Detailed Lecture on Proteins

1. UNIT 5
CHEMISTRY OF PROTEINS
by
Dr. Waqar Ahmad
Pharm-D (Gold Medalist)
M.Phil Pharmacy (QAU Islamabad) Pakistan.
Cell# 00923015820152

2. What is Protein?
Protein: an energy-yielding nutrient composed of
carbon, hydrogen, oxygen, and nitrogen.
• Differs from carbohydrates and fats because of
the presence of nitrogen.
• The body has at least 30,000 types of protein,
each with a different job.
• The building blocks of all protein molecules are
amino acids.

6. Structures and abbreviations of the standard amino acids

7. 20 Amino acids
Glycine (G)
Glutamic acid (E)Asparatic acid (D)
Methionine (M)
Threonine (T)Serine (S)Glutamine (Q)
Asparagine (N)Tryptophan (W)Phenylalanine (F)
Cysteine (C)
Proline (P)
Leucine (L)Isoleucine (I)Valine (V)Alanine (A)
Histidine (H)Lysine (K)
Tyrosine (Y)
Arginine (R)
White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic

14. Peptides and Proteins
20 amino acids are commonly found in protein.
These 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 (with side chain R1) forms a
covalent peptide bond with α-amino group of another amino acid ( with
the side chain R2) by removal of a molecule of water. The result is :
Dipeptide ( i.e. Two amino acids linked by one peptide bond). By the
same way, the dipeptide can then forms a second peptide bond with a
third amino acid (with side chain R3) to give Tripeptide. Repetition of
this process generates a polypeptide or protein of specific amino acid
sequence.

15. 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).

16. Examples on Peptides:
1- Dipeptide ( two amino acids joined by one peptide
bond):
Example: Aspartame which acts as sweetening agent being used
in replacement of cane sugar. It is composed of aspartic acid and
phenyl alanine.
2- Tripeptides ( 3 amino acids linked by two peptide bonds).
Example: GSH which is formed from 3 amino acids: glutamic acid,
cysteine and glycine. It helps in absorption of amino acids, protects
against hemolysis of RBC by breaking H2O2 which causes cell
damage.
3- octapeptides: (8 amino acids)
Examples: Two hormones; oxytocine and vasopressin (ADH).
4- polypeptides: 10- 50 amino acids: e.g. Insulin hormone

18. Food Sources of Protein
• Proteins in the diet can be provided from both
animal and plant sources.
• Factors that influence peoples protein choices:
1. Availability
2. Cost
3. Health Concerns
4. Food Preferences
5. Religious Beliefs
6. Environmental Factors

19. Food Sources of Protein
• Animal Sources of Protein
▫ The largest source of protein, especially in U.S.
▫ Beef,, Pork, Lamb, Poultry, & Fish.
▫ Other: Eggs, Milk, Yogurt, and Cheese
 Fast food chains provide the bulk of protein in teens
diets

20. Food Sources of Protein
• Meat is an excellent source of protein but can be
high in fat, the same is true for dairy.
• Considerably more expensive

21. Food Sources of Protein
• Plant Sources of Protein
▫ Can be found in grains, nuts, seeds, and legumes
 Legumes capture nitrogen making them more protein dense:
peanuts, kidney beans,
▫ Soybeans are a type of legume that can be converted to form
different types of food products – meat alternative

36. Protein Structure
Primary
Secondary
Tertiary
Quaternary
Assembly
Folding
Packing
Interaction
STRUCTURE
PROCESS

37. Hierarchical nature of protein structure
Primary structure (Amino acid sequence)
↓
Secondary structure （α-helix, β-sheet）
↓
Tertiary structure （Three-dimensional structure
formed by assembly of secondary structures）
↓
Quaternary structure （Structure formed by more
than one polypeptide chains）

38. Protein structure:
There are four levels of protein structure (primary, secondary,
tertiary and quaternary)
Primary structure:
• The primary structure of a protein is its unique sequence of
amino acids.
– Lysozyme, an enzyme that attacks bacteria, consists of a
polypeptide chain of 129 amino acids.
– The precise primary structure of a protein is determined by
inherited genetic information.
– At one end is an amino acid with a free amino group the
(the N-terminus) and at the other is an amino acid with a
free carboxyl group the (the C-terminus).

