Chapter 2: The Chemistry of Microbiology

1. Dr. Humann 08-28-14 MCB 3005 Chapter 2: The Chemistry of Microbiology

4. Matter anything that takes up space and has mass Atoms the smallest chemical units of matter

5. Electrons negatively charged subatomic particles circling a nucleus Nucleus structure containing neutrons and protons Neutrons uncharged particles Protons positively charged particles Atomic Structure

6. Figure 2.1 An example of a Bohr model of atomic structure. Electron shells + ) Proton (p Nucleus 0 ) Neutron (n – Electron (e )

7. Element composed of a single type of atom Atomic number equal to the number of protons in the nucleus Atomic mass (atomic weight) sum of masses of protons, neutrons, and electrons Defining Elements Atomic Number Element Atomic Mass

8. Periodic Table of the Elements

9. Hydrogen Carbon Oxygen Nitrogen Sulfur Phosphorous Common Elements of Life

10. Atoms of a given element that differ in the number of neutrons in their nuclei Isotopes 6 protons 6 neutrons 6 electrons 6 protons 7 neutrons 6 electrons 6 protons 8 neutrons 6 electrons

11. Stable isotopes Unstable isotopes Radioactive isotopes Release energy during radioactive decay Isotopes Radiolabel particles for analysis (research) Carbon-dating (research) Radiation therapy (health care) Sterilizing radiation (for decontamination) Energy

12. Nuclei determine identity, electrons determine chemical behavior Only the electrons of atoms interact Electrons occupy electron shells Valence electrons Electrons in outermost shell that interact with other atoms How are Electrons Arranged? = + First shell Second shell

13. Combining capacity of an atom Positive if atom has electrons to give up Negative if atom has spaces to fill Stable when outer electron shells contain eight electrons Valence H2O

14. What makes Argon and Neon different in terms of valence?

15. Atoms - Summary Electron Shell Nucleus Valence Electron Electron Proton Neutron What is this atom? What is the Atomic # and mass?

16. Chemical bonds atoms combine by sharing or transferring valence electrons Molecule two or more atoms held together by chemical bonds Compound a molecule composed of more than one element Electronegativity attraction of atom for electrons the more electronegative an atom, the greater the pull its nucleus exerts on electrons Generally based on # of protons and distance from nucleus to outer electron shell Chemical Bonds

17. Covalent bond Sharing of a pair of electrons by two atoms Nonpolar covalent bonds Shared electrons spend equal amounts of time around each nucleus Atoms with similar electronegativities No poles exist Covalent Bonds - Nonpolar

18. Polar Covalent Bonds Unequal sharing of electrons due to significantly different electronegativities Most important polar covalent bonds involve hydrogen Covalent Bonds - Polar

19. Ionic Bonds Occur when two atoms with vastly different electronegativities come together Atoms have either positive (cation) or negative (anion) charges Gain full + or - charges by gain/loss of electrons (thus changing the proton/electron balance) Cations and anions attract each other and form ionic bonds No electrons shared Typically form crystalline ionic compounds known as salts Chemical Bonds - Ionic

21. Hydrogen Bonds Electrical attraction between partially charged H+ and full or partial negative charge on same or different molecule Weaker than covalent bonds but essential for life Help to stabilize 3-D shapes of large molecules Chemical Bonds - Hydrogen

22. Chemical Bonds - Summary

23. The making or breaking of chemical bonds Involve reactants and products Biochemistry involves chemical reactions of living things 3 major types of reactions: Synthesis Decomposition Exchange Chemical Reactions

24. Involve the formation of larger, more complex molecules Require energy (endothermic) Common type is dehydration synthesis Water molecule formed All the synthesis reactions in an organism are called anabolism Synthesis Reactions Where the molecules bond

25. Break bonds within larger molecules to form smaller atoms, ions, and molecules Release energy (exothermic) Common type is hydrolysis Ionic components of water are added to products All the decomposition reactions in an organism are called catabolism Decomposition Reactions Where the molecules came apart

26. Involve breaking and forming covalent bonds Have endothermic and exothermic steps Involve atoms moving from one molecule to another Sum of all chemical reactions in an organism is called metabolism Exchange Reactions

