BIOCHEMISTRY

TYPES OF BONDS
A covalent bond is the sharing of a pair of valence electrons by two atoms
In some cases, two atoms are so unequal in their attraction for valence
electrons that the more electronegative atom strips an electron completely
away from its partner. The two resulting oppositely charged atoms (or
molecules) are called ions. A positively charged ion is called a cation, while a
negatively charged ion is called an anion.
Note that the transfer of an electron is not, by itself, the formation of a
bond; rather, it allows a bond to form because it results in two ions of
opposite charge.

 Even a molecule with nonpolar covalent bonds may have positively and
negatively charged regions. Electrons are not always evenly distributed;
at any instant, they may accumulate by chance in one part of a molecule
or another.
This results in ever-changing regions of positive and negative charge that
enable all atoms and molecules to stick to one another, which are known
as Van der Waals interactions.
Van der Waals interactions allow a gecko lizard to walk straight up a wall.
The Van der Waals interactions between the foot molecules and the
molecules of the walls surface are so numerous that despite their
individual weakness, together they can support the lizard.

PROPERTIES OF WATER
The water molecule is shaped like a wide V, with its two hydrogen atoms
and one oxygen atom and is joined by a single covalent bond.
Since oxygen is more electronegative than hydrogen, the electrons of
the covalent bond are closer to the oxygen than hydrogen, which results
in a partial negative charge for oxygen and partial positive
charge for hydrogen.
Water, therefore, is a polar molecule; there is not equal sharing of
electrons in the covalent bond.
The partially positive hydrogen of one molecule is attracted to the
partially negative oxygen of a nearby molecule. The two molecules are
then held together by a hydrogen bond.
Hydrogen bonds are very weak compared to covalent bonds.

 Cohesion: Two molecules of the same type bind together; two water
molecules are held together via hydrogen bonds.
Adhesion: Hydrogen bonds form between water and another polar molecule.
For example, water binds to plant cell walls to form a continuous column of
water in a plant.
Specific Heat: the amount of heat that must be absorbed or lost for 1 g of
that substance to change its temperature by 1C.
Hydrogen bonds restrict the motion of water molecules and increase the
temperature needed for these bonds to be broken, so water has a very high
specific heat. This allows waters temperature to remain very stable.
Heat of Vaporization: the quantity of heat a liquid must absorb for 1 g of it
to be converted from the liquid to the gaseous state. Waters high heat of
vaporization results from its hydrogen bonds. Evaporation

 As a liquid evaporates, the surface of the liquid that remains behind cools. This
evaporative cooling occurs because the molecules with the greatest kinetic
energy are the most likely to leave as gas.
Sweating is a form of evaporative cooling and allows the body to lower its
temperature if it gets too high.
Boiling Point: Waters high boiling point of 100 degrees C allows it to remain
liquid over a high range of temperatures.
Water is one of the few substances that are less dense as a solid than as a liquid,
so ice floats, which is really important because if ice sank, then eventually all
ponds, lakes, and even oceans would freeze solid, making life impossible on
Earth.
As the temperature falls to 0 degrees C, water molecules form a crystalline
lattice, with each water molecule hydrogen bonded to 4 other H20 molecules.
The hydrogen bonds keep the water molecule at a distance from each other,
which results in ice being 10% less dense than liquid water @ 4 degrees Celsius.

Ice: Hydrogen bonds are stable

Liquid water:
Hydrogen bonds break and re-form

 Solution: A liquid that is a completely homogeneous mixture of two or

more substances
Solvent: The dissolving agent of a solution
Solute: the substance that is dissolved
Water is a very versatile solvent, and it form shells around charged and
polar molecules, which prevent it from clumping together. Waters
partially negative oxygen pole attracts positively charged ions while its
positively charged hydrogen pole attracts negatively charged ions.
Hydrophilic: a water-loving substance-substances that dissolve in
water are hydrophilic such as polar molecules and ions.
Hydrophobic: a water-fearing substance- molecules that do not
dissolve in water are hydrophobic such as lipids and certain amino acids.

PROPERTIES OF CARBON
The key to an atoms chemical characteristics is its electron configuration.
Carbon has 4 valence electrons, which allow it to bond to four different
elements, assuming single bonding.

This tetravalence makes large, complex molecules possible

In most cases, carbon forms single or double covalent bonds.
Carbon chains form the skeletons of most organic molecules. The
skeletons vary in length and may be straight, branched, or arranged in
closed rings
Some carbon skeletons have double bonds, which vary in number and
location.
The valences of carbon and its most frequent molecules that it bonds to are
hydrogen, oxygen, and nitrogen

Methane

CH4

Ethane
C2H6

Ethylene

C2H4

HYDROCARBONS
Hydrocarbons are organic molecules consisting of only carbon and
hydrogen
Many organic molecules, such as fats, have hydrocarbon components
Hydrocarbons can undergo reactions that release a large amount of
energy
Examples: The gasoline that fuels a car consists of hydrocarbons, and the
hydrocarbon tails of fats serve as stored fuel for plant embryos (seeds) and
animals.

