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

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Flashcards in 1A: Structure & function of proteins and their constituent amino acids Deck (84):
1

Amino Acids

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

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Absolute Configuration at the α position (Optical Activity)

D (+) = clockwise rotation of polarized light
L (-) = counterclockwise rotation of polarized light

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Naturally occurring amino acids

L-Amino Acids

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Absolute Configuration at the α position (Stereochemistry)

R (right) vs S (left)

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Amino Acids as Dipolar Ions

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

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Acidic Amino Acids [2] (-)

Aspartic Acid (Aspartate)
Glutamic Acid (Glutamate)

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Basic Amino Acids [3] (+)

Arginine
Lysine
Histidine

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Hydrophobic/Lipophilic Amino Acids [8]

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

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Hydrophilic/Lipophobic Amino Acids [12]

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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Sulfur Linkage Reaction

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

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Importance of cystine

Important for tertiary structure

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How are peptide bonds formed?

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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How are peptide bonds broken?

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

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Primary Structure of Proteins

Linear sequence of amino acids, linked by peptide bonds

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Secondary Structures of Proteins

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

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Tertiary Structure of Proteins

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

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Importance of Proline

Introduces kinks that cause turns

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Importance of Cysteine/Cystine

Forms disulfide bonds

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Hydrophobic Bonding

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

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Quaternary Structure of Proteins

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

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Conformational Stability

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

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Denaturation

Occurs due to temperature, chemicals, enzymes and pH

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How does temperature denature?

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

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How do chemicals denature?

They break hydrogen bonds, disrupts all except peptide bonds

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How do enzymes denature?

They break down directly to peptide bonds

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How does pH denature?

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

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How does a solvation layer affect stability?

It decreases the amount of ionic interactions between proteins

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Isoelectric Point (Separation)

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

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Electrophoresis (Separation)

Separates charged particles using an electric field

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Agarose Gel Electrophoresis

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

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SDS-PAGE

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

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Non-Enzymatic Protein Function

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

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Function of Enzymes in Biological Reactions

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

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Types of Catalysis

Acid/Base
Covalent
Electrostatic

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Acid/Base Catalysis

Acids donate protons, bases accept protons

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Covalent Catalysis

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

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Electrostatic Catalysis

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

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Types of Enzymes

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

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Oxidoreductases

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

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Transferases

Transfer of a specific group from one substrate to another
e.g. Transaminase, Kinase

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Hydrolases

Hydrolysis of a substrate
e.g. Esterases, Digestive Enzymes

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Isomerases

Change of the molecular form of the substrate
e.g. Phosphoglucoisomerase, Hexoisomerase, Fumarase

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Lyases

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

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Ligases (Synthetases)

Joining of 2 molecules by the formation of new bonds
e.g. Citric Acid Synthetase

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Reduction of Activation Energy

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

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Saturation Kinetics

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

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What do enzymes NOT affect?

Keq, dG & Thermodynamics

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What do enzymes affect?

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

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Substrate Specificity

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

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Active Site Model of Enzyme Specificity

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

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Induced-Fit Model of Enzyme Specificity

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

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Cofactors

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

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Holoenzyme

Enzyme + cofactor

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Apoenzyme

Enzyme - cofactor

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Prosthetic Group

Tightly bound coenzyme

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Cosubstrates

Loosely bound coenzyme

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Coenzyme

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

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Water-Soluble Vitamins

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

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Fat-Soluble Vitamins

Vitamin A, D, E, K

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How do local conditions affect enzyme activity?

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

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Michaelis-Menten Kinetics Equation

E + S -> ES -> E + P

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Michaelis-Menten Approximations

Rapid Equilibrium & Steady-State

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Rapid Equilibrium Approximation

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

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Steady State Approximation

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

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Km (Michaelis Constant)

Breakdown[ES]/Formation[ES]

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Factors that affect Km

pH, temperature, ionic strength, nature of substrate

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Reaction Order (Enzyme Kinetics)

Zero Order; Rate is independent of substration formation

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Vmax/2 (1/2 Vmax)

Km

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Units of V

Moles/Time

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Units of Substrate

Molar

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Low Km indicates:

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

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High Km indicates:

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

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Cooperativity

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

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Positive Cooperativity & it's Curve

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

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Feedback Regulation

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

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Competitive Inhibition

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

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Noncompetitive Inhibition

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

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Mixed Inhibition

Inhibitor can bind to the allosteric site or the ES complex;
Decreases Vmax; Increases or Decreases Km

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Uncompetitive Inhibition

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

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Allosteric Enzymes

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

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Homotropic Allosteric Enzymes

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

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Heterotropic Allosteric Enzymes

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

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Covalently-Modified Enzymes

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

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Zymogen

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