27. Some important chemicals for life…

28. Most abundant substance in organisms Is considered an inorganic chemical (lacks carbon) Many special characteristics due to two polar covalent bonds Cohesive molecules – surface tension Excellent solvent Participates in many chemical reactions Water

29. Dissociated by water into component cations and anions Acid – dissociates into one or more H+ and one or more anions Base – binds with H+ when dissolved into water; some dissociate into cations and OH– Concentration of H+ in solution expressed using the pH scale Metabolism requires relatively constant balance of acids and bases Buffers prevent drastic changes in internal pH Acids & Bases

31. Compounds that dissociate in water into cations and anions other than H+ and OH– Cations and anions of salts are electrolytes Create electrical differences between inside and outside of cell Transfer electrons from one location to another Form important components of many enzymes Salts

32. Contain carbon and hydrogen atoms Atoms often appear in arrangements called functional groups Macromolecules – large molecules used by all organisms Lipids Carbohydrates Proteins Nucleic acids Monomers Basic building blocks of macromolecules Organic Macromolecules

33. Are all hydrophobic Four groups Fats Phospholipids Waxes Insoluble in water Steroids Roles in metabolism Ex. cholesterol Help keep membranes fluid Lipids Fats (triglycerides) Saturated Unsaturated Phospholipids (cell membranes) Hydrophilic Hydrophobic

34. Organic molecules composed of carbon, hydrogen, and oxygen (CH2O)n Functions Long-term storage of chemical energy Ready energy source Part of backbones of nucleic acids Converted to amino acids Form/are part of cell wall in animals, plants, microbes Involved in intracellular interactions between animal cells Carbohydrates

35. N-acetylglucosamine Monosaccharide Disaccharide Polysaccharide

36. Mostly composed of carbon, hydrogen, oxygen, nitrogen, and sulfur Roles in structure, enzymes, cell regulation, transport of cellular materials, host defense Made of amino acids (the type of “side group” affects interactions with other molecules) Covalent bonds between amino acids are called peptide bonds. Proteins

37. Amino acid 1 Peptide bond β-pleated sheet Amino acid 2 α-helix Hydrogen bond Amino acid 3 Ionic & hydrogen bonds Secondary structure Amino acid 4 β-pleated sheets Primary structure Amino acid sequence (polypeptide) α-helix Denaturation Amino acid substitution 3-D shapes 2 or more polypeptide chains Tertiary structure Quaternary structure

38. DNA and RNA are the genetic material of organisms and viruses RNA also acts as enzyme, binds amino acids, and helps form polypeptides Nucleic acid function DNA is genetic material of all organisms and of many viruses Carries instructions for synthesis of RNA and proteins Controls synthesis of all molecules in an organism Nucleic Acids

39. Nucleotides and nucleosides Nucleotides Monomers that make up nucleic acids Composed of three parts Phosphate Pentose sugar – deoxyribose or ribose One of five cyclic nitrogenous bases Nucleosides are nucleotides lacking phosphate Nucleic acid structure Three H bonds form between C and G Two H bonds form between T and A (DNA) or U and A (RNA) DNA is double stranded in most cells and viruses

40. Purines Pyrimidines Phosphate group Purine or pyrimidine nitrogenous base Adenine (A) (Used in DNA and RNA) Thymine (T) (Used in DNA) Pentose sugar Guanine (G) (Used in DNA and RNA) Cytosine (C) (Used in DNA and RNA) Uracil (U) (Used in RNA) Deoxyribose Ribose

41. 5' 3' A T Two hydrogen bonds G C Three hydrogen bonds A T 5' end Adenine base C G O C 5' 4' 1' C G Deoxyribose 3' 2' A Guanine base Phosphate Thymine base Sugar- phosphate backbones Cytosine base 3' end 5' 3' Antiparallel (go in opposite directions)

42. Phosphate groups & Energy • ATP (adenosine triphosphate) is the principal quick energy supply for cells. • Phosphate bonds are high energy bonds (more energy is released from them than from other covalent bonds). • Phosphates are important for many cellular activities. • Synthesis • Transport • Movement (locomotion)