The Chemical Basis of Life

1. The Chemical Basis of Life Chapter 2

2. Atoms and Molecules • Chemicals play many roles in an organisms life • DNA is a combination of chemical elements • Every cell has DNA • Every living thing contains cells • Organisms use chemical signals for many things including • Muscle movement, mating, and defense • This chapter deals with the place of chemicals in organisms

3. Studying the Role Of Chemicals in Organisms • Since chemicals play such an important role in organisms lives we use a reductionistic attitude to study it • Reductionism- In order to understand the whole, we study the parts • We reduce the biological hierarchy first

4. D. Organ: Flight muscle of a moth Rattlebox moth C. Cell and tissue: Muscle cell within muscle tissue Myofibril (organelle) B. Organelle: Myofibril (found only in muscle cells) Myosin Actin Atom A. Molecule: Actin Biological Hierarchy • Start at the organ level: • Organ: Flight muscle of moth • Cell and Tissue: Muscle cell and tissue • Organelle: Microfibril • Molecule: Actin (protein) • Elements • Atoms

5. Elements • A chemical element is a substance that cannot be broken down to other substances by ordinary chemical means • About 25 of the 92 naturally occurring elements are essential to life • Goiters are caused by iodine deficiency

6. Essential Elements • Carbon, hydrogen, oxygen, and nitrogen make up the bulk of living matter, but there are other elements necessary for life

7. Compounds • Compound: a substance containing two or more elements in a fixed ratio • More common than pure elements • Example: NaCl (salt) • Most compounds in living organisms contain at least 3 or 4 different elements • Carbon, hydrogen, oxygen, and nitrogen • Proteins like actin are made of these

8. Atoms • Elements consist of one kind of atom that is different form all other atoms of other elements • Smallest unit of matter that still retains the properties of the element in question • An atom consists of three basic types of subatomic particles: • Protons, electrons, and neutrons

9. 2 Protons Nucleus 2 Neutrons 2 Electrons A. Helium atom Figure 2.4A Atoms • Protons and neutrons are located in the core of the atom called the nucleus • Electrons surround the nucleus in a sort of orbit

10. Atoms • Protons are positively charged • Electrons are negatively charged • Neutrons are__?__?__ • The atom is held together by the attraction between the positively charged protons and the negatively charged electrons • The number of protons and the number of electrons are equal

11. Isotopes • Atoms of each element are distinguished by a specific number of protons, this is the element’s atomic number • Mass number- is the number of protons and neutrons in its nucleus • The number of neutrons may vary • Varying numbers of neutrons create isotopes

12. Radioactive Isotopes • Radioactive isotopes are unstable, and give off energy as the nucleus decays spontaneously • Radioactive isotopes can be useful tracers for studying biological processes • The body cannot tell the difference between regular carbon and radioactive carbon and the body takes up the compounds and uses them, thus leaving a radioactive trace

13. Radioactive Isotopes • Photographic film or Geiger counters can detect radioactivity • These are used to study basic chemical processes in organisms, such as photosynthesis and in diagnosis using radioactive anatomical imaging PET scan

14. Electrons • Arranged only at certain energy levels called shells • Inner shell holds 2 electrons • Outer shells hold 8 elections • The number of electrons in the outer shell determines the chemical reactivity of the element • If the shell is not full (2 or 8) then the element will interact with other elements in order to fill its outer shell

15. Outermost electron shell (can hold 8 electrons) Electron First electron shell (can hold 2 electrons) HYDROGEN (H) Atomic number = 1 CARBON (C) Atomic number = 6 NITROGEN (N) Atomic number = 7 OXYGEN (O) Atomic number = 8 Figure 2.6 Electrons

16. Hydrogen Helium First shell Oxygen Lithium Beryllium Carbon Nitrogen Fluorine Boron Neon Second shell Magnesium Sodium Aluminum Silicon Sulfur Argon Chlorine Phosphorus Third shell

