The Chemistry of Life

Basic Chemistry; Chemical Reactions; Acids and Bases; Water; Organic Molecules

Chemistry and Physiological Reactions

• Body is made up of many chemicals

• Chemistry underlies all physiological reactions:

– Movement, digestion, pumping of heart, nervous system

• Chemistry can be broken down into:

– Basic chemistry

– Biochemistry

Part 1 – Basic Chemistry

”Matter”

• Matter is anything that has mass and occupies space

– Matter can be seen, smelled, and/or felt

– Weight is mass plus the effects of gravity

• States of matter

– Matter can exist in three possible states:

• Solid: definite shape and volume

• Liquid: changeable shape; definite volume

• Gas: changeable shape and volume

“Energy”

• Energy is the capacity to do work or put matter into motion

• Energy does not have mass, nor does it take up space

• The greater the work done, the more energy it uses up

– Energy exists in two possible forms:

• Kinetic – energy in action

• Potential – stored (inactive) energy

– Energy can be transformed from potential to kinetic energy

• Stored energy can be released, resulting in action

• Forms of energy

– Chemical energy

• Stored in bonds of chemical substances

– Electrical energy

• Results from movement of charged particles

– Mechanical energy

• Directly involved in moving matter

– Radiant or electromagnetic energy

• Travels in waves (example: heat, visible light, ultraviolet light, and X rays)

• Energy form conversions

– Energy may be converted from one form to another

• Example: turning on a lamp converts electrical energy to light energy

– Energy conversion is inefficient

• Some energy is “lost” as heat, which can be partly unusable energy

• All matter is composed of elements

– Elements are substances that cannot be broken down into simpler substances by ordinary
chemical methods

• Four elements make up 96% of body:

– Carbon, oxygen, hydrogen, and nitrogen

– 9 elements make up 3.9% of body

– 11 elements make up

• Periodic table lists all known elements

• All elements are made up of atoms, which are:

– Unique building blocks for each element

– Smallest particles of an element with properties of that element

– What give each element its particular physical & chemical properties

• Atomic symbol

– One- or two-letter chemical shorthand for each element

• Example: “O” for oxygen, “C” for carbon

• Some symbols come from Latin names: “Na” (natrium) is sodium; “K” (kalium) is potassium
“Structure of Atoms”

• Atoms are composed of three subatomic particles:

– Protons

• Carry a positive charge (+)

• Weigh an arbitrary 1 atomic mass unit (1 amu) =1 dalton

– Neutrons

• Have no electrical charge (0)

• Also weigh 1 amu

– Electrons

• Carry a negative charge (−)

• Are so tiny they have virtually no weight (0 amu) =1/2000 dalton

• Protons and neutrons are found in a centrally located nucleus; electrons orbit around the nucleus

• Chemists devise models of how subatomic particles are put together

– Planetary model

– Orbital model

Two models of the structure of an atom

• Different elements contain different numbers of subatomic particles

– Hydrogen has 1 proton, 0 neutrons, and 1 electron

– Helium has 2 protons, 2 neutrons, and 2 electrons

– Lithium has 3 protons, 4 neutrons, and 3 electrons

• Identifying facts about an element include its atomic number, mass number, isotopes, and atomic
weight

Atomic structure of the three smallest atoms

• Atomic number

– Number of protons in nucleus

– Written as subscript to left of atomic symbol

• Example: 3Li

• Mass number

– Total number of protons and neutrons in nucleus

• Total mass of atom

– Written as superscript to left of atomic symbol

• Example: 7Li
• Isotopes

– Structural variations of same element

– Atoms contain same number of protons but differ in the number of neutrons they contain

• Atomic numbers are same, but mass numbers different

• Atomic weight

– Average of mass numbers of all isotope forms of an atom

“Isotopes of Hydrogen”

”Radioisotopes”

• Radioisotopes are isotopes that decompose to more stable forms

– Atom loses various subatomic particles

• Sometimes loss results in an isotope becoming a different element

– As isotope decays, subatomic particles that are being given off release a little energy

• This energy is referred to as radioactivity

• Can be detected and measured with scanners

Molecules and Compounds

• Most atoms chemically combine with other atoms to form molecules and compounds

– Molecule: general term for 2 or more atoms bonded together

– Compound: specific molecule that has 2 or more different kinds of atoms bonded together

• Example: C6H12O6

• Molecules with only one type of atom (H2 or O2 ) are just called molecules

“Mixture”

• Most matter exists as mixtures: two or more components that are physically intermixed

• Three basic types of mixtures

– Solutions

– Colloids

– Suspensions

Types of Mixture
“Solutions”

