Chemistry @ IU :: Chemistry C483

Questions asked often in office hours or via email will be posted under the question forum. Check it often as it is updated as least once a day. They question you have may already have been answered.

Questions asked between exams 2 & 3:

1. The structure of cofactors are very complex. Do I need to be able to draw these? What is important for each molecule?

YOU DO NOT HAVE TO DRAW THE COFACTORS BUT YOU NEED TO BE ABLE TO

RECOGNIZE THEM (IE IF I GIVE YOU A PAGE WITH STRUCTURES OF COFACTORS

YOU SHOULD BE ABLE TO NAME EACH ONE). YOU ALSO NEED TO KNOW WHAT

ATOMS OF THE COFACTOR ARE INVOLVED IN THE CHEMICAL REACTION. THESE

ARE SHOWN IN RED IN THE NOTES AND YOUR BOOK.

2. I am overwhelmed by the amount of information presented for exam 3. Can you give me a "hint" on how to study or what to focus on?

You are responsible for ALL material presented in Lecture 26-38, including the readings

listed on the syllabus (Chapter 7, 10, 11, 12, 13, 14, 16), and assigned discussion problems.

For metabolic pathways:

You need to memorize the reactions and regulation of glycolysis and gluconeogenesis.
You need to know the NET equation for pyruvate dehydrogenase, and regulation of this enzyme complex. You do not need to know the details of each enzyme complex.
For TCA, the reactions will be provided as shown in the figure posted with the lecture notes. You are responsible for the regulation of this cycle.
You are responsible for knowing the basics of the Oxidative Phosphorylation pathway. You should know the pathway that electrons take from NADH & FADH2 through this pathway. This pathway will not be provided.
For the pentose phosphate pathway, the reactions will be provided as shown in the figure posted with the lecture notes. You are responsible for the regulation of this cycle AND knowing which reactions occurs when.
Glycogen metabolism at a “cartoon” level. You should be able to explain how glycogen synthesis occurs but do not need to include enzyme names or push arrows for this mechanism. You should be able to explain how glycogen is degraded but do not need to include enzyme names or push arrows. (Can you explain/reproduce figures 12.10, 12.11, 12.12, 12.14). You should be able to calculate the energy generated from breakdown of glycogen molecule and understand how glycogen metabolism is regulated.
Triacylglyceride (TAG; fat) metabolism. You should be able to calculate the energy derived from oxidation of a fatty acid and understand how fat synthesis and degradation is regulated.
You should understand when each of the metabolic pathways we discussed is functioning, when it is off, when it is accelerated, and when it is slowed. You need to understand how all of the pathways are connected.
Review your sugar structures if you have forgotten them (Quiz 2 assignment).

Questions asked between exams 1 & 2:

1. I could not follow the chymotrypsin mechanism presented in class. Can you explain this again?

The point of showing this mechanism was to give an example of what happens in an

enzyme's active site, to show how enzymes discriminate between substrates, and to show

how amino acids of an enzyme are involved in the chemical reaction catalyzed. Here is a

figure showing how chymotrypsin cleaves peptide bonds: chymotrypsin mechanism

2. What makes an amino acid substitution conservative?

A substitution should be viewed as conservative if the two amino acids have: 1. Identical

charges; 2. Identical chemistry abilities (similar protonation states); 3. Similar H-bonding

patterns; 4. Similar size.

3. Will globin binding curves be discussed in detail in class?

Yes. I will go over hemoglobin and myoglobin in detail after discussing nonallosteric and

allosteric enzymes.

For questions & answers posted prior to exam 1, click this file: questions pre exam 1