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7/25/2019 Microsoft PowerPoint - BIOCHEMISTRY-1
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Week Content Week Content
1 Biochemistry-1 (introduction, week
bonds, water, buffer systems)
8 Biochemistry-6 (bioenergentics)
2 Biochemistry-1 (cont.) 9 Biochemistry-7(Glycolysis,
gluconeogenesis and pentose
3 Biochemistry-2 (amino acid ,
protein)
10 Biochemistry-7(cont.)/TA3
4 Biochemistry-3 (protein functions)
TA1
11 Biochemistry-8 (TCA cycle)
5 Biochemistry-4 (carbohydrates) 12 Biochemistry-9 (Lipid oxidation)
6 Biochemistry-5 (Lipids) 13 Biochemistry-10 (amino acid
degradation and urea cycle)
7 Overview-1/ TA 2 14 Biochemistry-10 (cont.)
Midterm test 15 Overview-1/ TA 4
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Thalidomide!Risk of severe, life-threatening birth defects caused by
thalidomide. "stereo-" means "three-dimensionality"
stereochemistry is the study of
chiral molecules
1957 in Germany
Teratogen: agent that can disturb the
Thalidomide must not be taken by women
who are pregnant or who could become
pregnant while taking this medication-
banned in 2012
Thalidomide is still used as a class of
medications called immunomodulatory
agents. It treats multiple myeloma by
strengthening the immune system to fight
cancer cells
development of an embryo or fetus
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2012
Sixth Edition 2012
Lehninger Principles of
Biochemistry
David L. Nelson (University of
Wisconsin-Madison) , Michael M. Cox(University of Wisconsin-Madison)
•ISBN-10: 1-4292-3414-8
•ISBN-13: 978-1-4292-3414-6
•Cloth Text , 1340 pages2009
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At Standford and Wiscosine
universities
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1
1
2
3
4
5
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7
8
6
910
6
9
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Will not be studied in this course!
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Score partitioning ( credits: 3 + 1)
• Attendance: at least 11/15 classes (requirement)
•Daily Quick Tests: 10% (Written or Multiple Choices)
• erm es :• A Final Test: 40% (Written or Multiple Choices)
• Experiments: 30% (100% of time for attendance;
quick tests, report, final test)
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Week-1
• Introduction
oun a ons• Water
• Buffering
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Creatures are different in characteristcs but
share common futures:
1. A high degree of chemical complexity
and microscopic organization (Fig 1-1a)2. Systems for extracting, transforming, and
using energy from the environment
3. Defined functions for each of an
organism's and regulated interactions
among them (organs, intracellular structure
Under electromicroscopy
Vertebrate
muscles
…
4. Mechanisms for sensing and responding
to alterations in their surroundings (Fig
1-1b)
5. A capacity for precise self-replication
and self-assembly (Fig 1-1c).
6. A capacity to change over time by gradual
evolution.
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BIOCHEMISTRYBIOCHEMISTRY
Which form is the first living matter?
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A Cell
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• Plasma membrane defines the periphery of the cell, …a barrier to the
free passage of inorganic ions and most other charged or polar
compounds..(Intake ions, molecules as needed and excretion the wastes).
•Cytoplasm = cytosol (soluble materials) + suspended particles.•Metabolites, intermediates in biosynthetic and degradative pathways
• Coenzymes , compounds essential to many enzyme-catalyzed reactions
• Ribosomes, synthesize proteins from amino acids
•Proteasomes, which degrade proteins no longer needed by the cell
• uc eus eu aryo e or a nuc eo pro aryo e
• Genome, complete set of genes, composed of DNA-is stored and
replicate
•Eukaryotes , consists of nuclear material enclosed within a double
membrane (nucleus membrane)
•Prokaryotes, consists of nucleoid not enclosed within a doublemembrane (nucleus membrane)
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Three Domain of Life
ProkaryoteEukaryote
Based on rRNA sequence similarity
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Energy source and Carbon source
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Escherichia coli - the Most-Studied Bacterium
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Step centrifugation Separation by centrifugation
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Three types of cytoskeletal filaments: actin filaments,
microtubules, and intermediate filaments
actin filaments -
" “
Microtubules: green
bovine pulmonary artery lung cell undergoing mitosis
centrosomes
(magenta)
chromosomes: blue
kinetochores : yellow
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Bound
Plasmid
Compartment
Supramolecular
Segregate
Hierarchy
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Carbon bonding: single, double, triple
For an example?
