CHEM106 General Chemistry II Course Competencies
Lsn 1: General Chemistry Review: Electronegativity, Electron Configuration, Lewis Structures, Molecular Geometry, Hybridization, Double Bonds, Aromatic Structure, Kinetic Energy Molecular Distribution, and Vapor Pressure
Electronegativity, charge distribution, and molecular bonding structure
Demonstrate an understanding of electronegativity; understand and be able to clearly explain the basis for electronegativity periodic trends in terms of fundamental laws of electrostatic interactions (Coulomb’s Law).
Understand how to use relative electronegativities of atoms to clearly depict charge distribution across chemical bonds. Be able to quickly predict the important partial charges on atoms within given molecules.
Electron configuration
For a given atom or ion, use the periodic table to quickly list its specific electron configuration
Understand the valence electron configuration of atoms and ions
Molecular structure
Draw molecular structures showing all bonds from a given molecular representation
Quickly draw complete Lewis structures, to include all nonzero formal charges, for a given molecule or ion
Predict electron arrangement, molecular geometry, hybridization, and bond angles around given atoms in molecules
Multiple bond structure
Know and discuss double/triple bond geometry and hybridization
Outline and diagram cis/trans geometry about carbon-carbon double bonds
Outline, discuss, and use aromatic electronic structure and geometry
Distribution of molecular kinetic energies
Calculate fractions of molecules having kinetic energies greater than a given energy at a given temperature
Graphically represent and be able to clearly explain the distribution of kinetic energies of a collection of molecules at various temperatures
Understand the kinetic energy conversions into potential energy necessary to separate molecules, to break bonds, or to react molecules
Vapor pressures
Use molecular structures to predict relative vapor pressures of given substances
Use the kinetic molecular distributions to explain how vapor pressures change with temperature
Lsn 2: Intermolecular Forces (Noncovalent Interactions): Ionic Interactions, Hydrogen Bonds, Van der Waals Interactions, Dipole-Dipole and Ion-Dipole Interactions, Repulsive Interactions, Water Solvation, and Hydrophobic Interactions
Noncovalent interactions and intermolecular forces
Understand and be able to clearly discuss and diagram the basis for attractions between molecules/ions to include ion hydration, hydrogen bonding, London dispersion, dipole-dipole, ion-dipole, and cation-p electron interactions.
Understand and use the relative magnitude (in kJ/mole) of chemical bonds (e.g. ionic, covalent and metallic) vs intermolecular forces (hydrogen bonding, London dispersion, dipole/dipole) interactions.
Quickly draw diagrams that clearly show appropriate partial charges and intermolecular interactions among a given set of molecules or ions.
Predict points of potential H-bond donors and acceptors for any given molecular structure.
Predict and discuss relative boiling points (also vapor pressure, melting points, viscosity, surface tension) from molecular structure
Lsn 3: Solubility and Lipids: Thermodynamics of Liquid-Liquid Solubility, Octanol-Water Distribution Equilibrium Constants [Partition Coefficients (P)], Phospholipid Components and Structure, Cell Membrane Structure and Properties
Solubility, thermodynamics, and equilibria
Understand and be able to clearly explain the thermodynamics of solution formation
Know what equilibria constants are; be able to relate equilibria constants to changes in Gibbs Free Energy
Partition coefficients (P)
Understand what is meant by the octanol-water partition coefficient (P) and clearly describe its significance
Solve problems involving P, log P, and drug concentrations or amounts distributed across water and 1-octanol phases
Be able to predict relative polarities and solubilities (hydrophilic/hydrophobic, lipophilic/lipophobic) of a given molecular structure
Phospholipids
Understand and be able to quickly draw molecular structures of components within phospholipid molecules
Relate the structure of phospholipids molecules to solubility
Membranes
Understand and draw the molecular structure of membranes
Understand and describe the forces that hold membranes together
Predict and explain how membrane fluidity changes with temperature, degree of saturation, and fatty acid chain length.
