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
2
Q
Protein is made up of 4 elements:
A
Carbon, hydrogen, oxygen, and nitrogen (CHON)
3
Q
Primary, holding first place, of first importance
A
“Proteios”
4
Q
FUNCTIONS OF PROTEINS
A
- Catalyst of chemical reactions (e.g. enzymes) -accelerates or speed up chemical reactions
- Transport and storage function (e.g. hemoglobin – transport of oxygen and carbon dioxide; Ferritin – stores iron)
- Coordinated motion (e.g. actin and myosin – involved in muscle contraction)
- Mechanical support (e.g. collagen – the most abundant fibrous protein in our body; keratin)
- Immune protection (e.g. antibodies from gamma globulins – produced by lymphocytes)
- Generation and transmission of nerve impulses (ex. neurotransmitters)
- Control of growth and differentiation (e.g. repressor proteins)
- Cell signaling (e.g. membrane receptors such as insulin receptors)
- Hormones (e.g. insulin, thyrotropin, somatotropin, luteinizing hormone, etc.)
- One of the major components of biological membranes
- Sole source of nitrogen???
- Constituents of respiratory pigments and occur in ETC (cytchromes, hgb, mgb)
- Exerting osmotic pressure (maintenance of fluid and electrocyte balance)
- Catabolized to supply energy (least function)
5
Q
CLASSIFICATION OF PROTEINS
A
SIMPLE PROTEINS
CONJUGATED PROTEINS
DERIVED PROTEINS
FIBROUS PROTEINS
GLOBULAR PROTEINS
6
Q
SIMPLE PROTEINS
A
Albumin Globulin Glutelin Prolamine Albuminoid Histone Protamine
7
Q
It is 💡soluble in water and 💡dilute aqueous salt sol’n: 💡heat coagulable
A
Albumin
8
Q
It is 💡insoluble in water; 💡soluble in aqueous salt sol’n; 💡heat coagulable
A
Globulin
9
Q
It is 💡soluble in dilute acids and alkalis; 💡heat coagulable
(e.g., plant proteins – glutenin [wheat], oryzenin [rice])
A
Glutelin
10
Q
It is 💡alcohol-soluble protein
e.g., seed proteins – zein (corn), gliadin (wheat)
A
Prolamine
11
Q
💡Least soluble (e.g., animal proteins – keratin, collagen
A
Albuminoid (Scleroprotein)
12
Q
It is a 💡basic protein; 💡soluble in water, dilute acid and alkali; found in 💡combination with DNA
A
Histone
13
Q
It is the 💡simplest; 💡basic; 💡soluble in water, dilute ammonia, acid and alkali; found in 💡spermatozoa
A
Protamine
14
Q
It is made up of a 💡protein portion and a 💡non-protein portion (prosthetic group).
A
CONJUGATED PROTEINS
15
Q
CONJUGATED PROTEINS
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Nucleoproteins Glycoproteins and proteoglycans Phosphoproteins Chromoproteins Lipoproteins Metalloproteins
16
Q
It contain 💡nucleic acid as the prosthetic group
A
Nucleoproteins
17
Q
It contain 💡carbohydrate
A
Glycoproteins and proteoglycans
Glycoproteins contain more proteins than carbs while proteoglycans contain more carbs than proteins
18
Q
They have 💡phosphoric acid residues
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Phosphoproteins
19
Q
It contain prosthetic groups that give 💡color (e.g., hemoglobin – heme group gives color)
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Chromoproteins
20
Q
It is associated with 💡lipids
e.g., chylomicron, LDL, HDL
A
Lipoproteins
21
Q
It contain 💡minerals
e.g., insulin, cytochrome
A
Metalloproteins
22
Q
It 💡partially digested proteins
A
Proteosomes & Peptones
23
Q
Classification of proteins based on the shape and certain physical characteristics
A
FIBROUS PROTEINS
GLOBULAR PROTEINS
24
Q
- 💡Tough
- Involved in 💡structural functions
- e.g., collagen, keratin
A
FIBROUS PROTEINS
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- It is involved in 💡mobile and 💡dynamic functions
| - e.g., enzymes, plasma proteins, hemoglobin
GLOBULAR PROTEINS
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Classification based on biologic functions:
```
Enzymes
Storage proteins
Regulatory proteins
Structural proteins
Protective proteins
Transport proteins
Contractile or motile proteins
```
27
Dehydrogenases, kinases, etc.
