Instructors for

Biochemistry II
Dr. Yongmei Qin ( Associate

Professor, director of Biochemistry II)

Tel.:6275-8885 (office); Room 214, New
Life Science Building;
E-mail: qinym@pku.edu.cn

Dr. Zengyi Chang ( , Professor

Tel: 6275-8822 (office); Room 204, New
Life Science Building;
E-mail: changzy@pku.edu.cn

Teaching Assistants for

Biochemistry II
Ruiyu Kang ( ) 6275-8056
Raymank@pku.edu.cn

Fangyuan Chen ( ):
faye@pku.edu.cn

Anastasia Ngozi( ) 62758056

anasha@pku.edu.cn

Did you ever ask these questions

How the nutrients that we are ingesting daily

become part of our body and allow growth to
occur (what is the fate of the sugar, fat,
protein and nucleic acids that enter our body
along with the food ?)
Why do we become fat by only eating sugar?
What is the molecular nature of the large
number of genetic diseases? How can we
find ways to prevent and treat them?
What does O2 do for us? And how is O2
produced by plants?
How do the various living organisms
produce and consume energy?

Biochemistry II
Metabolism: The totality of
the transformation of
biomolecules (matter) and
energy

Definition of Metabolism
The entire highly integrated and

regulated network of chemical

transformations (as stepwise metabolic
pathways catalyzed by many enzymes )
occurring in a living organism (through
which cells extract energy and reducing
power from its environment, as well as
synthesize the building blocks of its
macromolecules and then the
macromolecules themselves).

Coenzymes (vitamin

Amino acids
carbohydrate

hormones

nucleotide

Amino acid
lipids

22nd edition designed by Dr. Donald E. Nicholson

For maps of metabolic

pathways see:
http://www.iubmb-nicholson.org
/

metabolism is categorized
into two types
Catabolism (biodegradation): larger

molecules (nutrients and cell constituents)

are broken down (often via exergonic
reactions) to salvage (reuse) their
components or/and to generate energy.
Anabolism (biosynthesis): The generation
of biomolecules from simpler components
(often via endergonic reactions).

The Ying & Yang of Metabolism

(Fuels)

The Ying & Yang of Metabolism

Exergonic Oxidation
Biodegradation
Output of energy

Simpler
Metabolites

Complex
Metabolites

Input of energy

Endergonic Reduction
Biosynthesis

Major Roles of
Metabolism
Extract energy and reducing power from

the environment (photosynthesis and

oxidative degradation of nutrients).
Generation (interconversion) of all the
biomolecules for a living organism.

Thus comes the term

Dynamic Biochemistry

(Fuels)

The role of Metabolism

Extract energy and reducing power

ATP: Energy currency

Also for mobility,

transport of nutrients
and so on.

Generate all biomolecules

Classification of organisms
based on trophic (feed)
strategies
Autotrophssynthesize all cellular

components from simple inorganic

molecules (e.g, H2O, CO2, NH3, H2S).
HeterotrophsDerive energy from
oxidation of organic compounds (made
by autotrophs).

Metabolism in various
living organisms allow
carbon, oxygen and
nitrogen to be cycled in the
biosphere.
The cycling of matter is
driven by the flow of
energy in one direction
through the biosphere!

Metabolism allows the cycling of C/O

and the flow of energy in the biosphere

glucose

Producers

Consumers

H2O

Metabolism also
allows the cycling
of N in the biosphere

(NH4+)

NO3NO2-

General Features of
Metabolism
Occurs in specific cellular (tissue and organ) locations as a series of

enzyme-catalyzed linear, branched or circular reactions, or

pathways.
Highly coupled and interconnected (Every road leads to Rome).
Highly regulated (often reciprocally) to achieve the best economy
(Balanced supply and demand).
The number of reactions is large (over 1000), however, the number
of types of reactions is relatively small (what happens in animal
respiration happens in plant photosynthesis).
Well conserved during evolution: reflecting the unity of the life
phenomena (what happens in bacteria happens in human being).

