Chapter 2 The Chemical Basis of Life

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Chapter 2 The Chemical Basis of Life
AP 151 Introduction to Human Physiology
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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
• Composition of Matter 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 is occupied by
  electrons

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• Elements are
• arranged by atomic
• number
• 24 elements have a
• biological role
• 6 elements 98.5
• of body wt.
• Trace elements in
• minute amounts

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Atomic Number and Mass Number

• Atomic Number
• Equal to number of protons in each atom
• Equal to the number of electrons
• Mass (Atomic) Number
• Number of protons plus number of neutrons

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Identification of Elements
Figure 2.2
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Isotopes

• Isotopes two or more forms of the same element
  with same number of protons and electrons but
  different neutron number
• For example there are three types of hydrogen
  see diagram below
• Denoted by using symbol of element preceded by
  mass number as 1H, 2H, 3H
• Radioactive isotopes
• Forms of atoms that emit radioactivity such as
  gamma rays, which can then be measured
• Used clinically and in research
• Examples of uses
• Tracking hormone uptake
• Treating cancer

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Ions and Ionization

• Ions - an atom that carries a charge due to an
  unequal number of protons and electrons

• Ionization transfer of electrons from one atom
  to another (? stability of valence shell)

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Anions and Cations

• Anion
• atom that gained electrons (net negative charge)
• Cation
• atom that lost an electron (net positive charge)
• Ions with opposite charges are attracted to each
  other

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Electrolytes

• Salts that ionize in water to form body fluids
• capable of conducting electricity
• Electrolyte importance
• chemical reactivity
• osmotic effects (influence water movement)
• electrical effects on nerve and muscle tissue
• Imbalances cause muscle cramps, brittle bones,
  coma and death

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Molecules and Chemical Bonds

• Molecules
• two or more atoms covalently bonded
• Example a hydrogen molecule (H2)
• Compounds
• two or more atoms of different elements
  covalently bonded Example water (H2O)
• Molecular formula
• elements and how many atoms of each
• E.g., H2O - 2 hydrogens 1 oxygen
• E.g. 2 H2O 2 molecules of water
• Structural formula
• location of each atom
• structural isomers revealed

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Molecular Weight

• MW of compound sum of atomic weights of all the
  atoms in the molecule
• Calculate MW of glucose (C6H12O6)
• 6 C atoms x 12 amu each 72 amu
• 12 H atoms x 1 amu each 12 amu
• 6 O atoms x 16 amu each 96 amu
• Molecular weight (MW) 180 amu

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Chemical Bonds

• Electron shells, or energy levels, surround the
  nucleus of an atom
• Bonds are formed using the electrons in the
  outermost energy level
• ONLY electrons are used in forming chemical bonds

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Chemically Inert Elements

• Inert elements have their outermost energy level
  fully occupied by electrons nonreactive

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Chemically Reactive Elements

• Reactive elements do not have their outermost
  energy level fully occupied by electrons
• Are capable of sharing, gaining, or losing
  electrons and thus forming bonds

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Chemical Bonds Ionic Bonds

• Ionic bonds form between atoms by the transfer of
  one or more electrons
• Loss of electron(s) by one atom results in the
  gain of the electron(s) by another atome
• Ionic compounds form crystals instead of
  individual molecules
• Example NaCl (sodium chloride)
• Ions are charged atoms resulting from the gain or
  loss of electrons
• Cations have lost one or more electrons
• Indicated by a positive charge e.g., Na, K
• Anions have gained one or more electrons
• Indicated by a negative charge e.g., Cl-

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Formation of an Ionic Bond
Figure 2.5a
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Covalent Bonding

• Atoms share one or morepairs of electrons
• Single covalent two atoms share one pair of
  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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Single Covalent Bonds
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Double Covalent Bonds
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Polar and Nonpolar Molecules

• Electrons shared equally between atoms produce
  nonpolar molecules
• Unequal sharing of electrons produces polar
  molecules
• Atoms with six or seven valence shell electrons
  are electronegative
• Atoms with one or two valence shell electrons are
  electropositive

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Polar and Nonpolar Molecules

• Electrons shared equally between atoms produce
  nonpolar molecules
• Unequal sharing of electrons produces polar
  molecules
• Atoms with six or seven valence shell electrons
  are electronegative
• Atoms with one or two valence shell electrons are
  electropositive

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Nonpolar /Polar Covalent Bonds

• electrons shared equally

• electrons shared unequally

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Hydrogen Bonds

• An intermolecular force
• A bond that forms between molecules rather than
  within a molecule
• Weakest bond no sharing of electrons
• Attraction between polar molecules
• Positive hydrogen atoms attracted to negative
  oxygen atoms in a 2nd molecule
• Physiological importance
• play an important role in determining the shape
  of complex molecules
• Viz., proteins, nucleic acids