Clearly outline the role of cholesterol in cell membranes
Predict relative membrane permeability for a variety of types of molecules or ions
Fats, oils, and fatty acids
Know the structure of saturated, monounsaturated, polyunsaturated, and trans fats; describe associated health effects
Relate the melting points of fats and oils to molecular structure
Understand and explain what is meant by omega fatty acids
Lsn 4: Condensation and Hydrolysis Reactions: Alcohols and Carboxylic Acids, Triglyceride Formation, Polyphosphate and Phospholipid Formation
Molecules: carboxylic acids, fatty acids, amino acids, and alkaloids
Outline the structure of a carboxylic acid functional group and diagram its acid/conjugate base forms
Be able to draw the structure for fatty acids, to include those having one or more points of unsaturation
Condensation reactions
Use partial charges within molecules to outline the basic mechanism for condensation reactions
Outline the chemical reactions and mechanisms for the formation of phospholipids from molecular subcomponents
Predict and outline fundamental mechanisms for condensation reactions such as those between
Acids and alcohols
Phosphates and alcohols
Amino acids
Hydrolysis reactions
Outline the reactions involved in phospholipid hydrolysis
Outline peptide hydrolysis chemical equations
Lsn 5: Amino Acids: Structure, Chirality, Side Chain Polarity, Peptide Bond and Resonance, Peptide Condensation and Hydrolysis, Henderson-Hasselbalch Equation, Charge and pH, Solubility and P
Amino acids
Know and be able to quickly draw the general molecular structure of amino acids and be able to clearly diagram the acid/conjugate base forms for both the carboxylic acid and the amine functionalities
Be able to quickly draw the complete molecular structure showing all bonds for all of the following amino acids:
AA’s with nonpolar side chains [Alanine(Ala,A), Valine(Val,V), Leucine(Leu,L), Isoleucine(Ile,I), Phenylalanine(Phe,F)]
AA’s with polar uncharged side chains [Glycine(Gly,G), Serine(Ser,S), Threonine(Thr,T), Tyrosine(Tyr,Y), Cysteine(Cys,C), Asparagine(Asn,N), Glutamine(Gln,Q)]
AA’s with carboxylic acid side chains [Aspartic Acid(Asp,D), Glutamic Acid(Glu,E)]
AA’s with basic side chains [Lysine(Lys,K), Arginine(Arg,R), Histidine(His,H)]
Understand and explain amino acid chirality
Peptides
Understand how peptide bonds are formed and draw appropriate resonance structures to explain peptide bond geometry
Diagram and understand the mechanisms for condensation and hydrolysis reactions of peptides
Acid-base systems
Predict reactions of acids with water; predict reaction of bases with water.
Write and use equilibria expressions for dissociation of weak acids and bases, Ka and Kb; pKa’s
Know the Henderson-Hasselbalch equation: be able to understand and use.
Predict predominant (and relative amounts) of acid/base forms (e.g. COOH/COO-, NH3+/-NH2) present at a given pH.
Know what an alkaloid is and be able to quickly draw acid/conjugate forms of a given alkaloid.
Acid-base properties of amino acids
Predict acid-base forms of amino acids present at various pH’s
Relate pH to amino acid functional group solubility in lipids or water
Lsn 6: Protein Structure: Primary Structure, Disulfide Bonds, Secondary Structure - Alpha Helices and Beta Sheets, Tertiary/Quaternary Structures and Associated Noncovalent Interactions, Prions, PostTranslational Protein Modifications
Protein structure
Know the primary structure of peptides
Understand protein secondary structure; draw diagrams to represent the underlying reason for the formation of alpha helices and beta sheets
Understand the various types of interactions that can occur between side chains; draw appropriate diagrams and clearly discuss these
Understand protein tertiary and quaternary structures
Understand the underlying reasons for the structure of globular proteins
Lsn 7: Enzymes: Structure and Function: Enzyme Catalysis, Mechanism of Action, Active Site, Substrate Binding, Catalytic Roles, Michaelis-Menton Kinetics, Lineweaver-Burk Plots, Km and Vmax Determination, Turnover Numbers, KM and Substrate-Enzyme Affinity, Factors Affecting Reaction Rates, Rate Law, Arrhenius Equation, Activation Energy, Kinetic Molecular Distribution
Enzyme-substrate interactions
Be able to draw and to clearly explain reaction energy diagrams for enzyme-substrate interactions
Understand the effects of inhibitors and what is specifically meant by IC50
Understand and clearly explain the basis for important types of noncovalent enzyme-substrate interactions
Clearly describe the enzyme inhibition process
Michaelis-Menton kinetics
Write equilibria associated with enzyme-substrate interactions
