MPSC Notes - Protein Structure Parts - III

Protein Structure Parts - III

21. What is the secondary structure of a protein?

The secondary protein structure is generated by the manner its amino acids interact through the intermolecular bond. These interactions create a spatial conformation of the polypeptide filament. The two most studied secondary conformations of proteins are the alpha-helix and the beta-sheet.

22. What is the difference between the alpha-helix and the beta-sheet protein conformations?

Alpha-helix and beta-sheet conformations are the two main types of secondary structure of a protein molecule. According to the primary protein structure its secondary structure can be of one type or the other.

In the alpha-helix structure the polypeptide curls longitudinally by the action of hydrogen bonds forming a spiral, or helix. In the beta-sheet conformation the protein is more distended and the hydrogen bonds form a zig-zag-shaped protein structure called B-strand. Many assembled beta-strands make a beta-sheet.

23. What is the tertiary structure of a protein? What are the main types of tertiary structure?

The tertiary protein structure is a spatial conformation additional to the secondary structure in which the alpha-helix or the beta-sheet folds itself up. The forces that keep the tertiary structure generally are interactions between the –R groups of the amino acids and between other parts of the protein and water molecules of the solution.

The main types of tertiary structure of proteins are the globular proteins and the fibrous proteins.
24. What is the quaternary structure of a protein? Do all proteins have quaternary structure?

The quaternary protein structure is the spatial conformation due to interactions among polypeptide chains that form the protein.

Only those proteins made of two or more polypeptide chains have quaternary structure. Insulin (two chains), hemoglobin (four chains) and the immunoglobulins (antibodies, four chains) are some examples of protein having quaternary structure.
25. What is protein denaturation? Is there any change in the primary structure when a protein is denatured?

Secondary, tertiary and quaternary structures of proteins are spatial structures. Denaturation is modification in any of these spatial structures that makes the protein deficient or biologically inactive.

After denaturation the primary protein structure is not affected.
26. How can denaturation be classified regarding its reversibility?

Protein denaturation can be a reversible or an irreversible process, i.e., it may be possible or impossible to make the protein regain its original spatial conformation.

27. What are some factors that can lead to protein denaturation?

Protein denaturation can be caused by temperature variation, pH change, changes in the concentration of surrounding solutes and by other processes. Most proteins denature after certain elevation of temperature or when in very acid or very basic solutions. This is one of the main reasons that it is necessary for the organisms to keep stable temperature and pH.

28. Is it expected that a change in the primary, in the secondary or in the tertiary structure of a protein will produce more functional consequences?

Any change of the protein structure is relevant if it alters its biological activity. Changes in the primary protein structure are more important because they are modifications in the composition of the molecule and such composition determines all other structures of the protein.

29. In sickle cell anemia, a hereditary disease, there is substitution of one amino acid by another in one of the four polypeptide chains of hemoglobin. In this case are all of the structural levels of the protein modified?

In sickle cell disease there is a change in the primary protein structure of one of the polypeptide chains that form hemoglobin: the amino acid glutamic acid is substituted by the amino acid valine in the β chain. The spatial conformation of the molecule in addition is also affected and modified by this primary “mistake” and the modification also creates a different (sickle) shape to the red blood cells.

Modified, sickled, red blood cells sometimes aggregate and obstruct the peripheral circulation causing tissue hypoxia and the pain crisis typical of sickle cell anemia.

30. What is the difference between essential and natural amino acids?

Essential amino acids are those that the organism is not able to synthesize and that need to be ingested by the individual. Natural amino acids are those that are produced by the organism.

There are living species that produce every amino acid they need, for example, the bacteria Escherichia coli, that does not have essential amino acids. Other species, like humans, need to obtain essential amino acids from the diet. Among the twenty different known amino acids that form proteins humans can make twelve of them and the remaining eight need to be taken from the proteins they ingest with food.

The essential amino acids for humans are phenylalanine, histidine, isoleucine, lysine, methionine, threonine, tryptophane and valine.

31. What are respectively some remarkable functions of myosin, CD4, albumin, keratin, immunoglobulin, reverse transcriptase, hemoglobin and insulin?

Myosin is a protein that when associated with actin produces a muscular contraction. CD4 is a membrane protein of some lymphocytes, the cells that are infected by HIV. Albumin is an energy storage protein and also an important regulator of the blood osmolarity. Keratin is a protein with structural function present in the epidermis and skin appendages of vertebrates. Immunoglobulins are the antibodies, specific proteins that attack and inactivate strange agents that enter the body. Reverse transcriptase is the enzyme responsible for the transcription of RNA and formation of DNA in the life cycle of retroviruses. Hemoglobin is the protein that carries oxygen from the lungs to the cells. Insulin is a hormone secreted by the pancreas that participates in the metabolism of glucose.

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