Chemistry of microbiology Chapter 2

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Chemistry of microbiologyChapter 2
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Atoms

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

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Atomic Structure

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

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Atomic Structure
Figure 2.1
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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

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Isotopes

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

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Electron Configurations

• Only the electrons of atoms interact, so they
  determine atoms chemical behavior
• Electrons occupy electron shells
• Valence electrons electrons in outermost shell
  that interact with other atoms

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Electron Configurations
Figure 2.3b
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Figure 2.4
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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

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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

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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

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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

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Nonpolar Covalent Bonds
Figure 2.5a-b
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Nonpolar Covalent Bonds
Figure 2.5c-d
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Polar Covalent Bonds

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

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Polar Covalent Bonds
Water
Figure 2.7a
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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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Lipids

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

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Fats
Figure 2.15a
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Fats
Figure 2.15b
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Phospholipids
Figure 2.16a
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Phospholipids
Figure 2.16b-c
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Steroids
Figure 2.17a-b
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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

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Carbohydrates

• Types
• Monosaccharides
• Disaccharides
• Polysaccharides

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Monosaccharides
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Disaccharides
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Polysaccharides
Cellulose
Amylose (starch)
Glycogen
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Proteins

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

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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

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Amino Acids and the Peptide Bond
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Protein Structure
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Nucleic Acids

• DNA and RNA the genetic material of organisms
• RNA helps form polypeptides

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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)

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Figure 2.25a-b
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Nucleic Acid Structure
Figure 2.26a-b
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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

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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

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Table 2.5
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ATP
Figure 2.27