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MCAT > 1A: Structure & function of proteins and their constituent amino acids > Flashcards

1A: Structure & function of proteins and their constituent amino acids Flashcards

1
Q

Amino Acids

A

Contain a carboxylic group, alpha carbon, alpha amino group and alpha hydrogen

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2
Q

Absolute Configuration at the α position (Optical Activity)

A

D (+) = clockwise rotation of polarized light

L (-) = counterclockwise rotation of polarized light

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3
Q

Naturally occurring amino acids

A

L-Amino Acids

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4
Q

Absolute Configuration at the α position (Stereochemistry)

A

R (right) vs S (left)

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5
Q

Amino Acids as Dipolar Ions

A

Low pH = cationic
High pH = anionic
Isoelectric Point = Neutral Zwitterion

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6
Q

Acidic Amino Acids [2] (-)

A 
Aspartic Acid (Aspartate)
Glutamic Acid (Glutamate)
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7
Q

Basic Amino Acids [3] (+)

A

Arginine
Lysine
Histidine

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8
Q

Hydrophobic/Lipophilic Amino Acids [8]

A 
Alanine (A)
Valine (V)
Leucine (L)
Isoleucine (I)
Proline (P)
Methionine (M)
Phenylalanine (F)
Tryptophan (W)
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9
Q

Hydrophilic/Lipophobic Amino Acids [12]

A 
Glycine (G)
Serine (S)
Threonine (T)
Arginine (R)
Asparagine (N)
Aspartate (D)
Glutamate (E)
Glutamine (Q)
Cysteine (C)
Lysine (K)
Histidine (H)
Tyrosine (Y)
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10
Q

Sulfur Linkage Reaction

A

Cysteine-SH + HS-Cysteine -> Cystine-S-S-Cystine

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11
Q

Importance of cystine

A

Important for tertiary structure

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12
Q

How are peptide bonds formed?

A

The carboxyl group of one amino acid reacts with the amino group of a second amino acid; releases water a product

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13
Q

How are peptide bonds broken?

A

A water molecule is introduced into the peptide bond releasing a free amino acid from the peptide chain

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14
Q

Primary Structure of Proteins

A

Linear sequence of amino acids, linked by peptide bonds

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15
Q

Secondary Structures of Proteins

A

Consists of alpha helices and beta sheets; linked by hydrogen bonds

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16
Q

Tertiary Structure of Proteins

A

Chains of peptides folded onto themselves, linked by disulfide bonds, ionic interactions, van der waals, hydrogen bonds

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17
Q

Importance of Proline

A

Introduces kinks that cause turns

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18
Q

Importance of Cysteine/Cystine

A

Forms disulfide bonds

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19
Q

Hydrophobic Bonding

A

Occurs within the core of proteins between the non-polar/hydrophobic R-groups creating stability (hydrophobic collapse)

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20
Q

Quaternary Structure of Proteins

A

3D structure with multiple subunits of proteins interacting; linked by non-covalent interactions between subunits

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21
Q

Conformational Stability

A

The dG difference between the native state (folded) and unfolded state of a protein

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22
Q

Denaturation

A

Occurs due to temperature, chemicals, enzymes and pH

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23
Q

How does temperature denature?

A

It disrupts all bonding expect peptide bonds; this increases hydrophobic interactions since active globular proteins will fold

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24
Q

How do chemicals denature?

A

They break hydrogen bonds, disrupts all except peptide bonds

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25
Q

How do enzymes denature?

A

They break down directly to peptide bonds

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26
Q

How does pH denature?

A

Ionic bonds are broken down so tertiary and quaternary structures are disrupted

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27
Q

How does a solvation layer affect stability?

A

It decreases the amount of ionic interactions between proteins

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28
Q

Isoelectric Point (Separation)

A

Proteins move until they reach the pH equal to their isoelectric point in electrophoresis

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29
Q

Electrophoresis (Separation)

A

Separates charged particles using an electric field

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30
Q

Agarose Gel Electrophoresis

A

Separates nucleic acids; their negatively charged structures move toward the cathode and help with identification of sizes of particles

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31
Q

SDS-PAGE

A

Separates proteins based on mass but not charge; SDS neutralizes charge; smaller particles move through the gel faster

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32
Q

Non-Enzymatic Protein Function

A

Binding of molecules
Immune Function (Ab)
Movement (Dynein & Kinesin)
Transport (Hemoglobin)

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33
Q

Function of Enzymes in Biological Reactions

A

They act as catalysts, providing alternate pathways for reactions to occur; stabilize transition states

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34
Q

Types of Catalysis

A

Acid/Base
Covalent
Electrostatic

35
Q

Acid/Base Catalysis

A

Acids donate protons, bases accept protons

36
Q

Covalent Catalysis

A

Formation of covalent bonds in order to reduce energy for transition states; bonds are broken for the reuse of the enzyme

37
Q

Electrostatic Catalysis

A

Formation of ionic bonds with intermediates in order to stabilize the transition states in chemical reactions

38
Q

Types of Enzymes

A
  1. Oxidoreductases
  2. Transferases
  3. Hydrolases
  4. Isomerases
  5. Lyases
  6. Ligases (Synthetases)
39
Q

Oxidoreductases

A

Transfers hydrogen and oxygen atoms or electrons from one substrate to another
e.g. Dehydrogenase, Oxidase

40
Q

Transferases

A

Transfer of a specific group from one substrate to another

e.g. Transaminase, Kinase

41
Q

Hydrolases

A

Hydrolysis of a substrate

e.g. Esterases, Digestive Enzymes

42
Q

Isomerases

A

Change of the molecular form of the substrate

e.g. Phosphoglucoisomerase, Hexoisomerase, Fumarase

43
Q

Lyases

A

Nonhydrolytic removal of a group or addition of a group to a substrate
e.g. Decarboxylase, Aldolase

44
Q

Ligases (Synthetases)

A

Joining of 2 molecules by the formation of new bonds

e.g. Citric Acid Synthetase

45
Q

Reduction of Activation Energy

A

Enzymes reduce the energy of activation by providing alternate pathways for reactions; which increases the rate of the reaction

46
Q

Saturation Kinetics

A

The idea that as concentration of substrate increases, so does the rate of the reaction

47
Q

What do enzymes NOT affect?

