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Biochemistry Lecture
GBSN (Unit 6)
Chemistry of Proteins
by,
Miss Areesha Ahmad
Lecturer
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
Sigma
Epsilon
Any functional group
Alkane and Alkyl group
Alkanes are organic compounds that consist entirely of single-bonded
carbon and hydrogen atoms.
Alkyl group In organic chemistry, an alkyl group is an alkane missing one
hydrogen
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
Glycine
Alanine
Methyl group
In organic chemistry, a methyl group is an alkyl derived from methane (CH4), containing one carbon atom bonded to
three hydrogen atoms,
Serine
CH2OH (hydroxymethyl group)
Cysteine
CH2SH (thiol group)
Thiols are the sulfur analogue of alcohols (that is, sulfur takes the place of oxygen in
the hydroxyl (OH) group of an alcohol),
Methionine
C5H11NO2S
Side chain: Contains a sulfur atom
and a methyl group
Tyrosine
C9H11NO3
Tyrosine has a phenyl group
(a benzene ring) with a
hydroxyl group (OH)
attached to it, forming a
phenol.
Tryptophan
C11H12N2O2
Tryptophan's R-group is an indole ring
(a bicyclic structure with a benzene
ring fused to a five-membered ring
containing nitrogen).
Valine
C5H11NO2
The side chain consists of a
central carbon atom (part of the
R-group) bonded to two methyl
groups (CH3).
Most a – Amino Acids are chiral
• Most α-amino acids are chiral, meaning they have a carbon atom (the α-carbon) that is attached to
four different groups: an amino group (NH2) a carboxyl group (COOH) a hydrogen atom (H), and
a variable side chain (R group).
• This allows the compound to exist as a pair of mirror images that are not superimposable on each
other, similar to left and right hands.
• These mirror images are called enantiomers, and the amino acids form two stereoisomers.
• Biochemists use the L and D nomenclature to describe the configurations of these stereoisomers.
• All naturally occurring proteins from living organisms are made up of L amino acids.
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
• Nonpolar, aliphatic (7)
• Aromatic (3)
• Polar, uncharged (5)
• Positively charged (3)
• Negatively charged (2)
Aliphatic amino acids are non-polar and hydrophobic.
Nonpolar means
equal sharing of
electron
Polar: unequal sharing
of electrons.
Polar amino acids are hydrophilic
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
pH is a power of hydrogen ions.
• pH value is inversely related to the concentration of hydrogen ions in the solution..
• Higher concentration of hydrogen ions: lower pH (more acidic),
• lower concentration of hydrogen ions: higher pH (more basic).
Peptide Bond Formation: Amino acids join together to form a
peptide bond, releasing water.
• Amino Acid: The basic unit of peptides and proteins.
• Peptide: A short chain of amino acids.
• Dipeptide: A peptide with exactly two amino acids.
• Oligopeptide: A peptide with 2 to 20 amino acids.
• Polypeptide: A longer chain of amino acids, typically more than 20,
forming part or all of a protein.
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
The cytoskeleton is a structure that helps cells maintain their shape and internal organization
Microtubules and microfilaments is the proteins.
• Microtubules are made of tubulin
• Microfilaments are made of actin.
Actin filaments, usually in association with myosin, are responsible for many types of cell movements.
Myosin is the prototype of a molecular motor—a protein that converts chemical energy in the form of ATP to
mechanical energy, thus generating force and movement.
• A proteose is any of various water-soluble compounds that are produced during in-vitro or in-vivo
hydrolytic breakdown of proteins a little before producing amino acids
• Peptone, a protein decomposition product, is made by partial hydrolysis process of the protein originated
from beef, casein, milk powder, gelatin, soy protein, silk protein, fibrin, etc.
eg., pepsin
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
Rod like structure not soluble in water e.g.., collagen, keratin etc (key component of skin,
bones, muscles, and other body parts)
Fibrous proteins
Spherical shape. Soluble in water e.g., Antibody, enzymes etc
Globular proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
Tendon is a soft, fibrous, cord-like tissue that connects muscle to bone or another structure
Inert: Do not react with
other chemical
Colloids are very low diameter particles which are responsible for the turbidity or the color of surface water
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
Amino Acids
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
GBSN - Biochemistry (Unit 6) Chemistry of Proteins
Hydrogen bonds are
formed between the
carbonyl O of one
amino acid and the
amino H of another
Alpha Helix Structure
Beta-Pleated sheets
Two or more segments of a polypeptide chain overlap and form hydrogen bonds
Disulfide bond
A disulfide bond, also known as a disulfide bridge, is a covalent bond
formed between the sulfur atoms of two cysteine amino acids within a
protein. These bonds play a crucial role in stabilizing the three-
dimensional 3D structure of proteins.
Formation:
Disulfide bonds are formed through an oxidation reaction
between the thiol groups (–SH) of two cysteine residues.
The reaction releases two hydrogen atoms (H₂), resulting
in a bond between the two sulfur atoms (–S–S–).
Function
• These bonds are crucial for the stability and proper folding of proteins.
• Disulfide bridges can occur in both the secondary and tertiary structure of a protein,
providing stabilization to alpha helices and beta sheets and stabilize the overall (3D)
structure of the protein.
• In some cases, disulfide bonds can also influence the protein's quaternary structure by
linking different polypeptide chains.
• They create rigid connections that help hold the structure in place and prevent it from
unfolding.
• They may form between two cysteine residues in different regions of the protein, helping
to hold those regions together and maintain the protein's shape.
