amino acid and protein structure

2. PROTEINS
Proteins are Linear unbranched polymers of 20 different alpha amino acids
linked together by peptide bond
– a “polypeptide”
Definition:
Amino acid polymers of ≤50 amino acids are called
“polypeptides, peptides, oligopeptides, etc.”
Amino acids polymer of >50 amino acids are called “proteins.”

3. IMPORTANCE AND FUNCTION OF
PROTEINS
CATALYTIC: enzymes
Gene regulation: histones
TRANSPORT: haemoglobin (oxygen), albumin
(bilirubin , free fatty acids) and transferrin (iron)
COMMUNICATION: hormones (eg insulin) and
neurotransmitters
CONTRACTILE: actin, myosin (in muscle)
PROTECTIVE: Immunoglobulin, fibrinogen, blood
clotting factors, interferons
STRUCTURAL: cell membrane proteins, keratin
(hair), collagen
REGULATORY : calmodulin

4. Each AMINO ACID has
 An amino group,
 A carboxyl group,
 A hydrogen atom
 A specific side chain (R group)
All are
bonded
to the α-
carbon
atom
AMINO ACIDS
are the basic building blocks of
PROTEINS

5. ONLY L-AMINO ACIDS ARE CONSTITUENTS OF
PROTEINS.
5

6. CLASSIFICATION OF AMINO ACIDS
(1) Chemical classification (Side chain) classification
(2) Nutritional classification
(3) Metabolic classification

7. (1) CHEMICAL CLASSIFICATION

8. AMINO ACIDS

9. AMINO ACIDS

11. 2- NUTRITIONAL CLASSIFICATION
1- Non essential amino acids:
Amino acids that could be synthesized in the body, so they are not needed in the
diet.
2- Essential amino acids:
Amino acids that could not be synthesized in the body, so they have to be taken
in the diet, and their deficiency results in diseases
1- Non essential amino acids
• Glycine
• Alanine
• Serine
• Tyrosine
• Cysteine
• Asparagine
• Aspartic
• Glutamic acid
• Glutamine
• Proline
2- Essential amino acids
• Valine
• Leucine
• Isoleucine
• Threonine
• Methionine
• Arginine
• Lysine
• Histidine
• Phenylalanine
• Tryptophan

12. 3- METABOLIC CLASSIFICATION
Amino acids are classified according to their metabolic fate in the body into:
1. Glucogenic amino acids Amino
acids that can give glucose.
2. Ketogenic amino acids: Amino
acids that can give ketone bodies.
3. Glucogenic/ Ketogenic (Mixed) amino acids: Amino
acids that can give both ketone bodies and glucose.
Pure glucogenic Glucogenic and Ketogenic Pure
Ketogenic
Alanine, Arginine Asparagine,
Asparagine, Aspartate Cysteine,
Cysteine, Glutamate
Glutamine, Glycine Histidine,
Proline, Serine
Tyrosine, Phenylalanine
Tryptophan
Methionine, Threonine Valine Isoleucine Leucine

14. Neurotransmitte
rs
• Gamma amino butyric acid (GABA) Derivative of
glutamic acid
• Dopamine from Tyrosine
Mediator of allergic
reaction
• Histamine from Histidine
Thyroid Hormone
• Thyroxine from Tyrosine
EXAMPLES OF AMINO ACID
DERIVATIVE

15. BUILDING PROTEINS
Peptide bonds
 covalent bond between NH2 (amine) of one
amino acid & COOH (carboxyl) of another
 C–N bond
peptide
bond
dehydration
synthesis
H2O

16. Typical bonds in protein molecules
Covalent bonds
Non-covalent bonds
Peptide bond
Disulfide bond
Hydrogen bond
Ionic bond
Hydrophobic interactions

17. DISULFIDE BONDS
Two cysteine molecules
under oxidizing conditions
to form dissulfide bond
Intermolecular or
intramolecular cross-link
cystine, it is amino acid
formed when two cysteine
molecules or residues are
joined by a disulfide bond
C
H2
SH C
H2
S
H
C
H2
S
S
C
H2
[O]

18. Hydrogen bond
Non-covalent bonds: Hydrogen bond
Hydrogen bond formation

19. Ion bond (between oppositely charged radicals)
In strong acid:
-NH3+
-COOH
In strong base:
-NH2
-COO-
pH influences the strength of ion bonds

20. Polar radicals
Non-polar radicals
Hydrophobic interactions in
the formation of protein
structure
Hydrophobic interactions- between
hydrophobic (non-polar) radicals

21. Protein bonds: Summary

22. Levels or orders of proteins structure
 Primary structure
 Secondary structure
 Tertiary structure
 Quaternary structure

23. Primary structure
Definition:
The linear sequence of amino acids forming
the backbone of a protein.
• Peptides: di-, three-, tetra- peptides example glutathione
(tripeptide)
• Oligopeptides: up to 20 amino acids
• Polypeptides: from 20 to 50 amino acids

24.  Every polypeptide chain has a unique amino
acid sequence determined by genes.
 A single amino acid change in polypeptide
chain may change or completely abolish
protein function.
 Primary structure determines the higher levels
of protein organization.
Remember
Bonds in primary structure: Peptide and
disulfide bonds.

