Organic Chemistry
Organic molecules contain carbon
Abundant in living organisms
Macromolecules are large, complex
organic molecules
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Carbon
Carbon has 4 electrons in its outer shell
Needs 4 more electrons to fill the shell
It can make up to 4 bonds
Usually
single or double bonds
Carbon can form nonpolar and polar bonds
Molecules
with nonpolar bonds (like
hydrocarbons) are poorly water soluble
Molecules with polar bonds are more water
soluble
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Propionic Acid
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Functional Groups
Groups of atoms with special chemical
features that are functionally important
Each type of functional group exhibits the
same properties in all molecules in which it
occurs
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Isomers
Two structures with an identical molecular
formula but different structures and
characteristics
Structural isomers- contain the same
atoms but in different bonding
relationships
Stereoisomers- identical bonding
relationships, but the spatial positioning of
the atoms differs in the two isomers
Geometric
isomers- positioning around double bond
Enantiomers- mirror image of another molecule
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Four major types of organic
molecules and macromolecules
1.
2.
3.
4.
Carbohydrates
Lipids
Proteins
Nucleic acids
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Carbohydrates
Composed of carbon, hydrogen, and
oxygen atoms
Cn(H2O)n
Most of the carbon atoms in a
carbohydrate are linked to a hydrogen
atom and a hydroxyl group
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Monosaccharides
Simplest sugars
Most common are 5 or 6 carbons
Pentoses-
ribose (C5H10O5), deoxyribose
(C5H10O4)
Hexose- glucose (C6H12O6)
Different ways to depict structures
Ring
or linear
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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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Disaccharides
Carbohydrates composed of two
monosaccharides
Joined by dehydration or condensation
reaction
Broken apart by hydrolysis
Examples -sucrose, maltose, lactose
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Polysaccharides
Many monosaccharides linked together to
form long polymers
Examples
Energy
storage – starch, glycogen
Structural role – cellulose, chitin,
glycosaminoglycans
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Lipids
Composed predominantly of hydrogen and
carbon atoms
Defining feature of lipids is that they are
nonpolar and therefore very insoluble in
water
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Fats
Mixture of triglycerides
Also
known as triacylglycerols
Formed by bonding glycerol to three fatty
acids
Joined by dehydration or condensation
reaction
Broken apart by hydrolysis
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Fatty acids
Saturated-
all carbons are linked by single
covalent bonds
Tend to be solid at room temperature
Unsaturated-
contain one or more double
bonds
1 double bond- monounsaturated
2 or more – polyunsaturated
Tend to be liquids at room temperature (oils)
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Fats are important for energy storage
1
gram of fat stores twice as much energy as
1 gram of glycogen or starch
Fats can also be structural in providing
cushioning and insulation
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Phospholipids
Glycerol, 2 fatty acids and a phosphate
group
Amphipathic molecule
Phosphate
region- polar, hydrophillic
Fatty acid chains- nonpolar, hydrophobic
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Proteins
Composed of carbon, hydrogen, oxygen,
nitrogen, and small amounts of other
elements, notably sulfur
Amino acids are the monomers
Common
structure with variable R-group
20 amino acids
Side-chain determines structure and function
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Proteins
Joined by dehydration or condensation
reaction
Peptide
bond
Forms polypeptides (<50 amino acids)
Proteins are made up of 1 or more
polypeptides
Broken apart by hydrolysis
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Protein Structure
Primary
Secondary
Tertiary
Quaternary
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Primary structure
Amino acid sequence
Determined by genes
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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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Tertiary structure
Folding gives complex three-dimensional
shape
Sometimes final level of structure
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Quaternary structure
Made up of 2 or more polypeptides
Protein
subunits
Multimeric proteins
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5 factors promoting protein folding
and stability
1.
2.
3.
4.
5.
Hydrogen bonds
Ionic bonds
Hydrophobic effects
Van der Waals forces
Disulfide bridges
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Protein-protein interactions
Many cellular processes involve steps in
which two or more different proteins
interact with each other
Specific binding at surface
Use first 4 factors (Hydrogen bonds, Ionic bonds,
Hydrophobic effects, Van der Waals forces)
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Christian Anfinsen Showed That the Primary
Structure of Ribonuclease Determines Its
Three-Dimensional Structure
Prior to the 1960s, the mechanisms by which
proteins assume their three-dimensional
structures were not understood.
Christian Anfinsen, however, postulated that
proteins contain all the information necessary to
fold into their proper conformation without the
need for organelles or cellular factors
He hypothesized that proteins spontaneously
assume their most stable conformation based on
the laws of chemistry and physics
Ribonuclease experiment
Nobel Prize 1972
In vitro- no other cellular components present
Chemicals that disrupt bonds cause the enzyme
to lose function
Removal of those chemicals restored function
Even
in the complete absence of any cellular factors
or organelles, an unfolded protein can refold into its
functional structure
Christian Boehmer Anfinsen, Jr.
NIH and Johns Hopkins
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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
Store genetic information coded in the sequence of their
monomer building blocks
Ribonucleic
acid (DNA)
acid (RNA)
Involved in decoding this information into instructions for
linking together a specific sequence of amino acids to form a
polypeptide chain
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Nucleic Acids
Monomer is a nucleotide
Made up of phosphate group, a fivecarbon sugar (either ribose or
deoxyribose), and a single or double ring
of carbon and nitrogen atoms known as a
base
Sugar-phosphate backbone
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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 forms
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