(3D)
Only one polypeptide arranged in 3D structure
More than one polypeptide arranged in 3D structure
Assignment

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GBSN - Biochemistry (Unit 6) Chemistry of Proteins

  • 1. Biochemistry Lecture GBSN (Unit 6) Chemistry of Proteins by, Miss Areesha Ahmad Lecturer
  • 9. Alkane and Alkyl group Alkanes are organic compounds that consist entirely of single-bonded carbon and hydrogen atoms. Alkyl group In organic chemistry, an alkyl group is an alkane missing one hydrogen
  • 13. Alanine Methyl group In organic chemistry, a methyl group is an alkyl derived from methane (CH4), containing one carbon atom bonded to three hydrogen atoms,
  • 15. Cysteine CH2SH (thiol group) Thiols are the sulfur analogue of alcohols (that is, sulfur takes the place of oxygen in the hydroxyl (OH) group of an alcohol),
  • 16. Methionine C5H11NO2S Side chain: Contains a sulfur atom and a methyl group
  • 17. Tyrosine C9H11NO3 Tyrosine has a phenyl group (a benzene ring) with a hydroxyl group (OH) attached to it, forming a phenol.
  • 18. Tryptophan C11H12N2O2 Tryptophan's R-group is an indole ring (a bicyclic structure with a benzene ring fused to a five-membered ring containing nitrogen).
  • 19. Valine C5H11NO2 The side chain consists of a central carbon atom (part of the R-group) bonded to two methyl groups (CH3).
  • 20. Most a – Amino Acids are chiral • Most α-amino acids are chiral, meaning they have a carbon atom (the α-carbon) that is attached to four different groups: an amino group (NH2) a carboxyl group (COOH) a hydrogen atom (H), and a variable side chain (R group). • This allows the compound to exist as a pair of mirror images that are not superimposable on each other, similar to left and right hands. • These mirror images are called enantiomers, and the amino acids form two stereoisomers. • Biochemists use the L and D nomenclature to describe the configurations of these stereoisomers. • All naturally occurring proteins from living organisms are made up of L amino acids.
  • 22. • Nonpolar, aliphatic (7) • Aromatic (3) • Polar, uncharged (5) • Positively charged (3) • Negatively charged (2)
  • 23. Aliphatic amino acids are non-polar and hydrophobic. Nonpolar means equal sharing of electron
  • 24. Polar: unequal sharing of electrons. Polar amino acids are hydrophilic
  • 29. pH is a power of hydrogen ions. • pH value is inversely related to the concentration of hydrogen ions in the solution.. • Higher concentration of hydrogen ions: lower pH (more acidic), • lower concentration of hydrogen ions: higher pH (more basic).
  • 30. Peptide Bond Formation: Amino acids join together to form a peptide bond, releasing water.
  • 31. • Amino Acid: The basic unit of peptides and proteins. • Peptide: A short chain of amino acids. • Dipeptide: A peptide with exactly two amino acids. • Oligopeptide: A peptide with 2 to 20 amino acids. • Polypeptide: A longer chain of amino acids, typically more than 20, forming part or all of a protein.
  • 34. The cytoskeleton is a structure that helps cells maintain their shape and internal organization Microtubules and microfilaments is the proteins. • Microtubules are made of tubulin • Microfilaments are made of actin.
  • 35. Actin filaments, usually in association with myosin, are responsible for many types of cell movements. Myosin is the prototype of a molecular motor—a protein that converts chemical energy in the form of ATP to mechanical energy, thus generating force and movement.
  • 36. • A proteose is any of various water-soluble compounds that are produced during in-vitro or in-vivo hydrolytic breakdown of proteins a little before producing amino acids • Peptone, a protein decomposition product, is made by partial hydrolysis process of the protein originated from beef, casein, milk powder, gelatin, soy protein, silk protein, fibrin, etc. eg., pepsin
  • 39. Rod like structure not soluble in water e.g.., collagen, keratin etc (key component of skin, bones, muscles, and other body parts) Fibrous proteins
  • 40. Spherical shape. Soluble in water e.g., Antibody, enzymes etc Globular proteins
  • 42. Tendon is a soft, fibrous, cord-like tissue that connects muscle to bone or another structure
  • 43. Inert: Do not react with other chemical
  • 44. Colloids are very low diameter particles which are responsible for the turbidity or the color of surface water
  • 53. Hydrogen bonds are formed between the carbonyl O of one amino acid and the amino H of another Alpha Helix Structure
  • 54. Beta-Pleated sheets Two or more segments of a polypeptide chain overlap and form hydrogen bonds
  • 55. Disulfide bond A disulfide bond, also known as a disulfide bridge, is a covalent bond formed between the sulfur atoms of two cysteine amino acids within a protein. These bonds play a crucial role in stabilizing the three- dimensional 3D structure of proteins. Formation: Disulfide bonds are formed through an oxidation reaction between the thiol groups (–SH) of two cysteine residues. The reaction releases two hydrogen atoms (H₂), resulting in a bond between the two sulfur atoms (–S–S–).
  • 56. Function • These bonds are crucial for the stability and proper folding of proteins. • Disulfide bridges can occur in both the secondary and tertiary structure of a protein, providing stabilization to alpha helices and beta sheets and stabilize the overall (3D) structure of the protein. • In some cases, disulfide bonds can also influence the protein's quaternary structure by linking different polypeptide chains. • They create rigid connections that help hold the structure in place and prevent it from unfolding. • They may form between two cysteine residues in different regions of the protein, helping to hold those regions together and maintain the protein's shape.
  • 57. (3D) Only one polypeptide arranged in 3D structure
  • 58. More than one polypeptide arranged in 3D structure