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Lecture 1 Slides
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My office hours
2130 Pacific Hall
Mon 3:00-4:00
Tues 3:00-4:00
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Metabolic Biochemistry BIBC 102
hppt://courses.ucsd.edu/rhampton/bibc102
office hours 2130 Pac Hall
Mon 3:00- 4:00
Tues 3:00- 4:00
exams 1 midterm, 1 final
problem sets available on web
IAs sections: you each registered
How to take this class
1) Bring the lecture slides TO CLASS
you can:
a) Download the powerpoints
How to take this class
1) Bring the lecture slides TO CLASS
you can:
b) Download the lec 1-10 PDF
How to take this class
1) Bring the lecture slides TO CLASS
you can:
c) buy a packet at Soft reserves
-ready soon
-pages with holes
-2 slides per page (by popular demand)
How to take this class
2) Know everything on the study list
3) Know all the terms on the terms list
How to take this class
2) Know everything on the study list
3) Know all the terms on the terms list
4) Take advantage of the problem sets
Podcasting… with benefits
C6H12O6
podcasts on web ~24 hrs after class
An ongoing experiment…
iClicker 2 Why?
1) Allows instant feedback and
refocusing
2) Pleasantly anonymous
3) Facilitates my teaching
4) Provides easy source of points
iClicker 2
1) Get one. Must be “iClicker brand
Sold in UCSD bookstore
2) Bring it to class, use it
3) Credit given for participation
not correctness
In-class text messaging…
Ask… or
txt: 203 303 4320
make sure you can check your
UCSD email (@ucsd.edu)
Nelson, Cox and Lehninger 6th Ed.
sixth edition
fifth edition
Nelson, Cox and Lehninger 5th Ed.
As of past few years, NC&L is
suggested, but NOT required…
R-generated reading…
familiar
biomolecules
small biomolecules are “non-iterated”
but do have common functional groups
small biomolecules are “non-iterated”
small biomolecules are “non-iterated”
but do have common functional groups
fig1-16
the metabolic pathway
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Why study and understand metabolism?
0) Underlies every life process at some level
1) Obesity: a world-wide problem in health
2) Adult onset diabetes: a metabolic disease
3) Exercise and metabolism
4) Important in ageing, cancer and many other
maladies
5) Biofuel strategies for alternative energy
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catabolism
and
anabolism
Many levels of thinking
Many levels of thinking
Many levels of thinking
Many levels of thinking
Metabolism as a system
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The Stedman Institute at Duke U. School of Medicine
Chris
Newgard
The Stedman Institute at Duke U. School of Medicine
PROTEINS
an amino acid
an L amino acid
Amino
acids:
The
Molecular
Tool Box
fig3-5
Amino
acids:
The
Molecular
Tool Box
(G)
(L)
(D)
(M)
(I)
(S)
(P)
(T)
(N)
(C)
(Q)
(E)
(K)
fig3-5
(V)
(A)
(R)
(H)
(F)
(Y)
(W)
Amino
acids:
The
secret
practice
method
The peptide bond
A polypeptide with 5 residues
has distinct ends or
termini: N and C
Chemical independence of R groups
A commercial dipeptide
met-enkephalin: a neuropeptide
Tyr-Gly-Gly-Phe-Met
your own morphine
The a helix
The a helix
fig 4-4
The a helix
fig4-6
The b sheet
fig4-19
The b sheet
fig4-6
common b structures
fig4-19
examples of folded proteins
with a and b 2o structures
fig4-21
Levels of protein structure
fig3-23
heme: a cofactor
fig5-1
heme: a cofactor
fig5-1
heme at home…
fig5-3
Cofactors
molecular entity in addition to the amino acids
of the polypeptide
ions included in protein structure
discrete molecules
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ENZYMES: the key to metabolism
biological catalysts
proteins (for the whopping majority…)
encoded by genes
diseases, alleles, isozymes
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How did (and does) metabolism evolve?
1) chicken and egg issue in origin of metabolism
2) multiple intermediates
A
essential
B
C
D
non-essential intermediates
3) organism-specific metabolism
4) regulatory connections and strategies
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E
essential
fig6-4
fig6-4
enzymes increase the
rates of reactions
B.S. degree
in 21 min.
Energy map of a reaction
DG‡ is the activation energy
altering rate by catalysis
enzymes alter DG‡. period
how enzymes alter reactions: no enzyme
how enzymes alter reactions: plus enzyme
Main Enzymatic Catalytic Mechanisms
entropy reduction
acid-base catalysis
metal ion catalysis
covalent intermediates
other, stranger things…
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Main Enzymatic Catalytic Mechanisms
entropy reduction
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entropy reduction: reaction 1
fig6-7
entropy reduction: reaction 2
about 105 times faster
fig6-7
entropy reduction: reaction 3
about 108 times faster
fig6-7
Main Enzymatic Catalytic Mechanisms
entropy reduction
acid-base catalysis
recall from O-chem...
acids and bases enhance
rates of reactions like this
Main Enzymatic Catalytic Mechanisms
entropy reduction
acid-base catalysis
metal ion catalysis
ions as cofactors
Main Enzymatic Catalytic Mechanisms
entropy reduction
acid-base catalysis
metal ion catalysis
covalent intermediates
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Main Enzymatic Catalytic Mechanisms
entropy reduction
acid-base catalysis
metal ion catalysis
covalent intermediates
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other, stranger things…
“UN-REQUIRED” READING
not required, but interesting
READ
LIGAND BINDING
and
ENZYME CATALYSIS