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CHEMISTRY FOR BIOLOGIST Relevance of Chemistry to biology “Natural Law” Living Things are made up of Non-Living Components To understand the way living things function, it is necessary to understand basic chemical processes BASIC CHEMISTRY Living things had same materials (C,H,O) as many non-living materials, but living material had a different organization 1821 Friedrich Wohler Inorganic NH4+NCO- Organic NH2CONH2 MATTER Matter is anything that occupies space and has mass Properties: Color, Texture, odor, Taste Lattice –Repeat Units Crystalline: regular Geometric shape Amorphous- shapeless chocolate glass soot Physical Chemical Changes: Physical – H20 3 phases(solid, liquid, and gas) Chemical- composition Altered CH4 CO2 + H20 Structure: Elements of Life Elements: made up of Atoms - 92 occur naturally H- hydrogen O- oxygen Cl- chloride Na- sodium (latin: natrium) K- potassium (latin: kalium) Fe- iron (latin: ferrum) 20 Essential for Life CHOPKINS CAFÉ MIGHTY GOOD TRACE ELEMENTS: Mn,Ca,Co,Zn,B, Mo, Cl, Si Six elements comprise 99% of Bacterial dry weight CHNOPS ATOMS Atoms: composed of subatomic particles proton (+), neutrons, and electrons(-) # protons = atomic number defines atoms C=6 N=7 protons + neutrons = atomic mass protons + neutrons = atomic weight (Daltons) C: 6+6=12 Isotopes Isotopes are different Forms of Elements: Atomic Number the same but Atomic Weights Different (Neutrons greater Than Protons) Hydrogen - 1 proton, 0 neutrons (Elemental State) Deuterium - 1 proton, 1 neutron (Stable isotope) Tritium -1 proton, 2 neutrons (Radioisotopes) Radioisotopes are unstable and will degrade naturally 14C 32P 35S 3H Electron Configuration Atoms also have Electrons, negatively charged subatomic particles Arrangement Two dimensionally vs 3-D 1st shell - 2 electrons 2nd Shell - 8 Electrons 3rd Shell - 8 Electrons 4th Shell - 18 Electrons Outer shell 8 electrons *** Octet Number of electrons in outer shell determines bonding properties chemical behavior Valence Electrons Element C H O N P S He Ca Na Cl # e6 1 8 7 15 16 2 20 11 17 shell # 2+4 1 2+6 2+5 2+8+5 2+8+8 2 2+8+8+2 2+8+1 2+8+7 valence +4/-4 +1 -2 -3/+5 -3 +2/-6 0 +2 +1 -1 Molecules Atoms with less than 8 e- in outer shell interact chemically or they BOND To form molecules The # and type of BONDS depends on # of electrons Atoms share/lose or gain to reach stable state Octet Rule –tendency of atoms to have 8 electrons in outer orbit (unless the atom is H or P) “FOOLS “ THE ATOM /THINKS CORRECT # e- for Stability 02 0:0 N2 N N H2 H:H Compounds: Atoms With more than one Element 2H+ + 0-2- H20 Types of Chemical Bonds Covalent Ionic Hydrogen Types of Chemical Bonds Covalent Bonds- Shared Bonds- STRONG Bonds Non-polar covalent Bonds - EQUAL SHARED ELECTRONS •Hydrophobic Bonds •van der Waals forces Polar Covalent Bonds - UNEQUAL SHARED ELECTRONS Hydrophilic bonds (likes water) Some atoms attract electrons more strongly Electronegativity Fl 0 N P 9p 8P 7P 15P 4.0 3.5 3.0 2.1 IONIC Bonds/Weaker than Covalent Bonds VASTLY Different Electro negativity ELECTRONS are COMPLETELY REMOVED ELECTRONS ARE TRANSFERRED FROM 1 ATOM TO ANOTHER NaCl placed in water Compound is dissociated when “hydrated” H20 + NaCl Na+1 + Cl-1 Ions (Ionization) Cation Na+1 Anion Cl-1 Electrolytes Opposites attract- Electrical Attraction Between atoms Common Ions Cations monovalent: Na+, K+, H+, NH4+ divalent: Ca2+, Mg2+, Fe2+ Anions Cl-, OH-, HC03-,N03CO32- S042P043- Hydrogen