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CHAPTER 2
Small Molecules: Structure and Behavior
Atoms: The Constituents of Matter
 Matter is composed of atoms with positively
charged nuclei of protons and neutrons surrounded
by negatively charged electrons.
Main Elements Found in Living Organisms
Figure 2.1
Isotopes of an element differ in numbers
of neutrons
Figure 2.2
Some isotopes are unstable and are termed radioactive.
These radioisotopes are useful for many purposes.
Electrons are distributed in shells of orbitals
Each orbital contains a max of 2 electrons
Orbital Shell Representations for Several
Atoms
Figure 2.5
Interaction of atoms via sharing of electrons
generates molecules via bonding
Table 2.1
Covalent Bonds
Covalent bonds form when two atomic
nuclei share one or more pairs of
electrons. They have spatial orientations
that give molecules three-dimensional
shapes
Figure 2.6
Covalent Bonds
Combining electrons in all
the orbitals in a particular
level often occurs.
sp3 bonds of carbon are the
combination of the 2s orbital
and the 3 2p orbitals to form
4 sp3 orbitals which each
have a single electron that is
shared with the single
electron in H’s 1s orbital
Figure 2.7
table 02-02.jpg
Table
2.2
Table 2.2
Chemical Bonds: Linking Atoms
Together
 Nonpolar covalent bonds form when the
electronegativities of two atoms are approximately
equal
 Polar covalent bond in which one end is d+ and the
other is d– forms when atoms with strong
electronegativity (such as oxygen) bond to atoms
with weaker electronegativity (such as hydrogen)
 Hydrogen bonded to a strongly electronegative
atom can be donated to a H-bond
Polarity in bonding
Figure 2.8
figure 02-08.jpg
table 02-03.jpg
Table
2.3
Table 2.3
Ionic bonds
Complete
gain/loss of
electron to form
a charged species
Oppositely
charged ions
then interact
electrostatically
Figure 2.10
Hydrogen bonds
figure 02-09.jpg
 Hydrogen bonds form between a d+ hydrogen atom in
one molecule and a d– nitrogen, oxygen or sulfur atom
in another molecule or in another part of a large
molecule.
Polar solvents dissolve ionic & polar
substances
Figure 2.11
Polar & Non-polar Molecules
 Nonpolar molecules do not interact directly with
polar substances. They are attracted to each other
by very weak bonds called van der Waals forces.
 Van der Waals forces are the weak sharing of
electons between orbitals of molecules
Water: Structure and Properties
 Water’s molecular structure and capacity to form
hydrogen bonds give it unusual properties
significant for life.
Water: Structure and Properties
 Cohesion of water molecules results in a high
surface tension. Water’s high heat of vaporization
assures cooling when it evaporates.
 Solutions are substances dissolved in water.
Concentration is the amount of a given substance in
a given amount of solution. Most biological
substances are dissolved at very low
concentrations.
Chemical Reactions: Atoms Change
Partners
 In chemical reactions, substances change their
atomic compositions and properties. Energy is
either released or added. Matter and energy are not
created or destroyed, but change form.
Acids, Bases, and the pH Scale
 Acids are substances that donate hydrogen ions. Bases are
those that accept hydrogen ions.
 The pH of a solution is the negative logarithm of the
hydrogen ion concentration.
 pH=-log[H+]
 Values lower than pH 7 indicate an acidic solution.
 Values above pH 7 indicate a basic solution
pH Scale
Figure 2.18
Acids, Bases, and the pH Scale
 Buffers are systems of weak acids and bases that limit
the change in pH when hydrogen ions are added or
removed.
The Properties of Molecules
 Molecules vary in size, shape, reactivity, solubility,
and other chemical properties.
 Functional groups make up part of a larger
molecule and have particular chemical properties.
 The consistent chemical behavior of functional
groups helps us understand the properties of the
molecules that contain them.
Functional Groups
Figure 2.20 – Part 1
Functional Groups
Figure 2.20 – Part 2
Isomers
•Optical isomers
•rotate plain
polarized light
in opposite
directions
•Structural isomers
•Differ in
position of
functional
groups
Optical Isomers Figure
2.21
CHAPTER 3
Macromolecules: Their Chemistry and
Biology
Macromolecules: Giant Polymers
 Macromolecules are formed by covalent bonds
between monomers and include polysaccharides,
proteins, and nucleic acids.
 Lipids are crucial biomolecules, but are not
considered ‘macromolecules’
table 03-01.jpg
Table 3.1
Fatty Acid
Triglyceride
Phospholipid
Macromolecules: Giant Polymers
 Macromolecules have specific three-dimensional
shapes.
 Different functional groups give local sites on
macromolecules specific properties.
Condensation Reactions
 Monomers are joined by
condensation reactions.
Hydrolysis reactions
break polymers into
monomers.
 Joining of monomers is
typically called
polymerization
Proteins: Polymers of Amino Acids
 Functions of proteins include support, protection,
catalysis, transport, defense, regulation, and
movement. They sometimes require an attached
prosthetic group.
Proteins: Polymers of Amino Acids
 Twenty amino acids are found in proteins.
