“BIOCHEMISTRY NOTES”

UNIT 1:
Biochemistry – is the study of the chemical substance found in living organisms and the
chemical interactions of these substance with each other.

STATES OF MATTER - Chemistry is the science and study of the material world. It is
generally accepted that there are three states of matter, solid, liquid and gaseous, and the
chemicals that make up the materials of the world involve the chemical elements or molecules.
Biochemical substance – is a chemical substance found within a living organism.

-substance are divided into two groups; bioinorganic and bioorganic

Bioinorganic substances- include water and inorganic salts.
Bioorganic substances- include carbohydrates, lipids, proteins, and nucleic acid.

BIOINORGNIC
Water (about 70%)
SUBSTANCE

Substance that do Inorganic salts (about 5%)

BIOCHEMICAL not contain carbon
SUBSTANCE

BIOORGANIC Proteins (about 15%)

SUBSTANCE
Substance that Lipids (about 8%)
contain carbon
Carbohydrates (about 2%)

Nucleic acids (about 2%)

Properties of Carbon

Key Points
o Carbon has several allotropes, or different forms in which it can exist. These
allotropes include graphite and diamond, which have very different properties.
o Despite carbon’s ability to make 4 bonds and its presence in many compounds, it
is highly unreactive under normal conditions.
o Carbon exists in 3 main isotopes: 12C, 13C, 14C. 14C is radioactive and used in
dating carbon-containing samples (radiometric dating).

CARBON- is the chemical element with the symbol C and atomic number 6 (contains 6
protons
in its nucleus).
- The most common isotope of carbon has 6 protons and 6 neutrons, and has an
atomic mass of 12.0107 amu. 
- it is nonmetallic and tetravalent—making four electrons available to form covalent
chemical bonds.
- its ground state electron configuration is 1s22s22p2
- its oxidation state ranges from 4 to -4, and it has an electronegativity value of 2.55
on the Pauling scale.
- it is a solid, and sublimes at 3,642 °C

Carbon Allotropes
Carbon has several allotropes, or different forms
in which it exists. Interestingly, carbon allotropes span
a wide range of physical properties: diamond is the
hardest naturally occurring substance, and graphite is
one of the softest known substances. Diamond is
transparent, the ultimate abrasive, and can be an
electrical insulator and thermal conductor. Conversely,
graphite is opaque, a very good lubricant, a good
conductor of electricity, and a thermal insulator.
Allotropes of carbon are not limited to diamond and
graphite, but also include buckyballs (fullerenes),
amorphous carbon, glassy carbon, carbon nanofoam,
nanotubes, and others.
 Allotropes of Carbon Some allotropes of carbon:

a) diamond, b) graphite, c) lonsdaleite, d–f) fullerenes (C60, C540, C70); g) amorphous carbon, h) carbon nanotube.

Chemical Reactivity of Carbon

Carbon compounds form the basis of all known life on Earth, and the carbon-nitrogen
cycle provides some energy produced by the sun and other stars. Carbon has an affinity for
bonding with other small atoms, including other carbon atoms, via the formation of stable,
covalent bonds. Despite the fact that it is present in a vast number of compounds, carbon is
weakly reactive compared to other elements under normal conditions. At standard temperature
and pressure, it resists oxidation; it does not react with sulfuric acid, hydrochloric acid, chlorine,
or any alkali metals. At higher temperatures, carbon will react with oxygen to give carbon
oxides, and metals to give metal carbides.

Carbon has the ability to form very long chains of strong and stable interconnecting C-C
bonds. This property allows carbon to form an almost infinite number of compounds; in fact,
there are more known carbon-containing compounds than all the compounds of the other
chemical elements combined, except those of hydrogen (because almost all organic compounds
contain hydrogen as well).

Carbon Isotopes
Carbon has two stable, naturally occurring isotopes: carbon-12 and carbon-13. Carbon-12
makes 98.93% and carbon-13 forms the remaining 1.07%. The concentration of 12C is further
increased in biological materials because biochemical reactions discriminate against 13C.
Identification of carbon in NMR experiments is done with the isotope 13C. 14C is a radioactive
isotope of carbon with a half-life of 5730 years. It has a very low natural abundance
(0.0000000001%), and decays to 14N through beta decay. It is used in radiometric dating to
determine the age of carbonaceous samples (of physical or biological origin) up to about 60,000
years old.
In total, there are 15 known isotopes of carbon and the shortest-lived of these is 8C, which
decays through proton emission and alpha decay, and has a half-life of 1.98739 x 10 −21 seconds.
The exotic 19C exhibits a nuclear halo, which means its radius is appreciably larger than would be
expected if the nucleus were a sphere of constant density.

