CHEM106 General Chemistry II Course Competencies
Lsn 1: General
Chemistry I 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 Lewis
structures 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: Gen Chem I
Review - 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:
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, diagram, and
explain the equilibrium constant expression for Kd,
the dissociation constant for drug-receptor complex dissociation
- 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
- Understand cis- and trans-geometry and the formation of
trans-fats
- Relate the melting
points of fats and oils to molecular structure
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
- 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
Lsn 6: Acid-Base
Properties of Amino Acids: Henderson-Hasselbalch
Equation, Charge and pH, Solubility and pH
- 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
- Understand what isoelectric points (pI) are
and how to determine them from the pKa's
of amino acids
Lsn 7: 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
o Know the primary structure of peptides
o Understand protein secondary structure; draw diagrams to represent the
underlying reason for the formation of alpha helices and beta sheets
o Understand the various types of interactions that can occur between
side chains; draw appropriate diagrams and clearly discuss these
o Understand protein tertiary and quaternary structures
o Understand the underlying reasons for the structure of globular proteins
o Clearly discuss and diagram prions formation
process and their relevance
o Outline major functions of proteins in the human body
Lsn 8: Chemical
Kinetics: Factors Affecting Reaction Rates, Rate Law, Arrhenius Equation, Activation Energy, Kinetic Molecular
Distribution
- 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 how to
experimentally determine a reaction's activation energy using Arrhenius plots
- 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 9: Enzyme
Catalysis: Enzyme Catalysis Mechanism of Action, Active Site
Substrate Binding, Enzyme Inhibition, Competitive and Allosteric Inhibitors
- 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
Lsn 10: Enzyme Kinetics:
Michaelis-Menton Kinetics, Lineweaver-Burk
Plots, KM and Vmax
Determination, Turnover Numbers, KM and Substrate-Enzyme Affinity
- 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
Lsn 11: Mid-Term
Examination
Lsn 12: Receptors
as Drug Targets I: Neurotransmitters
and Hormones, Ion Channel and Membrane receptors, Receptor-Ligand
Interactions, Agonists and Antagonists, Sensitization, Tolerance, and
Dependence
- Know the molecular structures
for these neurotransmitters:
- Cathecholamines:
L-Dopa, dopamine, norepinephrine,
and epinephrine
- Amino Acids:
Glutamate, Aspartate, Glycine,
GABA (gamma-aminobutyric acid)
- 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 13: Receptors
as Drug Targets II: Receptors
as Drug Targets II: Affinity, Efficacy, and Potency; Dissociation Binding Equilibria, EC50, IC 50, and Scatchard
Plots
- 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
Lsn 14: Receptor
Structure and Signal Transduction I: Overview of Ion Channels,
G-Protein Coupled Receptors, Kinase-Linked Receptors,
Intracellular (Steroidal) Receptors
·
Receptors
o Understand the various types of drug receptors present within the human
body
o Understand the various types of receptor responses
o Understand receptor response differences to agonists and antagonists
Lsn 15: Ion
Channels and Thermodynamics: Ion Concentration Gradients,
Sodium-Potassium-ATP Pump Mechanism, Cell Membrane Potentials, Nernst Equation and Membrane Equilibrium Potentials, Free
Energy Changes of Ion Movement across Voltage and Concentration Gradients, Ion
Movements and Resulting Inhibitory/Excitatory Potential Changes
- 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
- 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
Lsn 16: Receptor
Structure and Signal Transduction II – GPCR’s: G-Protein Coupled Receptors Signaling
Mechanism of Action
·
Intracellular Receptors and
Zinc fingers
o Diagram and effectively 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
o Explain the underlying basis for the zinc finger mechanism of action in
steroidal interactions with DNA
o Discuss a new area of drug research that targets the zinc fingers in
estrogen receptors to treat breast cancer
Lsn 17: Receptor Structure and Signal
Transduction III: Steroids
and Intracellular Steroidal Receptors: Steroid Structure and Hydrophobicity, Complex Ions and Zinc Fingers, Steroidal
Receptors, Steroid-Receptor Mechanism of Action, Treatment of Hormone-Dependent
Breast Cancers
·
Steroid structure and
properties
o
Understand and draw the skeletal
structure for steroids
o
Discuss and predict the lipophilic/lipophobic properties of steroids
o
Explain the effects of anabolic
steroids and of each of the two classes of corticosteroids (mineralcorticoids
and glucocorticoids)
o
Outline where steroids are
produced, what their sources are, and how they work hormones in the human body
o
Discuss steroidal sex hormones
·
Nucleic acid structure
o Understand the structure of DNA and RNA to include the major components
and specific features
o Understand the condensation mechanism of action to form phosphate diester polynucleotides
o Clearly explain the underlying physical basis for the attractions
between the two strands of double helix DNA
·
Central dogma
o Understand and clearly describe how genetic information is encoded in
DNA
o Explain what a gene is, what it does, and the two roles of the major
regions (promoter and coding) of DNA gene templates
o Generate a possible DNA sequence for the coding of a given peptide
o 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
- Show how transition metal
ion valence electron energy levels shift as ions are introduced into
octahedral and tetrahedral ligand environments;
understand and be able to clearly explain the basis for these shifts
- Understand and
diagram the structure of important biochemical complexes to include iron
in hemoglobin, magnesium in chlorophyl and
cobalt in B-12.
- Outline the
mechanism of action for platinum compounds [e.g. cisplatin
PtCl2(NH3)2] as chemotherapeutic agents
for cancer patients
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
I: 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: Adrenergics II:
Lsn 22: Psychoactive
Drugs I - Stimulants:
Lsn 23: Psychoactive
Drugs II – Anti-Depressants:
Lsn 24: Psychoactive
Drugs III – Hallucinogens:
Lsn 25: Opium and 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 26: 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
Lsn 27: Test
2
Lsn 28: Review