Bonds Hydrogen Bonds are much weaker bonds that form between molecules Rather than within a molecule, e.g. H20 Biological molecules depend on H-Bonding to give shape & function DNA Proteins Bonds are individually weak but collectively “Strong” H-Bonds gives water its important Properties •Elements •Atoms •Molecules •Compounds •Bonds •Covalent •Electronegative •Dipole Separation of partial Charges •Ionic •Hydrogen Chemical Reactions Making and Breaking Chemical Bonds Reactants Atoms/ions/molecules Products Atoms/ions/molecules Speed of Chemical Reactions depend on: • Reactants Concentration • Temperature • Random collisions Types of Chemical Reactions 1. Synthesis / DEHYDRATION 2. Decomposition / hydration ADDS WATER 3. Exchange Reactions Decomposition Chemical Reaction CATABOLISM Reverse of synthesis Exothermic- Release energy Break bonds of larger molecules to form smaller molecule Hydrolysis- Water added to reactant C12H22011 + H20 C6H1206 SUCROSE GLUCOSE + C6H1206 FRUCTOSE Synthesis ANABOLISM Dehydration Synthesis: Two small molecules are joined together by covalent bonds and a water molecule is formed Small-R-OH + H-R-Small-- large Molecule + H20 Energy input required: Endothermic Reactions OH- removed form one Reactant H- removed from another Reactant Catabolic /Hydrolysis Reactions Overall energy is released X-Y + H2O X-H + OH-Y Anabolic/Synthesis Reactions Overall energy consuming reactions X-H + OH-Y X-Y + HOH Exchange Reactions A + BC AB + C + CD AD + BC AB C6H1206 + Glucose A-P-P-P ATP C6H1206-P + A-P-P Glucose-6P ADP Sum of Catabolic + Anabolic Rxn = METABOLISM PROPERTIES OF WATER 1) Water has Thermal Stability (HIGH SPECIFIC HEAT) 2) The High Heat Capacity which causes Evaporative Cooling 3) Due to Polarity & COHESIONESS, Water is an Excellent Solvent for Polar Compounds 4)Water Molecules are attracted to each Other giving Cohesion and Adhesion-Surface Tension 5) Solid Water Floats?? Acids, Bases and pH H+ = Minus an electron is a Proton H20 ---------- H+ + OH- SOLUTIONS WITH > H+ THAN OH- (Hydroxyl) is Acidic SOLUTIONS WITH > 0H- THAN H+ is Basic ACID: HCL----- H+ COOH--- H+ BASE: NaOH--- Na+ NH2----- NH3+ + Cl+ COO+ OH- pH Scale Measures Whether Solution is Acidic, Basic or Neutral pH= -log[H+] Neutral is pH 7, or [H+] Concentration of 10-7 Higher [H+] gives lower pH value [H+] = 10-3, pH = 3 Acidic [H+] = 10-12, pH = 12 BUFFERS BUFFERS CONSIST OF AN ACID AND ITS CORRESPONDING BASE Buffers Minimize Changes in pH by Absorbing or releasing H+ K2HP04 + H+---------- KH2P04 KH2P04 + OH+---------- K2HP04 Organic Compounds Carbon Skelton: C-C-C Hydrocarbon – Saturated-All H’s HYDROPHOBIC/NON POLAR Function Groups Added-Unsaturated Hydrophilic Contains Electronegative Elements O/N/P/S Carbon Building block of life Component of every organism Component of daily diet, fuel, clothing 6 million cps/1000/yr new 250,00 inorganic cpds Organic cpds- C-C covalent bondingSTABLE Inorganic cpds NO C-C Ionic bonding UN-Stable Organic Chemistry Biochemistry Hydrocarbons Alcohol Aldehyde Ketone Organic acid Carbon dioxide Stoichiometry of REDOX Processes • Oxidation Level, OX, Imaginary Charge of an Element being stabilized in a molecule compared with corresponding low stability of the single atom • Major elements in OM: C, O, H, N, S • ED Not EA Valence Electron Orbit N=2n2 • shell: 2 • 2nd shell:8 • 3rd shell: 18 st 1 Atomic # 1 6 7 8 11 12 15 16 17 Element H C N O Na Mg P S Cl 1st 1 2 2 2 2 2 2 2 2 2nd 3r 4 5 6 8 8 8 8 8 1 2 5 6 7