 
Chemical Reaction- is a process generally characterized by a chemical change in which the
starting materials (reactants) are different from the products.
-tend to involve the motion of electrons, leading to the formation and
breaking of chemical bonds.

Types of Chemical Reactions

1. Oxidation-Reduction or Redox Reaction

In a redox reaction, the oxidation numbers of atoms are changed. Redox
reactions may involve the transfer of electrons between chemical species.
The reaction that occurs when In which I2 is reduced to I- and
S2O32- (thiosulfate anion) is oxidized to S4O62- provides an example of a
redox reaction: 2 S2O32−(aq) + I2(aq) → S4O62−(aq) + 2 I−(aq)
2. Direct Combination or Synthesis Reaction
In a synthesis reaction, two or more chemical species combine to form a
more complex product. A + B → AB The combination of iron and sulfur to
form iron (II) sulfide is an example of a synthesis reaction: 8 Fe + S8 → 8 FeS
3. Chemical Decomposition or Analysis Reaction
In a decomposition reaction, a compound is broken into smaller chemical
species. AB → A + B The electrolysis of water into oxygen and hydrogen gas is
an example of a decomposition reaction: 2 H2O → 2 H2 + O2

4. Single Displacement or Substitution Reaction

A substitution or single displacement reaction is characterized by one element
being displaced from a compound by another element. A + BC → AC + B An example
of a substitution reaction occurs when zinc combines with hydrochloric acid. The zinc
replaces the hydrogen: Zn + 2 HCl → ZnCl2 + H2

5. Metathesis or Double Displacement Reaction

In a double displacement or metathesis reaction two compounds exchange bonds
or ions in order to form different compounds. AB + CD → AD + CB
An example of a double displacement reaction occurs between sodium chloride and silver
nitrate to form sodium nitrate and silver chloride. NaCl(aq) + AgNO3(aq) → NaNO3(aq)
+ AgCl(s)
 6. Acid-Base Reaction
An acid-base reaction is a type of double displacement reaction that
occurs between an acid and a base. The H+ ion in the acid reacts with the
OH- ion in the base to form water and an ionic salt:
HA + BOH → H2O + BA The reaction between hydrobromic acid (HBr)
and sodium hydroxide is an example of an acid-base reaction:
HBr + NaOH → NaBr + H2O
7. Combustion
A combustion reaction is a type of redox reaction in which a combustible
material combines with an oxidizer to form oxidized products and generate heat
(exothermic reaction). Usually, in a combustion reaction oxygen combines with
another compound to form carbon dioxide and water. An example of a
combustion reaction is the burning of naphthalene: C10H8 + 12 O2 → 10
CO2 + 4 H2O
8. Isomerization
In an isomerization reaction, the structural arrangement of a compound is
changed but its net atomic composition remains the same.
9. Hydrolysis Reaction
A hydrolysis reaction involves water. The general form for a hydrolysis
reaction is: X-(aq) + H2O(l) ↔ HX(aq) + OH-(aq)

Chemical Bonds- is a region that forms when electrons from different atoms interact with
each other.
-The electrons that participate in chemical bonds are the valence
electrons, which are the electrons found in an atom's outermost shell.
When two atoms approach each other these outer electrons interact.
Electrons repel each other, yet they are attracted to the protons
within atoms. The interplay of forces results in some atoms forming
bonds with each other and sticking together.

Atoms-are the basic building blocks of all types of matter.

- Atoms link to other atoms through chemicals bonds resulting from the strong attractive forces
that exist between the atoms.
Main Types of Chemical Bonds
1. ionic bond is formed when one atom accepts or donates one or more of its
valence electrons to another atom.
2.   covalent bond -is formed when atoms share valence electrons. 

The atoms do not always share the electrons equally, so a polar covalent bond may
be the result. When electrons are shared by two metallic atoms a metallic
bond may be formed. In a covalent bond, electrons are shared between two atoms.
The electrons that participate in metallic bonds may be shared between any of the
metal atoms in the region.

Predict Type of Chemical Bond Based on Electronegativity

If the electronegativity values of two atoms are similar:

 Metallic bonds form between two metal atoms.

