The Chemical Basis of Life

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The Chemical Basis of Life
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Basic Chemistry

• Matter, Mass, and Weight
• Matter anything that occupies space and has mass
• Mass the amount of matter in an object
• Weight the gravitational force acting on an
  object of a given mass
• Elements and Atoms
• Element the simplest type of matter with unique
  chemical properties composed of atoms of only
  one kind
• Atom smallest particle of an element that has
  chemical characteristics of that element

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Atomic Structure

• Atoms composed of subatomic particles
• Neutrons no electrical charge
• Protons one positive charge
• Electrons one negative charge
• Nucleus formed by protons and neutrons
• Most of the volume of an atom occupied by
  electrons

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Atomic Number and Mass Number

• Atomic Number equal to number of protons in each
  atom which is equal to the number of electrons
• Mass Number number of protons plus number of
  neutrons

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Isotopes and Atomic Mass

• Isotopes two or more forms of same element with
  same number of protons and electrons but
  different neutron number
• For example there are three types of hydrogen
• Denoted by using symbol of element preceded by
  mass number as 1H, 2H, 3H
• Atomic Mass average mass of naturally occurring
  isotopes

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Atomic Structure

• Central nucleus with electrons around it

• Several Energy Levels (2,8, ,)

• Octet rule

• Stable and reactive atoms

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Periodic Table

• Atomic number

• Symbol

• Molecular weight

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Chemical Reactions

• Two atoms share one or more electrons which helps
  the reach the octet requirement and be stable

• The bonded atoms make up a molecule. Whether it
  they are the same or different element

• The shared electrons can be shared equally
  between the two atoms (covalent bond) or may be
  taken predominantly by one of them leaving the
  new molecule with some electric charge (Ionic
  bond)

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Chemical Bonds

• The chemical bonds need energy to be created. By
  breaking a bond the energy of the bond is released

• The covalent bonds can be simple, double or
  triple. The amount of energy of every bond is
  additive

• Hydrogen bonds partial bond among charged ions.
  Much weaker than then former bonds

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Electrons and Chemical Bonding

• Intramolecular bonding occurs when outermost
  electrons are either shared with or transferred
  to another atom
• Ionic Bonding atoms exchange electrons
• Covalent Bonding two or more atoms share
  electron pairs
• Ion an atom loses or gains electrons and
  becomes charged
• Cation positively charged ion
• Anion negatively charged ion
• In an ionic bond, cations and anions are
  attracted to each other and remain close to each
  other

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Covalent Bonding

• Atoms share one or more pairs of electrons
• Single covalent two atoms share one pair of
  electrons
• Double covalent Two atoms share 4 electrons
• Nonpolar covalent Electrons shared equally
  because nuclei attract the electrons equally
• Polar covalent Electrons not shared equally
  because one nucleus attracts the electrons more
  than the other does

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Molecules and Compounds

• Molecules and compounds two or more atoms
  chemically combine to form an independent unit
• Example a hydrogen molecule (H2), water (H2O)
• Molecular Mass determined by adding up atomic
  masses of its atoms or ions
• Example NaCl (22.99 35.45)

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Intermolecular Forces

• Forces between molecules
• Result from weak electrostatic attractions
  between oppositely charged parts or molecules, or
  between ions and molecules
• Weaker than forces producing chemical bonding

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Intermolecular Forces Hydrogen Bonds

• Occur when the positively charged H of one
  molecule is attracted to the negatively charged
  O, N or F of another molecule
• For example, in water the positively charged
  hydrogen atoms of one water molecule bond with
  the negatively charged oxygen atoms of other
  water molecules
• Hydrogen bonds play an important role in
  determining the shape of complex molecules

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Intermolecular Forces Solubility and
Dissociation

• Solubility ability of one substance to dissolve
  in another
• For example, sugar or salt dissolves in water
• Dissociation or Separation in ionic compounds,
  cations are attracted to negative end and anions
  attracted to positive end of water molecules the
  ions separate and each becomes surrounded by
  water molecules
• Electrolyte dissociation of an ionic compound in
  water

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Electrolytes and Nonelectrolytes

• Electrolytes solutions made by the dissociation
  of cations () and anions (-) in water
• Have the capacity to conduct an electric current
• Currents can be detected by electrodes
• Nonelectrolytes solutions made by molecules that
  dissolve in water, but do not dissociate do not
  conduct electricity

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Chemical Reactions

• Atoms, ions, molecules or compounds interact to
  form or break chemical bonds
• Reactants substances that enter into a chemical
  reaction.
• Products substances that result from the
  reaction
• Chemical bonds are made (synthesis anabolism)
  and broken (decomposition catabolism) during
  chemical reactions
• Metabolism collective term used for the sum of
  all of the anabolic and catabolic reactions in
  the body

