2. What is the importance of proteins for living organisms?
Proteins play a fundamental role in nearly all biological processes. Due to their diversity, they can take on many different configurations and can play varied roles in cells and tissues.
Some protein functions are worthy noting: they have a structural function (cell membrane proteins, cytoskeleton proteins, connective tissue proteins), an enzymatic function (enzymes are proteins), an energy storage function (proteins can be broken down into acetyl-CoA to "feed" the Krebs cycle), an osmotic regulation function (albumin), a transportation function (membrane channels, respiratory pigments), an immune protection function (antibodies), a movement function (contractile proteins), an endocrine integration function (hormones) and a informative function (membrane receptors, intracellular signalers). There are also many proteins whose biological functions are not yet known.
Amino Acids and How They Form Proteins
3. What unit are proteins composed of?
The units that make up proteins are amino acids.
4. What is an oligopeptide? How is it different from a polypeptide?
The peptide molecule is the molecule formed by the bonding of amino acids through the peptide bond. An oligopeptide is a peptide composed of few amino acids (oligo = few). Polypeptides are peptides that contain many amino acids (poli = many), in general more than 50.
5. How many amino acids are known to form proteins in living organisms?
There are twenty different known amino acids that form proteins related to the genetic code of the living organisms.
There are still many other amino acids that are not yet known.
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The Chemical Composition of Amino Acids
6. Does every amino acid have a central carbon atom? To which organic group is that central carbon atom bound?
A carboxyl group –COOH, an amine group – NH₂, an hydrogen atom –H and a variable radical -R are necessarily bound to the central carbon atom of an amino acid.
7. How can amine groups be classified?
Amines can be classified into primary amines, in which one –R (variable radical) is attached to a –NH₂; secondary amines, in which one hydrogen atom of the NH₂ is substituted by another –R, thus leaving two –R; and tertiary amines, in which there are no hydrogen atoms bound to the nitrogen and with three –R instead.
8. What is the molecular structure of a carboxyl group?
Carboxyl groups (–COOH) have one carbon atom attached to one hydroxyl group through a simple bond and to one oxygen atom via a double bond. The carbon atom’s other bond site is available to other substances.
9. What is the flat structural representation of an amino acid molecule?
An amino acid molecule has a central carbon atom to which a carboxyl group is bound on one side and to which a –R (variable radical) is bound on the opposite side. Perpendicular to those ligands, an amine group is bound to the central carbon atom on one side, and a hydrogen atom is bound on its opposite side.
The bond between the carboxyl group and a carbon atom in which a hydrogen atom is laterally attached is the reason for the name “acid” in amino acids. The bond between an amine group and the central carbon gives the name “amino.”
10. What is the importance of the –R group (variable radical) in an amino acid molecule?
The –R group, also called a side-chain, is the variable part of the amino acid molecule. The –R group can be a complex chain of carbon atoms, a substitute methyl group (in this case forming the amino acid alanine) or even a sole hydrogen atom (forming glycine, the simplest amino acid). Therefore the –R group is important because it is what distinguishes the different amino acids.
11. How can the binding of two amino acids into a peptide formation be described?
A peptide is formed when a carbon atom from the carboxyl group of one amino acid is connected to the nitrogen atom of the amine group of another amino acid. Through that bond, the hydroxyl group of the carboxyl group and one hydrogen atom of the amine are lost resulting in the release of one water molecule.
12. What is the bond between two amino acids called?
The chemical bond between two amino acids is called a peptide bond.
13. Are the –R groups bound to the central carbon atoms involved in the bond between amino acids?
The peptide bond connects the nitrogen atom of the amine group of one amino acid to the carbon atom of the carboxyl group of another amino acid, releasing one molecule of water. Therefore, the –R groups do not participate in that bond.
14. Are the –H groups bound to the central carbon atoms involved in the peptide bond?
The central carbon atoms, the –R groups and the hydrogen atoms attached to the central carbon atoms do not participate in the peptide bond.
15. Are the amine and the carboxyl groups attached to central carbon atoms involved in the bond between amino acids?
Yes. The nitrogen of the amine group of one amino acid binds to the carbon atom of the carboxyl group of the other amino acid. The water molecule released from the formation of the peptide bond thus contains one hydrogen atom from the amine and an oxygen atom and the other hydrogen atom from the carboxyl group.
16. Does the chemical reaction to bind amino acids incorporate or release atoms? What are the chemical entities incorporated or released during this reaction?
The binding of amino acids via the peptide bond releases atoms. They are released in the form of one molecule of water.
Amino Acids Create Different Proteins
17. Can the same amount of amino acids create different proteins?
Different proteins with the same total number of amino acids may exist. In such cases, the difference depends on the types of amino acids or on the sequence in which they form the protein.