 Covalent bonds form between two non-metal atoms. Nonpolar covalent
bonds form when the electronegativity values are very similar, while polar
covalent bonds form when the electronegativity values are a little further apart.

If the electronegativity values of two atoms are different, ionic bonds are formed.

Origin of Organic Chemistry

- is the study of compounds that contain carbon. It is one of the major branches of chemistry.
- organic chemistry can be traced back to ancient times when medicine men extracted chemicals from
plants and animals to treat members of their tribes.
- didn't label their work as "organic chemistry", they simply kept records of the useful properties and uses
of things like willow bark which was used as a pain killer.
- was first defined as a branch of modern science in the early 1800's by Jon Jacob Berzelius.

Jon Jacob Berzelius

- classified chemical compounds into two main groups:

- organic if they originated in living or once-living matter

- inorganic if they came from "mineral" or non-living matter.
- Berzelius believed in Vitalism - the idea that organic compounds could only originate from
living organisms through the action of some vital force.

There are three generally accepted sources of organic compounds:

• carbonized organic matter
• living organisms
• invention/human ingenuity

Functional Groups and their Reactivity

Key Points
o Functional groups are collections of atoms that attach the carbon skeleton of an
organic molecule and confer specific properties.
o In organic chemistry, a functional group is a set of atoms within molecules
that function together to react in predictable ways.
o Functional groups undergo the same chemical reactions no matter how
large or small the molecule is.
o Covalent bonds link the atoms within functional groups and connect them
to the rest of the molecule.
o Examples of functional groups include the hydroxyl group, ketone group,
amine group, and ether group.

1. Hydroxyl Functional Group

Also known as the alcohol group or hydroxy group, the hydroxyl group is an oxygen
atom bonded to a hydrogen atom. Hydroxy groups link
biological molecules together via dehydration
reactions.
Hydroxyls are often written as OH on structures and
chemical formulas. While hydroxyl groups are not
highly reactive, they do readily form hydrogen bonds
and tend to make molecules that contain
them soluble in water. Examples of common
compounds containing hydroxyl groups are
alcohols and carboxylic acids.
2. Aldehyde Functional Group
Aldehydes are made up of carbon and oxygen double-bonded together and hydrogen bonded to
the carbon. An aldehyde may exist as either the keto or enol tautomer. The aldehyde group is
polar. Aldehydes have formula R-CHO.

3.Ketone Functional Group

A ketone is a carbon atom double bonded to an
oxygen atom that appears as a bridge between two
other parts of a molecule. Another name for this group
is the carbonyl functional group.

Note how the aldehyde is a ketone where one R is the

hydrogen atom.

4.Amine Functional Group

Amine functional groups are derivatives of ammonia
(NH3) where one or more of the hydrogen atoms are
replaced by an alkyl or aryl functional group.

5.Amino Functional Group

The amino functional group is a basic or alkaline group.
It's commonly seen in amino acids, proteins, and the
nitrogenous bases used to build DNA and RNA. The amino group is NH 2, but under
acidic conditions, it gains a proton and becomes NH3+.
Under neutral conditions (pH = 7), the amino group of an amino acid carries the +1
charge, giving an amino acid a positive charge at the amino portion of the molecule.

6.Amide Functional Group

Amides are a combination of a carbonyl group and an

amine functional group.

7.Ether Functional Group

An ether group consists of an oxygen

atom forming a bridge between two
different parts of a molecule.

Ethers have formula ROR.

8.Ester Functional Group

The ester group is another bridge group
consisting of a carbonyl group
connected to an ether group.

Esters have formula RCO2R.

9.Carboxylic Acid
Functional Group
Also known as the carboxyl functional group.

The carboxyl group is an ester where one substituent

R is a hydrogen atom.

The carboxyl group is usually denoted by -COOH

10.Thiol Functional Group

The thiol functional group is similar to the hydroxyl group except the oxygen atom in the
hydroxyl group is a sulfur atom in the thiol group.

Thiol functional group is also known as a sulfhydryl

functional group.

Thiol functional groups have formula -SH.

Molecules that contain thiol groups are also called

mercaptans.

11.Phenyl Functional Group

This group is a common ring group. It is a
benzene ring where one hydrogen atom is
replaced by the R substituent group.
Phenyl groups are often denoted by the
abbreviation Ph in structures and formulas.
Phenyl groups have formula C6H5.