1. Presentations Tuesday, May 8th ~7-10pm
Two groups will go during class that day

2. Exam #3 Next Friday Chapter 6 (and Lab Experiment 4)
General concepts of catalysis
Contributions of side chains/prosthetic groups to catalysis (eg. acid/base, metal-ion catalysis)
Enzyme kinetics
What do the variables/constants mean?
Types of inhibition? Mechanisms? Effects on constants?
Enzyme regulation
Why? How?

3. Chapter 7 Chapter 8 Representations of carbohydrate structures
Formation of ring structures and formation of glycosidic bond
Polymers, eg. starch vs. cellulose
Formation of sugar/protein hybrids (proteoglycans and glycoproteins: how and why?
Chapter 8

4. Nucleic acid chemistry
“Denaturation” of nucleic acids
‘unzipping’ the base pairs
Biologically: denaturation necessary for reading the genetic information (DNA replication, RNA polymerization)
Biochemically: denaturation necessary for manipulations of DNA/RNA (amplification (PCR), sequence determination)
Can be measured by ↑ UV absorption upon denaturation

5. Nucleic acid chemistry
“Denaturation” of nucleic acids
Easiest way: raise temperature
“Melting point” depends on strength of interaction between the two strands
What influences how strongly the strands interact?

7. Nucleic acid chemistry
Changes in the covalent structure of nucleotides
Can influence interaction with DNA-binding proteins
eg. methylation of bacterial DNA protects it from endogenous ‘nucleases’
Can cause a change in the genetic information
Mutation
May be “Silent”: much of our DNA is ‘junk,’ doesn’t code for protein/RNA
May affect protein function/expression
Damage/kill cell?
Weaken regulatory mechanisms: aberrant cell growth/tumor/cancer
Improve organism’s ‘fitness,’ fecundity

8. Base deamination Can happen spontaneously or via mutagenic chemicals
Altered base typically recognized by cell’s repair machinery, excised & replaced
100 events per cell per day

9. Depurination

10. UV damage: dimerization of pyrimidines

11. Other non-enzymatic changes to DNA
Oxidative damage: eg. through H2O2, free-radical metabolic intermediates
Cause a variety of changes, eg. base alterations, double-stranded DNA breaks
Cells have very good, yet imperfect repair mechanisms
DNA damage → mutation

12. Other functions of nucleotides
Energy storage

13. Other functions of nucleotides
Enzyme cofactors
Transfer of acyl group to other bio molecules
Acyl group attached to the free sulfhydryl

14. Other functions of nucleotides
Enzyme cofactors
NAD+
Accepts hydride (H+ + 2e-) to form NADH
Functions in redox chemistry

15. Other functions of nucleotides
FAD
Vitamin B2
Accepts 2H atoms (2H+ + 2e-) to form FADH2
Functions in redox chemistry