Fundamentals of Anatomy & Physiology Eleventh Edition Chapter 2

Chemistry

• Deals with the structure of matter.
• Includes:
  • Structure of atoms.
  • Basic chemical building blocks.
  • How atoms combine to form increasingly complex structures.

Atoms and Atomic Structure

• Matter: Anything that takes up space and has mass.
• Made up of atoms.
• Atoms join to form chemicals with different characteristics.
• Chemical characteristics determine physiology at molecular and cellular levels.
• Subatomic particles:
  • Protons: Positive charge, 1 mass unit.
  • Neutrons: Neutral, 1 mass unit.
  • Electrons: Negative charge, low mass.
• Atomic structure:
  • Atomic number: Number of protons.
  • Nucleus: Contains protons and neutrons.
  • Electron cloud: Spherical area containing electrons.
  • Electron shell: Two-dimensional representation of the electron cloud.
• Element: A pure substance composed of atoms of one kind.
  • The atomic number (number of protons) determines its chemical properties.
• Isotopes: Versions of elements based on mass number.
  • Mass number = number of protons + the number of neutrons.
  • Radioisotopes: Have radioactive nuclei.
    • Decay rate is expressed as half-life.
• Atomic weight: Average of the different atomic masses and proportions of different isotopes
• A mole (mol) has a weight in grams equal to the atomic weight of the element
• Electrons and energy levels
  • Electrons in the electron cloud determine the reactivity of an atom
  • Electron cloud contains shells, or energy levels, that can hold a limited number of electrons
    • Lower shells fill first
    • Outermost shell is the valence shell, and it determines bonding

Principal Elements in the Human Body:

• Oxygen (O): 65% of total body weight.
  • Significance: Component of water and other compounds; gaseous form is essential for respiration.
• Carbon (C): 18.6% of total body weight.
  • Significance: Found in all organic molecules.
• Hydrogen (H): 9.7% of total body weight.
  • Significance: Component of water and most other compounds.
• Nitrogen (N): 3.2% of total body weight.
  • Significance: Found in proteins, nucleic acids, and other organic compounds.
• Calcium (Ca): 1.8% of total body weight.
  • Significance: Found in bones and teeth; important for membrane function, nerve impulses, muscle contraction, and blood clotting.
• Phosphorus (P): 1.0% of total body weight.
  • Significance: Found in bones and teeth, nucleic acids, and high-energy compounds.
• Potassium (K): 0.4% of total body weight.
  • Significance: Important for proper membrane function, nerve impulses, and muscle contraction.
• Sodium (Na): 0.2% of total body weight.
  • Significance: Important for blood volume, membrane function, nerve impulses, and muscle contraction.
• Chlorine (Cl): 0.2% of total body weight.
  • Significance: Important for blood volume, membrane function, and water absorption.
• Magnesium (Mg): 0.06% of total body weight.
  • Significance: A cofactor for many enzymes.
• Sulfur (S): 0.04% of total body weight.
  • Significance: Found in many proteins.
• Iron (Fe): 0.007% of total body weight.
  • Significance: Essential for oxygen transport and energy capture.
• Iodine (I): 0.0002% of total body weight.
  • Significance: A component of hormones of the thyroid gland.
• Trace elements: Silicon (Si), fluorine (F), copper (Cu), manganese (Mn), zinc (Zn), selenium (Se), cobalt (Co), molybdenum (Mo), cadmium (Cd), chromium (Cr), tin (Sn), aluminum (Al), boron (B), and vanadium (V).
  • Significance: Some function as cofactors; the functions of many trace elements are poorly understood.

Molecules and Compounds

• Chemical bonds form molecules and compounds
  • Molecule: Two or more atoms joined by strong bonds.
  • Compound: Two or more atoms of different elements joined by strong or weak bonds.
  • Not all molecules are compounds and not all compounds consist of molecules
  • Molecular weight of a molecule or compound is the sum of the atomic weights of its atoms

Chemical bonds

• Involve sharing, gaining, and losing electrons.
• Three major types of chemical bonds
  • Ionic bonds
  • Covalent bonds
  • Hydrogen bonds

Ionic Bonds

• An ion is an atom with an electric charge.
• One atom—the electron donor—loses one or more electrons and becomes a cation.
• Another atom—the electron acceptor—gains those same electrons and becomes an anion.
• Ionic bonds are attractions between cations (positive ions) and anions (negative ions).

