UNIVERSITY OF THE VISAYAS - MAIN

BIOCHEMISTRY LECTURE

Prepared by: Mr. Rommeljun Solijon Datiles

LEARNING OBJECTIVES
At the end of the lesson, the student
should be able to:

1. identify the general structural features

of amino acids;

2. describe the chracteristics of primary,

s e c o n d a r y, t e r t i a r y, a n d q u a t e n n a r y
structure of proteins;

3. describe the main features of enzymes;

and

3. value the significant role of amino acids,

proteins and enzymes, and its use to
diagnose and treat diseases.
Proteins
 Of the four major groups of
biomolecules --- lipids, carbohydrates,
proteins, and nucleic acids ---
Proteins have the widest array of
functions.

Proteins are one of the most abundant

organic molecules in living systems
and have the most diverse range of
functions of all macromolecules.
 Proteins may be structural, regulatory,
contractile, or protective; they may serve
in transport, storage, or membranes; or
they may be toxins or enzymes.

Each cell in a living system may contain

thousands of proteins, each with a
unique function. Their structures, like
their functions, vary greatly. They are all,
however, polymers of amino acids,
arranged in a linear sequence.
Unlike lipids and carbohydrates, which the
body stores for use when needed.

Protein is not stored so it must be consumed

on a daily basis.

The current recommended daily intake for

adults is 0.8g of protein per kg of body
weight.

Since children need protein for both growth

and maintenance, the recommended daily
intake is higher.
• Keratin and collagen, for example
form long insoluble fibers, giving
strenght and support to tissues.

§ Hair, horns, hooves, and finger

nails are all made up of keratin.

§ Collagen is found in bone,

connective tissue, tendons, and
cartilage.
• Membrane proteins
transport small organic
molecules and ions across
cell membranes.

• Insulin, the hormone that

regulates blood glucose
level.
• Hemoglobin, which transports
oxygen from the lungs to tissues, are
proteins.

• Enzymes are proteins that catalyze

and regulate all aspects of cellular
function.
What are Proteins ?
• Proteins are biomolecules that contain many amide bonds, formed
by joining amino acids together.

• Proteins are long chains or polymers composed of a specific type of

amino acid known as an α-amino acid.

§ The word protein comes from the

greek proteios meaning “of first
importance.”

§ proteins occur widely in human

body, accounting for approximately
50% of its dry weight.
Proteins in the Human Body
Protein Types and Functions
How High Proteins Affect the Body
Amino Acids
 “Amino Acids are the organic
compounds that combine to form
proteins, hence they are referred to as
the building components of proteins.

These biomolecules are involved in

several biological and chemical
functions in the human body and are
the necessary ingredients for the
growth and development of human
beings. There are about 300 amino
acids that occur in nature.”
v Amino Acids
• To understand protein properties and structure, we must first learn the
amino acids that composed them.

Ø Amino acids are the fundamental building blocks of proteins

and nitrogenous backbones for compounds such as
neurotransmitters and hormones.
v Amino Acids

Ø Amino acids contain 2

functional groups -- Amino
group (NH2) and a
carboxyl group (COOH).

Ø The amino group is bonded

to the α carbon, the carbon
adjacent to the carbonyl
group, maing them α-
amino acids.
v Amino Acids
• Amino acids with an additionall COOH group in the side are called
acidic amino acids.

• those with an additional

basic N atom in the side
chain are called basic
amino acids.

• All others are neutral

amino acids.
Stereochemistry of Amino Acids
• L Amino acids have the -NH3+ group on the left side in the
Fischer projection, common naturally occurng amino acids are L
isomers.

• D Amino acids have -NH3+ group on the right side in the Fischer
projection. D amino acids occur infrequently in nature.
Exercise:
General Properties of Amino Acids

• They have a very high melting and boiling point.

• Amino acids are white crystalline solid substances.

• In taste, few Amino acids are sweet, tasteless, and bitter.

• Most of the amino acids are soluble in water and are

insoluble in organic solvents.
Types of Amino Acids

• Proteins have a variety of important roles in living organisms,

yet they are made from the same 20 L-amino acids.

