Chemistry and Chemical Reactions

Learning Outcomes

• 2-1 Describe an atom and how atomic structure affects interactions between atoms.
• 2-2 Compare the ways in which atoms combine to form molecules and compounds.
• 2-3 Distinguish among the major types of chemical reactions that are important for studying physiology.
• 2-4 Describe the crucial role of enzymes in metabolism.
• 2-5 Distinguish between inorganic compounds and organic compounds.
• 2-6 Explain how the chemical properties of water make life possible.
• 2-7 Explain what pH is and discuss its importance.
• 2-8 Describe the physiological roles of acids, bases, and salts and the role of buffers in body fluids.
• 2-9 Describe monomers and polymers, and the importance of functional groups in organic compounds.
• 2-10 Discuss the structures and functions of carbohydrates.
• 2-11 Discuss the structures and functions of lipids.
• 2-12 Discuss the structures and functions of proteins.
• 2-13 Discuss the structures and functions of nucleic acids.
• 2-14 Discuss the structures and functions of high-energy compounds.

Introduction to the Chemical Level

• Chemistry:
  • The science that deals with the structure of matter.
  • Includes the structure of atoms, basic chemical building blocks, and 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 together 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 that contains electrons.
  • Electron shell: Two-dimensional representation of electron cloud.
• Element:
  • A pure substance composed of atoms of one kind.
  • The atomic number (number of protons) in an atom determines its chemical properties.
• Isotopes:
  • Versions of elements based on mass number.
  • Mass number = number of protons plus 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.

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 Notation
  • The symbol of an element indicates 1 atom of that element. A number preceding the symbol of an element indicates more than 1 atom of that element.
  • A numerical subscript following the symbol of an element indicates the number of atoms of that element in a molecule.
  • In a description of a chemical reaction, the participants at the start of the reaction are called reactants, and the reaction generates one or more products. Chemical reactions are represented by chemical equations. An arrow indicates the direction of the reaction, from reactants (usually on the left) to products (usually on the right). Chemical reactions neither create nor destroy atoms; they merely rearrange atoms into new combinations. Therefore, the numbers of atoms of each element must always be the same on both sides of the equation for a chemical reaction. When this is the case, the equation is balanced.
  • A superscript plus or minus sign following the symbol of an element indicates an ion. A single plus sign indicates a cation with a charge of +1. (The original atom has given up 1 electron.) A single minus sign indicates an anion with a charge of -1. (The original atom has gained 1 electron.) If more than 1 electron is involved, the charge on the ion is indicated by a number preceding the plus or minus sign.
• 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 (positive ion).
  • Another atom—the electron acceptor—gains those same electrons and becomes an anion (negative ion).
  • Ionic bonds are attractions between cations and anions.
• 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 1°C
• 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
• 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 $pH = -log[H^+]$
• 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
• 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

• 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 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

• 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 (—NH2)
    • 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

• 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
• 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