A

Keq, dG & Thermodynamics

48
Q

What do enzymes affect?

A

Rate Constant, Kinetics, Forward & Reverse reaction (no change in equilibrium)

49
Q

Substrate Specificity

A

Substrate binds at the enzymes active site; their structure is specific to fit into the enzymes active site

50
Q

Active Site Model of Enzyme Specificity

A

The enzymes active site has a shape that accommodates the shape of the substrate

51
Q

Induced-Fit Model of Enzyme Specificity

A

Enzymes and their substrates conform to each others’ shape in order to bind together

52
Q

Cofactors

A

Inorganic molecules or Metal ions that certain enzymes use to catalyze a reaction/process

53
Q

Holoenzyme

A

Enzyme + cofactor

54
Q

Apoenzyme

A

Enzyme - cofactor

55
Q

Prosthetic Group

A

Tightly bound coenzyme

56
Q

Cosubstrates

A

Loosely bound coenzyme

57
Q

Coenzyme

A

Small, organic, non-protein molecules that carry chemical groups (electrons, atoms, functional groups) between enzymes; vitamin derivatives

58
Q

Water-Soluble Vitamins

A 
B Complex (B1, B2, B6, Folate, B12, Biotin, Pantothenate)
C
59
Q

Fat-Soluble Vitamins

A

Vitamin A, D, E, K

60
Q

How do local conditions affect enzyme activity?

A

pH, salt, temperature etc, can all affect the structure of the enzymatic protein and thus affect the availability of the active site

61
Q

Michaelis-Menten Kinetics Equation

A

E + S -> ES -> E + P

62
Q

Michaelis-Menten Approximations

A

Rapid Equilibrium & Steady-State

63
Q

Rapid Equilibrium Approximation

A

It states that E, S and the ES complex equilibrate rapidly so that the total enzyme concentration is equal to the concentration of free enzyme and the concentration of bound enzyme;

Etotal = Efree + ES

64
Q

Steady State Approximation

A

That the rate of formation of the ES complex is equal to the rate of breakdown of the ES complex

65
Q

Km (Michaelis Constant)

A

Breakdown[ES]/Formation[ES]

66
Q

Factors that affect Km

A

pH, temperature, ionic strength, nature of substrate

67
Q

Reaction Order (Enzyme Kinetics)

A

Zero Order; Rate is independent of substration formation

68
Q

Vmax/2 (1/2 Vmax)

A

Km

69
Q

Units of V

A

Moles/Time

70
Q

Units of Substrate

A

Molar

71
Q

Low Km indicates:

A

Not much substrate required to reach half maximal velocity; high affinity for the particular substrate

72
Q

High Km indicates:

A

A lot of substrate required to reach half maximal velocity; low affinity for the particular substrate

73
Q

Cooperativity

A

When a substrate binds to one subunit, the other subunits are stimulated and become active. It can be positive or negative

74
Q

Positive Cooperativity & it’s Curve

A

One oxygen molecule binds to the ferrous iron of a heme molecule which allows the other subunits heme to bind more molecules; Sigmoidal Shape

75
Q

Feedback Regulation

A

The product of a pathway inhibits or activates its pathway; it can be positive (activation) or negative (inhibition)

76
Q

Competitive Inhibition

A

Inhibitor competes with its substrate for the active site; can be overcome by increasing the amount of substrate; the Vmax is unchanged by the inhibitor; apparent Km increases

77
Q

Noncompetitive Inhibition

A

Inhibitor binds to the enzyme at an allosteric site which deactivates it; substrate still has access to the A/S but cannot catalyze the reaction as long as the inhibitor binds;
Decreases Vmax; Unchanged Km

78
Q

Mixed Inhibition

A

Inhibitor can bind to the allosteric site or the ES complex;

Decreases Vmax; Increases or Decreases Km

79
Q

Uncompetitive Inhibition

A

Inhibitor binds only to substrate-enzyme complex; Decrease Vmax; Decreases Km

80
Q

Allosteric Enzymes

A

Contain 2 binding sites, one for substrate & others for effectors (which change the conformation of the enzyme, noncovalently & reversibly)

81
Q

Homotropic Allosteric Enzymes

A

Acts as both the substrate for the enzyme and the effector of the enzyme’s activity

82
Q

Heterotropic Allosteric Enzymes

A

Acts only as the effector that regulates the enzyme’s activity; does not act as substrate

83
Q

Covalently-Modified Enzymes

A 
Covalent modification (phosphorylation) activates or inactivates the enzymes activity
e.g. Glycogen phosphorylase-a vs b
84
Q

Zymogen

A

Inactive enzyme precursor; upon hydrolysis or change of configuration of the active site

MCAT (31 decks)

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