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BIOCHEMISTRYBIOCHEMISTRYlephinga@hcmut.edu.vn

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)

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

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

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

At Standford and Wiscosine

universities

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)

• erm es :• A Final Test: 40% (Written or Multiple Choices)

• Experiments: 30% (100% of time for attendance;

quick tests, report, final test)

Week-1

• Introduction

oun a ons• Water

• Buffering

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

5. A capacity for precise self-replication

and self-assembly (Fig 1-1c).

6. A capacity to change over time by gradual

evolution.

BIOCHEMISTRYBIOCHEMISTRY

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

• 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)

Three Domain of Life

ProkaryoteEukaryote

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

actin filaments -

Microtubules: green

bovine pulmonary artery lung cell undergoing mitosis

centrosomes

(magenta)

chromosomes: blue

kinetochores : yellow

Plasmid

Compartment

Supramolecular

Segregate

Hierarchy

Carbon bonding: single, double, triple

For an example?

tetrahedral arrangement freedom of rotationrigid plan: not free rotate

Functional Groups in Biomolecules

Problem-1

Identification of

Functional

Groups

Acetyl

Acetyl-CoA: “acetyl group carrier” molecule

Balls and sticks

Fisher presentation

Group ordering byclockwise or counter

clockwiseCarbon monomeric

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-4Based 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

At pH= 7.0 = -log[H+]

log[H+] = 10-7

Water molecules are mainly in H20 form, very

low concentration of water’s ions

Water –ions interactions

Hydrogen bonding between a substrate and its enzyme

Water channel

Water – amphipathic molecular interactions

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*

Conjugate acid-base pairs consist of a proton donor

and a proton acceptor

acceptor

h f d Ti i / i

The titration curve of acetic acid Titration/titrate

deprotonated

After addition of each

increment of NaOH to the

acid-acetate buffer pair

,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.

Water and pH At H= 7.0 = -lo H+

lo H+ = 10-7

Buffering region ofNH3/NH4+ =?

Henderson-Hassenbalch equation: relation of pH, pKa

and concentrations of acid and conjugate base)

When pH = pKa?

[Conjugate base] = [ acid]

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?

Bi b t b ff i t

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 (KH

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

• 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

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