Chapter 2
Chemical
Principles
© 2013 Pearson Education, Inc. Lectures prepared by Christine L. Case
Copyright © 2013 Pearson Education, Inc.
Lectures prepared by Christine L. Case
The Structure of Atoms
▪ Chemistry is the study of interactions between
atoms and molecules
▪ The atom is the smallest unit of matter that enters
into chemical reactions
▪ Atoms interact to form molecules
▪ Atoms are composed of
▪ Electrons: negatively charged particles
▪ Protons: positively charged particles
▪ Neutrons: uncharged particles
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The Structure of Atoms
▪ Protons and neutrons are in the nucleus
▪ Electrons move around the nucleus
Figure 2.1 The structure
of an atom.
Electron shells
Proton (p+)
Nucleus
Neutron (n0)) Insert Fig 2.1
Electron (e−)
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Chemical Elements
▪ Each chemical element has a different number of
protons
▪ Isotopes of an element are atoms with different
numbers of neutrons. Isotopes of oxygen:
16 17 18
8
O 8
O 8
O
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Electronic Configurations
▪ Electrons are arranged in electron shells
corresponding to different energy levels
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Table 2.1 The Elements of Life
Insert Table 2.1
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How Atoms Form Molecules
▪ Atoms combine to complete the outermost shell
▪ The number of missing or extra electrons in this shell
is known as the valence
▪ Molecules hold together because the valence
electrons of the combining atoms form attractive
forces, called chemical bonds, between the atomic
nuclei
▪ A compound contains different kinds of atoms
H2O
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Ionic Bonds
▪ When the number of protons and electrons is equal
in an atom, there is electrical neutrality
▪ Ions are charged atoms that have gained or lost
electrons
Figure 2.2a Ionic bond formation.
Loss of Gain of
electron electron
Sodium atom Sodium ion Chlorine atom Chloride ion
(electron donor) (Na+) (electron acceptor) (Cl–)
A sodium atom (Na) loses one electron to an electron acceptor and forms a sodium ion (Na+).
A chlorine atom (Cl) accepts one electron from an electron donor to become a chloride ion (Cl–).
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Ionic Bonds
▪ Ionic bonds are attractions between ions of
opposite charge
▪ One atom loses electrons, and another gains electrons
Figure 2.2b Ionic bond formation.
Insert Fig 2.2b
Sodium chloride molecule
Sodium ion Chloride ion Na+ Cl–
(Na+) (Cl–)
NaCl
The sodium and chloride ions are attracted because of their opposite charges and are held
together by an ionic bond to form a molecule of sodium chloride.
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Covalent Bonds
▪ Covalent bonds form when two atoms share
one or more pairs of electrons
Figure 2.3a Covalent bond formation.
Diagram of Atomic Structure Structural Formula Molecular Formula
Insert Fig 2.3a or
Hydrogen atom Hydrogen atom Hydrogen molecule
A single covalent bond between two hydrogen atoms.
Figure 2.3b Covalent bond formation.
Diagram of Atomic Structure Structural Formula Molecular Formula
or
Carbon atom
Insert Fig 2.3b
Hydrogen atoms
Methane molecule
Single covalent bonds between four hydrogen atoms and a carbon atom, forming a
methane molecule.
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Water
▪ Inorganic
▪ Polar molecule
▪ Solvent
▪ Polar substances dissociate, forming solutes
NOTE: Between
the atoms, there
are covalent
Figure 2.4a Hydrogen bond bonds
formation in water.
Insert Fig 2.4a
Partial Charges
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Hydrogen Bonds
▪ Hydrogen bonds form when a hydrogen atom that
is covalently bonded to an O or N atom is attracted
to another N or O atom in another molecule
Figure 2.4b Hydrogen bond
formation in water.
