Supplemental Lecture (97/02/06 update) by Stephen T. Abedon (abedon.1@osu.edu)

  1. Chapter title: Proteins
    1. A list of vocabulary words is found toward the end of this document
    2. From their primary structure through their quaternary structure, from translation into chains of amino acids through their ultimate demise and denaturation, proteins are the most complex and sophisticated molecules known. Nothing less would do for controlling nearly every aspect of metabolism and biochemistry (as do those protein catalysts known as enzymes), as well as serving as proteinaceous but non-enzymatic regulators of metabolism. Proteins also play crucial structural and cell-to-cell signaling roles. Though not necessarily defining life, nothing goes farther in defining the complexity life is capable of than protein molecules.
  2. Protein
    1. Proteins are macromolecules (poly-amino acids) responsible for the bulk of the expression of an organism's phenotype (i.e., what you can see and sense of an organism--as opposed to simply the coded information contained in a organism's hereditary material).
    2. One important class of proteins are enzymes. There are many other kinds of proteins with many other roles including structural, regulatory, toxins, hormonal, etc.
  3. Amino acid
    1. The building blocks of proteins. Proteins are linear polymers of as many as hundreds of amino acids.
    2. Amino acids take their names from their structure which consists of an amino group (-NH2) and a carboxy group (-COOH) connected through a central carbon. Most amino acids (proline is the exception) have the formula 2HN-CHR-COOH where R is a variable side chain (i.e., attached to the central carbon):
      3. H   R OH 
\  | |  
N-C-C=O
/  |    
H   H
    3. R groups:
      1. There are 20 naturally occurring amino acids. That is, variations on R, that are incorporated into proteins (See text figure 1035.1).
    4. Amino acid R groups can be:
      1. nonpolar,
      2. hydrophilic (both ionizable and not ionizable), or
      3. have a variety of very diverse structures and special functions.
    5. All of these differences between R groups impact on the structure of proteins.
    6. Protein structural complexity:
      1. Because of variation among R groups, amino acids have diverse structures that define their roles in proteins.
      2. Stemming from this diversity among its building blocks, proteins have extremely complex structures which, per individual protein, typically require a great deal of effort to successfully discover and define.
  4. Zwitterion [dipolar ion]:
    1. Dissociation of the amino and carboxy groups occurs at physiological pH (i.e., approximately pH7).
    2. Consequently, amino acids tend to exist doubly ionized (below). Double ionized ions such as these are known as dipolar ions or Zwitterions. 
    H   R OH            H R O- 
 \  | |             | | |  
  N-C-C=O ------ +H-N-C-C=O
 /  |               | |    
H   H               H H
  5. Essential amino acids
    1. Some but not all organisms are able to synthesize all 20 amino acids directly from intermediates of carbohydrate metabolism.
    2. Those organisms which are unable to synthesize all 20 amino acids must obtain the amino acids they are not able to synthesize (or, in some cases, their anabolic intermediates) from their environment (e.g., food).
    3. These obligately environmentally obtained amino acids are called essential in that growth and ability to thrive is defective in their absence.
  6. Peptide bond [peptide]
    1. The bond that links amino acids together to form proteins (see illustration below).
    2. Individual peptide bonds are formed by a condensation reaction between two amino acids. The resulting molecule, consisting of two or more amino acid monomers, is called a peptide.
    3. Note that due to resonance, the peptide bond takes on a partial double bond character resulting in these bonds being more resistant to rotation (i.e., stiffer) than might otherwise be expected.
    4. See illustration below.
  7. Illustration, peptide bond

  8. Illustration, partially double peptide bond
  9. Di-, and tri- peptides and polypeptides
    1. Linear polymers of amino acids made up from 2 (dipeptide), 3 (tripeptide), or more than 3 amino acids (polypeptide).
    2. People use the term polypeptide and protein more or less interchangeably when referring to proteins consisting of a single subunit.
