Chapter 2

BASIC CHEMISTRY
Matter
 Anything that occupies space and has mass
 Matter may exist as one of three states
o Solid – definite shape and volume
o Liquid – definite volume; shape of container
o Gaseous – neither a definite shape nor volume
 Matter may be changed
o Physically
 Changes do not alter the basic nature of a substance
 Examples include changes in the state of matter (solid, liquid or
gas)
o Chemically
 Changes alter the chemical composition of the substance

Energy
 The ability to do work
 Has no mass and does not take up space
o Kinetic Energy – energy is doing work
o Potential energy – energy is inactive or stored
 Forms of energy
o Chemical energy – stored in chemical bonds of substances (ex: food)
o Electrical energy – results from movement of charged particles (ex:
movement of the neurons and nerve cells)
o Mechanical energy – energy directly involved in moving matter (ex: when
our muscles contract)
o Radiant energy – travel in waves, energy of the electromagnetic spectrum
(ex: x-ray, CT scan, MRI, diagnostic examination)
 Energy form conversions
o ATP (adenosine triphosphate) traps the chemical energy of food in its
bonds

Composition of Matter
 Elements – fundamental units of matter
o 96 percent of the body is made from four elements:
1. Oxygen (O) – most common; 65% of the body’s mass
2. Carbon (C)
3. Hydrogen (H)
4. Nitrogen (N)
 Periodic Table contains a complete listing of elements
Composition of Matter
 Atoms
o Building blocks of elements
o Atoms of elements differ from one another
o Atomic symbol is chemical shorthand for each element
 The Basic Atomic Sub particles
o Protons (p+) are positively charged
o Neutrons (n 0) are uncharged or neutral
o Electrons are (e−¿¿ ) are negatively charged

 All atoms are electrically neutral

o Number of protons equals number of electrons in an atom

o Positive and negative charges cancel each other out
 Ions are atoms that have lost or gained electrons

Identifying Elements

 To identify an element, we need to know the:

o Atomic Number – equal to the number of protons that the atom contains
 Unique to atoms of a particular element
 Indirectly tells the number of electrons in an atom
o Atomic Mass Number – sum of the protons and neutrons contained in an
atom’s nucleus
o Atomic Weight – approximately equal to the mass number of the element’s
most abundant isotope
  Isotopes
o Atoms that have the same number of protons and electrons but vary in the
number of neutrons
o Isotopes have the same atomic number but different atomic masses

Atomic Weights and Isotopes

 Radioisotope

o Heavy isotope of certain atoms

o Tends to be unstable
 o Decomposes to more stable isotope
 Radioactivity – process of spontaneous atomic decay
o Used to tag and trace biological molecules through the body

Molecules and Compounds

 Molecule – two or more atoms of the same elements combined chemically

 Example of a chemical reaction, shown as a chemical equation, resulting in a
molecule:
H (atom) + H (atom) → H 2 (molecule)
o The reactants are the atoms on the left
o The product is the molecule on the right, represented by a molecular
formula

 Compound – two or more atoms of different elements combined chemically to

form a molecule of a compound
 Example of a chemical reaction resulting in a compound:
4H + C → CH 4 (methane)

Chemical Bonds and Chemical Reactions

 Chemical reactions occur when atoms combine with or dissociate from other
atoms

 Chemical bonds are energy relationships involving interactions among the

electron reacting atoms

Types of Chemical Bonds

 Ionic Bonds
o Form when electrons are completely transferred from one atom to another
o Allow atoms to achieve stability through the transfer of electrons

 Ions
o Result from the loss or gain of electrons
 Anions have negative charge due to gain of electrons
 Cations have positive charge due to loss of electrons
 o Tend to stay close together because opposite charges attract

 Covalent Bonds
o Atoms become stable through shared electrons
o Electrons are shared in pairs
o Single covalent bonds share one pair of electrons

o Double covalent bonds share two pairs of electrons

o Covalent Bonds can be described as either nonpolar or polar

 Nonpolar covalent bonds
- electrons are shared equally between the atoms of the molecule

- electrically neutral as a molecule

 - example: carbon dioxide
 Polar covalent bonds
- Electrons are not shared equally between the atoms of the molecule
- Molecule has a positive and negative side, or pole
- Example: water

 Hydrogen
Bonds
o
Extremely
weak chemical bonds
o Formed when a hydrogen atom is attracted to the negative portion, such
as an oxygen or nitrogen atom, of a polar molecule
o Responsible for the surface tension of water
o Important for forming intramolecular bonds, as in protein structure

Patterns of Chemical Reactions

 Synthesis reaction (A + B → AB)
o Atoms or molecules combine together to
form a larger, more complex molecule
o Energy is absorbed for bond formation
o Underlies all anabolic (building) activities
in the body

 Decomposition
reaction (AB → A + B)
o Molecule is broken down into
smaller molecules
o Chemical energy is released
o Underlies all catabolic (destructive)
activities in the body

