biochemistry - institut teknologi...
TRANSCRIPT
What is Biochemistry?
• Biochemistry = chemistry of life.
• Biochemists use physical and chemical principles to explain biology at the molecular level.
• Basic principles of biochemistry are common to all living organism
How does biochemistry impact you?
• Medicine
• Agriculture
• Industrial applications
• Environmental applications
Principle Areas of Biochemistry
• Structure and function of biological macromolecules
• Metabolism – anabolic and catabolic processes.
• Molecular Genetics – How life is replicated. Regulation of protein synthesis
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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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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Nucleoid region contains the DNA •Cell membrane & cell wall • Contain ribosomes (no membrane) to make proteins in their cytoplasm
Contain 3 basic cell structures: • Nucleus • Cell Membrane • Cytoplasm with organelles
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Characteristic Bio-membranes and Organelles
Mitochondrion Surrounded by a double membrane with a series of folds called cristae. Functions in energy production through metabolism. Contains its own DNA, and is believed to have originated as a captured bacterium.
Plasma Membrane A lipid/protein/carbohydrate complex, providing a barrier and containing transport and signaling systems. Nucleus Double 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. Ribosomes Protein 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 apparatus A 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.
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Vacuoles Membrane surrounded "bags" that contain water and storage materials in plants.
Peroxisomes or Microbodies Produce and degrade hydrogen peroxide, a toxic compound that can be produced during metabolism.
Cell wall Plants have a rigid cell wall in addition to their cell membranes Cytoplasm enclosed by the plasma membrane, liquid portion called cytosol and it houses the membranous organelles.
Cytoskeleton Arrays of protein filaments in the cytosol. Gives the cell its shape and provides basis for movement. E.g. microtubules and microfilaments.
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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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How did organic complex molecules evolved from more simple molecules?
• Urea was synthesized by heating the inorganic compound ammonium cyanate (1828)
• This showed that compounds found exclusively in living organisms could be synthesized from common inorganic substances
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Many Important Biomolecules are Polymers
• Biopolymers - macromolecules created by joining many smaller organic molecules (monomers)
• Condensation reactions join monomers (H2O is removed in the process)
• Residue - each monomer in a chain
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Water • About 60-90 percent of an organism is water
Water is used in most reactions in the body Water is called the universal solvent
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.
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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 Monomers Cells 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
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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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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
Testosterone Estrogen
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 body
Enzymes 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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Enzymes:
• Active site - a cleft or groove in an enzyme that binds the substrates of a reaction
Egg white lysozyme
The nature and arrangement of amino acids in the active site make it specific for only one type of substrate. (accepts just one enaniomer)
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Concepts of Life
Life is characterized by
• Biological diversity: lichen, microbes, jellyfish, sequoias, hummingbirds, manta rays, gila monsters, & you
• Chemical unity: living systems (on earth)
obey the rules of physical and organic chemistry – there are no new principles
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The Energetics of Life
• Photosynthetic organisms capture sunlight energy and use it to synthesize organic compounds
• Organic compounds provide energy for all organisms
Using toxic O2 to generate energy
2 H2O à O2 + 4e- + 4H+ (photosynthesis)
Glucose + 6O2 à 6CO2 + 6H2O + Energy
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Life needs (3) CHEMICAL MECHANISMS, to:
• Harness energy • Drive sequential chemical reactions • Synthesize & degrade macromolecules • Maintain a dynamic steady state • Self-assemble complex structures • Replicate accurately & efficiently • Maintain biochemical “order” vs outside
Chemical reaction types encountered in biochemical processes
1. Nucleophilic Substitution • One atom of group substituted for another
2. Elimination Reactions • Double bond is formed when atoms in a molecule is removed
3. Addition Reactions: • Two molecules combine to form a single product. • A. Hydration Reactions • Water added to alkene > alcohol (common addition pathway)
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4. Isomerization Reactions. • Involve intramolecular shift of atoms or groups
5. Oxidation-Reduction (redox) Reactions • Occur when there is a transfer of e- from a donor to
an electron acceptor
6. Hydrolysis reactions • Cleavage of double bond by water.
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Biochemical Reactions • Metabolism: total sum of the chemical reaction happening in a
living organism (highly coordinated and purposeful activity) a. Anabolism- energy requiring biosynthetic pathways b. Catabolism- degradation of fuel molecules and the production of
energy for cellular function
• All reactions are catalyzed by enzymes
• The primary functions of metabolism are: a. acquisition & utilization of energy b. Synthesis of molecules needed for cell structure and functioning (i.e. proteins, nucleic acids, lipids, & CHO c. Removal of waste products
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Even though thousands of pathways sound very large and complex in a tiny cell:
• The types of pathways are small
• Mechanisms of biochemical pathways are simple
• Reactions of central importance (for energy production & synthesis and degradation of major cell components) are relatively few in number
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Energy for Cells
• Living cells are inherently unstable.
