Course No: Agri Science 302

Descriptive Title: ADVANCED BIOCHEMISTRY

Course Description: Molecular structure and functions of proteins, carbohydrates, lipids and nucleic acids; introduction to properties, reaction kinetics and catalytic reaction of enzymes at the molecular and cellular levels.

Credit: Three (3) units(9 hours lecture per week for 6 weeks)

COURSE OUTLINE

1. Introduction

2. The Cell

Types of CellsCell StructureBiomolecules – an OverviewWater

3. Nucleic Acids

General Properties and StructureThe Central Dogma of Molecular BiologyMutationsRecombinant Technology

CloningPolymerase Chain Reaction

4. Proteins

Amino AcidsGeneral PropertiesClassificationAmino Acids as Buffers

PolypeptidesThe Peptide BondsBiological FunctionsLevels of Protein ArchitectureDenaturationResolution and Analysis of ProteinsProtein Sequencing

EnzymesClassification and NomenclatureAllosterismEnzyme KineticsEnzyme Inhibition

Introduction to MetabolismNitrogen Metabolism

Digestion, Absorption and Transport of Amino AcidsDegradation of Amino Acids

Metabolic Fate of the Carbon SkeletonMetabolic fate of Nitrogen

5. Bioenergetics

Free Energy, High Energy Compounds and Coupled ReactionsBiological Redox Reactions

Reduction Potentials and Nernst EquationElectron Transport System and ATP Synthesis: Mechanism and

Inhibition

6. Carbohydrates

General Properties, Function and StructureCarbohydrate Catabolism

GlycolysisGlycogenolysisKrebs CycleHexose Monophosphate Shunt

Carbohydrate AnabolismGluconeogenesisGlycogenesisPhotosynthesis: C3,CAM, and C4 Plants

7. Lipids

General properties and StructureSaponifiable LipidsNon-safonifiable lipids

Biological Membranes: Functions and StructureLipid Metabolism

Digestion, Absorption and Transport of FatsCatabolic Pathways

LipolysisBeta Oxidation of Fatty Acids

Anabolic PathwaysFatty Acid SynthesisKetogenesisFat SynthesisCholesterol Biosynthesis – an Overview

8. Integration of Metabolism

References:

1. Koolman, J. and K.H. Roehm. 2005. Color Atlas of Biochemistry. 2nd Edition. Thieme New York, 333 Seventh Avenue, New York, NY 10001 USA

2. Berg, J.M., J.L. Tymoczko, and L. Stryer. Biochemistry. 5th Edition.3. Nelson, D.L. and M.M. Cox. Lehninger Principles of Biochemistry. 4th Edition. 4. McKee, T. and J.R. McKee. 2003. Biochemistry: The Molecular Basis of Life. 3rd

Edition. McGraw-Hill, Inc., 1221 Avenue of Americas, New York, NY 10020 USA5. Gumport, R.I., F.H. Deis, N.C. Gerber. 2002. Student Companion to Accompany

Biochemistry. 5th Edition. W.H. Freeman and Company, New York6. Murray, R.K., D.K Granner, P.A. Mayes and V.W. Rodwell. 2003. Harper’s Illustrated

Biochemistry. 26th Edition. Lange Medical Books/McGraw-Hill, New York

What is Biochemistry?

– the science which is concerned with the chemical constituents of living cells and with the reactions and processes they undergo

– major objective: the complete understanding, at the molecular level, of all of the chemical processes associated with living cells

– study of the molecular basis of life

Properties of Living Systems

1. Living systems are complex systems and yet highly organized.

- complex systems: composed of a lot of chemical substances; large number of components

- highly organized: many parts each has specific function/s, these functions are coordinated and interrelated

2. Living systems have the capacity for self-replication and self-assembly.

- reproductive ability; faithful copying of traits – genes, DNA

3. Living systems are capable of growth, movement, repair, adaptation and evolution.

- they are capable for sensing and responding to alterations in their surroundings and constantly adjust to these changes by adapting their internal chemistry.

- movement: response to stimuli- evolve: mutation

4. Living systems have the capacity of extracting, transforming and using energy from the environment.

- reproduction, growth, movement – activities that need energy- energy in the forms of mononucleotides (GTP, CTP, UTP, ATP – universal currency of

energy) and/or reducing equivalent dinucleotides (NAD, FAD).

