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Chemistry of microbiology Chapter 2

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1 Chemistry of microbiology Chapter 2

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

3 Atomic Structure Electrons – negatively charged subatomic particles circling a nucleus Nucleus – contains neutrons and protons Neutrons – uncharged particles Protons – positively charged particles

4 Atomic Structure Figure 2.1

5 Atomic Structure Element – composed of a single type of atom
Atomic number – equals the number of protons in the nucleus Atomic mass (atomic weight) – sum of masses of protons, neutrons, and electrons 12 C 6 23 Na 11

6 Isotopes Elements that differ in number of neutrons in their nuclei are isotopes Stable isotopes Unstable isotopes Release energy during radioactive decay

7 Electron Configurations
Only the electrons of atoms interact, so they determine atom’s chemical behavior Electrons occupy electron shells Valence electrons – electrons in outermost shell that interact with other atoms

8 Electron Configurations
Figure 2.3b

9 Figure 2.4

10 Chemical Bonds Outer electron shells are stable when contain eight electrons Valence – combining capacity of an atom Positive if has electrons to give up Negative if has spaces to fill Chemical bonds – when 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

11 Chemical Bonds Principal types of chemical bonds Covalent
Nonpolar covalent bonds Polar covalent bonds Ionic bonds Hydrogen bonds – weak forces that combine with polar covalent bonds

12 Covalent Bonds Covalent bond – sharing of a pair of electrons by two atoms Electronegativity – attraction of atom for electrons; the more electronegative an atom, the greater the pull its nucleus exerts on electrons

13 Nonpolar Covalent Bonds
Atoms with similar electronegativities Shared electrons spend equal amount of time around each nucleus No poles exist Carbon atoms critical to life; forms four nonpolar covalent bonds with other atoms Organic compounds contain carbon and hydrogen atoms

14 Nonpolar Covalent Bonds
Figure 2.5a-b

15 Nonpolar Covalent Bonds
Figure 2.5c-d

16 Polar Covalent Bonds Unequal sharing of electrons due to significantly different electronegativities Most important polar covalent bonds involve hydrogen Allows for hydrogen bonding

17 Polar Covalent Bonds Water Figure 2.7a

18 Ionic Bonds Formed by a transfer of electrons
Creating ions: positive (cation) and negative (anion) Cations and anions attract each other and form ionic bonds (no electrons shared) Typically form crystalline ionic compounds known as salts

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

20 Chemical Reactions The making or breaking of chemical bonds
Involve reactant(s) and product(s) A + B  C + D Q + R  S T U + V Three categories of chemical reactions Synthesis reactions Decomposition reactions Exchange reactions

21 Synthesis Reactions Involve the formation of larger, more complex molecules Important type – dehydration synthesis Water molecule formed Require energy (endothermic) All the synthesis reactions in an organism are called anabolism

22 Decomposition Reactions
Break bonds within larger molecules to form smaller atoms, ions, and molecules Release energy (exothermic) Common type – hydrolysis Bond broken as the ionic components of water are added to products All the decomposition reactions in an organism are called catabolism

23 Exchange Reactions Involve breaking and forming covalent bonds, and involve endothermic and exothermic steps Atoms moved from one molecule to another Sum of all chemical reactions in an organism is called metabolism

24 Water Most abundant substance in organisms
Most of its special characteristics due to two polar covalent bonds Water molecules are cohesive – surface tension Excellent solvent Remains liquid across wide range of temperatures Can absorb significant amounts of energy without changing temperature Participates in many chemical reactions


26 Acids and Bases 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- Metabolism requires relatively constant balance of acids and bases Concentration of H+ in solution is expressed using the pH scale Buffers prevent drastic changes in internal pH

27 Salts Compounds that dissociate in water into cations and anions other than H+ and OH- (NaCl -----Na+ + Cl- ) Cations and anions of salts are electrolytes Create electrical differences between inside and outside of cell Transfer electrons from one location to another Important components of many enzymes

28 Organic Macromolecules
Contain carbon and hydrogen atoms Atoms often appear in certain common arrangements – functional groups Macromolecules Lipids Carbohydrates Proteins Nucleic Acids Monomers – basic building blocks of macromolecules

29 Lipids Not composed of regular subunits, but are all hydrophobic Types
Fats and oils (triglycerides) Phospholipids Steroids

30 Fats Figure 2.15a

31 Fats Figure 2.15b

32 Phospholipids Figure 2.16a

33 Phospholipids Figure 2.16b-c

34 Steroids Figure 2.17a-b

35 Carbohydrates 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 cell wall Involved in intercellular interactions between animal cells

36 Carbohydrates Types Monosaccharides Disaccharides Polysaccharides

37 Monosaccharides

38 Disaccharides

39 Polysaccharides Cellulose Amylose (starch) Glycogen

40 Proteins Mostly composed of carbon, hydrogen, oxygen, nitrogen, and sulfur Functions Structure Enzymatic catalysis Regulation Transportation Defense and offense

41 Amino Acids The monomers that make up proteins
Most organisms use only amino acids in the synthesis of proteins Side groups affect how amino acids interact with one another and how a protein interacts with other molecules A covalent bond (peptide bond) formed between amino acids by dehydration synthesis reaction

42 Amino Acids and the Peptide Bond

43 Protein Structure

44 Another Look at Protein Structure

45 Primary structure

46 Secondary structure

47 Tertiary structure

48 Quaternary structure


50 Nucleic Acids DNA and RNA: the genetic material of organisms
RNA helps form polypeptides

51 Nucleotides The monomers that make up nucleic acids
Composed of three parts Phosphate Pentose sugar – deoxyribose or ribose One of five cyclic nitrogenous bases Adenine (A) Guanine (G) Cytosine (C) Thymine (T) Uracil (U)

52 Figure 2.25a-b

53 Nucleic Acid Structure
Figure 2.26a-b

54 Nucleic Acid Structure
H bonds form between C and G and between T and A in DNA U and A in RNA DNA is double stranded in most cells and viruses Two strands are complementary Two strands are antiparallel

55 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

56 Table 2.5

57 ATP Figure 2.27

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