( A)

General approaches for

studying metabolism
Purification and Chemical characterization

of metabolites;
Tracing the fates of certain biomolecules in
living subjects (via such chemical labels as
isotopes).
Isolation of genetic mutants having genetic
defects.
Identification and characterization of
enzymes.

Issues for current and

future investigation on
metabolism

Continue to unveil new pathways and new regulation

strategies of metabolism.
Studies on enzymes.
Observation of metabolic processes in intact living
organisms (e.g., in the brains under various states)
Metabolism differences among various organisms or
various states of the same organism (for diagnosing and
treating such diseases as cancer, infections of bacteria
or viruses, obesity, etc; to understand aging).
Appropriate and inappropriate nutrition.
Biotechnological application of knowledge learned from
metabolic studies in medicine, agriculture and industry.

Nobel Prizes in revealing

the Metabolism of living
matter (1)

1907, Eduard Buchner: cell-free fermentation.

1922, Archibald B. Hill: production of heat in the muscle?;

Otto Meyerhof: fixed relationship between the

consumption of oxygen and the metabolism of lactic acid
in the muscle.
1923, Frederick Grant Banting, John James Richard
Macleod: discovery of insulin.
1929, Arthur Harden, Hand von Euler-Chelpin:
fermentation of sugar and fermentative enzymes .
1929, Christiaan Eijkman: antineuritic vitamin; Sir
Frederick Gowland Hopkins: growth-stimulating vitamins .
1931, Otto Heinrich Warburg: nature and mode of action of
the respiratory enzyme.

Nobel Prizes in revealing

the Metabolism of living
matter
(2)
1934,
George
Hoyt
Whipple,
George
Richards Minot,

William Parry Murphy: liver therapy in cases of

anaemia.
1937, Albert Szent-Gyorgyi: biological combustion,
vitamin C and the catalysis of fumaric acid .
1943, Henrik Carl Peter Dam: discovery of vitamin K;
Edward Adelbert Doisy: chemical nature of vitamin K .
1947, Carl Cori and Gerty Cori: catalytic conversion
of glycogen; Bernardo Houssay: hormone of the
anterior pituitary lobe in the metabolism of sugar .
1950, Edward Calvin Kendall, Tadeus
Reichstein,Philip Showalter Hench: hormones of the
adrenal cortex, their structure and biological effects.
1953, Hans Krebs: citric acid cycle; Fritz Lipmann:
role of co-enzyme A in metabolism .
1955, Axel Hugo Theodor Theorell: nature and mode
of action of oxidation enzymes.

Nobel Prizes in revealing

the Metabolism of living
matter (3)

1961, Melvin Calvin: carbon dioxide assimilation

in plants.
1964, Konrad Bloch, Feodor Lynen: cholesterol
and fatty acid metabolism.
1971, Earl W. Sutherland, Jr.: mechanisms of the
action of hormones.
1978, Peter Mitchell: chemiosmotic theory of
biological energy transfer.
1982, Sune K. Bergstrm, Bengt I. Samuelsson,
John R. Vane: prostaglandins and related
biologically active substances .
1985. Michael S. Brown, Joseph L. Goldstein:
regulation of cholesterol metabolism .

Nobel Prizes in revealing

the Metabolism of living
matter
(4)
W. Black, Gertrude B. Elion, George
1988, Sir James

H. Hitchings: principles for drug treatment.

1988, Johann Deisenhofer, Robert Huber, Hartmut
Michel: photosynthetic reaction centre .
1992, Edmond H. FischerEdwin G. Krebs: reversible
protein phosphorylation as a biological regulatory
mechanism.
1994, Alfred G. GilmanMartin Rodbell: G-proteins and
the role of these proteins in signal transduction in
cells.
1997, Paul D. Boyer, John E .Walker: synthesis of ATP.
1998, Robert F. Furchgott, Louis J. Ignarro, Ferid
Murad: nitric oxide as a signalling molecule in the
cardiovascular system.