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Hydrogen Bonds
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Solvency

• Solvency - ability to dissolve other chemicals
• Hydrophilic (charged substances) dissolve easily
  in water
• Hydrophobic (neutral substances) do not easily
  dissolve in water
• Water universal solvent
• More solutes are soluble in water than any other
  solvent
• metabolic reactions and transport of substances

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Properties of Water

• Universal solvent
• More solutes are soluble in water than in any
  other solvent
• Due mainly to its polarity
• Chemical reactivity
• Water participates in chemical reactions
• water ionizes into H and OH-
• water ionizes other chemicals (acids and salts)
• water is involved in hydrolysis (digestion) and
  dehydration synthesis (formation) reactions

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Properties of Water As a Solvent

• Polar water molecules overpower the ionic bond in
  NaCl-
• forming hydration spheres around each ion
• water molecules negative pole faces Na,
  positive pole faces Cl-

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Properties of Water Thermal Stability of Water

• 3. Water used to transport solutes and heat
• Recall that 90-92 of plasma is water
• All solutes and heat are transported in blood
• Allows heat generated in one region to be
  disbursed over entire body
• 4. Water stabilizes internal temperature
• Has high heat capacity
• hydrogen bonds inhibit temperature increases by
  inhibiting molecular motion
• water can absorb large amounts of heat without
  large changes in temperature
• Has high heat of vaporization (see
  http//health.howstuffworks.com/sweat2.htm)
• effective coolant
• 1 ml of sweat removes 500 calories of heat

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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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Acids and Bases Salts and Buffers

• Acid a proton (H) donor or any substance that
  releases hydrogen ions HCl ? H Cl
• Base a proton acceptor or any substance that
  binds to or accepts hydrogen ions
• NaOH ? Na OH
• Salt a compound consisting of a cation other
  than a hydrogen ion and an anion other than a
  hydroxide ion. Example NaCl, KCl
• Buffer a substance which prevents wide
  fluctuations in pH

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Acid-Base Concentration (pH)

• Acidic solutions have higher H concentration and
  therefore a lower pH
• pH from 0-7
• Alkaline solutions have lower H concentration
  and therefore a higher pH
• pH from 7-14
• Neutral solutions have equal H and OH
  concentrations

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The pH Scale

• Refers to the hydro- gen 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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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
• Chemical equations contain
• Number and type of reacting substances, and
  products produced

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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
• Dehydration synthesis synthesis 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
• CO2 H2O ? H2CO3 ? H HCO3-

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Oxidation-Reduction (Redox) Reactions

• Oxidation
• molecule loses electrons and releases energy
• oxygen is often the electron acceptor
• Reduction
• molecule gains electrons and energy
• Oxidation-reduction (redox) reactions
• Electrons are often transferred as hydrogen atoms
• Citric acid -2H a-ketoglutaric
  acid
• NAD 2H
  NADH H
• NAD and FAD are commonly used to accept hydrogens
  from cpds undergoing oxidation (like citric acid
  in the above example)

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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
• Example insulin
• Functions regulate processes, aid transport,
  protection, muscle contraction, structure, energy
• Nucleic Acids composed of carbon, hydrogen,
  oxygen, nitrogen, and phosphorus.
• Examples ATP, DNA, RNA

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Organic Molecules and Carbon

• Carbon has only 4 valence electrons
• bonds readily to gain 4 more valence electrons
• Forms long chains, branched molecules and rings
• serves as the backbone for organic molecules
• Carries a variety of functional groups

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Functional Groups

• Atoms attached to carbon backbone
• Determines chemical properties of the cpd. to
  which it is attached

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Carbohydrates Monosaccharides

• Simple sugars
• General formula is CH2O
• Six-carbon sugars (hexoses) like glucose,
  fructose, and galactose are important in the diet
  as energy sources (C6H12O6)
• structural isomers same molecular but different
  structural formula
• Five-carbon sugars (pentoses) are components of
  ATP, DNA and RNA ribose and deoxyribose

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Carbohydrates Disaccharides

• Two simple sugars bound together by dehydration
  synthesis (loss of water with formation of new
  cpd._
• Examples sucrose (Glu Fru), lactose (Glu
  Galac), maltose (Glu Glu)
• Are isomers C12H22O11 Why not C12H24O12?
• Digested through hydrolysis reactions
• Note the reversible reaction below

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Carbohydrates Polysaccharides