 Exchange reaction
AB + C → AC + B
And
AB + CD → AD + CB
o Involves simultaneous synthesis and
decomposition reactions as bonds are both
made and broken
o Switch is made between molecule parts, and
different molecules are made
  Most chemical reactions are reversible
 Reversibility is indicated by a double arrow
o When arrows differ in length, the longer arrow indicates the more rapid
reaction or major direction of progress
 Factors influencing the rate of chemical reactions are shown in Table 2.4

Biochemistry: The Chemical Composition of Living Matter

Inorganic Compounds Organic Compounds

 Lack carbon  Contain carbon

 Tend to be small, simple  All are large, covalent molecules
molecules  Include carbohydrates, lipids,
 Include water, salts, and many (not proteins, and nucleic acids
all) acids and bases

INORGANIC COMPOUND
 Water
o Most abundant inorganic compound in the body
o Accounts for two-thirds of the body’s weight
o Vital properties include:
 High heat capacity
 Polarity/solvent properties
 Chemical reactivity
 Cushioning

 High heat capacity

→ Water absorbs and releases a large amount of heat before it
changes temperature
→ Prevents sudden changes in body temperature

 Polarity/solvent properties
→ Water is often called the “universal solvent”
→ Solvents are liquids or gases that dissolve smaller amounts of
solutes
→ Solutes are solids, liquids, or gases that are dissolved or
suspended by solvents
→ Solution forms when solutes are very tiny
 → Colloid forms when solutes of intermediate size form a translucent
mixture

 Chemical reactivity
→ Water is an important reactant in some chemical reactions
→ Reactions that require water is known as hydrolysis reactions
→ Example: water helps digest food or break down biological
molecules

 Cushioning
→ Water serves a protective function
→ Examples: cerebrospinal fluid protects the brain from physical trauma, and
amniotic fluid protects a developing fetus

 Salt
o Ionic compound
o Contain cations other than H +¿¿ and anions other than OH-
o Easily dissociate (break apart) into ions in the presence of water
o All salts are electrolytes
o Electrolytes are ions that conduct electrical currents
o Vital to many body functions

 Example: sodium and potassium ions are essential for nerve

impulses
 Acids
o Electrolytes that disassociate (ionize) in water and release hydrogen ions (
H +¿¿ )
o Proton ( H +¿¿ ) donors
o Example: HCI → H +¿¿ + Cl-
o Strong acids ionize completely and liberate all their protons
o Weak acids ionize incompletely

 Bases
o Electrolytes that dissociate (ionize) in water and release hydroxyl (OH-)
o Proton ( H +¿¿ ) acceptors
o Example: NaOH → Na+ ¿¿ + OH-

 Neutralization reaction
o Type of exchange reaction in which acids and bases react to form water
and a salt
o Example: NaOH + H 2O + NaCl

 pH (power of Hydrogen)
o pH measures relative concentration of hydrogen (and hydroxide) ions in
body fluids
o pH scale is based on the number of protons in a solution
o pH scale runs from 0 to 14 (0-7 is acids, 8-14 is bases)
o Each successive change of 1 pH unit represents a tenfold change in H +¿¿
concentration
o Neutral
 7 is neutral
 Neutral means that the number of hydrogen ions exactly equals the
number of hydroxyl ions
o Acidic solutions have a pH below 7
 More H +¿¿ than OH-
o Basic solutions have a pH above 7
+¿¿
 Fewer H than OH-
o Buffers – chemicals that can regulate pH change
Note that:

 If pH increases (8-14), the hydrogen ion decreases.

Neutralization reaction happens when acid and bases are combined thus producing
water and salt.

 If pH decreases (7-0), the hydrogen ion increases.

ORGANIC COMPOUND
  Polymer – chainlike molecules made of many
similar or repeating units (monomers)
 Many biological molecules are
polymers, such as carbohydrates and
proteins

There are two reactions that happens in organic compound:

1. Dehydration synthesis – monomers are joined to from polymers through the

removal of water molecules
o A hydrogen ion is removed from one monomer while a hydroxyl group is
removed from the monomer it is to be joined with
o Water is removed at the site where monomers are joined (dehydration)

2. Hydrolysis – polymers are broken down into monomers through the addition of

water molecules
o As a water molecule is added to each bond, the bond is broken, and the
monomers are released

 Carbohydrates

o Contain carbon, hydrogen, and oxygen

o Include sugars and starches
o Classifies according to size and solubility in water
 Monosaccharides – simple sugars and the structural units of the
carbohydrate group
 Disaccharides – two simple sugars joined by dehydration synthesis
 Polysaccharides – long-branching chains of linked simple sugars

 Monosaccharides – simple sugars

o Single-chain or single-ring structures
 o Contain three to seven carbon atoms
o Examples: glucose (blood sugar), fructose, galactose, ribose, deoxyribose
a. simple sugar (monosaccharides)

 Disaccharides – two simple sugars joined by dehydration synthesis

o Examples include sucrose, lactose, and maltose
o Too large to pass through cell membranes
b. double sugar (disaccharide)

 Note that:
Glucose + Galactose = Lactose + Water
Glucose + Fructose = Sucrose + Water
Glucose + Glucose = Maltose + Water

