Module 2 Flashcards

Question

Cytoskeletal Proteins

Answer 1

Structural proteins that are responsible for cell shape, cell migration, and cell signaling. ## Footnote **Ex:** Actin, Tubulin

Answer 2

An Actin polymer that forms part of a network to control cell shape, cell migration, and muscle contraction.

Answer 3

A type of cytoskeletal protein complex that is critical to cell structure and cell function. ## Footnote **Ex:** Vimentin, Laminin, Keratin

Answer 4

Proteins that span the width of a cell membrane and allow polar/charged molecules to enter/exit the cell. ## Footnote The two classes of membrane transport proteins are **passive transporters** and **active transporters**.

Answer 5

A membrane transport protein that allows specific molecules to enter/exit the cell while moving down their concentration gradient. ## Footnote **Ex:** Porins, Ion Channels

Answer 6

A membrane transport protein requiring energy to induce protein conformational changes that open/close a gated channel (and pump molecules against their concentration gradient). ## Footnote * Active transporters obtain energy from either **ATP hydroylsis** or **ionic gradients**. * **Ex:** Ca²⁺-ATPase

Answer 7

* Membrane Receptors * Nuclear Receptors * Intracellular Signaling Proteins

Answer 8

A transmembrane protein that changes conformation upon binding of a cognate ligand molecule. ## Footnote **Ex:** Erythropoietin Receptor (Growth Hormone Receptor); Insulin Receptor (Receptor Tyrosine Kinase); Adrenergic Receptors (G Protein-Coupled Receptor)

Answer 9

A transcription factor that regulates gene expression in response to ligand binding. ## Footnote **Ex:** Glucocorticoid Receptor, Vitamin D Receptor, Estrogen Receptor, Progesterone Receptor

Answer 10

A protein that functions as a molecular switch by undergoing conformational changes in response to incoming signals (e.g. receptor activation). ## Footnote **E:** Protein Kinases, Phosphatases, Intermolecular Adaptor Proteins, Site-Specific Proteases

Answer 11

Proteins that function to ensure the integrity of genomic DNA throughout a cell's lifespan. ## Footnote **Ex:** DNA Synthesis Enzymes, DNA Repair Enzymes, DNA Recombination Enzymes, RNA Synthesis Enzymes

Answer 12

A monomeric globular transport protein concentrated in muscle tissue that functions in Oxygen storage.

Answer 13

A tetrameric globular transport protein that transports Oxygen from the lungs to the tissues via the circulatory system. ## Footnote Hemoglobin is the major protein in red blood cells (i.e. accounts for 35% of the cells' dry weight).

Answer 14

An Fe²⁺ porphoryin complex that functions as a prostethic group to bind Oxygen. ## Footnote The Fe ion *must* be in the 2+ oxidation state for Oxygen binding to occur.

Answer 15

* **Myoglobin:** Single Polypeptide w/ 1 Heme Group * **Hemoglobin:** Four Polypeptides w/ 4 Heme Groups ## Footnote * Less than 20% of amino acids are identical between Myoglobin and Hemoglobin. * Myoglobin and Hemoglobin *share* the globin fold conformation.

Answer 16

* Two α-Subunits + Two β-Subunits (Each Possess 1 Heme Group) * Dimer of Heterodimers (α₁β₁ + α₂β₂) = Heterotetramer * Eight α-Helices (Globin Fold) per Subunit

Answer 17

A protein folding pattern that contains eight **α-helices**. ## Footnote **Ex:** Myoglobin, Hemoglobin

Answer 18

Six ## Footnote * **Four** coordination bonds are with Nitrogens *in the plane* of the porphyrin ring. * **One** coordination bond is *above* the plane of the porphyrin ring. * **One** coordination bond is *below* the plane of the porphyrin ring.

Answer 19

A Histidine residue in globin proteins that coordinates with the Fe²⁺ of the porphyrin ring (either *above* or *below* the plane of the ring).

Answer 20

A Histidine residue in globin proteins that forms a hydrogen bond with O₂ (when O₂ is bound to the porphyrin ring) to stabilize its intereaction with the Heme group.

Answer 21

The O₂ forms a **coordination bond** with the Fe²⁺ of the porphoryin ring (either *above* or *below* the plane of the ring).

Answer 22

* **Unbound O₂:** The Heme group is *puckered* (i.e. Fe²⁺ is NOT in the plane of the porphyrin ring) because of the larger Fe²⁺ ionic radius. * **Bound O₂:** The Heme group is *planar* (i.e. Fe²⁺ IS in the plane of the porphyrin ring) because of the smaller Fe²⁺ ionic radius. ## Footnote The binding of O₂ to the Heme group moves His F8 (and the entire F Helix) toward the Heme group.