Hydrogen
bond
Insert Fig 2.4b
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Molecular Weight and Moles
▪ The sum of the atomic
weights in a molecule is
the molecular weight H2O
▪ One mole of a substance
2H =21 =2
is its molecular weight in
grams O = 16
MW = 18
1 mole weighs 18 g
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Chemical Reactions
▪ Chemical reactions involve the making or breaking
of bonds between atoms
▪ A change in chemical energy occurs during a
chemical reaction
▪ Endergonic reactions absorb energy
▪ Exergonic reactions release energy
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Synthesis Reactions
▪ Occur when atoms, ions, or molecules combine
to form new, larger molecules
Combines
to form
A + B AB
Atom, ion, Atom, ion, New molecule
or molecule A or molecule B AB
▪ Anabolism is the synthesis of molecules in a cell
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Decomposition Reactions
▪ Occur when a molecule is split into smaller
molecules, ions, or atoms
Breaks
down into
AB A + B
New molecule Atom, ion, Atom, ion,
AB or molecule A or molecule B
▪ Catabolism is the decomposition reactions in a cell
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Exchange Reactions
▪ Are part synthesis and part decomposition
NaOH + HCl NaCl + H2O
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Reversible Reactions
▪ Can readily go in either direction
▪ Each direction may need special conditions
Heat
A + B AB
Water
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Important Biological Molecules
▪ Organic compounds always contain carbon and
hydrogen
▪ Inorganic compounds typically lack carbon
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Water
▪ Inorganic
▪ Polar molecule
▪ Solvent
▪ Polar substances dissociate, forming solutes
NOTE: Between
the atoms, there
are covalent
Figure 2.4a Hydrogen bond bonds
formation in water.
Insert Fig 2.4a
Partial Charges
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Water
▪ H+ and OH− participate in chemical reactions
R—R + H2O → R—OH + H—R
Maltose + H2O → Glucose + Glucose
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Figure 2.5 How water acts as a solvent for sodium chloride (NaCl).
Sodium ion
Insert Fig 2.5in water
dissolved
Sodium chloride crystal
Chloride ion
dissolved in water
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Water
▪ H bonds absorb heat
▪ Makes water a temperature buffer (i.e., it resists changes
in temp)
Figure 2.4b Hydrogen bond
formation in water.
Hydrogen
bond
Insert Fig 2.4b
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Figure 2.6 Acids, bases, and salts.
HCl NaOH NaCl
Insert Fig 2.6
Acid Base Salt
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Acids
▪ Substances that dissociate into one or more H+
e.g. HCl → H+ + Cl−
HCl
Figure 2.6a Acids, bases,
and salts.
Insert Fig 2.6a
Acid
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Bases
▪ Substances that dissociate into one or more OH−
e.g. NaOH → Na+ + OH− NaOH
Figure 2.6b Acids, bases,
and salts.
Insert Fig 2.6b
Do not confuse OH- with –OH,
the functional group.
Base
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Salts
▪ Substances that dissociate into cations and anions,
neither of which is H+ or OH−
e.g. NaCl → Na+ + Cl− NaCl
Figure 2.6c Acids, bases, and
salts.
Insert Fig 2.6c
Salt
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Acid-Base Balance
▪ The amount of H+ in a solution is expressed as pH
▪ pH = −log10[H+]; pH means potential of hydrogen
▪ Increasing [H+] increases acidity
▪ Increasing [OH−] increases alkalinity
▪ pH 7 is neutral, i.e. [H+] and [OH−] are equal
▪ Most organisms grow best between pH 6.5 and 8.5
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Figure 2.7 The pH scale. pH scale
Stomach acid
Lemon juice
Grapefruit juice
Wine
Acidic solution Tomato juice
Urine
Insert Fig 2.7 Milk
Pure water
Human blood
Seawater
Neutral solution
Milk of magnesia
Household ammonia
Household bleach
Oven cleaner
Basic solution Limewater
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Structure and Chemistry: Organic
Molecules
▪ The chain of carbon atoms in an organic molecule
is the carbon skeleton
▪ Functional groups are responsible for most of
the chemical properties of a particular organic
compound
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Table 2.4 Representative Functional Groups and the Compounds in Which They Are Found (Part 1 of 2)
Insert Table 2.4
(two slides if possible)
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Table 2.4 Representative Functional Groups and the Compounds in Which They Are Found (Part 2 of 2)
Insert Table 2.4
(two slides if possible)
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Functional Groups
▪ Identify the functional groups in an amino acid (this
is the building block of proteins to be discussed
later)
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Organic Compounds
▪ Small organic molecules can combine into large
macromolecules
▪ Macromolecules are polymers consisting of many
small repeating molecules
▪ The smaller molecules are called monomers
Polymers
▪ Monomers join by dehydration synthesis or
condensation reactions
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Carbohydrates
▪ Cell structures and energy sources
▪ Consist of C, H, and O with the formula (CH2O)n
▪ Monosaccharides are simple sugars with three to
seven carbon atoms
▪ Disaccharides are formed when two
monosaccharides are joined in a dehydration
synthesis
▪ Disaccharides can be broken down by hydrolysis
Figure 2.8 Dehydration synthesis and hydrolysis.