Enzymes
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Ferritin, myoglobin
Storage proteins
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Myoglobin, DNA-binding proteins
Regulatory proteins
30
Elastin, reticulin, collagen
Structural proteins
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Immunoglobulin, blood clotting factors
Protective proteins
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Plasma lipoprotein
Transport proteins
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Actin, myosin
Contractile or motile proteins
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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
PEPTIDES
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Consisting of 💡2 to 10 amino acids
Oligopeptides
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Peptides with significant biologic activities
```
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)
```
37
- 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
Glutathione (gamma-glutamyl-L-cysteinylglycine)
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- 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
(1) Oxytocin
| (2) Vasopressin
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- 💡Pentapeptide; 💡opioid peptides
| - 💡Relieve pain; bind to receptors in the brain and 💡induce analgesia
Met-enkephalin and Leu-enkephalin
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- It has 💡28 amino acid residues
| - It stimulates the 💡production of a dilute urine
Atrial natriuretic factor
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- It stimulate the 💡perception of pain
Substance P and bradykinin
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- It has 💡29 amino acid residues
| - It 💡opposes the action of insulin; 💡increases blood sugar level
Glucagon
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- With 💡39 amino acid residues; 💡stimulates adrenal cortex
Corticotropin
44
- It is 💡artificial sweetener
Aspartame (L-aspartylphenylalanine methyl ester)
45
Formation of Peptide Bond
- 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
Evidences that a peptide bond exist in proteins
(+) 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
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N-terminal residue
- It has free alpha amino group
C-terminal residue
- It has a free alpha carboxyl group
Parts of the peptide chain
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PROTEIN LEVELS OF STRUCTURAL ORGANIZATION
PRIMARY STRUCTURE
SECONDARY STRUCTURE
TERTIARY STRUCTURE
QUATERNARY STRUCTURE
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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
PRIMARY STRUCTURE
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The backbone of a protein refers to the __.
Atoms that participate in the formation of peptide bonds
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The 3-D shape of a folded polypeptide is a result of the __.
Interactions among the R groups
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It is due to the 💡formation of hydrogen bonds 💡between peptide bonds
SECONDARY STRUCTURE
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Two types of secondary structure:
o Coils or helices – INTRAchain hydrogen bonding (within the same structure)
o Sheets or pleats – INTERchain hydrogen bonding
54
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
Alpha-helix
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Alpha-helix is stabilized by __ formed bet.
Inter-residue hydrogen bonds
56
In alpha helix, each peptide bond participates in __.
Hydrogen bonding
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An alpha-helix forms spontaneously as it is the __, most stable conformation for a polypeptide chain.
Lowest energy
58
Factors that destabilize the alpha-helix:
Presence of adjacent similarly charged amino acids
Presence of adjacent bulky R groups.
Presence of proline
59
Why does the presence of proline destabilize the alpha-helix?
- Contains rigid ring that prevents the N-C bond from rotating
- No N-H group available to form intrachain hydrogen bonds
60
It is a 💡second most commonly occurring protein 2° structure
💡“Zigzag”
Beta-pleated Sheet
61
Beta-pleated sheet is formed when 2 or more almost fully extended polypeptide chains lie __ such that hydrogen bonding occurs between adjacent peptide chains.
Side by side
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In beta-pleated sheet, hydrogen bonds are __, which stabilizes the sheet.
Interchain
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R groups lie __ the zigzagging planes of the pleated sheet and are nearly __ to them.