Covalent Bonds

• Strong bonds involving shared electrons.
• One electron is donated by each atom to make the pair of electrons.
• Sharing one pair of electrons is a single covalent bond.
• Sharing two pairs of electrons is a double covalent bond.
• Sharing three pairs of electrons is a triple covalent bond.
• Nonpolar covalent bonds
  • Equal sharing of electrons between atoms that have equal pull on the electrons
• Polar covalent bonds
  • Unequal sharing of electrons because one atom has a disproportionately strong pull on the electrons
  • Form polar molecules—like water

Hydrogen Bonds

• Weak polar bonds between adjacent molecules based on electrical attractions.
• Involve attractions between a slight positive charge and a slight negative charge
• Hydrogen bonds between $H_2O$ molecules cause surface tension

States of Matter

• Solid: Constant volume and shape.
• Liquid: Constant volume but changes shape.
• Gas: Changes volume and shape.

Chemical Reactions

• In a chemical reaction
  • Either new bonds are formed or existing bonds are broken
  • Reactants: Materials going into a reaction.
  • Products: Materials coming out of a reaction.
  • Metabolism: All of the reactions that are occurring at one time.
• Energy: The capacity to do work
• Work: Movement of an object or change in matter
• Kinetic energy: Energy of motion
• Potential energy: Stored energy
• Chemical energy: Potential energy stored in chemical bonds

Types of Chemical Reactions

• Decomposition
• Synthesis
• Exchange
• Reversible

Decomposition Reaction (Catabolism)

• Breaks chemical bonds.
• $AB → A + B$
• Hydrolysis reaction
• $AB + H_2O → AH + BOH$

Synthesis Reaction (Anabolism)

• Forms chemical bonds.
• $A + B → AB$
• Dehydration synthesis (condensation) reaction
• $AH + BOH → AB + H_2O$

Exchange Reaction

• Involves decomposition first, then synthesis
• $AB + CD → AD + CB$

Reversible Reactions

• $A + B ↔ AB$
• At equilibrium, the amounts of chemicals do not change even though the reactions are still occurring
  • Reversible reactions seek equilibrium, balancing opposing reaction rates
  • When reactants are added or removed, reaction rates adjust to reach a new equilibrium

Enzymes

• Biochemical reactions
  • In cells, do not occur spontaneously
  • Activation energy is the amount of energy needed to start a reaction
  • Enzymes are protein catalysts that lower the activation energy of reactions

Exergonic Reactions

• Release energy.

Endergonic Reactions

• Absorb energy.

Inorganic and Organic Compounds

• Nutrients: Essential molecules obtained from food.
• Metabolites: Molecules made or broken down in the body.
• Inorganic compounds: Carbon dioxide, oxygen, water, and inorganic acids, bases, and salts.
• Organic compounds: Molecules containing carbon and hydrogen.
  • Carbohydrates, proteins, lipids, and nucleic acids.

Properties of Water

• Water ($H_2O$)
  • Accounts for up to two-thirds of total body weight
  • Produces solutions—uniform mixtures of two or more substances
    • A solution consists of a solvent, or liquid, and solutes
    • Solutes are the dissolved substances
  • Universal solvent: Many molecules are water-soluble
  • Reactivity: Water serves as a reactant in some reactions
  • High heat capacity: Heat capacity is the heat required to raise the temperature of a unit mass of a substance 1ºC
  • Lubrication: To moisten and reduce friction
• Properties of aqueous solutions
  • Water is a polar molecule
  • Many inorganic compounds split into smaller molecules via dissociation in water
  • Ionization is dissociation into ions
  • Polar water molecules form hydration spheres around ions and small polar molecules that keep them in solution

Important Electrolytes That Dissociate in Body Fluids

• $NaCl$ (sodium chloride) $→ Na^+ + Cl^-$
• $KCl$ (potassium chloride) $→ K^+ + Cl^-$
• $Ca<em>3(PO</em>4)<em>2$ (calcium phosphate) $→ Ca^{2+} + PO</em>4^{2-}$
• $NaHCO<em>3$ (sodium bicarbonate) $→ Na^+ + HCO</em>3^-$
• $MgCl_2$ (magnesium chloride) $→ Mg^{2+} + 2Cl^-$
• $Na<em>2HPO</em>4$ (sodium hydrogen phosphate) $→ 2Na^+ + HPO_4^{2-}$
• $Na<em>2SO</em>4$ (sodium sulfate) $→ 2Na^+ + SO_4^{2-}$
• Electrolytes and body fluids
  • Electrolytes are inorganic ions that conduct electricity in solution
  • Electrolyte imbalance seriously disturbs vital body functions
• Hydrophilic and hydrophobic compounds
  • Hydrophilic
    • hydro- = water, -philos = loving
    • Includes ions and polar molecules
    • Interact with water
  • Hydrophobic
    • phobos = fear
    • Includes nonpolar molecules, fats, and oils
    • Do not interact with water
• Colloids and suspensions
  • Colloid
    • A solution containing dispersed proteins or other large molecules
    • Example: blood plasma
  • Suspension
    • Contains large particles that settle out of solution
    • Example: whole blood