18. Are proteins with the same number of their respective amino acid components necessarily identical?
While many proteins share the same number of each of their different amino acid components, for example, 50 alanines, 70 glycines and 20 histidines, the sequences in which these amino acids are connected may be very different. Therefore, if two or more proteins have the same number of each of their amino acid components, they are not necessarily identical.
19. What is the essential condition for one protein molecule to be identical to another protein molecule?
For a protein molecule to be identical (exactly) to another protein molecule, it is necessary for the sequences of amino acids that form them to be identical.
20. What is the primary structure of a protein? What is the importance of the primary structure?
The primary structure of a protein is the linear sequence of amino acids that form the molecule.
The primary structure is the basis of identity of the protein. Modification of only one amino acid in the primary structure creates a different protein. This different protein can be inactive or can even have other biological functions.
21. What is the secondary structure of a protein?
The secondary structure of a protein is generated by the way in which its amino acids interact through the intermolecular bond. These interactions create a spatial conformation of the polypeptide chain. The two most studied secondary conformations of proteins are the alpha-helix and the beta-sheet.
22. What is the difference between alpha-helix and beta-sheet protein conformations?
Alpha-helix and beta-sheet conformations are the two main types of secondary structures of a protein molecule. Depending on the primary protein structure, its secondary structure can be of one type or the other.
In the alpha-helix structure, the polypeptide curls longitudinally through the action of hydrogen bonds, forming a spiral or helix. In the beta-sheet conformation, the protein is more extended and the hydrogen bonds form a zig-zag-shaped protein structure called a beta-strand. Many beta-strands put together make a beta-sheet.
23. What is the tertiary structure of a protein? What are the main types of tertiary structures?
The tertiary structure of a protein is a spatial conformation in addition to the secondary structure, in which the alpha-helix or the beta-sheet folds itself up. The forces that maintain the tertiary structure are generally interactions between the –R groups of the amino acids, other parts of the protein and the water molecules of the solution.
The main types of tertiary structure of proteins are globular proteins and fibrous proteins.
24. What is the quaternary structure of a protein? Do all proteins have a quaternary structure?
The quaternary structure of a protein is the spatial conformation caused by interactions between the polypeptide chains that form the protein.
Only proteins made up of two or more polypeptide chains have a quaternary structure. Insulin (two chains), hemoglobin (four chains) and immunoglobulins (antibodies, four chains) are some examples of protein with a quaternary structure.
Protein Denaturation and Structural Changes
25. What is protein denaturation? Are there any changes in the primary structure when a protein is denatured?
The secondary, tertiary and quaternary structures of a protein are spatial structures. Denaturation is a 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 according to its reversibility?
Protein denaturation can be reversible or irreversibl. That means that it may be possible or impossible for the protein to 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 elevations in temperature or when in very acidic or very alkaline solutions. This is one of the main reasons that it is necessary for organisms to mantain a stable temperature and pH.
28. Do changes in the primary, secondary or tertiary structure of a protein normally have consequences for their function?
Any changes in the structure of a protein are relevant if they alter its biological activity. Changes in the primary structure of a protein are the most important because they are modifications in the composition of the molecule, and that composition determines all the other structures of the protein.
29. In sickle cell anemia, a hereditary disease, one amino acid is substituted 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. In addition, the spatial conformation of the molecule is also affected and modified by this primary “mistake”, which also creates a different (sickle) shape for red blood cells.
Modified, sickle-shaped, red blood cells sometimes accumulate and obstruct peripheral blood circulation, causing tissue hypoxia and the acute pain typical of sickle cell anemia.
The Difference Between Essential and Nonessential Amino Acids
30. What is the difference between essential and nonessential amino acids?
Essential amino acids are those that the body is not able to synthesize and which need to be ingested by the individual. Nonessential amino acids are those that are produced by the body.
There are living species that produce every amino acid they need. For example, the bacteria Escherichia coli does not have essential amino acids. Other species, like humans, need to obtain essential amino acids from their diet. Among the twenty different known amino acids that form proteins humans can produce twelve of them and the remaining eight need to be taken from proteins ingested through food.
The essential amino acids for humans are phenylalanine, histidine, isoleucine, lysine, methionine, threonine, tryptophane and valine.
Examples of Important Proteins
31. What are some of the remarkable functions of myosin, CD4, albumin, keratin, immunoglobulin, reverse transcriptase, hemoglobin and insulin?
Myosin is a protein that when bound to actin produces a muscle 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 blood osmolarity. Keratin is a protein with a structural function and which is present in the epidermis and skin appendages of vertebrates. Immunoglobulins are antibodies, specific proteins that attack and inactivate foreign agents that enter the body. Reverse transcriptase is the enzyme responsible for the transcription of RNA and the formation of DNA in the life cycle of retroviruses. Hemoglobin is the protein that carries oxygen from the lungs to cells. Insulin is a hormone secreted by the pancreas that participates in the metabolism of glucose.