Assignment 2_MSE693A

1.Write general structure of amino acid, and label each important group.
Answer; - Structure of amino acid have 4 major group that can be seen in the following figure also.
 Alpha carbon
 Side chain (R- group)
 Amino group
 Carboxylic group

2.In brief, describe the types of non-covalent bonds govern the shape of protein?
Answer: - in proteins generally single covalent bond are responsible for rotation of the bond that
result in several configuration. But the non-covalent bond, limit these configurations by containing
some specific configuration. Some general type of non-covalent force in proteins are followings
-Hydrogen bonds
– Ionic bonds
– van der Waals attractions (dispersion or London forces)
– Hydrophobic forces; have a major role in protein folding in solvent. Interaction of polar and non-
polar group are different in water or solvent that result in a specific shape of protein.
• Conformation depending on the environment
 3.Describe the α-helix and β-structure of protein.
Answer
generally alpha helix structure of protein is formed because of hydrogen bonding between N_H and
C=O group that present in the polypeptide backbone of the protein
betta sheets can be form by either interaction between parallel chains (polypeptide run in same
orientation) or anti-parallel chains (polypeptide run in opposite orientation).
4.Describe the protein structure with its several levels of organisation
Answer: -
Protein structure have several of organisation that can be categorized in the following way
primary structure; these are the fundamental structure of protein that made of covalently
bonded amino acids
– Amino acid sequence
• Secondary structure; these structures are driven from the primary structure of protein
because of no-covalent bonding between the amino- acid sequence or peptide backbone
– α helices and β sheets
• Tertiary structure: as peptide backbone interaction define the secondary structure,
similarly side chain interaction lead to the tertiary structure of protein. Means Interactions
of side chains of protein within the secondary structure leads to tertiary structure. The side
chain interaction in the tertiary structure are following;
Non-polar or hydrophobic interactions, Polar or hydrophilic interactions, Salt bridges (ionic
interactions)
Disulphide bonds – covalent bonds formed between –SH groups of two cysteine residues
– Three-dimensional conformation such as Fibrous, Globular proteins and Lipid-soluble
membranous proteins
• Quaternary structure
– it is a complex structure of proteins that form by more than one polypeptide chain. Two
or more protein chains interacting to form a complex protein such as Hemoglobin.
The interaction the quaternary structure are the combination of all interaction of other
structure (primary, secondary and tertiary structure )
• Protein domains
– Part of a polypeptide that can fold independently into a compact, stable structure.