Understanding Atoms: The Building Blocks of Matter and Life

1. The Chemistry of Life Chapter 2

2. Atoms • The study of chemistry begins with this basic unit of matter • Comes from the Greek atomos = “unable to cut”

3. Protons • Same mass as a neutron • Positively charged particles • Found in nucleus (center of atom) • The # of protons determine the element

4. Neutrons • Same mass as a proton • Neutral charge • Found in nucleus • The # of neutrons determine the isotope

5. Electron • Negatively charged particle • 1/1840 the mass of a proton • Constantly in motion in shells surrounding the nucleus • Attracted to positive protons, but stay outside of the nucleus due to their energy • The # of electrons determine the charge

7. Element • A pure substance that consists entirely of one type of atom • Represented by one or two letter symbols • Atomic Number – the number of protons; unique to each element

8. Isotopes • Isotopes – atoms of the same element that have different numbers of neutrons (ex: Carbon-12; Carbon-13; Carbon-14 pg. 36) • Radioactive Isotopes – isotopes whose nuclei are unstable and break down at a constant rate over time

9. Element • Mass number – the sum of protons and neutrons (daltons) • Atomic Mass – the “weighted” avg. of the masses of an element’s isotopes; units are Atomic Mass Unit (amu)

10. Compounds • A substance formed by the chemical combination of two or more elements in definite proportions • Shorthand through the chemical formula; H2O, NaCl • The chemical and physical properties of compounds are usually very diff than the individual elements’ properties

11. Chemical bond • What holds compounds and molecules together • Covalent Bond; Ionic Bond; Hydrogen Bond • Van der Waals Forces

12. Covalent Bond • Forms when electrons are shared between atoms • The moving electrons are located in a region bt the atoms where the orbitals of the atoms overlap • Sharing of two electrons – single covalent bond • Sharing of four electrons – double covalent bond • Sharing of six electrons – triple covalent bond • Molecule – structure that results when atoms are joined together by covalent bonds; smallest unit of most compounds ex: water

13. Ionic Bond • Forms when one or more electrons are transferred from one atom to another • An atom that loses electrons → becomes positively charged • An atom that gains electrons → becomes neg. charged • IONS – atoms that gain or lose electrons • The attraction bt Ions is strong and it is called an ionic bond ex: NaCl

14. Hydrogen Bond • Not as strong as covalent or ionic bonds • The strongest of the bond that can for between molecules • Due to polarity • Most common in water molecules

15. Van der Waals Forces • Intermolecular forces of attraction bt molecules due to unequal sharing of electrons • Due to the difference in the attraction of electrons • They can hold molecules together, especially when the molecules are large

17. Properties of Water • Water • “blue planet” → water covers ¾ of the earth’s surface • Single most abundant compound in most living things • One of the few compounds that is a liquid at temps found on earth • Water expands as it freezes • Ice is less dense than liquid water, so it floats

18. Water Molecule • Neutral (pos charge on its 10protons balance out 10 electrons) • Polarity • O2 pulls Hydrogen’s electrons toward itself • O2 has a slight neg charge; Hydrogens have a slight pos charge • Polar molecule – a molecule in which the charges are unevenly distributed (molecule is like a magnet with the poles)

19. Water Molecule • Hydrogen Bonds • Between nearby molecules due to polarity • COHESION – an attraction bt molecules of same substance • ADHESION – an attraction bt molecules of diff substances

20. Solutions and Suspensions • Water isn’t always pure; usually a mixture • Mixture – a material composed to two or more elements or compounds that are physically mixed together but not chemically combined (salt and pepper; sugar and sand)

21. Mixture • Solutions – components are equally distributed throughout the sln • Solute – sub that is dissolved • Solvent – sub in which the solute dissolves (Ex: salt and water)

22. Mixture • Suspension – mixtures of water and non-dissolved material (Ex: sugar and water; blood)

23. Acids and Bases • Water molecules can react to form ions • Use double arrows to show can happen either direction H2O  H+ + OH – Water  hydrogen ion + hydroxide ion

24. Acids and Bases • pH scale = measurement system that indicates the concentration of H+ ions in a solution • Scale ranges from 0 to 14 • At 7, concentration of H+ and OH- are equal creating a neutral solution • Below a pH of 7, solutions are considered acidic (more H+ ions) • Above a pH of 7, solution are considered basic (less H+ ions, more OH-)

25. Acids and Bases • Acids • Any compound that forms H+ ions in solution; donates H+ increases concentrations of H+ • Below 7 on scale • Strong acids, like those produced by your stomach are 1-3 on pH scale

26. Acids and Bases • Bases • A compound that produces OH- ions in sln OR takes H+ out of sln • Also known as alkaline solutions • Above 7 on the pH scale • Strong bases are 11-14 on the pH scale