• Based on the body’s capability to synthesize, amino acids can

be categorized into 2 types:

Ø Essential amino acids

Ø Nonessential amino acids.
Ø Semiessential amino acids
 Types of Amino Acids

Ø Essential amino Ø Nonessential Ø Semiessential

acids: amino acids: amino acids:

• Essential amino acids • Nonessential amino • Semiessential

are the amino acids acids need not be amino acids are
which have to be taken in through diet growth-promoting
taken in through diet as they can be amino acids.
as they “CAN NOT” produced by the body they’re only
be produced by the essential when
body body is stress/ill.
Types of Amino Acids
Zwitterion

• Since amino acid contains a base (NH2 group) and an acid COOH),
proton transfer from the acid to the base forms a salt called a
zwitterion, which contains both a positive and a negative charge.

• These salts have high melting points and are water soluble.
Essential Amino Acids
v Lysine

• Lysine is necessary for promoting the

formation of antibodies, hormones, and
enzymes and in the development and
fixation of calcium in bones.

• An amino acid released in the hydrolysis of

many common proteins but present in small
amounts or lacking in certain plant proteins;
e.g., gliadin from wheat, zein from corn
(maize).
v Methionine
• Methionine is used in the treatment of kidney
stones, maintaining healthy skin and also used
in controlling invade of pathogenic bacteria.

• Sulfur-containing amino acid obtained by the

hydrolysis of most common proteins

• Methionine accounts for about 5 percent of the

weight of egg albumin; other proteins contain
much smaller amounts of methionine.
• It is one of several so-called essential amino acids
for mammals and fowl; i.e., they cannot synthesize
it.
v Phenylalanine
• Phenylalanine helps in maintaining a
healthy nervous system and in boosting
memory power.

• Human hemoglobin (the oxygen-carrying

pigment of red blood cells) is one of the richest
sources of phenylalanine, yielding 9.6 percent by
weight.

• First isolated in 1881 from lupine seedlings,

phenylalanine is one of several essential amino
acids for fowls and mammals; i.e., they cannot
synthesize it and require dietary sources.
v Threonine
• Threonine helps in promoting the
functions of the immune system.

• One of the last amino acids to be

isolated (1935), threonine is one of
several so-called essential amino acids;
i.e., animals cannot synthesize it and
require dietary sources
v Tryptophan
• Tryptophan is involved in the production of
vitamin B3 and serotonin hormones. This
serotonin hormone plays a vital role in
maintaining our appetite, regulating sleep
and boosting our moods.

• Tryptophan is used by the body to manufacture

several important substances, including the
neurotransmitter serotonin and the vitamin niacin.

• Diets poor in tryptophan can lead to pellagra, a

disease resulting from niacin deficiency; however,
this disease is now rare in developed countries.
v Histidine
• Histidine is involved in many enzymatic
processes and in the synthesizing of both red
blood cells (erythrocytes) and white blood
cells (leukocytes).

• A particularly rich source, hemoglobin (the

oxygen-carrying pigment of red blood cells) yields
about 8.5 percent by weight of histidine.

• Histamine, a compound involved in the

physiological processes associated with allergic
reactions, is formed in the human body by
decarboxylation of histidine.
v Isoleucine
• Isoleucine plays a vital role in the formation
of haemoglobin, stimulating the pancreas to
synthesize insulin, and transporting oxygen
from the lungs to the various parts.

• First isolated in 1904 from fibrin, a protein

involved in blood-clot formation, isoleucine is one
of several so-called essential amino acids for
chicks, rats, and other higher animals, including
man; i.e., they cannot synthesize it and require
dietary sources.
v Leucine
• Leucine is involved in promoting protein
synthesis and growth hormones.

• Among the first of the amino acids to be

discovered (1819), in muscle fibre and wool, it is
present in large proportions (about 15 percent) in
hemoglobin (the oxygen-carrying pigment of red
blood cells) and is one of several so-called
essential amino acids for rats, fowl, and humans;
i.e., they cannot synthesize it and require dietary
sources.
v Valine

• Valine acts as an important component in

promoting muscle growth.

• It is one of several so-called essential amino acids

for fowl and mammals; i.e., they cannot synthesize
it and require dietary sources.

• It is synthesized in plants and microorganisms

from pyruvic acid (a product of the breakdown of
carbohydrates)
Nonessential Amino Acids
v Alanine

• Alanine functions by removing toxins from

our body and in the production of glucose and
other amino acids.

