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Amino Acids and Proteins

 Amino Acids as Source of Other Compounds

• Tyrosine is the source of a group of excitatory

neurotransmitters and hormones called
‘catecholamines‘, which include epinephrine
(adrenaline), norepinephrine (noradrenaline) and
dopamine.
• They are called that because each of them contains
the catechol (aromatic) ring that is part of the
tyrosine side chain.
• Tyrosine is also the source for the pigment melanin
and the thyroid hormones thyroxine (T4) and
thriiodothyronine (T3). 3
Catecholamines biosynthesis from tyrosine
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• Tryptophan is the source of ‘indolamines‘ (a.k.a.
‘tryptamines‘). That is, biogenic amines containing
the indole ring of tryptophan’s side chain.

• The most well-known indolamine is the

neurotransmitter serotonin, involved in the
regulation of mood, appetite, and sleep.

• Another well-known indolamine is melatonin, which

regulates the sleep-wake cycle (circadian rhythm) in
humans.
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Conversion of Tryptophan to Serotonin 6
• Histidine is the source of histamine, local mediator
of inflammation and the immune response to certain
pathogens.

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• Glutamate is the source of gamma-amino-butyric-
acid (GABA), a major inhibitory brain
neurotransmitter.

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• Glutamate, along with glycine and cysteine, also
creates the tri-peptide glutathione – a compound
that fights oxidative stress caused in our body by free
radicals.

• N-acetylcysteine, the derivative of the amino acid

cysteine, is used for treating naphthalene toxicity.
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• Serine is used to build phosphatidylserine and
phosphatidylethanolamine, two phospholipids
building the membranes of our cells.

• Serine is also the precursor of ceramide, a waxy

molecule composed of sphingosine and a fatty acid
found in cell membranes.

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• Arginine is the precursor of creatine (an energy
reservoir in our muscles), nitrogen oxide (a mediator
of blood vessel constriction), citrulline (an
antioxidant), and a group of polyamines that have
various physiological and cellular roles.

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• Coenzyme A is important for central metabolism in
all life forms. It is crucial to their ability to derive
energy for foodstuff, as well as to build fatty acid,
cholesterol and the neurotransmitter acetylcholine.
It is made from the amino acid cysteine and from
pantothenic acid (vitamin B5).
• S-adenosylmethionine is a molecule built from the
amino acid methionine and the adenosyl group of
ATP. It is a common and important enzymatic
cofactor, needed for numerous biochemical reactions
that involve methylation.

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Production of Amino Acids from Other
Amino Acids or Compounds

Amino Acids in Red; Other Compounds in Blue

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Amino Acids in Red; Other Compounds in Blue
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 Phenylketonuria (PKU)
• Phenylketonuria (PKU) is an autosomal recessive
metabolic genetic disorder characterized by a
mutation in the gene for the hepatic enzyme
phenylalanine hydroxylase (PAH), rendering it
nonfunctional.
• This enzyme is necessary to metabolize the amino
acid phenylalanine (Phe) to the amino acid tyrosine.

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• When PAH activity is reduced, phenylalanine
accumulates and is converted into phenylpyruvate
(also known as phenylketone), which is detected in
the urine.
• Untreated PKU can lead to mental retardation,
seizures, and other serious medical problems. The
mainstream treatment for classic PKU patients is a
strict PHE-restricted diet supplemented by a medical
formula containing amino acids and other nutrients.
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 Amino acids as acid and base
• When an amino acid is dissolved in water, it
exists in solution as the dipolar ion, or zwitter
ion (German for “hybrid ion”).
• A zwitter ion can act as either an acid (proton
donor) or a base (proton acceptor).

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• Substances having this dual nature are
amphoteric and are often called ampholytes.
• A simple monoamino monocarboxylic α-
amino acid, such as alanine, is a diprotic acid
when fully protonated—it has two groups, the
-COOH group and the -NH3 group that can
yield protons

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 Isoelectric point
• The isoelectric point (pI) is the pH value at
which the molecule carries no electrical
charge or the negative and positive charges
are equal. The PH at which amino acids are
present in zwitterion form.

