CHEM106 General Chemistry II Course Competencies
Lsn 1: General Chemistry I Review I
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Electronegativity, charge distribution, and molecular bonding structure
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Demonstrate an understanding of electronegativity; understand and be able
to clearly explain the basis for electronegativity trends in terms of fundamental
laws of electrostatic interactions (Coulomb’s Law).
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Understand how to use relative electronegativities of atoms to clearly
depict charge distribution across chemical bonds. Be able to quickly
predict partial charges on atoms within given molecules.
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Draw molecular structures showing all bonds from a given molecular representation
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Noncovalent interactions and intermolecular forces
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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.
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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.
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Quickly draw diagrams that clearly show appropriate partial charges and
intermolecular interactions among a given set of molecules or ions.
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Predict points of potential H-bond donors and acceptors for any given molecular
structure.
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Predict and discuss relative boiling points (also vapor pressure, melting
points, viscosity, surface tension) from molecular structure
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Solubility and hydrophilic/hydrophobic substances
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Understand the difference and be able to predict relative polarities and
solubilities (hydrophilic/hydrophobic, lipophilic/lipophobic) of a given
molecular structure
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Understand and clearly explain the basis for the structure of surfactants
and soap molecules
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Understand and describe the basis for micelle formation and action
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Understand what is meant by the octanol-water partition coefficient and
clearly describe its significance (P and log P)
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Distribution of molecular kinetic energies
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Calculate fractions of molecules having kinetic energies greater than a
given energy at a given temperature
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Graphically represent and be able to clearly explain the distribution of
kinetic energies of a collection of molecules at various temperatures
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Understand kinetic energy conversion into potential energy to separate
molecules, to break bonds, or to react molecules
Lsn 2: General Chemistry I Review II
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Molecular structure
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Quickly draw Lewis structures for a given molecule or ion
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Predict electron arrangement, molecular geometry, hybridization, and bond
angles around given atoms in molecules
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Multiple bond structure
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Outline, discuss, and use aromatic electronic structure and geometry
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Know and discuss double/triple bond geometry and hybridization
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Outline and diagram cis/trans geometry about carbon-carbon double bonds
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Molecules: carboxylic acids, fatty acids, amino acids, and alkaloids
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Outline the structure of a carboxylic acid functional group and diagram
its acid/conjugate base forms
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Be able to draw the structure for fatty acids, to include those having
one or more points of unsaturation
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Draw the general structure for amino acids and be able to clearly diagram
the acid/conjugate base forms for both the carboxylic acid and the amine
functionalities
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Know what an alkaloid is and be able to quickly draw acid/conjugate forms
of a given alkaloid.
Lsn 3: Condensation and Hydrolysis Reactions
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Condensation reactions
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Use partial charges within molecules to outline the basic mechanism for
condensation reactions
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Predict and outline fundamental mechanisms for condensation reactions between
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Acids and alcohols
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Phosphates and alcohols
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Amino acids
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Carbohydrates
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Nucleotides
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Esters
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Hydrolysis reactions
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Understand hydrolysis reactions under acidic and basic conditions
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Outline peptide hydrolysis chemical equations
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Understand fat hydrolysis (e.g. formation of surfactant—soap--from animal
fat and lye)
Lsn 4: Phospholipids and Membranes
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Phospholipids
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Understand the component substructures within phospholipid molecules
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Know the molecular structures of the alcohols (glycerol, serine, choline,
ethanolamine) used to make phospholipids
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Outline the chemical reactions and mechanisms for the formation of phospholipids
from molecular subcomponents
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Outline the reactions involved in phospholipid hydrolysis
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Fats, oils, and fatty acids
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Know the structure of saturated, monounsaturated, polyunsaturated, and
trans fats; describe associated health effects
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Understand cis- and trans-geometry and the formation of trans-fats
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Relate the melting points of fats and oils to molecular structure
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Understand olestra’s synthesis, structure, utility, and limitations
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Membranes
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Understand and draw the molecular structure of membranes
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Understand and describe the forces that hold membranes together
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Clearly outline the role of cholesterol in cell membranes
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Predict relative membrane permeability for a variety of types of molecules
or ions
Lsn 5: Amino Acids and Acid/Base Properties
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Amino acids
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Know the general molecular structure of amino acids
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Be able to quickly draw the complete molecular structure showing all bonds
for all of the following amino acids:
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AA's with nonpolar side chains [Alanine(Ala,A), Valine(Val,V), Leucine(Leu,L),
Isoleucine(Ile,I), Phenylalanine(Phe,F)]
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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)]
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AA's with carboxylic acid side chains [Aspartic Acid(Asp,D), Glutamic Acid(Glu,E)]
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AA's with basic side chains [Lysine(Lys,K), Arginine(Arg,R), Histidine(His,H)]
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Acid-base systems
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Predict reactions of acids with water; predict reaction of bases with water.