ISOMERS
Isomers are compounds with the same molecular formula but
different structures and properties

Structural isomers have different covalent arrangements

of their atoms
Cis-trans isomers have the same covalent bonds but differ
in spatial arrangements due to the inflexibility of double
bonds.
Enantiomers are isomers that are mirror images of each
other that differ this way because of an asymmetric carbon.
Very important in the Pharmaceutical Industry

Structural isomers

Cis-trans isomers
Enantiomers
cis isomer

trans isomer

FUNCTIONAL GROUPS
A number of characteristic groups can replace the hydrogens attached to skeletons of organic
molecules
Functional groups are the components of organic molecules that are most commonly involved
in chemical reactions
The number and arrangement of functional groups give each molecule its unique properties

The seven functional groups that are most important in the chemistry of life:

Hydroxyl group
Carbonyl group
Carboxyl group
Amino group
Sulfhydryl group
Phosphate group
Methyl group

POLYMERS & MONOMERS

Carbohydrates, proteins, and nucleic acids are chain-like molecules called
polymers.
Lipids technically arent polymers.
Polymers consist of a long molecule consisting of many similar or
identical monomers linked by covalent bonds.
Monomers are connected by a reaction in which two molecules are
covalently bonded to each other, with the loss of a water molecule; this is
known as a dehydration reaction, aka condensation reaction.
Hydrolysis is the opposite: use water to break down polymers into
monomers.

CARBOHYDRATES
Monosaccharides (simple sugars) have molecular formulas that are
multiples of CH2O.
Trademarks of a sugar: multiple hydroxyl groups and a carbonyl group. A
sugar is either a ketose or aldose sugar depending on the placement of
the carbonyl group.
Another way sugars are differentiated are their arrangements around an
asymmetrical carbon.
Ex: Glucose, Fructose, Galactose, Ribose.
Monosaccharides, particularly glucose, are major nutrients for cells.

 Disaccharides consist of two monosaccharides joined by a

glycosidic linkage (covalent bond that joints two monosaccharides
together, which is formed in a condensation reaction).
Most common disaccharide is sucrose, and its monomers are fructose
and alpha-glucose.
Other examples: lactose (alpha-glucose+galactose) and maltose (alpaglucose+alpa-glucose).

 Polysaccharides are macromolecules, polymers with a few hundred to a few

thousand monosaccharides joined by glycosidic linkages.
Animals and plants use polysaccharides in order to store excess sugars.
Plants store starch, an alpha-glucose polymer, in organelles called plastids.
The simplest form of starch is amylose, which is unbranched.
Amylopectin is a more complex form of starch and is branched.
Animals store glycogen, an alpha-glucose polymer, mainly in the liver and
skeletal muscles.
Hydrolysis of glycogen or starch releases glucose when demand for sugar
increases in the animal or plant, respectively.

 There are also polysaccharides that have structural purposes such as cellulose,
which is the primary material in building plant cell walls.
Cellulose is a beta-glucose polymer, and is never branched.
Parallel cellulose molecules are grouped into units known as microfibrils.
Another structural polysaccharide is chitin, which also is a beta-glucose
polymer. Chitins glucose monomers have a nitrogen branching off the 2nd
carbon.
Chitin is found in arthropods to build their exoskeletons, and fungi use chitin to
build their cell walls instead of cellulose.

LIPIDS
Lipids are not considered true polymers. The only trait that all of them
share is that they mix poorly, or not all, with water.
Lipids are hydrophobic and mainly consist of hydrocarbon regions.
Examples of lipids include waxes, oils, fats, phospholipids, and steroids.

TRIGLYCERIDES
Fats, aka triglycerides, consist of a glycerol and fatty acids.
Glycerol is an alcohol; each of its 3 carbons have a hydroxyl group.
Fatty acids have a carboxyl group but otherwise, consist of hydrocarbon
regions.
When a fat is being made, three fatty acid molecules are joined to glycerol
by an ester linkage, which is formed by a dehydration reaction between a
hydroxyl group and a carboxyl group.
Major function of fats is energy storage. Fats also aid in insulation and
cushions vital organs.
If a fat has no double bonds, it is saturated. Ex: butter.
If a fat has one or more double bonds, it is unsaturated. Ex: olive oil.

PHOSPHOLIPIDS
A phospholipid has only two fatty acids attached to glycerol, and the third
hydroxyl group of glycerol is joined to a phosphate group, which makes the
phospholipid amphipathic(has both hydrophilic and hydrophobic regions).
It also adds a slight negative charge to the head of the phospholipid.
Phospholipids are the major building blocks of cell membranes.
Steroids are lipids with a carbon skeleton that consists of 4 fused skeletons.
Examples include cholesterol and testosterone.

PROTEINS
Monomer: Amino Acids, which has an amino group and carboxyl group. It
also has a R group (sidechain) that adds certain properties to that specific
amino acid.
Functions of proteins include hormones, defense, storage, and enzymes.
The covalent bond between a dipeptide (two amino acids) is known as a
peptide bond.
Proteins are either fibrous(long fibers) or globular (spherical). Most
enzymes are globular.
There are 4 levels of protein structure.

NUCLEIC ACIDS
Nucleic acids are polymers made of monomers called nucleotides.
Nucleotides consist of a nitrogenous base, a 5 carbon sugar, and a
phosphate group.
Nitrogenous bases for DNA: Adenine, Guanine, Cytosine, Thymine.
RNA has the same except Thymine is replaced with Uracil.
Adenine and Guanine are Purines (2 rings) while the rest are pyrimidines
(1 ring).
Nucleotides are joined together via a phosphodiester linkage, which
makes the phosphate group linking with the sugar of the nucleotides.