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 Peptide bonds
• A covalent bond joining the α-amino group of
one amino acid to the carboxyl group of
another with the loss of a water

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 Peptide
• Peptides are short chains of amino acids linked by
peptide bonds. Long chains of amino acids are called
proteins. Chains of fewer than twenty amino acids are
called oligopeptides, and include dipeptides,
tripeptides, and tetrapeptides. A polypeptide is a
longer, continuous, unbranched peptide chain
• Dipeptide = contains 2 amino acid units. Tripeptide =
contains 3 amino acid units. Tetrapeptide = contains 4
amino acid units. Oligopeptide = contains not more
than 10 amino acid units.

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 Protein
• Biochemical compounds: Polymers of amino
acids
• Composition: one or more polypeptides
(amino acids)
• Structure: folded into
a globular or fibrous form
• Function: It carries out several biological
functions.

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Importance and function of protein
1. cell structure: cytoskeleton (mircrofilamints,
microtubules)
2. contractile machinery of muscle: Actin Myosin
3. Oxygen transport: Hemoglobin
4. Search for foreign invaders: Antibodies
5. Reaction catalysis: Enzymes
6. Sensing and responding: Receptors
7. Many other functions previously explained in
amino acids section

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Biological Function of Proteins

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Levels of protein structure

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 Primary Structure
• The simplest level of protein structure,
primary structure, is simply the sequence of
amino acids in a polypeptide chain. For
example, the hormone insulin has two
polypeptide chains, A and B, shown in diagram
below.

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 Secondary Structure
• The next level of protein structure, secondary structure,
refers to local folded structures that form within a
polypeptide due to interactions between atoms of the
backbone. (The backbone just refers to the polypeptide chain
apart from the R groups – so all we mean here is that
secondary structure does not involve R group atoms.)
• The most common types of secondary structures are the α
helix and the β pleated sheet. Both structures are held in
shape by hydrogen bonds, which form between the carbonyl
O of one amino acid and the amino H of another.

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 Tertiary Structure
• The overall three-dimensional structure of a
polypeptide is called its tertiary structure. The
tertiary structure is primarily due to
interactions between the R groups of the
amino acids that make up the protein.

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 Quaternary Protein
• Many proteins are made up of a single
polypeptide chain and have only three levels
of structure (the ones we’ve just discussed).
However, some proteins are made up of
multiple polypeptide chains, also known as
subunits. When these subunits come together,
they give the protein its quaternary structure.
• Examples : hemoglobin, DNA polymerase,
ribosomes, antibodies, and ion channels

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Ways of Classification of proteins?

1. Classification of proteins based on the

structure
2. Classification of proteins based on function
3. Classification of Proteins Based on
Composition
4. Classification of Proteins based on solubility

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 1. Classification of proteins based on
the structure
• a. Fibrous Proteins
• In this classification proteins, The polypeptide chains are elongated
and wound about an axis in a helical shape. These are structural
proteins. They can be extracellular and will then be insoluble in
water and have a protective function:
• α keratin hair
• fibroin silk
• elastin of the skin
• collagen tendons
• They can also be intracellular
include myosin and tropomyosin muscle cells. careful not to
confuse fibrous and filamentary (globular proteins attached to each
other).

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• b. Globular proteins
• Soluble in water, they are spherical. They have much more
complex than the fibrous protein structure, but they have
a much greater variety of biological activities. The best
example of Globular protein is MyoGlobin.
• They can be membrane and then have roles as:
• Carrier
• Receptors
• Ion channel
• GAP links
• Cell adhesion proteins
• They may be soluble and be plasma such as albumin,
protein hormones such as LH, cytosolic proteins circulating
proteins such as Calmodulin.

