Lecture 3: The Chemistry of Life PDF

Lecture 3: The Chemistry of Life  Today Elements and atoms – Radioisotopes – Electron shell models Chemical bonds Properties of water Acids and bases Introduction to organic molecules  Chemical Elements Elements – Consist only...

Lecture 3: The Chemistry of Life  Today Elements and atoms – Radioisotopes – Electron shell models Chemical bonds Properties of water Acids and bases Introduction to organic molecules  Chemical Elements Elements – Consist only of a single substance (type of atom) – 94 elements occur naturally on Earth – Mix and match to form all ordinary matter  Chemical Elements  What are the most common elements in living organisms?  Chemical Elements Different materials consist of different types and proportions of elements Human Earth’s Crust Ocean Oxygen 61.0% Oxygen 46.0% Oxygen 85.7% Carbon 23.0 Silicon 27.0 Hydrogen 10.8 Hydrogen 10.0 Aluminum 8.2 Chlorine 2.0 Nitrogen 2.6 Iron 6.3 Sodium 1.1 Calcium 1.4 Calcium 5.0 Magnesium 0.1 Phosphorus 1.1 Magnesium 2.9 Sulfur 0.1 Potassium 0.2 Sodium 2.3 Calcium 0.04 Sulfur 0.2 Potassium 1.5 Potassium 0.03  Atoms Atoms – smallest particles that retain properties of an element Consist of subatomic particles – Protons (+) Nucleus – Neutrons (zero charge) 0 0 – Electrons (–)  Atoms Properties of atoms – Atomic number = number of protons – All atoms of an element have the same atomic number  Atoms Properties of atoms – Mass number = number of protons + number of neutrons – Isotopes vary in mass number (but not atomic number) Carbon-12 Carbon-13 Carbon-14 6 protons 6 protons 6 protons 6 neutrons 7 neutrons 8 neutrons 98.9% 1.1% < 0.1%  Atoms Radioisotopes – Unstable nucleus that emits energy and particles – Radioactive decay transforms radioisotope into different element, at a fixed rate  Atoms Radioisotopes – Unstable nucleus that emits energy and particles – Radioactive decay transforms radioisotope into different element, at a fixed rate  Atoms Uses of radioisotopes: – Dating of rocks and fossils – Tracers – Cancer treatment  Atoms Electrons – Negatively charged – Repel one another – Attracted to protons → Orbit around the nucleus – In a neutral atom, # p = # e  Atoms Electron shells – Orbitals of different energy levels – Hold a certain number of electrons – Shells closer to nucleus are lower energy, and filled first 1st shell: 2nd shell: Up to 2 Up to 8 electrons electrons  Atoms Electron shells – Periodic table row = number of shells – Periodic table column = number of electrons in outer shell H He Bulk elements Li Be Trace elements B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe  Draw shell models of lithium (Li) and carbon (C).  Atoms Electron shells – Full shells are stable – Unfilled outer shells react with shells of other atoms  Which of these atoms are likely to gain or lose electrons? Why?  Atoms electron loss Electron shells 11 11 – Left side of periodic table: Atoms tend to lose electrons, Sodium atom Sodium ion 11 p + 11 p + forming positively charged ion 11 e – 10 e – charge: 0 charge: +1 electron gain – Right side of periodic table: Atoms tend to gain electrons, 17 17 forming negatively charged ion Chlorine atom Chloride ion 17p + 17p + 17e – 18e – charge: 0 charge: -1  Atoms Electron shells – Periodic table tells you how elements will behave!  Chemical Bonds Chemical bond – union between electron structures of atoms Molecule – two or more atoms joined together Chemical formula H2O  Chemical Bonds Chemical reaction – breaking/reforming of bonds in molecules  Which biologically important reaction is this?  Count the numbers of atoms of each element on both sides of the equation.  Types of Chemical Bonds Ionic bonds – Attraction between positive ion and negative ion NaCl, sodium chloride (table salt)  Types of Chemical Bonds Covalent bonds – Atoms share a pair or pairs of electrons to fill outer shells Nonpolar – electrons Polar – electrons pulled more shared equally towards one atom – e H H  Why? e + +  Types of Chemical Bonds Hydrogen bonds – Weak attraction between polar regions of molecules Water: positive H poles attracted to negative O poles  Types of Chemical Bonds Hydrogen bonds – Weak attraction between polar regions of molecules  Properties of Water Water is fundamentally important to life Special properties: – Polarity – Solvent – Temperature stability – Cohesion  Properties of Water Polarity – Water molecules formed by polar covalent bonds – Polarity is attractive to other polar molecules What is this called?  Properties of Water Polarity – Determines how other substances will interact with water – Hydrophilic substances – Hydrophobic substances Polar Nonpolar Form hydrogen bonds Repelled by water with water  Examples?  Examples?  Properties of Water Water is a good solvent – A liquid that dissolves other substances (solutes) – Ions dissolve easily in water, because water molecules surround them  Properties of Water Water is a good solvent – Polar molecules also dissolve easily  Properties of Water Water stabilizes temperature – Temperature = movement energy of molecules – Liquid water can absorb a lot of heat without changing temperature  Why?  Properties of Water Water stabilizes temperature – Energy input breaks hydrogen bonds → evaporation – Energy loss causes hydrogen bonds to lock into a lattice → ice formation Some molecules too Too energized to bond All molecules bonded close to bond  Properties of Water Evaporation Water cohesion from leaves – Water molecules resist separation Why? Water pulled into roots Surface tension Capillary action  Acids and Bases Water molecules can separate into hydrogen (H+) and hydroxide (OH–) ions pH – measure of the concentration of H+ in a solution – Negative relationship – more H+ ions means a lower pH – Order of magnitude scale (1 = 10X)  Acids and Bases Pure water has a pH of 7 Acids – Donate H+ when dissolved in water – Acidic solutions have pH < 7 Bases – Accept H+ or release OH– when dissolved in water – Basic solutions have pH > 7 Lower pH More H+ pH Scale Acidic pH 7 Neutral Higher pH Less H+ Basic  Acids and Bases Buffers – Set of chemicals that help stabilize pH – A weak acid and a weak base work as a pair – Alternately accept or release H+ to counter external shifts in pH  Acids and Bases Buffers – Example: bicarbonate buffer system in human blood If pH rises, carbonic acid dissociates into bicarbonate and H+ If pH lowers, bicarbonate binds H+ to form carbonic acid H+ + HCO3– ↔ H2CO3  Why are buffers important to a living organism?  Organic Molecules Organic compounds: – Carbon-based – With hydrogen and others covalently bonded – Essential molecules of life Carbohydrates Lipids Proteins Nucleic acids  Organic Molecules Living things are based on carbon  Why? Element Human Hydrogen 62% Mostly water Oxygen 24% Carbon 12% Most of the rest! Nitrogen 1.2% Phosphorus 0.2% Calcium