1. 1 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. *See separate FlexArt PowerPoint slides for all figures and tables pre-inserted into PowerPoint without notes and animations. Chapter 02 Molecules of Life

2. Why Study Chemistry?  The science that deals with the basic properties of matter  Chemical substances undergo changes and interact with one another in chemical reactions  Metabolism is the use of nutrients for energy or for making substances of cells  Understanding the basic principles of chemistry is essential to understanding metabolic processes in living things Understanding microbial metabolism aids understanding human metabolism

3. A Glimpse of History  Louis Pasteur (1822–1895) often considered father of bacteriology  Started career as chemist for French wine industry  Studied tartaric and paratartaric acids Form thick crusts within wine barrels Identical chemical composition Affect polarized light differently Observed paratartaric acid crystals had two different structures Realized paratartaric acid composed of mixture of stereoisomers

4. Atoms and Elements  Atoms Basic unit of all matter Made up of three major components Protons –Positively charged Electrons –Negatively charged Neutrons –Uncharged

5. Atoms and Elements  Atom Protons and neutrons are found in the nucleus Account for the “weight” of the atom –Atomic mass Electrons orbit the nucleus Have relatively little mass –Do not contribute to the mass of the atom »Approximately 2,000 electrons = 1 proton Protons and electrons are equal in a uncharged atom i.e.,complete atom = # of Protons + # of Neutrons

6. 2.1. Atoms and Elements  Atoms distinguished by atomic number Number of protons in nucleus  Also atomic mass Sum of protons and neutrons (electrons too light) E.g., hydrogen (one proton, no neutrons) has atomic number and mass of 1 Protons ONLY PROTONS + NEUTRONS

7. 2.1. Atoms and Elements  Elements consist of only one type of atom Cannot be chemically separated into simpler parts Living matter primarily composed of four Hydrogen, carbon, oxygen, nitrogen Atoms of an element can have different mass numbers Same # of protons, different # of neutrons Termed isotopes

8. 2.1. Atoms and Elements  Electrons are arranged in shells around nucleus First shell can hold up to 2 Next and subsequent shells can hold up to 8 Inner shells (closer to nucleus) fill first Biological molecules follow “octet rule” Most stable with full outer shell Electrons farther from nucleus have higher energy level Valence electrons are those in outer shell Important in bond formation C C 6 Mass number Atomic number Element symbol 6e – 6p + 6n 0 (a) 12 (b) (c) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

9. Structure of Four Biologically Important Atoms

11. Chemical Bonds and the Formation of Molecules  Atoms are most stable when the outer orbital contains the maximum number of electrons 2, 8, 8 etc.  To fill outer orbitals atoms form bonds with other atoms to fill outer orbitals Bonds are formed with the sharing or the gain or loss of electrons Molecules are formed when atoms bond together

12. Chemical Bonds and the Formation of Molecules  There are several types of chemical bonds They also vary in strength  Chemical bonds include Covalent bonds Ionic bonds Hydrogen bonds

13. Covalent Bonds  Covalent bonds form when atoms share electrons One pair of shared electrons = one covalent bond Carbon bonds with hydrogen to form organic molecules Other compounds are inorganic Covalent bonds are strong Difficult to break at biological temperatures Requires enzymes HHH 4 C C H H HH C H H + Methane Each hydrogen atom needs one electron to fill its valence. Carbon needs four electrons to fill its valence. Chemical formula Each line represents a shared pair of electrons. Space-filling model Ball-and-stick model CH 4 (b) (a) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

14. Covalent Bonds  Achieve stability through the sharing of electrons between atoms Creates a strong bond Difficult to break Requires significant energy usually in the form of heat Never break spontaneously at physiological temperatures –Enzyme required to break at lower temperature Bonds can be polar or non-polar

15. Covalent Bonds  Non-polar and Polar Covalent bonds may have an equal or unequal attraction for the shared electrons Non-polar covalent Bonds formed between identical atoms or between atoms that have similar attraction –H-H or C-H

17. Covalent Bonds Polar covalent bond One atom has a greater attraction to the electrons than the other –Produces a slight charge within the molecule »One part of the molecule with be slightly negatively charged and one molecule with by slightly positively charged Electrons are unequally shared

