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1. Amino Acids and proteins
By Alemu Adela
DBU
2018

2. Objectives
• Describe the structures of amino acids
• List the biological importance of amino acids and
proteins
• Understand the basis of amino acid classification
• List the properties of amino acids
• Describe the structural classification of proteins
• Know the structure and functions of heme
proteins(Hemoglobin and myoglobin)

3. Amino Acids
• Amino Acids are the building and functional units of proteins.
• 300 amino acids occur in nature. Only 20 of them occur in proteins.
Structure of amino acids:
• Each amino acid has 4 different groups attached to the same
tetrahedral carbon atom. :
Amino group,
COOH gp,
Hydrogen atom and
Side Chain distinct R-groups, that distinguish one amino acid from
another,
R
N.B.Proline* has cyclic structure other than the common amino acid
structure(imino acid)

4. Biomedical Importance
• They are polymerized to form proteins.
• the L-α-amino acids and their derivatives functions as :-
Source of energy, nerve transmission and the biosynthesis of
carbohydrates, porphyrins, purines, pyrimidines and urea.
• Short polymers of amino acids called peptides perform
prominent roles in the:-
Neuroendocrine system as hormones, hormone-releasing
factors, neurotransmitters.
Detoxification of free radicals(GSH)
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5. Classification of amino acids
I- Chemical classification: is based on the R group of the AA
According to net charge on amino acid,
R
Classified in to three:
1. Neutral amino acids
2. Basic amino acids
3. Acidic amino acids

6. A- Neutral amino acids includes
1- Glycine R= H
2- Alanine R= CH3
3- Branched chain amino acids: R is branched such as in:
a- Valine R= isopropyl
b- Leucine R= isobutyl
c- Isoleucine R = is isobutyl
4-Sulfur containing amino acids: Cysteine & Methionine
5-hydroxy amino acids: Serine and Threonine
6- aromatic amino acids:- Phenyl alanine, Tyrosine & Tryptophan
7- Amides: Aspargine and Glutamine
8- Proline (imino acids ): In proline, amino group enters in the ring
formation being α-imino gp

9. B- Basic amino acids:
Contain two or more NH2 groups or nitrogen atoms that act as a base
At physiological pH, basic amino acids will be positively charged.
Lysine, Arginine (contains guanido group) and Histidine are basic AAs

10. C- Acidic Amino acids:
At physiological pH will carry negative charge
Aspartic acid (aspartate) and Glutamic acid (glutamate)are
acidic amino acids

11. According to polarity of side chain (R):
A- Polar amino acids:
• R contains polar hydrophilic group so can forms hydrogen bond with
H2O and are predominantly found on the exterior surfaces of proteins
in aqueous solution
 In those amino acids, R may contain:
1- OH group
2- SH group
4- NH2 group
5- COOH group
B- Non polar amino acids:
• R is alkyl hydrophobic group which can’t enter in hydrogen bond
formation and reside predominantly in the interior of proteins

14. II- Nutritional classification:
1- Essential amino acids: These amino acids can’t be formed in the body
and so, it is essential to be taken in diet. Their deficiency affects growth,
health and protein synthesis.
2- Semiessential amino acids: These are formed in the body but not in
sufficient amount for body requirements especially in children.
Summary of essential and semiessential amino acids:
Villa HM = Ten Thousands Pound
V= valine i= isoleucine l= lysine l= leucine
A = arginine* H= histidine* M= methionine
T= tryptophan Th= threonine P= phenyl alanine*
* = phenyl alanine, arginine and histidine are semiessential
3- Non essential amino acids: These are the rest of amino acids that are
formed in the body in amount enough for adults and children. They are
the remaining 10 amino acids.

15. III- Metabolic classification:
According to metabolic or degradation products of amino acids
they can be:
1- Ketogenic amino acids: which give ketone bodies . Lysine
and Leucine are the only pure ketogenic amino acids.
2- Mixed ketogenic and glucogenic amino acids: which
give both ketonbodies and glucose.These are: isoleucine, phenyl
alanine, tyrosine and tryptophan.
3- Glucogenic amino acids: Which give glucose. They include
the rest of amino acids. These amino acids by catabolism yields
products that enter in glycogen and glucose formation.

