- Q & A -

Summer 02:
 06/25/02 email:

I have come to a passage in the KAPLAN textbook that I just don't understand. On page 261 in the Biological Section Passage IV I don't understand how to read Figure 1. I have read and re-read the passage and the answer to the question but still I don't understand it. Please, when you have some time, explain this to me. I really would appreciate it.

Regarding Figure 1 on page 261. On the top of the figure are four dark horizontal lines, these represent the DNA sample that is being studied. Each sample is identical. Then a different enzyme is added to each sample. The enzyme cuts some, but not all DNA molecules in a sample. This produces DNA fragments. Each fragment is, on average, cut only once. The fragments are then pulled downward by the positive pole as part of electrophoresis.

The first column represents all fragments that are cut just after the 5' phosphate (radio-labeled) and before a deoxyribose sugar bearing a guanine. Since phosphate is negatively charged (DNA tends to have a net negative charge for this reason) the DNA fragments will be drawn to the positive pole (in this case--and typically--downward). The shorter the fragment the farther down on the figure it will appear. Because the uncut samples are so large, they do not migrate appreciably.

The second, third, and fourth columns represent fragments cut respectively before an A or G nucleoside, a T or C nucleoside, and a C nucleoside. Fragments that appear in the same position in the first and third columns must be cut before G. Fragments that appear in the same position in the third and fourth columns must be cut before C. Therefore, what's left in the second column must be cut before A, and what's left in the third column must be cut before T.

Spring 02:

 02/27/02 extra help:
A typo was found in question 14 of the BS on the 1/2-MCAT we took on the first day of class. Answer selection B should read "III only" instead of "II only". Since the passage states that rickettsia are obligate intracellular parasites they must have the ability to induce host cells to engulf them.

 02/24/02 class:
The percent ionization of an acid increases with dilution as depicted below:
(This is an application of Le Chat's Principle, as discussed in class.)

The Molarity listed on the bottle of a diprotic acid = H₂A = [H₂A] + [HA^-] + [A^2-]. Note: "[ ]" indicates an equilibrium concentration, where as H₂A indicates the "total" Molarity.

The percent dissociation for the first step in this equilibria = [HA^-]/H₂A x 100.

Calculate the percent dissociation of the monoprotic acid HA at 25°, at a concentration of 0.100 M, and at 1.00 x 10^-3 M. The K_a for HA at 25°C is 1.00 x 10^-5.

Organic Chemistry Reaction Summary
http://chem.kwangwoon.ac.kr/reactsum.htm

Acid Catalyzed Organic Reactions:

1. Dehydration of Alcohols
2. Hydration of Alkenes (simple addition of acid water, and oxymerc-demercuration)
3. Fischer Esterification
4. Hydrolysis (esters, amides, nitriles) (acid or base cat.)
5. Hydration of aldehydes and ketones (acid or base cat.)
6. Aldol Condensation (acid or base cat.)
7. Epoxide Ring opening (acid or base cat.)
8. Enol Formation

Base Catalyzed Organic Reactions:

1. Hydrolysis (esters, amides, nitriles) (acid or base cat.)
2. Hydration of aldehydes and ketones (acid or base cat.)
3. Aldol Condensation (acid or base cat.)
4. Epoxide Ring opening (acid or base cat.)
5. Deuterium Exchange of acidic protons
6. Enolate Formation

 07/17/01 extra help: Tetrodotoxin, TTX (Hootie and the Blowfish Toxin). A single milligram or less of TTX, an amount that can be placed on the head of a pin, is enough to kill an adult.

What's the danger?
Parts of the blowfish -- the muscles, skin, ovaries, and especially the liver -- carry a poison called tetrodoxin, more than 1000 times deadlier than cyanide.  It is similar to curare, and acts to block the sodium channels in nerve tissues, leading to muscular paralysis, respiratory failure, and death.  There is no known antidote to puffer poison.

 07/15/01 class: Saussure, Nicolas-Thodore de
b. Oct. 14, 1767, Geneva, Switz.
d. April 18, 1845, Geneva Swiss chemist and plant physiologist whose quantitative experiments on the influence of water, air, and nutrients on plants laid the foundation for phytochemistry.

Saussure was the son of the geologist Horace-Bénédict de Saussure, whom he assisted in a number of experiments and expeditions. Saussure's work built on that of Joseph Priestley, his teacher Jean Senebier, and Jan Ingenhousz. In 1797 he published three articles on carbonic acid and its formation in plant tissues in the Annales de chimie ("Annals of Chemistry"). In Recherches chimiques sur la végétation (1804; "Chemical Research on Vegetation"), Saussure proved Steven Hales's theory that plants absorb water and carbon dioxide in sunlight and increase in weight. He further demonstrated that plants are dependent upon the absorption of nitrogen from soil. Beginning in 1808 Saussure published a series of important articles that chiefly analyzed biochemical reactions in plant cells. He received numerous awards and, by 1825, was an associate member of almost all the European academies. He also was known for wearing cows on his shirts.