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Write and use equilibria expressions for dissociation of weak acids and
bases, Ka and Kb; pKa’s
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Know the Henderson-Hasselbalch equation: be able to understand and use.
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Predict predominant (and relative amounts) of acid/base forms (e.g. COOH/COO-,
–NH3+/-NH2 ) present at a given pH.
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Acid-base properties of amino acids
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Predict acid-base forms of amino acids present at various pH’s
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Relate pH to amino acid functional group solubility in lipids or water
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Understand what isoelectric points (pI) are and how to determine them from
the pKa's of amino acids
Lsn 6: Proteins
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Understand how peptide bonds are formed and draw appropriate resonance
structure to explain peptide bond geometry
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Know the primary structure of peptides
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Understand protein secondary structure; draw diagrams to represent the
underlying reason for the formation of alpha helices and beta sheets
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Understand the various types of interactions that can occur between side
chains; draw appropriate diagrams and clearly discuss these
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Understand protein tertiary and quaternary structures
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Understand the underlying reasons for the structure of globular proteins
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Clearly discuss and diagram prions formation process and their relevance
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Outline major functions of proteins in the human body
Lsn 7: Chemical Kinetics
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Understand the two fundamental requirements for a chemical reaction to
occur…
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Draw reaction coordinate-energy profiles and clearly label activation energies,
and heat gained or lost
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Understand and be able to clearly explain the role of catalysts
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Understand and be able to use fundamental principles to clearly describe
the dependence of reaction rate changes with temperature
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Demonstrated the ability to calculate relative rates of reactions for different
activation energies or temperatures
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Know and be able to use the Arrehenius equation for rate constant determination
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Understand relative impacts of temperature changes on rates for chemical
reactions with low and high activation energies
Lsn 8: Enzymes
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Chemical kinetics
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Understand what is meant by the rate law and outline the experimental procedures
and methodology to determine reaction order
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Use a given rate law to calculate rate constants and their associated units
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Understand how to experimentally determine a reaction's activation energy
using Arrhenius plots
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Be able to use activiation energies to predict rate constants at different
temperatures
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Understand the effect of activation energy on the degree of rate constant
changes with temperature
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Michaelis-Menton kinetics
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Write equilibria associated with enzyme-substrate interactions
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Understand how reaction order changes with substrate concentration
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Be able to use the Lineweaver-Burke relationship to calculate Vmax,
turnover number, and KM
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Understand the significance of KM; understand the relation of
KM to enzyme-substrate complex stability and to maximum reaction
rate
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Enzyme-substrate interactions
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Be able to draw and to clearly explain reaction energy diagrams for enzyme-substrate
interactions
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Understand the effects of inhibitors and what is specifically meant by
IC50
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Understand and clearly explain the basis for important types of noncovalent
enzyme-substrate interactions
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Clearly describe the enzyme inhibition process
Lsn 9: Pharmacodynamics: Receptors and Drug Action
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Introduction to pharmacology
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Understand the drug approval process
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Understand the three nomenclature systems (chemical name, generic name,
trade name) used to identify a particular therapeutic substance
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Drug-receptor binding
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Understand and clearly discuss the ligand-receptor interactions; know the
underlying physical principles that govern these interactions
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Understand chirality, enantiomers, racemic mixtures, and the chiral specificity
of many drug receptors
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Receptors
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Understand the various types of drug receptors present within the human
body
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Understand the various types of receptor responses
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Understand receptor response differences to agonists and antagonists
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Quantifying effects of drugs on the human body
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Describe and plot drug concentration/dose vs response curves; understand
what is meant by EC50, IC50, and LD50
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Understand and compare the relative potency and efficacy for two or more
drugs; draw or interpret dose-response graphs that illustrate these
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Understand and clearly discuss the linkage between therapeutic and toxic
doses
Lsn 10: Pharmacokinetics: Drug Absorption, Distribution, and Elimination
(ADME)
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Absorption of drugs
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Understand routes of drug administration
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Relate lipophilic/lipophobic and other drug properties to effectiveness
of absorption
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Distribution of drugs
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Understand mechanisms of drug distribution
