Cumulative Final Exam

Question 1

Non-Covalent Interactions

Answer 1

• Hydrogen Bonds
• Ionic/Electrostatic Interactions
• Hydrophobic Interactions
• Van der Waals Interactions

Question 2

Van der Waals Interactions

Answer 2

Weak intermolecular interactions that occur between the dipoles of nearby electrically neutral molecules.

Question 3

Hydrophobic Interactions

Answer 3

The tendency of hydrophoic molecules to pack closely together to mimize contact/interaction from water (when in an aqueous environment).

Question 4

Henderson-Hasselbalch Equation

Answer 4

Question 5

What causes the pH value to be less than the pK_a value?

Buffer Systems

Answer 5

[Conjugate Base] < [Acid]

[A^–] < [HA]

Question 6

What causes the pH value to be greater than the pK_a value?

Buffer Systems

Answer 6

[Conjugate Base] > [Acid]

[A^–] > [HA]

Question 7

What causes the pH value to be equal to the pK_a value?

Buffer Systems

Answer 7

[Conjugate Base] = [Acid]

[A^–] = [HA]

Question 8

What is a state function?

Answer 8

A variable/function determined solely by the start conditions and end conditions (and not the path/speed of the process).

Question 9

What does the ∆G value represent?

Answer 9

The magnitude of the driving force (energy magnitude) needed to pull/bring a system to its equilibrium point.

Equilibrium: ∆G = 0 kJ/mol

Question 10

Equation: ∆G

Any State

Answer 10

Question 11

Equation: ∆G°’

Equilibrium State

Answer 11

Question 12

Relationship: ∆G° vs. K_eq

Answer 12

• K_eq > 1: ∆G is Negative (Reaction Favors Product Formation)
• K_eq < 1: ∆G is Positive (Reaction Favors Reactant Formation)
• K_eq = 1: ∆G is Zero (Reaction is at Equilibrium)

Question 13

Why are living organisms never at equilibrium?

Answer 13

Living organisms require a constant input of energy to maintain homeostasis (which shifts the organism’s energy system away from equilibrium).

Question 14

How is ADP + P_i more thermodynamically favorable than ATP?

Answer 14

• Charge Separation: The ADP + P_i form possesses fewer negative charges on the same compound.
• Solvation: The ADP + P_i form is better solvated by water due to the split into two negatively charged compounds.
• Resonance Stabilization: The ADP + P_i form possesses more resonance forms to increase stabilization via electron delocalization.

Question 15

Energy Charge

Answer 15

A measure of the current energy state within a cell in terms of ATP, ADP, and AMP.

Question 16

How does Hydrogen-bonding occur within an alpha helix?

Protein Secondary Structure

Answer 16

Hydrogen bonds form between the amino group (of one amino acid) and a carboxyl group (of another amino acid) four amino acids away.

The alpha helix Hydrogen bonds connect Residue_n and Residue_n+4.

Question 17

Alpha Helix: Rise vs. Pitch

Answer 17

• Rise: The vertical distance between two consecutive amino acids.
• Pitch: The vertical distance spanning one complete turn of the helix.

Pitch = (Rise Distance) × (Number of Residues)

Question 18

Why are antiparallel β sheets more stable than parallel β sheets?

Answer 18

Antiparallel β sheets possess more optimal lengths and geometries of Hydrogen bonds between adjacent β strands, which results in higher levels of structural stability.

Question 19

Types of Side-Chain Interactions

Protein Tertiary Structure

Answer 19

• Hydrophobic Interactions
• Disulfide Bonds
• Electrostatic Interactions

Question 20

Protein Structure: Domain vs. Subunit

Answer 20

• Domain: One distinct region (with a unique function) of a single polypeptide chain.
• Subunit: One distinct polypeptide chain of a multi-polypeptide protein.

Question 21

Methods of Determining 3-D Protein Structure

Answer 21

• X-Ray Crystallography
• Nuclear Magnetic Resonance (NMR)
• Cryo-Electron Microscopy (CryoEM)

Question 22

Which levels of protein structure are impacted by protein denaturation?

Answer 22

• Secondary
• Tertiary
• Quaternary

Question 23

What are the causes of protein denuration?

Answer 23

• Excess Heat
• pH Variations
• Detergents
• Chemical Agents (Urea, GdmCl, βME)

Question 24

How does β-Mercaptoethanol cause protein denuration?

Answer 24

β-Mercaptoethanol breaks disulfide bonds (S—S) linking spatially adjacent amino acids.

Question 25

How does Urea cause protein denuration?

Answer 25

Urea disrupts the intramolecular *polar interactions* (electrostatic attractions) within a polypeptide/protein.

Question 26

**Takeaways:** Haber-Anfinsen Experiments

Answer 26

* Proteins will spontaneously fold into their native conformations under *physiological conditions*. * A protein's primary structure (amino acid sequence) dictates its 3-D/tertiary structure.

