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

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?

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

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

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?

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

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

Depurination

UV damage: dimerization of pyrimidines

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

Other functions of nucleotides Energy storage

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

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

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