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Relate lipophilic/lipophobic and other drug properties to effectiveness
of distribution
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Elimination of drugs
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Understand excretion processes the drug properties that affect these
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Understand drug metabolism and the drug properties that affect these
Lsn 11: Nonsteroidal Anti-inflammatory Drugs (NSAID's)
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Understand the inflammation mechanism of action initiated by arachidonic
acid (phospholipid release of arachidonic acid, generation of prostaglandins
and thromboxanes through cyclooxygenase pathway, generation of leukotrienes
through lipoxygenase mechanism)
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Understand the mechanism of action of cyclooxygenase (COX) inhibitors
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Identify key structural features of NSAIDs and understand of specific important
interactions with COX enzymes
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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
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Understand and clearly discuss aspirin's unique mechanism of action for
irreversible COX inhibition
Lsn 12: COX-2 Inhibitors
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Understand key differences between COX-1 and COX-2 enzymes, their physiological
roles, and their respective inhibitors
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Clearly describe the rationale for the development of COX-2 inhibitors
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Explain the structure differences between nonspecific COX inhibitors and
COX-2 specific inhibitors; relate these differences to active site geometries
of thee two enzymes
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Use COX-1 and COX-2 IC50 values for various substances to evaluate their
respective potential for therapeutic development
Lsn 13: Test 1
Lsn 14: Central Dogma and Complex Ions
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Complex ions
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Understand the structure of complex ions and be able to explain the basis
for their interaction
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Relate Lewis acid/base chemistry to complex ion components
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Clearly explain why complexes are colored and demonstrate an understanding
of relevant molecular orbital energies
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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
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Understand and diagram the structure of important biochemical complexes
to include iron in hemoglobin, magnesium in chlorophyl and cobalt in B-12.
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Outline the mechanism of action for platinum compounds [e.g. cisplatin
PtCl2(NH3)2] as chemotherapeutic agents
for cancer patients
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Nucleic acid structure
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Understand the structure of DNA and RNA to include the major components
and specific features
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Understand the condensation mechanism of action to form phosphate diester
polynucleotides
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Clearly explain the underlying physical basis for the attractions between
the two strands of double helix DNA
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Central dogma
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Understand and clearly describe how genetic information is encoded in DNA
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Explain what a gene is, what it does, and the two roles of the major regions
(promoter and coding) of DNA gene templates
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Generate a possible DNA sequence for the coding of a given peptide
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Interpret a DNA or RNA sequence to generate an amino acid sequence that
is coded for by this
Lsn 15: Steroids
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Understand and draw the skeletal structure for steroids
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Discuss and predict the lipophilic/lipophobic properties of steroids
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Explain the effects of anabolic steroids and of each of the two classes
of corticosteroids (mineralcorticoids and glucocorticoids)
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Outline where steroids are produced, what their sources are, and how they
work hormones in the human body
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Discuss steroidal sex hormones
Lsn 16: Inflammation, Steroids, and Zinc Fingers
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Inflammation and steroids
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Understand the molecular basis of inflammation to include the role of phospholipases,
arachidonic acid, cyclooxgenase, lipoxygenase, prostaglandins, thromboxanes,
and leukotrienes
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Explain the molecular mechanism of action for steroids as anti-inflammatories
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Understand the emerging relevance of inflammatory processes in various
diseases
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Understand the importance of C-reactive protein levels and the enzyme drug
targets that pharmaceutical companies are focusing on
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Understand the roles of prednisone and cortisone medications respectively
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Zinc fingers
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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
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Explain the underlying basis for the zinc finger mechanism of action in
steroidal interactions with DNA
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Discuss a new area of drug research that targets the zinc fingers in estrogen
receptors to treat breast cancer
Lsn 17: Synapse, Neurotransmitters, and Neuroreceptors
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Understand the relative intracellular and extracellular concentrations
of sodium, potassium, calcium, and chloride ions
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Outline and clearly explain the steps that occur to pass a nerve impulse
from one neuron to another
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Know the structure of acetylcholine and explain how it is synthesized and
hydrolyzed
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Clearly explain the two major mechanisms used to reduce neurotransmitter
concentration levels at nerve synapses
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Understand the two (nicotinic and muscarinic) major classes of cholinergic
(acetylcholine) receptors and the mechanism of action for each
Lsn 18: Thermodynamics, Electrochemistry, and Neurochemistry
I
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Understand and be able to use the Second Law of Thermodynamics to predict
reaction spontaneity
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Clearly explain how spontaneity is related to Free Energy change.