  10. Peptide polarity
    1. Note the polarity of the dipeptide formed above. That is, one end has an -NH2 group and the other a -C00H group and therefore the amino acids are arranged R to R' in the -NH2 to -C00H direction.
    2. When mRNAs are translated (i.e., synthesized) into polypeptides, the first end produced is the amino (-NH2) end. That is, new amino acids are added one by one to the -COOH end. 
      3.   R'    R''          R'''           R'    R''   R'''  
  |     |            |              |     |     |     
H-N-C-C-N-C-C-OH + H-N-C-C-OH -- H-N-C-C-N-C-C-N-C-C-OH
  | ||| | |||        | |||          | ||| | ||| | |||   
  H H O H H O        H H O          H H O H H O H H O
    3. The same figure as that directly above, but with the "below the chain" hydrogens removed (i.e., ignored) for the sake of clarity, is shown as follows: 
      4. R'    R''          R'''           R'    R''   R'''  
|     |            |              |     |     |     
H-N-C-C-N-C-C-OH + H-N-C-C-OH -- H-N-C-C-N-C-C-N-C-C-OH
||    ||           ||             ||    ||    ||   
O     O            O              O     O     O
    4. Polypeptides thus are synthesized in the -NH2 to -COOH direction (i.e., we speak of the sequence of a polypeptide in terms where the first amino acid "added" is in the first position, the second added is in the second position, etc.). By convention polypeptides are consequently listed and read in the -NH2 to -COOH direction, e.g., as follows (a random sequence of amino acids):
          1     2     3     4     5     6     7       
2HN-(ala)-(lys)-(thr)-(ser)-(ser)-(lys)-(leu)-COOH
  11. Protein primary structure
    1. The sequence of amino acids in a polypeptide.
    2. Note that amino acids have polarity (i.e., 2HN-CHR-COOH), are always linked in the same orientation in a given polypeptide by a peptide bond, and polypeptides are linear polymers. Consequently, the primary structure of a protein has polarity.
    3. The next higher level of structure is called secondary structure.
    4. See text figure 1035.2.
  12. Protein secondary structure [Alpha helix, Beta sheet]
    1. Repetitive folding of a polypeptide chain into certain types of consistent structure.
    2. These secondary structures are known as alpha helices and beta sheets.
    3. The next higher level of structure is called tertiary structure.
    4. See text figure 1035.2.
  13. Protein tertiary structure
    1. The complete 3-dimensional structure (in addition to the repetitive structures described as secondary structure) of a folded polypeptide.
    2. The next higher level of structure is called quaternary structure.
    3. See text figure 1035.2.
  14. Protein quaternary structure
    1. More than one polypeptide:
      1. The 3-dimensional structure of more than one polypeptide chain which are intimately nestled together to form a multi-subunit protein.
      2. Note that whereas the minimum number of polypeptides necessary to display primary, secondary, or tertiary structure is one, a protein must be made up of at least two polypeptides before it may display quaternary structure.
    2. See text figure 1035.2.
  15. Multi-subunit protein
    1. Two or more polypeptide chains that operate as a single, functional unit. Each of the polypeptide chains is referred to as a subunit. The entire grouping of polypeptides is considered to be a single protein.
  16. Conjugated protein
    1. A protein that consists of more than just polymers of amino acids. Such things as sugars, nucleic acids, metal atoms, lipids, or phosphate groups may be bound to a protein to form a conjugated protein.
  17. Glycoprotein
    1. A protein conjugated to a carbohydrate.
  18. Lipoprotein
    1. A protein conjugated to a lipid.
  19. Denaturation
    1. A process of destruction of a protein's higher order structure (i.e., secondary structure and above).
    2. Denaturation may be effected by temperature, salt concentrations, or extremes of pH. The classic example of denaturation is the denaturation of egg albumen you effect (i.e., make happen) when cooking breakfast.
    3. As protein complexity increases, the likelihood that proper refolding (a.k.a., renaturation) may occur becomes less likely. This is because the steps a polypeptide chain must take to properly fold are often sequential and assisted by other proteins.