18. Covalent Bonds  Covalent bonds can be non-polar or polar Non-polar: equal sharing of electrons Polar: unequal sharing of electrons One atom more electronegative than other Important in biological systems –Result in hydrogen bonds Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H O H (a)(b) Decreasing electron density Increasing electron density –– ++ ++

19. Ionic Bonds  Formed by atoms gaining or losing electrons to obtain stability Electrons completely leave first atoms and become part of outer orbital of second atom Loss and gain of electrons leads to charged atoms (ions) –Atom that loses electrons becomes positively charged –Atom that gains electron becomes negatively charged  Charged atoms are attracted to each other and form a bond between ions (opposites attract) Ionic bond

20. Cations (positive charge) Anions (negative charge)  Ionic bonds form because of strong attraction between negative and positive charges Relatively weak bonds Ionic Bonds  Ionic bonds formed by atoms gaining or losing electrons Produces charged atoms, or ions Cl – e–e– NaCl Na + Cl – Cl Na + Na (a) (b) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

21. Ionic Bonds  Ionic bonds are weaker than covalent bonds Bonds dissociate in water Easily broken at room temperature Approximately 100 time weaker than covalent bonds  Important among weak forces holding biological molecules together

22. Hydrogen Bonds  Weak bonds formed from the attraction of positively charged hydrogen atoms Hydrogen atoms in polar molecules are attracted to negatively charged atoms or molecules Most commonly oxygen or nitrogen Hydrogen bonds occur between molecules such as water and DNA Covalent bonds are formed within the molecules –Hydrogen bonds hold molecules together –Covalent bonds hold atoms together

23. Molarity  A mole is 6.022 x 10 23 particles A mole of one compound has the same # of molecules as a mole of any other E.g., 1 mole NaCl = 58.4 g; 1 mole KCl = 74.55 g Each example has a different mass, but the same number of molecules!  Molarity (M) of solution is # moles dissolved in 1 liter H 2 O E.g., a 1 M solution of NaCl is 58.4 g dissolved in 1 liter H 2 O To calculate one mole of NaCl: ∑ Na = 22.9 + Cl= 35.5 = 58.4 g

24. Hydrogen bonds  Hydrogen bonds Form between hydrogen and other electronegative elements (O or N) Increased number provides stability to molecules Water: a polar molecule Hydrogen Bonding

25. Polar Compounds and Hydrogen Bonding

26. Chemical Compounds of the Cell  Most important molecule is water Importance of water depends on its unusual bonding properties

27. 2.3. Chemical Components of the Cell  Water Makes up over 70% of all living organisms by weight Polar molecule Hydrogen bonding explains properties Ice: each water molecule forms 4 hydrogen bonds Liquid: hydrogen bonds continually form and break Liquid water Ice Water molecule ++ ++ ––

28. Water as a Biological Solvent  Polarity Cytoplasm is aqueous and contains polar molecules Promotes hydrogen bonding (stability) Promotes interaction within biomolecules Forces nonpolar molecules (lipids) to aggregate  Cohesiveness H bonds are dynamic: forming, breaking, re-forming Responsible for water’s important properties: 1.High surface tension, 2.High specific heat 3.Surface ice insulates underlying water – prevents freezing (aquatic organisms can survive)

29. Water  Polar nature makes water an excellent solvent Dissolves polar compounds and those with +/– charge These compounds are hydrophillic “Water loving” Non-polar molecules are hydrophobic “Water fearing” Water with dissolved substances freezes at lower temperatures Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Salt crystal (NaCl) Water molecules Na + Cl – ++ –– –– –– –– –– ++ ++ ++ ++ Na + Cl –

30. Polarity and Water Molecules Positive polar end of water surrounds the negative ions Negative polar end of water surrounds the positive ions

31. Hydrogen Bonding Between Water Molecules 2D surface hydrogen bonds are stronger than the 3D in the middle of the volume

32. Strong Surface Tension of Water

33. Acids, Bases, and pH  Acid: A hydrogen ion (H + ) or proton donor  Base: A proton acceptor, or a hydroxyl ion (OH - ) donor  pH scale: relates proton concentration to pH (logarithmic scale) pH= log (1/[H + ] The molar concentration of H +