Glucose Fructose Sucrose
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Carbohydrates
▪ Oligosaccharides consist of 2 to 20
monosaccharides (some sources 3-10
monosaccharides)
▪ Polysaccharides consist of tens or hundreds of
monosaccharides joined through dehydration
synthesis
▪ Starch, glycogen, dextran, and cellulose are polymers of
glucose that are covalently bonded differently
▪ Chitin is a polymer of two sugars repeating many times
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Lipids
▪ Primary components of cell membranes
▪ Consist of C, H, and O
▪ Are nonpolar and insoluble in water
Simple Lipids
▪ Fats or triglycerides
▪ Contain glycerol and fatty acids; formed by
dehydration synthesis
Carboxyl group Hydrocarbon chain
Figure 2.9a,b Structural formulas
of simple lipids.
Insert Fig 2.9a
Fatty acid (palmitic acid),
C15H31COOH
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Glycerol
Figure 2.9c Structural formulas of simple lipids.
Ester linkage
Palmitic acid (C15H31COOH) + H2O
(saturated)
Stearic acid (C17H35COOH) + H2O
(saturated)
cis configuration
Molecule
Molecule ofof fat
fat
(triglyceride)
(triglyceride)
Oleic acid (C17H33COOH) + H2O
(unsaturated)
▪ Saturated fat: no double bonds
▪ Unsaturated fat: one or more double bonds in the
fatty acids
▪ Cis: H atoms on the same side of the double bond
▪ Trans: H atoms on opposite sides of the double bond
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Complex Lipids
▪ Contain C, H, and O +
P, N, or S
▪ Membranes are made
of phospholipids
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Steroids
▪ Four carbon rings with an –OH group attached to one ring
▪ Part of membranes (of animal cells, mycoplasmas, fungi, and plants)
(mycoplasmas use lanosterol; Figure 2.11 Cholesterol, a steroid.
fungi use ergosterol; plants use
phytosterols)
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Proteins
▪ Are essential in cell structure and function
▪ Enzymes are proteins that speed chemical reactions
▪ Transporter proteins move chemicals across
membranes
▪ Flagella are made of proteins
▪ Some bacterial toxins are proteins
Amino Acids
▪ Proteins consist of subunits called amino acids
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Figure 2.12 Amino acid structure.
Side Cyclic
group side
Amino
group
group
Insert Fig 2.12
Carboxyl
group
Generalized amino acid Tyrosine
▪ Exist in either of two stereoisomers: D or L
▪ L-forms are most often found in nature
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Figure 2.13 The L- and D-isomers of an amino acid, shown with ball-and-stick models.
Mirror
L-amino acid D-amino acid
Insert Fig 2.13
Left hand Right hand
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Peptide Bonds
▪ Peptide bonds between amino acids are formed
by dehydration synthesis
Figure 2.14 Peptide bond formation by dehydration synthesis.
Peptide bond
Dehydration
synthesis
Insert Fig 2.14
Water
Glycine Alanine Glycylalanine
(a dipeptide)
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Proteins
▪ Consist of subunits called amino acids.
amino acid
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Table 2.4.1
Proteins NOTE: 3 amino acids structures below are incorrect; they are correct
in the 12th edition
amino acid
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Table 2.4.2
Levels of Protein Structure
▪ The primary structure is a polypeptide chain
Figure 2.15a Protein structure.
Peptide bonds
(a) Primary structure:
polypeptide strand
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Levels of Protein Structure
▪ The secondary structure occurs when the amino
acid chain folds and coils in a regular helix or pleats
Figure 2.15b Protein structure.