Understand how reaction order changes with substrate concentration
Be able to use the Lineweaver-Burke relationship to calculate Vmax, turnover number, and KM
Understand the significance of KM; understand the relation of KM to enzyme-substrate complex stability and to maximum reaction rate
Chemical kinetics
Understand the two fundamental requirements for a chemical reaction to occur…
Draw reaction coordinate-energy profiles and clearly label activation energies, and heat gained or lost
Understand and be able to clearly explain the role of catalysts
Understand and be able to use fundamental principles to clearly describe the dependence of reaction rate changes with temperature
Arrehenius equation
Know and be able to use the Arrehenius equation for rate constant determination
Demonstrated the ability to calculate relative rates of reactions for different activation energies or temperatures
Understand and be able to calculate a reaction's activation energy from given rate constants at different temperatures
Understand relative impacts of temperature changes on rates for chemical reactions with low and high activation energies
Be able to use activation energies to predict rate constants at different temperatures
Rate law
Understand what is meant by the rate law and outline the experimental procedures and methodology to determine reaction order
Use a given rate law to calculate rate constants and their associated units
Lsn 8: Enzymes as Drug Targets: Active Site Inhibitors, Allosteric Inhibition, Competitive / Uncompetitive / Non-Competitive
Inhibitors, Suicidal Substrates
Enzyme inhibition
Understand and fully explain the basis for competitive enzyme inhibition
Understand and fully explain the basis for noncompetitive enzyme inhibition
Illustrate and discuss the effects of various types of inhibition on maximum reaction velocities and on substrate concentrations required to achieve half of the maximum reaction velocities
Discuss what is meant by suicidal inhibitors and use your understanding of condensation reactions to predict the specific mechanism of action for a given active site and inhibitor structures.
Lsn 9: Medical Approaches to Inflammation I: Nonsteroidal Anti-Inflammatory Drugs (NSAID's)
Inflammation
Understand the overall molecular basis of inflammation
Cyclooxygenase (COX) inhibitors
Understand the mechanism of action of cyclooxygenase (COX) inhibitors
Identify key structural features of NSAIDs and understand of specific important interactions with COX enzymes
Understand the specific interaction between the NSAID carboxylic group and the COX Arg-120 side chain; describe and effectively explain the effect upon KM values that occur when neutral glutamine is substituted for Arg-120
Understand and clearly discuss aspirin's unique mechanism of action for irreversible COX inhibition
COX-2 Inhibitors
Understand key differences between COX-1 and COX-2 enzymes, their physiological roles, and their respective inhibitors
Clearly describe the rationale for the development of COX-2 inhibitors
Explain the structure differences between nonspecific COX inhibitors and COX-2 specific inhibitors; relate these differences to active site geometries of thee two enzymes
Use COX-1 and COX-2 IC50 values for various substances to evaluate their respective potential for therapeutic development
Lsn 10: Medical Approaches to Inflammation II: Steroidal Anti-Inflammatory Drugs
Steroid structure and properties
Understand and draw the skeletal structure for steroids
Discuss and predict the lipophilic/lipophobic properties of steroids
Outline where steroids are produced, what their sources are, and how they work hormones in the human body
Inflammation and steroids
Understand the overall molecular basis of inflammation
Explain the molecular mechanism of action for steroids as anti-inflammatories
Understand the emerging relevance of inflammatory processes in various diseases
Central dogma
Understand and clearly describe how genetic information is encoded in DNA
Explain what a gene is, what it does, and the two roles of the major regions (promoter and coding) of DNA gene templates
Generate a possible DNA sequence for the coding of a given peptide
Interpret a DNA or RNA sequence to generate an amino acid sequence that is coded for by this
Complex ions
Understand the structure of complex ions and be able to explain the basis for their interaction
Relate Lewis acid/base chemistry to complex ion components
Clearly explain why complexes are colored and demonstrate an understanding of relevant molecular orbital energies
Understand and describe the structure of important biochemical complexes such as iron in hemoglobin.
