Chapter 0

Organic Chemist
ry
 Organic Ch 2
emistry
Outline

Organic vs Inorganic
Functional Groups and Isomers
Macromolecules
Carbohydrates
Lipids
Proteins
Nucleic Acids
 Organic Ch 3
emistry
Organic Molecules
Inorganic – Chemistry of elements other than carbon
Organic – Carbon-based chemistry
Inorganic Organic
Usually with Always contain
+ & - ions carbon and hydrogen
Usually Always
ionic bonding covalent bonding
Always with Often quite large, with
few atoms many atoms
Often associated with Usually associated
nonliving matter living systems
Carbohydrates as structural materials 4
 Organic Ch 5
emistry
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
Can produce long carbon chains like octane
Can produce ring forms like cyclohexane
Octane & Cyclohexane 6
 Organic Ch 7
emistry
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
 Biologically Important Organic Ch 8
emistry
Functional Groups
Group Structure Compound Significance
Hydroxyl R OH Alcohols Polar, forms H-bonds; some sugars
and amino acids Example: Ethanol

O
Polar, formsRH-bonds; some sugars
Aldehydes
C Example: Ethanol Polar; some sugars
Example: Formaldehyde
and amino acids; H
Carbonyl O some sugars Polar; some sugars
Polar; Ketones
Example:
R C R Formaldehyde Example: Acetone

O
Polar; Carboxylic
some sugars
Carboxyl R CExample: Acids
Acetone
Polar, acidic; fats and amino acids
Example: Acetic acid
OH
Polar, acidic;
R N H
fats andAmines
amino acids
Amino H
Polar, basic; amino acids
Example: Tryptophan
Example: Acetic
Polar, acidic; acidamino acids
some
Sulfhydryl R
Polar,SHbasic; Thiols
amino
Example: Adenosine triphosphateacids
Disulfide Bonds; some amino acids
Example: Ethanethiol
Example:
Disulfide Bonds;
O someTryptophan
amino acids
Example:
Phosphate Ethanethiol
R C R Organic Polar, acidic; some amino acids
Phosphates Example: Adenosine triphosphate
OH
 Organic Ch 9
emistry
Isomers

Isomers - organic molecules that have:

Identical molecular formulas, but
Differing internal arrangement of atoms
 Organic Ch 10
emistry
Macromolecules
Some molecules 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:
Category Example Subunit(s)
Lipids Fat Glycerol & fatty acids
Carbohydrates Polysaccharide Monosaccharide
Proteins Polypeptide Amino acid
Nucleic Acids DNA, RNA Nucleotide
Common 11
Foods
 Organic Ch 12
emistry
Dehydration and Hydrolysis
Dehydration - Removal of water molecule
Used to connect monomers together to make
polymers
Polymerization of glucose monomers to make
starch
Hydrolysis - Addition of water molecule
Used to disassemble polymers into monomer
parts
Digestion of starch into glucose monomers
Specific enzymes required for each reaction
Accelerate reaction
Are not used in the reaction
Synthesis and 13
Degradation
of Polymers
 Four Classes of Organics: Organic Ch 14
emistry
1 - Carbohydrates
Monosaccharides:
Single sugar molecule
Glucose, ribose, deoxyribose
Disaccharides:
Contain two monosaccharides joined during
dehydration reaction
Sucrose
Polysaccharides:
Polymers of monosaccharides
Starch, cellulose, chitin
Popular Models for 15
Representing
Glucose Molecules
 Synthesis and 16
Degradation
of Maltose, a Disaccharide
 Carbohydrates Examples: Organic Ch 17
emistry
Monosaccharides

Single sugar molecules

Quite soluble and sweet to taste
Examples
Glucose (blood), fructose (fruit) and galactose
­ Hexoses - Six carbon atoms
­ Isomers of C6H12O6
Ribose and deoxyribose (in nucleotides)
­ Pentoses – Five carbon atoms
­ C5H10O5 & C5H10O4
 Carbohydrates Examples: Organic Ch 18
emistry
Disaccharides
Contain two monosaccharides joined by
dehydration reaction
Soluble and sweet to taste
Examples
Sucrose
­ Table sugar, maple sugar
­ One glucose and one fructose joined by
dehydration
Maltose
­ Malt sugar
­ Two glucoses joined by dehydration
 Carbohydrates Examples: Organic Ch 19
emistry
Polysaccharides (1)
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
 Carbohydrates Examples: Organic Ch 20
emistry
Polysaccharides (2)
More polysaccharide examples
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
 Starch 21
Structure and
Function
 Glycogen 22
Structure and
Function
 Cellulose 23
Structure and
Function
 Four Classes of Organics: Organic Ch 24
emistry
2 - Lipids
Insoluble in water
 Long chains of repeating CH2 units
 Renders molecule nonpolar
Types of Lipids

Type Organismal Uses Human Uses

Long-term energy storage &
Fats thermal insulation in animals Butter, lard
Long-term energy storage in
Oils plants and their seeds Cooking oils

Phospholipids Component
membrane
of plasma
No-stick pan spray
Component of plasma
Steroids membrane; hormones Medicines

