This video explains more on protein in biochemistry

1. Amino Acids and Proteins:
Structures and Chemistry
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2. AMINO ACIDS

3. CHEMICAL NATURE OF AMINO
ACIDS
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4. Amino acids are simple organic compounds with both amino and
carboxyl groups as their functional groups
Carboxyl group
What are amino acids?
Amino group
α

5. α
β
γ
δ
ε

6. STEREOISOMERISM
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7. ➢ Chirality defines compounds with an atom with four different groups
attached to it. Such atom is called chiral atom
L- amino acid
D- amino acid

8. CLASSIFICATION OF AMINO
ACIDS
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9. R-group

10. Non-polar aliphatic R-groups
Glycine Alanine Proline Valin
e
Leucine Isoleucine Methionine

11. Aromatic R-groups
Phenylalanine Tyrosin Tryptophan

13. Polar uncharged R-groups
Cysteine
Threonine
Serine
Asparagine Glutamine

14. Formation of disulfide bond

15. Positively charged R-groups
Lysin Histidine
Arginine

16. Negatively charged R-group
Aspartate Glutamate

17. Source

18. Essential and non-essential amino acids

19. Abbreviation of amino acids
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20. Essential and non-essential amino acids

21. ACID-BASE PROPERTIES OF AMINO ACIDS
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22. Amphoteric nature of amino acids
At physiological pH carboxyl group of amino acids are unprotonated
At physiological pH amino group of amino acids are protonated

39. PEPTIDE BOND
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42. STRUCTURE OF PROTEINS
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43. 1. Primary
2. Secondary
3. Tertiary and
4. Quaternary protein structure
Types of protein structure

44. PRIMARY STRUCTURE
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45. Primary structure of a protein is the linear sequence of the amino acids in
a protein.
The order/sequence of amino acid is that the N-terminal end (end with
free α-amino group) is to the left while the C-terminal end, carrying the α-
carboxyl group, is to the right and are read from N-terminal to the C-
terminal end of the peptide
In naming a polypeptide, the amino acid residues except the C-terminal
amino acid, have their suffixes (-ine, -an, -ic, or –ate) changed to –yl. For
example glutamylglycylvalylisoleucine

47. SECONDARY STRUCTURE
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48. Secondary structure of proteins is the particularly stable arrangements of
amino acid residues giving rise to recurring structural patterns.
This ordered arrangement in a protein confers the regular conformational
forms upon that protein.
Examples of secondary structures frequently found in proteins are the ⍺-
helix, 𝞫-sheet and 𝞫-bend.
These structural conformations are stabilized by hydrogen bonds.

49. α-helix
➢ This is the most common of the secondary structures found among the
globular proteins.
➢ The formation of the α-helix is spontaneous and is stabilized by H-bonding
between amide nitrogens and carbonyl carbons of peptide bonds spaced
four residues apart.
➢ The orientation of H-bonding produces a helical coiling of the peptide
backbone such that the R-groups extend outward from the central axis to
avoid steric hindrances with each other.
➢ Each turn of α-helix contains 3.6 amino acids residues, thus amino acid
residues spaced three or four residues apart in primary sequence are
spatially close together when folded in the α-helix.

50. α-helix
➢ Examples of proteins with with α-helix include keratins (fibrous protein),
major components of hair and skin.
➢ The number of disulphide bonds between constituent polypeptide chains
defines their rigidity. Another example is myoglobin, although a globular
protein and a flexible molecule.

51. α-helix structure

53. ➢ Examples of proteins with with α-helix include keratins (fibrous protein),
major components of hair and skin.
➢ The number of disulphide bonds between constituent polypeptide chains
defines their rigidity. Another example is myoglobin, although a globular
protein and a flexible molecule.

54. The following amino acids are not found in α-helix structure of protein
1. Proline
2. Glutamate, aspartate, histidine, lysine and arginine
3. Tryptophan, tyrosine and phenylalanine
4. Valine and isoleucine
Note the disruption of α-helix is important as it introduces additional folding
of the polypeptide backbone to allow the formation of globular proteins

55. β-sheet
➢ In this form of secondary structure, all the peptide bond components are
involved in hydrogen bonding.
➢ Unlike α-helix, β-sheet is composed of 2 or more different peptide chains or
segments of polypeptide chains of at least 5 – 10 amino acids.
➢ They are arranged either antiparallel to each other (N-terminal and C-
terminal of the β-strands alternating) or parallel to each other (all N-
terminal of the β-strands aligned in the same direction).
➢ Hydrogen bonding between the amide nitrogen, and carbonyl carbon
stabilize the folding and the alignment of stretches of the polypeptide
backbone beside each other.

56. β-sheet
➢ As opposed to a linearly contiguous region of the backbone in α-helix,
hydrogen-bonding residues in β-sheet are perpendicular to the polypeptide
backbone.
➢ The compactness of globular protein is made possible because of β –bends
that reverse of the direction of polypeptide chain. This is made possible due
to the presence of four amino acid residues, proline (causes kink in the
polypeptide chain), glycine (smallest R-group).
➢ Formation of hydrogen bonds and ionic bonds stabilizes the β-bends.

