Daily Goals/Objectives
(Will be updated daily)

Class # 02A
Goals/Objectives:  After class, students will be able to .....
1 1/15 TU A2 .
2 1/17 TH A4
  • explain the differences between mixtures and pure substances

  • explain the differences between elements and compounds

  • explain how to separate mixtures into pure substances

  • explain the differences between physical and chemical properties

  • explain characteristics of scientific theories and how such theories differ from other ways to explaining or describing the world

3 1/21 M A6
  • explain the differences among scientific laws, hypotheses and theories

  • name specific example of scientific laws and their associated explanatory theories

  • explain in simple mathematical and graphical analyzes the gas laws and how kinetic molecular theory explains these laws

  • explain the difference between independent, dependent and controlled variables

  • given simple rules draw structure of  molecules containing C, H, N and O

4 1/23 W A2
  • explain the difference between correlation and causation, and the role of confounding (3rd variable in understanding causation
  • state the differences between types of medical studies conducted to study benefit and harm
  • describe different types of biases that affect validity of medical studies
  • draw Lewis dot symbols of elements
  • define ionization energies and use tables of them to infer the octet rule
  • use Lewis Dot Symbols to explain ionic  bonding



1/25 F A4

  • use Lewis Dot Symbols to explain ionic and covalent bonding
  • write formulas for simple salts based on Lewis Dot structure
  • draw Lewis structure (without nonbonded electrons pairs) based on the octet rule for compounds of C, H, N, and O
  • define electronegativity and partial charges and use them to predict if covalent bonds are polar or nonpolar.
  • draw Lewis structure (with nonbonded electrons pairs and formal charges) based on the octet rule for compounds of C, H, N, and O and expanded octets for P and S

1/29 TU A6


  • draw Lewis structures for common inorganic and organic molecules.

  • identify slight charges, full formal charges, nonpolar and polar covalent bonds in molecules

  • from simple formulas draw Lewis structures and line drawings for simple organic molecules

  • state the geometry of electrons clouds around an atom when there are 2, 3, or 4 clouds extending from the central atom.


1/31 TH A2

  • use Lewis structures to determine the overall geometry of electron clouds and of the bonded to a central atom

  • use Lewis structures determine if a molecule as a whole is polar or nonpolar

  • state relationships between molecular polarity of a molecule and physical properties such as ease and rate of evaporation, melting and boiling points and solubility in solvents

  •  Qz: Lewis structure


2/4 M A4



  • describe common intermolecular forces (ion-ion, dipole-dipole, H-bonds, and van der Waals or London forces

  • draw Lewis structures showing appropriate intermolecular forces between molecules.

  • given the Lewis structure predict the solubility of a substance in water or a nonpolar organic solvent

  • qz:  geometry and polarity



2/6 W A6


  • Qz: acetic acid/water and IMFs 

  • explain the meaning of red, blue and gray/white in the color coding used in computer models showing electron density and charges (full and partial) in small and large molecules

  • define single and double chain amphiphiles and draw cartoons of them showing the types of structures they form in water

  • use Lewis structure to explain differential solubility of salts in water

  • define and give examples of electrolytes and nonelectrolytes

  • define acid and base, strong and weak acid/base

  • using Lewis structures draw the mechanism for acid/base reactions for binary acids (HX) and oxyacids

  • from the Lewis structure, predict which proton is likely to be donated to a base in an acid/base reaction


2/8 F B2


  • identify acids, bases, conjugate acids and conjugate bases in an acid/base chemical reaction

  • explain the difference and list examples of strong/weak acids and strong/weak bases

  • explain the difference between strong, weak, and nonelectrolytes, and classify glucose, ethanol, acidic acid and HCl as one of these.

  • explain the difference between OH- (in salts and aqueous solution) vs -OH (covalently attached to other atoms

  • given simple solubility rules, predict if a precipitation reaction will occur when two aqueous salt solutions, especially those with molecular anions  are mixed.

  • Cu: The 1st reactions




2/12 TU B4



Qz: acid/base

  • explain the trend in acidity of HF, HCl, HBr, and HI from comparing their conjugate bases

  • explain from chemical equations and the Lewis structure of conjugate bases why the two carbon molecule acetic acid is considered a weak acid in water and the two carbon molecule ethanol is not.

  • define pH and determine the pH given the [H3O+] concentration

  • define redox reactions and identify oxidizing agent, reducing agent. 

  • Determine the oxidation numbers for an atom or ion in a molecule or molecular ion

  • give examples of strong oxidizing /reducing agents



2/14 TH B6



  • classify a given reaction as acid/base, precipatation, or redox;

  • state the type of reaction for the Lab 2 Cu experiment.


