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Biochemistry > Cumulative Final Exam > Flashcards

Cumulative Final Exam Flashcards

1
Q

Non-Covalent Interactions

A
  • Hydrogen Bonds
  • Ionic/Electrostatic Interactions
  • Hydrophobic Interactions
  • Van der Waals Interactions
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2
Q

Van der Waals Interactions

A

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

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3
Q

Hydrophobic Interactions

A

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

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4
Q

Henderson-Hasselbalch Equation

A
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5
Q

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

Buffer Systems

A

[Conjugate Base] < [Acid]

[A–] < [HA]

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6
Q

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

Buffer Systems

A

[Conjugate Base] > [Acid]

[A–] > [HA]

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7
Q

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

Buffer Systems

A

[Conjugate Base] = [Acid]

[A–] = [HA]

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8
Q

What is a state function?

A

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

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9
Q

What does the ∆G value represent?

A

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

Equilibrium: ∆G = 0 kJ/mol

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10
Q

Equation: ∆G

Any State

A
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11
Q

Equation: ∆G°’

Equilibrium State

A
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12
Q

Relationship: ∆G° vs. Keq

A
  • Keq > 1: ∆G is Negative (Reaction Favors Product Formation)
  • Keq < 1: ∆G is Positive (Reaction Favors Reactant Formation)
  • Keq = 1: ∆G is Zero (Reaction is at Equilibrium)
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13
Q

Why are living organisms never at equilibrium?

A

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

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14
Q

How is ADP + Pi more thermodynamically favorable than ATP?

A
  • Charge Separation: The ADP + Pi form possesses fewer negative charges on the same compound.
  • Solvation: The ADP + Pi form is better solvated by water due to the split into two negatively charged compounds.
  • Resonance Stabilization: The ADP + Pi form possesses more resonance forms to increase stabilization via electron delocalization.
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15
Q

Energy Charge

A

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

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16
Q

How does Hydrogen-bonding occur within an alpha helix?

Protein Secondary Structure

A

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 Residuen and Residuen+4.

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17
Q

Alpha Helix: Rise vs. Pitch

A
  • 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)

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18
Q

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

A

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

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19
Q

Types of Side-Chain Interactions

Protein Tertiary Structure

A
  • Hydrophobic Interactions
  • Disulfide Bonds
  • Electrostatic Interactions
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20
Q

Protein Structure: Domain vs. Subunit

A
  • Domain: One distinct region (with a unique function) of a single polypeptide chain.
  • Subunit: One distinct polypeptide chain of a multi-polypeptide protein.
21
Q

Methods of Determining 3-D Protein Structure

A
  • X-Ray Crystallography
  • Nuclear Magnetic Resonance (NMR)
  • Cryo-Electron Microscopy (CryoEM)
22
Q

Which levels of protein structure are impacted by protein denaturation?

A
  • Secondary
  • Tertiary
  • Quaternary
23
Q

What are the causes of protein denuration?

A
  • Excess Heat
  • pH Variations
  • Detergents
  • Chemical Agents (Urea, GdmCl, βME)
24
Q

How does β-Mercaptoethanol cause protein denuration?

A

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

25
Q

How does Urea cause protein denuration?

A

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

26
Q

Takeaways: Haber-Anfinsen Experiments

A
  • 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.
27
Q

Takeaways: Haber-Anfinsen Experiments

A
  • 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.
28
Q

Models: Protein Folding

A
  • Hydrophobic Collapse Model
  • Framework Model
  • Nucleation Model
29
Q

Chaperones: Clamp-Type vs. Chamber-Type

A
  • Clamp-Type: Heat-Shock Protein (Smaller)
  • Chamber-Type: Chaperonin Protein (Larger)

Chaperone Protein: A protein that binds to partially/improperly folded proteins and utilizes ATP hydrolysis to facilitate proper protein folding.

30
Q

Examples: Diseases of Protein Misfolding

A
  • 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)
31
Q

Column Chromatography: Three Types

A
  • 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

Column Chromatography: A protein purification method that separates proteins based on differential physical/chemical interactions with a solid gel matrix.

32
Q

Anion Exchanger vs. Cation Exchanger

Ion-Exchange Chromatography

A
  • Anion Exchanger: Positively Charged Matrix (e.g. DEAE)
  • Cation Exchanger: Negatively Charged Matrix (e.g. CMC)
33
Q

SDS-PAGE

A

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).

SDS-Page separates proteins on the basis of size to estimate the molecule weight of particular proteins.

34
Q

Isoelectric Point

pI

A

The pH value at which a protein has no/neutral net charge.

Isoelectric Focusing (IEF): A gel filtration technique that separates proteins on the basees of their isoelectric point.

35
Q

Isoelectric Focusing: pH vs. pI

A
  • 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.
36
Q

Effect of pH on O2-Hemoglobin Affinity

A
  • Higher pH = Higher Binding Affinity
  • Lower pH = Lower Binding Affinity
37
Q

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

A

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.

38
Q

Which factors increase the stability of Hemoglobin’s T state?

A
  • Lower [O2]
  • Lower pH
  • Carbamylation
  • Higher [2,3-BPG]
  • Higher [CO2</sub]
  • Higher [Competitive Binders]

Competitive Binders: CO, SO, CN–

39
Q

Which factors increase the stability of Hemoglobin’s R state?

A
  • Higher [O2]
  • Higher pH
  • Lower [2,3-BPG]
  • Lower [CO2</sub]
  • Lower [Competitive Binders]

Competitive Binders: CO, SO, CN–

40
Q

Fetal Hemoglobin vs. Adult Hemoglobin

A
  • 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.
41
Q

Mutation: Sickle Cell Anemia

β Chain

A

Amino Acid #6: Glutamine → Valine

42
Q

Which types of catalysis are utilized by Serine proteases?

A
  • Acid-Base Catalysis
  • Covalent Catalysis

Serine Protease: An enzyme that cleaves the peptide backbone of proteins via a Serine nucleophile (within the enzyme’s active site).

43
Q

Examples: Serine Proteases

A
  • Chymotrypsin
  • Trypsin
  • Elastase
44
Q

Serine Proteases: Catalytic Triad

A
  • Serine
  • Histadine
  • Aspartate
45
Q

Which type of catalysis is utilized by Enolase?

A

Metal-Ion Catalysis

46
Q

Turnover Number (kcat)

A

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

47
Q

What does the Specificity Constant represent?

A

Catalytic Efficiency of an Enzyme

The specificity constant is dependent upon the enzyme’s affinity to the substrate and the enzyme’s catalysis rate.

48
Q
A

Biochemistry (7 decks)

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