• An especially rich source of L-alanine is silk

fibroin, from which the amino acid was first
isolated in 1879.

• Alanine is one of several so-called nonessential

amino acids for birds and mammals; i.e., they can
synthesize it from pyruvic acid (formed in the
breakdown of carbohydrates) and do not require
dietary sources.
v Asparagine
• Asparagine is mainly involved in the
transportation of nitrogen into our body cells,
formations of purines and pyrimidine for the
synthesis of DNA, the development of the nervous
system and improving our body stamina.

• First isolated in 1932 from asparagus, from which its

name is derived, asparagine is widely distributed in
plant proteins.

• It is one of several so-called nonessential amino acids

in warm-blooded animals: they can synthesize it from
aspartic acid.
v Aspartic acid

• Aspartic acid plays a major role in metabolism

and in promoting the synthesis of other amino
acids.

• First isolated in 1868 from legumin in plant seeds,

aspartic acid is one of several so-called
nonessential amino acids for mammals; i.e., they
can synthesize it from oxaloacetic acid (formed in
the metabolism of carbohydrates) and do not
require dietary sources.
v Glutamic acid
• Glutamic acid acts as a neurotransmitter and is
mainly involved in the development and
functioning of the human brain.

• Certain plant proteins (e.g., gliadin) yield as much as

45 percent of their weight as glutamic acid; other
proteins yield 10 to 20 percent.

• Much of this content may result from the presence of

a related substance, glutamine, in proteins; glutamine
is converted to glutamic acid when a protein is
hydrolyzed.
v Glycine
• Glycine is helpful in maintaining the proper cell
growth, and its function, and it also plays a vital
role in healing wounds. It acts as a
neurotransmitter.

• Sweet-tasting, it was among the earliest amino acids

to be isolated from gelatin (1820). Especially rich
sources include gelatin and silk fibroin.

• Glycine is one of several so-called nonessential amino

acids for mammals; i.e., they can synthesize it from
the amino acids serine and threonine and from other
sources and do not require dietary sources.
v Proline
• Proline is mainly involved in the repairing of the
tissues in the formation of collagen, preventing
the thickening and hardening of the walls of the
arteries (arteriosclerosis) and in the regeneration
of new skin.

• Unlike other amino acids, proline, first isolated from

casein (1901), is readily soluble in alcohol. Collagen,
the principal protein of connective tissue, yields about
15 percent proline.

• It is one of several so-called nonessential amino acids;

i.e., animals can synthesize it from glutamic acid and
do not require dietary sources.
v Serine
• Serine helps in promoting muscle growth and
in the synthesis of immune system proteins.

• First isolated in 1865 from sericin, a silk protein,

serine is one of several so-called nonessential
amino acids for mammals; i.e., they can
synthesize it from glucose and do not require
dietary sources.

• Serine and some of its derivatives (e.g.,

ethanolamine) are also important components of
a class of lipids (phospholipids) found in
biological membranes.
Semiessential Amino Acids
v Arginine
• Arginine helps in promoting the synthesis of
proteins and hormones, detoxification in the
kidneys, healing wounds, and maintaining a
healthy immune system.

• amino acid obtainable by hydrolysis of many

common proteins but particularly abundant in
protamines and histones, proteins associated with
nucleic acids.

• First isolated from animal horn (1895), arginine

plays an important role in mammals in the
synthesis of urea, the principal form in which
these species excrete nitrogen.
v Cysteine
• Cysteine acts as an antioxidant and provides
resistance to our body; it is important for
making collagen. It affects the texture and
elasticity of the skin

• -containing nonessential amino acid. In peptides and

proteins, the sulfur atoms of two cysteine molecules
are bonded to each other to make cystine, another
amino acid.

• The bonded sulfur atoms form a disulfide bridge, a

principal factor in the shape and function of skeletal
and connective tissue proteins and in the great
stability of structural proteins such as keratin.
v Glutamine
• Glutamine promotes a healthy brain function
and is necessary for the synthesis of nucleic
acids – DNA and RNA.

• First isolated from gliadin, a protein present in

wheat (1932), glutamine is widely distributed in
plants; e.g., beets, carrots, and radishes.