16. Amphoteric properties :
have both basic and acidic groups and so can act as base or acid.
Neutral amino acids exist in aqueous solution as “ Zwitter ion” i.e.
contain both positive and negative charge.
Thus, amino acids can act as buffers.
Chemical properties:
1- Reactions due to COOH group:
Salt formation with alkalis,
Ester formation with alcohols,
Amide formation with amines
 Decarboxylation
-2- Reactions due to NH2 group:
Deamination and reaction with ninhydrin reagent.
Ninhydrin reagent reacts with amino group of amino acid
yielding blue colored product. The intensity of blue color indicates
quantity of amino acids present.
Properties of amino acids

17. Peptides
The 20 amino acids are linked together through “peptide bond forming
peptides and proteins (what’s the difference?).
 The chains containing less than 50 amino acids are called “peptides”,
while those containing greater than 50 amino acids are called “proteins”.
Peptide bond formation:
α-carboxyl group of one amino acid forms a covalent peptide bond with
α-amino group of another amino acid by removal of a molecule of water.
The result is : Dipeptide
By the same way, the dipeptide can then forms a second peptide bond
with a third amino acid to give Tripeptide.
Repetition of this process generates a polypeptide or protein of specific
amino acid sequence.

18. Peptide bond formation:
- Each polypeptide chain starts on the left side by free amino group of the
first amino acid enter in chain formation . It is termed N- terminus
- Each polypeptide chain ends on the right side by free COOH group of the
last amino acid and termed C-terminus

19. Glutathione
 Glutathione is a tripeptide formed from 3
AAs:  -glu, cys and gly.
 It is formed in liver cytoplasm by the
help of ATP and  -glutamyl-cysteine
synthetase and glutathione synthetase.
 Glutathione exists in 2 states: reduced
(GSH); and oxidized (GSSH). GSH is
involved in a number of reduction
reactions that helps protect cells against
damage from reactive oxygen species
(ROS).
 Regeneration of GSH from GSSH is
catalyzed by glutathione reductase, which
uses NADPH as a reductant.
 It is also important for amino acid
intestinal absorption and transportation,
and used as a Coenzyme for a number of
enzymes
19
GSSH

20. Proteins
• Proteins are physically and functionally complex
macromolecules.
• Perform multiple critically important roles.
Maintains cell shape and integrity: cytoskeleton
Form the contractile machinery of muscle: Actin and myosin
Protects from foreign invaders: antibodies
Catalyze reactions: Enzymes
Enable cells to sense and respond: Receptors
Transport small molecules and ions: hemoglobin
• These functions and others arise from specific binding
interactions and conformational changes in the
structure of a properly folded proteins

21. • The linear sequence of amino acids
(primary structure) folds into helices
or sheets (secondary structure)
• Which pack into a globular or
fibrous domain (tertiary structure).
• Some individual proteins self-
associate into complexes (quaternary
structure)
• complexes can consist of tens to
hundreds of subunits
(supramolecular assemblies)
Protein structure

22. Primary structure
• The linear sequence of amino acids
• This structural level stems from amino acids chemically
bound through peptide bonds
• Determine the three dimensional structure of proteins
• A knowledge of the primary structure of proteins is
essential in order to diagnose genetic diseases
• Abnormal sequences of amino acids typically lead to
improper folding in the resulting protein, which can
then produce a loss of its function

23. Secondary structure
• The local structure of the polypeptide chain
• Determined by hydrogen bond interactions between
the carbonyl oxygen group of one peptide bond and
the amide hydrogen of another nearby peptide bond.
Two types
1. α-helix
2. The β-pleated sheet

24. α-helix
• The α-helix is a rod-like structure with
the peptide chain tightly coiled and the
side chains of amino acid residues
extending outward from the axis of the
spiral.
• Intrachain hydrogen bonds maintain
the coiled structure
• Each turn of the helix contains 3.6 amino
acids
• Proline disrupts an -helix (kink)

25. The β-pleated sheet
• An extended structure as opposed to the
coiled α-helix
• All of the peptide bond moieties
involved in hydrogen bonding to create a
pleated sheet structure
• It is pleated because the carbon-carbon
(C-C) bonds are tetrahedral and cannot
exist in a planar configuration
• It can be parallel or anti parallel depend
on the direction of the poly peptide chain
that forms it

26. A β-pleated sheet.

27. Tertiary structure
• Three-dimensional, folded and
biologically active conformation of
a protein
• This structure reflects the overall
shape of the molecule
Stabilized by
1. Covalent disulfide bonds
2. Hydrogen bonds
3. Salt bridges(ionic interaction)
4. Hydrophobic interactions

28. Domains and folds
• Domains and. A section of protein structure sufficient to
perform a particular chemical or physical task such as binding
of a substrate or other ligand.
• Folds: Within a domain, a combination of secondary
structural elements forms a fold, such as the nucleotide
binding fold, or an actin fold. Folds are defined by their
similarity in a number of different proteins.