34. pH of Aqueous Solutions  pH is measure of [H + ] in m/l Water tends to split into H + (acidic) and OH – (basic) Pure water has equal concentrations (each 10 –7 M) Product of [H + ] and [OH – ] is always 10 –14 M Ten-fold increase in [H + ] decreases [OH – ] by factor of ten Each log unit represents ten- fold change in [H + ] Buffers stabilize pH of solutions 10 –14 10 –7 10 0 More basic (higher pH) More acidic (lower pH) 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0 H + ion concentration (molarity) 1MNaOH Drain cleaner Lye Household ammonia Milk of magnesia Detergent solution Seawater Blood NEUTRAL Milk Urine Unpolluted rainwater Black coffee Beer Vinegar Cola Lemon juice Stomach acid Battery acid pH Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

35. pH Values of Some Common Substances

36. Elements and Small Molecules in Cell  ~1% dry weight is inorganic ions Na + (sodium) K + (potassium) Mg 2+ (magnesium) Ca 2+ (calcium) Fe 2+ (iron) Cl – (chloride) PO 4 3– (phosphate) SO 4 2– (sulfate)  Organic compounds Have important functional groups

37. Elements and Small Molecules in Cell  Adenosine triphosphate (ATP) Energy currency of cell Three negatively charged phosphate groups repel Bonds inherently unstable, easily broken Releases energy to drive cellular processes High energy phosphate bonds denoted by ~ ATP  ADP + Pi O O O – P OO O O – P O O O – P O – N N N N Adenosine Phosphate groups High-energy bonds Ribose OH Adenine CH 2 NH 2 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

38. Macromolecules and Their Component Parts  Macromolecules are very large Macro = large  Biological macromolecules are divided into four classes Proteins Polysaccharides (carbohydrates) Lipids Nucleic acids

39. Macromolecules and Their Component Parts  All macromolecules are polymers Poly = many Large molecules formed by joining smaller subunits together Joining subunits together involves dehydration reaction –H 2 O is removed during chemical reaction »Reaction termed dehydration synthesis

40. Macromolecules and Their Component Parts  Macromolecules are broken down into smaller subunits Instead of removing H 2 O, a molecule of H 2 O is added Reaction termed hydrolytic reaction or hydrolysis

41. Dehydration Synthesis H H OH H H H2OH2O Water comes out = Dehydration A new molecule is synthesized Dehydration Synthesis 2 Separate molecules to be joined

42. 2.4. Proteins  Proteins  More than half of dry weight of cell  Versatile, many important roles Catalyze reactions Transport molecules Move cells Provide cellular framework Sense and respond to conditions outside cell Regulate gene expression

43. Amino Acids  Proteins made up of amino acids Infinite possible combinations of 20 amino acids Protein characteristics depend mainly on shape Shape determined by amino acid sequence Amino acids share common structure Side chain (R group) differs All except glycine exist as stereoisomers Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CCN+N+ H R H HH O–O– O Side chain— “R” is the general designation for a side chain Carboxyl group— negatively charged at neutral pH Amino group— positively charged at neutral pH W C Y W C YXX Mirror D-Amino acidL-Amino acid

44. Amino Acid Subunits  All amino acids have the following shared features A carboxyl group (COO - ) An amino group (NH 2 + ) A central carbon A side chain The side chain differentiates the amino acids Amino acids are subdivided based on similarities of the side chain

45. Peptide Bonds and Their Synthesis  The amino acids that form proteins are held together by peptide bonds Unique type of covalent bond Formed between the interaction of the carboxyl group of one amino acid and the amino group of the following amino acid –Reaction causes the release of water and the formation of a peptide bond

46. Hydrolysis (lysis, i.e. break apart with water) C O || - - C N | H - | H | H | R1R1 H2OH2O HOH | Starting with peptide bonded amino acids Bring in water Break water bonds break peptide bond and add water parts End with separate amino acids | CC OH N | H - O || - | H | R2R2 | Water has been used to break (lyse) a bond This is called Hydrolysis