Answer 23

The structural changes of Hemoglobin/Myoglobin under different physiological conditions results in altered affinities for O₂.

Answer 24

P = Protein L = Ligand PL = Protein-Ligand Complex

Answer 25

An equilibrium constant for the binding of two molecules (e.g. a protein and a ligand to form a protein-ligand complex). ## Footnote **Units:** M^–1

Answer 26

An equilibrium constant for the dissociation of two molecules (e.g. a protein-ligand complex unbinding to yield a protein and a ligand). ## Footnote **Units:** K_d

Answer 27

## Footnote The K_d is the **inverse** of the K_a equation.

Answer 28

A **lower affinity** between the two molecules (i.e. *more* of the dissociated protein and ligand are present). ## Footnote A lower K_d value indicates a **higher affinity** between the two molecules.

Answer 29

The ligand concentration at which 50% of potential ligand binding sites are occupied. ## Footnote K_d: [L] at θ = 0.5

Answer 30

The fraction of protein binding sites that are occupied by ligands.

Answer 31

Hyperbolic

Answer 32

The partial pressure of a ligand at which 50% of potential binding sites are occupied. ## Footnote **P₅₀:** pX at θ = 0.5

Answer 33

* **P₅₀:** Used when the ligand is a gaseous compound (e.g. O₂) * **K_d:** Used when the ligand is a solid/liquid compound (e.g. Drug Compounds)

Answer 34

* Binding of Regulatory Molecules * Covalent Modification * Proteolytic Processing

Answer 35

An enzyme regulatory mechanism involving the *noncovalent* binding of biomolecules/proteins to an enzyme subunit. ## Footnote The effect of reversible inhibition can be *decreased* by diluting a reaction (with more substrate).

Answer 36

An enzyme regulatory mechanism involving the *covalent* binding of an inhibitory molecule to catalytic groups on an enzyme's active site. ## Footnote Irreversible inhibition is *not affected* by diluting a reaction with more substrate (since the covalent bonds remains intact regardless of enzyme/inhibitor concentration).

Answer 37

* Competitive Inhibitors * Uncompetitive Inhibitors * Mixed Inhibitors

Answer 38

A molecule that decreases enzymatic efficiency by inhibiting/blocking substrate binding at the enzyme's active site. ## Footnote Competitive inhibitors bind to the free enzyme at the active site (or at a location overlapping with the active site).

Answer 39

A molecule that decreases enzymatic efficiency by binding to the enzyme-substrate complex and altering the active site conformation. ## Footnote Uncompetitive inhibitors bind to the enzyme-substrate complex at a location other than the active site (i.e. an *allosteric* site).

Answer 40

A molecule that decreases enzymatic efficiency by altering the active site conformation (before *or* after substrate binding). ## Footnote Mixed inhibitors bind to the free enzyme *or* the enzyme-substrate complex a location other than the active site (i.e. an *allosteric* site).

Answer 41

Equilibrium Dissocation Constant for Enzyme-Inhibitor Complex ## Footnote **K_I** describes the *affinity* of an inhibitor for an enzyme.

Answer 42

Equilibrium Dissocation Constant for Enzyme-Substrate-Inhibitor Complex ## Footnote **K_I** describes the *affinity* of an inhibitor for an enzyme-substrate complex.

Answer 43

* **v_max**: Decreases * **K_m-app**: Unaffected

Answer 44

* **v_max**: Decreases * **K_m-app**: Decreases

Answer 45

* **v_max**: Decreases * **K_m-app**: Increases

Answer 46

* **v_max**: Decreases * **K_m-app**: Decreases

Answer 47

**Slope (K_m/v_max):** Increases **Y-Intercept (1/v_max):** Increases **X-Intercept (-1/K_m):** Unaffect ## Footnote Noncompetitive inhibition causes the Linewaver-Burk plot to *pivot leftward* about the x-intercept.

Answer 48

**Slope (K_m/v_max):** Unaffected **Y-Intercept (1/v_max):** Increases **X-Intercept (-1/K_m):** Increases ## Footnote Uncompetitive inhibition causes the Linewaver-Burk plot to shift *right*.

Answer 49

Increases [S] Requirement ## Footnote Competitive inhibition shifts the Michaelis-Menten graph *rightward*.

Answer 50

**Slope (K_m/v_max):** Increases **Y-Intercept (1/v_max):** Unaffected **X-Intercept (-1/K_m):** Increases ## Footnote Competitive inhibition causes a *leftward pivot* about the y-intercept of the Linewaver-Burk plot.