• Constant flow of energy prevents them from becoming disorganized.
• Cells obtains energy mainly by the oxidation of bio-molecules (e- transferred from 1 molecule to another and in doing so they lose energy)
• This energy captured by cells & used to maintain highly organized cellular structure and functions
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ENVIRONMENTAL BIOCHEMISTRY
METABOLIC RESPONCES TO THE ENVIRONMENTAL FACTORS AND THE LIMITS OF CHANGES THERE OF,LEADING TO ADAPTATION.
EFFECTS OF VARIATION IN ATMOSPHERIC TEMPERATURE & CHEMICAL STRESS IN FORM OF AIR, WATER AND FOOD POLLUTION.
ALTERATION IN ATMOSPHERIC TEMPERATURE
EXPOSURE TO COLD STRESS
TYPES OF INJURY: LOCAL(FROSTBITE) & GENERAL(HYPOTHERMIA)
COMPENSATORY MECHANISM
1. SHIVERING PHASE (INVOLVEMENT OF SKELETAL MUSCLE)
2. NON SHIVERING PHASE (NON SHIVERING THERMOGENESIS OR CHEMICAL THERMOGENESIS)
~NUTRITIONAL MODIFICATION
INCREASED COMBUSTION,RISE IN TYROSINE TRANSAMINASE & TRYPTOPHANPYRROLASE ALSO INCREASE IN ARGINASE.
~LIPID METABOLISM
DECREASE IN TOTAL FFA,ROLE OF BROWN ADIPOSE TISSUE
~CALORIGENIC SHUNT
INCREASED GLYCOLYSIS,GLUCONEOGENESIS,ROLE OF ETC.
~HORMONAL EFFECT
ROLE OF THYROID HOMONE
EXPOSURE TO HEAT
HEAT BALANCE & HEAT STRESS (MUST BE DISSIPATED)
VARIOUS FACTOR EFFECTING IT.
EFFECTS OF HEAT STRESS
~HEAT STROKE
~HEAT HYPERPYREXIA
~HEAT EXHAUSTION
~HEAT SYNCOPE
CHEMICAL STRESS AND POLLUTION
AIR POLLUTION
1.POLLUTANTS & CONTAMINANTS
2.SOURCE
INDUSTRIAL
COMBUSTION
MOTOR VEHICLE
MISCELLANEOUS
3.INDICATORS
SULPHURDIOXIDE
SMOKE INDEX
SUSPENDED PARTICLES
HEALTH EFFECTS OF AIR POLLUTION
1. OXIDES OF SULPHUR INJURY TO RESPIRATORY SYSTEM
DAMAGE TO LUNG TISSUE
2. OXIDES OF CARBON
CO2 ADAPTATION:CHANGE IN ACID BASE EQUILIBRIUM
CO TOXICITY: HYPOXIA,REACTION WITH Hb.
3. PHOTOCHEMICAL OXIDANTS
SECONDARY PRODUCTS OF NITROGEN OXIDE
EYE AND LUNG IRRITATION , ASTHMA
4. PARTICULATES
PULMONARY ABNORMALITIES
SIDEROSIS(IRON) ASBESTOSIS(ASBESTOS)
ANTHRACOSIS(SOOT) BYSSINOSIS(COTTON DUST)
SILICOSIS(SILICA) BAGASSOSIS(SUGARCANE,RICE)
1.ORGANIC POLLUTANTS
a. SEWAGE,WASTE FROM TANNRIES,PAPER MILLS, FOOD
PROSSESING INDUSTRIES.
