Chapter 3

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 Organic Chemistry
. Organic molecules contain Carbon (C) and Hydrogen (H)

. Organic molecules are very common in living organisms

. Macromolecules are large, complex organic molecules

. 4 categories of macromolecules:
- Carbohydrates
- Lipids
- Proteins
- Nucleic Acids

A bacterial cell contains about 5000 different organic molecules and a plant or animal cell
contains about 10.000

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 Inorganic Substances Organic Molecules

Usually contains positive and negative ions Always contains carbon and hydrogen

Usually ionic bonding Always covalent bonding

Always contains small number of atoms Often quite large, with many atoms

Often associated with non living matter Usually associated with living
organisms

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 Carbon Atom
C has 4 electrons in its outer shell

Needs 4 more electrons to fill the shell

It can make up to 4 covalent bonds with C,H,N,O, or S

Usually single or double bonds

C can form nonpolar (C,H) and polar bonds (O,N)

. Molecules with nonpolar bonds (like hydrocarbons) are
poorly water soluble

. Molecules with polar bonds are more water

soluble

C-C bonds are short and therefore stable at different

temperatures.
.Shorter bonds tend to be stronger and more stable than
longer bonds between 2 large atoms

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 R: C backbone

Functional Groups
The carbon chain of an organic molecule is called its
skeleton or backbone.

The reactivity of an organic molecule is dependent

on the attached functional group.

Functional groups are specific combinations of

bonded atoms that always react in the same way,
regardless of the particular carbon skeleton.

Functional groups determine the polarity of an

organic molecule and also the types of reaction it will
undergo.

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 The four class of organic molecules
and macromolecules
Carbohydrates, lipids, proteins, and nucleic acids are referred to as macromolecules
because of their large size.
They all have different polymers, and basic building blocks, called ‘monomers’

Polymers are made up of monomers.

Examples:
Protein, a folded peptide chain (polymer) can contain hundreds of amino acids
(monomers);
Nucleic acid (DNA or RNA) (polymer) can contain hundreds of nucleotides (monomers).

How can polymers get so large?

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Polymer formation:
Dehydration =
Reaction that fuses (puts
together) compounds (monomer)
that results in
loss of water- Removal of
water molecule.

Polymer degradation:
Hydrolysis =
Reaction that breaks down
compound by the
addition of water

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 Stearic acid (fatty acid)

Glycerol
Example of dehydration reaction:
Formation of triglyceride from:
glycerol + fatty acids

Triglyceride
Example of hydrolysis reaction:
Breakdown of sucrose to form:
glucose + fructose

hydrolysis
 Carbohydrates
An immediate energy source in living organisms

Large molecule

Composed of C, H, and O atoms

General formula: Cn(H2O)n

Most of the C atoms in a carbohydrate are linked to a H atom and a OH group

Plays structural roles in a variety of organisms

The term carbohydrates include single sugar molecules and also chains of sugars

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 Carbohydrates: Monosaccharides
Simplest sugars: Monosaccharides (mono, single
and sacchar, sugar).
Monosaccharides are the monomers of larger
sugars (disaccharides & polysachharides).

Contains much energy (in its bonds)

Molecular formula for a single sugar is a multiple of

CnH2nOn.

Sugars have many hydroxyl groups, and this polar

functional group makes them soluble in water.

Most common are 5 or 6 carbons

Pentoses: 5C (component of RNA and DNA
molecules)
ribose (C5H10O5); found in RNA
deoxyribose (C5H10O4); found in DNA
Hexose: 6C
glucose (C6H12O6); water soluble

Different ways to depict structures

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Ring or linear
 Glucose isomers
Structural isomers: different arrangement of same elements
Glucose and galactose

Stereoisomers:

Geometric isomers:above
or below ring
α- and β-glucose

Enantiomers: mirror image

D- and L-glucose

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Geometric isomers:above or below ring
α- and β-glucose

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Enantiomers: mirror image
D- and L-glucose

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 Carbohydrates: Disaccharides
Disaccharides are composed of 2 monosaccharides

Joined by dehydration (condensation) reaction

Broken apart by hydrolysis

Examples:
. Sucrose = Glucose (6C) + Fructose (5C),
-Sucrose is the form in which sugar is transported in plants;
-Sugar we use to sweeten our food

. Maltose = Glucose + Glucose [malt sugar]

. Lactose = Glucose + Galactose [milk sugar]

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 Carbohydrates:
Many monosaccharides linked together to
Polysaccharides
form long polymers = polysaccharides

