Transcript Chapter 25 Organic and Biological Chemistry

Organic and
Biological
Chemistry
Organic and
Biological
Chemistry
Organic Chemistry
• Organic chemistry is the chemistry
of carbon compounds.
• Carbon has the ability to form long
chains.
• Without this property, large
biomolecules such as proteins,
lipids, carbohydrates, and nucleic
acids could not form.
Organic and
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Chemistry
Structure of Carbon Compounds
• There are three hybridization states and
geometries found in organic compounds:
– sp3 Tetrahedral
– sp2 Trigonal planar
– sp Linear
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Hydrocarbons
• There are four basic
types of hydrocarbons:
–
–
–
–
Alkanes
Alkenes
Alkynes
Aromatic hydrocarbons
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Chemistry
Properties of Alkanes
• The only van der Waals force is the London
dispersion force.
Organic and
• The boiling point increases with the length Biological
Chemistry
of the chain.
Alkanes
• Alkanes contain only single bonds.
• They are also known as saturated
hydrocarbons.
– They are “saturated” with hydrogens.
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Chemistry
Formulas
• Lewis structures of alkanes look like this.
• They are also called structural formulas.
• They are often not convenient, though…
Organic and
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Chemistry
Formulas
…so more often condensed formulas are used.
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Chemistry
Structure of Alkanes
• Carbons in alkanes are sp3 hybrids.
• They have a tetrahedral geometry and 109.5°
bond angles.
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Chemistry
Structure of Alkanes
• There are only bonds in alkanes.
• There is free
rotation about the
C—C bonds.
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Chemistry
Isomers
Isomers have
the same
molecular
formulas, but the
atoms are
bonded in a
different order.
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Chemistry
Organic Nomenclature
• There are three parts to a compound name:
– Base: This tells how many carbons are in the
longest continuous chain.
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Chemistry
Organic Nomenclature
• There are three parts to a compound name:
– Base: This tells how many carbons are in the
longest continuous chain.
– Suffix: This tells what type of compound it is.
Organic and
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Chemistry
Organic Nomenclature
• There are three parts to a compound name:
– Base: This tells how many carbons are in the
longest continuous chain.
– Suffix: This tells what type of compound it is.
– Prefix: This tells what groups are attached to the
chain.
Organic and
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Chemistry
How to Name a Compound
1. Find the longest chain in
the molecule.
2. Number the chain from
the end nearest the first
substituent encountered.
3. List the substituents as a
prefix along with the
number(s) of the
carbon(s) to which they
are attached.
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Biological
Chemistry
How to Name a Compound
If there is more than
one type of
substituent in the
molecule, list them
alphabetically.
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Biological
Chemistry
Cycloalkanes
• Carbon can also form ringed structures.
• Five- and six-membered rings are most stable.
– They can take on conformations in which their bond
angles are very close to the tetrahedral angle.
– Smaller rings are quite strained.
Organic and
Biological
Chemistry
Reactions of Alkanes
• Alkanes are rather unreactive due to
the presence of only C—C and C—H
-bonds.
• Therefore, they make great nonpolar
solvents.
Organic and
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Chemistry
Alkenes
• Alkenes contain at least one carbon–carbon
double bond.
• They are unsaturated.
– That is, they have fewer than the maximum number of
hydrogens.
Organic and
Biological
Chemistry
Structure of Alkenes
• Unlike alkanes, alkenes cannot rotate freely
about the double bond.
– The side-to-side overlap in the -bond makes this
impossible without breaking the -bond.
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Chemistry
Structure of Alkenes
This creates
geometric isomers,
which differ from
each other in the
spatial arrangement
of groups about the
double bond.
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Chemistry
Properties of Alkenes
Structure also affects the physical properties
of alkenes.
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Chemistry
Nomenclature of Alkenes
• The chain is numbered so the double bond gets the
smallest possible number.
• cis-Alkenes have the carbons in the chain on the
same side of the molecule.
• trans-Alkenes have the carbons in the chain on
opposite sides of the molecule.
Organic and
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Chemistry
Alkynes
• Alkynes contain at least one carbon–carbon triple
bond.
• The carbons in the triple bond are sp-hybridized
and have a linear geometry.
• They are also unsaturated.
Organic and
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Chemistry
Nomenclature of Alkynes
4-methyl-2-pentyne
• The method for naming alkynes is analogous
to the naming of alkenes.
• However, the suffix is -yne rather than -ene.
Organic and
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Chemistry
Reactions of Alkynes
• Alkynes undergo many of the same reactions
alkenes do.
• As with alkenes, the impetus for reaction is
the replacement of -bonds with -bonds.