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Synthetic Reactions

• Two or more reactants chemically combine to form
  a new and larger product. Anabolism.
• Chemical bonds made energy stored in the bonds.
• Responsible for growth, maintenance and repair
• Hydrolysis synthetic reaction where water is a
  product
• Produce chemicals characteristic of life
  carbohydrates, proteins, lipids, and nucleic acids

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Decomposition Reactions

• A large reactant is broken down to form smaller
  products. Catabolism.
• Chemical bonds broken energy released.
• Hydrolysis water is split into two parts that
  contribute to the formation of the products
• Example the breakdown of ATP to form ADP and
  inorganic phosphate with a concomitant release of
  free energy

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Reversible Reactions

• Chemical reactions in which the reaction can
  proceed either from reactants to products or from
  products to reactants.
• Equilibrium rate of product formation is equal
  to rate of reactant formation
• Example CO2 and H formation in plasma

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Oxidation-Reduction Reactions

• Oxidation loss of an electron by an atom
• Reduction gain of an electron by an atom
• Oxidation-Reduction Reactions the complete or
  partial loss of an electron by one atom is
  accompanied by the gain of that electron by
  another atom
• Synthetic/decomposition reactions can be
  oxidative reduction reactions
• Reactions can be described in more than one way

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Energy the capacity to do work

• Potential Energy energy stored in chemical
  bonds energy that could do work if it were
  released. Breaking chemical bonds releases
  energy.
• Kinetic Energy does work and moves matter
• Mechanical Energy energy resulting from the
  position or movement of objects
• Chemical Energy form of potential energy in the
  chemical bonds of a substance
• Heat Energy energy that flows between objects of
  different temperatures

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ATP and Potential Energy
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Heat Energy

• When a chemical bond is broken and energy is
  released, only some of that energy is used to
  manufacture ATP.
• Energy that is released but not captured is
  released as heat.
• The heat used by humans to maintain body
  temperature.

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Speed of Chemical Reactions

• Temperature affects rate of reaction.
• Increase in temperature means increase of kinetic
  energy.
• Molecules move faster, collide harder and more
  frequently.
• Concentration of reactants.
• As concentration of reactants increases, rate of
  reaction increases.
• A decrease of O2 in cells can cause death as rate
  of aerobic chemical reactions decreases.
• Catalysts substances that increase the rate of
  chemical reactions without being permanently
  changed or depleted
• Enzymes proteinaceous catalysts that increase
  the rate of chemical reactions by lowering the
  activation energy necessary for reaction to begin
• Activation Energy minimum energy reactants must
  have to start a chemical reaction

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Activation Energy and Enzymes
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Chemistry

• Inorganic Chemistry generally, substances that
  do not contain carbon
• Water, oxygen
• Exceptions CO, CO2, and HCO3-
• Organic Chemistry study of carbon-containing
  substances. Those that are biologically active
  are called biochemicals.

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Water

• High specific heat large amount of heat required
  to raise temperature of water
• Stabilizes body temperature
• Protection
• Lubricant, cushion
• Participates in chemical reactions
• Many reactions take place in water
• Dehydration and hydrolysis
• Serves as a mixing medium

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Mixtures, Solutions and Measures of Concentration

• Mixture substances physically but not chemically
  combined
• Suspension materials separate unless stirred.
  Sand and water.
• Colloid dispersal of tiny particles through a
  medium. Milk.
• Solution mixture of liquids, gasses, or solids
  that are uniformly distributed and chemically
  combined
• Solvent that which dissolves the solute
• Solute that which dissolves in the solvent
• Concentration measure of number of particles of
  solute per volume of solution
• Unit used by physiologists is osmolality
• Concentration of body fluids influences movement
  of fluid into and out of cells.

