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biochemistry > Protein Chemistry > Flashcards

Protein Chemistry Flashcards

1
Q

These are are 💡complex organic nitrogenous substances with 💡very high molecular weights (>50 amino acid residues)

They consist of largely or entirely of 💡alpha-amino acids united in peptide linkage

A

PROTEINS

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2
Q

Protein is made up of 4 elements:

A

Carbon, hydrogen, oxygen, and nitrogen (CHON)

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3
Q

Primary, holding first place, of first importance

A

“Proteios”

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4
Q

FUNCTIONS OF PROTEINS

A
  1. Catalyst of chemical reactions (e.g. enzymes) -accelerates or speed up chemical reactions
  2. Transport and storage function (e.g. hemoglobin – transport of oxygen and carbon dioxide; Ferritin – stores iron)
  3. Coordinated motion (e.g. actin and myosin – involved in muscle contraction)
  4. Mechanical support (e.g. collagen – the most abundant fibrous protein in our body; keratin)
  5. Immune protection (e.g. antibodies from gamma globulins – produced by lymphocytes)
  6. Generation and transmission of nerve impulses (ex. neurotransmitters)
  7. Control of growth and differentiation (e.g. repressor proteins)
  8. Cell signaling (e.g. membrane receptors such as insulin receptors)
  9. Hormones (e.g. insulin, thyrotropin, somatotropin, luteinizing hormone, etc.)
  10. One of the major components of biological membranes
  11. Sole source of nitrogen???
  12. Constituents of respiratory pigments and occur in ETC (cytchromes, hgb, mgb)
  13. Exerting osmotic pressure (maintenance of fluid and electrocyte balance)
  14. Catabolized to supply energy (least function)
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5
Q

CLASSIFICATION OF PROTEINS

A

SIMPLE PROTEINS

CONJUGATED PROTEINS

DERIVED PROTEINS

FIBROUS PROTEINS

GLOBULAR PROTEINS

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6
Q

SIMPLE PROTEINS

A 
Albumin
Globulin
Glutelin
Prolamine
Albuminoid
Histone
Protamine
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7
Q

It is 💡soluble in water and 💡dilute aqueous salt sol’n: 💡heat coagulable

A

Albumin

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8
Q

It is 💡insoluble in water; 💡soluble in aqueous salt sol’n; 💡heat coagulable

A

Globulin

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9
Q

It is 💡soluble in dilute acids and alkalis; 💡heat coagulable
(e.g., plant proteins – glutenin [wheat], oryzenin [rice])

A

Glutelin

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10
Q

It is 💡alcohol-soluble protein

e.g., seed proteins – zein (corn), gliadin (wheat)

A

Prolamine

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11
Q

💡Least soluble (e.g., animal proteins – keratin, collagen

A

Albuminoid (Scleroprotein)

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12
Q

It is a 💡basic protein; 💡soluble in water, dilute acid and alkali; found in 💡combination with DNA

A

Histone

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13
Q

It is the 💡simplest; 💡basic; 💡soluble in water, dilute ammonia, acid and alkali; found in 💡spermatozoa

A

Protamine

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14
Q

It is made up of a 💡protein portion and a 💡non-protein portion (prosthetic group).

A

CONJUGATED PROTEINS

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15
Q

CONJUGATED PROTEINS

A 
Nucleoproteins
Glycoproteins and proteoglycans
Phosphoproteins
Chromoproteins
Lipoproteins
Metalloproteins
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16
Q

It contain 💡nucleic acid as the prosthetic group

A

Nucleoproteins

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17
Q

It contain 💡carbohydrate

A

Glycoproteins and proteoglycans

 Glycoproteins contain more proteins than carbs while proteoglycans contain more carbs than proteins

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18
Q

They have 💡phosphoric acid residues

A

Phosphoproteins

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19
Q

It contain prosthetic groups that give 💡color (e.g., hemoglobin – heme group gives color)

A

Chromoproteins

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20
Q

It is associated with 💡lipids

e.g., chylomicron, LDL, HDL

A

Lipoproteins

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21
Q

It contain 💡minerals

e.g., insulin, cytochrome

A

Metalloproteins

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22
Q

It 💡partially digested proteins

A

Proteosomes & Peptones

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23
Q

Classification of proteins based on the shape and certain physical characteristics

A

FIBROUS PROTEINS

GLOBULAR PROTEINS

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24
Q
  • 💡Tough
  • Involved in 💡structural functions
  • e.g., collagen, keratin
A

FIBROUS PROTEINS

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25
Q
  • It is involved in 💡mobile and 💡dynamic functions

- e.g., enzymes, plasma proteins, hemoglobin

A

GLOBULAR PROTEINS

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26
Q

Classification based on biologic functions:

A 
Enzymes
Storage proteins
Regulatory proteins
Structural proteins
Protective proteins
Transport proteins
Contractile or motile proteins
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27
Q

Dehydrogenases, kinases, etc.