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Chemistry
Aromatic Hydrocarbons
• Aromatic hydrocarbons are cyclic hydrocarbons that
have some particular features.
• There is a p-orbital on each atom.
– The molecule is planar.
• There is an odd number of electron pairs in the system.
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Chemistry
Aromatic Nomenclature
Many aromatic
hydrocarbons are
known by their
common names.
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Chemistry
Reactions of Aromatic
Compounds
• In aromatic
compounds, unlike
in alkenes and
alkynes, each pair of
-electrons does not
sit between two
atoms.
• Rather, the
electrons are
delocalized; this
stabilizes aromatic
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compounds.
Biological
Chemistry
Reactions of Aromatic
Compounds
• Due to this stabilization, aromatic compounds
do not undergo addition reactions; they
undergo substitution.
• In substitution reactions, hydrogen is
replaced by a substituent.
Organic and
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Chemistry
Structure of Aromatic
Compounds
• Two substituents on a benzene ring could
have three possible relationships:
– ortho-: On adjacent carbons.
– meta-: With one carbon between them.
– para-: On opposite sides of ring.
Organic and
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Chemistry
Reactions of Aromatic
Compounds
Halogenation
Friedel-Crafts Reaction
Reactions of aromatic compounds often
require a catalyst.
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Chemistry
Functional
Groups
The term functional
group is used to
refer to parts of
organic molecules
where reactions
tend to occur.
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Chemistry
Alcohols
• Alcohols contain one or more hydroxyl groups,
—OH.
• They are named
from the parent
hydrocarbon; the
suffix is changed to
-ol and a number
designates the
carbon to which the
hydroxyl is
attached.
Organic and
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Chemistry
Alcohols
• Alcohols are much
more acidic than
hydrocarbons.
– pKa ~15 for most
alcohols.
– Aromatic alcohols
have pKa ~10.
Organic and
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Chemistry
Ethers
• Ethers tend to be quite unreactive.
• Therefore, they are good polar solvents.
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Chemistry
Carbonyl Compounds
• The carbonyl group
is a carbon-oxygen
double bond.
• Carbonyl
compounds include
many classes of
compounds.
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Chemistry
Aldehydes
In an aldehyde, at
least one hydrogen
is attached to the
carbonyl carbon.
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Chemistry
Ketones
In ketones, there
are two carbons
bonded to the
carbonyl carbon.
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Chemistry
Carboxylic Acids
• Acids have a
hydroxyl group
bonded to the
carbonyl group.
• They are tart tasting.
• Carboxylic acids are
weak acids.
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Chemistry
Esters
• Esters are the
products of
reactions
between
carboxylic acids
and alcohols.
• They are found in
many fruits and
perfumes.
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Chemistry
Amides
Amides are formed
by the reaction of
carboxylic acids with
amines.
Organic and
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Chemistry
Amines
• Amines are organic bases.
• They generally have strong, unpleasant
odors.
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Chemistry
Chirality
• Carbons with four different groups attached to
them are handed, or chiral.
• These are optical isomers or stereoisomers.
• If one stereoisomer is “right-handed,” its
enantiomer is “left-handed.”
Organic and
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Chemistry
Chirality
S-ibuprofen
• Many pharmaceuticals are chiral.
• Often only one enantiomer is clinically
active.
Organic and
Biological
Chemistry
Amino Acids and Proteins
• Proteins are polymers
of -amino acids.
• A condensation
reaction between the
amine end of one
amino acid and the
acid end of another
produces a peptide
bond.
Organic and
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Chemistry
Amino Acids and Proteins
• Hydrogen bonding in
peptide chains causes
coils and helices in the
chain.
• Kinking and folding of
the coiled chain gives
proteins a
characteristic shape.
Organic and
Biological
Chemistry
Amino Acids and Proteins
• Most enzymes are
proteins.
• The shape of the
active site
complements the
shape of the substrate
on which the enzyme
acts; hence, the “lockand-key” model. Organic and
Biological
Chemistry
Carbohydrates
Simple sugars are
polyhydroxy
aldehydes or ketones.
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Chemistry
Carbohydrates
• In solution, they form
cyclic structures.
• These can form chains
of sugars that form
structural molecules
such as starch and
cellulose.
Organic and
Biological
Chemistry
Nucleic Acids
Two of the building blocks of
RNA and DNA are sugars
(ribose or deoxyribose) and
cyclic bases (adenine,
guanine, cytosine, and
thymine or uracil).
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Chemistry
Nucleic Acids
These combine with
a phosphate to form
a nucleotide.
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Chemistry
Nucleic Acids
Nucleotides combine
to form the familiar
double-helix form of
the nucleic acids.
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Chemistry