BIOCHEMISTRY LECTURE NOTES
Protons and neutrons are at
Created by: Chedriel Kien Q. Ballo
Introduction to Biochemistry
Covalent bonds
Overview of Central Themes in Biochemistry.  subatomic particles between atoms.)
- Simple building blocks, such as amino
acids, are used to generate complex
biochemical structures, such as
proteins. Proteins play diverse roles in
the cell, including structural, transport,
and catalysis. The information for the
generation of such complex structures
is encoded in nucleic acids. The flow of
this information is regulated in a
complex fashion. The entire process is
fueled by metabolic processes that
generate energy from organic energy
sources and use this energy to
synthesize complex molecules.
Chemical Bonding and Biochemical Structures
- The elements that are commonly found
in biochemical molecules are among
the most abundant on earth, this
includes carbon, oxygen, nitrogen,
sulfur, and phosphorous.
- Atoms are made up of subatomic
particles: protons, neutrons, and
electrons.
the center of the atom and have a mass
of 1 atomic mass unit (a.m.u) each.
Each proton has a positive charge (+1),
while neutrons are neutral (they carry
no charge). Each electron has a negative
charge (-1) and zero mass. Two atoms
that differ by the number of neutrons
are called isotopes of the same
element.
- One characteristic of the atoms of the
major elements is that they are able to
form molecules through formation of
covalent bonds with other atoms.
- Covalent bonds represent the sharing of
the electrons (negatively charged
The number of covalent bonds that can
form is dictated by the number of
unpaired electrons in the outer valence
shell of the atom.
- The electron shells are divided into
atomic orbitals. Each atomic orbital
holds at most 2 electrons. The s orbital
is spherically symmetric. The three p
orbitals (px, py, pz) are bi-lobed, have a
defined direction in space, and hold a
total of 6 electrons. The 1st shell
consists of the 1s orbital, and can hold 2
electrons. the 2ndshell contains the 2S
and the 2Px, 2Py, and 2Pz orbitals and
can thus hold 8 electrons. The 3rd shell
contains the 3S, 3Px, 3Py, 3Pz, and the
five 3d orbitals. Since the 3d orbitals are
 very high in energy, it is reasonable to
consider that the 3rd shell really
contains 8 electrons as well. For most
elements that are found in biological
systems it is sufficient to consider the
1st shell, the 2nd shell, and the 3S and 3P
orbitals as the third shell

Electronic Number of Hybrid

Atom Generation of Hybrid Atomic Orbitals.
Configuration bonds Orbitals
-  The top section shows the generation
of three sp2  orbitals from an s orbital
and two p orbitals. The three
H 1s1 1 sp2  orbitals all lie in the same plane
and are 120o  from each other. The
bottom section show the generation of
3×sp2 + four sp3  orbitals from an s orbital and
C 1s2 2s2 2p2 4 pz or 4× three p orbitals. The resultant
sp3 sp3  orbitals form a tetrahedron, with
an angle of 109o  between each orbital.
3 (4 when 3×sp2 +
2 2 3 Covalent bonds 
N 1s  2s  2p protonat pz or 4×
ed) sp3
- indicate the sharing of electrons
between atoms. Usually two half-filled
2 (3 when 3×sp2 +
2 2 4 orbitals combine to form the bond.
O 1s  2s  2p protonat pz or 4×
Hence hydrogen forms one bond while
ed) sp3
carbon forms four.

Chirality
2
S 3s23p4
(usually) - When a molecule cannot be
superimposed on its mirror image, it is
said to be chiral. Biochemical processes
P 3s23p3 5 are often able to distinguish between
chiral molecules, thus it is important to
be able to identify if a compound is
chiral or not. Carbon, when
- Carbon, nitrogen, and oxygen, usually sp3 hybridized, is tetrahedral. If the four
form hybrid orbitals, that show a groups attached to the carbon are
mixture of s and p character, e.g. different, then the molecule containing
that carbon is chiral, and the carbon
sp3hybrid orbitals, as dicussed below.
itself is refereed to as a chiral center.
Planer groups, such as carbon
hybridized as sp2, are not chiral,
because the plane of the molecule
 forms a mirror plane within the
molecule itself, thus the mirror images
are identical.
Functional Groups
Amino acids
- Organic compounds containing amine
(-NH2) and carboxylic acid (-COOH)
functional groups, along with a side-
chain specific to each amino acid; the
different side-chains produce different
biochemical properties for each
compound; 20 different amino acids are
encoded by the genetic code, though a
small number of other amino acids exist
in some cells.