pH and Homeostasis

• pH
  • The negative logarithm of the hydrogen ion concentration of a solution in moles per liter
  • Neutral pH
    • A balance of $H^+$ and $OH^-$
    • Pure water = 7.0
  • Acidic pH (lower than 7.0)
    • High $H^+$ concentration
    • Low $OH^-$ concentration
  • Basic( or alkaline)pH(higher than 7.0)
    • Low $H^+$ concentration
    • High $OH^-$ concentration
  • pH of human blood
    • Ranges from 7.35 to 7.45
  • pH scale
    • Has an inverse relationship with $H^+$ concentration
      • More $H^+$ ions means lower pH, fewer $H^+$ ions means higher pH

Acids, Bases, and Salts

• Acid (proton donor)
  • A solute that adds hydrogen ions to a solution
  • Strong acids dissociate completely in solution
• Base (proton acceptor)
  • A solute that removes hydrogen ions from a solution
  • Strong bases dissociate completely in solution
• Weak acids and weak bases
  • Fail to dissociate completely
  • Help to balance the pH
• Salt
  • Solute that dissociates into cations and anions other than hydrogen ions and hydroxide ions
• Buffers and pH control
  • Buffers stabilize pH of solutions
    • Buffer systems often involve a weak acid and its related salt (weak base)
    • Neutralize strong acids or strong bases
    • Carbonic acid–bicarbonate buffer system is very important in humans
  • Antacids
    • Use sodium bicarbonate to neutralize hydrochloric acid in the stomach

Monomers and Polymers

• Each macromolecule of life is made up of monomer subunits
  • Identical monomers (molecules) join together to form a polymer

Carbohydrates

• Organic molecules
  • Contain H, C, and usually O
  • Are covalently bonded
  • Contain functional groups that determine their chemistry
  • Include carbohydrates, lipids, proteins, and nucleic acids
• Carbohydrates
  • Contain carbon, hydrogen, and oxygen in a 1:2:1 ratio
  • Some are isomers—molecules with the same molecular formula but different structures

Types of Carbohydrates

• Monosaccharides
  • Simple sugars with three to seven carbon atoms
  • Glucose, fructose, galactose
• Disaccharides
  • Two monosaccharides condensed by dehydration synthesis
  • Sucrose, maltose
• Polysaccharides
  • Polymers of many sugars condensed by dehydration synthesis
  • Glycogen, starch, cellulose

Lipids

• Mainly hydrophobic molecules such as fats, oils, and waxes
• Made mostly of carbon and hydrogen atoms
• Include
  • Fatty acids
  • Eicosanoids
  • Glycerides
  • Steroids
  • Phospholipids and glycolipids
• Fatty acids
  • Long chains of carbon and hydrogen with a carboxyl group (COOH) at one end
  • Relatively nonpolar, except the carboxyl group
  • Fatty acids may be
    • Saturated with hydrogen
      • No double bonds in the hydrocarbon tail
    • Unsaturated (one or more double bonds in tail)
      • Monounsaturated = one double bond
      • Polyunsaturated = two or more double bonds

Eicosanoids

• Cannot be synthesized, so must be obtained from the diet
• Derived from a fatty acid called arachidonic acid
• Leukotrienes: Active in the immune system
• Prostaglandins
  • Short-chain fatty acids
  • Local hormones

Glycerides

• Fatty acids attached to a glycerol molecule
• Monoglyceride—glycerol plus one fatty acid
• Diglyceride—glycerol plus two fatty acids
• Triglycerides—glycerol plus three fatty acids
  • Also called triacylglycerols or neutral fats
  • Have three important functions
    • Energy source
    • Insulation
    • Protection

Steroids

• Four-ringed carbon structures with an assortment of functional groups
• Examples include
  • Cholesterol: Component of plasma (cell) membranes
  • Sex hormones such as estrogen and testosterone
  • Steroid hormones such as corticosteroids and calcitriol
  • Steroid derivatives called bile salts