57. β-sheet

60. β-helix structure

61. Super-Secondary Structure
➢ Some proteins such as the globular proteins are constructed by combining
structural elements (α-helices, β-sheets, nonrepetitive sequences).
➢ These form the core region, which are connected by loop regions (e.g β-
bends) at the surface of the protein.
➢ This structure is usually produced by packing side chains from adjacent
secondary structural elements close to each other

63. TERTIARY STRUCTURE
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64. ➢ Tertiary structure is the complete three-dimensional structure of the
polypeptide units of a given protein.
➢ The primary structure of a polypeptide chain determines its tertiary
structure.
➢ Included in this description is the spatial relationship of 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.
➢ Secondary structures of proteins often constitute distinct domains.
Therefore, tertiary structure also describes the relationship of different
domains to one another within a protein.
➢ The interactions of different domains is governed by several forces:

66. FORCES CONTROLLING PROTEIN STRUCTURE
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67. 1. Hydrogen bonding
2. Hydrophobic forces
3. Electrostatic forces
4. van der waals forces

69. QUATERNARY STRUCTURE
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70. ➢ Proteins containing 2 or more different polypeptide chains are held in
association by the same non-covalent forces that stabilize the tertiary
structures of proteins.
➢ Proteins with multiple polypeptide chains are oligomeric proteins.
➢ The structure formed by monomer-monomer interaction in an oligomeric
protein is known as quaternary structure.
➢ Oligomeric proteins can be composed of multiple identical polypeptide
chains or multiple distinct polypeptide chains.
➢ Proteins with identical subunits are termed homo-oligomers. Proteins
containing several distinct polypeptide chains are termed hetero-oligomers.
➢ Haemoglobin is a protein with quaternary structure

75. Collagen consist of three chains that are wind around each other to form tiple helix.
Collagen contain approximately 1,000 amino acids and one-third are glycine. The
sequence Gly-X-Y occurs frequently. X= proline and Y = hydroxyproline
Osteogenesis imperfecta (OI) is predominantly characterized by a generalized
decrease in bone mass (osteopenia) and by brittle bones. The disorder is frequently
associated with blue sclerae, dental abnormalities (dentinogenesis imperfecta),
progressive hearing loss, and a positive family history. Biochemical defect The
disorder is caused by mutations in the genes that code for type I procollagen (ie,
COL1A1 and COL1A2). Amino acids with bulky side chain replaces glycine
Scurvy (vitamin C deficiency): hydroxylation of proline residues is decreased and
unstable form of collagen is produced leading to abnormal development of bone,
teeth, blood vessels and other structures rich in collagen. Bleeding gum and poor
wound healing are usually observed.

76. Emphysema is a lung disease characterized by destruction of the alveolar
walls. Its causes are complex but airway infection, cigarette smoking, air
pollution and familial factors are involved. A deficiency in plasma α1-
Antitrypsin leads to the development of emphysema and less frequently hepatic
disease.
In healthy individuals, the lungs contain a natural enzyme called neutrophil
elastase that, under normal circumstances, helps the lungs by digesting
damaged, aging cells and bacteria. This process promotes healing of the lung
tissue. Unfortunately this enzyme is nonspecific in nature and eventually attacks
the lung tissue instead of helping it heal. That is where alpha antitrypsin (AAT)
comes into action, by destroying the enzyme before it can cause actual damage
to healthy lung tissue. It promotes the lungs to function normally. When there is
not enough AAT, however, the lung tissue will continue to be destroyed, which
may lead to the chronic lung disease, emphysema.

77. The two common deficiency variants of a1-antitrypsin, S and Z, result from
point mutations in the α1- antitrypsin gene and are named on the basis of their
slower electrophoretic mobility on isoelectric focusing analysis compared with
the normal M allele. S α1-antitrypsin (264Glu→Val) is found in up to 28
percent of Southern Europeans and, although it results in plasma α1-antitrypsin
levels that are 60 percent of the M allele, it is not associated with any
pulmonary sequelae. This is usually sufficient to protect the lungs from the
effects of elastase in people who do not smoke. The Z variant (342Glu→Lys)
results in a more severe deficiency that is characterized, in the homozygote, by
plasma α1-antitrypsin less than 15 percent of normal, and patients are likely to
develop panacinar emphysema at a young age; 50 percent of these patients will
develop liver cirrhosis, because the A1AT is not secreted properly and instead
accumulates in the liver.

78. For optimal function, the hemoglobin ⍺- and 𝛽- globin chains must have the
proper structure and be synthesized in a 1:1 ratio. A large excess of one subunit
over the other results in the class of diseases called thalassemias. This disease
provides resistance to malaria in heterozygous state just like sickle cell anemia.
1. single amino acid replacement mutations that give rise to an unstable
globin subunit is one mechanism by which thalassemia arises.
2. The most common are mutations that result in decreased synthesis of of one
subunit
3. ⍺-thalassemia result from the complete gene deletion

79. Hemoglobinopathies: Disorders in the structure or amount of the globin chains
HbS is composed of two normal ⍺-chains and two 𝛽-globin chains with the sickle
cell variant. The change in the amino acid composition from a glutamate to a valine
in the 𝛽-chain allows sickle hemoglobin to separate from normal adult. hemoglobin
by electrophoresis.
In heterozygous individuals with sickle cell trait, the sickle cell allele provides some
protection against malaria. The infected red blood cells of individual with normal
HbA develop protrusions that attach to the lining of capillaries, occluding the
vessels and preventing oxygen from reaching cells in the affected region leading to
cell death.
In heterozygous individuals, HbS in infected cells aggregates into long fibre that
cause the cell to become distorted. The distorted cells containing malaria parasite
are preferentially recognized by the spleen and are rapidly destroyed. Thus ending
the life of the parasite

80. Hemoglobinopathies: Disorders in the structure or amount of the globin chains
2. Another common hemoglobin variant HbC result from a Glu - to - Lys
replacement in the same position as HbS mutation. This produces to effect (a)
promotes water loss from the cell by activating the K+ transporter by an
unknown mechanism resulting in a higher than normal concentration of
hemoglobin within the cell
(b) lowers the solubility hemoglobin in the homozygote resulting in a
tendency of the mutant hemoglobin to precipitate within the red cell.
Although, unlike sickle cell anemia, the cell does not become deformed.
Homozygotes for HbC have mild hemolytic anemia