• Solutions

– Are homogeneous mixtures, meaning particles are evenly distributed throughout

– Solvent: substance present in greatest amount

• Usually a liquid, such as water

– Solute(s): substance dissolved in solvent

• Present in smaller amounts

“Colloids”

• Colloids

– Also known as emulsions; are heterogeneous mixtures, meaning that particles are not evenly
distributed throughout mixture

– Some undergo sol-gel (solution to gel) transformations

(cytosol)

“Suspensions”

• Suspensions

– Heterogeneous mixtures that contain large, visible solutes that do settle out

– Example: mixture of water and sand

”Chemical Bonds”

• Chemical bonds are “energy relationships” between electrons of reacting atoms

• Electrons are the subatomic particles that are involved in all chemical reactions

“Roles of Electrons in Chemical Bonding”

• Electrons can occupy areas around nucleus called electron shells

– Each shell contains electrons that have a certain amount of kinetic and potential energy, so shells are
also referred to as energy levels

– Depending on its size, an atom can have up to 7 electron shells

• Octet rule (rule of eights)

– Atoms desire 8 electrons in their valence shell

– Desire to have 8 electrons is driving force behind chemical reactions

– Most atoms do not have full valence shells

“Chemically inert and reactive elements”

Types of Chemical Bonds

• Three major types of chemical bonds

– Ionic bonds

– Covalent bonds

– Hydrogen bonds

“Ionic Bonds”

• Ionic bonds

– Ions are atoms that have gained or lost electrons and become charged

– Ionic bonds involve the transfer of valence shell electrons from one atom to another, resulting in ions
• One becomes an anion (negative charge)

– Atom that gained one or more electrons

• One becomes a cation (positive charge)

– Attraction of opposite charges results in an ionic bond

Formation of ionic bond

• Covalent bonds

– Covalent bonds are formed by sharing of two or more valence shell electrons between two atoms

– Allows each atom to fill its valence shell at least part of the time

– Two types of covalent bonds:

• Polar and nonpolar covalent bonds

2 e – single

4 e – double

6 e- triple

Formation of covalent bonds

– Nonpolar covalent bonds

• Equal sharing of electrons between atoms

• Results in electrically balanced, nonpolar molecules such as CO2

• Polar covalent bonds

– Unequal sharing of electrons between 2 atoms

– Results in electrically polar molecules

– Atoms have different electron-attracting abilities, leading to unequal sharing

• Atoms with greater electron-attracting ability are electronegative, and those with less are
electropositive
“Hydrogen bonds”

• Hydrogen bonds

– Attractive force between electropositive hydrogen of one molecule and an electronegative

– Common between dipoles such as water

– Also act as intramolecular bonds, holding a large molecule in a three-dimensional shape

Chemical Equations

• Chemical reactions occur when chemical bonds are formed, rearranged, or broken

• These reactions can be written in symbolic forms called chemical equations

• Chemical equations contain:

– Reactants: substances entering into reaction together

– Product(s): resulting chemical end products

– Amounts of reactants and products are shown in balanced equations

“Types of Chemical Reactions”

• Three main types of chemical reactions:

1. Synthesis (combination) reactions involve atoms or molecules combining to form larger, more
complex molecule

• Used in anabolic (building) processes

A + B → AB

Synthesis
2. Decomposition reactions involve breakdown of a molecule into smaller molecules or its constituent
atoms (reverse of synthesis reactions)

• Involve catabolic (bond-breaking) reactions

AB → A + B

3. Exchange reactions, also called displacement reactions, involve both synthesis and decomposition

• Bonds are both made and broken

AB + C → AC + B

and

AB + CD → AD + CB
4. Reversible Reactions

• All chemical reactions are theoretically reversible

A + B ←→ AB

• Chemical equilibrium occurs when the rate of product formation is equal to the rate of reactant
formation.

Rate of Chemical Reactions

• The speed of chemical reactions can be affected by:

– Temperature: increased temperatures usually increase rate of reaction

– Concentration of reactants: increased concentrations usually increase rate

– Particle size: smaller particles usually increase rate

– Catalysts increase the rate of reaction without being chemically changed or becoming part of the
product

• Enzymes are biological catalysts

“Biochemistry”

• All chemicals either organic or inorganic

– Inorganic compounds

• Water, salts, and many acids and bases

• Do not contain carbon

– Organic compounds

• Carbohydrates, fats, proteins, and nucleic acids

• Contain carbon, are usually large, and are covalently bonded

• Both equally essential for life

Water

• Most abundant inorganic compound

– Accounts for 60%–80% of the volume of living cells

• Most important inorganic compound because of its properties

– High heat capacity

– High heat of vaporization

– Polar solvent properties

– Reactivity

– Cushioning

“Water Properties”

