Chapter 3: Organic Chemistry
(Outline)
 Organic vs. Inorganic
 Functional Groups and Isomers
 Macromolecules
 Carbohydrates
 Lipids
 Proteins
 Nucleic Acids
Organic Molecules
 Inorganic – Chemistry of elements other than
carbon
 Organic – Carbon-based chemistry
Carbon Atom
 Carbon atoms:
 Contain a total of 6 electrons
 Only four electrons in the outer shell
 Very diverse as one atom can bond with up to
four other atoms
 Often bonds with other carbon atoms to make
hydrocarbons – chains of carbon atoms bonded
exclusively to hydrogen atoms
 Can produce long carbon chains like octane
 Can produce ring forms like cyclohexane
Functional Groups and Isomers
 Functional groups:
 Specific combinations of bonded atoms
 Attached as a group to other molecules
 Always react in the same manner, regardless of
where attached
 Determine activity and polarity of large organic
molecules
 Many functional groups, but only a few are
of major biological importance
Functional Groups
 Six functional groups are of biological
importance
 Hydroxyl group (–OH)
 Carbonyl group (C=O)
 Carboxyl group (HO–C=O)
 Amino group (–NH2)
 Sulfhydryl group (–SH)
 Phosphate group
Functional Groups - Hydroxyl
 Composed of a hydrogen atom bonded to
an oxygen atom: -OH
 Organic molecules containing a hydroxyl
group are known as alcohols
 Polar
 Forms hydrogen bonds; present in sugars
and some amino acids
Example: Methanol
Functional Groups - Carbonyl
 Composed of a carbon atom double-bonded
to an oxygen atom: C=O
 Polar
 If at the end of the skeleton: aldehyde
 If within the skeleton: ketone
 Present in sugars
Formaldehyde
Acetone
Functional Groups - Carboxyl
 Composed of an oxygen double bonded to a
carbon atom that is also bonded to a
hydroxyl group (hydroxyl group + carbonyl
group = carboxyl group)
 Organic molecules containing a carboxyl
group are known as carboxylic acids
 Polar, acidic
 Present in fatty acids, amino
acids
Example: acetic acid
Functional Groups - Amino
 Composed of a nitrogen atom bonded to
two hydrogen atoms: -NH2
 Organic molecules containing an amino
group are known as amines
 Polar
 Forms hydrogen bonds
 Present in amino acids
Example: Glycine
Functional Groups - Sulfhydryl
 Composed of a sulfur atom bonded to a
hydrogen atom: -SH
 Organic molecules containing a sulfhydryl
group are known as thiols
 Forms disulfide bonds
 Present in some amino acids
Example: Ethanethiol
Functional Groups - Phosphate
 An ion composed of a phosphate ion
covalently attached by one of its oxygen
atoms to the carbon skeleton
 Polar, acidic
 Present in nucleotides, phospholipids
Un-ionized form
Isomers
 Isomers - organic molecules that have:
 Identical molecular formulas, but
 Differing internal arrangement of atoms
Macromolecules
 Some molecules are called macromolecules because
of their large size
 Usually consist of many repeating units
 Resulting molecule is a polymer (many parts)
 Repeating units are called monomers
 Some examples:
Making & Breaking Macromolecules
 Dehydration (synthesis)
 Macromolecule is assembled by removing an –OH
group from one subunit and an H from other
subunit
 Thus removing a water molecule (H2O) for every
subunit that is added to a macromolecule
 Also called water-losing reaction
 Energy is required to break the chemical bonds
when water is extracted
 Cells must supply energy to assemble
macromolecules
Making & Breaking Macromolecules
 Hydrolysis (digestion)
 Macromolecules are disassembled into their
constituent parts by adding an –OH group to
form one subunit and an H to form the other
subunit
 Thus adding a water molecule for every
macromolecule that is disassembled
 Energy is released when the energy storing
bonds are broken
Synthesis & Degradation
of Polymers
 Polymers - large molecules consisting of long chains
of repeating subunits (monomers)
The 4 major classes of organics:
1. Carbohydrates
 Loosely defined group of molecules that contain C,
H, and O in molecular ratio of 1:2:1, with an
empirical formula of (CH2O)n
 Are named based on the number of sugar units they
contain
 Monosaccharides
one sugar unit (mono-)
 Disaccharides
two sugar units (di-)
 Polysaccharides
many sugar units (poly-)
Carbohydrates Examples:
Monosaccharides
 Single sugar molecules
 Quite soluble and sweet to taste
 Play central role in energy storage
 Examples
 Glucose, fructose & galactose
 Hexoses - Six carbon atoms
 Isomers of C6H12O6
 Ribose and deoxyribose
 Pentoses – Five carbon atoms
 C5H10O5 & C5H10O4
Carbohydrates Examples:
Disaccharides
 Contain two monosaccharides joined by a
covalent bond
 Soluble and sweet to taste