A

Enzymes

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28
Q

Ferritin, myoglobin

A

Storage proteins

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29
Q

Myoglobin, DNA-binding proteins

A

Regulatory proteins

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30
Q

Elastin, reticulin, collagen

A

Structural proteins

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31
Q

Immunoglobulin, blood clotting factors

A

Protective proteins

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32
Q

Plasma lipoprotein

A

Transport proteins

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33
Q

Actin, myosin

A

Contractile or motile proteins

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34
Q

These are amino acid polymers with 💡low molecular weights, typically consisting of 💡less than 50 amino acids.

Chains of amino acid residue linked by a 💡peptide bond

They have 💡more than 10 amino acid residues

A

PEPTIDES

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35
Q

Consisting of 💡2 to 10 amino acids

A

Oligopeptides

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36
Q

Peptides with significant biologic activities

A 
Glutathione (gamma-glutamyl-L-cysteinylglycine)
Oxytocin and vasopressin
Met-enkephalin and Leu-enkephalin
Atrial natriuretic factor
Substance P and bradykinin
Glucagon
Corticotropin
Aspartame (L-aspartylphenylalanine methyl ester)
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37
Q
  • It is a tripeptide
  • It is a 💡reducing agent; due to 💡–SH group
  • It protects the cell from the destructive effects of 💡oxidation by peroxides
  • It works with 💡glutathione peroxidase to decompose hydrogen peroxide into water and oxygen
A

Glutathione (gamma-glutamyl-L-cysteinylglycine)

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38
Q
  • It contain 💡nine amino acid residues
  • (1) __ stimulates 💡contraction of uterine muscle during childbirth
  • (2) __ is an 💡antidiuretic hormone; stimulates 💡water reabsorption in the kidney
A

(1) Oxytocin

(2) Vasopressin

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39
Q
  • 💡Pentapeptide; 💡opioid peptides

- 💡Relieve pain; bind to receptors in the brain and 💡induce analgesia

A

Met-enkephalin and Leu-enkephalin

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40
Q
  • It has 💡28 amino acid residues

- It stimulates the 💡production of a dilute urine

A

Atrial natriuretic factor

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41
Q
  • It stimulate the 💡perception of pain
A

Substance P and bradykinin

42
Q
  • It has 💡29 amino acid residues

- It 💡opposes the action of insulin; 💡increases blood sugar level

A

Glucagon

43
Q
  • With 💡39 amino acid residues; 💡stimulates adrenal cortex
A

Corticotropin

44
Q
  • It is 💡artificial sweetener
A

Aspartame (L-aspartylphenylalanine methyl ester)

45
Q

Formation of Peptide Bond

A
  • You should have at least 2 amino acid residues
  • The carboxyl group of the 1st amino acid will react with the amino group of the 2nd amino acid forming a C=O-N-H bond (peptide bond)
  • Are Cis configurations and has a more rigid bond
  • Dehydration process
46
Q

Evidences that a peptide bond exist in proteins

A

 (+) Biuret test
 Relatively few titratable amino and carboxyl functions
 Hydrolyzed by enzymes which are specific for the peptide bond
 X-ray diffraction studies proved the existence of peptide linkages between amino acids in hemoglobin and myoglobin

47
Q

N-terminal residue
- It has free alpha amino group

C-terminal residue
- It has a free alpha carboxyl group

A

Parts of the peptide chain

48
Q

PROTEIN LEVELS OF STRUCTURAL ORGANIZATION

A

PRIMARY STRUCTURE
SECONDARY STRUCTURE
TERTIARY STRUCTURE
QUATERNARY STRUCTURE

49
Q

o It is the 💡quantitative amino acid composition
o It is the 💡sequence of amino acids
o 💡Number of peptide chains

 Most abundant amino acid in proteins:
o Leucine, Alanine, Glycine, Serine, Valine, Glutamic acid

 Rarest:
o Trp, Cys, Met, His

A

PRIMARY STRUCTURE

50
Q

The backbone of a protein refers to the __.

