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Unformatted text preview: Chapter 2: The Chemistry of Life
Bonnie S. Gunn Lecturer UTPA Definitions Matter Definition States of matter Forms of Energy Chemical Electrical Mechanical Radiant (electromagnetic) Can be converted from Can be converted from one form to another
ATP (adenosine triphosphate) ATP (adenosine triphosphate) Energy Definition Types of energy Potential Kinetic Elements Periodic table Atoms Composition of matter Smallest particle of an element that has the properties of the element Atomic symbol Nucleus Protons (positive charge, 1 amu) Neutrons (no charge, 1 amu) Electrons (negative charge, 0 amu) orbit the nucleus Planetary versus orbital model Different numbers of protons, neutrons, and electrons Atomic number: the number of protons in the nucleus (1H), (2He), etc. Mass number: mass of all protons and neutrons (# of amu); He 2+2 = 4 Isotopes: two or more atomic variants vary in mass number Have the same number of protons and electrons but differ in number of neutrons Identifying Elements Atom structure and isotopes Common elements of the Human body
CHON 4 most common CaPPS Last 4 2nd P for potassium (K) Atoms and isotopes Atomic weight: The average of the relative weights (mass numbers) of all the isotopes of an element, accounting for their abundance in nature. Radioisotopes: Process of atomic decay Can be detected using scanners so are useful in medicine and research Halflife: time a radioisotope takes to lose half its energy Molecules and mixtures Molecule: two or more atoms held together by chemical bonds If they are the same kind it is a simple molecule (molecule of that atom) Compound: two or more atoms (of different kinds) held together by chemical bonds A molecule is the smallest particle of a compound that still has the characteristics of the compound Mixtures Two or more components that are physically intermixed Solutions Homogeneous mixtures of components (liquid, solid, gas) Solutes (component in smaller amount) Solvents (dissolving medium) Heterogeneous mixtures with large solute particles Sol gel transformation (fluid to solid state) Colloids (emulsions) Suspensions Heterogeneous mixtures with solutes that settle out Solution Concentration Described as a % of the solute (e.g. 20% solution) Molarity Moles per liter Mole: is the sum of the atomic weight (molecular weight) measured in grams (gram molecular weight) Glucose: C6H12O6 C H O
Atom # 6 12 6 x x x Atomic Weight 12.011 1.008 15.999 = = = Total Total weight 72.066 12.096 95.994 180.156 A one molar solution Glucose: C6H12O6 Atom C H O # 6 12 6 Atomic Weight 12.011 1.008 15.999 Total weight 72.066 12.096 95.994 180.156 x x x = = = Total Measure 180.156 grams of glucose and ADD enough water to make one Liter of solution (1000 ml) Thus Molarity is measured in moles/Liter. Abbreviation: 1.0 M Why be so complex? Precision!!! 1.0 M solution of ANY substance contains EXACTLY the same number of solute particles 6.02 X 1023 solute particles Called Avogardo's number Mixtures versus compounds Mixtures No chemical bonds Can be strained, filtered, evaporated to separate compounds Homogeneous or heterogeneous Compounds Chemical bonds Break bonds to separate Homogeneous What is a chemical bond? An energy relationship between electrons of 2 atoms Electron shells Region of space around the nucleus of the atom Concentric rings There are 7 known Outermost shell termed the Valence shell 1 with 2 electrons 6 with 8 electrons Energy shells Each shell is a different energy level If the energy shell is full, the element is Potential energy depends on which shell the electron is in chemically inert Noble gases (ex. He, Ne) Beyond the second shell, atoms can carry more than 8 electrons per shell, but only are reactive with 8 of these electrons (octet rule) Chemically active elements Types of chemical bonds Ionic Covalent Hydrogen Ionic bonds Ionic Atoms can transfer electrons Anion: electron acceptor Cation: electron donor charge + charge Opposites attract: ions stay close together, forming the bond Most are salts, that form crystals (like NaCl) Ionic bondattraction of these ions to each other Covalent bonds Atoms share electrons, having an orbit common to both atoms Each atom has its outer shell filled atleast part of the time Multiple covalent bonds Atoms can share more than a single electron pair, forming double or triple bonds Polar and nonpolar molecules Molecules can be balanced (Nonpolar) Molecules can be unbalanced (polar) Electrons shared evenly Nonsymetrical particles Atoms have different abilities to attract electrons Electronegativity What is it? What causes it? Comparisons of ionic and covalent bonds Hydrogen bonding Due to polarity of molecules Weak bonds formed between hydrogen and another atom Important as intramolecular bonds, giving shape and stability to proteins and other biomolecules Surface tension of water Chemical Equations Represent chemical reactions Reactants yields products i.e. C6H12O6 + 6 O2 6 CO2 + 6 H2O + ATP When chemical bonds are formed, rearranged, or broken Solid vs liquid vs gas (Why do these reactions happen faster in a gas? Chemical reactions Anabolic Synthesis (or combination) reaction Catabolic Decomposition reaction Exchange (displacement) reactions Bonds both synthesized and broken Parts exchanged between molecules, forming new molecules Oxidationreduction reactions (Redox) Used in the production of ATP Losing electrons (electron donor): Oxidized Gaining electrons (electron acceptor): Reduced
