BCH 2333/2733

BCH 2333/2733
Test #4/#5 or Midterm 2 Review Sessions
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Protein Binding and
Michaelis-Menton Kinetics

Review Session Details
  • Understanding general ligand binding (i.e. formulate equation and associate it to Kd)
  • Learn to manipulate the simple Kd equation into complex ones
  • Graphically understand how protein-ligand system is interpreted
  • Cooperativity in ligand binding (i.e. Hill plot)
  • Assess the two types of cooperativity models (MWC vs. KNF model)
  • Apply protein-ligand cooperativity to oxygen transport in the body
  • Understand enzyme catalysis graphically and in-terms of Gibbs free energy
  • Understanding the Briggs-Haldane model and the steady-state approximation
  • Measuring the rate of enzymatic reactions with Michaelis-Menten enzyme kinetics
  • Understand the Michaelis-Menten equation
  • Graphically understand how to interpret Michaelis-Menten enzyme kinetics
  • Graphically understand the lineweaver-burke plot (double reciprocal of Michaelis-Menten graph)
  • Fully understand the following kinetic parameters: KM, Kd, kcat, kcat/KM

BCH2333/2733: Protein Binding and Michaelis-Menten Kinetics

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Enzyme Inhibition,
Catalysis and Regulation

Review Session Details
  • Understand general mechanism for enzyme catalysis (i.e. catalysis via induced fit, covalent catalysis, acid-base catalysis, catalysis by approximation and metal-ion catalysis)
  • Using specific case studies, learn to identify which type of catalysis is being used by enzyme
  • Learn how cofactors and coenzymes are involved in enzyme catalysis (with specific examples)
  • Understand how allosteric binding can lead to feedback activation or inhibition (will use Aspartate transcarbamoylase (ATCase) to understand concept)
  • Learn other forms of enzyme regulations such as: isozymes, reversible covalent modification, proteolytic cleavage and transcriptional control
  • Learn how various types of reversible inhibitors can affect Michaelis-Menten parameters (Km and Vamx)
  • Graphically understand how to determine which type of reversible inhibitor is present using a Line-weaver Burke plot
  • Learn about the different types of irreversible inhibitors

BCH2333/2733: Enzyme Catalysis, Regulation and Inhibition

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Test #3 or Midterm 2 Review Sessions

$40

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Protein Folding
and Structure

Review Session Details
  • Review amino acid side chain properties (i.e. pKa, charges, stereochemistry, trans/cis amide bonds)
  • Understand the 3 main dihedral angles regulating secondary structure (phi, psi and omega)
  • Apply dihedral angles to Ramachandran plot
  • Relate secondary structures to Ramachandran plot
  • Properties of helices (i.e. residues per turn, pitch, H-bonding, simple calculations, drawing helical wheel)
  • Properties of Beta-sheets (i.e. length per residue, H-bonding, types of turns, simple calculations)
  • Domains vs. motifs
  • How to identify type of quaternary structure (i.e. C2, C3, D2, D3 etc.)
  • Thermodynamics involved for protein folding
  • Understand what facilitates folding of proteins

BCH2333/2733: Protein Folding and Structure

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Lipids, Protein Binding and
Nucleic Acid Structures

Review Session Details
  • Review primary DNA structure (i.e. base tautomerization, classic base pair H-bonding, c2/c3 endo sugar rings)
  • Understand the inter- and intramolecular interaction in a DNA double helix
  • Analyse and understand DNA secondary structures (i.e. DNA helices: A, B, and Z)
  • Remembering Chargaff's Rule
  • Understand properties of triple DNA helices (H-DNA)
  • Palindromes and formation of hairpins and
  • DNA denaturation and melting curves
  • Types of lipids and their structures
  • Lipid membrane properties (i.e. fluidity, lateral and transverse diffusion, and cholesterol)
  • Fatty acid nomenclature
  • Understanding general ligand binding (i.e. formulate equation and associate it to Kd)
  • Learn to manipulate the simple Kd equation into complex ones
  • Graphically understand how protein-ligand system is interpreted
  • Cooperativity in ligand binding (i.e. Hill plot)
  • Assess the two types of cooperativity models (MWC vs. KNF model)
  • Apply protein-ligand cooperativity to oxygen transport in the body

BCH2333/2733: Nucleic Acid Structures, Lipids and Protein Binding

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Test #1/#2 or Midterm 1 Review Sessions

$40

for 3.5 Hours of Tutoring

Thermodynamics, Buffers
and Carbohydrates

Review Session Details
  • Review Session will include tutoring with problem solving from past Midterms/Tests
  • Types of intermolecular interactions in biochemistry (i.e. ionic and dipole interactions)
  • The hydrophobic effect
  • Three thermodynamic parameters: ∆H, ∆S and ∆G
  • ∆G and equilibrium constants (Keq) of biochemical reactions
  • Using the H-H equation to solve for pH, pKa and concentration of buffer
  • Switch between line structure and Fisher projection for sugars
  • Sugar stereochemistry (i.e. D/L sugars, enantiomers, diastereomers, epimers)
  • Structural difference between Ribose, Glucose, Mannose and Galactose and Fructose
  • The concept of mutarotation about the anomeric carbon
  • Learn to convert between Fisher projections, Haworth projection and line structures
  • Sugar function in a cellular context

BCH2333/2733: Thermodynamics, Buffers and Carbohydrates

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Amino acids, Peptides
and
Nucleic Acids

Review Session Details
  • Review Session will include tutoring with problem solving from past Midterms/Tests
  • Understand how to assess amino acid stereochemistry
  • Switch between line structure and Fisher projection for amino acids
  • Learn the mechanism for the formation of a amide bond
  • Review 20 natural amino acids and their pKas
  • Amino acid charge at various pH and its isoelectric point (pI) values
  • Composition of DNA and RNA nucleic acids
  • DNA structure (i.e. base tautomerization, classic base pair H-bonding, c2/c3 endo sugar rings)
  • Understand the inter- and intramolecular interaction in a DNA double helix
  • Analyse and understand DNA secondary structures (i.e. DNA helices: A, B, and Z)
  • Drawing oligomers of DNA and RNA
  • Mechanism for the formation of a phosphodiester bond
  • Identifying nucleic acid base pairing and tautomers

BCH2333/2733: Amino acids, peptides and nucleic acids

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Session Instructor
ABDULLAH AKBAR, PhD
Abdullah is a top-rated tutor with 10+ years of teaching experience.
­

­As a recent PhD graduate from the University of Ottawa, he has worked along with many of the CHM BCH 2333/2733 Professors. His lesson plans will always begin with must-know fundamental concepts and end with examples from previous midterms and final exam questions.

Recommended by 200+ uOttawa students. Join one of his review sessions and decide for yourself!