Biochemistry for Environmental Health

Lecture 1

Ahmad Razali IshakDepartment of Environmental HealthFaculty of Health SciencesUiTM Puncak Alam

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Biochemistry

Biochemistry has become the foundation for understanding all biological

processes.

It has provided explanations for the causes of many diseases in humans,

animals and plants

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What is Biochemistry ? • Biochemistry is the application of chemistry to

the study of biological processes at the cellular and molecular level.

• It emerged as a distinct discipline around the beginning of the 20th century when scientists combined chemistry, physiology and biology to

investigate the chemistry of living systems by:

A. Studying the structure and behavior of the complex molecules found in biological material and

B. the ways these molecules interact to form cells, tissues and whole organism

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Practical application of Biochemistry

1. In medicine and health care• Enzymes as a marker for disease e.g. Lactate

dehydrogenase (hearth attack can be diagnosed by an increase of IDH from hearth muscle

• Acetyl cholinesterase (Ace) important in controlling certain nerve impulse. Many pesticides interfere with this enzyme

2. Designer drugs- new and improved antibiotics and chemotherapy agents.

3. In agriculture- herbicides, pesticides, genetics engineering4. Chemical industries-synthesis and detoxification

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Principles of Biochemistry • Cells (basic structural units of living organisms) are highly

organized and constant source of energy is required to maintain the ordered state.

• Living processes contain thousands of chemical pathways. Precise regulation and integration of these pathways are required to maintain life

• Certain important pathways e.g. Glycolysis is found in almost all organisms.

• All organisms use the same type of molecules: carbohydrates, proteins, lipids & nucleic acids.

• Instructions for growth, reproduction and developments for each organism is encoded in their DNA

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Biochemical Evolution

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CH4, H2O, NH3, HCN

How did organic complex molecules evolved from more simple molecules?

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Types of element in organism

• 90 element in earth, only 27 component essential in organism.

• In earth, 4 most abundant element are oxygen, silicone, aluminum and Ferum.

• In organism, 4 most abundant element are hydrogen, oxygen, carbon and nitrogen.-most endurance element with different types of process in organism. 7

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Cont..

• H, C, O, N can form covalent bond by sharing pair of electrons

• This 4 types of elements form a large number of different types of compound

• 3 from this element (O,N,C) can share either 1 or 2 pair of electron which produce single ore double bond.

• This make this element can form different types of chemical bonds.

• This element also very light and can form very strong covalent bond.

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Cont..

• Carbon can share 4 electron pairs thus can form 4 covalent bond with 4 other carbon element -forming the straight chain/cyclic for different types of organic molecules.

• C also produce different types of functional group since it can form covalent bond with N, O and sulfur.

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Cont..

• C also permit the 3 dimensional structure for biomolecule since it can form tetrahedron configuration with other carbon

• No other element like C which can form different in size, configuration different types of bond with functional group.

• Unique characteristics of C enable a hierarchy of molecule organization in cell

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Revision-basic chemistry

• Covalent bond- sharing of pairs of electrons between atoms

• Hydrogen bond- interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group

• Van der Waal force- Van der Waals forces include attractions between atoms, molecules, and surfaces, as well as other intermolecular forces

• Disulphide bond- a covalent bond, usually derived by the coupling of two thiol groups. The linkage is also called an SS-bond or disulfide bridge

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Cont..

• Covalent bond

• Hydrogen bond

• Van der waals force

• Disulphide bond

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Table 1-1, p. 4

Molecular Organisation of a cell

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Cells• Basic building blocks of life• Smallest living unit of an organism• Grow, reproduce, use energy, adapt, respond to their

environment• Many cannot be seen with the naked eye• A cell may be an entire organism or it may be one of billions

of cells that make up the organism

• Basis Types of Cells

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Fig. 1-11, p. 17

Table 1-3, p. 15

Characteristic Bio-membranes and Organelles

MitochondrionSurrounded by a double membrane with a series of foldscalled cristae. Functions in energy production through metabolism. Contains its own DNA, and is believed to have originated as a captured bacterium.

Plasma MembraneA lipid/protein/carbohydrate complex, providing a barrier and containing transport and signaling systems. NucleusDouble membrane surrounding the chromosomes and the nucleolus. Pores allow specific communication with the cytoplasm. The nucleolus is a site for synthesis of RNA making up the ribosome

Chloroplasts (plastids)Surrounded by a double membrane, containing stacked thylakoid membranes. Responsible for photosynthesis, the trapping of light energy for the synthesis of sugars. Contains DNA, and like mitochondria is believed to have originated as a captured bacterium.

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Rough endoplasmic reticulum (RER)A network of interconnected membranes forming channels within the cell. Covered with ribosomes (causing the "rough" appearance) which are in the process of synthesizing proteins for secretion or localization in membranes.RibosomesProtein and RNA complex responsible for protein synthesis

Smooth endoplasmic reticulum (SER)A network of interconnected membranes forming channels within the cell. A site for synthesis and metabolism of lipids. Also contains enzymes for detoxifying chemicals including drugs and pesticides.