 Polysaccharides – long, branching chains of linked simple sugars

o Large, insoluble molecules
o Function as storage products
o Examples include starch and oxygen

 Lipids
o Most abundant are triglycerides, phospholipids, and steroids
o Contain carbon, hydrogen, and oxygen
 Carbon and hydrogen outnumber oxygen
o Insoluble in water, but soluble in other lipids
 Lipids (continued)
 Triglycerides or neutral fats
o Source of stored energy
o Composed of two types of building blocks – fatty acids and one glycerol
molecule
 Saturated fatty acids
 Unsaturated fatty acids
 o Fatty acid chains of triglycerides
 Saturated fats
- Contain only single covalent bonds
- Chains are straight
- Exist as solids at room temperature since molecules closely pack
together
 Unsaturated fats
- Contain one or more double covalent bonds, causing chains to kink
- Exist as liquid oils at room temperature
- “Heart healthy”

 Trans fats
- Oils that have been solidified by the addition of hydrogen atoms at
double bond sites
- Increases risk of heart diseases

 Omega-3 fatty acids

- Found in cold-water fish and plant sources, including flax, pumpkin,
and chia seeds; walnuts and soy foods
- Appear to decrease risk of heart disease

 Phospholipids
o Contain two fatty acids chains rather than three; they are hydrophobic
(water-fearing)
o Phosphorus-containing polar “head” carries an electrical charge and is
hydrophilic (water-loving)
o Charged “head” region interacts with water and ions while the fatty acid
chains “tails” do not
o Form cell membranes
 Steroids
o Formed of four interlocking rings
o Include cholesterol, bile salts,
vitamin D, and some hormones
o Some cholesterol is ingested from
animal products; the liver also
makes cholesterol
o Cholesterol is the basis for all
steroids made in the body

 Proteins
o Account for over half of the body’s organic matter
 Provide for construction materials for body tissues
 Play a vital role in cell function
 Act as enzymes, hormones, and antibodies
o Contain carbon, oxygen, hydrogen, nitrogen, and sometimes sulfur
o Built from building blocks called amino acids
 Amino acids structure
- Contain an amine group ( NH 2)
- Contain an acid group (COOH)

- Vary only by R-groups

o Protein Structure
 Polypeptides contain fewer than 50 amino acids
 Proteins contain more than 50 amino acids
 Large, complex proteins contain 50 to thousands of amino acids
 Sequence of amino acids produces a variety of proteins
o Structural levels of proteins
  Primary structure – strand of amino acid “beads”
 Secondary structure – chains of amino acids twist or bend
- Alpha helix – resembles a metal spring
- Beta-pleated sheet – resembles pleats of a skirt or sheet of
paper folded into a fan
 Tertiary Structure – compact, ball-like (globular) structure
 Quaternary structure – result of a combination of two or more
polypeptide chains

o Fibrous (structural) proteins

 Appear in body structures
 Exhibit secondary, tertiary, or even quaternary structure
 Bind structures together and exist in body tissues
 Stable proteins
 Examples include collagen and keratin
 o Globular (functional) proteins
 Function as antibodies, hormones, or enzymes
 Exhibit at least tertiary structure
 Hydrogen bonds are critical to the maintenance of structure
 Can be denatured and no longer perform physiological roles
 Active sites “fit” and interact chemically with other molecules

  Enzymes
o Act as biological catalysts
o Increase the rate of chemical reactions
o Bind to substances at an active site to catalyze reactions
o Can be recognized by their – ase suffix
 Hydrolase
 Oxidase
 Nucleic acids
o Form genes
o Composed if carbon, oxygen, hydrogen, nitrogen, and phosphorus atoms
o Largest biological molecules in the body
o Two major kinds:
 DNA
 RNA
o Nucleic acids are built from building blocks called nucleotides
o Nucleotides contain three parts
1. A nitrogenous base
 A = Adenine
 G = Guanine
 C = Cytosine
 T = Thymine
 U = Uracil
2.

Pentose (five-carbon) sugar

3. A phosphate group

 Deoxyribonucleic acid (DNA)

o The genetic material found within the cell’s nucleus
o Provides instructions for every protein in the body
o Organized by complementary bases to form a double-stranded helix
o Contains the sugar deoxyribose and the bases adenine, thymine,
cytosine, and guanin
o Replicates before cell division
 Ribonucleic
acid (RNA)
o Carries out DNA’s instructions for protein synthesis
o Created from a template of DNA
o Organized by complementary bases to form a single-stranded helix
o Contains the sugar ribose and the bases adenine, uracil, cytosine, and
guanine
o Three varieties are messenger, transfer, and ribosomal RNA

 Adenosine triphosphate (ATP)

o Composed of a nucleotide built from ribose sugar, adenine base, and
three phosphate groups
o Chemical energy used by all cells
o Energy is released by breaking high-energy phosphate bondf

o ADP (adenosine diphosphate) accumulates as ATP is used for energy

o ATP is replenished by oxidation of food fuels
o Three examples of how ATP drives cellular work is shown below