29. V. Quaternary structure of proteins
• Is the arrangement (spatial relationships ) of polypeptide
subunits
If two subunits – dimeric
If three subunits – trimeric
If several subunits – multimeric
• Subunits held together by intermolecular forces (e.g.
hydrogen bonds, ionic bonds, hydrophobic interactions)
• Subunits may either operate independently of each other,
or may work cooperatively (e.g. hemoglobin)

30. Denaturation of proteins
• Occurs when the protein’s secondary and tertiary structures
are disrupted
• Does not lead to hydrolysis of peptide bonds
• Denaturing agents include heat, organic solvents, mechanical
mixing, strong acids or bases, detergents, and lead and
mercury ions
• Most proteins remain permanently disordered once
denatured and become insoluble
• Denaturation may be reversible (under ideal conditions)

31. Classification
Proteins can be classified as globular and fibrous
• Globular proteins
Compact and roughly spherical
have axial ratios(the ratio of their shortest to longest
dimensions) of not over 3
Most enzymes and heme proteins are globular proteins
• Fibrous proteins
Adopt highly extended conformations.
Possess axial ratios of 10 or more
Many structural proteins.

32. Hemoglobin and myoglobin
 Globular hemeproteins important for oxygen binding
 The proteins by themselves cannot bind oxygen.
 They employ heme, the porphyrin ring, for the purpose.
 Has a very similar primary structure
 Myoglobin is a single polypeptide that has one O2 binding
site
 Hemoglobin is a tetramer composed of two different types
of subunits with 4 O2 binding site
 A comparison between myoglobin and hemoglobin
illustrates the advantages of a multisubunit quaternary
structure.

33. 33
Myoglobin
 153 AA, single polypeptide with tertiary structure →water
soluble
 Found mainly in muscle tissue where it serves as intracellular
reservoir of oxygen.
 Binds very tightly with oxygen and releases it only at very low
partial pressure of oxygen i.e. at the time of extreme oxygen
deprivation in muscles.
 The released oxygen can then be utilized for the metabolic
activity of muscle cells.

34. Conti….
 80% made up of α-helical secondary structure with 8 separate
right handed regions, designated A -H
 Interior of the molecule is largely hydrophobic, non-polar AAs
 Surface of the molecule carries the polar/ionic AAs
 Primarily stabilized by non-covalent forces but no disulfide bonds
 Carries a heme prosthetic group inserted into a hydrophobic
pocket
 Each heme is a protoporphyrin-IX moiety and contains one
central coordinately bound iron atom
 Iron is normally in the ferrous (Fe2+) form and serves as the
oxygen binding site

35. 35
Physiological importance of Myoglobin
 Myoglobin in tissues (especially in muscle) accepts oxygen
from Hb in circulating arterial blood
 The p50 (oxygen partial pressure required for half saturation)
for myoglobin is very low
 At the oxygen concentration existing in tissues, myoglobin is
nearly saturated
 only in rapidly exercising muscle or conditions of hypoxia
(extreme oxygen deprivation) would myoglobin give away its
oxygen
 Due to its hyperbolic oxygen dissociation curve and very
low p50, myoglobin is unsuitable for the transport of oxygen

36. hemoglobin
• Hemoglobins are tetramers Consists of four globin subunit and
four heme prosthetic group found in erythrocytes
• Heme prosthetic group binds oxygen
• The subunit composition of the principal hemoglobins are α2
β2 (HbA; normal adult hemoglobin), α2 γ2(HbF; fetal
hemoglobin), α2 S2(HbS; sickle cell hemoglobin),
• Responsible for binding oxygen in the lung and transporting the
bound oxygen throughout the body
• The quaternary structure of hemoglobin leads to physiologically
important cooperative interactions between the subunits

37. Structure of hemoglobin

38. O2 binds to HGB cooperatively
• When oxygen binds to the first subunit of deoxyhemoglobin it
increases the affinity of the remaining subunits for oxygen
• As additional oxygen is bound to the second and third subunits,
oxygen binding is further, incrementally, strengthened, so that at the
oxygen tension in lung alveoli, hemoglobin is fully saturated with
oxygen
• As oxyhemoglobin circulates to deoxygenated tissue, oxygen is
incrementally unloaded(removed) and the affinity of hemoglobin for
oxygen is reduced. Thus at the lowest oxygen tensions found in very
active tissues the binding affinity of hemoglobin for oxygen is very
low allowing maximal delivery of oxygen to the tissue.
• This phenomenon of tetrameric proteins are termed as Cooperative
interactions, and have critical importance in aerobic life