Answer 51

**Slope (K_m/v_max):** Increases **Y-Intercept (1/v_max):** Increases **X-Intercept (-1/K_m):** Increases

Answer 52

**Slope (K_m/v_max):** Increases **Y-Intercept (1/v_max):** Increases **X-Intercept (-1/K_m):** Decreases

Answer 53

* **v_max**: Unaffected * **K_m-app**: Increases

Answer 54

Competitive Inhibition

Answer 55

A type of mixed inhibition in which the inhibitor compound has *equal affinity* for the free enzyme and the enzyme-substrate complex. ## Footnote * Noncompetitive inhibitors bind to the free enzyme *or* the enzyme-substrate complex at a location other than the active site (i.e. an *allosteric* site).

Answer 56

An enzymatic regulatory mechanism in which a metabolic pathway's end product serves as an inhibitor of the first enzyme in the pathway.

Answer 57

Substrate-binding to one subunit of a cooperative enzyme changes the substrate affinity at other enzyme subunits.

Answer 58

The enzyme's catalytic activity can increase/decrease significantly over a small range of substrate concentrations.

Answer 59

**C₆R₆** (Association of Two C₃R₃ Complexes) ## Footnote * **C =** Catalytic Subunit * **R =** Regulatory Subunit

Answer 60

An inactive enzyme precursor that is activated by a proteolytic cleavage (either auto-cleavage *or* trans-cleavage) reaction.

Answer 61

A model of enzyme catalysis in which rigid physical/chemical complementarity between the substrate and the enzyme are required for the reaction to occur.

Answer 62

A model of enzyme catalysis in which an enzymatic conformational change will occur upon binding of the substrate.

Answer 63

The process of stabilizing a particular enzyme conformation that is preferred for ligand binding.

Answer 64

* Active sites *exclude excess solvents* from the reaction environment. * Active sites bring reactive *functional groups in close proximity* to the substrate. * Active sites facilitate *optimal/reactive orientations* of the substrates.

Answer 65

No ## Footnote Enzymes *decrease the activation energy* of a reaction, *not* the ground energy states of the reactants and products.

Answer 66

No ## Footnote Enzymes change *the rate* at which a reaction proceeds, *not* the ratio of products and reactants at equilibium.

Answer 67

Enzymes increase the reaction rate in both directions by the same amount, so the overall product-to-reactant ratio remains unchanged.

Answer 68

The enzyme catalyst will *decrease the activation energy* of the reaction by (1) *properly orienting the substrates* for a reaction to occur and (2) providing an *alternative path to product formation*. ## Footnote * Enzymes *stabilize the transition state* of a reaction (to lower the activation energy barrier). * The *entropy change of a reaction is reduced* by properly orienting the substrates for a reaction.

Answer 69

A small inorganic molecule (often a metal ion) that assists with the catalytic reaction mechanism within an enzyme's active site. ## Footnote **Ex:** Fe²⁺, Mg²⁺, Mn²⁺, Cu²⁺, Zn²⁺, Ni²⁺, K⁺, Se, Mo

Answer 70

The catalytically *active* form of an enzyme that possesses a *bound* cofactor.

Answer 71

The catalytically *inactive* form of an enzyme that *lacks* its cofactor.

Answer 72

An type of enzyme cofactor that possesses *organic* components. ## Footnote **Ex:** NADH, FADH₂, TPP, Biotin, CoA,THF, PLP, Lipoamid, Cobalamin

Answer 73

A type of coenzyme that is *permanently* associated with an enzyme. ## Footnote **Ex:** Heme Group (Globin Proteins)

Answer 74

A loosely bound molecule that is *transformed into a co-product* during the course of an enzymatic reaction. ## Footnote **Ex:** NAD⁺/NADH, NADP⁺/NADPH

Answer 75

An enzyme containing a *nucleophilic serine amino acid* within the active site that functions to *cleave the peptide backbone* of dietary proteins. ## Footnote **Ex:** Chymotrypsin

Answer 76

Chymotrypsin consists of *three* individual polypeptide chains that are covalently linked by disulside bonds. ## Footnote * The **three** individual polypeptide chains were formed from the cleavage of a single nascent polypeptide chain. * The enzyme active site sites on the enzyme's surface (to allow easy access to the polymer substrates).

Answer 77

A set of *three* amino acids in **serine proteases** that form a hydrogen-bonded network required for catalysis.

