer 11

Tertiary structure

Question 12

what level of protein organization is Assemble subunits

Answer 12

Quaternary structure

Question 13

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

Answer 13

PRIMARY STRUCTURE

Question 14

It determines the native conformation of the peptide/protein.

Answer 14

PRIMARY STRUCTURE

Question 15

What level of organization is the Spike protein

Answer 15

Primary structure

Question 16

full name of SARS-CoV-2

Answer 16

Severe acute respiratory syndrome coronavirus 2

Question 17

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

Answer 17

SECONDARY STRUCTURE

Question 18

Spatial arrangement of the atoms in the polypeptide chain

Answer 18

SECONDARY STRUCTURE

Question 19

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

Answer 19

SECONDARY STRUCTURE

Question 20

Does the primary structure dictates the secondary structure?

Answer 20

Yes

Question 21

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

Answer 21

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

Question 22

What kinds of structure can be found in a secondary structure

Answer 22

• α-Helix
• β-sheet
• Random coil

Question 23

Spiral structure

Answer 23

SECONDARY STRUCTURE: α-HELIX

Question 24

Stabilized by intramolecular hydrogen bonds

Answer 24

SECONDARY STRUCTURE: α-HELIX

Question 25

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

Answer 25

SECONDARY STRUCTURE: α-HELIX

Question 26

Pitch: 5.4Å

Answer 26

SECONDARY STRUCTURE: α-HELIX

Question 27

H-bonds are parallel to helical axis

Answer 27

SECONDARY STRUCTURE: α-HELIX

Question 28

All R groups point outward from helix

Answer 28

SECONDARY STRUCTURE: α-HELIX

Question 29

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

Answer 29

SECONDARY STRUCTURE: α-HELIX

Question 30

Enumerate the CONSTRAINTS TO STABILITY OF HELIX

Answer 30

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

Question 31

What are the examples of helix breakers

Answer 31

Pro Gly

Question 32

(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

Answer 32

Pro

Question 33

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

Answer 33

Gly

Question 34

what are strong helix formers

Answer 34

Small hydrophic residues like (Ala, Leu)

Question 35

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

Answer 35

SECONDARY STRUCTURE: β-PLEATED SHEET

Question 36

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

Answer 36

SECONDARY STRUCTURE: β-PLEATED SHEET

Question 37

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

Answer 37

SECONDARY STRUCTURE: β-PLEATED SHEET

Question 38

H-bonds form are adjacent between β- strands.

Answer 38

SECONDARY STRUCTURE: β-PLEATED SHEET

Question 39

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

Answer 39

SECONDARY STRUCTURE: β-PLEATED SHEET

Question 40

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

Answer 40

SECONDARY STRUCTURE: β-PLEATED SHEET

Question 41

These are non-repetitive structures.

Answer 41

SECONDARY STRUCTURE: RANDOM COILS

Question 42

An irregular or unique conformation

Answer 42

SECONDARY STRUCTURE: RANDOM COILS

Question 43

Combinations of α and β-strands

Answer 43

SUPERSECONDARY STRUCTURES

Question 44

What are examples of SUPERSECONDARY STRUCTURES

Answer 44

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

Question 45

repetitive supersecondary structures

Answer 45

Motif

Question 46

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

Answer 46

TERTIARY STRUCTURE

Question 47

Stabilized by numerous interactions between amino acid side chains.

Answer 47

TERTIARY STRUCTURE

Question 48

What does a Tertiary Structure contain?

Answer 48

* Covalent bonds (e.g. disulfide bond between 2 cys) * H-bonds * Salt bridges (electrostatic) * Hydrophobic interaction

Question 49

polypeptide chain arranged in long strands or sheets

Answer 49

Fibrous proteins

Question 50

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

Answer 50

Secondary structure

Question 51

What is the function of fibrous proteins?

Answer 51

Strucutral (strength and support)

Question 52

What are examples of fibrous proteins

Answer 52

Collagen and Keratin

Question 53

Most are water insoluble

Answer 53

Fibrous proteins

Question 54

polypeptide chain folded into compact, spherical structure

Answer 54

Globular proteins

Question 58

What does globular proteins consist of many types of?