 Play a role in the transport of sugars
 Examples
 Sucrose
 Table sugar, maple sugar
 One glucose and one fructose joined by
dehydration
 Maltose
 Also known as malt sugar
 Two glucoses joined by dehydration
Synthesis and Degradation
of Maltose, a Disaccharide
Carbohydrates Examples:
Polysaccharides
 Polymers of monosaccharides
 Low solubility; not sweet to taste
 Examples
 Starch
 Polymer of glucose
 Used for short-term energy storage
 Plant starch


Often branched chain
Amylose, corn starch
 Animal starch


Unbranched
Glycogen in liver and muscles
Starch
Structure and Function
Glycogen
Structure and Function
Carbohydrates Examples:
Polysaccharides
 Cellulose
Long, coiled polymer of glucose
Glucoses connected differently than in starch
Structural element for plants
Main component of wood and many natural
fibers
 Indigestible by most animals




 Chitin




Polymer of glucose
Each glucose with an amino group
Very resistant to wear and digestion
Arthropod exoskeletons, cell walls of fungi
Cellulose
Structure and Function
Chitin
The 4 major classes of organics:
2. Lipids
 Insoluble in water
 Long chains of repeating CH2 units
 Renders molecule nonpolar
Types of Lipids:
Triglycerides
 Triglycerides (Fats)
 Structure = glycerol + 3 fatty acids
 Glycerol = a 3-carbon alcohol with each
carbon bearing a hydroxyl group
 Fatty acids = long hydrocarbon chains
(ranging from 4 to 36 carbons) ending in a
carboxyl group
 The 3 fatty acids of a triglyceride
are not necessarily the same
Dehydration Synthesis of
Triglyceride
 Three fatty acids attached to each glycerol molecule
 Carboxylic acid at one end
 Carboxylic acid connects to –OH on glycerol in
dehydration reaction
Triglycerides
 Functions
 Long-term energy storage
 Efficient energy storage molecules because
of their high concentrations of C-H bonds
 Insulation
 The fat (blubber) beneath the skin in
marine animals
 Cushioning
 Excellent shock absorber and provides
natural 'cushioning' to vital organs
Saturated & Unsaturated fats
 Based on absence/ presence of double bonds
between C atoms and number of H atoms
 Saturated fats
 All internal C atoms are bound to at least two H
atoms, no double bonds between C atoms
 results in maximum number of H atoms
therefore, said to be saturated with H
 Tend to be straight and fit close together
 Most are solid at room temperature
 Example: butter
Saturated & Unsaturated fats
 Unsaturated fats
 Double bonds between at least one pair of
C atoms
 results in less than maximum number of
hydrogen atoms therefore, said to be
unsaturated
 Have low melting points because the fatty
acids chains can’t closely align
 double bonds cause kinks
 Most are liquid at room temperature
 Example: vegetable oil
Fat & Fatty Acids
Types of Lipids:
Phospholipids
 Derived from triglycerides
 Modified fats with two fatty acid chains rather than
three
 Two fatty acids attached instead of three
 Third fatty acid is replaced by a phosphate group
 The fatty acids are nonpolar and hydrophobic
 The phosphate group is polar and hydrophilic
 Molecules self arrange when placed in water
 Polar phosphate “heads” next to water
 Nonpolar fatty acid “tails” overlap and exclude
water
 Spontaneously form double layer & a sphere
 Structure of cell membranes = phospholipid bilayer
Phospholipids form Membranes
Types of Lipids:
Steroids
 Steroids – lipids composed of four fused C rings
 Hormones
 Regulatory
 Cholesterol
 Found in eukaryotic cell membrane
 Bile salts (emulsify fats)
 Different steroids are created by varying
functional groups attached to the rings
 High levels of cholesterol in the blood may
contribute to cardiovascular disease
Steroid Diversity
Types of Lipids:
Waxes
 Long-chain fatty acid bonded to a long-chain
alcohol
 High melting point
 Waterproof coating on leaves, bird feathers,
mammalian skin, arthropod exoskeleton
 Resistant to degradation
The 4 major classes of organics:
3. Proteins
 Classification of proteins according to biological
function
 Support – Collagen in ligaments & tendons
 Enzymes – biological catalysts
 Transport – Hemoglobin; membrane proteins
 Defense – Antibodies
 Hormones – Many hormones; insulin
 Motion – Contractile proteins; actin & myosin in
muscles, microtubules
Protein Subunits:
The Amino Acids
 Made up of various combinations of 20
types of repeating subunits called amino
acids
 are joined together by peptide bonds
 are organic molecules
 consist of
 two characteristic end groups
 a side group (or side chain)
Structure of Amino Acids
 Each amino acid has a central carbon atom
(the alpha carbon)
 Two end groups
 an amino group (-NH2)
 a carboxyl group (-COOH)