• Chains of glucose subunits Polymers
• Glycogen formed by animals energy storage
• Liver synthesizes after a meal and breaks it down
  between meals
• 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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Carbohydrate Functions

• All digested carbohydrates converted to glucose
  and oxidized to make ATP
• Conjugated carbohydrate bound to lipid or
  protein
• glycolipids
• external surface of cell membrane
• glycoproteins
• external surface of cell membrane
• mucus of respiratory and digestive tracts
• proteoglycans
• gels that hold cells and tissues together
• joint lubrication
• rubbery texture of cartilage

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Lipids Fats

• Contain C, H, and O, but the proportion of oxygen
  in lipids is less than in carbohydrates
• Hydrophobic organic molecules
• Examples Triglycerides, Phospholipids, Steroids,
  Eicosanoids
• Ingested and broken down by hydrolysis
• Triglycerides composed of glycerol and 3 fatty
  acids
• Fatty acids may be saturated or unsaturated
• Saturated (no double bonds between carbons)
• Unsaturated (one or more double bonds between
  carbon atoms)
• Functions protection, insulation, energy source
• See next slide

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Lipids Triglycerides
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Lipids Phospholipids

• Phospholipids modified triglycerides with two
  fatty acid groups and a phosphorus group
• Polar (hydrophilic) at one end nonpolar
  (hydrophobic) at the other.
• Function important structural component of cell
  membranes

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Lipids Steroids

• Steroids flat molecules with four
  interlocking hydro- carbon rings
• All are derived from cholesterol

• Cholesterol
• important component of cell membranes
• produced only in animal liver cells
• naturally produced by our body

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Eicosanoids

• Derived from arachidonic acid (a fatty acid)
• Hormone-like chemical signals between cells
• Includes prostaglandins produced in all tissues
• role in inflammation, blood clotting, hormone
  action, labor contractions, blood vessel diameter

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Representative Lipids Found in the Body

• Neutral fats found in subcutaneous tissue and
  around organs
• Phospholipids chief component of cell membranes
• Steroids cholesterol, bile salts, vitamin D,
  sex hormones, and adrenal cortical hormones
• Fat-soluble vitamins vitamins A, D, E, and K
• Eicosanoids prostaglandins, leukotriens, and
  thromboxanes
• Lipoproteins transport fatty acids and
  cholesterol in the bloodstream

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Proteins
Macromolecules composed of combinations of 20
types of amino acids bound together by peptide
bonds

• Contain C, H, O, N
• Amino acids building blocks of protein
• Contain an amino group (NH2), carboxyl (COOH)
  group, and a radical group (R-)
• Peptide bonds covalent bonds formed between
  amino acids during protein synthesis

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Levels of 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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Fibrous and Globular Proteins

• Fibrous proteins
• Extended and strandlike proteins
• Examples keratin, elastin, collagen, and certain
  contractile fibers
• Globular proteins
• Compact, spherical proteins with tertiary and
  quaternary structures
• Examples antibodies, hormones, and enzymes

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Types of Proteins

• Structural - collagen, keratin
• Transport - Hb, ? and ? globulins
• Contractile - actin and myosin in muscle
• Regulatory - hormones
• Immunologic - antibodies (IgG, IgA)
• Clotting - thrombin and fibrin
• Osmotic - albumin in plasma
• Catalytic - enzymes

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Protein Denuaturation

• Reversible unfolding of proteins due to drops in
  pH and/or increased temperature

Figure 2.18a
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Protein Denaturation

• Irreversibly denatured proteins cannot refold and
  are formed by extreme pH or temperature changes

Figure 2.18b
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Nucleic Acids

• Composed of carbon, oxygen, hydrogen, nitrogen,
  and phosphorus
• Their structural unit, the nucleotide, is
  composed of N-containing base, a pentose sugar,
  and a phosphate group
• Five nitrogen bases contribute to nucleotide
  structure adenine (A), guanine (G), cytosine
  (C), thymine (T), and uracil (U)
• Two major classes DNA and RNA
• Informational molecules
• Other important nucleotides
• ATP, cAMP

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DNA Deoxyribonucleic acid

• 100 million to 1 billion nucleotides long
• 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

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How ATP Drives Cellular Work
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Turnover Rates of Different Cell Types

• TR refers to the average time between synthesis
  and recycling of the compound
• Liver
• Total protein 5-6 days
• Enzymes 1 hr to several days
• Glycogen 1-2 days
• Cholesterol 5-7 days
• Muscle
• Total protein 30 days
• Glycogen 12-24 hours
• Neurons
• Phospholipids 200 days
• Cholesterol 100 days
• Fat cell
• Triglycerides 15-20 days