Department of Physics and Biochemical Sciences

PBS-BCH-221
BSc in Biomedical Engineering
Proteins and amino acids
Facilitator: Bernadetta Phiri Mando (Mrs)
 Proteins and amino acids
• Proteins are most abundant molecules of living system and have
high molecular weights.
• Proteins are made up of carbon, hydrogen, oxygen and nitrogen
and in some cases sulfur and phosphorus.
• Proteins are macromolecules made up of linear polymers of
amino acids so named because the amino group is bonded to the
α-carbon atom (central carbon).
 Amino acids
• The physical and chemical • Amino acid general structure:
properties of a protein are
determined by its constituent
amino acids.
• It is the side group that makes
each amino acid unique
• The individual amino acid subunits
are joined by amide linkages called Peptide bond:
peptide bonds.
• Amino acids are thus building
blocks of proteins.
 Amino acids cont..
• The central carbon atom is called α-carbon • In L isomers –NH2 group is
which is linked to four different groups: present to the left and in D-
• Carboxyl (–COOH) group, amino (NH2) isomers –NH2 group is present
group, hydrogen -H, and -R group also to the right of α-carbon.
called side chain. • There are 20 standard amino
• Because of binding with four different acids present in proteins of
groups, α-carbon of amino acids is chiral or biological system. These amino
asymmetric. acids are L-isomers.
• Because of this asymmetric, α-carbon
amino acids are present in two optically
active forms or mirror image forms;
• L isomers and the D isomers.
• R can be -H as in the case of glycine or it
can be a -CH3 as in alanine.
 Characteristics of amino acids:
Amino acids are basic units of protein.
All amino acids have at least one acidic carboxylic acid (-COOH)
group and one basic amino (-NH2) group.
Amino acids are colorless, crystalline solid
They are mostly soluble in water and insoluble in organic solvent
Only L- form of amino acids are found in Proteins in human body. If
D-form is present, it is converted into l-form by enzymes in liver.
More than 300 amino acids are found in nature but only 20 amino
acids are standard and present in protein because they are coded by
the gene.
Other non-standard amino acids are modified amino acids and called
non-protein amino acids
 Standard amino acids
• The standard acids differ form each other in the structure of
the side chain bonded to their α-carbon.
• The standard amino acids can be grouped according to their
side chains .
• Each standard amino acid has a three-letter abbreviation and
a one-letter symbol for use in writing protein structures.
• These standard amino acids are:
Glycine, alanine, valine, leucine, isoleucine, proline,
phenylalanine, tyrosine, serine, threonine, aspartic acid,
asparagine, glutamic acid, glutamine, cysteine, methionine,
histidine, trptophan, lysine and arginine.
Standard amino acids structure
Standard amino acids structure cont..
 Classification of amino acids
• Amino acids are classified in different group as follows:
 Classification on the basis of nutrition
 Classification on the basis of R-group
 Classification on the basis of catabolism
 Classification of amino acids on the basis of Nutrition:
• Can be classified further into essential amino acids or non-essential amino
acids
• Human beings can synthesize about half of the amino acids needed to make
proteins.
• Amino acids that can be synthesized by the human body are called non-
essential amino acids.
• Examples include: glycine, alanine, arginine, asparagine, aspartic acid, glutamic
acid, glutamine, proline, serine, cysteine and tyrosine.
• Essential amino acids are those that cannot be synthsised by the body
but are obtained from food sources/diet.
• Examples include:
• Threonine (Thr), Lysine (Lys),Valine (Val), Phenylalanine (Phe), Tryptophan
(Trp), Methionine (Met), Histidine (His), Leucine (Leu), Isoleucine (Ile).
 Classification of amino acids on the basis of Nutrition:

• Proteins that provide all the essential amino acids in about the right
proportions for human nutrition are called complete proteins.
• Examples of complete proteins are those in meat, fish, milk, and
eggs.
• About 50 g of complete protein per day is adequate for adult
humans.
• Proteins that are severely deficient in one or more of the essential
amino acids are called incomplete proteins.
Classification of amino acids on the basis of Nutrition: cont..
• Plant proteins are generally incomplete.
• Rice, corn, and wheat are all deficient in lysine.
• Rice also lacks threonine, and corn also lacks tryptophan.
• Beans, peas, and legumes have the most complete proteins among
the common plants, but they are deficient in methionine.
• Plant proteins can be chosen to be complementary, with some
foods supplying amino acids that others lack.
• Another alternative is to supplement the vegetarian diet with a rich
source of complete proteins such as milk or eggs.
Classification on the basis of R-group
The physical and chemical properties of a protein are
determined by its constituent amino acids based on the
properties of their R groups particularly their polarity, or
tendency to interact with water at biological pH (near pH
7.0).
• A: Hydrophobic/aliphatic amino acids
• Are amino acids in which R-group is non-polar (water-
insoluble)
• Examples: Glycine, Alanine,Valine, leucine, Isoleucine,
Methionine, Proline.
Non-polar, aliphatic amino acids cont..
 Non-polar, aliphatic amino acids cont..
• R- group of alanine, valine, leucine, and isoleucine tend to cluster
together within proteins, stabilizing protein structure through
hydrophobic effect.
• Glycine has the simplest structure. Although it is most easily grouped
with the nonpolar amino acids, its very small side chain makes no real
contribution to interactions driven by the hydrophobic effect.
• Methionine, one of the two sulfur-containing amino acids, has a slightly
nonpolar thioether group in its side chain.
• Proline has an aliphatic side chain with a distinctive cyclic structure.
• The secondary amino (imino) group of proline residues is held in a rigid
conformation that reduces the structural flexibility of polypeptide
regions containing proline.
 B. Aromatic R Groups
• Examples: Phenylalanine, tyrosine, and tryptophan
• They are relatively nonpolar (hydrophobic).
• All can contribute to the hydrophobic effect.
• The hydroxyl group of tyrosine can form hydrogen bonds,
and it is an important functional group in some enzymes.
• Tyrosine and tryptophan are significantly more polar than
phenylalanine because of the tyrosine hydroxyl group and the
nitrogen of the tryptophan indole ring.
Aromatic R Groups cont..
 C. Polar hydrophilic amino acids
• Amino acids in which R-group is polar/hydrophilic
• i. Polar, uncharged R Groups
• The R groups are more soluble in water/more hydrophilic because
they contain functional groups that form hydrogen bonds with water.
• Examples: serine, threonine, cysteine, asparagine, and glutamine.
• Polarity of serine and threonine is contributed by their hydroxyl
groups, and that of asparagine and glutamine by their amide groups.
• Cysteine is an outlier here because its polarity, contributed by its
sulfhydryl group, is quite modest. Cysteine is a weak acid and can
make weak hydrogen bonds with oxygen or nitrogen
Polar, uncharged R Groups amino acids
 ii. Polar, positively charged (Basic) R Groups
• The most hydrophilic R groups are
those that are either positively or
negatively charged.
• Examples of positively charged R
group amino acids at pH 7.0:
• Lysine, arginine and histidine
• Lysine has a second primary amino
group on its aliphatic chain
• Arginine has a positively charged
guanidinium group
• and histidine has an aromatic
imidazole group.
 iii. Negatively Charged (Acidic) R Groups
• Amino acids in which R-group
is acidic or negatively charged
at pH 7.0
• Examples:
aspartate/aspartic acid
and glutamate/glutamic
acid, each of which has a
second carboxyl group.
 Classification on the basis of catabolism
• Amino acids are broken down into • Based on
six major products, all of which enter the catabolism:
the citric acid cycle:
• Glucogenic amino acids,
• Pyruvate, acetyl-CoA, oxaloacetate,
• Ketogenic amino acids
alpha-ketoglutarate, succinyl-CoA, or
fumarate. • Mixed amino acids
(both Glucogenic and
• From here the carbon skeletons are
Ketogenic).
diverted to gluconeogenesis or
ketogenesis or are completely
oxidized to CO2 and H2O.
 Glucogenic amino acids
• Glucogenic amino acids are amino acids that can be
converted into glucose via gluconeogenesis.
• Glucogenic amino acids form pyruvate or other glucose
precursors as intermediate such as alpha-ketoglutarate,
succinyl Co-A, Fumarate, and oxaloacetate.
• Examples: alanine, arginine, asparagine, aspartic, cysteine,
glutamic, glutamine, glycine, histidine, methionine, proline,
serine and valine.
 Ketogenic amino acids
• Are amino acids that form acetyl CoA or acetoacetylCoA.
• These are precursors for ketone bodies.
• These amino acids cannot produce glucose because the carbon
atoms in the ketone body are degraded into carbon dioxide in
the citric acid cycle.
• Examples: Lysine and leucine.
• Although Ketogenic amino acids fail to produce glucose, they can be
used for ketogenesis or lipid synthesis.
• Ketogenesis is the biochemical process of forming ketone bodies
from the breakdown of Ketogenic amino acids or fatty acids.
Ketone bodies are in three types as Acetoacetate, Acetone, and β-
hydroxybutyrate.
 Mixed amino acids
• Mixed amino acids (both glucogenic and ketogenic) since they can give
rise to both glucose precursors and fatty acid precursors.
• Examples: isoleucine, phenylalanine, threonine, tryptophan, and
tyrosine.
 Uncommon amino acids

• Uncommon amino acids also have important functions.