2/18 M B2

 Test 1


2/20 W B4





  • rank and explain your ranking for stability, basicity, reactivity, relative energy of a series of negatively charge species produced in aqueous solutions

  • draw curved arrow mechanisms showing the attack, bond making/breaking and products produced (including any leaving groups) at carbonyl carbons in the following functional groups: aldehydes, ketones, and carboxylic acid derivatives including anhydrides, esters, and amides

LONG WEEKEND 2/21-2/22

2/26 TU B6

  • rank the reactivity of carboxylic acid derivatives towards cleavage by OH-

  • explain in words and draw a simple mechanism showing the hydrolysis of carboxylic acid derivatives

  • define a sugar

  • draw a mechanism which show hows glucose can cyclize and the difference between alpha and beta forms

  • identify simple 6 carbon sugars from their structure

  • identify sugars and linkages in simple dissacharides and polysaccharides


2/28 TH B2

Qz: carbonyl chemistry

  • identify important functional groups in DNA and RNA

  • define fats/lipids

  • draw the line structure of fatty acids from symbolic notation

  • review the interactions of single and double chain lipids in water

  • draw a mechanism to show the hydrolysis of triacylglycerides

  • draw a line structure of an amino acid and dipeptide, noting the N and C terminus and the side chains

  • identify polar charged, polar and nonpolar side chains

  • explain the likely location in a folded protein of nonpolar and polar charged side chains based on analogy to micelle formation


3/3 M B4

 Mol. Model


  • identify and describe the characteristics of the protein backbone and side chains, especially with respect to polarity and capacity to form H bonds

  • define primary, secondary, tertiary, and quaternary protein structure

  • draw conclusions from interactive web-based molecular models of DNA, proteins, and protein complexes concerning the structure and function of biological molecules

  • identify alpha helices and beta sheets in proteins

  • define transcription and translation

  • state the Central Dogma of Biology

  • Given a gene sequence and the genetic code, determine the amino acid sequence of the corresponding protein


3/5 W B6


  • predict likely effects of mutations in genes on the structure and function of proteins, especially when changes in size and polarity of the amino acids occur

  • draw mechanisms showing how acid/base reactions of amino acid side chains on the surface of a protein change the charge state of the protein

  • draw mechanisms showing how ATP can react with water, an alcohol (ROH) or an alcohol side chain of Tyr, Ser and Thr, leading to the phosphorlyation of proteins

  • define kinase and protein kinase.


3/7 F C2

Tu 1

Qz:  kinases

  • define signal transduction, primary and secondary messenger, kinase and phosphatase

  • explain the individual steps in the hormone activation of glycogen phosphorylase given a diagram of the steps

  • state which steps amplify the initial signal (hormone binding)

  • explain how individual activation steps in the glycogen phosphorylase pathway are reversed

  • differentiate between kinases activated by second messengers and those that are directly activated by primary messengers (receptor kinases)




3/11 Tu C4

No lab  today

  • explain the individual steps in the activation of gene transcription through signal transduction by a hormone or other external signal

  • describe structural features of proteins (RNA polymerase, transcription factors) and DNA (promoter, TATA box, response elements) required for their interaction and control of gene expression


3/13 Th C6


  • explain the two drive forces that contribute to ion flow across a membrane of a neuron

  • given ion concentrations in and outside of the cell, predict changes in ion flow and transmembrane potential when specific ion channels are open

  • associate the role of specific membrane receptors and channels with changes in membrane permeabilities and transmembrane potentials during neuron activation


3/25 TU C2


  • explain how neuron firing can be activated or inhibited by neurotransmitters

  • explain given a diagram how alcohol and benzodiazepines affect neuron activity through the GABA channel

  • give examples of typical short term and long term effects by neurotransmitters on neurons


3/27 TH C4

Lb5: EtoH1A - make


Neural effects of ethanol and addictive drugs:  long term

Risk Analysis 


3/31 M C6

Test 2


4/2 W C2


  • define mole
  • determine the number of grams in one mole of any substance
  • given the number of grams of a substance determine the number of moles
  • given the number of grams of a reactant (or product), determine the number of grams of a product (or reactant) produced in a chemical reaction
  • determine which reactant is in excess or limiting in a chemical reaction
  • define various types of concentration units:  mass percent (mass solute/volume solution) and volume percent (volume solute/volume solution), molarity (moles solute/L solution)
  • given the molarities of two reacting solutions, determine the molarity, moles, and grams of products produced.