 Each consists of an amino group, a carboxyl group,
a hydrogen, and a side chain bonded to the a
carbon atom.
table 03-02a.jpg
Amino Acids
Table 3.2 – Part 1
Amino Acids
table 03-02bc.jpg
Proteins: Synthesis
 Amino acids are covalently
bonded together by peptide
linkages or peptide bond
 Chemically this is an amide
bond
 Each amino acid is called a
residue
 Reaction proceeds leaving the
amino terminus of the 1st aa
and the carboxyl terminus of the
last aa unmodified (free)
Proteins: Structure
 Polypeptide chains of proteins are folded into
specific three-dimensional shapes
 There are 4 levels of structure




Primary (1o) – amino acid sequence
Secondary (2o) – localized structures of adjacent residues
Tertiary (3o) – folding of units of secondary structure
Quaternary – association of multiple individual proteins
(subunits) to form a functional complex
Protein Structure
H-bonds stabilize 2o structures
Protein Structure
Figure 3.5 – Part 2
3.5 –
Part 2
Covalent bonds (disulfide bridges), H-bonds & ionic bonds (salt
bridges) stabilize 3o and 4o structures
Protein Structure
The SH groups of cysteine residues
can form disulfide bridges that link
distant regions of proteins together
Figure 3.3
figure 03-03.jpg
figure 03-07.jpg
3.7
Figure 3.7
Proteins: Structure
• Chemical interactions
important for binding of
proteins to other molecules.
• H-bonds
• Van der Waals interactions
• Ionic interactions
Proteins: Structure
 Proteins can be
denatured
 heat, acid, or
chemicals
 Loss of tertiary and
secondary structures
and biological
function.
Proteins: Structure
 Proper folding of proteins is critical for their function
 Chaperonins assist protein folding
Carbohydrates: Sugars and Sugar
Polymers
• Monosaccharides
3-carbons – trioses
• 5-carbons - pentoses
• 6-carbons – hexoses
• Disaccharides
• Two monosaccharides
• Maltose
• Sucrose
• Lactose
• Oligosaccharide
• <10 glycoside residues
• Polysaccharide
• >10 glycoside residues
•
Carbohydrates: Structures
Hemiacetal forms
Carbohydrates Structure
Glyceraldehyde
4 carbon sugar is erythrose
Carbohydrates Structure
Isomers
figure 03-12b.jpg
Carbohydrate Polymerization
Glycosidic linkages may have either a or b orientation in space
Numbering of bond refers to carbon position of hemiacetal ring
Carbohydrate polymerization
Figure 3.14 – Part 1
An unbranched polysaccharide
Carbohydrate polymerization
Figure 3.14 – Part 2
Branched chain polysaccharides
Carbohydrates modified sugars
• Chemically modified
monosaccharides
• Phosphates,
• Acetyl groups
• Sulfates
• Amino groups
• Derivative of glucosamine
polymerizes to form the
polysaccharide chitin
• Used as the basis of arthropod
exoskeletons
• Proteoglycans & Glycoproteins
• Proteins with attached
carbohydrates
• Heparin sulfate
• Chondroitin sulfate
Nucleic Acids: Informational
Macromolecules
• In cells, DNA is the hereditary material. DNA and
RNA play roles in protein formation.
Nucleotide Structures
Nucleotides – The Sugars
Nucleotides – The Bases
Nucleosides – Sugar + Base
Nucleotide – Nucleoside + Phosphates
Nucleic Acids – Polymers of Nucleotides
Nucleic Acid Structure
Nucleic Acids
 Complementary Base Pairing
 A-T or U
 G-C
 Watson-Crick Pairing
 Specificity
 Fidelity of DNA replication
 Fidelity of transcription
 Fidelity of any nucleic acid-nucleic acid
interaction
 ie. mRNA – tRNA
 Hybridization
 Our manipulation of nucleic acids
16S rRNA Secondary
Structures
tRNA Secondary Structure
DNA Double Helix
Figure 3.18
Major Groove
Minor Groove
Spacing of base-pairs – 3.4Å
Helix diameter ~ 20Å
10 base-pairs per helical turn
DNA – The Genetic Material
 Genes
 Coding sequences
 Regulatory sequences
 Genes encode proteins
 Information flow
 DNA  RNA  protein
 Central Dogma
 DNA sequences
Nucleic Acids: Manipulation
 Molecular Biology
• DNA amplification – PCR
• DNA cloning – gene isolation and identification
• DNA sequencing – gene characterization
• DNA-RNA & DNA-DNA hybridization – Gene
Chips
Lipids
 Fatty Acids
 Triglycerides
 Phospholipids
 Steroids
 Steroid hormones
 Retinoids
Fatty Acids
Triglyceride Formation
Figure 3.19
Phospholipids:
• Phospholipids have a
hydrophobic hydrocarbon “tail”
and a hydrophilic “head”
group.
• Head group
• Phosphate connection
• Base
• Choline
• Ethanolamine
• Sugar
• Inositol
• Amino acid
• Serine
Lipid Bilayer Formation
Figure 3.22
Steroid Lipids:
• Carotenoids trap light energy in green plants. β-Carotene can be
split to form vitamin A (retinol), a lipid vitamin.
All-trans retinol
Steroid Lipids
Figure 3.24