• Examples: 4-hydroxyproline, a derivative of proline, and 5-
hydroxylysine, derived from lysine.
• 4-hydroxyproline is found in plant cell wall proteins, and both
are found in collagen, a fibrous protein of connective tissues.
 The role of proline
• In humans, proline is important in the formation of
collagen.
• Proline and hydroxyproline (proline derivative) are
major amino acid in the collagen protein which contain
three chains of polypeptides
• This collagen forms the major extracellular
components in connective tissues e.g skin, tendons,
cartilage, ligaments, vessels and bones.
 Hydroxylation of proline
Hydroxlation means a chemical process that introduces
a hydroxyl group (-OH) into an organic compound.
• Hydroxylation of proteins occurs as a post-translational
modification,-OH added to protein and is catalyzed by
enzymes.
• Most frequently hydroxylated amino acid residue in
human proteins is proline. Lysine is too hydroxylated.
because collagen makes up about 25–35% of the protein
in our bodies and 15% is hydroxyproline at every 3rd
residue in its amino acid sequence
 Hydroxylation cont..
• Hydroxylation process requires;
Enzymes; prolyl 4-hydroxylase, prolyl 3-hydroxylase and lysyl 5-
hydroxylase.
 Iron, molecular oxygen and α-ketoglutarate to carry out the
oxidation
 Ascorbic acid (vitamin C)/ascorbate for the continued activity
of prolyl hydroxylases and to return the iron to its reduced
state.
• Hence ascorbate functions as a cofactor.
• How is hydroxylation of proline connected to scurvy?
 Hydroxylation Mechanism
• Proline hydroxylation occurs at C-4 by the action of
enzyme.
• Enzyme activates o2, and reaction is assisted by Fe2+ that
tightly binds to it to activate o2.
The other o2 is taken up by α-ketoglutarate to produce
succinate.
• Formation of a complex that inactivates the enzyme.
• Ascorbate reactivate the enzyme by reducing the ferric
ion and gets oxidized to dehydroxyascorbate.
Proline hydroxylation
 Hydroxylation of proline cont..
• Hydroxyproline is plays an essential role in forming and
folding of collagen.
 This maintains and stabilizes the collagen triple helix
structure by forming inter-strand hydrogen bonds.
• Collagen synthesized in the absence of ascorbate
(vitamin C) is less stable and fragile than the normal
protein.
 Collagen
• Forms connective fibers in tissues such as skin, ligaments,
cartilage, bones and teeth.
It acts as a shock absorber and reduces friction.
It helps to heal cartilage and cushion joints.
Its fibers keep bones and blood vessels strong, and anchor
our teeth to gums.
• Hence impaired hydroxylation of proline have devastating
consequences e.g weak connective tissue that lead to
SCURVY.
Collagen structure
SCURVY
• Scurvy is deficiency disease caused by impaired
hydroxylation of collagen due to lack of Ascorbic acid
(vitamin C)/Ascorbate
• Vitamin C is required for the continuous activity of
prolyl hydroxylases and collagen formation.
Vitamin C/Ascorbic Acid

• It is a water soluble vitamin.

• Unlike other mammals, human beings do not have the
ability to make their own vitamin, hence we must
obtain vitamin C from our diet.
• It is found in a varieties of foods and plays important
roles in the body.
Ascorbic acid structure
 Functions of vitamin C
• Has a number of functions and these are;
Ascorbate plays a role in collagen, hormone and amino acid
formation.
It is essential for wound healing and facilitates recovery
from burns.
It also functions as an antioxidants from damage by free
radicals and can also regenerate other antioxidants like
Vitamin E.
It supports immune system function. It helps to synthesize
neurotransmitter, norepinephrine critical to brain
function.
Function of scurvy cont..
• Facilitates iron absorption in the body.

• It also synthesizes carnitine, a small molecule that is

essential for the transport of fat to mitochondria, for
conversion to energy.
 Symptoms of scurvy

• Blood vessel fragility

• loosened teeth which will
eventually fall out in the
advanced stages of scurvy
• Bleeding gums
 Symptoms of scurvy
• Skin lesions
• loss of appetite
• rashes, particularly on your
legs; generally looking like
tiny red blisters and
eventually large purple
blotches.
• slow wound healing
• anaemia
• Swollen legs
 Prevention of scurvy
• Eating foods that are rich in
Vitamin C can prevent scurvy.
• The richest sources are fruits
and vegetables. Common rich
sources are citrus fruits and
their juices.
Citrus fruits: lemons, oranges,
grapefruits.
Vegetables: cabbages, green
peppers, tomatoes, potatoes.
 Sources of Vitamin C cont..
• Other sources of vitamin C
are;
• Carrots, paprika, spinach,
strawberries, papaya, broccoli,
Liver, cereals.
• All these will supply the body
with Ascorbic acid needed
for the formation of collagen.
Treatment of scurvy
• Involves administering Vitamin C supplements by
mouth or by injection following recommended
dosage.
REFERENCES
• Lehninger A. L., Lee, D.M & Michael, M.C (2017). Principles of
Biochemistry (7th ed.). W. H. Freeman & Company Ltd.
• Berg J.M, Tymoczko J & Sryer L(2001). Biochemistry (5th ed.).
W.H Freeman and Company and Sumanas.
• Gropper, S.S & Smith, J.L (2013). Advanced nutrition and human
Metabolism (6th ed.) Yollanda Cossio, Belmont.
 Practice questions
1. Draw the structural formula of an 5. With the aid of chemical
amino acid. equation or structures, describe
2. Draw the structures of the how impaired hydroxylation of
following amino acids: proline lead into scurvy.
a. Sulfur-containing amino acids
b. Aromatic amino acids
3. With examples, explain the
difference between glucogenic
amino acids and ketogenic amino
acids.
4. Describe the classes of amino
acids.
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