Intracellular Receptors and Zinc fingers
Diagram and discuss the structure of zinc fingers; clearly show the amino acid residues that interact with the zinc ion and how zinc fingers affect protein shape
Explain the underlying basis for the zinc finger mechanism of action in steroidal interactions with DNA
Discuss a new area of drug research that targets the zinc fingers in estrogen receptors to treat breast cancer
Lsn 11: Receptors as Drug Targets I: Neurotransmitters and Hormones, Receptor-Ligand Interactions, Agonists, Antagonists, Partial Agonists, Inverse Agonists, Treatment of Hormone-Dependent Breast Cancers, Mechanisms of Actions for active ingredients in Advair
Drug-receptor binding
Understand and clearly discuss the ligand-receptor interactions; know the underlying physical principles that govern these interactions
Understand chirality, enantiomers, racemic mixtures, and the chiral specificity of many drug receptors
Know, diagram, and explain the equilibrium constant expression for Kd, the dissociation constant for drug-receptor complex dissociation
Receptors
Understand and describe some of the various classes of drug receptors present within the human body
Understand the various types of receptor responses
Understand receptor response differences to agonists, partial agonists, antagonists, and inverse agonists
Lsn 12: Receptors as Drug Targets II: Affinity, Efficacy, and Potency; Sensitization, Tolerance, and Dependence, Dissociation Binding Equilibria, EC50, IC 50
Affinity, Efficacy and Potency
Define, illustrate and demonstrate an understanding of affinity, efficacy, and potency
Sensitization, Tolerance, and Dependence
Illustrate, describe, and discuss the mechanism of action of the desensitization process that can occur due to prolonged receptor activation by an agonist
Illustrate, describe, and discuss the mechanism of action of the sensitization process that can occur due to prolonged receptor binding of antagonists
Discuss the molecular basis for tolerance and dependence.
Neurotransmitter molecular structures
Acetylcholine
Dopamine, norepinephrine, epinephrine, and serotonin [5-Hydroxytryptamine (5-HT)]
Glutamate, GABA (gamma-aminobutyric acid)
Lsn 13: Nucleic Acids as Drug Targets
Nucleic acid structure
Understand the structure of DNA and RNA to include the major components and specific features
Understand the condensation mechanism of action to form phosphate diester polynucleotides
Clearly explain the underlying physical basis for the attractions between the two strands of double helix DNA
Cancer Chemotherapy Treatments
Outline the mechanism of action for platinum compounds [e.g. cisplatin PtCl2(NH3)2] as chemotherapeutic agents for cancer patients
Describe the historical development of and outline the mechanism of action for nitrogen mustards as chemotherapeutic agents for cancer patients
Describe the mechanism of action for 5-Fluorouracil (5-FU) as a chemotherapeutic agent for cancer patients
Lsns 1-13: Mid-Term Examination
Lsn 14-15: Receptor Structure and Signal Transduction I-II - Overview and Thermodynamics of Ion Channels: Ion Concentration Gradients, Cell Membrane Potentials, Nernst Equation and Membrane Equilibrium Potentials, Ion Movements and Resulting Inhibitory/Excitatory Potential Changes Ion Channels, Sodium-Potassium-ATP Pump Mechanism, Free Energy Changes of Ion Movement across Voltage and Concentration Gradients
Ion Channels
Understand the relative intracellular and extracellular concentrations of sodium, potassium, calcium, and chloride ions
Understand the sodium-potassium pump mechanism to maintain ion concentration gradients and the array of energetics associated with this
Describe what an ion channel is and the specific properties of the substance that forms the channel
Outline the difference and define what is meant by voltage-gated and ligand-gated ion channels.
Describe the structure of voltage gated sodium ion channels and potassium ion channels to explain how they work. Understand the role of these ion channels in moving nerve pulses down an axon
Understand the role and the basic general mechanism of G-Protein Coupled Receptors (GPCR) in cell signaling processes; explain the importance of these receptors in the pharmaceutical industry
Understand and be able to clearly explain the physical basis for the selectivity of sodium and potassium ion channels
Understand how increased permeability can affect voltage-gated ion channels
Neurochemistry
Be able to relate concentrations to associated electric potentials (e.g. Nernst Equation) and changes in Free Energy
Demonstrate the ability to calculate Free Energy changes, equilibrium constants, and electric potentials associated with given reactions
Explain and calculate cell membrane potentials associated with ion concentration gradients
Relate resting membrane potential to ion permeability and to intracellular/extracellular concentrations
Calculate Free Energy changes necessary to move substances across concentration gradients and to move ions across potential gradients
Thermodynamics
Understand and be able to use the Second Law of Thermodynamics to predict reaction spontaneity
Clearly explain how spontaneity is related to Free Energy change.