A

Atoms that participate in the formation of peptide bonds

51
Q

The 3-D shape of a folded polypeptide is a result of the __.

A

Interactions among the R groups

52
Q

It is due to the 💡formation of hydrogen bonds 💡between peptide bonds

A

SECONDARY STRUCTURE

53
Q

Two types of secondary structure:

A

o Coils or helices – INTRAchain hydrogen bonding (within the same structure)

o Sheets or pleats – INTERchain hydrogen bonding

54
Q

 Linus Pauling 1951

 The H atom attached to a peptide N and the carbonyl O of the residue 4th in line behind in the primary structure

 Amino acid R groups extend outward from the helix.

IT HAS A 3.6 AA RESIDUE PER 360 DEGREES TURN

A

Alpha-helix

55
Q

Alpha-helix is stabilized by __ formed bet.

A

Inter-residue hydrogen bonds

56
Q

In alpha helix, each peptide bond participates in __.

A

Hydrogen bonding

57
Q

An alpha-helix forms spontaneously as it is the __, most stable conformation for a polypeptide chain.

A

Lowest energy

58
Q

Factors that destabilize the alpha-helix:

A

 Presence of adjacent similarly charged amino acids
 Presence of adjacent bulky R groups.
 Presence of proline

59
Q

Why does the presence of proline destabilize the alpha-helix?

A
  • Contains rigid ring that prevents the N-C bond from rotating
  • No N-H group available to form intrachain hydrogen bonds
60
Q

 It is a 💡second most commonly occurring protein 2° structure
 💡“Zigzag”

A

Beta-pleated Sheet

61
Q

Beta-pleated sheet is formed when 2 or more almost fully extended polypeptide chains lie __ such that hydrogen bonding occurs between adjacent peptide chains.

A

Side by side

62
Q

In beta-pleated sheet, hydrogen bonds are __, which stabilizes the sheet.

A

Interchain

63
Q

R groups lie __ the zigzagging planes of the pleated sheet and are nearly __ to them.

A

Above or below

Perpendicular

64
Q

Two arrangements of Beta-sheets:

A

Antiparallel beta-sheet

Parallel beta-sheets

65
Q

o Neighboring H bonded polypeptide chains run in 💡opposite directions
o More 💡stable and 💡optimal

A

Antiparallel beta-sheet

66
Q

o The hydrogen bonded chains 💡extend in the same direction

A

Parallel beta-sheets

67
Q

Factors that destabilize the beta-pleated sheets

A

 Bulky R groups

 R groups with like charges

68
Q

 💡Combinations of secondary structure
 Occur as part of a 💡larger functional unit
 Have a 💡particular function
 Have 💡different functions in different proteins
 Have roughly 💡10 to 40 amino acid residues each

A

Supersecondary structures or Motifs

69
Q

Common Supersecondary Structures:

A 
o Helix-loop-helix
o Coiled-coil motif
o Beta-alpha-beta unit
o Hairpin
o Zinc finger
o Leucine zipper
o Greek key
70
Q

 💡3-dimensional structure
 💡Protein conformation (shape)
 Indicates how secondary structural features – helices, sheets, bends, turns and loops assemble to form domains.

A

TERTIARY STRUCTURE

71
Q

TERTIARY STRUCTURE results from?

A

Further folding of a polypeptide with regions of α-helix and/or beta-sheet, into a closely packed, nearly spherical shape.

72
Q

Amino acid residues that are 💡distant from each other in the primary structure 💡come into close proximity when the __.

A

Polypeptide folds

73
Q

When polypeptide folds, proteins become more __; most __ are excluded from the proteins’ interior making interactions between polar and nonpolar AA possible

A

Compact

Water molecules

74
Q

Large globular proteins (>200 AA) often contain several 💡compact units called __.