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Acids and Bases Salts and Buffers

• Acid a proton donor or any substance that
  releases hydrogen ions
• Base a proton acceptor or any substance that
  binds to or accepts hydrogen ions
• Salt a compound consisting of a cation other
  than a hydrogen ion and an anion other than a
  hydroxide ion. Example NaCl
• Buffer a solution of a conjugate acid-base pair
  in which acid and base components occur in
  similar concentrations

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The pH Scale

• Refers to the Hydrogen ion concentration in a
  solution
• Neutral pH of 7 or equal hydrogen and hydroxide
  ions
• Acidic a greater concentration of hydrogen ions
• Alkaline or basic a greater concentration of
  hydroxide ions

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Oxygen and Carbon Dioxide Important Inorganic
Compounds

• Oxygen (O2) required in the final step in the
  series of reactions used to extract energy from
  food.
• Carbon dioxide (CO2) produced during the
  catabolism of organic compounds.
• Metabolic waste product.
• Combines with water in plasma and forms H thus
  affecting acid/base balance

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Organic Chemistry Biochemicals

• Carbohydrates composed of carbon, hydrogen,
  oxygen.
• Divided into monosaccharides, disaccharides,
  polysaccharides
• Example glucose
• Energy sources and structure
• Lipids composed mostly of carbon, hydrogen,
  oxygen.
• Relatively insoluble in water.
• Example anabolic steroids
• Functions protection, insulation, physiological
  regulation, component of cell membranes, energy
  source
• Proteins composed of carbon, hydrogen, oxygen,
  nitrogen, sometimes iodine.
• Example insulin
• Functions regulate processes, aid transport,
  protection, muscle contraction, structure, energy
• Nucleic Acids composed of carbon, hydrogen,
  oxygen, nitrogen, phosphorus.
• Examples ATP, DNA, RNA

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Carbohydrates Monosaccharides

• Simple sugars.
• Six-carbon sugars like glucose, fructose, and
  galactose are important in the diet as energy
  sources.
• Five-carbon sugars are components of ATP, DNA and
  RNA

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Carbohydrates Disaccharides

• Two simple sugars bound together by dehydration
• Examples sucrose, lactose, maltose

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Macro molecules

• Carbohydrates

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Carbohydrates Polysaccharides

• Long chains of many monosaccharides.
• Storage molecules for monosaccharides and form
  part of cell surface markers
• Glycogen formed by animals.
• Starch and cellulose formed by plants
• Starch in food is used as a source of
  monosaccharides
• Cellulose in food acts as fiber (bulk) in the
  diet

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Simple molecules

• Methane, Ethane, Propane, rings

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Macro molecules

• Polymers

• Long chain lipids

• Carbohydrates

• Proteins

• Nucleic acids

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Lipids Fats

• Ingested and broken down by hydrolysis
• Triglycerides composed of glycerol and fatty
  acids
• Functions protection, insulation, energy source

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Macro molecules

• Long chain amphipatic molecules Phospholipids

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Lipids Phospholipids

• Polar (hydrophilic) at one end nonpolar
  (hydrophobic) at the other.
• Function important structural component of cell
  membranes

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Lipids Steroids

• Cholesterol, bile salts, estrogen, testosterone.
• Carbon atoms arranged in four rings
• Functions physiological regulators and component
  of cell membranes

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Cell Membrane

• Double layer of phospholipids

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Proteins

• Amino acids building blocks of protein
• Peptide bonds covalent bonds formed between
  amino acids during protein synthesis

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Protein Structure

• Primary sequence of amino acids in the
  polypeptide chain
• Secondary folding and bending of chain caused by
  hydrogen bonding
• Tertiary formation of helices or of pleated
  sheets caused in part by S-S bonds between amino
  acids
• Quaternary two or more proteins associate as a
  functional unit

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Enzymes Protein Catalysts

• Lower the activation energy necessary for a
  reaction to occur bring reactants into close
  proximity
• Three-dimensional shape contains an active site
  where reactants attach.
• Induced Fit Hypothesis enzymes change shape to
  accommodate the shape of specific reactants
• Enzyme names usually end in ase and often have
  the same word stem as the reactant for example a
  lipid is a reactant for lipase.
• Cofactors combine with active site and make
  nonfunctional enzymes functional
• Organic cofactors called coenzymes

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Nucleotides

• Composed of a five-carbon sugar, a nitrogenous
  base, and a phosphate
• Include the nucleic acids (DNA and RNA) and ATP

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DNA Deoxyribonucleic acid

• Genetic material of cells copied from one
  generation to next
• Composed of 2 strands of nucleotides
• Each nucleotide contains one of the organic bases
  of adenine or guanine (which are purines) and
  thymine or cystosine (which are pyrimidines).

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RNA Ribonucleic acid

• Similar to a single strand of DNA
• Four different nucleotides make up organic bases
  except thymine is replaced with uracil
  (pyrimidine)
• Responsible for interpreting the code within DNA
  into the primary structure of proteins.

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Adenosine Triphosphate (ATP)

• Energy currency of the body
• Provides energy for other chemical reactions as
  anabolism or drive cell processes as muscle
  contraction
• All energy-requiring chemical reactions stop when
  there is inadequate ATP