biochemistry is the study of organic chemistry, mainly the compounds known as carbohydrates, lipids,...
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THE CHEMISTRY OF LIFE
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THE CHEMISTRY OF LIFEBiochemistry is the study of organic chemistry, mainly the compounds known as carbohydrates, lipids, proteins, and nucleic acids.
All living things are made up of various chemical compounds.
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The Nature of MatterAtoms are the basic building blocks of matter
Elements are substances which are made of only one kind of atom
Compounds are a combination of two or more kinds of atoms in a defined proportion
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Structure of Atoms
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Structure of AtomsNucleus – made up of protons (+ charge, 1 atomic mass unit) and neutrons (no charge, 1 atomic mass unit) # of protons = # of neutrons
Electrons – orbit the nucleus (- charge, very little mass) determine the chemistry of atoms first energy level contains up to 2 electrons outside levels can hold up to 8 electrons when an electron orbital is full the atom is chemically inactive if orbital in not full the atom “looks” to
gain, lose, or share electrons with other atoms
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Structure of Atoms
http://www.classzone.com/cz/books/bio_09/resources/htmls/animated_biology/unit1/bio_ch02_0059_ab_atombond.html (Great Review of atoms and bonding!)
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Mass number & Atomic NumberAtomic number is equal to the number of protons
Mass number (atomic mass) is equal to the number of protons plus the number of neutrons
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Isotopes Atom of an elements that has a different number of neutrons from that of other atoms of the same element
Radioactive isotopes are unstable and break down at a constant rate over time (some can be used as tracers)
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Isotopes of Carbon
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Chemical Bonding Ionic bonds – Fig. 2-3 – form when atoms gain or lose electrons, become chemically charged and are attracted to each otherhttp://www.dnatube.com/video/366/Ionic-Bond
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Chemical Bonding Covalent bonds – Fig. 2-4 – formed when atoms share one or more pairs of electronshttp://www.dnatube.com/video/1290/Covalent-bond
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Chemical Bonding Van der Waals forces – Fig. 2-5 – a slight attraction that develops between the oppositely charged regions of nearby molecules
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Properties of WaterH2O – most important inorganic compound; All organisms need H2O to survive. Formed by polar covalent bonds between hydrogen & oxygen
inorganic – contains no carbon/hydrogen
bondsorganic – contains carbon
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Properties of WaterPolar Covalent Bonds are formed when partial positive (+) and partial negative (-) charges are formed as a result of unequal sharing of electrons
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Properties of WaterPolar Covalent Bonds are formed when partial positive (+) and partial negative (-) charges are formed as a result of unequal sharing of electrons
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Properties of Water – Hydrogen BondsHydrogen bonds are weak electrical attractions between the partial negative charge of one molecule and the partial positive charge of a different moleculehttp://www.youtube.com/watch?v=lkl5cbfqFRM
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Properties of Water Cohesion is the attraction of molecules of the same substance (Fig. 2-8). Because of cohesion of H2O molecules, H2O is able to store a lot of heat. This ability to store heat protects organisms from damaging changes in temperature
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Properties of Water Adhesion is the attraction between molecules of one substance and molecules of another substance; adhesion makes H2O one of the best solvents
http://www.youtube.com/watch?v=EBfGcTAJF4o&NR=1
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Solutions & SuspensionsMixtures of two or more elements or compounds that are
physically NOT chemically combined
Solution – mixtures in which the molecules of the substances are evenly distributed between the solvent and the solute
Suspension – mixture of water and nondissolved materials
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Acids, Bases, and pHpH is a measurement of the H+ concentration in a solution
Water (H2O) is a neutral molecule (neither acidic or basic) which will dissociate into and equal number of H+ and OH- and is the basis of pH comparison
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Acids, Bases, and pHpH is a measurement of the H+ concentration in a solution
The pH scale (Fig. 2-10)
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Acids, Bases, and pHpH is a measurement of the H+ concentration in a solution
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Acids, Bases, and pHpH is a measurement of the H+ concentration in a solution
•pH of water is 7•Acids have a greater [H+] than [OH-] pH is less than 7•Bases have a greater [OH-] than [H+] pH is greater than 7
•Buffers are weak acids or bases that can react with strong acids or bases to help prevent sharp sudden changes in pH (maintain homeostasis)