Golgi apparatusA series of stacked membranes. Vesicles (small membrane surrounded bags) carry materials from the RER to the Golgi apparatus. Vesicles move between the stacks while the proteins are "processed" to a mature form. Vesicles then carry newly formed membrane and secreted proteins to their final destinations including secretion or membrane localization. Lysosymes

A membrane bound organelle that is responsible for degrading proteins and membranes in the cell, and also helps degrade materials ingested by the cell. 20

VacuolesMembrane surrounded "bags" that contain water and storage materials in plants.

Peroxisomes or MicrobodiesProduce and degrade hydrogen peroxide, a toxic compound that can be produced during metabolism.

Cell wallPlants have a rigid cell wall in addition to their cell membranes

Cytoplasmenclosed by the plasma membrane, liquid portion called cytosol and it houses the membranous organelles.

CytoskeletonArrays of protein filaments in the cytosol. Gives the cell its shape and provides basis for movement. E.g. microtubules and microfilaments.

http://www.biology.arizona.edu copyright © 1997 - 2004.. 21

22Biochemistry

Biolog. Nanostructures

Fig. 1-1, p. 2

Bio-molecules• Just like cells are building blocks of tissues likewise molecules

are building blocks of cells.

• Animal and plant cells contain approximately 10, 000 kinds of molecules (bio-molecules)

• Water constitutes 50-95% of cells content by weight.

• Ions like Na+, K+ and Ca+ may account for another 1%

• Almost all other kinds of bio-molecules are organic (C, H, N, O, P, S)

• Infinite variety of molecules contain C.

• Most bio-molecules considered to be derived from hydrocarbons.

• The chemical properties of organic bio-molecules are determined by their functional groups. Most bio-molecules have more than one. 24

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Biomolecules – Structure

• Building block• Simple sugar• Amino acid• Nucleotide• Fatty acid

• Macromolecule• Polysaccharide• Protein (peptide)• RNA or DNA• Lipid

Anabolic

Catabolic

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Linking MonomersCells link monomers by a

process called dehydration synthesis (removing a

molecule of water)

This process joins two sugar monomers to make a double

sugar

Remove H

Remove OH

H2O Forms

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Breaking Down Polymers• Cells break down

macromolecules by a process called hydrolysis (adding a molecule of water)

Water added to split a double sugar

Sugars

• Carbohydrates most abundant organic molecule found in nature.• Initially synthesized in plants from a complex series of reactions involving photosynthesis.• Basic unit is monosaccharides.• Monosaccharides can form larger molecules e.g.

glycogen, plant starch or cellulose.

Functions• Store energy in the form of starch (photosynthesis

in plants) or glycogen (in animals and humans).• Provide energy through metabolism pathways and

cycles.• Supply carbon for synthesis of other compounds.• Form structural components in cells and tissues.

• Intercellular communications 28

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Monosaccharides -Polysaccharides

Glycosidic bonds connecting glucose residues are in red

Glucose - Cellulose

Fatty acids - Lipids

• Are monocarboxylic acid contains even number C atoms

• Two types: saturated (C-C sb) and unsaturated (C-C db)

• Fatty acids are components of several lipid molecules.

• E,g. of lipids are triacylglycerol, steriods (cholestrol, sex hormones), fat soluble vitamins.

Functions• Storage of energy in the form of fat• Membrane structures• Insulation (thermal blanket)• Synthesis of hormones

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Triglyceride

Glycerol Fatty Acid Chains

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Structure of a biological membrane

• A lipid bilayer with associated proteins

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Steroids

•The carbon skeleton of steroids is bent to form 4 fused rings

Cholesterol is the “base steroid” from which your body produces other steroids

Estrogen & testosterone are also steroids

Cholesterol

TestosteroneEstrogen

Synthetic Anabolic Steroids are variants of testosterone

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Nucleic Acids

•Store hereditary information

Contain information for making all the body’s proteins

Two types exist --- DNA & RNA

Amino acids - Proteins:

• Amino acids: • Building blocks of proteins.

• R Group (side chains) determines the chemical properties of each amino acids.

• Also determines how the protein folds and its biological function.

• Functions as transport proteins, structural proteins, enzymes, antibodies, cell receptors.

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Proteins as Enzymes

• Many proteins act as biological catalysts or enzymes

Thousands of different enzymes exist in the bodyEnzymes control the rate of chemical reactions by weakening bonds, thus lowering the amount of activation energy needed for the reaction -> Catalysator

-> No not interfere with the equilibrium of reaction

-> Enzymes are reusable !!!!

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Macromolecules

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Macromolecules

Thank You

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