Waxes Wear resistance; retain water Candles, polishes

Blubber 25
Types of Lipids: 26
Triglycerides
 Types of Lipids: Organic Ch 27
emistry
Triglycerides (1)
Triglycerides (Fats)
Long-term energy storage
Backbone of one glycerol molecule
­ Three-carbon alcohol
­ Each has an OH- group
Three fatty acids attached to each glycerol
molecule
­ Long hydrocarbon chain
 Saturated- no double bonds between carbons
 Unsaturated - 1 double bonds between carbons

­ Carboxylic acid at one end

­ Carboxylic acid connects to –OH on glycerol in
dehydration reaction
Dehydration Synthesis of Triglyceride 28
from Glycerol and Three Fatty Acids
 Types of Lipids: Organic Ch 29
emistry
Phospholipids (2)
Phospholipids
Derived from triglycerides
Glycerol backbone
Two fatty acids attached instead of three
Third fatty acid replaced by 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
Phospholipids Form 30
Membranes
 Types of Lipids: Organic Ch 31
emistry
Steroids & Waxes (3)
Steroids
Cholesterol, testosterone, estrogen
Skeletons of four fused carbon rings
Waxes
Long-chain fatty acid bonded to a long-chain
alcohol
­ High melting point
­ Waterproof
­ Resistant to degradation
Steroid Diversity 32
Waxes 33
 Four Classes of Organics: Organic Ch 34
emistry
3 -Proteins

Functions
 Support – Collagen
 Enzymes – Almost all enzymes are proteins
 Transport – Hemoglobin; membrane proteins
 Defense – Antibodies
 Hormones – Many hormones; insulin
 Motion – Muscle proteins, microtubules
 Protein Subunits: Organic Ch 35
emistry
The Amino Acids
Proteins are polymers of amino acids
Each amino acid has a central carbon atom
(the alpha carbon) to which are attached
 a hydrogen atom,
 an amino group –NH2,
 A carboxylic acid group –COOH,
 and one of 20 different types of –R
(remainder) groups
There are 20 different amino acids that make
up proteins
All of them have basically the same structure
except for what occurs at the placeholder R
Structural Formulas for 36
the
20 Amino Acids
 Proteins: Organic Ch 37
emistry
The Polypeptide Backbone
Amino acids joined together end-to-end
 COOH of one AA covalently bonds to the NH2
of the next AA
 Special name for this bond - Peptide Bond
­ Two AAs bonded together – Dipeptide
­ Three AAs bonded together – Tripeptide
­ Many AAs bonded together – Polypeptide
 Characteristics of a protein determined by
composition and sequence of AA’s
 Virtually unlimited number of proteins
Synthesis and Degradation of a 38
Peptide
 Protein Molecules: Organic Ch 39
emistry
Levels of Structure
Primary:
 Literally, the sequence of amino acids
 A string of beads (up to 20 different colors)
Secondary:
 The way the amino acid chain coils or folds
 Describing the way a knot is tied
Tertiary:
 Overall three-dimensional shape of a polypeptide
 Describing what a knot looks like from the outside
Quaternary:
 Consists of more than one polypeptide
 Like several completed knots glued together
Levels of Protein 40
Organization
Examples of Fibrous 41
Proteins
 Organic Ch 42
emistry
Protein-folding Diseases

Assembly of AA’s into protein extremely

complex
Process overseen by “chaperone” molecules
 Inhibit incorrect interactions between R
groups as polypeptide grows
 Defects in these chaperones can corrupt the
tertiary structure of proteins
 Mad cow disease could be due to mis-folded
proteins
 Four Classes of Organics: Organic Ch 43
emistry
4 -Nucleic Acids

Polymers of nucleotides
Very specific cell functions
DNA (deoxyribonucleic acid)
­ Double-stranded helical spiral (twisted ladder)
­ Serves as genetic information center
­ In chromosomes
RNA (ribonucleic acid)
­ Part single-stranded, part double-stranded
­ Serves primarily in assembly of proteins
­ In nucleus and cytoplasm of cell
 The Nucleotides of Organic Ch 44
emistry
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 45
DNA Structure 46
RNA Structure 47
 Organic Ch 48
emistry
Comparison of DNA & RNA

Table 3.4
Feature DNA RNA
Sugar Deoxyribose Ribose
Cytosine, guanine; Cytosine, guanine;
Bases adenine, thymine adenine, uracil
Double-stranded;
Strands Pairing across strands Mostly single stranded
Helix Yes No

Function Heredity; cellular

control center
Interprets genetic info;
protein synthesis
Chromosomes of cell Cell nucleus and
Where nucleus cytoplasm
 Organic Ch 49
emistry
Other Nucleic Acids
ATP (adenosine triphosphate) is composed of
adenine, ribose, and three phosphates
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
ATP 50
 Organic Ch 51
emistry
Review

Organic vs Inorganic
Functional Groups and Isomers
Macromolecules
Carbohydrates
Lipids
Proteins
Nucleic Acids
 Ending Slide Chapter 03

Organic Chemist
ry