Nobel Prizes in revealing

the Metabolism of living
matter
(5)
1999, Gunter Blobel: protein localization.

2000, Arvid Carlsson, Paul Greengard, Eric

R. Kandel: signal transduction in the

nervous system.
2001, Leland H. Hartwell, Tim Hunt, Sir Paul
Nurse: regulators of the cell cycle.
2002, Sydney Brenner, H. Robert Horvitz,
John E. Sulston: regulation of organ
development and programmed cell death.
2004, Aaron Ciechanover, Avram Hershko,
Irwin Rose: ubiquitin-mediated protein
degradation.

Major aspects that will be

covered in Biochemistry II
General principles for bioenergetics.
Oxidative degradation of fuels (glycolysis,

oxidation, ketoacid oxidation, citric acid cycle), generating NADH, FADH 2,

ATP, and CO2.
Oxidation of NADH and FADH2 by O2 and generation of ATP and
H2O (respiratory chains, ATP synthase).
Biosynthesis of carbohydrates (including photosynthsis), fatty
acids, amino acids, and nucleotides.
Metabolites, chemical reactions, enzymes, regulations, with wide
applications in medicine, agriculture, and biotechnology.

How to study metabolism

Compare and relate (interconnect) the chemical reactions

(Where are you in the metabolism network ?)

Try to contemplate on the ways the living organisms used to
achieve a balanced and dynamic steady state ( How could
the multilayered regulation cooperate so effectively ?).
Understand the classical experiments and thoughts that led
to the revelation of the knowledge described ( Does He/she
deserve the Nobel Prize?).
Be aware of the nature of the data (Could this observations
from in vitro studies be extended to what happens in vivo ?).
Understand the aspects that need further studies ( Do I still
have a chance to win a Nobel Prize ?).

Enjoy Biochemistry II:

a course that will
allow you to learn
what life is really all
about.

Scoring policies for this

course
Tests (attendance): 10%;
Critical reading of a research paper
(one paper for each two students):
15%;
Final Exam: 75%.

Dat Chapter
e

Lecturer

Sept. 12

Over view of metabolism and Chapter 13: Principles of Bioenergetics

Dr. Zengyi Chang

Sept. 19

Chapter 14

Dr. Zengyi Chang

Sept. 26

Chapter 16 The Citric Acid Cycle

Oct. 10

Chapter 17 Fatty Acid Catabolism

Dr. Yongmei Qin

Oct. 17

Chapter 18 Amino Acid Oxidation & Production of Urea

Dr. Yongmei Qin

Oct. 24

Chapter 18 Amino Acid Oxidation & Production of Urea

Dr. Yongmei Qin

Oct. 31

Chapter 19 Oxidative phosphorylation and photophosphorylation

Dr. Zengyi Chang

Nov. 7

Chapter 19 Oxidative phosphorylation and photophosphorylation

Dr. Zengyi Chang

Nov. 14

Chapter 14 GLuconeogenesis
Chapter 15 Principles of Metabolic regulation: Glucose and GLycogen

Dr. Yongmei Qin

Nov. 21

Chapter 20 Carbohydrate Biosynthesis in plants

Dr. Yongmei Qin

Nov. 28

Chapter 21 Lipid biosynthesis

Dr. Yongmei Qin

Dec. 5

Chapter 21 Lipid biosynthesis

Dr. Yongmei Qin

Dec. 12

Chapter 22
molecules

Dec. 19
Dec 26

Glycolysis & and Pentose phosphate pathway

Biosynthesis of amino acids, nucleotides and related

Chapter 22 Biosynthesis of amino acids, nucleotides and related

molecules
Chapter 23

Integration and hormonal regulation of mammalian

Dr. Zengyi Chang

Dr. Zengyi Chang

Dr. Zengyi Chang
Dr. Zengyi Chang