BIOCHEMICALS

I) Basic Physics and Chemistry

A) Energy:
We speak oI energy in two Iorms; Kinetic in 'motion and Potential 'stored.
Kinetic: 1 Thermal molecular motion
2 Radiant movement oI photons
3 Electric movement oI charged particles
Potential: 1 Chemical bond
2 Chemical gradient (across a barrier)
3 Electrical potential (voltage)

1
st
Law oI Thermodynamics Energy can neither be created nor destroyed but can be
converted Irom Iorm to Iorm.
2
nd
Law oI Thermodynamics A natural process that starts in one equilibrium state and
ends in another will go in the direction that causes the entropy (statistical probability oI
randomness or disorder) oI the system plus the environment to increase.

Biological systems (i.e. Cells) must disorder their environment to maintain their degree
oI order. They do this by interconversion oI radiant and bond energy Irom external
sources into internal organized energy stores in chemical bonds and gradients. Thus a
basic Iamiliarity with chemical principles is Iundamental to an understanding oI cellular
activities.
B) Chemical interactions ('Bonds)
1) Ionic Bond a transIer oI electrons, oppositely charged ions attract.
2) Covalent Bond a sharing oI electrons. The 'valence oI and atom is
indicative oI the number oI electrons it can share. In a non-polar covalent
bond electrons are shared equally. In a polar covalent bond there is unequal
sharing.
3) 'Hydrogen Bond the attraction oI a member (partial negative) oI a polar
covalent bond with the hydrogen oI chemicals containing e.g. O-H or N-H
groups.
Example: Water a polar H-bonding solvent Ior biological systems.
Hydrophilic substances are polar or charged.
Hydrophobic substances are non-polar organics.
Amphipathic substances have extensive non-polar regions wit charger or polar
ends.
4) Van der Waals Attraction transient and opposing dipoles in nearby atoms.
This attraction is important Ior interaction oI non-polar substances.
5) 'Hydrophobic Bond is not a true bond. Rather it reIers to the energy
required to a non-polar molecule between interacting polar molecules or polars
between non-polars
C) Some Carbon Chemistry
Living systems are based upon the versatile chemistry oI the carbon atom. It can
interact (bond) with many other elements. It has a valence oI Iour with its bonds
distributed in a tetrahedral and oIten asymmetric Iashion. Since it can also bond with
other carbon atoms in single or double (planner) interactions large macromolecules are
possible.

Aliphatic C-H and aromatic C
6
H
6
linkages are non-polar i.e. hydrophobic.
CO and C-N linkages are polar and thereIore hydrophilic.

Alcohol - R-C-OH Aldehyde R CHO Ketone R (CO) R

Acid R- (CO) OH Ester R (CO) OR

Amine R C NH
2
Amide R- (CO) NHR


II) Organic Biomolecules
The primary Biomolecules include:
Carbohydrates
Lipids
Nucleotides and Nucleic Acids
Amino Acids and Proteins

A) Carbohydrates
Carbohydrates get their name Irom their general chemical Iormula Cn(H
2
O)
n
.
'Head group is and aldehyde trailed by multi alcohols. OIten these react creating a
ring structure.
Carbohydrates have two 'Iorms, simple sugars and complex carbohydrates.
Simple sugars (Figure 2)
monosaccharides e.g. glucose, Iructose, galactose
disaccharides e.g. sucrose, lactose, maltose
Primary use: energy source or building block.
Complex Carbohydrates - (Figure 3)
Carbohydrate polymers produced by condensation oI simple sugars.
Uses:
Energy storage
Plants Starch, amylose and amylopectin 1-4 linkage
Animals Glycogen 1-4 and 1-6 linkages, highly branched.

Structural (oIten 1-4 linkage)
1) Cellulose plant cell wall, indigestible 'Iiber
2) Glycosaminoglycan ABAB repeats used in the extracellular
matrix oI animal tissues.
3) Chitin unbranched polymer oI N-Acetylglucosamine. Used as
an exoskeletal element by some animals.

B) Lipids
Composed primarily oI carbons and hydrogens with only small amounts oI oxygen.
ThereIore they are relatively water insoluble and yield substantial amounts oI energy
when 'burned. Important subtypes include:
1) Fatty acids and Triacylglycerols: (Figure 4)
Fatty acids come as saturated or unsaturated with the carbon chain length usually
in multiples oI 2. Their primary use is as a source oI energy or as a building block.
Triacylglycerols (Iats and oils) are composed oI 3 Fatty acids linked to glycerol
and are used primarily as an energy storage Iorm.

2) Sterols: (Figure 4)
The carbon/hydrogen 'chain is Iormed into a multi-ring structure. These
compounds Iunction in membranes and as 'hormones.
3) Phospholipids: (Figure 5)
These compounds have a structure similar to triacylglycerols. However one Iatty
acid is replaced by a polar or charged 'head group that contains PO
4
. This
organization produces an amphipathic compound ideal Ior the construction oI cell
membranes.


C) Nucleotides and Nucleic Acids
Nucleotides are built oI 3 components: (Figure 6)
1) a phosphate group
2) a pentose sugar
3) a 'nitrogenous base
Biologically signiIicant nitrogenous bases;
Purines aromatic, heterocyclic Iused 6 and 5 atom rings Adenine and Guanine
Pyrimidines - single 6 unit aromatic ring Cytosine, Thymine and Uracil
These can condense with #1 carbon oI a pentose sugar (ribose or deoxyribose) to Iorm a
nucleoside. A phosphate can link to the #5 carbon oI a nucleoside Iorming a
nucleotide. Mono, di, and triphosphate Iorms are common biologically.

Nucleotides have multiple Iunctions:
1) as modiIying groups Ior other molecules
2) as building blocks Ior nucleic acids
3) Ior chemical potential (bond) energy transIer

Energy transIer Iunction: At cellular pH phosphate groups will be charged. Thus ATP
will have multiple nearby negative charges. Charge:charge repulsion 'strains the
phosphoanhydride bond. Thus Iorming it requires and input oI energy some oI which
can be 'harvested when the bond is broken. ATP, then, can 'transIer energy Irom
one chemical system to another i.e. it can 'couple energy yielding and energy
requiring reactions. (Figure 7) (Figure 8)

Nucleic Acids DNA (Figure 9)
Polymerized by condensation oI the 3`OH oI the sugar with the 5` phosphate oI a
second nucleotide. (By convention we describe the sequence 5` 3`).
The pentose is deoxyribose, the bases are AGTC.
There are two nucleic acid strands running antiparallel.
The sugar/phosphate backbone is on the 'outside.
The bases stack in parallel planes, using vander Waals and 'hydrophobic interactions
to stabilize their position.
Base pairing purine to pyrimidine (2 ring to 1 ring) uses 2 or 3 'H-bonds.
The 'natural B-Form oI DNA shows a right-handed twist, with one complete turn
every 3.4nm (~10.6 base pairs) and exposes a major and minor groove.
DNA is 'Ilexible i.e. can be 'bent by unique sequences or bound proteins.


Nucleic Acids RNA (Figure 10)
Single stranded, also described 5`3`
Bases AGC and U, ribose sugar exposed 2`OH make RNA more 'reactive
Structures;
Local Stem loops and hairpins
Global 3D speciIic conIigurations
Recent work indicates that conIigurations and reactivity allow some RNAs to act as
speciIic reaction catalysts i.e. as 'ribozymes.