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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 andmolecular level.
It emerged as a distinct discipline around thebeginning of the 20th century when scientistscombined chemistry, physiology and biology toinvestigate 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 andwhole organism
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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 maintainthe 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 foreach 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 DNACell membrane & cell wall Contain ribosomes (no membrane)to make proteins intheir cytoplasm
Contain 3 basic cell structures: Nucleus Cell Membrane Cytoplasm with organelles
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Two Main Types of Eukaryotic Cells
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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 acaptured bacterium.
Plasma Membrane A lipid/protein/carbohydrate complex, providing a barrier andcontaining transport and signaling systems.
Nucleus Double membrane surrounding the chromosomes and the nucleolus.Pores allow specific communication with the cytoplasm. Thenucleolus is a site for synthesis of RNA making up the ribosome
Chloroplasts (plastids) Surrounded by a double membrane, containing stacked thylakoidmembranes. Responsible for photosynthesis, the trapping of lightenergy for the synthesis of sugars. Contains DNA, and likemitochondria is believed to have originated as a capturedbacterium.
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.
Rough endoplasmic reticulum (RER) A network of interconnected membranes forming channels within thecell. Covered with ribosomes (causing the "rough" appearance) whichare 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 containsenzymes for detoxifying chemicals including drugs and pesticides .
Golgi apparatus A series of stacked membranes. Vesicles (small membranesurrounded bags) carry materials from the RER to the Golgiapparatus. Vesicles move between the stacks while the proteins are"processed" to a mature form. Vesicles then carry newly formedmembrane and secreted proteins to their final destinations includingsecretion or membrane localization.
Lysosymes A membrane bound organelle that is responsible for degradingproteins and membranes in the cell, and also helps degrade materialsingested by the cell. 8
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Vacuoles Membrane surrounded "bags" that contain water and storagematerials in plants .
Peroxisomes or Microbodies Produce and degrade hydrogen peroxide, a toxiccompound 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 cytosoland it houses the membranous organelles.
CytoskeletonArrays of protein filaments in the cytosol. Gives the cell itsshape and provides basis for movement.E.g. microtubules and microfilaments.
http://www.biology.arizona.edu copyright 1997 - 2004. . 9
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10Biochemistry
Biolog. Nanostructures
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Biochemical Evolution
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CH 4, H 2O, NH 3, HCN
How did organic complex molecules evolved frommore simple molecules?
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How did organic complex molecules evolvedfrom more simple molecules?
Urea was synthesized by heating the inorganiccompound ammonium cyanate (1828)
This showed that compounds found exclusively in livingorganisms could be synthesized from common inorganicsubstances
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The Urey-Miller experiment (1950)
Some amino acids could be produced:
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Many Important Biomoleculesare Polymers
Biopolymers - macromolecules created by joining manysmaller 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 percentof an organism is water
Water is used inmost reactions inthe body
Water is calledthe universalsolvent
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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 monomersto make a double sugar
Remove
H
Remove OH
H2O Forms
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Breaking Down Polymers Cells break down
macromolecules bya process calledhydrolysis (addinga molecule ofwater)
Water added to split a double sugar
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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.
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Monosaccharides -Polysaccharides
Glycosidic bonds connectingglucose residues are in red
Glucose - Cellulose
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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, sexhormones), 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 ofsteroids is bent to form4 fused rings
Cholesterol is the
base steroid fromwhich your bodyproduces othersteroids
Estrogen &testosterone are alsosteroids
Cholesterol
TestosteroneEstrogen
Synthetic Anabolic Steroids are variants of testosterone
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Nucleic Acids
Store hereditary informationContain information for making all thebodys proteins
Two types exist --- DNA & RNA
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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 byweakening bonds, thus lowering the amount ofactivation 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
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Concepts of LifeLife is characterized by
Biological diversity: lichen, microbes, jellyfish, sequoias, hummingbirds, mantarays, gila monsters, & you
Chemical unity: living systems (on earth)obey the rules of physical and organicchemistry there are no new principles
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Life needs 3 things :
(1) ENERGY , which it mustknow how to:
Extract Transform Utilize
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The Energetics of Life
Photosyntheticorganisms capturesunlight energy and useit to synthesize organiccompounds
Organic compoundsprovide energy for allorganisms
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Glycolysis: the preferred way for theformation of ATP
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Life needs (2) SIMPLE MOLECULES ,which it must know how to:
Convert Polymerize Degrade
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Life needs (3) CHEMICALMECHANISMS , 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
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Trick #1: Life uses chemical coupling todrive otherwise unfavorable reactions
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Trick #2: Life uses enzymes to speed upotherwise slow reactions
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How does an enzyme do it,thermodynamically?
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How does an enzyme do it,mechanistically?
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Chemical reaction types encountered inbiochemical 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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Summary of Key Concepts
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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 pathwaysb. 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 energyb. Synthesis of molecules needed for cell structure and
functioning (i.e. proteins, nucleic acids, lipids, & CHOc. Removal of waste products
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Even though thousands of pathways sound verylarge and complex in a tiny cell:
The types of pathways are small
Mechanisms of biochemical pathways are simple
Reactions of central importance (for energyproduction & synthesis and degradation of major cellcomponents) 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 anotherand in doing so they lose energy)
This energy captured by cells & used to maintain
highly organized cellular structure and functions
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