Monosaccharides are connected to each

other by glycosidic linkages (bonds)

Short-term energy storage

Large molecules can’t pass through plasma

membrane (not soluble in water, and much
larger than sugar)

When an organism requires energy,

polysaccharides are broken down to
release simple sugar molecules

Glucose molecules can be stored by

organisms as different macromolecules.
Glycosidic linkages/bonds:
Energy storage molecules:
between monosaccharides to form
Starch in plants, (energy storage) disaccharides or polysaccharides
Glycogen in animals, (energy storage)
Structural role :
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Cellulose (plants), chitin (insects and fungi),
 Carbohydrates: Polysaccharides
(Energy Storage Molecules)
Starch: is a mixture of two complex carbohydrates:
amylose and amylopectin, both of which are polymers
of glucose. It is used by plants as a way to store
excess glucose.

Glycogen: Animals store glucose as glycogen

(granules in liver); polysaccharide of glucose, which
functions as the primary short-term energy storage in
animal cells.

Hormones control release and storage of glucose:

Insulin released from the pancreas promotes
the storage of the glucose as glycogen.
Glucagon, another hormone released from the
pancreas stimulates glycogen breakdown into
glucose.

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 Carbohydrates: Polysaccharides
(Structural Molecules)
Cellulose:
. Most abundant (common) of all the Cellulose
carbohydrates.
. Polymer of -glucose
. Cell walls in plants contain cellulose.
. Parallel glucose chains → cellulose

Chitin:
. Form the external skeleton of many
insects and the cell wall of fungi.
. The sugar monomer of chitin have
nitrogen-containing groups attached to
them.

Glycosaminoglycans:
. Found in animals.
. Abundantly found in cartilage.
. Tend to have sugar monomers with
carboxyl and sulfate groups.
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 Lipids
Organic molecules

Composed predominantly of H and C atoms (hydrocarbon chains).

Defining feature of lipids is that they are nonpolar. (Hydrogen bonded only to carbon
have no tendency to form hydrogenated bonds with water molecules) and therefore
very insoluble in water.

Lipids (fats) used for both insulation and long-term energy storage by animals.
Plants use oil instead of fat for a long-term energy storage

Phospholipids and steroids: other important lipids found in living things.

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 Lipids: Fats
Mixture of triglycerides (Also known triacylglycerols); long-term energy storage

Formed by bonding glycerol to three fatty acids; joined by dehydration or condensation reaction

Broken apart by hydrolysis

Glycerol: compound with three OH groups (OH is polar group- glycerol soluble in water).
Fatty acid consists of long hydrocarbon (R) chain with a carboxyl (-COOH) group at one end.

Chemical formula of fatty acid: R-COOH

Fat and oils formation: Acid portions (carboxyl) of the three fatty acids react with the -OH group of
glycerol during a dehydration reaction.
 Lipids: Fats (contd)
The three fatty acids can be all different, all the same, or only two the same.

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 Lipids: Fats (contd)
Fatty acids are either saturated or unsaturated.

Saturated fatty acids:

. Have no double bonds between the carbon atoms. All carbons are linked by
single covalent bonds.

. Tend to be solid at room temperature

Unsaturated fatty acids:

. contain one or more double bonds in the carbon chain
- 1 double bond: monounsaturated
- 2 or more: polyunsaturated

. Tend to be liquids at room temperature (plant oils)

Fats are important for energy storage: 1g of fat stores twice as much energy
as 1 g of glycogen or starch

Fats can also be structural in providing cushioning and insulation

 Saturated and unsaturated fatty acids

saturated
unsaturated

saturated
unsaturated

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Lipids: Phospholipids
Phospholipids: membrane components,
contains phosphate group.

Instead of third fatty acid attached to

glycerol as in fat, there is a polar
phosphate group.

Amphipathic molecule
Hydrophilic heads (phosphate region)
hydrophobic tails (Fatty acid chains)

Arrange themselves so polar heads

are adjacent to water.

Bulk of cell plasma membrane consists of

phospholipid bilayer.

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 Lipids: Steroids
Have skeletons of 4 interconnected carbon rings
Usually not very water soluble
3 types of steroids:
Cholesterol, estrogen and testosterone

Cholesterol is the precursor of several other

steroids, such as testosterone and estrogen.

Testosterone and estrogen differ only by the

functional group attached to the same carbon
skeleton, and yet have a profound effect on the
body and the sexuality of an animal.