Phylogeny of the Three Domains of Life

Structural Hierarchy of Living Systems

elements building blocks macromolecules supramolecular assemblies

organelles cells tissues organs organs system organism

Elements   : Only about 30 of the more than 90 naturally occurring chemical

elements are essential to organisms.Bulk: C, H, N, O, Na, K, Ca, P, S, ClTrace: Mg, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Se, Mo, I

Building blocksamino acids (proteins)monosaccharides (carbohydrates)nucleotides (DNA, RNA)fatty acids and glycerol (lipids)

Macromoleculesmade up of monomers or building blocks (nucleotides, amino acids; glucose)

Supramolecular assembliese.g. membrane : macromolecules interacting with each other; they form assembly; bi-lipid layer e.g. the cell surface

Organelles

Cell

- the basic unit of structure and function in a living organism- the simplest unit in a living system where you an observe the attributes of life- microscopic; 0.1 to several hundreds micrometer in diameter

- Types of cells:

1. prokaryotic cells: Greek words “pro” (before) and “karyon” (nucleus) do not have membrane –bound organelles

bacteria have no nucleus; just nucleoid region where DNA and RNA synthesis occur

2. eukaryotic cells: Greek words “eu” (true) and “karyon” (nucleus) have true nucleus membrane bound plants, fungi, animals, protists much larger than prokaryotic cells—commonly 5 to 100 _m in diameter, with cell

volumes a thousand to a million times larger than those of bacteria possess mitochondria, endoplasmic reticulum, Golgi complexes, and

lysosomes. Plant cells also contain vacuoles and chloroplasts

Cell Structures and their Functions

(a) Animal Cell

(b) Plant Cell

The Biomolecules

- the molecules that make up living organisms- these are biochemical substances inside living or biological systems- 2 groups: bio-organic and bio-inorganic

Bio-organic molecules:lipids (non-polymeric)nucleic acidscarbohydratesprotein (most abundant- 15%)

Bio-inorganic molecules:water: most abundant biochemical substance; 50-95% of living systems

water-soluble salts or ions: electrolytes ( Na+, K+, Mg2+, Ca2+)

Water

- considered as the medium of life- compose 50-95% of the body- ¾ of the earth’s surface- can exists in different states: : ice, vapor, liquid- molecular formula: H2O; the oxygen is more electronegative (greater capacity to attract

electrons) than hydrogen- water molecules are bent; the bond angle is 104.5o

- structure of the water molecule:

- water is polar: the electron distribution in hydrogen-oxygen bonds is displaced towards the oxygen;

Water is a polar compound: capable of dipole-dipole (negative to positive) interactioncapable of H bonding in the pure state with FON

compoundscapable of dissolving ionic compounds (e.g. NaCl)

Physical properties of water:

1. Water can dissolve wide array of substances: H2O is life sustaining

2. Water has high heat capacity (the amount of energy that must be added or removed to change the temperature of 1 gram of a substance 1o C). The specific heat of liquid water is 4.18 J/goC (one among the highest). This is possible due to its ability to form H bonds in the pure state.

Due to its high heat capacity, the amount of water in the body has a bearing in the body temperature. The fluctuation in body temperature is not that wide or extreme in range because water in the body can absorb enormous amount of heat. Water acts as an effective modulator of climatic temperature. It can absorb and store solar energy and release it slowly.

3. Water is a cohesive substance. Cohesion - phenomenon – molecules of a compound are held together by H bonds. This is due to the ability of water to form H bonds in the pure state. This property is responsible for capillary action which is necessary in plant nourishment. Substances are dissolved in water- water are cohesive- column of water strong to take substance upward.

4. Water has high heat of vaporization (the energy required to vaporize, or change from liquid to gas, one mole of a liquid at a pressure of one atmosphere). This is due to the ability of water to form H bonds. 1 calorie = 4.18 J; 540 calories needed to vaporize liquid H2O;

This is necessary to avoid dehydration among living organisms.

5. Water expands when frozen.- at 4oC : density of water is highest- below 4oC density is low- ice is less densed than liquid water, ice floats in water.- Why solid water is less densed than liquid water? Why water expands when it freezes?

Water molecules:solid state – fixed particleliquid state – has some mobilitygaseous state – freely moving

H bonding is directional; frozen fixed position; less denser due to the presence of pockets not filled in. D=M/V; solid water less denser than liquid water.

Is the condition that solid water is less denser than liquid water essential to life?Yes, it is essential to marine life forms in environmental bodies of water e.g. in

Alaska. Water on top is frozen; at the bottom, water is liquid. When water freezes (less densed), it goes up . The layer of ice on top protects the living things below the ice surface from the cold temperature above. The ice surface acts as insulator.

6. Acid –base property of water: buffer system; pH regulation