39. High orders of Protein structure
• A functional protein is not just a polypeptide chain, but one or more polypeptides
precisely twisted, folded and coiled into a molecule of unique shape (conformation).
This conformation is essential for some protein function e.g. Enables a protein to
recognize and bind specifically to another molecule e.g. hormone/receptor;
enzyme/substrate and antibody/antigen.
•

40. 2- Secondary structure:
Results from hydrogen bond
formation between hydrogen of –NH
group of peptide bond and the carbonyl
oxygen of another peptide bond.
According to H-bonding there are two
main forms of secondary structure:
α-helix: It is a spiral structure resulting
from hydrogen bonding.
β-sheets: is another form of secondary
structure in which two or more
polypeptides (or segments of the same
peptide chain) are linked together by
hydrogen bond between H- of NH- of one
chain and carbonyl oxygen of adjacent
chain (or segment).

41. • Tertiary structure is determined
by a variety of interactions (bond formation)
among R groups and between R groups and the
polypeptide backbone.
a. The weak interactions include:
 Hydrogen bonds among polar side chains
 Ionic bonds between
charged R groups ( basic and acidic amino
acids)
 Hydrophobic
interactions among
hydrophobic ( non polar) R
groups.

42. b. Strong covalent bonds include disulfide bridges, that form
between the sulfhydryl groups (SH) of cysteine monomers,
stabilize the structure.

43. • Quaternary structure: results from the aggregation (combination) of two or more
polypeptide subunits held together by non-covalent interaction like H-bonds,
ionic or hydrophobic interactions.
• Examples on protein having quaternary structure:
– Collagen is a fibrous protein of three polypeptides (trimeric) that are
supercoiled like a rope.
• This provides the structural strength for their role in connective tissue.
– Hemoglobin is a globular protein with four polypeptide chains (tetrameric)
– Insulin : two polypeptide chains (dimeric)

45. PROPERTIES
OF
PROTEINS
•Physical Properties
•Chemical Properties

46. PHYSICAL PROPERTIES
 contains carbon, hydrogen, oxygen, nitrogen and
small amount of sulphur.
 composed of amino acids that are linked together
by peptide bonds
 act as catalysts, enzymes that speed up the rate of
chemical reactions
 provides structural support for cells
 transports substances across cell membrane
 provides a defense mechanism against pathogens
(antibodies)
 responds to chemical stimuli
 secretes hormones.

47. TO DETERMINE MOLECULAR NATURE
•In order to determine the nature of the molecular and
ionic species that are present in aqueous solutions at
different pH's, we make use of the Henderson -
Hasselbalch Equation.

48. ISOELECTRIC POINT
 the negatively and positively charged molecular
species are present in equal concentration. This
behavior is general for simple (difunctional) amino
acids.

49. ELECTROPHORESIS
 The distribution of charged species in a sample can
be shown experimentally by observing the
movement of solute molecules in an electric field,
using the technique of electrophoresis.

51. What is Protein?
• The protein we consume can be altered and
changed but can never return to its initial form.
This is called denaturation. This can be seen
when you add heat to an egg (it changes from a
runny fluid to a solid mass). The shapes of the
protein molecules in these foods have changed.
– Factors that cause denaturation:
1. Heat
2. Acids
3. Bases
4. Alcohol

52. CHEMICAL PROPERTIES
 Denaturation of Proteins
Denaturation is a process in
• which proteins or nucleic acids lose the
quaternary structure, tertiary structure and
secondary structure which is present in their
native state, by application of some external
stress or compound such as a strong acid or
base, a concentrated inorganic salt, an organic
solvent (e.g., alcohol or chloroform), radiation or
heat.

