Biochemistry Review

Proteins


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1. As with carbohydrates, proteins can act as food reserves or structural molecules.

2. Other equally vital roles played by proteins include chemical messengers or hormones, oxygen transportation in the circulation of blood, the contractile properties necessary for movement, and as antibodies which defend us against invading organisms.

3. Probably the most important responsibility of proteins is their role as enzymes -- biologically active catalysts.

4. The smallest subunits of a protein are the amino acids which are joined together into a linear chain

5. If a pair of amino acids are linked together by a peptide bond (covalent) the result is called a dipeptide.

6. The enzyme-mediated dehydration synthesis eventually results in a linear chain of amino acids called a polypeptide.

7. Proteins range in size between 50 amino acids subunits to some with 70-80 thousand amino acid subunits.

8. Biochemists know of about twenty primary amino acids found in proteins. Secondary amino acids are derived from the primary ones. This seemingly limited number of subunits is actually more than enough to create the multitude of unique properties exhibited by proteins.

9. All amino acids have the same core structure. The central or alpha carbon is bonded to 3 side groups and a hydrogen. -NH2 is the amino group, COOH is the carboxyl group, and R is the variable group.

10. In its ionized state an amino acid may have either a positive or a negative charge.

11. The R or variable groups of amino acids may be categorized into 4 types:

  • nonpolar-- such as the methyl group.
  • polar -- such as NH2 or OH
  • positively charged -NH3+
  • negatively charged - COO-

12. One of the polar but uncharged amino acids, cysteine contains a sulfhydryl side group. The presence of this and similar amino acids is very important to protein structure. Explain why.

* The sulfhydryl group in one part of a polypeptide chain can covalently bond to a sulfhydryl in another region thus stabilizing a particular folding pattern in the mature protein.

13. Illustrate the formation of a peptide bond. Circle the atoms which combine to form water and draw the structural formula of the resulting dipeptide.

Use the space below to show the dipeptide.

 

14. Each carboxyl-amino linkage is a special covalent bond called a peptide bond, and the complete polypeptide has an N-terminal or amino end and a C-terminal or carboxyl end.

15. Proteins may have as many as four levels of organization, and most have at least three.

16. Describe the salient features of each level of protein structure

primary level = linear arrangement of amino acids held together by peptide bonds.

secondary level = coiling to form an alpha helix or beta pleated sheet due to hydrogen bonding.

tertiary level = highly specific folding into a three-dimensional structure.

(list the four principle forces responsible for tertiary structure)
  1. covalent bonds (sulfhydryl groups
  2. hydrogen bonds
  3. ionic bonds
  4. hydrophobic interactions

quaternary level = two or more polypeptides combined to form a functional protein.

17. The tertiary level of organization is possible because of regions in the polypeptide chain where the alpha helix does not form. Theses regions are called linker regions.

18. When a protein loses its functional 3D shape it is said to be denatured.

19. A common (and usually permanent) cause of this loss of protein function is excessively high temperatures. Other denaturing agents are __________, ____________, and certain chemicals (usually labeled toxin, or poison).

20. A simple protein contains only amino acids in one or more polypeptides. Many proteins are conjugated or bound in some way to some other chemical - something extra - called a prosthetic group.

21. List three types of conjugated proteins and their prosthetic group.

(a) glycoproteins have - carbohydrates

(b) chromoproteins have- pigments (heme for example)

(c) lipoproteins- lipids

22. The prosthetic group of a protein often determines function. For example the catalytic activities of many enzymes are dependent on a prosthetic group called a cofactor.

23. Many proteins function by temporarily binding to one molecule or another. Describe the importance binding has for the following molecules or substrates.

(a) oxygen - transport by hemoglobin from lungs to muscle cells

(b) antigen - binds to an antibody which protects against disease agents

(c) cell surface - transports food molecules into a cell

24. Structural proteins which maintain the physical form of vertebrates include the following extracellular varieties: collagen, elastin, and keratin.

25. Collagen makes up about 25% of the protein in humans is the connective tissue found in tendons, ligaments, and muscle coverings called sarcomeres.

26. Keratin is an intracellular protein forming the horny layer of dead skin cells. It is however found extracellularly as hair, feathers (birds), claws or nails (most mammals), horns (rhinoceros), antlers (deer), and scales (reptiles and birds)