Transcript organic compounds

Organic Compounds
and Biomolecules
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Organic Compounds
 It used to be thought that only living things could synthesize
the complicated carbon compounds found in cells
 German chemists in the 1800’s learned how to do this in the
lab, showing that “organic” compounds can be created by
non-organic means.
 Today, organic compounds are those that contain carbon.
(with a few exceptions such as carbon dioxide and diamonds)
Carbon’s Bonding Pattern
 Carbon has 4 electrons in its outer shell. To satisfy the octet
rule, it needs to share 4 other electrons. This means that each
carbon atom forms 4 bonds.
 The 4 bonds are in the form of a tetrahedron, a triangular
pyramid.
 Carbon can form long chains and rings, especially with
hydrogens attached.
 Compounds with just carbon and hydrogen are “hydrocarbons”:
non-polar compounds like oils and waxes.
Carbon atoms form 4 tetrahedral single bonds. Two carbon
atoms sharing a single bond can rotate around the single bond.
Two carbon atoms sharing a double bond are closer and
cannot rotate about the double bond. The carbons and the
atoms bound to them form a plane.
Functional Groups
Most of the useful behavior of organic compounds comes from
functional groups attached to the carbons. A functional group
is a special cluster of atoms that performs a useful function.
Organic Molecules and Functional Groups
Functional Groups:
• An atom or a group of atoms.
• Chemical and physical properties.
• The reactive part of the molecule.
• Have C—C and C—H bonds.
• Many organic molecules possess other structural
features:
 Heteroatoms—atoms other than carbon or
hydrogen, example: N, S, P, etc.
  Bonds—the most common  bonds occur in
C—C and C—O double bonds.
• Heteroatoms and  bonds confer reactivity on a particular
molecule.
 Heteroatoms have lone pairs and create electrondeficient sites on carbon.
  Bonds are easily broken in chemical reactions.
 A  bond makes a molecule a base and a nucleophile.
The C—C and C—H bonds are form the carbon backbone or
skeleton to which the functional group is attached.
• Ethane and molecules like it are very unreactive:
• Ethanol has an OH group attached to its backbone. Ethanol has lone
pairs and polar bonds that make it reactive with a variety of reagents.
Hydrocarbons
Hydrocarbons are compounds made up of only the elements
carbon and hydrogen. They may be aliphatic or aromatic.
• Aromatic hydrocarbons: had strong characteristic odors.
• The simplest aromatic hydrocarbon is benzene.
• When a benzene ring is bonded to another group, it is called
a phenyl group.
Examples of Molecules Containing C-Z  Bonds
Compounds Containing the C=O Group:
• This group is called a “carbonyl group”.
• The polar C—O bond makes the carbonyl carbon an
electrophile, while the lone pairs on O allow it to react as a
nucleophile and base.
• The carbonyl group also contains a  bond that is more
easily broken than a C—O  bond.
Molecules Containing the C=O Functional Group
A functional group determines all of the following
properties of a molecule:
1.
bonding and shape
2.
type and strength of intermolecular forces
3.
physical properties
4.
nomenclature
5.
chemical reactivity
Biomolecules
• Biomolecules are organic compounds found in biological
systems.
• There are four main families of biomolecules:
 Protein (amino acids),
 Carbohydrate (monosaccharide),
 Lipids and
 Nucleic acid (nucleotides).
• Biomolecules often have several functional groups.
Intermolecular Forces
 Intermolecular forces are also referred to as noncovalent
interactions or nonbonded interactions.
 There are several types of intermolecular interactions.
 Ionic compounds contain oppositely
charged.
 These ionic interactions are much
stronger than the intermolecular
forces present between covalent
molecules.
• Covalent compounds are composed of discrete
molecules.
• The nature of the forces between molecules
depends on the functional group present.
• There are three different types of interactions:
shown below in order of :
 van der Waals forces
 dipole-dipole interactions
 hydrogen bonding
increasing strength
Van der Waals Forces
 van der Waals forces are also known as London forces.
 They are weak interactions caused by momentary changes in
electron density in a molecule.
 They are the only attractive forces present in nonpolar
compounds.
Even though CH4 has no net dipole, at any
one instant its electron density may not be
completely symmetrical, resulting in a
temporary dipole.
This can induce a temporary dipole in
another molecule. The weak interaction of
these temporary dipoles constituents van
der Waals forces.
 All compounds exhibit van der Waals forces.
 The surface area of a molecule determines the strength of the van
der Waals interactions between molecules. The larger the surface
area, the larger the attractive force between two molecules, and
the stronger the intermolecular forces.
 van der Waals forces are also affected by polarizability.
 Polarizability is a measure of how the electron cloud around an
atom responds to changes in its electronic environment.
Larger atoms, like iodine, which have
more loosely held valence electrons,
are more polarizable than smaller
atoms like fluorine, which have more
tightly held electrons.
Thus, two F2 molecules have little
attractive force between them since the
electrons are tightly held and temporary
dipoles are difficult to induce.