47. Protein Structure Determinants:  Hydrogen bonding  Polar groups  Non-polar groups  Covalent bonds N H HH CCCNCCNCC O OHH OHH RR RR Primary Structure The primary structure can fold into a pleated sheet, or turn into a helix. (a) Secondary Structure (b) Tertiary Structure (c) Secondary Structure Quaternary Structure (d)  -pleated sheet  -helix

48. Protein Structure  Proteins have four structures Primary Secondary Tertiary Quaternary

49. Protein Structure  Primary structure Sequence of amino acids In large part determines other protein features

50. Protein Structure  Secondary structure Primary structure folds into new configuration Helical structure –Alpha (α) helix Pleated structure –Beta (β) sheet New configuration results from weak bonds formed between amino acids

51. Protein Structure  Tertiary structure 3 dimensional structure 2 major shapes Globular Fibrous Becomes functional protein

52. Protein Denaturation  Proteins must have specific shape to have proper function Environmental conditions can break bonds within the protein Causes shape change –Shape change causes protein to stop functioning »Called denaturation  Denaturation can be reversible or irreversible Environment determines reversibility

53. Carbohydrates  Carbohydrates are diverse group of molecules with various sizes  Play important roles in all organisms including Common source of food and energy Form part of nucleic acids Form part of bacterial cell wall

54. Carbohydrates  Carbohydrates contain carbon, hydrogen and oxygen in 1:2:1 ratio Each carbon atom is bound to two hydrogen atoms and one oxygen atom CH 2 O  Polysaccharide large molecules made of carbohydrate molecules  Oligosaccharide short chains of carbohydrates  Monosaccharide Single carbohydrate molecule

55. Carbohydrates  Monosaccharide Classified by number of carbons in molecule Most common monosaccharides 5 and 6 carbon sugars –5 carbon sugars = pentose »Ribose and deoxyribose –6 carbon sugars = hexose »Glucose, fructose and galactose

56. Carbohydrates  Disaccharides Produced by joining two monosaccharides through dehydration synthesis Lactose and sucrose most common in nature Glucose + galactose = lactose Glucose + fructose = sucrose Maltose less common Glucose + glucose = maltose

57. 2.5. Carbohydrates  Monosaccharides have single unit 5-carbon include ribose, deoxyribose 6-carbon include glucose, galactose, fructose, mannose Structural isomers: distinct properties, names Can exist in alpha (α) or beta (β) form depending on location of hydroxyl group Glucose CH 2 OH 6 H 4 H H H OH HOOH H O CH 2 OH 6 5 HO H O OH H H H H 1 2 3 4 5 1 2 3 CH 2 OH 6 H 4 H H OH HOOH H H O 5 1 2 3 CH 2 OH 6 5 H H 4 OH O CH 2 OH OH H Fructose Galactose 3 1 2 Mannose Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 5 O 3 HH H H 2 41 5 O H 3 H H H 2 41 CH 2 OH Ribose β formα form OH Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

58. Carbohydrates  Polysaccharides Serve different function Cellulose most abundant organic molecule on earth Polymer of glucose molecules Principle constituent in plant cell wall Glycogen is carbohydrate storage molecule of animals and some bacteria Polymer of glucose subunits Dextran storage molecule for carbon and energy for some bacteria Polymer of glucose subunits

59. Cellulose

60. Starch

61. Nucleic Acids  Two types of nucleic acid DNA Carry genetic code in all cells RNA Decodes sequence of amino acids to produce proteins Sub units of nucleic acids are nucleotides

62. DNA  Master molecule Determines specific properties of the cell  Nucleotides are composed of three units Nitrogen containing ring compound Nitrogenous base –Purine »Adenine and guanine –Pyrimidine »Thymine and cytosine Five carbon sugar molecule Deoxyribose Phosphate molecule

63. DNA  Nucleotides are joined through covalent bonding Bond created between phosphate of one nucleotide and sugar of the adjacent through dehydration synthesis Phosphate molecule acts as a bridge between the number 3 (3’) carbon of one sugar and the number 5 (5’) carbon of the adjacent –Results in a sugar phosphate backbone