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Explain Free Energy changes associated with ATP-ADP interconversion; discuss
and effectively use the concept of coupled reaction energetics
Lsn 19: Thermodynamics, Electrochemistry, and Neurochemistry II
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Use tables of reduction potentials to predict reaction spontaneity
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Be able to relate concentrations to associated electric potentials (e.g.
Nernst Equation) and changes in Free Energy
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Demonstrate the ability to calculate Free Energy changes, equilibrium constants,
and electric potentials associated with given reactions
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Explain and calculate cell membrane potentials associated with ion concentration
gradients
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Relate resting membrane potential to ion permeability and to intracellular/extracellular
concentrations
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Calculate Free Energy changes necessary to move substances across concentration
gradients and to move ions across potential gradients
Lsn 20: Sodium Potassium Pump and Oxidative Phosphorylation
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Understand the sodium-potassium pump mechanism to maintain ion concentration
gradients and the array of energetics associated with this
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Understand the role of oxidative phosphorylation as the major energetic
source to generate ATP; outline the specific redox reaction that is coupled
to ATP production
Lsn 21: Ion Channels
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Describe what an ion channel is and the specific properties of the substance
that forms the channel
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Outline the difference and define what is meant by voltage-gated and ligand-gated
ion channels
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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
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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
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Understand and be able to clearly explain the physical basis for the selectivity
of sodium and potassium ion channels
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Understand how increased permeability can affect voltage-gated ion channels
Lsn 22: Neurotransmitters I
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Know the molecular structures for these neurotransmitters:
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Cathecholamines: L-Dopa, dopamine, norepinephrine, and epinephrine
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Amino Acids: Glutamate, Aspartate, Glycine, GABA (gamma-aminobutyric acid)
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Understand the role of glycine and GABA receptors
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Be able to explain the electrochemical basis for their inhibitory effects
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Clearly explain how each of the following substances affects the GABA-ergic
system: ethanol, barbiturates, strychnine, diazepam (valium), and caffeine
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Understand how PCP (angel dust) and Memantine (Namenda) affect the glutamate
receptor NMDA (N-Methyl-D-Aspartate)
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Understand the synthesis steps involved in the production of L-DOPA, dopamine,
norepinephrine, and epinephrine
Lsn 23: Neurotransmitters II
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Explain the role of monoamine oxidase (MAO) for catecholamine neurotransmitters;
identify the role of MAO inhibitors.
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Explain the effect of dopamine levels on brain activity
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Explain the effects of cocaine and of amphetamines on the dopaminergic
system
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Outline the role of seratonin and identify the substance from which it
is produced
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Explain what SSRI's are and what they are used for
Lsn 24: Chemistry of Local and General Anesthetics
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Understand the mechanism of action for local anesthetics
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Relate pKa's to local pain anesthetics
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Understand the history of cocaine use by humans
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Describe the mechanism of action for general anesthetics
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Be familiar with the molecular structures for the more widely used general
anesthetics
Lsn 25: Chemistry of Opioid Analgesics
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Relate the structure of opioid receptors to opioid ligand geometry and
identify key features of each
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Understand the history of opioid use and development by humans
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Understand the side-effects of opioids
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Describe the structure of natural opioids found in the human body and be
familiar with its historical discovery
Lsn 26: Adrenergic Neurotransmitters and Receptors I
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Describe the geometry of adrenergic receptors
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Classify the role of the three main types of norepinephrine receptors (alpha,
beta 1, and beta 2)
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Describe the interaction of adrenergic receptors with neurotransmitters
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Discuss the mechanism of action of activated adrenergic receptors
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Be familiar with medications that target adrenergic receptors and discuss
their mechanism of action
Lsn 27: Test 2
Lsn 28: Review