    4. Thus, denaturation is often or usually synonymous with permanent loss of protein function.
  20. Links
    1. Proteins: Structure and Diversity (Molecular Biology for Beginners)
    2. Principles of Protein Structure
  21. Vocabulary
    1. Alpha helix
    2. Amino acid
    3. Beta sheet
    4. Conjugated protein
    5. Denaturation
    6. Dipeptide
    7. Essential amino acids
    8. Glycoprotein
    9. Lipoprotein
    10. Multi-subunit protein
    11. Partially double peptide bond, illustration
    12. Peptide bond
    13. Peptide bond, illustration
    14. Peptide polarity
    15. Polypeptide
    16. Primary structure
    17. Protein
    18. Quaternary structure
    19. Secondary structure
    20. Tertiary structure
    21. Tripeptide
    22. Zwitterion
  22. Practice questions
    1. Which is not true about amino acids? (circle correct answer) [PEEK]
      1. 20 naturally occurring
      2. diverse structures
      3. R groups are all non-polar
      4. proteins consist of linear, amino acid polymers
      5. all of the above
      6. none of the above
    2. What is the minimum number of polypeptides that must be found in a protein exhibiting tertiary structure? [PEEK]
    3. Draw a tripeptide having R groups consisting of -CH3, -H, and -CHCH3CH3. [PEEK]
    4. A process that destroys protein quaternary structure, tertiary structure, secondary structure, and function, but not primary structure, may be described (generally) as? [PEEK]
    5. When a protein is dissolved in water, the amino acids found in its interior are likely to have R groups which are (circle correct answer) [PEEK]
      1. hydrophilic
      2. charged
      3. highly reduced
      4. polar
      5. all of the above
      6. none of the above
    6. Tell me the specific name of an actual protein (e.g., collagen is a protein---don't use collagen as an answer). [PEEK]
    7. A protein can contain hundreds of amino acid monomers, but how many different kinds of naturally occurring amino acids are there? [PEEK]
    8. Name the type of biomolecule responsible for directly displaying or directly catalyzing most of the chemical complexity you associate with biological systems. [PEEK]
    9. What chemical aspect of amino acids results in their having different properties such that the chemical and physical properties of polypeptides vary with both amino acid content and amino acid order? (short answer, less than 10 words) [PEEK]
    10. According to convention (and because this is the order in which polypeptides are synthesized), __________ is the order that amino acids are numbered in chains. [PEEK]
      1. amino to carboxy.
      2. carboxy to amino.
      3. 5' to 3'.
      4. 3' to 5'.
      5. 5 to 3.
      6. 3 to 5.
    11. Give the name of one type of protein secondary structure. (short answer, less than 5 words) [PEEK]
    12. Due to resonance the peptide bond is actually intermediate in properties between those associated with a single bond and those associated with a double bond. In what way do you think this might affect the polypeptides, for example, as they fold into their native (i.e., normal/natural) structure? (short answer, less than 10 words) [PEEK]
  23. Practice question answers
    1. iii, R groups are (not) all nonpolar
    2. one
    3. See illustration below:
      4.   3HC O   H O   CHCH3CH3
  | ||  | ||  |           
H-N-C-C-N-C-C-N-C-COOH      
  | |   | |   | |           
  H H   H H   H H
    4. Denaturation
    5. iii, highly reduced
    6. RNA polymerase, lysozyme, phosphofructokinase, etc.
    7. 20
    8. proteins, enzymes OK.
    9. R groups.
    10. i, amino to carboxy; i.e., from the amino end (start numbering) through the carboxy end (stop numbering).
    11. alpha helix or beta pleated sheet.
    12. stiffens the backbone thus further limiting the total number of conformations it is able to explore during folding.
  24. References
    1. Raven, P.H., Johnson, G.B. (1995). Biology (updated version). Third Edition. Wm. C. Brown publishers, Dubuque, Iowa. pp. 50-56.