“Chemical structure of a standard

amino acid in its unionised form. “R”
represents a group of atoms that varies
for each specific type of amino acid.”
Important Functional Groups in Biochemistry.
ATP
-  Alkanes and benzene aromatic rings do
not contain polar atoms (e.g. N and O), - Adenosine 5’-triphosphate; used in all
and therefore do not interact with cells, often called the “biological
water, a polar solvent. Consequently molecular unit of currency” of
intracellular energy transfer.
they usually leave the aqueous phase.
This hydrophobicbehavior is very
important in the self-assembly of many
biochemical structures, such as proteins
and membranes. The remaining
compounds have some polar atoms and
thus interact with water to a greater
extent. Imidazole is found in the amino
acid Histidine and plays an important
role in the catalytic activity of many
enzymes. The guanidinium group is Chemical structure of adenosine 5’-
found on the amino acid arginine and triphosphate
the indole group is found in the amino
acid tryptophan. Biotechnology

- Biotechnology is the use of living

Definition of common biochemical terms
systems and organisms to develop,
 Technical terms in simplified form
 make or modify products or processes
for specific use.
Carbohydrate (saccharide)
- Molecules consisting of carbon,
hydrogen and oxygen atoms; can exist
as monosaccharides, disaccharides,
oligosaccharides, and polysaccharides;
important biological compounds
include sugars, starch, and cellulose,
performing important cellular roles
such as energy storage and structural
components.
Chemical structures of two stereoisomers of
erythrose, a 4-carbon monosaccharide. The
structures show D-erythrose (left) and L-
erythrose (right).
DNA
- Deoxyribonucleic acid: (A) polymer of
deoxyribonucleotides that carries the
genetic instructions used in the growth,
development, functioning and
reproduction of all known living
organisms; (B) most DNA molecules
consist of two strands coiled around
each other to form a double helix, with
base pairs between each strand.
Representations of the structure of
deoxyribonucleic acid (DNA). (A) Chemical
structure of DNA, highlighting the base pairs
that connect the two strands. (B) Molecular
structure of DNA, highlighting how the two
strands coil around each other to form a
double helix. Source: bio.libretexts.org CC BY-
NC-SA 3.0
Free energy
- Used in thermodynamics to describe
the amount of energy that is available
in any system to perform “work” (the
energy transferred between
components undergoing any physical
process). It is often designated with the
symbol “G”.
Lipid
- Small molecules, made of a
hydrocarbon chain that terminates with
a carboxylic acid group (-COOH), which
confer the molecule with a polar,
hydrophilic end attached to the non-
polar, hydrophobic end that is insoluble
in water; key important biological
compounds include fats, waxes, sterols,
fat-soluble vitamins, glycerides and
phospholipids; main biological functions
include storing energy, signaling, and
acting as structural components of cell
membranes.
 - Long, continuous, and unbranched
chain of amino acids, each joined to the
next by a peptide bond.

`
Chemical structure of lipid, showing the
hydrophilic end to the left of the
diagram.
Chemical structures of polypeptide
Nucleotide containing 10 amino acids, each indicated
their 3-letter abbreviation.
- Organic molecules that serve as the
monomers of nucleic acids, like DNA
and RNA; each nucleotide is composed RNA
of a nitrogenous base, a five-carbon - Ribonucleic acid (RNA): polymer of
ring sugar moiety (ribose or ribonucleotides involved in various
deoxyribose), and at least one biological roles in coding, decoding,
phosphate group. regulation, and expression of genes;
most RNA molecules consist of a single
strand, which can fold into specific 3-
dimensional structures.

Chemical structure of nucleotide

monomer.

Physiology

- Physiology is the scientific study of the

normal function in living systems. As a
sub-discipline of biology, it focuses on
how organisms, cells, and biomolecules
carry out the chemical or physical
functions that exist in all living systems.
Chemical structure of single chain RNA,
Protein (polypeptide)
highlighting that each ribose contains a
free hydroxyl group (OH).
Thermodynamics - Large, complex molecules that are
important in biological cells. Typically
- Thermodynamics is the area of science
these are synthesized within cells due
concerned with heat and temperature
to anabolic reactions that start from
and their relationship with energy and
smaller, precursor molecules. Common
work. It describes the behaviour of
forms of macromolecules include fats,
these quantities and is governed by the
nucleic acids (DNA and RNA),
four fundamental laws of
polysaccharides and proteins (also
thermodynamics, irrespective of the
referred to as polypeptides).
composition or specific properties of
the material or system in question.

Glucose

- Glucose is a carbohydrate (sugar) with

the molecular formula C6H12O6. It is
important for most cells because it
allows them to gain energy to grow and
divide. It occurs in different chemical
forms with one, known as dextrose,
occurring widely in nature. Glucose is
stored as a polymer, in plants as starch
and in animals as glycogen, for times
when the organism will need it.

Macromolecule
Sources:
Open Learning Initiative: Register for a Course (n.d). Retrieved from
https://oli.cmu.edu/jcourse/workbook/activity/page?
context=de60381d0a0001dc2c4deada32e0f09
Definitions of common biochemical terms – Biochemistry (n.d). Retrieved from
https://www.futurelearn.com/courses/biochemistry/14/steps/818276