4/4 F C4

Lb5: EtoH1B - make

  • state the difference between aerobic and anerobic catabolism

  • state the main metabolic and chemical goals in the catalolism of carbohydrates and lipids

  • given the glycolytic pathway identify important chemical features required of the pathway in catabolic pathway.

  • describe the roles of NAD+ and O2 and their utilization in anaerobic and aerobic metabolism

  • describe the biochemical properties of NAD+ and NADH in glycolysis and how their relative amounts are regulated during anaerobic exercise conditions in the respiring muscle and in the liver.



4/8 TU C6


4/10 TH D2




  • describe you impression of the video on the 1918 influenza pandemic
  • given a description of the influenza virus, draw structures showing its segmented RNA genome, its major surface proteins, and its interactions with human epithelial cells
  • describe the life cycle of the virus from binding to budding of new viruses from the infected cell
  • describe how RNA viruses are more susceptible to mutations during replication than occurs during DNA replication

4/14 M D4

Lb6: EtoH2 - oxidation

  • review the life cycle of the virus

  • describe the role of hemagglutinin and neuraminidase in binding of the virus to cells, and release of virus from infected cells.

  • explain the difference between antigenic drift and shifts

  • explain how segmented RNA viruses can reassort to produce new strains associated with pandemics

  • explain how pandemic viruses originate


4/16 W D6

  • review the life cycle of the virus and antigenic shift/drift
  • describe the binding target of viral hemagglutin on human cells
  • describe difference in the 1918 H1 protein that allowed it to jump from avian to human hosts
  • differentiate between the innate and adaptive immune system (IS)
  • state the different type of "foreign enemy" or antigenic targets that the IS must recognize
  • given a diagram describe the molecules involved in the interaction of macrophages and dendritic cells which present peptides from engulfed targets bound on MHCII proteins to T cell receptors on immune T helper cells
  • given a diagram describe the molecules involved in the interaction of T cells (e.g. cytotoxic T cells) and virally infected or tumor cells which present peptides from viral or tumor antigens bound on MHCI proteins to T cell receptors on immune T cells
  • given a diagram describe how the T cells recognize foreign peptide:MHC complexes on antigen-presenting cells but not MHC  complexes with host peptides

4/18 F D2


  • explain why two immune cells (an innate antigen-presenting macrophage and T helper cell) are required for immune cell stimluation
  • give reasons why presentation of foreign peptides processed inside antigen presenting cells helps in mounting an immune response against foreign antigens while protecting self cells;
  • given a diagram describe the molecules involved in the general detection and interaction of macrophages and dendritic cells of the innate immune system from TOLL receptors with pathogens associated molecular patterns found on/and bacteria, fungi, protozoans, and some viruses 
  • descirbe the production and role of cytokines in the immune resposne
  • describe drugs and their targets used to treat influenza infections
  • describe the production and types of vaccines against influenza

4/22Tu D4

Lb7: EtoH3 - combust


  • compare the chemical features of the hydrolysis of carboxylic acid anhydrides, ester, amides, phosphoanhydrides and mixed anhydrides
  • list the desired reactions/products for an anaerobic pathway (glycolysis) that takes a 6C carbohydrate (Glucose) to 2 3C molecules (pyruvate)
  •  list the desired reactions/products for an aerobic pathway (pyruvate dehydrogenase and Krebs cycle) that takes a pyruvate to CO2 and water
  • given a diagram, explain features/functions of mitochondrial electron transport/ATP synthesis (oxidative phosphorylation



4/25 F D6


  • given the glycolytic pathway and Krebs cycle and electron transport pathways in the mitochondria, identify the steps where oxidation of specific molecules is coupled to ATP synthesis

  • describe in the step identified above the energetic coupling necessary to synthesize ATP

  • describe how NAD+ is regenerated so that glycolysis and Kreb's cycle can continue


4/29 Tu D2


  • list the desired reactions/products for the catabolism of fatty acids to CO2 and water
  • state the types of CHO and lipid energy storage molecules and under what conditions they are released for energy production or stored for energy reserves
  • Given an overall summary of the catabolism of CHO and lipids, explain why excess CHO can be converted to fats but excess fatty acids can't be converted to CHO
  • describe what determines if fatty acids in lipid cells are esterified to form triacylglycerides or released from the cells for energy use;
  • state how CHO and fat metabolism in fat cells are integrated
  • describe the contrasting roles of glucagon and insulin in control of CHO and lipid metabolism
  • given a signal transduction pathway explain how insulin binding to fat and muscle cells lead to glucose uptake
  • state the differences between type I and type II diabetes.

5/1 Th  D4

Lb8: TBA


Test 3


5/5 TH D6






5/9, Friday

1:00-3:00  PM