C6H12O6 + 6 O2 6 CO2 + 6 H2O + ATP Energy flow of reactions Endergonic Exergonic Chemical equalibrium Factors influencing the rate of chemical reactions Temperature (why?) Particle size (why?) Catalysts Concentration (why?) Increase the rate of reactions without becoming biologically changed themselves Enzymes (The study of the chemical composition and reactions of living matter) Inorganic compounds: Biochemistry Organic compounds: Do not contain carbon Water, salt, acids, bases, etc Contain carbon Covalently bonded Often large Proteins, lipids, etc. BOTH are important! 6080% of the volume of cells Numerous properties Inorganic compounds and the importance of water High heat capacity High heat of vaporization Polar solvent properties Reactivity (hydrolysis, dehydration synthesis) Cushioning Salts An ionic compound with cations other than H+ and an ions other than OH Na+, K+, Cl Dissociate into ions when in water An ion is a charged particle (often in solution) All ions are electrolytes they conduct an electrical current in solution Acids Have a sour taste Proton donors A substance that releases hydrogen: H+ When dissolved in water acids release the proton (hydrogen) and an Anion i.e. HCl H+ + Cl The anion causes the acidity H is written first in the molecular formula! Bases Bitter taste Proton acceptors A substance that accepts hydrogen: H+ When dissolved in water they release hydroxyl ions and an Cation i.e. NaOH Na+ + OH The cation causes the base The pH scale Neutralization Why Mix Acids and Bases? HCl + NaOH H+ + Cl + Na+ + OH Get neutral products!! NaCl + H2O Buffers Buffers keep the body from having large, rapidly occurring changes in pH Complex system of strong and weak acids and bases exchanging ions Essentially, change in pH not as extreme i.e. carbonic acidbicarbonate system with buffer than without Organic compounds What is so special about Carbon (C)? Valence shell has 4 electrons Polymers are formed from monomers Isommers have the same molecular Electroneutral: never gains or loses electrons Can form single, double, triple, or quadruple covalent bonds Can form long chains, rings, and complex forms necessary for biological structures formula but are arranged differently Carbohydrates Sugars Monosaccharides Disaccharides Polysaccarides Lipids Fats Neutral fats: triglygerides (saturated, unsaturated) Other lipids: phospholipids Phospholipids: modified triglycerides two fatty acid chains and a phosphorus group These have polar and nonpolar sections Other lipids: Steroids Flat molecules with interlocking rings Cholesterol Hydrocortisone Testosterone Estrogen Other lipids: Eicosanoids Derived from 20C fatty acid (arachidonic acid) Prostaglandins Blood clotting Inflammation Labor contrations Proteins 1030% of cell mass Structural and biochemical properties Derived from amino acids Linkage of amino acids and peptide bonds 20 common types of amino acids Amine (NH2)and an organic acid group ( COOH) Linked by dehydration synthesis CN linkage created termed a peptide bond (strong) How many proteins can be formed from 20 molecules? 20! = 243,290,008,176,640,000 types Yes, that is quadrillion... What about their shape? Alpha helix Beta pleated sheet Combined forms? Structural levels of proteins Primary Secondary Tertiary and sequence of aa Quaternary globular molecule two or more chains What difference does and folding make? Glucose molecules stored by plants folding: starch Ex. Potato Ex. Celery folding: cellulose Fibrous versus globular proteins Fibrous (structural) Collagen Globular (functional) Chemically active and functional in numerous processes Protein denaturation Globular proteins are unstable, due to reliance on hydrogen bonding. Heat breaks hydrogen bonds, changing the 3D (three dimensional) shape of the protein Molecular chaperones Globular proteins Help proteins achieve their functional 3 dimensional shape Some proteins are enzymes Enzymes globular proteins catalyze reactions (up to 1,000,000 X increase in speed!) specific Act on substrate (reactant in an enzymatic reaction) Holoenzymes (2 parts) Two parts Most Apoenzyme (protein) Cofactor If from a vitamin, it is termed a coenzyme Enzyme Action Energy of activation (EA) amount of energy required to start (prime) the reaction Effect of enzymes 3 steps for enzyme activity Nucleic Acids (DNA and RNA) DNA: Deoxyribonucleic acid RNA: Ribonucleic acid Double stranded, nucleus Encodes the information necessary for life Genetic information Single stranded, cytoplasm Five nucleotides Adenine: purine Thymine: pyramidine in DNA Guanine: purine Cytosine: pyramidine The structure of DNA The macrostructure of DNA Adenine:Thymine Guanine:Cytosine 2 hydrogen bonds 3 hydrogen bonds Double helix Phosphate sugar backbone Adenosine Triphosphate (ATP) The molecule responsible for providing energy within cells "energy currency of the cell Adenosine + sugar + phosphate Breaking phosphate bond by hydrolysis releases energy What can ATP be used for? H2O ATP ADP + iP + energy H2O The End ...
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