17. How does an electron fill its out shell? • When two atoms with incomplete outer shells react, they either give up or receive electrons, causing a bond • Chemical bond: Two types of chemical bonds: • Ionic Bonds • Convalent bonds

18. + Na Cl Na Cl Na Sodium atom Cl Chlorine atom Na+ Sodium ion Cl– Chloride ion Ionic Bonds • Attractions between ions of opposite charge hold them together • Ion- molecule with an electrical charge from loosing or gaining an electron

19. Covalent Bonds • Two atoms share electrons • Two or more atoms held together by covalent bonds are called molecules • Single bonds • Double bonds

20. (–) (–) O H H (+) (+) Figure 2.9 Polar Molecules • Consists of two hydrogen molecules covalently bonded to a single oxygen atom • Shared electrons • An atoms attraction for the shared electrons is called its electronegativity • If the molecule shares the electron equally it is called nonpolar • If the electrons are pulled more closely to one atom than to the others, the stronger pulling atom becomes slightly negative and the other slightly positive, this makes the molecule polar

21. Hydrogen bond Figure 2.10A Water • Due to it’s polarity, water has some unusual properties • The partially charged atoms are attracted to neighboring molecules and form weak bonds called hydrogen bonds

22. Water • Water exists on earth in all three physical states: • What are they? • Where are they? • Life exists on earth because of the properties of water and its abundance

23. Water • Cohesive nature of water • Allows plants to uptake water from the roots • Surface tension of water allows small insects to walk on water • Makes it more difficult to heat and cool water • Takes up a lot of heat when the atmosphere is hot, therefore cools the atmosphere and releases heat in cold times as it cools and warms the atmosphere • Evaporative Cooling- perspiration

24. Water • Frozen water is less dense than liquid water • Fewer molecules in ice than an equal volume of liquid • Ice floats Ice Water ICE Hydrogen bonds are stable

25. Water as a Solvent • Solution- liquid consisting of a homogenous mixture of two or more substances • Solvent- dissolving agent • Solute- substance being dissolved • Aqueous solution- solution where water is the solvent • Because of its polarity, water is an excellent solvent

26. Acidic and Basic Solutions • In aqueous solutions some of the water molecules dissociate (come apart) and form ions • Hydrogen ions (H+) • Hydroxide ions (OH-) • For chemical processes to function within organisms the right balance of (H+) and (OH-) ions • Pure water is a neutral solution

27. pH scale 0 1 Acidic and Basic Solutions Battery acid Lemon juice, gastric juice 2 3 Grapefruit juice, soft drink, vinegar, beer Increasingly ACIDIC (Higher concentration of H+) Acidic solution • Acid- chemical compound that donates H+ ions • Base- chemical compound that donates OH- ions • pH scale measures acidity • 0-7 is acidic, 8-14 is basic • Buffers- resist changes in pH by accepting H+ ions 4 Tomato juice 5 Rain water 6 Human urine Saliva NEUTRAL [H+]=OH–] 7 Pure water Human blood, tears 8 Seawater Neutral solution 9 10 Increasingly BASIC (Lower concentration of H+) Milk of magnesia 11 Household ammonia 12 Household bleach 13 Oven cleaner Basic solution 14

28. Acidic solution Basic solution Neutral solution

29. 2 H2O 2 H2 + O2  Figure 2.17A Chemical Reactions • The structure of atoms and molecules determines the way they behave • Chemical reactions rearrange molecules and ions and change the way they behave • Chemical reaction- process leading to chemical changes in matter Reactants Products

30. Beta-carotene Vitamin A (2 molecules) Figure 2.17B Living Cells and Chemical Reactions

32. The Molecules of Cells Chapter 3

33. ORGANIC COMPOUNDS AND THEIR POLYMERS • Nearly all molecules created by cells are composed of carbon molecules • Carbon can be bonded to itself or to elemental atoms • Organic Compounds-compounds synthesized by cells and containing carbon • Carbon has the ability to synthesize large, diverse molecules

34. Carbon • Carbon has only four electrons in it’s outer shell that holds eight • Very reactive with many other atoms • The shape of a molecule, which depends partly on its bond angles, usually helps to determine its angles • The chain of carbon atoms in organic molecules is called the carbon skeleton

35. Carbon Space-filling model Structural formula Ball-and-stick model • Carbon can form four covalent bonds • It can join with other carbon atoms to make chains or rings • Over 2 million organic, carbon-containing compounds are known Methane The four single bonds of carbon point to the corners of a tetrahedron.