Dipole-Dipole Interactions
 Dipole–dipole interactions are the attractive forces between the
permanent dipoles of two polar molecules.
 Consider acetone (below). The dipoles in adjacent molecules align
so that the partial positive and partial negative charges are in close
proximity. These attractive forces caused by permanent dipoles are
much stronger than weak van der Waals forces.
Hydrogen Bonding
Hydrogen bonding typically occurs when a hydrogen atom bonded
to O, N, or F, is electrostatically attracted to a lone pair of electrons
on an O, N, or F atom in another molecule.
Note: as the polarity of an organic molecule increases, so does
the strength of its intermolecular forces.
Physical Properties—Boiling Point
 The boiling point of a compound is the temperature at which liquid
molecules are converted into gas.
 In boiling, energy is needed to overcome the attractive forces in
the more ordered liquid state.
 The stronger the intermolecular forces, the higher the boiling
point.
 For compounds with approximately the same molecular weight:
Consider the example below. Note that the relative strength of the
intermolecular forces increases from pentane to butanal to 1butanol. The boiling points of these compounds increase in the
same order.
For two compounds with similar functional groups:
 The larger the surface area, the higher the boiling point.
 The more polarizable the atoms, the higher the boiling point.
Consider the examples below which illustrate the effect of size
and polarizability on boiling points.
Liquids having different boiling points can be separated in the
laboratory using a distillation apparatus, shown in Figure below:
Physical Properties—Melting Point
 The melting point is the temperature at which a solid is converted
to its liquid phase.
 In melting, energy is needed to overcome the attractive forces in
the more ordered crystalline solid.
 The stronger the intermolecular forces, the higher the melting point.
 Given the same functional group, the more symmetrical the
compound, the higher the melting point.
 Because ionic compounds are held together by extremely strong
interactions, they have very high melting points.
 With covalent molecules, the melting point depends upon the
identity of the functional group. For compounds of approximately
the same molecular weight:
• The trend in melting points of pentane, butanal, and 1butanol parallels the trend observed in their boiling points.
• Symmetry also plays a role in determining the melting points of
compounds having the same functional group and similar
molecular weights, but very different shapes.
• A compact symmetrical molecule like neopentane packs well into a
crystalline lattice whereas isopentane, which has a CH3 group
dangling from a four-carbon chain, does not. Thus, neopentane
has a much higher melting point.
Solubility
• Solubility is the extent to which a compound, called a solute,
dissolves in a liquid, called a solvent.
In dissolving a compound, the
energy needed to break up the
interactions between the
molecules or ions of the solute
comes from new interactions
between the solute and the
solvent.
 Compounds dissolve in solvents having similar kinds of
intermolecular forces.
 “Like dissolves like.”
 Polar compounds dissolve in polar solvents. Nonpolar or
weakly polar compounds dissolve in nonpolar or weakly polar
solvents.
 Water and organic solvents are two different kinds of solvents.
 Water is very polar since it is capable of hydrogen bonding with
a solute.
 Many organic solvents are either nonpolar, like carbon
tetrachloride (CCl4) and hexane [CH3(CH2)4CH3], or weakly
polar, like diethyl ether (CH3CH2OCH2CH3).
 Most ionic compounds are soluble in water, but insoluble in
organic solvents.
• An organic compound is water soluble only if it contains one
polar functional group capable of hydrogen bonding with the
solvent for every five C atoms it contains. For example, compare
the solubility of butane and acetone in H2O and CCl4.
Since butane and acetone are both organic compounds having a C—C and
C—H backbone, they are soluble in the organic solvent CCl4. Butane, which
is nonpolar, is insoluble in H2O. Acetone is soluble in H2O because it contains
only three C atoms and its O atom can hydrogen bond with an H atom of H2O.
 To dissolve an ionic compound, the strong ion-ion interactions
must be replaced by many weaker ion-dipole interactions.
When an ionic solid is dissolved in
H2O, the ion-ion interaction are
replaced by ion-dipole interactions.
Though these forces are weaker,
there are so many of them that they
compensate for stronger ionic bonds.
 The size of an organic molecule with a polar functional group
determines its water solubility.
 A low molecular weight alcohol like ethanol is water soluble
since it has a small carbon skeleton of  five C atoms),
compared to the size of its polar OH group.
 Cholesterol has 27 carbon atoms and only one OH group. Its
carbon skeleton is too large for the OH group to solubilize by
hydrogen bonding, so cholesterol is insoluble in water.
• The nonpolar part of a molecule that is not attracted to H2O is
said to be hydrophobic.
• The polar part of a molecule that can hydrogen bond to H2O is
said to be hydrophilic.
• In cholesterol, for example, the hydroxy group is hydrophilic,
whereas the carbon skeleton is hydrophobic.
Application—Vitamins
Vitamins are either lipid or water soluble.
Application—Soap
Soap molecules have two distinct parts - a hydrophilic
portion composed of ions called the polar head, and a
hydrophobic carbon chain of nonpolar C—C and C—H
bonds, called the nonpolar tail.