Above or below
Perpendicular
64
Two arrangements of Beta-sheets:
Antiparallel beta-sheet
| Parallel beta-sheets
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o Neighboring H bonded polypeptide chains run in 💡opposite directions
o More 💡stable and 💡optimal
Antiparallel beta-sheet
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o The hydrogen bonded chains 💡extend in the same direction
Parallel beta-sheets
67
Factors that destabilize the beta-pleated sheets
Bulky R groups
| R groups with like charges
68
💡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
Supersecondary structures or Motifs
69
Common Supersecondary Structures:
```
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
💡3-dimensional structure
💡Protein conformation (shape)
Indicates how secondary structural features – helices, sheets, bends, turns and loops assemble to form domains.
TERTIARY STRUCTURE
71
TERTIARY STRUCTURE results from?
Further folding of a polypeptide with regions of α-helix and/or beta-sheet, into a closely packed, nearly spherical shape.
72
Amino acid residues that are 💡distant from each other in the primary structure 💡come into close proximity when the __.
Polypeptide folds
73
When polypeptide folds, proteins become more __; most __ are excluded from the proteins’ interior making interactions between polar and nonpolar AA possible
Compact
| Water molecules
74
Large globular proteins (>200 AA) often contain several 💡compact units called __.
Domains
75
Types of Interactions that stabilize Tertiary Structure
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
- 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
Molecular chaperons
77
Enzymes involved in protein folding
Peptidyl prolyl cis-trans isomerase
| Protein-disulfide isomerase
78
Family of enzymes also known as 💡Cyclophilins
| Promotes the 💡maturation of native proteins
Peptidyl prolyl cis-trans isomerase
79
Facilitates the 💡formation of disulfide bonds that 💡stabilize a protein’s native conformation
Protein-disulfide isomerase
80
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).
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
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
QUATERNARY STRUCTURE
82
*Each polypeptide component is called a __.
subunit
83
Are those with 💡more than one subunit.
Oligomeric proteins
84
These are 💡identical subunits
Protomers
85
Interactions that 💡hold subunits together
Hydrophobic interactions
Electrostatic interactions
Hydrogen bonds
Interpolypeptide disulfide bonds
86
The 💡principal forces that hold the subunits together
INTERACTION BETWEEN NON-POLAR GROUPS
Hydrophobic interactions
87
They contribute to the 💡proper alignment of the subunits
INTERACTION BETWEEN R-GROUPS OF BASIC AND ACIDIC AA
Electrostatic interactions
88
- 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.
DENATURATION OF PROTEINS
89
Denatured proteins exists in a set of __.
Partially folded states
90
Disrupt the weak interactions in a protein, primarily hydrogen bonds.
Denatured proteins
91
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
Renaturation
92
DENATURING AGENTS
Physical agents
Chemical agents
93
- Extremes of pH and temperature
- High pressure
- Ultraviolet light
- Ultrasound
Physical agents
94
- Organic solvents
– Acids, alkali, urea, guanidine
- Detergents
Chemical agents
95
ALTERATION
CHEMICAL ALTERATION
PHYSICAL ALTERATIONS
BIOLOGICAL ALTERATIONS
96
o Decrease in solubility – most visible effect in globular proteins
o Many chemical groups which were inactive become exposed and more readily detectable
CHEMICAL ALTERATIONS
97
o Increased viscosity
o Decreased rate of diffusion o increased levorotation
o Cannot be crystallized
PHYSICAL ALTERATIONS
98
o Increased digestibility
o Enzymatic or hormonal activity is destroyed
o Antibody functions are altered
BIOLOGICAL ALTERATIONS
99
Responsible for formation of protein primary structure
Amide bond
100
At physiologic pH this pair of amino acids can form ionic bonds which stabilizes the quaternary structure of
proteins
Histidine-lysine
101
It is a pair of amino acids can be sites of
| glycocidation in a protein molecule
Threonine-asparagine