 A side group (-R)
 bonded to the α C atom between the two end
groups
 varies from one amino acid to another
 determines the unique chemical properties of
the amino acid
Examples of amino acid side groups
 Grouped into three
chemical classes based
on their side groups
 Non-polar
(e.g. leucine)
 Polar (e.g. serine)
 Ionized (e.g. lysine)
Proteins:
The Polypeptide Backbone
 Amino acids joined together end-to-end
 COOH of one amino acid covalently bonds to the
NH2 of the next amino acid
 Special name for this bond - Peptide Bond
 2 amino acids bonded together – Dipeptide
 3 amino acids bonded together – Tripeptide
 Many amino acids bonded together – Polypeptide
 Characteristics of a protein are determined by
composition and sequence of amino acids
 Virtually unlimited number of proteins
Synthesis and Degradation of a
Peptide
Protein Molecules:
Levels of Structure
 Four levels of organization of protein structure
 Primary – refers to the linear sequence of amino
acids that make up the polypeptide chain
 Secondary – refers to the formation of a regular
pattern of twists or folds of the polypeptide chain
 Tertiary – refers to the three-dimensional globular
structure formed by bending and twisting of the
polypeptide chain
 Quaternary – refers to the fact that some proteins
contain more than one polypeptide chain
Levels of Structure
 Primary level
 result from the specific amino acid sequence
producing a long chain with a carboxylic acid
group on one end and an amino group on the
other
 slight change in primary structure can be
detrimental
 one dimensional
Levels of Structure
 Secondary level
 results from H-bonding between individual
amino acids of the polypeptide chain
 two dimensional
 two patterns of H bonding
 α (alpha) helix
 β pleated sheets
 Fibrous proteins are either mostly
alpha helices or beta pleated
sheets
Secondary structure
 Alpha Helix
 polypeptide chain in coiled
 hydrogen bonds between every 4th amino acid
 α helices are numerous in proteins in hair and
horn
 Beta Pleated Sheet
 chain folded back with regions of chain parallel
to itself
 hydrogen bonds hold it in this conformation
 spider silk and silkworm silk are mostly
β pleated sheets
Levels of Protein Organization
Levels of Structure
 Tertiary level
 Final folded shape of protein resulting from
hydrophobic interactions with water, globular
(three dimensional)
 Hydrogen bonds, ionic bonnds and covalent
bonds may also contribute to tertiary structure
 Disulfide bonds (S-S); cysteine
 Denaturation – process by which a protein
changes its shape (tertiary & secondary) or even
unfolds when its “tolerance range” for some
factor is exceeded
 Results from breaking hydrogen bonds, disrupting
polar – nonpolar interactions
Levels of Structure
 Quaternary level
 when two or more polypeptide chains associate
to form a functional protein
 each polypeptide chain with its primary,
secondary & tertiary structure
 Examples:
 Collagen – 3 helical polypeptides super-coiled
forming a strong fibrous protein
 Hemoglobin – 4 polypeptide chains: 2 identical
alpha and 2 identical beta chains each with a
central heme (iron) unit
The 4 major classes of organics:
4. Nucleic acids
 Nucleic acids
 long polymers of repeating subunits called
nucleotides
 are the information storage devices of cells
 two types
 DNA
 deoxyribonucleic acid
 RNA
 ribonucleic acid
Nucleic acids
 DNA
 Double-stranded helical spiral (twisted ladder)
 Serves as genetic information center (blueprint)
in genes or chromosomes
 Specifies the amino acid sequence of proteins
through the sequences of nucleotides
 RNA
 Part single-stranded, part double-stranded
 Serves primarily in assembly of proteins
 In nucleus and cytoplasm of cell
The Nucleotides of
Nucleic Acids
 Three components:
 A phosphate group,
 A pentose sugar (ribose or deoxyribose), and
 A nitrogenous base (4 kinds in DNA, 3 kinds in
RNA, 3 common to both
 Nucleotide subunits connected end-to-end to
make nucleic acid
 Sugar of one connected to the phosphate of the
next
 Sugar-phosphate backbone
Nucleotides
DNA & RNA
Comparison of DNA & RNA
Other Nucleic Acids
 ATP (adenosine triphosphate) is composed of
adenine, ribose, and three phosphates
 Nucleotides play critical roles in molecules which
serve as the energy currency of the cell
 In cells, one phosphate bond is hydrolyzed – yields:
 The molecule ADP (adenosine diphosphate)
 An inorganic phosphate molecule pi
 Energy
 Other energy sources used to put ADP and pi back
together again
 Other high energy molecules (NAD+, nicotinamide
adenine dinucleotide and FAD+,flavin adenine dinucleotide)
ATP