BioC 3021 Section 001

Second Exam Structures to Learn

Sugars: glyceraldehyde, ribose, glucose, galactose, fructose, glycerol, 2-deoxy-ribofuranose, N-Acetyl glucosamine,
amylose, amylopectin, glycogen and cellulose showing correct linkages. know alpha and beta forms of glucose
Lipids: stearic acid, oleic acid, elaidic acid, tristearin, phosphatidic acid, phosphatidyl serine
Nucleic Acids: the five nucleotides, ATP, a DNA chain and an RNA chain showing phosphodiester linkages and correct
5 to 3 polarity, DNA and RNA duplexes showing hydrogen bonding between bases, AZT
NOTE: you should still know the structures of all the amino acids, you might be asked to draw any that we have
looked at in protease mechanisms
Second Exam Concepts to Know
1. ENZYMES
Know how concentrations of substrate, free enzyme, ES complex, and product change during a reaction.
Understand a V versus [S] plot and a double reciprocal plot; be able to draw both plots given data.
Know how to determine Km and Vmax and their significance.
Understand competitive and noncompetitive inhibitors and their effects on Km, Vmax.
Know how p-nitrophenyl acetate reveals chymotrypsin mechanism.
For chymotrypsin: know mechanism, catalytic triad, and how enzyme determines substrate specificity.
Be able to draw the serine protease catalytic triad of Asp 102, His 57, and Ser 195:
-with substrate bound prior to first catalytic step
- as second tetrahedryl transition state
- as acid component of substrate is released at the end of the reaction
-you should be able to follow each proton that moves but you dont need to follow electrons
Know the six modes of enzyme catalysis with specific examples of enzymes that use them (where appropriate).
Understand transition state: definition, significance, transition state analogs, and enzyme binding affinity.
For aspartic acid protease: know mechanism, how enzyme determines substrate specificity, inhibitors:
-be able to draw starting form
-be able to draw tetrahedral intermediate
-know the origin and fate of all protons that move
Understand gram-positive cell wall, glycoprotein transpeptidase, beta-lactam antibiotics and beta-lactamases.
Know some examples of how drug designers have tried to respond to beta-lactamases.
You do not need to know the structures of penicillin drugs .
Know the parts of the rennin-angiotensin system, ACE inhibitors: how they work but you do not need to know structures.
However, given a protease inhibitor, you should be able to find the 'fake' peptide bond.
2. CARBOHYDRATES
Draw the monosaccharides as listed above, know what epimers and anomers are and how to tell alpha vs. beta.
Know the ring closure reactions for glucose and fructose.
Understand alpha and beta linkages.
Know the storage and structural polysaccharides: examples, structure, significance, H-bonding.
3. LIPIDS
Know the structures of fatty acids, triglycerides and phospholipids listed above,
Know role of cholesterol in membranes but don't have to know structure.
Understand membranes: lipid arrangement, protein arrangements, hydropathy plot, MDR, aquaporin.
Be able to discuss ABO blood groups, Rh factor.
4. NUCLEIC ACIDS
Draw structures of mono- and polynucleotides listed above, and know properties of DNA, RNA.
Be able to describe non-Watson Crick base pairing in RNA, RNA enzymes.
Be able to discuss reverse transcriptase inhibitors.
Also remember hemoglobin: - effect of pH, BPG, CO on hemoglobin