Download Organic Chemistry

Organic
Chemistry
Ch. 3 - Organic Molecules
1
p. 36 text
Inorganic – Chemistry of elements other than carbon
Organic – Carbon-based chemistry
Inorganic
Organic
Usually with
+ & - ions
Always contain
carbon and hydrogen
Usually
ionic bonding
Always
covalent bonding
Always with
few atoms
Often quite large, with
many atoms
Often associated with
nonliving matter
Usually associated
living systems
Carbohydrates as structural materials
2
Organic
Chemistry
3
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
4
Organic
Chemistry
5
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
Functional Groups (Fig. 3.2)
Organic
Chemistry
6
Group Structure Compound Significance
forms H-bonds; some sugars
R OH
Hydroxyl
Alcohols Polar,
and amino acids Example: Ethanol
O
Polar, formsRH-bonds;
some
sugars
Polar; some sugars
Aldehydes
Example: Formaldehyde
C
and amino acids;HExample: Ethanol
Carbonyl
O some sugars Polar; some sugars
Polar;
Ketones
Example: Acetone
Example:
Formaldehyde
R CR
O
Carboxylic
Polar;
some
sugars
Polar, acidic; fats and amino acids
R
Carboxyl
CExample:Acids
AcetoneExample: Acetic acid
OH
H and amino acids
Polar, basic; amino acids
Polar,
acidic;
fats
R
N
Amino
Amines
Example: Tryptophan
H
Example:
Acetic
acidamino acids
Polar, acidic;
some
Disulfide Bonds; some amino acids
R
SH
Sulfhydryl
Thiols
Example: Ethanethiol
Example:
Adenosine
triphosphate
Polar, basic;
amino acids
Example: Tryptophan
O
Organic
Polar, acidic; some amino acids
R POH some
Example: Adenosine triphosphate
Disulfide Bonds;
amino
acids
Phosphate
Phosphates
Example: Ethanethiol
OH
Organic
Chemistry
Isomers
Isomers - organic molecules that have:
Identical molecular formulas, but
Differing internal arrangement of atoms
7
Organic
Chemistry
8
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 Foods
9
Organic
Chemistry
10
Dehydration and Hydrolysis
Dehydration (condensation) - Removal of
water molecule
Connects monomers together to make
polymers
Glucose monomers condense to make starch
Hydrolysis - Addition of water molecule
Disassembles 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 Degradation
of Polymers
11
Four Classes of Organics:
1 - Carbohydrates
Monosaccharides:
Single sugar molecule
Glucose, ribose, deoxyribose
Disaccharides:
Contain two monosaccharides
Sucrose
Polysaccharides:
Polymers of monosaccharides
Starch, glycogen, cellulose, chitin
Organic
Chemistry
12
Popular Models for Representing
Glucose Molecules
13
Synthesis and Degradation
of Maltose, a Disaccharide
14
Carbohydrates Examples:
Monosaccharides
Organic
Chemistry
15
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
Carbohydrates Examples:
Disaccharides
Organic
Chemistry
16
Two monosaccharides joined by dehydration
Soluble and sweet to taste
Examples
Sucrose
- Table sugar, maple sugar
- One glucose and one fructose joined together
Maltose
- Malt sugar
- Two glucoses joined together
Carbohydrates Examples:
Polysaccharides (1)
Organic
Chemistry
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
17
Carbohydrates Examples:
Polysaccharides (2)
Organic
Chemistry
More polysaccharide examples
Cellulose
- Long, coiled polymer of glucose
- Structural element for plants
- Indigestible by most animals
Chitin
- Polymer of glucose
- Very resistant to wear and digestion
- Arthropod exoskeletons, cell walls of fungi
18
Starch
Structure and Function
19
Glycogen
Structure and Function
20
Cellulose
Structure and Function
21
Organic
Chemistry
Four Classes of Organics:
2 - Lipids
22
Insoluble in water


Long chains of repeating CH2 units
Renders molecule nonpolar
Types of Lipids
Type
Organismal Uses
Fats
Long-term energy storage &
thermal insulation in animals Butter, lard
Oils
Long-term energy storage in
Cooking oils
plants and their seeds
Component of plasma
Phospholipids membrane
Human Uses
No-stick pan spray
Steroids
Component of plasma
membrane; hormones
Waxes
Wear resistance; retain water Candles, polishes
Medicines
Blubber
23
Types of Lipids:
Triglycerides
24
Types of Lipids:
Triglycerides (1)
Organic
Chemistry
25
Triglycerides (Fats)
Long-term energy storage
Backbone of one glycerol molecule
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
Dehydration Synthesis of Triglyceride
from Glycerol and Three Fatty Acids
26
Types of Lipids:
Phospholipids (2)
Organic
Chemistry
27
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 Membranes
28
Types of Lipids:
Steroids & Waxes (3)
Organic
Chemistry
29
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
30
Waxes
31
Four Classes of Organics:
3 -Proteins
Organic
Chemistry
32
Functions
 Support – Collagen
 Enzymes – Almost all enzymes are proteins
 Transport – Hemoglobin; membrane proteins
 Defense – Antibodies
 Hormones – Many hormones; insulin
 Motion – Muscle proteins, microtubules
Organic
Chemistry
33
Protein Subunits:
The Amino Acids
Proteins are polymers of amino acids
Each amino acid has a central carbon atom 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 the
20 Amino Acids
34
Proteins:
The Polypeptide Backbone
Organic
Chemistry
35
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 Peptide 36
Protein Molecules:
Levels of Structure
Organic
Chemistry
37
Primary:
 Literally, the sequence of amino acids
Secondary:
 The way the amino acid chain coils or folds
Tertiary:
 Overall three-dimensional shape of a
polypeptide
Quaternary:
 Consists of more than one polypeptide
Levels of Protein Organization
38
Examples of Fibrous Proteins
39
Organic
Chemistry
40
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:
4 -Nucleic Acids
Organic
Chemistry
41
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)
- Single-stranded
- Serves primarily in assembly of proteins
- In nucleus and cytoplasm of cell
The Nucleotides of
Nucleic Acids
Organic
Chemistry
42
Three components:
- A phosphate group,
- A pentose sugar (ribose or deoxyribose), and
- A nitrogenous base (4 kinds in DNA, 4 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
43
DNA Structure
44
RNA Structure
45
Organic
Chemistry
Comparison of DNA & RNA
Table 3.4
Feature
DNA
Sugar
Deoxyribose
Bases
Strands
Cytosine, guanine;
Cytosine, guanine;
adenine, thymine
adenine, uracil
Double-stranded;
Pairing across strands Single stranded
Helix
Yes
cellular
Function Heredity;
control center
Where
RNA
Ribose
No
Interprets genetic info;
protein synthesis
Chromosomes of cell Cell nucleus and
nucleus
cytoplasm
46
Organic
Chemistry
47
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
48