64. 2.6. Nucleic Acids  Nucleotides include nucleobase Purines adenine (A), guanine (G) Two fused rings Pyrimidines cytosine (C), thymine (T) Single ring structure Uracil (U) is found only in RNA O H H H N N N H H H H H H H N H N N O H N N N H N H H O N O N O O N N Purines (double ring) Pyrimidines (single ring) NH 2 Adenine (A) (both DNA and RNA) Guanine (G) (both DNA and RNA) Cytosine (C) (both DNA and RNA) Uracil (U) (RNA only) Thymine (T) (DNA only) NH 2 CH 3 H Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

65. DNA  DNA in living organisms is a double stranded helical molecule Strands are held together by hydrogen bonding between the nitrogen bases Specific pairing between bases –Adenine binds to thymine »A-T or T-A –Guanine binds to cytosine »G-C or C-G Bases are complementary

66. RNA  Involved in decoding DNA  Structure is similar to DNA Differs in a number of ways Thymine is replaced by uracil –There is no thymine base in RNA The sugar is ribose in place deoxyribose RNA is generally shorter Exists as a single stranded molecule not double stranded

67. 2.7. Lipids  Lipids are non-polar, hydrophobic molecules Diverse group defined by this physical property Highly soluble in organic solvents E.g., ether, benzene, chloroform Not composed of similar subunits  Simple lipids contain carbon, hydrogen, oxygen Fats most common Glycerol linked to fatty acids via dehydration synthesis Fatty acids are long chains of bonded C, H atoms with carboxyl group at one end RC O R + + C O RC O HC H HC HC H RC O RC O RC O HC H O HCO HC H O Triglyceride (fat) Dehydration synthesis (b) Glycerol3 fatty acids 3 H 2 O HO OH Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

68. Lipids  Critical component of the cell membrane Membranes act a gatekeepers to the cell Often determines what enters or leaves the cell  Heterogeneous group of molecules Made up of different subunits  Defining feature Insoluble in water  Smallest of the four macromolecules  Can be divided into two general classes Simple lipids Compound lipids

69. Simple Lipids  Contain only carbon, hydrogen and oxygen  Most common are called fats Solid at room temperature Made of glycerol and fatty acids Fatty acids are long hydrocarbon chains plus an acid group (COOH) at the end Glycerol is carbon hydrogen chain with three hydroxyl (OH) groups attached –Allows for the binding of three fatty acids to one glycerol »Triglyceride Fatty acids bond to glycerol covalently through dehydration synthesis

70. 2.7. Lipids  Fatty acids: two groups Saturated: no double bonds Tails pack tightly so solid at room temperature (fats) Unsaturated: double bonds Kinks prevent tight packing so liquid at room temperature (oils) Monounsaturated: 1 double bond Polyunsaturated: >1 double bond Most natural fatty acids are cis: hydrogens attached to same side of double bond Trans have hydrogens on opposite sides of double bond Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. C H H C H H C H H C O C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H CH H H C H H C H H C H H C HO O C H H C H H C H H C H H C H C H H C H C H H C H H C H H C H H C H H C H H C H H H Saturated fatty acid (palmitic acid) Unsaturated fatty acid (oleic acid) Double bond HO (a)

71. 2.7. Lipids  Compound lipids include other elements  Phospholipids important Phosphate group linked to polar molecule Yields hydrophilic head group Hydrophobic fatty acid tails Form lipid bilayer with polar heads oriented outward toward aqueous environments Essential component of cytoplasmic membranes  Lipoproteins, lipopolysaccharides also compound lipids O O O–O– O P O O CO CO CH2H2 CH2H2 CH R Phospholipid bilayer Phospholipid Polar head group Hydrophilic head Hydrophobic tail Phosphate group Glycerol Unsaturated fatty acidSaturated fatty acid Watery exterior of cell Watery interior of cell CH 2 CH 3 CH CH 2 CH 3 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

72. Simple Lipids  Steroids are also considered simple lipids  Differ from fats in structure and function Structure consists of four- membered ring  Classified as lipid because steroids are insoluble in water  If one of the rings has a hydroxyl (OH) group attached it is classified as a sterol Example: cholesterol