27. Acids and Bases • Buffers • Weak acids or bases that can react with strong acids or bases to prevent sharp, sudden changes in pH • Impt in maintaining homeostasis in body (ex: blood pH)

28. Carbon Compounds • Organic Chemistry • The study of all compounds that contain bonds between carbon atoms • Originally thought to be only compounds produced by living organisms • Friedrich Wӧhler (1828) synthesized urea from ammonium cyanate

29. Properties of Carbon • Four valence electrons – 4 single strong covalent bonds • Ability to form large, complex molecules • Single, double or triple covalent bonds • Different shapes: linear, branch, rings (pg 44)

31. Macromolecules • “giant molecule” • Formed by Polymerization – large compounds are built by joining smaller ones together • Monomers join to form Polymers • Four types of organic compounds found in living things: Carbohydrates, Lipids, Nucleic Acids, and Proteins

32. Carbohydrates • Compounds made up of carbon, hydrogen and oxygen atoms usually in a ration of 1:2:1 • Living things use carbs as their main source of energy • Starch; Glucose

33. Carbohydrates • Monomers are simple sugars or monosaccharides; in milk, fructose • Main source of energy • Sugars = immediate energy for all cell activity • Starches = stored extra sugar as complex carbs • Monosaccharides = single sugar molecules • Disaccharides = 2 monosaccharide molecules joined by a covalent bond • Polysaccharides = large maacromolecules formed from many monosacc. Joined by covalent bonds

34. Lipids • A large and varied group of biological molecules made mostly from carbon and hydrogen atoms • Monomoers are fatty acid + glycerol (generally)

35. Lipids • Hydrophobic hydrocarbons • Fats, oils and waxes • Saturated Fatty Acids = fatty acid with all single bonded Cs • Unsaturated Fatty Acids = fatty acid with 1+ double bond • Polyunsaturated Fatty Acids = fatty acid with 2+ double bonds

36. Nucleic Acids • Contain hydrogen, Oxygen, Nitrogen, Carbon and Phosphorous • Monomers are Nucleotides = consists of three parts • A 5-Carbon Sugar • A phosphate group • A nitrogenous base • Store and transmit hereditary or genetic info • Ribonucleic Acids (RNA) – contains sugar ribose • Deoxyribonucleic Acids (DNA) – contains the sugar deoxyribose

38. Proteins • Contain nitrogen as well as carbon, hydrogen and oxygen • Monomers are Amino Acids = compounds with an amino group (-NH2) on one and a carboxyl group (-COOH) on the other end • More than 20 diff amino acids are found in nature • Amino acids differ in their R group (may be acidic, basic, polar, nonpolar, etc)

39. Proteins • Each protein has a specific role • Control the rate of rx • Regulate cell processes • Form bones and muscle • Transport substances into or out of cells • Help fight disease

40. Proteins • Up to four levels of organization • Primary = sequence of amino acids in the protein chain • Secondary = amino acids within the chain can be coiled or folded(alpha helix and beta pleats) • Tertiary = interactions bt AA • Quaternary = multiple chain interact

41. Protein structure

42. Chemical Rx • Process that changes or transforms one set of chemicals into another • Mass and energy are conserved • Some occur slow • Some occur fast • ALWAYS involve changes in the chemical bonds that join atoms in compounds Reactants Products

43. Chemical Reactions • When you exhale, you release CO2. It goes into your bloodstream, where it dissolves in water to be transported to your lungs CO2 + H2O H2CO3 carbon dioxide + water carbonic acid

44. Energy in Reactions • Always an exchange in energy during a chemical rx • Energy released may come in several forms including heat, light, sound • Energy is neither created nor destroyed, but rather stored in the chemical bonds

45. Energy in Rxns • Spontaneous chemical rxns – takes little energy to release a lot • Nonspontaneouschemrxns – takes a lot of energy to release very little • The energy that is put into the chemrxn is the Activation Energy • Some chemrxns require so much energy they would not occur w/o a Catalyst – sub that speeds up the rate of a chemrxn by lowering the activation energy

46. Enzyme Action • Enzymes – proteins that act a biological catalysts; they speed up chemrxns that take place in cells • For Chemrxns to occur must need several things to occur • Activation energy • Reactants must collide(at right angle) • Chem bonds must be broken • Chem bonds must be formed

47. Energy-Absorbing Rxns

48. Enzyme-Substrate Complex • Enzymes provide the site where reactants can be brought together to react; those reactants are known as Substrates – reactants of enzyme-catalyzed rxns

49. Enzyme-Substrate Complex • Substrates bind to the ACTIVE SITE of the enzyme • The active site and substrates have complementary shapes = lock and key • Enzyme and substrates are held together by intermolecular forces • Binding forms the enzyme-substrate complex • Complex must be maintained during the chemical rxn • Upon completion of rxn, the products are released and the enzyme is ready for another rxn

50. Enzyme-Substrate Complex