Question 27

**Takeaways:** Haber-Anfinsen Experiments

Answer 27

* Adding **βME + Urea** to an active RNaseA resulted in an **unfolded/nonfunctional RNaseA**. * Removing **βME + Urea** simultaneously from the unfolded RNaseA resulted in **functional RNaseA** with **correct disulfide bonds**. * Removing **βME first** and **Urea second** from the unfolded RNaseA resulted in a **nonfunctional RNaseA** with **random disulfide bonds**. * Adding **trace βME** to the improperly folded RNaseA resulted in a **functional RNaseA** with **correct disulfide bonds**.

Question 28

**Models:** Protein Folding

Answer 28

* Hydrophobic Collapse Model * Framework Model * Nucleation Model

Question 29

**Chaperones:** Clamp-Type vs. Chamber-Type

Answer 29

* **Clamp-Type:** Heat-Shock Protein (Smaller) * **Chamber-Type:** Chaperonin Protein (Larger) ## Footnote **Chaperone Protein:** A protein that binds to partially/improperly folded proteins and utilizes ATP hydrolysis to facilitate proper protein folding.

Question 30

**Examples:** Diseases of Protein Misfolding

Answer 30

* Cystic Fibrosis (CFTR Mutation) * Alzheimer's Disease (Amyloid Plaques) * Huntington's Disease (Polyglutamine Track Expansion) * Mad Cow Disease (Prion Protein) * Creutzfeldt-Jakob Disease (Prion Protein)

Question 31

**Column Chromatography:** Three Types

Answer 31

* **Ion-Exchange Chromatography:** Separation Based on Charge Difference * **Affinity Chromatography:** Separation Based on Binding Affinity to Target Ligand * **Gel-Filtration Chromatography:** Separation Based on Size ## Footnote **Column Chromatography:** A protein purification method that separates proteins based on differential physical/chemical interactions with a solid gel matrix.

Question 32

Anion Exchanger vs. Cation Exchanger | Ion-Exchange Chromatography

Answer 32

* **Anion Exchanger:** Positively Charged Matrix (e.g. DEAE) * **Cation Exchanger:** Negatively Charged Matrix (e.g. CMC)

Question 33

SDS-PAGE

Answer 33

A gel electrophoresis technique that utilizes a polyacrylamide gel matrix (frame-supported molecular sieve) and the sodium dodecyl sulfate detergent (to coat proteins with a negative charge). ## Footnote **SDS-Page** separates proteins on the basis of size to estimate the molecule weight of particular proteins.

Question 34

Isoelectric Point | pI

Answer 34

The pH value at which a protein has **no/neutral** net charge. ## Footnote **Isoelectric Focusing (IEF):** A gel filtration technique that separates proteins on the basees of their isoelectric point.

Question 35

**Isoelectric Focusing:** pH vs. pI

Answer 35

* **pH < pI:** The protein will move towards the cathode (–) due to having a net *positive charge*. * **pH > pI:** The protein will move towards the anode (+) due to having a net *negative charge*. * **pH = pI:** The protein will be stationary due to having a net *neutral charge*.

Question 36

Effect of pH on O₂-Hemoglobin Affinity

Answer 36

* **Higher pH =** Higher Binding Affinity * **Lower pH =** Lower Binding Affinity

Question 37

How does **elevated [2,3-BPG]** at higher altitudes impact O₂-Hemoglobin binding?

Answer 37

Elevated [2,3-BPG] creates a **greater fractional saturation difference** between the lungs and the tissues, which results in more offloading of O₂ to the tissues at high altitudes.

Question 38

Which factors **increase** the stability of Hemoglobin's T state?

Answer 38

* Lower [O₂] * Lower pH * Carbamylation * Higher [2,3-BPG] * Higher [CO_2–

Question 39

Which factors **increase** the stability of Hemoglobin's R state?

Answer 39

* Higher [O₂] * Higher pH * Lower [2,3-BPG] * Lower [CO_2–

Question 40

Fetal Hemoglobin vs. Adult Hemoglobin

Answer 40

* Fetal Hemoglobin has a higher O₂ affinity than adult Hemoglobin, which enables O₂ to diffuse from the mother to the fetus during pregnancy. * Fetal Hemoglobin possesses γ subunits (in place of the adult Hemoglobin's β subunits), which have a decreased affinity for 2,3-BPG.

Question 41

**Mutation:** Sickle Cell Anemia | β Chain

Answer 41

**Amino Acid #6:** Glutamine → Valine

Question 42

Which types of catalysis are utilized by Serine proteases?

Answer 42

* Acid-Base Catalysis * Covalent Catalysis ## Footnote **Serine Protease:** An enzyme that cleaves the peptide backbone of proteins via a Serine nucleophile (within the enzyme's active site).

Question 43

**Examples:** Serine Proteases

Answer 43

* Chymotrypsin * Trypsin * Elastase

Question 44

**Serine Proteases:** Catalytic Triad

Answer 44

* Serine * Histadine * Aspartate

Question 45

Which type of catalysis is utilized by Enolase?

Answer 45

Metal-Ion Catalysis

Question 46

Turnover Number (k_cat)

Answer 46

The rate of (substrate → product) conversion at a single enzyme when that enzyme is fully saturated.

Question 47

What does the Specificity Constant represent?

Answer 47

Catalytic Efficiency of an Enzyme ## Footnote The specificity constant is dependent upon the **enzyme's affinity to the substrate** and the **enzyme's catalysis rate**.