P1254156806JkiMz

1
Evolutionary tailoring of retroviral immunity
genes, by Sara Sawyer, Research Scientist,
F red Hutchinson Cancer Research Center, Seattle,
WA Wed. Nov. 15 400 PM BI 234
Join Sara for pizza lunch (FREE!!!) at noon on
Wednesday in BI 415 .They can ask about grad
school, postdoc'ing, AIDS research, surfing,
anything...!
2
16-Nov-06 Seminar Prof. Myriam Cotten, Pacific
Lutheran University. "A Solid-State NMR Study of
Lipid-Bound Piscidin Implications of Peptide
Secondary Structure, Topology, and Fast Dynamics
for Antimicrobial Function." 400 p.m. SL 130
3
17-Nov-06 Bowling for Chemistry. Come join the
Chem Club for an evening of fun at 20th Century
Lanes on State Street. 600 p.m.
4
Chapter 13 Enzymes!!
5
Number Classification Biochemical Properties
1. Oxidoreductases Act on many
chemical groupings to add or remove hydrogen
atoms. 2. Transferases Transfer functional
groups between donor and acceptor
molecules. Kinases are specialized
transferases that regulate metabolism by
transferring phosphate from ATP to other
molecules. 3. Hydrolases Add water across a bond,
hydrolyzing it. 4. Lyases Add water, ammonia or
carbon dioxide across double bonds, or remove
these elements to produce double bonds.
5. Isomerases Carry out many kinds of
isomerization L to D isomerizations, mutase
reactions (shifts of chemical groups) and
others. 6. Ligases Catalyze reactions in which
two chemical groups are joined (or ligated)
using ATP.
6
1.Addition or removal of water
a.Hydrolases - these include esterases,
carbohydrases, nucleases, deaminases, amidases,
and proteases b.Hydrases such as
fumarase, enolase, aconitase and carbonic
anhydrase 2.Transfer of electrons
a.Oxidases b.Dehydrogenases
7
3.Transfer of a radical
a.Transglycosidases - of monosaccharides
b.Transphosphorylases and phosphomutases - of a
phosphate group c.Transaminases - of
amino group d.Transmethylases - of a
methyl group e.Transacetylases - of an
acetyl group 4.Splitting or forming a C-C bond
a.Desmolases 5.Changing geometry or
structure of a molecule a.Isomerases
6.Joining two molecules through hydrolysis of
pyrophosphate bond in ATP or other
triphosphate a.Ligases
8
Oxidoreductases--catalyze redox reactions
Usually require a coenzyme
Ethanol NAD ? Acetaldehyde NADH H
Enzymes receive common names reflecting their
function, either in the forward or reverse
direction.
The enzyme for this reaction is called
Alcohol Dehydrogenase
9
Transferases-transfer functional groups
Kinases transfer phosphates from ATP (or GTP)
e.g Hexokinase Glucose ATP?glc-6-P ADP
Hydrolases catalyze hydrolytic cleavages
Proteases are hydrolases
10
Lyases catalyze group elimination to form
double bonds
e.g. Enolase (glycolysis)
2-Phosphoglycerate ? H2O phosphoenol- pyruv
ate
Isomerases--duh, interconvert isomers
e.g. phosphoglucose isomerase
Glucose-6-phosphate ? Fructose-6-phosphate
11
Ligases--join to substrates together at the
expense of ATP
e.g. DNA Ligase
Joins Okazaki fragments during DNA replication
Some bacterial ligases substitute NAD as the
energy source.
12
Coenzymes

• Enzymes often require the participation of other
  small molecules to carry out a particular
  reaction.
• These small molecules, called coenzymes, are
  metabolic derivatives of vitamins.
• Vitamins are nutrients required in small amounts
  by organisms. Vitamin deficiencies usually
  present as metabolic disorders, e.g. scurvy

13
Table 13-1 The Common Coenzymes.
14
Table 13-2 Vitamins That Are Coenzyme Precursors.
Page 464
15
Figure 13-2 The structures and reaction of
nicotinamide-adenine dinucleotide (NAD) and
nicotinamide adenine dinucleotide phosphate
(NADP).
Page 461
16
Figure 13-4 Structures of nicotinamide and
nicotinic acid.
Page 464
17
Enzyme Activities Are Regulated at Various Levels

• Transcription
• Processing
• Translation
• Post-translational modification
• Transient modification (e.g. phosphorylation)
• Allosteric Effectors

18
Figure 13-5 The rate of the reaction catalyzed by
ATCase as a function of aspartate concentration.
Page 465
19
Figure 13-6 Schematic representation of the
pyrimidine biosynthesis pathway.
Page 466
20
Figure 13-7a X-Ray structure of ATCase. (a)
(left) T-state ATCase along the proteins
molecular threefold axis of symmetry (right)
R-state ATCase along the proteins molecular
threefold axis of symmetry.
Page 467
21
Figure 13-7b X-Ray structure of ATCase. (b)
(left) T-state ATCase along the proteins
molecular twofold axis of symmetry (right)
R-state ATCase along the proteins molecular
twofold axis of symmetry.
Page 467
22
Figure 13-8 Comparison of the polypeptide
backbones of the ATCase catalytic subunit in the
T state (orange) and the R state (blue).
Page 468
23
Figure 13-9 Schematic diagram indicating the
tertiary and quaternary conformational changes in
two vertically interacting catalytic ATCase
subunits.
Page 469
24
(No Transcript)
25
(No Transcript)
26
Styer p.277
27
Stryer p. 278
28
(No Transcript)