Proteins
• A protein is a naturally-occurring,
unbranched polymer in which the
monomer units are amino acids.
o A biopolymer of α-amino acids
o From the Greek word proteios
meaning "primary" or "holding the
first place."
o Gerard Johann Mulder coined the
word protein
• Proteins are most abundant molecules in the
cells after water – account for about 15% of
a cell’s overall mass.
• Elemental composition - Contain Carbon
(C), Hydrogen (H), Nitrogen (N), Oxygen
(O), most also contain Sulfur (S).
• The average nitrogen content of proteins is
15.4% by mass.
• Also present are Iron (Fe), Phosphorus (P)
and some other metals in some specialized
protein.
Amino Acids: The Building Blocks for
Proteins
• An amino acid is an organic compound that
contains both an amino (-NH2) and
carboxyl (-COOH) groups attached to the
same carbon atom.
o The position of carbon atom is Alpha
(a)
o -NH2 group is attached at alpha (a)
carbon
o -COOH group is attached at alpha (a)
carbon atom
• R = side chain –vary in size, shape, charge,
acidity, functional groups present, hydrogen-
bonding ability, and chemical reactivity.
o >700 amino acids are known
o Based on common “R” groups, there
are 20 standard amino acids
• All amino acids differ from one another by
their R-groups
• Standard amino acids are divided into four
groups based on the properties of R-groups
• Non-polar amino acids: R-groups are non-
polar
o Such amino acids are hydrophobic-
water fearing (insoluble in water)
o 9 of the 20 standard amino acids are
non-polar
o When present in proteins, they are
located in the interior of protein where
there is no polarity
Polar amino acids: R-groups are polar
Three types: Polar neutral; Polar acidic; and
Polar basic
• Polar-neutral: contains polar but neutral
side chains
o Seven amino acids belong to this
category
• Polar acidic: Contain carboxyl group as part
of the side chains
o Two amino acids belong to this category
• Polar basic: Contain amino group as part of
the side chain
o Two amino acids belong to this category
Nomenclature
• Common names assigned to the amino
acids are currently used.
1. Three letter abbreviations - widely used for
naming:
– First letter of amino acid name is
compulsory and capitalized followed by next
two letters not capitalized except in the case
of Asparagine (Asn), Glutamine (Gln) and
tryptophan (Trp).
2. One-letter symbols - commonly used for
comparing amino acid sequences of
proteins:
– Usually the first letter of the name
– When more than one amino acid has the
same letter the most abundant amino acid
gets the 1st letter.