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 Waxes
Long-chain fatty acid bonds with a long-chain alcohol, secreted onto plant leaves
and insect cuticles

Very nonpolar and hydrophopic: provide a barrier to water loss

High melting point: Solid at normal temperature.

Waterproof

Resistant to degradation

Structural elements in bee colonies (bee hives)

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 Proteins
Diverse functions:
- Support: keratin (hair, nail, ligaments..)
- Enzymes: bring reactants together
- Transport: channel and carrier protein (plasma membrane) allow substance to
enter and exit cells. Hemoglobin: transport of oxygen.
- Defense: antibodies (combine with foreign subjects and prevent them from
destroying cells)
- Hormones: eg. insulin regulates blood glucose
- Motion: eg. actin and myosin allow parts of cells to move and cause muscles
to contract

Composed of C, H, O, N, and small amounts

of other elements, notably S

Amino acids are the monomers of proteins

• 20 different amino acids
• Common structure with variable R-group
• Side-chain (R) determines structure
and function
• Bond to a hydrogen atom, an
amino group -NH2, an carboxyl group -COOH, and an R (remainder) group.
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Proteins: Amino The 20 different amino acids:

Acids Structure
Amino acids are usually
classified by properties
of the side chain into
four groups:
◼ acidic,
◼ basic,
◼ hydrophilic (polar),
◼ hydrophobic
(nonpolar).

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29
 Proteins: Peptide bond formation
Image:Peptidformationball.svg

. Amino acids are joined by

dehydration or condensation
reaction through a covalent bond
called “peptide bond”.

. Peptide: Two or more amino acids

bonded together.

. Polypeptide : Chain of many amino

acids joined by peptide bonds.

. Proteins are made up of 1 or more

polypeptides that are folded

. Peptide bonds are broken apart by

hydrolysis
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 C-terminus
N-terminus

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Protein Structure
Primary:
Sequence of amino acids.

Secondary:
Polypeptide coils or folds in
a particular fashion. Hydrogen
bonding often holds the
secondary structure

Tertiary:
Folding and twisting that results
in final three dimensional shape
of a polypeptide.

Quaternary:
Consists of more than one
polypeptide.
For example, hemoglobin
or DNA polymerase
Tertiary structure of ribonuclease A (only 1 peptide) 32
 Protein structure
Primary structure:
. Amino acid sequence
. Determined by genes

Secondary structure:
. Chemical and physical interactions
cause folding
. Irregular or repeating
. α helices and β pleated sheets
- Key determinants of a protein’s
characteristics

. “Random coiled regions”

- Not α helix or β pleated sheet
- Shape is specific and important
to function
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 The five factors promoting protein
folding and stability
1. H-bonds (hydrogen bonds): promote protein folding and stability

2. Ionic bonds: ionic and polar interactions promote folding and stability

3. Hydrophobic effects: avoid water contact

4. Van der Waals forces: atoms that have weak attractions

5. Disulfide bridges: covalent bonds that link 2 cysteine amino acids that
contain sulfthydryl group

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 Protein-protein interactions

Many cellular processes involve steps in

which two or more different proteins
interact with each other

Very specific binding at surface

Use first 4 factors

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 Proteins Contain Functional Domains
Within Their Structures
Module or domains in proteins have distinct structures and function

Signal transducer and activator of transcription (STAT) protein example

Each domain of this protein is involved in a distinct biological function

Proteins that share one of these domains also share that function
 Nucleic Acids
Responsible for the storage, expression, and transmission of genetic information
Two classes
 Deoxyribonucleic acid (DNA)
◼ Store genetic information coded in the sequence of their monomer building blocks
 Ribonucleic acid (RNA)
◼ Involved in decoding this information into instructions for linking together a specific
sequence of amino acids to form a polypeptide chain
Monomer is: nucleotide
Nucleotides are connected to each other by phosphodiester bonds (on each strand).
Made up of phosphate group, a 5C sugar (pentose sugar), either ribose (in RNA) or
deoxyribose (in DNA) single or double ring of C and N atoms known as a nitrogen base
Sugar-phosphate backbone

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Structure of a DNA strand The double-stranded structure of DNA
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Nucleotides classification in 2 main groups

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 DNA vs. RNA
DNA RNA
Deoxyribonucleic acid Ribonucleic acid
Deoxyribose Ribose
Thymine (T) Uracil (U)
Adenine (A), guanine (G), cytosine (C)
used in both
2 strands; double helix Single strand
1 form Several types: mRNA,
tRNA, rRNA… 40