25. Definition: Spatial folding of the polypeptide
chain in properly arranged, repetitive
structures.
Formed as a result of hydrogen bonds
between the carbonyl oxygen (C = O) and the
amide hydrogen (N-H) of the polypeptide
chain and does not depend on the side
radicals.
Secondary structure
Three types of secondary structures:
 α-helix,
 β-sheet,
 β-turn.

26. 1- Alpha (α) helix
The carbonyl oxygen of each
peptide bond is linked to a
hydrogen bond with the amide
hydrogen of the fourth amino acid
towards the C-terminus.

27. 2- Beta (β) –pleated
sheet
In a β pleated sheet, two or more
segments of a polypeptide chain line
up next to each other, forming a
sheet-like structure held together by
hydrogen bonds.
Two types of β pleated sheet include:
Anti-parallel beta sheets:
polypeptide chains run in an
opposite direction
Parallel – run in the same
direction with longer looping
sections between them
3-  turns occur frequently
whenever strands in  sheets
change the direction.

28. Complete three-dimensional
shape of a given protein.
Conformation.
Represent the spatial
relationship of the different
secondary structures to one
another within a polypeptide
chain and how these
secondary structures
themselves fold into the
three-dimensional form of
the protein.
Tertiary structure

29. Tertiary structure is based on various types of interactions
between the side-chains of the peptide chain depend on all
types on bonds expect peptide one.

30. DOMAINS
A domain is a basic structural unit of a
protein that can fold into a stable structure
independently and perform a function
Different domains can impart different
functions to proteins
Proteins can have one to many domains
depending on protein size

31.  Quaternary structure describes the joining of
two or more polypeptide subunits.
 The subunits each have their own tertiary
structure.
 Bonds – non-covalent interactions.
 Subunits can either function independently or
work co-operatively.
 Dissociation of a subunit results in loss of
function.
QUATERNARY STRUCTURE

32. Denaturation
It is the destruction of the secondary, tertiary and quaternary
structures of a protein molecule.
Causes: Physical agents: - as heat, high pressure, strong
shaking, X-rays and ultraviolet rays.
Chemical agents: - as urea, guanidine, alcohol, string acids and
alkalies.

33. Effects of denaturation :-
Chemical changes: - exposure of the hidden, inactive
chemical groups and becomes easily detectable.
Physical changes: - includes ↑ viscosity and ↓ solubility of
the protein and its precipitation at its iso-electric point.
Biological changes: - it leads to :
↑ Digestibility by proteolytic enzymes.
Loss of enzymatic, hormonal and antigenic properties.

34. OVERALL SHAPE
– the over all shape of protein divided into:
Two classes of proteins are classified on the
basis of their axial ratio (ratio of length to
breadth):
(a) Globular proteins: have axial ratio less
than 10. They are compactly folded
polypeptide chains like insulin, albumin
and globulins.
(b) Fibrous proteins: have an axial ratio
greater than 10 . The polypeptide chains
coiled in spiral or helix and cross linked
by hydrogen bonds like keratin, collagen
and fibrin

36. Solubility of proteins
The proteins have different solubility in water and salt solution
examples :
1- Albumin : present in egg white (ovalbumin), milk (lactalbumin) and
blood plasma
• They are proteins of high biological value i.e. contain all essential
amino acids and easily digested.
• are soluable in water and salt solution
•Heat coagulable
• precipitated by full saturation with ammonium sulfate
•Molecular weight 68,000 dalton .

37. 2 - Globulins: present in egg white (ovaglobulin), milk
(lactglobulin) and blood plasma
They are proteins of high biological value i.e. contain all
essential amino acids and easily digested.
these are insoluble in water, but soluble in salt solution
heat coagulable
precipitated by half saturation with ammonium sulfate
Molecular weight 150,000 dalton .
Plasma globulins include:

38. 3- SCLEROPROTEINS

39. CLASSIFICATION OF PROTEINS
According to their hydrolytic products:
Simple proteins : on hydrolysis gives
amino acids only.
Conjugated (compound) protein:
contain beside protein a prosthetic
group like phosphoproteins and
lipoproteins.
Derived proteins: products of
hydrolysis of proteins like proteoses
and peptones and small peptides

40. Conjugated protein
Each conjugated protein consists of a
simple protein combined with nonprotein
component.
The nonprotein component is
called a prosthetic group. According
to the type of this group conjugated
protein can be subclassified into
several types like:

41. 1- NUCLEOPROTEINS
Nucleo-Proteins
Histones and protamines

conjugated with nucleic acids
like DNA and RNA.
Plays role in Genetic

information.

42. 2- PHOSPHOPROTEINS
Phospho-Proteins
Proteins conjugated with

phosphoric acid.
Examples:

Casein in milk.

Vitellin in egg yolk.


43. 3- LIPOPROTEIN

44. 4- METALLOPROTEIN

45. 5- CHROMOPROTEIN

46. DERIVED PROTEINS
Derived proteins are proteins derived by
partial to complete hydrolysis from the
simple or conjugated proteins by the action
of acids, alkalies or enzymes. They include
two types of derivatives:
•primary-derived proteins
•secondary-derived proteins

47. Primary Derived Proteins
These are denatured or

co-agulated proteins.
Example : Egg proteins

48. SECONDARY DERIVED
PROTEIN