• Important in cellular metabolism in animals,

glutamine is the only amino acid capable of readily
crossing the barrier between blood and brain and,
with glutamic acid, is thought to account for about
80 percent of the amino nitrogen (―NH2) of brain
tissue.
v Tyrosine
• Tyrosine plays a vital role in the production of
the thyroid hormones -T3 and T4, in
synthesizing a class of neurotransmitters and
melanin, which are natural pigments found in
our eyes, hair, and skin.

• tyrosine is particularly abundant in insulin (a

hormone) and papain (an enzyme found in fruit of
the papaya), which contain 13 percent by weight.

• Tyrosine is one of several so-called essential amino

acids for certain animals; i.e., they cannot
synthesize it and require dietary sources.
Polypeptides
v Peptides
• When amino acids are joined together by amide bonds, they form larger
molecules called peptides and proteins.

Ø A covalent bond is produced when the carboxyl group of one

amino acid is joined to the amino group of another with the
removal of a molecule of water.
v Peptides

Ø A dipeptide has two amino acids joined together by onee amino

bond.

• The -NH3+ group of one

amino acid forms an amide
bond with the caroboxylate
(-COO-) of another amino
acid, and the elements of
H2O are removed.
v Peptides

Ø A tripeptide has three amino acids joined together by two amide

bonds.
v Peptides
Ø The fundamental linkage in all protein structures is generated by
the chemical bond established between amino acids. The carboxyl
group (COOH) of one amino acid links with the amino group
(NH2) of another to produce the sequence CONH and release
water in a peptide bond (H2O).
v Peptides

Ø The amino acid with the free -NH3+ group on the α carbon is
called the N-terminal amino acid.

Ø The amino acid with the free -COO- group on the α carbon is called
the C-terminal amino acid.
v Peptides Nomenclature
• Peptides are named as derivatives of the C-terminal amino acid.

Ø Name all other amino acids from left to right as substituents of the
C-terminal amino acid.
Ø Change the -ine or -ic acid ending of the amino acid name to the
suffix -yl
v Peptides Nomenclature
• Thus peptide A, which has serine as its C-terminal amino acid, is
named as alanylserine. Peptide B, which has alanine as its C-
terminal amino acid, is named serylalanine.

A B
Exercise:

• Identify the N-terminal and C-terminal amino acid in each peptide.

(A) Arg-His-Asn-Tyr (B) Val-Thr-Pro-Phe

(C) (D)
v Peptides
v Polypeptides
Ø Polypeptides and Proteins both have amino acids joined
together in long linear chains, but the term protein is usually
reserved for polymers of more than 40 amino acids.
v Polypeptides Functions
Ø Proteins and peptides are key biological components that carry out important
tasks in cells. Proteins, for example, give cells their form and respond to
signals from the extracellular environment. Peptides play an important
function in controlling the activity of other substances. Proteins and peptides
are structurally similar, consisting of chains of amino acids bound together by
peptide bonds (also called amide bonds).

Ø Peptides, on the other hand, can be classified into oligopeptides, which have a
small number of amino acids, and polypeptides, which have a large number of
amino acids. One or more polypeptides are linked together to make proteins.
As a result, proteins are essentially very long peptides. In reality, some
researchers use the term peptide to refer to oligopeptides, or short amino acid
chains, while the term polypeptide is used to refer to proteins or chains of 50
or more amino acids.
v Proteins
Ø To understand proteins, the large polymers of amino acids that
are responsible for so much of the structure and function of all
living cells, we must four levels of structure, called the primary,
secondary, tertiary and quaternary structure of proteins.
v Proteins
v Proteins Structure
v Primary Structure
Ø The Primary structure of a protein is the particular sequence of
amino acids that is joined together by together by peptide bonds.
Ø The most important element of this primary structure is the amide
bond that joins the amino acids.

The peptide bond between two amino acids is

depicted. The shaded quadrilateral represents
planar nature of this bond. By "planar" we
mean that the 2 alpha carbons, the nitrogen,
and carbon and oxygen associated with the
peptide bond all lie in a single plane (the
peptide bond is resistant to twisting). However,
each amino acid can twist relative to the next
amino acid between the C alpha and C carbons.
Attribution: Marc T. Facciotti
v Primary Structure
Ø The linear sequence of amino acids in the polypeptide chain are held
together by peptide bonds and result in the N-C-C-N-C-C patterned
backbone.
Ø The primary structure is coded for in the DNA, a process you will
learn about in the Transcription and Translation modules.

