BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | PROTEIN STRUCTURE | NOTED BY FAKHRY (IG @SFAKHRYM)
v Overview
o The linear consequence of the linked amino acids contains the information necessary to generate a protein molecule with a unique
three-dimensional shape that determines function
• Protein serves in many roles (e.g., Enzymes, hormone, receptor, antibodies, structural components, transporter of other
compound, and contractile elements in muscle)
o The complexity of protein structure is best analyzed by considering the molecule in terms of four organizational levels: primary,
secondary, tertiary, and quaternary
1
, BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | PROTEIN STRUCTURE | NOTED BY FAKHRY (IG @SFAKHRYM)
v PRIMARY STRUCTURE
o It consists of the amino acid sequence along the chain
• Understanding the primary structure of protein is important because many genetic diseases result in proteins with
abnormal amino acid sequence
• The linear polymer of amino acids contains polarity. By convention, the beginning of any polypeptide chain is at the α-
amino group and at the end is at the α-carboxyl group
• Each amino acid is called residue. The polypeptide chain consists of repeating units that make backbone. The variable
portion of the polypeptide are the side chains
• The polypeptide chain has the ability to form many hydrogens bonds
§ Hydrogen-bond donor: N-H group
§ Hydrogen-bond acceptor: C=O group
o Peptide Bond
o Amino acids are joined covalently by peptide bonds; It joins the α-carboxyl group of each amino acid to the α-amino group of
the next amino acid in the protein chain (condensation reaction)
o Peptide bonds are resistant to conditions that denature proteins, such as heating and high concentrations of urea
o Prolonged exposure to a strong acid or base at elevated temperatures is required to break these bonds enzymatically
o All amino acid sequences are read from the N- to the C-terminal end
o Linkage of >= 50 amino acids through peptide bonds is called a polypeptide, or protein
o Each component of amino acid is called a residue because it is the portion of the amino acid remaining after the atoms of water
are lost in the formation of the peptide bond.
§ When a peptide is named, all amino acid residues have their suffixes (-ine, -an, -ic, or -ate) changed to -yl, with the
exception of the C-terminal amino acid
• Example, a tripeptide composed of an N-terminal valine, a glycine, and a C-terminal leucine is called
valyglycyleucine
• The peptide bond has a partial double-bond character, that is, it is shorter than a single bond and is rigid, and planar
§ This prevents free rotation around the bond.
• However, the bonds between the α-carbon and the α-amino or α-carboxyl groups can be freely rotated (although
they are limited by the size and character of the R-groups)
§ This structure is due to interactions between electrons of the double bond of the carbonyl group and those of the C–N
bond, such that the latter acquires partial (about 40%) double-bond properties.
2
v Overview
o The linear consequence of the linked amino acids contains the information necessary to generate a protein molecule with a unique
three-dimensional shape that determines function
• Protein serves in many roles (e.g., Enzymes, hormone, receptor, antibodies, structural components, transporter of other
compound, and contractile elements in muscle)
o The complexity of protein structure is best analyzed by considering the molecule in terms of four organizational levels: primary,
secondary, tertiary, and quaternary
1
, BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | PROTEIN STRUCTURE | NOTED BY FAKHRY (IG @SFAKHRYM)
v PRIMARY STRUCTURE
o It consists of the amino acid sequence along the chain
• Understanding the primary structure of protein is important because many genetic diseases result in proteins with
abnormal amino acid sequence
• The linear polymer of amino acids contains polarity. By convention, the beginning of any polypeptide chain is at the α-
amino group and at the end is at the α-carboxyl group
• Each amino acid is called residue. The polypeptide chain consists of repeating units that make backbone. The variable
portion of the polypeptide are the side chains
• The polypeptide chain has the ability to form many hydrogens bonds
§ Hydrogen-bond donor: N-H group
§ Hydrogen-bond acceptor: C=O group
o Peptide Bond
o Amino acids are joined covalently by peptide bonds; It joins the α-carboxyl group of each amino acid to the α-amino group of
the next amino acid in the protein chain (condensation reaction)
o Peptide bonds are resistant to conditions that denature proteins, such as heating and high concentrations of urea
o Prolonged exposure to a strong acid or base at elevated temperatures is required to break these bonds enzymatically
o All amino acid sequences are read from the N- to the C-terminal end
o Linkage of >= 50 amino acids through peptide bonds is called a polypeptide, or protein
o Each component of amino acid is called a residue because it is the portion of the amino acid remaining after the atoms of water
are lost in the formation of the peptide bond.
§ When a peptide is named, all amino acid residues have their suffixes (-ine, -an, -ic, or -ate) changed to -yl, with the
exception of the C-terminal amino acid
• Example, a tripeptide composed of an N-terminal valine, a glycine, and a C-terminal leucine is called
valyglycyleucine
• The peptide bond has a partial double-bond character, that is, it is shorter than a single bond and is rigid, and planar
§ This prevents free rotation around the bond.
• However, the bonds between the α-carbon and the α-amino or α-carboxyl groups can be freely rotated (although
they are limited by the size and character of the R-groups)
§ This structure is due to interactions between electrons of the double bond of the carbonyl group and those of the C–N
bond, such that the latter acquires partial (about 40%) double-bond properties.
2