DECREASE DISSOLVED OXYGEN
PATHOGENIC MICROORGANISM , EUTROFICATION
b. SYNTHETIC ORGANIC CHEMICALS
( PLASTIC,PAINTS,PHARMA WASTE)
c. PESTICIDES
CLASSIFICATION
~CHLORINATED HYDROCARBON
(DDT,ALDRIN,DIELDRIN) ENTERS FOOD CHAIN
~CHLOROPHENOXY ACID
(ATRAZINE 2,4-‐D)
~ORGANOPHOSPHORUS
( MALATHIONE,DIAZINONE) NEUROTOXIC,INHIBITOR
OF CHOLINESTERASE .
2.INORGANIC POLLUTANTS
HEAVY METAL POLLUTANTS
~ENTER INTO FOOD CHAIN
~AFFINITY FOR SULPHUR;ATTACK SULPHUR BONDS IN ENZYMES
~OTHER VULNARABLE SITES ARE COOH OF PROTEIN ALSO BIND TO CELL
MEMBRANE.
A. ORGANIC MERCURIAL: INCECTISIDES & BACTERICIDES, NEUROLOGICAL
DISORDERS
B. CADMIUM: UNCOUPLER OF OXIDATIVE PHOSPHORYLATION
C. BERYLLIUM :PHOSPHATE INHIBITOR
D.STRONTIUM :COMPETITOR FOR CALCIUM IN BONE
E. LEAD
~GUIDELINES ON PREVENTING LEAD POISONING BY US CDC.
~ANY CHILDREN UNDER 6 YEARS OF AGE WITH BLOOD LEAD
LEVEL <10 μg/dl
~IN ADULTS ITS < 60 μg/dl
~SOURCE -‐-‐ UBIQUITOUS IN ENVIRONMENT (PAINTS & TETRAETHYL
LEAD)
~CLINICAL FEATURES
IN CHILDREN IS MENTAL RETARDATION,SLOW LEARNING,
BEHAVIOURAL CHANGES, LOSS OF 4-‐5 IQ POINTS FOR EACH
10 μg/dl OF BLOOD LEAD
IN ADULTS MENIFESTATIONS ARE NEUROPATHY
ENCEPHALOPATHY , ABDOMINAL PAIN & SEVERE ANEMIA.
~LEAD INHIBIT
ALA-‐SYNTHASE, ALA DEHYDRATASE, FERRO CHELATASE
F. ARSENIC
SOURCE : FRUIT SPRAYS , RAT POISON , PESTICIDES ETC.
TOXIC EFFECTS: DIZZINESS CHILLS CRAMPS & PARALYSIS
INHIBIT SH ENZYME INTERFERES WITH CELLULAR METABOLISM
ALSO CAUSES INTRAVASCULAR HEMOLYSIS.
FOOD POLLUTION
I. PROCESSING OF FOOD
• PRE PACKAGING -‐-‐ CONTAMINATION BY salmonella & staphylococcus aureus.
• PACKING – BOTULISM
• FOOD ADDITIVES – ANILINE , CYLAMATE , MONOSODIUM GLUTAMATE
II. NATURAL TOXIN
• LATHYRISM—NEUROTOXIN PRODUCE BY Lathyrus sa*vum
• FAVISM—IN G6PD DEFICIENT INDIVIDUALS
• ALKALOIDS—MUSCARINE IN MUSHROOMS
• GOITROGENS—THIOOXAZOLIDON DERIVATIVES (CABBAGE,TURNIP)
THIOCYANATES & ISOTHIOCYANATES (RAPESEEDS,MUSTARD)
III.STORAGE CONTAMINATION
FUNGAL GROWTH IN MOIST CONDITION
~AFLATOXIN,ERGOTOXIN
IV.ADULTRATION OF FOOD
~EPIDEMIC DROPSY
~ENDEMIC ASCITES
SUMMARY OF THE CHAPTER
ENVIRONMENTAL BIOCHEMISTRY
ALTERATION IN CHEMICAL STRESS & POLLUTION ATMOSPHERIC TEMPERATURE AIR WATER FOOD ~COLD STRESS ~SOURCES FACTORS ~HEAT STRESS ~INDICATORS ~PROCESSING ~HEALTH EFFECT ~NATURAL TOXINS ~OTHER EFFECT ~DURING STORAGE ACID RAIN ~ADULTERATION GREENHOUSE EFFECT GLOBAL WARMING ~SOURCE ~ORGANIC ~INORGANIC HEAVY METAL(LEAD,ARSENIC) ~OTHERS