Chemistry of microbiology Chapter 2

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

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

Atomic Structure Figure 2.1

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

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

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

Electron Configurations Figure 2.3b

Figure 2.4

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

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

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

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

Nonpolar Covalent Bonds Figure 2.5a-b

Nonpolar Covalent Bonds Figure 2.5c-d

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

Polar Covalent Bonds Water Figure 2.7a

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

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

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

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

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

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

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

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

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

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

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

Fats Figure 2.15a

Fats Figure 2.15b

Phospholipids Figure 2.16a

Phospholipids Figure 2.16b-c

Steroids Figure 2.17a-b

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

Carbohydrates Types Monosaccharides Disaccharides Polysaccharides

Monosaccharides

Disaccharides

Polysaccharides Cellulose Amylose (starch) Glycogen

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

Amino Acids The monomers that make up proteins Most organisms use only 20-21 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

Amino Acids and the Peptide Bond

Protein Structure

Another Look at Protein Structure

Primary structure

Secondary structure

Tertiary structure

Quaternary structure

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

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)

Figure 2.25a-b

Nucleic Acid Structure Figure 2.26a-b

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

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

Table 2.5

ATP Figure 2.27