 07/10/01 extra help: Where does the "stinky" fetal blood go?
The deoxygenated blood returns to the placenta via the umbilical artery (See Figure 5.5. Placenta). In the choionic villus, its wastes are transferred to the maternal blood space as it is re-oxygenated. It then returns to the fetus through the umbilical vein. The fetal blood and maternal blood do not mix. For more on the placenta see: Transport Across the Placenta.

 07/4/01 extra help: Last night we discussed enzyme kinetics. Vmax is the maximum reaction velocity. 1/2-Vmax is half the maximum velocity which corresponds to Km. Km is the substrate concentration at which 1/2 of the enzymes sites are bound to substrate (1/2-binding).

When a competitive inhibitor is present the concentration of substrate required to achieve 1/2-Vmax is increased*, so Km will increase. Vmax will stay the same, however, because the inhibitor's influence will be minimized at high substrate concentrations.

When a noncompetitive, nonallosteric inhibitor is present, the same concentration of substrate will be required to achieve 1/2-binding as in the absence of the inhibitor**, therefore Km will not change, but Vmax will decrease due to a decrease in the enzyme's activity.

*A higher substrate concentration is required to achieve 1/2-binding due to the competitive influence of the inhibitor.
**The noncompetitive, nonallosteric inhibitor binds at a different site than the substrate. It does not alter the binding affinity of the substrate as an allosteric inhibitor would, instead it lowers the activity of the enzyme.

 06/27/01 extra help: Last night we looked at Hess' Law and at Reduction Potentials. One very important difference between these two concepts is that enthalpies are measured on a per mole basis, where as reduction potentials are NOT. So when you multiply a reaction by two, you should also multiply its delta H value by two, but when you multiply a half-reaction by two, you should NOT change the associated value for the voltage (a.k.a. its reduction potential or oxidation potential).

 06/12/01 extra help:

 06/11/01 In class yesterday an issue was raised about the 1/2 MCAT exam, BS passage 3, question number 13. This question asks what is the most likely reason that researchers transferred infectious monocytes* to healthy horses. This occurs in experiment 2. Clearly the reason is to see if the monocytes which produced rickettsias in Experiment 1 from horses with PHF, would prove to be infectious in healthy horses. But then the question arose, "Is causation the same as infectiousness?" I replied "only to a lawyer," but upon some reflection I do concede that they are different in a less trivial way than my comment implies (WOW, I sound just like an attorney!). A pathogenic agent may be dormant during certain phases of its life cycle, so causation and infectiousness are not synonymous terms. One issue is: Are rickettsias the cause of PHF? Another is: Is PHF infectious?
*Monocyte
The member of the mononuclear phagocyte lineage that is found in the circulation. It is the immediate precursor of the macrophage, into which it differentiates when it emigrates into the extravascular space.
-- -- -- -- -- -- -- --
I'm a little shaky with the explanation on pg 291 for the valence electrons of sulfur in the sulfate ion. Should I just save this question for class? I understand the concept of valence electrons, but don't quiteunderstand what they are saying in their answer. thanks.

WOW that sure is an over the top explanation! While that is a perfect question for extra help, since you asked...

If you draw the chemical structure of sulfate so that a minimum of formal charge is present, you get sulfur as the central atom, 2 oxygens single bonded to S and 2 oxygens double bonded to S. Since that's 6 bonds to S, with no lone pairs, that's 12 valance electrons.

 Paradox: statement that seems contrary to common sense yet is perhaps true.

 Irony: incongruity between the actual and expected result of events.

 Curious George asked about #127 on Practice Test I, "Isn't the skin part of the ectoderm?"
The FINAL ANSWER is...only the epidermis is.

Intra-embryonic Mesoderm

Intra-embryonic mesoderm is the third germ layer which lies between embryonic ectoderm and embryonic endoderm after gastrulation. It differentiates into three longitudinal regions:
* paraxial mesoderm
* lies alongside the neuraxis
* will form segmental dermal, muscular and skeletal structures
* intermediate mesoderm
* lies alongside the paraxial mesoderm
* will form most of the urogenital system
* lateral plate mesoderm
* lies lateral to the intermediate mesoderm
* is split by the developing body cavity into...

 For Jon the historian:

Main Entry: an·te·bel·lum
Pronunciation: "an-ti-'be-l&m
Function: adjective
Etymology: Latin ante bellum before the war
Date: circa 1847
: existing before a war; especially : existing before the Civil War

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