• High heat capacity

– Ability to absorb and release heat with little temperature change

– Prevents sudden changes in temperature

• High heat of vaporization

– Evaporation requires large amounts of heat

– Useful cooling mechanism

• Polar solvent properties

– Dissolves and dissociates ionic substances

– Forms hydration (water) layers around large charged molecules

• Example: proteins

– Body’s major transport medium

• Reactivity

– Necessary part of hydrolysis and dehydration synthesis reactions

• Cushioning

– Protects certain organs from physical trauma

• Salts are ionic compounds that dissociate into separate ions in water

– Separate into cations (positively charged molecules) and anions (negatively charged)

• Not including H+ and OH– ions

“Acid- Base Balance”

• Acids and bases are both electrolytes

– Ionize and dissociate in water

• Acids

– Are proton donors: they release hydrogen ions (H+ ), bare protons (have no electrons) in
solution

– Important acids

• HCl (hydrochloric acid), HC2H3O2 (acetic acid, abbreviated HAc), and H2CO3 (carbonic acid)

“Bases”

• Bases

– Are proton acceptors: they pick up H+ ions in solution

• Example: NaOH → Na+ + OH–

– When a base dissolves in solution, it releases a hydroxyl ion (OH – )

– Important bases

• Bicarbonate ion (HCO3 – ) and ammonia (NH3 )

“ph”

• pH: Acid-base concentration

– pH scale is measurement of concentration of hydrogen ions [H+ ] in a solution

– The more hydrogen ions in a solution, the more acidic that solution is

– The scale ranges from 0 to 14.

– Neutral solutions have equal numbers of H+ and OH– ions

• All neutral solutions are pH 7

• Pure water is pH neutral

– pH of pure water = pH 7: [H+ ] = 10–7 m

– Alkaline (basic) solutions have low [H+] but high pH

“ABG”

• The Respiratory System (Acid); CO2 is a volatile acid

– If you increase your respiratory rate (hyperventilation) you "blow off" CO2 (acid) therefore decreasing
your CO2 acid—giving you ALKALOSIS

– If you decrease your respiratory rate (hypoventilation) you retain CO2 (acid) therefore increasing your
CO2 (acid)—giving you ACIDOSIS

• The Renal System (Base); the kidneys rid the body of the nonvolatile acids H+ (hydrogen ions) and
maintain a constant bicarb (HCO3). Bicarbonate is the body’s base

– You have Acidosis when you have excess H+ and decreased HCO3- causing a decrease in pH.

– You have Alkalosis when H+ decreases and you have excess (or increased) HCO3- base.

• Compensation

– The respiratory system can effect a change in 15-30 minutes

– The renal system takes several hours to days to have an effect.

“The Big Four”

❑ Respiratory Acidosis: pH < 7.35 (Normal: 7.35 - 7.45) CO2 > 45 (Normal: 35 – 45)

❑Respiratory Alkalosis: pH > 7.45 (Normal: 7.35 - 7.45) CO2 < 35 (Normal: 35 – 45)

❑Metabolic Acidosis pH < 7.35 (Normal: 7.35 - 7.45) HCO3- < 22 (normal: 22 – 26)

❑Metabolic Alkalosis pH > 7.45 (Normal: 7.35 - 7.45) HCO3- > 26

• Organic molecules contain carbon

• Carbon is electroneutral

• Major organic compounds: carbohydrates, lipids, proteins, and nucleic acids

• Many are polymers

– Chains of similar units called monomers (building blocks)

• Synthesized by dehydration synthesis

• Broken down by hydrolysis reactions

“Carbohydrates”

• Carbohydrates include sugars and starches

• Contain C, H, and O

– Hydrogen and oxygen are in 2:1 ratio

• Three classes

– Monosaccharides: one single sugar

• Monomers: smallest unit of carbohydrate

– Disaccharides: two sugars

– Polysaccharides: many sugars

• Polymers are made up of monomers of monosaccharides

“Monosaccharides”

• Monosaccharides

– Simple sugars containing three to seven carbon atoms

– (CH2O)n : general formula

• n = number of carbon atoms

– Monomers of carbohydrates

– Important monosaccharides

• Pentose sugars – Ribose and deoxyribose

• Hexose sugars – Glucose (blood sugar)

• Disaccharides

– Double sugars

– Too large to pass through cell membranes

– Important disaccharides

• Sucrose, maltose, lactose

– Formed by dehydration synthesis of two monosaccharides

• glucose + fructose → sucrose + water

• Polysaccharides

– Polymers of monosaccharides

• Formed by dehydration synthesis of many monomers

– Important polysaccharides

• Starch: carbohydrate storage form used by plants

• Glycogen: carbohydrate storage form used by animals

– Not very soluble

Lipids

• Contain C, H, O, but less than in carbohydrates, and sometimes contain P

• Insoluble in water

• Main types:

– Triglycerides or neutral fats

– Phospholipids

– Steroids

– Eicosanoids
Triglycerides

• Triglycerides can be constructed of:

– Saturated fatty acids

• All carbons are linked via single covalent bonds, resulting in a molecule with the maximum
number of H atoms (saturated with H)

• Solid at room temperature (Example: animal fats, butter)

– Unsaturated fatty acids

• One or more carbons are linked via double bonds, resulting in reduced H atoms (unsaturated)

• Liquid at room temperature (Example: plant oils, such as olive oil)

• Trans fats – modified oils; unhealthy

• Omega-3 fatty acids – “heart healthy”

“Phospholipids”

• Phospholipids

– Modified triglycerides

• Glycerol and two fatty acids plus a phosphoruscontaining group

– “Head” and “tail” regions have different properties

• Head is a polar region and is attracted to water

• Tails are nonpolar and are repelled by water

– Important in cell membrane structure

“Steroids”

• Steroids

– Consist of four interlocking ring structures

– Common steroids: cholesterol, vitamin D, steroid hormones, and bile salts

– Most important steroid is cholesterol

• Is building block for vitamin D, steroid synthesis, and bile salt synthesis

• Important in cell plasma membrane structure

• Eicosanoids

– Many different ones

– Derived from a fatty acid (arachidonic acid) found in cell membranes

– Most important eicosanoids are prostaglandins

• Play a role in blood clotting, control of blood pressure, inflammation, and labor contractions

“Proteins”

• Comprise 20–30% of cell mass

• Have most varied functions of any molecules

– Structural, chemical (enzymes), contraction (muscles)

• Contain C, H, O, N, and sometimes S and P

• Polymers of amino acid monomers held together by peptide bonds

• Shape and function due to four structural levels

• All proteins are made from 20 types of amino acids

– Joined by covalent bonds called peptide bonds

– Contain both an amine group and acid group

– Can act as either acid or base

– Differ by which of 20 different “R groups” is present

“Enzymes and Enzymes Activity”

• Enzymes: globular proteins that act as biological catalysts

– Catalysts regulate and increase speed of chemical reactions without getting used up in the process

– Lower the energy needed to initiate a chemical reaction

• Leads to an increase in the speed of a reaction

• Allows for millions of reactions per minute!

– Most functional enzymes, referred to as holoenzymes, consist of two parts

• Apoenzyme (protein portion)

• Cofactor (metal ion) or coenzyme (organic molecule, often a vitamin)

– Enzymes are specific

• Act on a very specific substrate

– Names usually end in –ase and are often named for the reaction they catalyze

• Example: hydrolases, oxidases

“Nucleic Acids”

• Nucleic acids, composed of C, H, O, N, and P, are the largest molecules in the body

• Nucleic acid polymers are made up of monomers called nucleotides

– Composed of nitrogen base, a pentose sugar, and a phosphate group

• Two major classes:

– Deoxyribonucleic acid (DNA)

– Ribonucleic acid (RNA)

“DNA”

• DNA holds the genetic blueprint for the synthesis of all proteins

– Double-stranded helical molecule (double helix) located in cell nucleus

– Nucleotides contain a deoxyribose sugar, phosphate group, and one of four nitrogen bases:

• Purines: adenine (A), guanine (G)

• Pyrimidines: cytosine (C) and thymine (T)

• DNA holds the genetic blueprint for the synthesis of all proteins (cont.)

– Bonding of nitrogen base from strand to opposite strand is very specific

• Follows complementary base-pairing rules:

– A always pairs with T

– G always pairs with C

• RNA links DNA to protein synthesis and is slightly different from DNA

– Single-stranded linear molecule is active mostly outside nucleus

– Contains a ribose sugar (not deoxyribose)

– Thymine is replaced with uracil

– Three varieties of RNA carry out the DNA orders for protein synthesis

• Messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)

“ATP”

• Chemical energy released when glucose is broken down is captured in ATP (adenosine triphosphate)

• ATP directly powers chemical reactions in cells

– Offers immediate, usable energy needed by body cells

• Structure of ATP

– Adenine-containing RNA nucleotide with two additional phosphate groups

“Cellular respiration”

• Anaerobic phase

- In the absence of oxygen, glucose is partially broken down by a series of catabolic reactions into
pyruvic acid.

• Aerobic phase

- In the presence of oxygen, glucose is completely broken down into carbon dioxide and water.