The primary structure of a protein is depicted

here as "beads on a string" with the N-
terminus and C-terminus labeled. The order in
which you would read this peptide chain would
begin with the N-terminus as Glycine,
Isoleucine, etc and end with methionine.
v Secondary Structure
Ø The three-dimensional
arrangement of localized
regions of a protein is called
its secondary structure.
These regions arise due to
hydrogen bonding the N-H
proton of one amide and the
C=O oxygen of another.

Ø Two arrangements that are

particularly stable are called
the α-helix and the β-
pleated sheet.
v Secondary Structure
The α-helix and β-pleated sheet are
secondary structures of proteins that
form because of hydrogen bonding
between carbonyl and amino groups
in the peptide backbone. Although the
interactions drawn are all between the
atoms of the backbone, certain
sequences of amino acids have a
propensity to disrupt an α-helix, while
others have a propensity to disrupt a
β-pleated sheet.
v Tertiary Structure

Ø The three-dimensional shape

adopted by the entire peptide chain
is called its tertiary structure.

Ø A peptide generally folds into a

shape that maximizes its stability.
In the aqueous environment of the
cell, protiens often fold in such as to
place a large number of polar and
charged groups on their outer
surface, to maximize the dipole-
dipole and hydrogen bonding
interactions with water.
v Tertiary Structure
v Tertiary Structure
v Quaternary Structure
Ø The shape adopted when two or more
folded polypeptide chains come
together into one protein complex is
called the quaternary structure.

Ø In nature, some proteins are formed

from multiple proteins, also known
as subunits, and the interaction of
these subunits forms the quaternary
structure.

Ø Weak interactions between the

subunits help to stabilize the overall
structure.
v Quaternary Structure

Ø For example, hemoglobin consists

of two subunits, encoded by the
alpha- and betaglobin genes.

Ø This protein complex also carries

the prosthetic group hemoglobin.

Ø The multi-subunit structure of

this protein complex gives it
regulatory characteristics not
shared by its single-subunit
cousin, myoglobin.
v Quaternary Structure
Assignment:
1. Draw the structure of each dipeptide:

(a) Gly-Phe (b) Gln-Ile (c) Leu-Cys

2. (a) Draw the structures of the two possible dipeptides that can formed
by combining leucine and asparagine. (b) In each dipeptide label the N-
and C-terminal amino acids. (c) Name each peptide using -three
abbreviations.

3. Identify the N-terminal amino acid in the tetrapeptide

alanylglycylleucylmethtionine. (b) what is the C-terminal amino acid?
(c) Write the peptide using three-letter sybmols for amino acids.
Enzymes
v Enzymes

• The human body is composed of different types of cells, tissues

and other complex organs.

• For efficient functioning, our body releases some chemicals to

accelerate biological processes such as respiration, digestion,
excretion and a few other metabolic activities to sustain a
healthy life.

• Hence, enzymes are pivotal in all living entities which govern

all the biological processes.
v Enzymes
• We conclude the discussion of proteins with enzymes, proteins that
serve as biological catalyst in all living organisms.

Ø Enzymes are crucial to the biological reactions that occur in the

body, which would otherwise often proceed too slowly to be of
any use.
v Enzymes Functions
The enzymes perform a number of functions in our bodies. These
include:
• Enzymes help in signal transduction. The most common enzyme
used in the process includes protein kinase that catalyzes the
phosphorylation of proteins.
• They break down large molecules into smaller substances that
can be easily absorbed by the body.
• They help in generating energy in the body. ATP synthase is the
enzyme involved in the synthesis of energy.
• Enzymes are responsible for the movement of ions across the
plasma membrane.
• Enzymes perform a number of biochemical reactions, including
oxidation, reduction, hydrolysis, etc. to eliminate the non-
nutritive substances from the body.
• They function to reorganize the internal structure of the cell to
regulate cellular activities.
v Enzymes
v Enzymes
v Enzymes Classification
• Earlier, enzymes were assigned names based on the one who discovered
them. With further research, classification became more comprehensive.