Biochemistry 2EE3

Metabolism and Physiological Chemistry

Instructor: Dr. Boris Zhorov

Website: http://www.learnlink.mcmaster.ca
Textbook: Fundamentals of Biochemistry. Econd Edition D. Voet, J. G. Voet, and C. W. Pratt. Wiley & Sons Inc. 2006 Questions: Students are encouraged to ask questions in the class and during the office hours. Office Hours: Instructor: Thursdays 4:30-5:20 HSC-4H29 Fei Geng Wednesdays 4:30-5:20 MDCL-3411 Revecca Zhu Thursdays 4:30-5:20 MDCL-3411

Evaluation of Student Performance

Multiple-choice midterm tests The final multiple-choice examination The final grade will be calculated as follows: Midterm 1 30% Midterm 2 30% Final examination 40%

Purpose
A brief introduction to proteins, enzymes and gene expression followed by a more detailed treatment of energy and intermediary metabolism with emphasis on physiological chemistry
Intermediary metabolism: enzyme-catalyzed processes within cells that extract energy from nutrient molecules and use that energy to construct cellular components.

Learning Objectives
Understanding principles and major concepts of biochemistry related to structure and function of biological macromolecules, energy production and utilization by living organisms, metabolic pathways, and mechanisms of integration and regulation of metabolism

What is Biochemistry?
Biochemistry is an interdisciplinary science combining biology and chemistry Biochemistry forms the basis for many applied sciences, e. g., biotechnology, nutrition and molecular medicine (drug design and gene therapy) Biochemistry overlaps other fundamental disciplines, e.g. physiology, molecular biology, immunology, and pharmacology

Major Issues Addressed by Biochemistry

How do biological molecules interact with each other? How is genetic information stored and expressed? How does the cell synthesize and degrade biological molecules? How is energy conserved and used by the cell? What are the mechanisms for organizing biological molecules What are chemical and three- dimensional structures of biological molecules?

Origin of Life. Cell

Learning Objectives
How did simple organic molecules emerge on Earth? What is the prebiotic area? Major chemical elements of the living cells Most common functional groups in biochemistry Chemical evolution Prokaryotic and eukaryotic cells

Prebiotic Era
Certain biochemical features are common to all modern organisms Earth formation: 4.6 billion years ago Earliest fossil organisms: 3.5 billion years old Prebiotic era: 1.1 billion years

Evidence for Early Life on Earth

Living stromatolites contain layers of sediment intermixed with different microbe types Look identical to ancient stromatolites that date back to 3.5 billion years ago (3.5 Gya) Indirect evidence for photosynthesis at 3.5 Gya

Large Mats in Western Australia

Early Life on Earth

Individual fossilized cells in ancient rock dating 3.2-2.5 billion years

Experiments by Miller and Urey (1953)

Electrical sparks Glycine + Alanine + Glutamic CH4 + NH3 + H2O +H2 acid + Aspartic acid + other Components of primordial simple organic compounds
atmosphere

Elemental Composition of the Human Body

Major Ionic Components (mM) of the Seawater and Extracellular Fluid

Ion Na+ Mg2+ Ca2+ K+ Cl-

Seawater 468 53 10 10 550

Exracellular fluid 145 1.5 2.5 4 115

Common Functional Groups in Biochemistry

Chemical Evolution: Polymerization

Chemical Evolution: Replication of Polymers

Complementarity between specific pairs of monomers: Anion is complementary to Cation H-bond Acceptor is complementary to H-bond Donor

Figure 1- 5 . Polymer serves as a template for the assembly of a complementary polymeric molecule

Stages of Prebiotic Evolution

Macromolecules gain a quality of self-perpetuation Primordial environment becomes enriched with molecules that are best able to survive and multiply Natural selection (competition for monomers) favors certain types of self-replicating macromolecules Ensembles of certain macromolecules sequester and become protected with a boundary

Cell
High local concentration of components High efficiency of chemical reactions Increased concentrations of certain microelements Modern organisms: eukaryotes and prokaryotes Greek: Eu (true), Pro (before), karyon (kernel) Synthesize required compounds from simpler but more abundant precursors Enzymes and energy producing metabolic pathways

Prokaryotes
Various types of bacteria Have relatively simple structures Only unicellular organisms Most numerous and widespread organisms on Earth Range in size from 1 to 10 m Do not have intracellular membranes

E. coli
Escherichia coli (E. coli) is the best- characterized prokaryote. Inhabits the mammalian colon. Contains millions of molecules representing 3,000 to 6,000 different compounds

Eukaryotic Cell
An animal cell may contain 100,000 different types of molecules Are 10 to 100 m in diameter Have membraneenclosed organelles Have nucleus and cytoskeleton

Evolution
Multicellular organisms arouse about 700- 900 million years ago Mitochondria may have evolved from a free- living bacteria that formed symbiotic relationships with primordial eukaryotes Charles Darwin (1809- 1882), British naturalist.Revolutionized biology with his theory of evolution based on natural selection. His most famous works are Origin of Species (1859) and The Descent of Man (1871).