Phospholipids and Glycolipids

• Both can be synthesized by our cells
• Contain a diglyceride attached to either a phosphate group (phospholipid) or a sugar (glycolipid)
• Generally, both have hydrophilic heads and hydrophobic tails
• Structural lipids—components of plasma membranes

Proteins

• Are the most abundant and important organic molecules
• Contain basic elements
  • Carbon (C), hydrogen (H), oxygen (O), and nitrogen (N)
• 20 amino acids are monomers that combine to form proteins (polymers)

Seven Major Protein Functions

• Support: Structural proteins
• Movement: Contractile proteins
• Transport: Transport(carrier) proteins
• Buffering: Regulation of pH
• Metabolic regulation: Enzymes
• Coordination and control: Hormones
• Defense: Antibodies

Protein Structure

• Long chains of amino acids
• Each amino acid consists of
  • Central carbon atom
  • Hydrogen atom
  • Amino group (—$NH_2$)
  • Carboxyl group (—$COOH$)
  • Variable side chain, or R group

Linking Two Amino Acids Together

• Requires dehydration synthesis between
  • Amino group of one amino acid and the carboxyl group of another amino acid
  • Forms a peptide bond
  • Resulting molecule is a peptide
  • Polypeptides are tripeptides and larger peptides

Protein Shape

• Primary structure: The sequence of amino acids along a polypeptide
• Secondary structure: Hydrogen bonds form spirals or pleats
• Tertiary structure: Coiling and folding produce three-dimensional shape
• Quaternary structure: Final protein complex produced by interacting polypeptide chains
• Fibrous and globular proteins
  • Globular proteins
    • Soluble spheres with active functions
    • Shape is based on tertiary structure
  • Fibrous proteins
    • Structural sheets or strands
    • Shape is based on secondary or quaternary structures

Enzymes are Catalysts

• Proteins that lower the activation energy of a chemical reaction
• Not changed or used up in the reaction
• Substrates (reactants) bind to an active site on an enzyme
• Enzymes exhibit
  • Specificity—catalyze only one type of reaction
  • Saturation limits—enzymes become saturated
  • Regulation—by other cellular chemicals
• Cofactors and enzyme function
  • Cofactor: An ion or molecule that binds to an enzyme before substrates can bind
  • Coenzymes: Nonprotein organic cofactors (vitamins)
• Temperature and pH affect enzyme function
  • Denaturation: Change in shape and loss of function due to heat or pH
• Glycoproteins and proteoglycans
  • Glycoproteins: Large proteins + small carbohydrates
    • Include enzymes, antibodies, hormones, and components of plasma membranes
    • Mucus production
  • Proteoglycans: Large polysaccharides + polypeptides
    • Increase viscosity of fluids

Nucleic Acids

• Large organic molecules found in the nucleus
• Store and process information
• Deoxyribonucleic acid (DNA)
  • Determines inherited characteristics
  • Directs protein synthesis
  • Controls enzyme production
  • Controls metabolism
• Ribonucleic acid (RNA)
  • Controls intermediate steps in protein synthesis

Structure of Nucleic Acids

• DNA and RNA consist of long chains of nucleotides (monomers), which contain
  • A pentose sugar (deoxyribose or ribose)
  • Phosphate group
  • Nitrogenous base (A, G, T, C, or U)
• DNA and RNA
  • DNA consists of a pair of nucleotide chains
    • Called complementary strands
    • Hydrogen bonds between opposing nitrogenous bases hold the strands together
    • Forms a twisting double helix
  • RNA consists of a single chain of nucleotides
    • Messenger RNA (mRNA)
    • Transfer RNA (tRNA)
    • Ribosomal RNA (rRNA)

Complementary Base Pairs

• Purines pair with pyrimidines
  • DNA
    • Adenine (A) bonds to thymine (T)
    • Cytosine (C) bonds to guanine (G)
  • RNA
    • Uracil (U) replaces thymine (T)

High-Energy Compounds

• Most high-energy compounds are derived from nucleotides
• Phosphorylation: The process of adding a phosphate group to another molecule
  • Produces a high-energy bond

Types of High-Energy Compounds

• Adenosine monophosphate (AMP): Nucleotide that contains one phosphate group
• Adenosine diphosphate (ADP): Contains two phosphate groups
• Adenosine triphosphate (ATP): High-energy compound containing three phosphate groups
• Adenosine triphosphatase (ATPase): Enzyme that catalyzes the conversion of ATP to ADP