Hydrogen bond
(b) Secondary structure: Helix
helix and pleated sheets
(with ONE polypeptide
strand)
Insert Fig 2.15b
Pleated sheet
Disulfide
bridge
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Levels of Protein Structure
▪ The tertiary structure occurs when the helix
folds irregularly, forming disulfide bridges, hydrogen
bonds, and ionic bonds between amino acids in the
chain
Figure 2.15c Protein structure.
Hydrophobic interaction
Polypeptide
Hydrogen strand
bond
Insert Fig 2.15c
Disulfide bridge
(c) Tertiary structure: (between cysteine
folded helix and molecules)
pleated sheet
Ionic bond
Details of bonds associated
with tertiary structure
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Levels of Protein Structure
▪ The quaternary structure consists of two or more
polypeptides
Figure 2.15d Protein structure.
Insert Fig 2.15d
(d) Quaternary structure:
two or more polypeptides
in their folded states
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Figure 2.15 Protein structure. Peptide bonds
(a) Primary structure: Hydrogen bond
polypeptide strand
(b) Secondary structure:
helix and pleated sheets
(with ONE polypeptide
strand) Helix
Pleated sheet
Hydrophobic interaction
Insert Fig 2.15a
2.15
Disulfide
bridge Polypeptide
Hydrogen strand
(c) Tertiary structure: bond
folded helix and
pleated sheet Disulfide bridge
(between cysteine
molecules)
Ionic bond
(d) Quaternary structure:
two or more polypeptides
in their folded states
Details of bonds associated
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Levels of Protein Structure
▪ Conjugated proteins consist of amino acids and
other organic molecules
▪ Glycoproteins
▪ Nucleoproteins
▪ Lipoproteins
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Nucleic Acids
▪ Consist of nucleotides
1: once nucleotide is incorporated
▪ Nucleotides consist of 3: before incorporation as the bldg. block
▪ Pentose
▪ Phosphate group(s) (1, 2, or 3)
▪ Nitrogen-containing (purine or pyrimidine) base
▪ Nucleosides consist of
▪ Pentose
▪ Nitrogen-containing base
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DNA
▪ Deoxyribonucleic acid
▪ Has deoxyribose
▪ Exists as a double helix
▪ A hydrogen bonds with T
▪ C hydrogen bonds with G
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Adenine and Thymine (as well as Cytosine and Guanine, not shown here)
are nitrogenous bases or nucleobases.
Figure 2.16 The Structure of DNA.
Phosphate Sugar Adenine (A) Thymine (T) Sugar Phosphate
Adenine nucleotide Hydrogen bonds Thymine nucleotide
Individual DNA nucleotides are composed of a The carbon atoms in the
deoxyribose sugar molecule covalently bonded sugars are identified by adding a
to a phosphate group at the 5’ carbon, and to a marker, ’ (for example, 5’,
nitrogen-containing base at the 1’ carbon. The pronounced “5-prime”). This
two nucleotides shown here are held together differentiates them from the
by hydrogen bonds. carbon atoms in the nucleo-
bases, such as Thymine.
Insert Fig 2.16
Sugars DNA double helix
Sugar-phosphate backbone
Phosphates
DNA’s double-helical, ladder-
The sugar-phosphate backbone of one strand is like form is made up of many
upside down, or antiparallel, relative to the nucleotides base pairs
backbone of the other strand. forming the rungs, and the
repeating sugar-phosphate
combination,
forming the backbone.
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RNA
▪ Ribonucleic acid
▪ Has ribose
▪ Is single-stranded (but can fold over onto itself)
▪ A hydrogen bonds with U
▪ C hydrogen bonds with G
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Figure 2.17 A uracil nucleotide of RNA. Uracil (U)
Phosphate
Insert Fig 2.17
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ATP
▪ Adenosine triphosphate
▪ Has ribose, adenine, and three phosphate groups
Figure 2.18 The structure of ATP.
Adenosine Adenine
Phosphates
Insert Fig 2.18
Ribose
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ATP
▪ Is made by dehydration synthesis
▪ Is broken by hydrolysis to liberate useful energy
for the cell
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Q: What are the biologically important
organic macromolecules?
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