Explain Free Energy changes associated with ATP-ADP interconversion; discuss and effectively use the concept of coupled reaction energetics
Lsn 16: Receptor Structure and Signal Transduction III – GPCR’s: G-Protein Coupled Receptors Signaling Mechanism of Action
Understand the role and the basic general mechanism of G-Protein Coupled Receptors (GPCR) in cell signaling processes; explain the importance of these receptors in the pharmaceutical industry
Lsn 17: Receptor Structure and Signal Transduction IV – Kinase-Linked Receptors: General Principles, Structure and Activation Mechanism of Tyrosine-Kinase Receptors, Tyrosine Kinase-Linked Receptors, Signal Transduction Involving Kinase-Linked Receptors
Lsn 18: Cholinergics I: Nervous System, Cholinergic System, Acetylcholine Structure & Receptor Binding
Outline and clearly explain the steps that occur to pass a nerve impulse from one neuron to another
Know the structure of acetylcholine and explain how it is synthesized and hydrolyzed
Clearly explain the two major mechanisms used to reduce neurotransmitter concentration levels at nerve synapses
Understand the two (nicotinic and muscarinic) major classes of cholinergic (acetylcholine) receptors and the mechanism of action for each
Lsn 19: Cholinergics II: Cholinergic Antagonists, Acetylcholinesterase Inhibitors
Lsn 20: Adrenergics: Geometry of adrenergic receptors, main types of norepinephrine receptors, interaction of adrenergic receptors with neurotransmitters, MOA of activated receptors
Describe the geometry of adrenergic receptors
Classify the role of the three main types of norepinephrine receptors (alpha, beta 1, and beta 2)
Describe the interaction of adrenergic receptors with neurotransmitters
Discuss the mechanism of action of activated adrenergic receptors
Be familiar with medications that target adrenergic receptors and discuss their mechanism of action
Lsn 21: Psychoactive Drugs I -- Stimulants and Tranquilizers:
Lsn 22: Psychoactive Drugs II – Anti-Depressants:
Understand how PCP (angel dust) and Memantine (Namenda) affect the glutamate receptor NMDA (N-Methyl-D-Aspartate)
Understand the synthesis steps involved in the production of L-DOPA, dopamine, norepinephrine, and epinephrine
Understand the role of glycine and GABA receptors
Be able to explain the electrochemical basis for their inhibitory effects
Clearly explain how each of the following substances affects the GABA-ergic system: ethanol, barbiturates, strychnine, diazepam (valium), and caffeine
Explain the role of monoamine oxidase (MAO) for catecholamine neurotransmitters; identify the role of MAO inhibitors.
Explain the effect of dopamine levels on brain activity
Explain the effects of cocaine and of amphetamines on the dopaminergic system
Outline the role of seratonin and identify the substance from which it is produced
Explain what SSRI's are and what they are used for
Lsn 23: Psychoactive Drugs III – Anti-Psychotics and Hallucinogens:
Lsn 24: Psychoactive Drugs IV – Cannabinoids, Opium & Opioid Analgesics:
Relate the structure of opioid receptors to opioid ligand geometry and identify key features of each
Understand the history of opioid use and development by humans
Understand the side-effects of opioids
Describe the structure of natural opioids found in the human body and be familiar with its historical discovery
Lsn 25: Chemistry of Local and General Anesthetics:
Understand the mechanism of action for local anesthetics
Relate pKa's to local pain anesthetics
Understand the history of cocaine use by humans
Describe the mechanism of action for general anesthetics
Be familiar with the molecular structures for the more widely used general anesthetics
Lsns 14-25: Second Half-Term Examination
Lsns 1-25: Comprehensive Final Examination