Answer 58

seconday structures

Question 58

They are largely water soluble.

Answer 58

Globular proteins

Question 59

what is the functions of globular proteins?

Answer 59

Metabolic (catalyctic, transport)

Question 59

what are some examples of globular proteins

Answer 59

Enzymes and Hemoglobin

Question 60

It refers to spatial arrangement of polypeptide subunits.

Answer 60

QUATERNARY STRUCTURE

Question 61

subunit

Answer 61

monomer

Question 62

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

Answer 62

QUATERNARY STRUCTURE

Question 63

how is subunits stabilized?

Answer 63

noncovalent interactions

Question 64

dimer

Answer 64

2 subunits

Question 65

trimer

Answer 65

3 subunits

Question 66

tetramer

Answer 66

4 subunits

Question 67

Glucose Homeostatic Proteins

Answer 67

INSULIN AND GLUCAGON

Question 68

Control carbohydrate metabolism by binding on specific receptors

Answer 68

INSULIN AND GLUCAGON

Question 69

Synthesized at the pancreas

Answer 69

INSULIN AND GLUCAGON

Question 70

what does the pancreas produce?

Answer 70

Insulin Glucagon

Question 71

β-cells

Answer 71

Insulin

Question 72

α-cells

Answer 72

Glucagon

Question 73

Hormone of nutrient abundance

Answer 73

INSULIN

Question 74

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

Answer 74

insulin

Question 75

86 AA

Answer 75

proinsulin

Question 76

function insulin

Answer 76

51 AA

Question 77

29 AA

Answer 77

C peptide

Question 78

What are major targets for insulin are?

Answer 78

* liver * Skeletal muscle * adipose tissue

Question 79

The net result is fuel storage

Answer 79

INSULIN

Question 80

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

Answer 80

GLUCAGON

Question 81

Its major target is the liver

Answer 81

Glucagon

Question 82

Glucagons major target is the liver, where it promotes:

Answer 82

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

Question 83

Fed state: insulin dominates causes?

Answer 83

Glucose oxidation Glycogen synthesis Fat syntheis Protein synthesis

Question 84

Fasted stat: glucagon dominates

Answer 84

Glycogenolysis Gluconeogenesis

Question 85

Hemeproteins

Answer 85

HEMOGLOBIN & MYOGLOBIN

Question 86

What is major or role HEMOGLOBIN & MYOGLOBIN

Answer 86

* Hemoglobin: O2 transport * Myoglobin: O2 storage

Question 87

O2 transport

Answer 87

Hemoglobin

Question 88

O2 storage

Answer 88

Myoglobin

Question 89

it is a Tetramer

Answer 89

Hemoglobin

Question 90

what is the primary structure of hemoglibin

Answer 90

* α = 141 aa * β = 146 aa

Question 91

the is secondary structure of hemoglobin

Answer 91

helical

Question 92

what is secondary structure of hemoglobin

Answer 92

Helical

Question 93

What is tertiary structure of hemoglobin

Answer 93

Globular

Question 94

What is the 4th structure of hemoglobin

Answer 94

4 folded chain in tetrahedral arrangement

Question 95

aka as antibodies

Answer 95

IMMUNOGLOBULIN

Question 96

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

Answer 96

Immunoglobulin

Question 97

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

Answer 97

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

Question 98

what is immunoglobulin comprised of? (CVH)

Answer 98

* Constant regions * Variable regions * Hinge

Question 99

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

Answer 99

IgA

Question 100

Cell attached antibody which functuon is still under study

Answer 100

IgD

Question 101

Antibody responsible for allergic reactions

Answer 101

IgE

Question 102

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

Answer 102

IgG

Question 103

The antibody whichh serves as protection for primary infections

Answer 103

IgM

Question 104

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

Answer 104

DENATURATION

Question 105

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

Answer 105

DENATURATION

Question 106

Enumerate the PROTEIN DENATURATION

Answer 106

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

Question 107

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

Answer 107

Chaotropic agents

Question 108

What does altered protein sequence contain two categories

Answer 108

Normal protein function Altered protein function