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 2. Classification of proteins based on
function
• They may be involved in:
• The structure and support is the case of collagen, elastin, glycoproteins
membrane
• The contraction: actin, myosin
• The cell adhesion proteins such as GAP junctions and proteins such
as cadherin,
• The reception signal such as membrane insulin receptors or intracellular
steroid receptors
• The signal transduction, a typical example being formed by the membrane
protein G (see the course on cellular communication )
• a signal: they can be informative molecule as growth factors (EGF) and
Follicular stimulating hormones (FSH),
• the immunity, the role of immunoglobulin
• the transportation such as haemoglobin (O 2 ) and transferrin (iron)
• the catalysis: therefore these proteins also play a role in metabolism,
replication and DNA transcription, muscle contraction, cell signalling.

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3. Classification of Proteins Based on
Composition

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 3. Classification of Proteins Based on
Composition
• If they are carbohydrates that are added in an amount between 5 and 40% of the
molecule, the protein is called glycoproteins and glycosylated proteins. If the
proportion of carbohydrates to pass more than 90% of the molecule, one blade of
peptidoglycan, they have passive protection.
• There are two main types of proteins. Those containing only amino acids
are holoproteins.
• Those containing a protein moiety (the apoprotein ) and a non-protein portion
are hemoproteins.
• Both parts are linked in various ways: covalent
bonds, ionic, hydrogen, hydrophobic. This non-protein portion may be a
group prosthetic ( inducing the emergence of new biological properties setting, as
heme in haemoglobin).
• The element can be added to one or more metal cofactors (Cu, Zn, …)
that metalloprotein.
• A chromoprotein contains a pigment and a phosphoprotein comprises one or
more inorganic phosphates.
• Also exist nucleoproteins by adding acid nucleic, and lipoproteins by addition of
lipids.

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 4. Classification of Proteins based on
solubility
• Proteins can be divided into two categories:
fibrous, which tend to be insoluble in water, and
globular, which are more soluble in water.
• Globular proteins are highly branched proteins
usually soluble in water. Insulin and Albumin are
the common fibrous proteins.
• Globular proteins having hydrophilic amino acids on
their surface are soluble in water. It is because the
hydrophilic amino acids can make hydrogen bonds
and other polar linkages with water molecules
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 Physical properties of Proteins
• Colloidal Nature
• A colloid is a kind of solution in which the
size of the solute particles is intermediate
between those in true solution and those in
suspension. Examples of colloids
are mayonnaise, milk, butter
• Because of their giant size, the proteins exhibit
many colloidal properties, such as; Their diffusion
rates are extremely slow and they may produce
considerable light-scattering in solution, thus
resulting in visible turbidity (Tyndall effect)

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 Physical properties of Proteins

• Denaturation
in biology, process modifying the
molecular structure of a protein. Denaturation
involves the breaking of many of the weak
linkages, or bonds (e.g., hydrogen bonds), within
a protein molecule that are responsible for the
highly ordered structure of the protein in its
natural (native) state.

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 Denaturation and protein folding
• Each protein has its own unique shape. If the temperature or pH of a
protein's environment is changed, or if it is exposed to chemicals, these
interactions may be disrupted, causing the protein to lose its three-
dimensional structure and turn back into an unstructured string of amino
acids. When a protein loses its higher-order structure, but not its primary
sequence, it is said to be denatured. Denatured proteins are usually non-
functional.
• For some proteins, denaturation can be reversed. Since the primary
structure of the polypeptide is still intact (the amino acids haven’t split
up), it may be able to re-fold into its functional form if it's returned to its
normal environment. Other times, however, denaturation is permanent.
One example of irreversible protein denaturation is when an egg is fried.
The albumin protein in the liquid egg white becomes opaque and solid as
it is denatured by the heat of the stove, and will not return to its original,
raw-egg state even when cooled down.
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The End

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