A

Domains

75
Q

Types of Interactions that stabilize Tertiary Structure

A

 Hydrophobic interactions
 Electrostatic interactions (salt bridges)
 Hydrogen bonds (Found in Serine and Threonine, Enhances solubility of proteins)
 Covalent bonds (Disulfide bridges- Covalent linkage of 2 Cysteine residue usually seen on Immunoglobulins)

76
Q
  • Proteins that have the net effect of 💡increasing the rate of correct folding by 💡binding newly synthesized polypeptides before they are completely polypeptide
  • 💡Assist in the translocation of polypeptide chains across membranes
  • e.g. heat-shock proteins, chaperonins
A

Molecular chaperons

77
Q

Enzymes involved in protein folding

A

 Peptidyl prolyl cis-trans isomerase

 Protein-disulfide isomerase

78
Q

 Family of enzymes also known as 💡Cyclophilins

 Promotes the 💡maturation of native proteins

A

Peptidyl prolyl cis-trans isomerase

79
Q

 Facilitates the 💡formation of disulfide bonds that 💡stabilize a protein’s native conformation

A

Protein-disulfide isomerase

80
Q

 They are discrete, 💡independent folding units within the 3D structure that perform a particular task such as 💡binding of a substrate or other ligand.
 They consist of 💡combinations of several units of supersecondary structures (motifs).

A

Domains or Lobes

 Size of domains varies from 25-30 to about 300 amino acid residues, with an average of about 100 amino acid

81
Q

 Exhibited only by proteins containing 💡more than one polypeptide chain.
 Most proteins with molecular masses 💡above 100 kD, consist of more than one polypeptide chain.
 Describes the characteristic manner in which the individual, folded polypeptide chains fit each other or interact with one another so that they can act as one single molecule

A

QUATERNARY STRUCTURE

82
Q

*Each polypeptide component is called a __.

A

subunit

83
Q

Are those with 💡more than one subunit.

A

Oligomeric proteins

84
Q

These are 💡identical subunits

A

Protomers

85
Q

Interactions that 💡hold subunits together

A

Hydrophobic interactions
Electrostatic interactions
Hydrogen bonds
Interpolypeptide disulfide bonds

86
Q

The 💡principal forces that hold the subunits together

INTERACTION BETWEEN NON-POLAR GROUPS

A

Hydrophobic interactions

87
Q

They contribute to the 💡proper alignment of the subunits

INTERACTION BETWEEN R-GROUPS OF BASIC AND ACIDIC AA

A

Electrostatic interactions

88
Q
  • Occurs when a protein 💡loses its native secondary, tertiary and/or quaternary structure; there is 💡cleavage of noncovalent bonds.
  • Always correlated with the 💡loss of a protein’s function.
A

DENATURATION OF PROTEINS

89
Q

Denatured proteins exists in a set of __.

A

Partially folded states

90
Q

Disrupt the weak interactions in a protein, primarily hydrogen bonds.

A

Denatured proteins

91
Q

Certain globular proteins 💡regain their native structure and biologic activity if returned to conditions in which the native conformation is stable- a process called __.

Except Collagen

A

Renaturation

92
Q

DENATURING AGENTS

A

Physical agents

Chemical agents

93
Q
  • Extremes of pH and temperature
  • High pressure
  • Ultraviolet light
  • Ultrasound
A

Physical agents

94
Q
  • Organic solvents
    – Acids, alkali, urea, guanidine
  • Detergents
A

Chemical agents

95
Q

ALTERATION

A

CHEMICAL ALTERATION

PHYSICAL ALTERATIONS

BIOLOGICAL ALTERATIONS

96
Q

o Decrease in solubility – most visible effect in globular proteins
o Many chemical groups which were inactive become exposed and more readily detectable

A

CHEMICAL ALTERATIONS

97
Q

o Increased viscosity
o Decreased rate of diffusion o increased levorotation
o Cannot be crystallized

A

PHYSICAL ALTERATIONS

98
Q

o Increased digestibility
o Enzymatic or hormonal activity is destroyed
o Antibody functions are altered

A

BIOLOGICAL ALTERATIONS

99
Q

Responsible for formation of protein primary structure

A

Amide bond

100
Q

At physiologic pH this pair of amino acids can form ionic bonds which stabilizes the quaternary structure of
proteins

A

Histidine-lysine

101
Q

It is a pair of amino acids can be sites of

glycocidation in a protein molecule

A

Threonine-asparagine

biochemistry (11 decks)

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