Answer 78

* Ser195 (C Chain) * His 57 (B Chain) * Asp102 (B Chain)

Answer 79

Polypeptide Substrate ⟶ Carboxyl-Terminal Fragment + Amino-Terminal Fragment ## Footnote * **Phase 1:** The polypeptide substrate is cleaved to release the *carboxyl-terminal fragment*. * **Phase 2:** The enzyme active site is regerated via release of the *amino-terminal fragment*.

Answer 80

1. The polypeptide **substrate binds** to the enzyme active site. 2. The aromatic**His57 Nitrogen deprotonates Ser195** to enable the Ser195 Oxygen to nucleophilically attack the polypeptide's carbonyl Carbon (to form an Oxyanion intermediate). 3. **Electron rearrangment** at the Oxyanion intermediate causes the polypeptide substrate to deprotonate His57 (and cleave its C_tetrahedral—N bond). 4. The **carboxyl-terminal fragment is released** from the enzyme active site. 5. An **H₂O** molecule enters the enzyme active site. 6. The aromatic**His57 Nitrogen deprotonates the H₂O** molecule to create an OH^– nucleophile. 7. The **OH^– nucleophile attacks the Acyl-enzyme** intermediate's carbonyl Carbon (to form an Oxyanion intermediate). 7. **Electron rearrangment** at the Oxyanion intermediate causes the polypeptide substrate to deprotonate His57 (and cleave its C_tetrahedral—O bond). 8. The **amino-terminal fragment is released** from the enzyme active site (to regenerate the functional catalytic triad within the enzyme active site).

Answer 81

1. The polypeptide *substrate binds* to the enzyme active site. 2. *His57 removes a proton from Ser195* to enable the Serine Oxygen to nucleophilically attack the polypeptide's carbonyl Carbon. 3. *His57 protonates the polypeptide's amino group* to cleave the polypeptide. 4. The carboxyl-terminal *fragment is released* from the enzyme active site. 5. An H₂O molecule enters the enzyme active site. 6. *His57 deprotonates the H₂O* molecule to created an OH^– nucleophile that attacks the Acyl-enzyme intermediate's carbonyl Carbon. 7. His57 protonates Ser195 to cleave the acyl-enzyme intermediate and relase the amino-terminal fragment from the enzyme active site. 8. The functional catalytic triad is regenerated within the enzyme active site.

Answer 82

The Oxyanion hole stabilizes Oxyanion (O^–) intermediates formed during the proteolytic cleavage reaction. ## Footnote **Oxyanion Hole:** Terminal Hydrogens of Gly193 and Ser195.

Answer 83

A numerical constant that reflects how quickly a substrate is converted into product as a function of time (under a defined set of conditions). ## Footnote * **First-Order Reaction:** s^–1 * **Second-Order Reaction:** M^–1s^–1 * **Third-Order Reaction:** M^–2s^–1

Answer 84

A state of a reaction in which [ES] remains relatively constant over an intial reaction period.

Answer 85

* Steady-State Conditions * First-Order Reaction * Single Enzyme

Answer 86

The substrate concentration at which the reaction rate is one-half its maximum value. ## Footnote **K_m:** [S] @ 0.5(v_max)

Answer 87

The enzyme has a high catalytic activity (i.e. is highly effective) at lower substrate concentrations. ## Footnote (A high K_m value indicates that the enzyme has high catalytic activity *only* at higher substrate concentrations.)

Answer 88

The plot pivots *rightward* about the x-intercept to yield a *lower* y-intercept and a *less steep* slope. ## Footnote * **K_m:** Remains Constant * **v_max:** Increases

Answer 89

* Enzymes with Cooperative Binding * Enzymes that Slowly Release Products

Answer 90

The maximum catalytic activity of an enzyme under saturating levels of substrate. ## Footnote The **k_cat** value is the number of conversions of substrate to product at a single active site per unit time (when the enzyme is saturated).

Answer 91

## Footnote [E_t] = [E] + [ES]

Answer 92

No ## Footnote An enzyme's catalytic efficiency is best described by the **specificity constant** (k_cat/K_m).

Answer 93

A ratio that measures the catalytic efficiency of an enzymatic reaction (to compare *two different* enzyme reactions or to compare the same enzyme reaction with *two different* substrates).

Answer 94

Moderately Efficient

Answer 95

Very Efficient

Answer 96

* CO₂ * H⁺ * 2,3-Biphosphoglycerate

Answer 97

An allosteric regulation mechanism in which the regulatory molecule affects the binding affinity of a different molecule(s). ## Footnote Heterotropic allostery involves the regulatory molecule binding to a location distinct from the protein's primary site (i.e. a secondary site).