BIOCHEMISTRY

lephinga@hcmut.edu.vn

Week

Content

Week

Content

Biochemistry-1 (introduction, week

bonds, water, buffer systems)

Biochemistry-6 (bioenergentics)

Biochemistry-1 (cont.)

Biochemistry-7(Glycolysis,
gluconeogenesis and pentose
phosphate pathway)

Biochemistry-2 (amino acid ,

protein)

10

Biochemistry-7(cont.)/TA3

Biochemistry-3 (protein functions)

TA1

11

Biochemistry-8 (TCA cycle)

Biochemistry-4 (carbohydrates)

12

Biochemistry-9 (Lipid oxidation)

Biochemistry-5 (Lipids)

13

Biochemistry-10 (amino acid

degradation and urea cycle)

Overview-1/ TA 2

14

Biochemistry-10 (cont.)

Midterm test

15

Overview-1/ TA 4

Thalidomide!

1957 in Germany

Risk of severe, life-threatening birth defects caused by

thalidomide.
"stereo-" means "three-dimensionality"
stereochemistry is the study of
chiral molecules

Teratogen: agent that can disturb the

development of an embryo or fetus
Thalidomide must not be taken by women
who are pregnant or who could become
pregnant while taking this medicationbanned 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

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 pages

2012

2009

At Standford and Wiscosine

universities

1
1
2
3
4
5

6
7
8
9
10
6
9

Will not be studied in this course!

Score partitioning ( credits: 3 + 1)

Attendance: at least 11/15 classes (requirement)
Daily Quick Tests: 10% (Written or Multiple Choices)
A Midterm Test: 20%
A Final Test:
40% (Written or Multiple Choices)
Experiments:
30% (100% of time for attendance;
quick tests, report, final test)

Week-1

Introduction
Foundations
Water
Buffering

Under electromicroscopy

Vertebrate
muscles

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
and functions)

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.

BIOCHEMISTRY

Which form is the first living matter?

A Cell

 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
Nucleus (eukaryote) or a nucleoid (prokaryote)
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 double
membrane (nucleus membrane)

Three Domain of Life

Prokaryote

Eukaryote

Based on rRNA sequence similarity

Energy source and Carbon source

Escherichia coli - the Most-Studied Bacterium

Step centrifugation

Separation by centrifugation

Three types of cytoskeletal filaments: actin filaments,

microtubules, and intermediate filaments
bovine pulmonary artery

Microtubules: green
actin filaments "stress fibers: red
chromosomes: blue

lung cell undergoing mitosis

centrosomes
(magenta)

kinetochores : yellow

Bound
Plasmid
Compartment
Supramolecular
Segregate
Hierarchy

Carbon bonding: single, double, triple

tetrahedral arrangement

freedom of rotation

For an example?
rigid plan: not free rotate

Functional Groups in Biomolecules

Problem-1
Identification of
Functional
Groups

Acetyl-CoA: acetyl group carrier molecule

Acetyl

Balls and sticks

Fisher presentation

Carbon monomeric

Group ordering by
clockwise or counter
clockwise

H- in the back (of the paper)

broad array
skeleton
Metabolism
Metabolite
Functional group
Molecular configuration
Substituent
Chiral carbon
Sterioisomer
steriospecific
conformation
rotation
Complementary match

Problem-2

Problem-3
Identify the chiral center(s) in isoproterenol

Hen ph
qun

Thuc xt gin
ph qun

Problem-4
Based on the characteristics of the molecule s would you separate (a)
amino acids from fatty acids and (b) nucleotides from glucose?

Why melting points are different among solvent molecules ?

Hydrogen bonding

43

Roles: Solubilisation/ interactions/ structural functions

Water

At pH= 7.0 = -log[H+] log[H+] = 10-7

Water molecules are mainly in H20 form, very
low concentration of waters ions

45

Water ions interactions

46

Hydrogen bonding between a substrate and its enzyme

47

Water channel

48

Water amphipathic molecular interactions

49

a hydronium ion
Proton hopping. Short "hops"
of protons between a series
of hydrogen-bonded water
molecules 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
molecule some distance away
(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*

Conjugate acid-base pairs consist of a proton donor

and a proton acceptor
acceptor
donor

The titration curve of acetic acid

A-

HA

pKa

Titration/titrate
deprotonated

acid-acetate buffer pair

HA/AAfter addition of each
increment of NaOH to the
acetic acid solution, the pH
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) to
its deprotonated form,
acetate (CH:COO ) The
points so obtained yield the
titration curve.

Water and pH
At pH= 7.0 = -log[H+] log[H+] = 10-7

A pair of a week Acid and its conjugate base?

CH3COONH3
R-SH
H2PO42PO43-

Buffering region of
NH3/NH4+ =?

Henderson-Hassenbalch equation: relation of pH, pKa

and concentrations of acid and conjugate base)

When pH = pKa?
[Conjugate base] = [ acid]

59

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

Change when adding acid or base to a buffering system?

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.

Common buffers are being used in a biochemitry lab

Acid phosphoric/ phosphate (KH2PO4/K2HPO4 , 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 36.2
Glycine/NaOH (NH2/NH3 +), pH 9.6
Tris -base/HCl, pH 7.0 9.0
HEPES/NaOH, pH 6.88.2
MOPS/NaOH, pH 6.5 7.9
MES/NaOH, pH 5.5 7.0
64