Cumulative Final Exam Flashcards
Non-Covalent Interactions
- Hydrogen Bonds
- Ionic/Electrostatic Interactions
- Hydrophobic Interactions
- Van der Waals Interactions
Van der Waals Interactions
Weak intermolecular interactions that occur between the dipoles of nearby electrically neutral molecules.
Hydrophobic Interactions
The tendency of hydrophoic molecules to pack closely together to mimize contact/interaction from water (when in an aqueous environment).
Henderson-Hasselbalch Equation
What causes the pH value to be less than the pKa value?
Buffer Systems
[Conjugate Base] < [Acid]
[A–] < [HA]
What causes the pH value to be greater than the pKa value?
Buffer Systems
[Conjugate Base] > [Acid]
[A–] > [HA]
What causes the pH value to be equal to the pKa value?
Buffer Systems
[Conjugate Base] = [Acid]
[A–] = [HA]
What is a state function?
A variable/function determined solely by the start conditions and end conditions (and not the path/speed of the process).
What does the ∆G value represent?
The magnitude of the driving force (energy magnitude) needed to pull/bring a system to its equilibrium point.
Equilibrium: ∆G = 0 kJ/mol
Equation: ∆G
Any State
Equation: ∆G°’
Equilibrium State
Relationship: ∆G° vs. Keq
- 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)
Why are living organisms never at equilibrium?
Living organisms require a constant input of energy to maintain homeostasis (which shifts the organism’s energy system away from equilibrium).
How is ADP + Pi more thermodynamically favorable than ATP?
- 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.
Energy Charge
A measure of the current energy state within a cell in terms of ATP, ADP, and AMP.
How does Hydrogen-bonding occur within an alpha helix?
Protein Secondary Structure
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.
Alpha Helix: Rise vs. Pitch
- 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)
Why are antiparallel β sheets more stable than parallel β sheets?
Antiparallel β sheets possess more optimal lengths and geometries of Hydrogen bonds between adjacent β strands, which results in higher levels of structural stability.
Types of Side-Chain Interactions
Protein Tertiary Structure
- Hydrophobic Interactions
- Disulfide Bonds
- Electrostatic Interactions
Protein Structure: Domain vs. Subunit
- Domain: One distinct region (with a unique function) of a single polypeptide chain.
- Subunit: One distinct polypeptide chain of a multi-polypeptide protein.
Methods of Determining 3-D Protein Structure
- X-Ray Crystallography
- Nuclear Magnetic Resonance (NMR)
- Cryo-Electron Microscopy (CryoEM)
Which levels of protein structure are impacted by protein denaturation?
- Secondary
- Tertiary
- Quaternary
What are the causes of protein denuration?
- Excess Heat
- pH Variations
- Detergents
- Chemical Agents (Urea, GdmCl, βME)
How does β-Mercaptoethanol cause protein denuration?
β-Mercaptoethanol breaks disulfide bonds (S—S) linking spatially adjacent amino acids.
How does Urea cause protein denuration?
Urea disrupts the intramolecular polar interactions (electrostatic attractions) within a polypeptide/protein.
Takeaways: Haber-Anfinsen Experiments
- 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.
Takeaways: Haber-Anfinsen Experiments
- 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.
Models: Protein Folding
- Hydrophobic Collapse Model
- Framework Model
- Nucleation Model
Chaperones: Clamp-Type vs. Chamber-Type
- 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.
Examples: Diseases of Protein Misfolding
- 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)
Column Chromatography: Three Types
- 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.
Anion Exchanger vs. Cation Exchanger
Ion-Exchange Chromatography
- Anion Exchanger: Positively Charged Matrix (e.g. DEAE)
- Cation Exchanger: Negatively Charged Matrix (e.g. CMC)
SDS-PAGE
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.
Isoelectric Point
pI
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.
Isoelectric Focusing: pH vs. pI
- 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.
Effect of pH on O2-Hemoglobin Affinity
- Higher pH = Higher Binding Affinity
- Lower pH = Lower Binding Affinity
How does elevated [2,3-BPG] at higher altitudes impact O2-Hemoglobin binding?
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.
Which factors increase the stability of Hemoglobin’s T state?
- Lower [O2]
- Lower pH
- Carbamylation
- Higher [2,3-BPG]
- Higher [CO2</sub]
- Higher [Competitive Binders]
Competitive Binders: CO, SO, CN–
Which factors increase the stability of Hemoglobin’s R state?
- Higher [O2]
- Higher pH
- Lower [2,3-BPG]
- Lower [CO2</sub]
- Lower [Competitive Binders]
Competitive Binders: CO, SO, CN–
Fetal Hemoglobin vs. Adult Hemoglobin
- 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.
Mutation: Sickle Cell Anemia
β Chain
Amino Acid #6: Glutamine → Valine
Which types of catalysis are utilized by Serine proteases?
- 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).
Examples: Serine Proteases
- Chymotrypsin
- Trypsin
- Elastase
Serine Proteases: Catalytic Triad
- Serine
- Histadine
- Aspartate
Which type of catalysis is utilized by Enolase?
Metal-Ion Catalysis
Turnover Number (kcat)
The rate of (substrate → product) conversion at a single enzyme when that enzyme is fully saturated.
What does the Specificity Constant represent?
Catalytic Efficiency of an Enzyme
The specificity constant is dependent upon the enzyme’s affinity to the substrate and the enzyme’s catalysis rate.
