Winter 2011 Biol/Chem 472
Metabolism
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Instructor: Gerry Prody
Office CB444
Office hrs: TBA
gerry@chem.wwu.edu
http://lightning.chem.wwu.edu/dept/facstaff/prody/
prody-472.htm
Welcome to Biochemistry
The required textbook for this
course is:
LEHNINGER
Principles of
Biochemistry 5/e
by David L. Nelson and Michael M. Cox
(©2008, W.H. Freeman & Company)
Free Companion Website
This site is chock full of resources to help you
succeed in the course.
www.whfreeman.com/lehninger5e
Student Media Resources
www.whfreeman.com/lehninger5e
• Interactive quizzes help you practice for
exams
• Animated Enzyme Mechanisms and
Animated Biochemical Techniques help
you understand key mechanisms and
techniques at your own pace
• Molecular Structure Tutorials allow you to
explore in more depth the molecular
structures included in the text
• Living Graphs illustrate key equations from
the book allowing you to do what if
scenarios by changing the parameters
• Lecture Companion Art allow you to print
figures and tables for note-taking and review
Additional Saleable Supplement:
The Absolute Study Guide & Solutions
Manual
It combines an innovative study guide with a reliable solutions manual
providing extended solutions to the end-of-chapter problems in the
textbook. It includes for each chapter:
- Major Concepts: A roadmap through the chapter
- What to Review: Questions that recap key points from previous
chapters
- Discussion Questions: Designed for individual review, study
groups, or classroom discussion
- A Self-Test: “Do you know the terms?”; crossword puzzles;
multiple-choice, fact-driven questions; and questions that ask
students to apply their knowledge
To learn more contact your local bookstore.
Need support?
1-800-936-6899 Monday-Friday, 9-5 EST
techsupport@bfwpub.com
What is Biochemistry?
• the systematic torture of students with
copious incomprehensible jargon, cryptic
fomulae, and impossible insoluble problems.
“Biochemistry is the study of Life as a process that can be understood.”
Primary Objective: understand the molecular mechanisms
that constitute the living state (“Molecular Logic”)
Lehninger: “Molecular Logic”
“A living cell is a self-assembling, self-regulating,
self-replicating isothermal open system of organic
molecules operating on a principle of maximum
economy of parts and processes; it promotes many
consecutive, linked organic reactions for the transfer
of energy and for the synthesis of its own
components by means of organic catalysts that it
produces itself.”
Biol/Chem 471; Biol/Chem 472 ; Biol/Chem 473
Elemental composition of the earth’s surface, including crust,
oceans and atmosphere.
Element
Oxygen
Silicon
Aluminum
Iron
Calcium
Sodium
Potassium
Magnesium
Hydrogen
Titanium
Chlorine
Carbon
All others
Percent by mass
49.1
26.1
7.5
4.7
3.4
2.6
2.4
1.9
0.88
0.58
0.19
0.09
0.56
Page 29
Table 1-3 Elemental Composition
of the Human Body.
Map of the
major
metabolic
pathways in a
typical cell.
Biol/Chem 472 Expected Outcomes
• draw enzymatic reactions correctly
• correctly calculate DGº’ and DG for a given step
or a series of steps in a pathway
• rationalize and/or predict features of pathway
regulation and describe regulatory mechanisms
• recognize how concentrations of metabolites
are regulated and the impact that changes in
flux and/or concentration will have on other
processes.
Note that figures labeled as Ch 11 come
from Voet and Voet. You can find
analogous figures in your text.
Page 357
Figure 11-1 The stereochemical relationships, shown in Fischer projection, among the D-aldoses with three to six carbon atoms.
Page 358
Figure 11-2 The stereochemical relationships among the D-ketoses with three to six carbon atoms.
Page 358
Figure 11-3
The reactions of alcohols
with (a) aldehydes to form hemiacetals and
(b) ketones to form hemiketals.
Figure 11-4
Cyclization reactions for hexoses.
Page 359
Figure 11-5 The anomeric monosaccharides a-D-glucopyranose and
b-D-glucopyranose, drawn as both Haworth projections and ball-andstick models.
Oxidation of sugars to acids: If the oxidation
occurs at C1, it’s an “-onic” acid. If at C6, it’s
“-uronic.”
Page 361
Figure 11-8
The acid-catalyzed
condensation of a-D-glucose with methanol
to form an anomeric pair of methyl-Dglucosides.
Some hexose derivatives important in biology
Figure 11-11 N-Acetylneuraminic acid in its linear and pyranose forms.