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Carbon Compounds Carbon compounds contain carbon and usually hydrogen; most occur naturally only in bodies & products of living things
Electron Structure of Carbon
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Characteristics of CarbonCarbon can bond with a variety of other elements
Carbon can bond to other carbon molecules (Fig. 2-11)
Carbon can form single, double or triple bonds
Carbon can be bonded into long chains, branches, or rings
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MacromoleculesDehydration synthesis – a reaction in which 2 molecules are bonded together by the removal of one H+ and one OH- to form H2O and another compound http://www.youtube.com/watch?v=b7TdWLNhMtM&NR=1
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MacromoleculesHydrolysis – a reaction in which a complex molecule is broken apart into simpler molecules by the addition of H2O
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CarbohydratesOrganic compounds of C, H, & O; ratio of H to O is always 2:1
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CarbohydratesOrganic compounds of C, H, & O; ratio of H to O is always 2:1
Function of Carbohydrates
Energy storage (Fig. 2-13) starch is stored form of sugar in plants glycogen is stored form of sugar in animals
Support cellulose is found in
plant cell walls chitin forms the
exoskeletons of
insects &arthropods
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LipidsOrganic compounds made up of C, H, & O, but much less O than
carbs.Structure of Lipids – Fats are made up of 1 glycerol and three fatty acids (Fig. 2-14)
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LipidsOrganic compounds made up of C, H, & O, but much less O than
carbs.Structure of Lipids – Phospholipids are the major
component of cell membranes (Fig. 7-12)
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LipidsOrganic compounds made up of C, H, & O, but much less O than
carbs.Lipids also serve as:
insulationenergy storageprotection – organs; waxy cuticle on the surface
of leaves
Lipids are non-polar – will not dissolve in water
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Nucleic AcidsDNA, RNA – compounds that contain phosphorus (P) and
nitrogen (N) in addition to C, H, & OStructure of DNA – double helix – Fig. 12-7Function of DNA – hereditary material, base pairs
act as a code that determines what proteinswill be made
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Nucleic AcidsDNA, RNA – compounds that contain phosphorus (P) and
nitrogen (N) in addition to C, H, & O
Structure of RNA – Fig. 12-12 – single chain of nucleic acids that are involved in protein synthesis
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Proteins Compounds that contain N as well as C, H, & O, some also
contain sulfur (S) and very small amounts of phosphorus (P)
StructureFig. 2-17
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Proteins Compounds that contain N as well as C, H, & O, some also
contain sulfur (S) and very small amounts of phosphorus (P)
FunctionStructural – cartilage, bone, muscle
Hormones – chemical messengers (ex. – insulin)
Antibodies – prevent disease
Enzymes – speed up reactions
Transport proteins are found in cell membranes
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Chemical Reactions & EnzymesChemical reactions involve the breaking of bonds in reactants and the formation of new bonds in products
Reactants – elements or compounds that enter into a reaction
Products – elements or compounds that are produced by a reaction
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Chemical Reactions & EnzymesEnergy in Reactions is either released or absorbed (Fig. 2-19)
Energy releasing reaction – the energy stored in the reactants is greater than the energy stored in the products (usually occurs spontaneously)
Energy absorbing reaction – the energy stored in the products is greater than the energy stored in the reactants (requires energy to initiate)
Activation energy – energy required to initiate a reaction
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Chemical Reactions & Enzymes
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Chemical Reactions & Enzymes
http://www.classzone.com/cz/books/bio_09/resources/htmls/animated_biology/unit1/bio_ch02_0052_ab_exoendo.html
This link is a great review of difference between exothermic and enothermic reactions
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Chemical Reactions & EnzymesEnzymes are protein catalysts that are necessary for most of the chemical reactions that occur in living cells
Catalyst – substance that brings about a reaction without being changed itself; can be re-used
Enzymes – lower the activation energy, energy needed to break bonds, therefore reactions can occur quickly and at normal body temps. (Fig. 2-20)
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Chemical Reactions & Enzymes
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Enzyme Actions – Fig. 2-21Substrate – substance that enzyme acts uponEnzymes are specific for their substrates
Active site – the region on the surface of an enzyme where substrate molecules attachhttp://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.html
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Chemical Reactions & EnzymesRegulation of Enzyme Activity
Only small amounts of enzymes are needed because each molecule is re-used
Temperature – most enzymes work best at normal body temperatures
pH – different enzymes work best at different ranges of pH
Concentration of substrate & enzyme determines reaction rate as long as both are freely accessible to each other (up to a certain point)