54.  Denaturation occurs because the bonding interactions
responsible for the secondary structure (hydrogen
bonds to amides) and tertiary structure are disrupted.
 In tertiary structure there are four types of bonding
interactions between "side chains" including: hydrogen
bonding, salt bridges, disulfide bonds, and non-polar
hydrophobic interactions. which may be disrupted.
 Therefore, a variety of reagents and conditions can
cause denaturation. The most common observation in
the denaturation process is the precipitation or
coagulation of the protein.

55. HEAT
Heat can be used to disrupt hydrogen bonds
and non-polar hydrophobic interactions. This
occurs because heat increases the kinetic
energy and causes the molecules to vibrate so
rapidly and violently that the bonds are
disrupted. The proteins in eggs denature and
coagulate during cooking. Other foods are
cooked to denature the proteins to make it
easier for enzymes to digest them. Medical
supplies and instruments are sterilized by
heating to denature proteins in bacteria and
thus destroy the bacteria.

56. ALCOHOL DISRUPTS HYDROGEN BONDING:
 Hydrogen bonding occurs between amide groups in the
secondary protein structure. Hydrogen bonding between "side
chains" occurs in tertiary protein structure in a variety of amino
acid combinations. All of these are disrupted by the addition of
another alcohol.
 A 70% alcohol solution is used as a disinfectant on the skin.
This concentration of alcohol is able to penetrate the bacterial
cell wall and denature the proteins and enzymes inside of the
cell. A 95% alcohol solution merely coagulates the protein on
the outside of the cell wall and prevents any alcohol from
entering the cell. Alcohol denatures proteins by disrupting the
side chain intramolecular hydrogen bonding. New hydrogen
bonds are formed instead between the new alcohol molecule
and the protein side chains.

57. ACIDS AND BASES DISRUPT SALT BRIDGES:
 Salt bridges result from the neutralization of an
acid and amine on side chains. The final interaction
is ionic between the positive ammonium group and
the negative acid group. Any combination of the
various acidic or amine amino acid side chains will
have this effect.
 The denaturation reaction on the salt bridge by the
addition of an acid results in a further straightening
effect on the protein chain as shown in the graphic
on the left.

58. HEAVY METAL SALTS
 Heavy metal salts act to denature proteins in much the same
manner as acids and bases. Heavy metal salts usually
contain Hg+2, Pb+2, Ag+1 Tl+1, Cd+2 and other metals with high
atomic weights. Since salts are ionic they disrupt salt bridges in
proteins. The reaction of a heavy metal salt with a protein
usually leads to an insoluble metal protein salt.
 This reaction is used for its disinfectant properties in external
applications. For example AgNO3 is used to prevent gonorrhea
infections in the eyes of new born infants. Silver nitrate is also
used in the treatment of nose and throat infections, as well as
to cauterize wounds.
 Mercury salts administered as Mercurochrome or Merthiolate
have similar properties in preventing infections in wounds.

59. Acids
 Acidic protein denaturants
include:
 Acetic acid[8]
 Trichloroacetic acid 12% in water
 Sulfosalicylic acid
Solvents
 Most organic solvents are
denaturing, including:
 Ethanol
 Methanol
Cross-linking reagents
 Cross-linking agents for proteins
include:[citation needed]
 Formaldehyde
 Glutaraldehyde
 Chaotropic agents
 Chaotropic agents include:
 Urea 6 – 8 mol/l
 Guanidinium chloride 6 mol/l
 Lithium perchlorate 4.5 mol/l
Disulfide bond reducers[edit]
 Agents that break disulfide
bonds by reduction include:[citation
needed]
 2-Mercaptoethanol
 Dithiothreitol
 TCEP (tris(2-
carboxyethyl)phosphine)
Other
 Picric acid
 Radiation
 Temperature

60. Example of denaturation that occurs in our
living:
1. Denaturation of human hair
 The extent to which fatty acid oxygenases are
activated in the normal epidermis is not known
2. In cooking eggs
 cooking eggs turns them from runny to solid
 cooking food makes it more digestible.
3. Milk forms a solid curd on standing
 ·
 ·
 ·
 ·
 ·
bacteria in milk grows
forms lactic acid
protonates carboxylate groups
becomes isoelectric
coagulates into a solid curd