Page 363
Sialic acid
BOX 7-1 FIGURE 1 The glucose oxidase reaction, used in the
measurement of blood glucose. A second enzyme, a peroxidase
catalyzes the reaction of the H2O2 with a colorless compound
to produce a colored product, which is measured
spectrophotometrically.
What is the second enzyme? 474 folks…
BOX 7-1 FIGURE 2 The
nonenzymatic reaction of
glucose with a primary amino
group in hemoglobin begins
with (1) formation of a Schiff
base, which (2) undergoes the
Amadori rearrangement to
generate a stable product;
(3) this ketoamine can
further cyclize to yield GHB.
(4) Subsequent reactions
generate advanced glycation
end products (AGEs), such as
ε-N-carboxymethyllysine and
methylglyoxal, compounds
that (5) can damage other
proteins by cross-linking
them, causing pathological
changes.
Which of these are
reducing sugars?
Which are nonreducing?
Page 365
Figure 11-13 Electron
micrograph of the cellulose fibers
in the cell wall of the alga
Chaetomorpha melagonium.
Page 365
Figure 11-14 The primary
structure of cellulose.
Page 365
Figure 11-15 Proposed
structural model of cellulose.
Cell wall
architecture
Pectins
extensin
Common sugars found in
plant polysaccharides
Pectin structures
Cross-bridging and esterification
in pectins
A spotted June beetle (Pelidnota punctata), showing
its surface armor (exoskeleton) of chitin.
Page 366
Figure 11-16 Structure of
chitin.
Page 366
Figure 11-17a a-Amylose. The D-glucose residues of
a-amylose are linked by a(1  4) bonds (red).
Page 366
Figure 11-17b
a-Amylose. This
regularly repeating polymer forms a lefthanded helix.
Page 367
Figure 11-18a
Amylopectin. Its
primary structure near one of its a(1  6)
branch points (red).
Page 367
Figure 11-18b
Amylopectin. (b) Its bushlike
structure with glucose residues at
branch points indicated in red.
Page 368
Figure 11-20 The disaccharide repeating
units of the common glycosaminoglycans.
Page 373
Figure 11-23 Schematic diagram
comparing the cell envelopes of (a) grampositive bacteria and (b) gram-negative
bacteria.
Both + and - walls
NAM
Page 373
NAG
Figure 11-24a
Chemical
structure of
peptidoglycan.
(a) The repeating
unit of
peptidoglycan.
Page 373
Figure 11-24b Chemical structure of
peptidoglycan. (b) The S. aureus bacterial cell
wall peptidoglycan.
Figure 11-25 Structure of
penicillin. From yeast
Page 374
Prevents crosslinking of
peptides
Alexander Fleming
Page 374
Figure 11-26 Enzymatic
inactivation of penicillin.
Page 376
Figure 11-29a N-Linked oligosaccharides.
(a) All N-glycosidic protein attachments occur
through a b-N-acetylglucosamino–Asn bond
to Asn–X–Ser/Thr.
Page 376
Figure 11-29c
N-Linked
oligosaccharides. (c) Some examples of Nlinked oligosaccharides.
Page 376
Figure 11-30 Some common O-glycosidic
attachments of oligosaccharides to
glycoproteins (red).
Figure 11-33a The surfaces of
(a) a normal mouse cell as seen in the electron
microscope. (b) a cancerous cell as seen in the
electron microscope.
Page 378
Agglutinated with Conconavalin A--specific for glc and man
a
b
Living cells are not
at equilibrium!
Concentrations of reactants and
products are typically far from the
equilibrium values (Q  Keq).
DG = DG + RTlnQ
o'
We must consider “steady state”
concentrations of these species for
the determination of DG.
Homeostatic
conditions
Fig 16.2
Catabolic
pathways
Anabolic
pathways
See Figure 16.3
Figure 16.20
Figure 16.25
°
°’
Table 16.3
31P NMR of
human muscle:
Before exercise
1 min of exercise
Pi
ATP
phosphocreatine
19 min of exercise
gab
10 min after exercise
Reduced substrates
+
Oxidized cofactors
Oxidized substrates
+
Reduced cofactors
Fig 17.3
Least oxidized
Most oxidized
Page 567
Figure 16-21b Some overall coupled reactions involving ATP.
(b) The phosphorylation of ADP by phosphoenolpyruvate
to form ATP and pyruvate.
Biol/Chem 472 Expected Outcomes
• draw enzymatic reactions correctly
• correctly calculate DGº’ and DG for a given step
or a series of steps in a pathway
• rationalize and/or predict features of pathway
regulation and describe regulatory mechanisms
• recognize how concentrations of metabolites
are regulated and the impact that changes in
flux and/or concentration will have on other
processes.
“Alfonse, Biochemistry makes my head hurt!!”
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