When soap is dissolved in H2O, the molecules form micelles with the nonpolar tails in
the interior and the polar heads on surface. The polar heads are solvated by ion-dipole
interactions with H2O molecules.
Application—The Cell Membrane
Phospholipid contain an ionic or polar head, and two long nonpolar hydrocarbon tails. In aqueous
environment, phospholipids form a lipid bilayer, with the polar head oriented toward aqueous exterior and
nonpolar tails forming hydrophobic interior. Cell membranes are composed largely of this lipid bilayer.
Transport Across a Cell Membrane:
• Polar molecules and ions are transported across cell membranes
encapsulated within molecules called ionophores.
• Ionophores are organic molecules that complex cations. They have a
hydrophobic exterior that makes them soluble in the nonpolar interior
of the cell membrane, and a central cavity with several oxygens
whose lone pairs complex with a given ion.
Transport Across a Cell Membrane:
Several synthetic ionophores have also been prepared, including
one group called crown ethers.
Crown ethers are cyclic ethers containing several oxygen atoms
that bind specific cations depending on the size of their cavity.
Influence of Functional Groups on Reactivity
Recall that:
• Functional groups create reactive sites in molecules.
• Electron-rich sites react with electron poor sites.
All functional groups contain a heteroatom, a  bond or both,
and these features create electron-deficient (or electrophilic)
sites and electron-rich (or nucleophilic) sites in a molecule.
Molecules react at these sites.
An electron deficient carbon reacts with a nucleophile,
symbolized as: Nu¯ in reactions. An electron-rich carbon
reacts with an electrophile, symbolized as E+ in reactions.
For example, alkenes contain a C—C double bond, an
electron-rich functional group with a nucleophilic  bond. Thus,
alkenes react with electrophiles E+, but not with other electron
rich species like OH¯ or Br¯.
On the other hand, alkyl halides possess an electrophilic
carbon atom, so they react with electron-rich nucleophiles.
Biomolecules
Biomolecules are complex, but are made up of simpler components
Proteins, nucleic acids, polysaccharides and lipids are the most
abundant biomolecules and always exist in organism
Carbohydrate:
 Complex carbohydrates: polysaccharides (starch, cellulose)
 "Simple sugars" monosccharides (glucose, fructose and
galactose) and disaccharides (sucrose, maltose and lactose)
Lipids
Proteins
Protein (Polypeptide): are organic compounds made of amino acids arranged in a
linear chain polymer and joined together by peptide bonds between the carboxyl
and amino groups of adjacent amino acid residues
Primary structure of Proteins
Secondary structure of Proteins
Tertiary & Quarternary
Structure of Proteins
Nucleotides
Polynucleotides (DNA & RNA)
Combination Biomolecules
 Lipoproteins (blood transport molecules)
 Glycoproteins (membrane structure)
 Glycolipids (membrane receptors)
Chemically identical Biologically different
Taste receptors can differentiate between diastereoisomers
Why is Sugar Sweet?
Our tongues recognize the molecules of sugar by their shape! The sugar molecules fit
specially-shaped cavities in our tongues. When these "pits" are filled, our nerves send a
signal to the brain shouting, YAHOO, sweet!
Evolution has programmed our brains to find nutritious material tasty and label organic
material which we can not digest as yucky! Recent research suggests that sugar is addictive,
just like drugs. Sugar and the taste of sweet stimulate the brain by activating beta endorphin
receptor sites.
In 2003, studies that focused on brain chemicals, known as opioids showed that some
addictive drugs like heroin or morphine activate the opioid system to produce a pleasurable
response. Whether through opioids or some other brain chemical, the scientists suspect that
sweets like drugs can activate an "incentive system" in the brain that helps reinforce
behaviors. In 2008, Bart Hoebel , a professor of psychology at Princeton University,
explained that ".. evidence from an animal model suggests that bingeing on sugar can act in
the brain in ways very similar to drugs of abuse."
You ask someone, why is sugar sweet, and they will most likely say, because it tastes
nice. Or they will give you the answer related to the specially-shaped cavities in our
tongues. Or they will say because our brains like it. All are possible answers. But I think
that sugar is sweet because of its importance to survival and because of evolution. Animal
species which could easily identify and develop a liking for this Universal Currency, Sugar,
survived and propagated.
Sugar contains some of the most important energy-rich dietary components necessary
for our survival. Sugar can be easily and quickly absorbed by the blood giving us vital
energy to keep us alive. Energy that keeps our hearts pumping, our brains functioning,
our muscles moving such that it keeps us alive and on our feet. Other foods, like fats or
starch, may need first to be processed and converted into simpler forms or to sugar to
be useful in the same way.
Enzymatic
Mechanism
Substrate
Product
Enzyme
Enzyme
Argininimide (colored) stereospecifically fitting within
an RNA a pocket (grey)
RNA pocket
Argininimide
Oxidation reactions generally release energy
More
reduced
More
oxidized