Instructors for Biochemistry

Instructors for Biochemistry

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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).


carbohydratecarbohydrate

Amino acidsAmino acids

Coenzymes (vitamines)Coenzymes (vitamines)

Amino acidsAmino acids

hormoneshormones

nucleotidesnucleotides

lipidslipids

22nd edition designed by Dr. Donald E. Nicholson22nd edition designed by Dr. Donald E. NicholsonDownloaded from

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For maps of metabolic pathways see:

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


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 MetabolismDownloaded from www.pharmacy123.blogfa.com

(Fuels)

Exergonic Oxidation

Complex Metabolites

Endergonic Reduction

The Ying & Yang of Metabolism

SimplerMetabolites

BiodegradationBiodegradation

BiosynthesisBiosynthesis

Output of energyOutput of energy

Input of energyInput of energy


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)

Extract energy and reducing power

ATP: Energy currency

Generate all biomolecules

The role of Metabolism

Also for mobility,transport of nutrients

and so on.


Classification of organisms based on trophic (“feed”)

strategies• Autotrophs—synthesize all cellular

components from simple inorganic molecules (e.g, H2O, CO2, NH3, H2S).

• Heterotrophs—Derive 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

H2O

glucose

Producers Consumers


Metabolism also allows the cycling

of N in the biosphere

(NH4+)

NO3-

NO2-


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”).


(乙酰辅酶 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.



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“.Downloaded from



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. Bergström, Bengt I. Samuelsson, John R.

Vane: prostaglandins and related biologically active substances.

• 1985. Michael S. Brown, Joseph L. Goldstein: regulation of cholesterol metabolism.



matter (4)• 1988, Sir James W. Black, Gertrude B. Elion, George 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.



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, FADH2, 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%.


Date Chapter LecturerSept. 12 Over view of metabolism and Chapter 13: Principles of Bioenergetics Dr. Zengyi Chang

Sept. 19 Chapter 14 Glycolysis & and Pentose phosphate pathway Dr. Zengyi Chang

Sept. 26 Chapter 16 The Citric Acid Cycle Dr. Zengyi Chang

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 Biosynthesis of amino acids, nucleotides and related molecules

Dr. Zengyi Chang

Dec. 19 Chapter 22 Biosynthesis of amino acids, nucleotides and related molecules

Dr. Zengyi Chang

Dec 26 Chapter 23 Integration and hormonal regulation of mammalian metabolism

Dr. Zengyi ChangDownloaded from


Instructors for Biochemistry

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