36. Forms of Carbon Skeletons Propane Ethane Length. Carbon skeletons vary in length. • Straight of Branched • Vary in length • Arranged in Rings • Hydrocarbons- Compounds containing only H and C • Compounds with the same # of H and C but with different forms are called Isomers Isobutane Butane Branching. Skeletons may be unbranched or branched. 2-Butene 1-Butene Double bonds. Skeletons may have double bonds, which can vary in location. Cyclohexane Benzene Skeletons may be arranged in rings. Rings.

37. Functional Groups • The groups of atoms that usually participate in chemical reactions • Attached to the carbon skeleton • Can be polar, which makes them water soluble • Compounds can contain several functional groups

38. Functional Groups

39. Functional Groups • Hydroxyl group (-OH)- oxygen is bonded to the carbon skeleton • Compounds containing a hydroxyl group are called alcohols • Amino group (-NH2)- nitrogen bonded to carbon skeleton and hydrogens bonded to nitrogen • Compounds containing an amino group are called amines

40. Carbonyl Groups • Carbon atom linked by a double bond to an oxygen atom • Ketone- carbonyl group within the chain • Aldehyde- carbonyl group at the end of the chain • Carboxylic Acid- carbonyl group at the end of the chain, and attached to a hydroxyl group

41. Macromolecules • Most organic molecules are large macromolecules made up of smaller molecules • Thousands of connected atoms • Examples: • Proteins • DNA • Lipids

42. Polymers • Polymer- a large molecule consisting of many identical or similar units strung together • Monomer- The units that serve as the building blocks of polymers • Essentially universal between organisms • The diversity of polymers accounts for the uniqueness of each organism

43. Dehydration Synthesis • Monomers are linked together to form polymers by a process called dehydration synthesis Short polymer Unlinked monomer Dehydration reaction Longer polymer

44. Hydrolysis • Breakdown of polymers, break the bonds between polymers by adding a water molecule Hydrolysis

45. Four Classes of Large Molecules • Carbohydrates • Proteins • Nucleic Acids • Lipids

46. Carbohydrates • A class of molecules ranging from small sugar molecules to large polysaccharides • Monosaccharides- carbohydrate monomers, single-unit sugars • Disaccharides- two monosaccharides linked together, double-sugars • Polysaccharides-hundreds to thousands of monosaccharides linked together

47. Glucose- aldehyde Fructose- ketone Monosaccharides • Molecular formulas that are some multiple of CH2O • Sugars have two trademark elements: • A number of hydroxyl groups (-OH) and a Carbonyl Group • Monosaccharides are the fuels for cellular work

48. Glucose Glucose Maltose Disaccharides • Disaccharides are formed when two monosaccharides link together • The two monosaccharides link by dehydration synthesis • Sucrose = fructose + glucose

49. Polysaccharides • Polymers of many monosaccharides linked together by dehydration synthesis • Starch- Storage polysaccharide in plant tissues as granules • Glycogen- Storage polysaccharide in animals, stored in liver and muscle tissue as granules • Cellulose- Building material in plants, most abundant organic material on earth, cannot be hydrolyzed by animals

50. Starch granules in potato tuber cells Glucosemonomer STARCH Glycogen granules in muscle tissue GLYCOGEN Cellulose fibrils ina plant cell wall CELLULOSE Cellulosemolecules Figure 3.7 Polysaccharides