39. In other words
• The binding of the first oxygen to HGB causes
Profound changes in the quaternary structure of HGB
accompany the high-affinity O2 induced transition of
hemoglobin from the low-affinity T (taut) state to the
high-affinity R (relaxed) state.
• These changes significantly increase the affinity of the
remaining unoxygenated hemes for O2 as subsequent
binding events require the rupture of fewer salt bridges
• Result in easier access of oxygen to the iron atom of the
second heme and thus a greater affinity of the
hemoglobin molecule for a second oxygen molecule.
• The low affinity HG is known as the taut (T) state
• The high affinity HGB is known as relaxed(R) state

40. Hemoglobin saturation:
Is the % of hemoglobin molecules carrying oxygen
depends on PO2 of the blood:
• When PO2 is high, as in pulmonary capillaries, O2
binds with the Hb
• when PO2 is low, as in tissue capillaries, O2 is
released from the Hb

41. P50 of Hb
• The quantity P50 is the partial pressure of O2 that half-
saturates a given hemoglobin.
• If the P50 is low, Hb has a higher affinity for O2
• For example, values of P50 for HbA and HbF are 26 and 20
mm Hg, respectively.
• In the placenta, this difference enables HbF to extract
oxygen from the HbA in the mother’s blood.

43. transport of CO2 from the tissues to the blood with delivery of
O2 to the tissues.

44. CO2 and O2 Transport by Hb
• Hemoglobin transports 15% of CO2 and protons from
peripheral tissues to the lungs.
• Much of the remaining CO2 is carried as bicarbonate, which
is formed in erythrocytes by the hydration of CO2 to carbonic
acid (H2CO3) →by carbonicanhydrase.
• At the pH of venous blood, H2CO3 dissociates into
bicarbonate and a proton →lower pH of peripheral tissues,
stabilizes the T state and thus enhances the delivery of O2.

45. In the lungs O2 binds to deoxyhemoglobin protons are
released and combine with bicarbonate to form carbonic
acid.
Dehydration of H2CO3 catalyzed by carbonic anhydrase
forms CO2, which is exhaled. This phenomena known as the
Bohr effect
A low Po2 in peripheral tissues promotes the synthesis of
2,3-BPG in erythrocytes
BPG therefore stabilizes deoxygenated (T state) hemoglobin by
forming additional salt bridges

46. Regulation of oxygen binding
• CO2, H+, and Cl– exert negative effects on
hemoglobin binding O2
• Increased 2,3-BPG concentration favors conversion
of R form Hb to T form Hb and increases oxygen
delivery by Hb to the tissue.

47. 47
Carbon Monoxide poisoning
 Carbon monoxide concentration is high in smoke from
fire/ vehicular exhaust / cigarette.
 Oxygen and CO compete with each other for Hb
binding
 CO binds with affinity 200 times that of oxygen,
 CO concentration of 1/200 that of oxygen can saturate
50% of Hb.

48. Carbon Monoxide poisoning
 When 30-50% of Hb is saturated with CO
Throbbing
headache
Confusion
Fainting
 When the saturation reaches 80% → rapidly fatal
 Oxygen, at high concentration, displaces CO from hemoglobin
→CO poisoning can be overcome by elevated pO2
 Treatment → O2 resuscitation

49. Hemoglobinopathies
1. Sickle cell anemia (HbS)
• Caused by a mutation glutamic acid is substituted by valine
at AA 6.
• Results in hemoglobin tetramers that aggregate into arrays
upon deoxygenation in the tissues.
• This aggregation leads to deformation of the red blood cell
making it relatively inflexible and unable to traverse the
capillary beds.
• At the end it leads to clogging of the fine capillaries.

50. 50
Hemoglobinopathies
Sickle Cells and malaria
 Individuals heterozygous for sickle-cell Hb have a higher
resistance to malaria
 Plasmodium falciparam spends a portion of its life cycle in RBCs
 The increased fragility of the sickled cells tends to interrupt this
cycle.
 Malarial parasite decreases the pH in RBCs and the low pH
increases the sickling of the cells.
 The parasite into the cells promotes sickling, followed by lysis.
• Sickled cells have low concentrations of K+ , which is highly
unsuitable for the parasite to survive.

51. Hemoglobinopathies
2. Thalassemias
• Are the result of abnormalities in hemoglobin
synthesis
• Deficiencies in β-globin synthesis result in the β-
thalassemias which causes premature red cell
destruction in the bone marrow and spleen.
• Deficiencies in α-globin synthesis result in the α-
thalassemias which leads to reduced oxygen carrying
capacity.