tetrahedral arrangement freedom of rotationrigid plan: not free rotate
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Functional Groups in Biomolecules
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Problem-1
Identification of
Functional
Groups
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Acetyl
Acetyl-CoA: “acetyl group carrier” molecule
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Balls and sticks
Fisher presentation
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Group ordering byclockwise or counter
clockwiseCarbon monomeric
H- in the back (of the paper)
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•broad array
•skeleton
•Metabolism
•Metabolite
•Functional group
•Molecular configuration
•Substituent
•Chiral carbon
•Sterioisomer
•steriospecific
•conformation
•rotation
•Complementary match
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Problem-2
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Problem-4Based on the characteristics of the molecule s would you separate (a)
amino acids from fatty acids and (b) nucleotides from glucose?
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Why melting points are different among solvent molecules ?
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Hydrogen bonding
S
43
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Water
45
At pH= 7.0 = -log[H+]
log[H+] = 10-7
Water molecules are mainly in H20 form, very
low concentration of water’s ions
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Water –ions interactions
46
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Hydrogen bonding between a substrate and its enzyme
47
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Water channel
48
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Water – amphipathic molecular interactions
49
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Proton hopping. Short "hops"
of protons between a series
of hydrogen-bonded watermolecules result in an extremely
rapid net movement of a proton
over a long distance.
As a hydronium ion (upper left)
gives up a proton, a water
a hydronium ion
(lower right) acquires one,
becoming a hydronium ion.
Proton hopping is much faster
than true diffusion and explains
the remarkably high ionic
mobility of H+ ions compared
with other monovalent cations
such as Na* and K*
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Conjugate acid-base pairs consist of a proton donor
and a proton acceptor
donor
acceptor
h f d Ti i / i
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The titration curve of acetic acid Titration/titrate
deprotonated
After addition of each
increment of NaOH to the
pKa
acid-acetate buffer pair
A-
HA/A-
,of the mixture is measured .
This value is plotted
against the amount of NaOH
added, expressed as a
fraction of the total NaOH
required to convert all the
acetic acid (CH3COOH) toits deprotonated form,
acetate (CH:COO ) The
points so obtained yield the
titration curve.
HA
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Water and pH At H= 7.0 = -lo H+
lo H+ = 10-7
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Buffering region ofNH3/NH4+ =?
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Henderson-Hassenbalch equation: relation of pH, pKa
and concentrations of acid and conjugate base)
59
When pH = pKa?
[Conjugate base] = [ acid]
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TWO especially important biological buffers are the
phosphate and bicarbonate systems.
The phosphate buffer system acts in the cytoplasm and is maximally
effective at a pH close to its pKa, of 6.86 thus tends to resist pH
changes in the range between about 5.9 and 7.9.
An effective buffer in biological fluids; in mammals, for example,
extracellular fluids and most cytoplasmic compartments have a pH in
the range of 6.9 to 7.4
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Change when adding acid or base to a buffering system?
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Bi b t b ff i t
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Bicarbonate buffering system
pCO2 is expressed in kilopascals (kPa; typically,
4.6 to 6.7 kPa) and 0.23 is the corresponding
solubility coefficient for CO2 in water; thus the term
0.23 x pCO2 = 1.2 kPa. Plasma HCO3- ~ 24 mM
Bicarbonate buffer system is an effective. The
physiological buffer near pH 7.4, because the
H2CO3 of blood plasma is in equilibrium with a
large reserve capacity of CO2(g) in the air space of
the lungs.
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Common buffers are being used in a biochemitry lab
•Acid phosphoric/ phosphate (KH
2
PO4/K2HPO
4, pKa=6.8)
• Carbon dioxide (CO2)/NaHCO3 , pH 5.4-7.4
• NH3/NH4+, pKa= 9.25
• Acid acetic/Na-acetate, pKa 4.76
• Acid citric/Na-citrate, pH 3 6.2
64
• Glycine/NaOH (NH2/NH3 +), pH 9.6• Tris -base/HCl, pH 7.0 9.0
• HEPES/NaOH, pH 6.8 8.2
• MOPS/NaOH, pH 6.5 7.9
• MES/NaOH, pH 5.5
7.0
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