Biochem Chapter 4: Protein 3D Structure

6. Why is rotation about the peptide bond prohibited, and what are the consequences of the lack of rotation?

The peptide bond has partial double bond character, which prevents rotation. This lack of rotation constrains the conformations of the peptide backbone and limits possible structures.

15. List some of the difference between a-helix and B-strand.

A- HELIX: is a condensed, coiled structure, with R groups bristling outwards from the axis of the helix. The distance between two adj aa is 1.5. B-STRAND: a fully extended poplypeptide chain, side chains of the aa point in opposite directions, distance between adj aa is 4.5. Both structures are stabilized by hydrogen bonding between components of the polypeptide backbone.

13. Differentiate between amino acid composition and amino acid sequence

Composition - the amino acids that make of the protein Sequence- is the same as the primary structure, the sequence of amino acids from the amino terminal to the carboxyl terminal.

25. The shape of hair is determined in part by the pattern of disulfide bonds in keratin, its major protein. How can curls be induced.

Disulfide bonds in hair are broken by adding thiol-containing regent and applying gentle heat. the hair is curled and an oxidizing agent is added to reform disulfide bonds to stabilize the desired shape.

23. Glycine is a highly conserved amino acid in the evolution of proteins. Why?

Glycine has the smallest side chain which is often essential for peptide chains to make tight turns or closely approach one another

28. The a and B subunits of hemoglobin bear a remarkable structural similarity to myoglobin. However, in the subunits of the hemoglobin, residues that are hydrophilic in myoglobin are hydrophobic. Why?

Hemoglobin is a tetramer, myoglobin is a monomer. The hydrophobic residues on the surface of hemoglobin subunits probably takes part in Van der Waals interactions with similar regions of the other subunits and are sheilded from the water environment by these interactions.

21. Many of the loops on the proteins that have been described are composed of hydrophilic amino acids, WHY?

Loops tend to be surface proteins, exposed to the environment. Because many proteins exist in an aqueous environment, the exposed loops are hydrophilic so as to interact with the water.

18. Would you expect Pro-X-peptide bonds to tend to have cis formations like those of X-Pro bonds? Why or why not?

No The pro-X bond would have the characteristics of any other peptide bond. The steric hinderance in X-pro arises because the R group of Pro is bonded to the amino group. Hence in X-pro, the proline R group is near the R groups of X, which would not be in the case of Pro-X

16. What are the levels of protein structure? Describe the type of bonds characteristics of each level

Primary - peptide bond Secondary - local hydrogen bonds between compenents of the polypep backbone Tertiary - varies types of noncovalent bonds between R groups that are very far apart in the primary structure Quaternary - various noncovalent bonds between R groups on the surface of subunits

12. Define the term "side chain" in the context of amino acid or protein structure.

Side chain is the functional group attacked to the alpha carbon atom of an amino acid

27. Proteins that span biological membranes often contain a-helices. Given the insides of membranes are highly hydrophobic, predict what type 0f amino acids will be in such a helix. What is an a-helix particularly suitable for existence in the hydrophobic environment of the interior of a membrane.

The aa would be hydrophobic in nature. An alpha helix is especially suitable for crossing a membrane because all of the amide hydrogen atoms and carbonyl oxygen atoms of the peptide backbone take part in intrachain hydrogen bonds, thus stabilizing these polar atoms in a hydrophobic environment.

1. How can you account for the stability of the peptide bond in light of the fact that hydrolysis releases considerable energy?

The energy barrier that must be crossed to go from the polymerized state to the hydrolyzed state is large even though the reaction is thermodynamically favorable.

20. A mutation that changes an alanine residue in the interior of a protein into valine is found to lead to loss of activity. However, activity is regained when a second mutation at a different position changes an isoleucine to glycine. How might this second mutation lead to a restoration of activity?

The first mutation destroys the activity because valine occupies more space than alanine does, and so the protein must take a difference shape, assuming that this residue lies in the closely packed interior. The second mutation restores activity because of a compensatory reduction in volume. Glycine is smaller than isoleucine

11. What is meant by the term polypeptide backbone?

The nitrogen - alpha carbon - corbonyl carbon repeating unit

22. How would each of the following treatments contribute to protein denaturation? a. heat b. addition of hydrophobic detergents c. large changes in pH

a. increases the thermal energy in the chain. the weak bonds holding the chain in the correct form would not be able to withstand the wiggling of the backbone, and the tertiary structure would be lost. Often the denatured chains would interact with each other, forming large complexes b. detergents turn the protein inside out. the hydrophobic interior of the protein would interact with the detergent, whereas the hydrophilic residue would interact with one another and not with the environment. c. all ionic interactions, not just hydrogen bonding, would be disrupted, resulting in protein denature.

7. Matching! a. primary structure b. peptide (amide bond) c. disulfide bond d. phi angle e. psi angle f. Ramachandran plot g. a helix h B pleated sheet i. B strand j. secondary structure 1. forms between two cysteine amino acids 2. a rodlike structure with a tightly coiled backbone 3. angle of rotation about the bond between the N atom and the a-carbon 4. fully extended polypeptide chain 5. formed by hydrogen bonds between parallel or antiparallel chains 6. regular repeating 3D structures 7. the bond responsible for primary structures 8. sequence of amino acids in protein 9. angle of rotation between the alpha carbon and the carbonyl carbon atom 10. a plot of phi and psi angles

a. primary structure- sequence of amino acids in a protein b. pepside(amide) bond - the bond responsible for primary structures. c. disulfide bond - forms between two cysteine amino acids d. phi angle - the angle of rotation about the bond between the N atom and the alpha carbon e. psi angle- angle of rotation between the alpha carbon and the carbonyl carbon atom f. Ramachandran plot - a plot of phi and psi angles g. alpha helix - a rod like structure with a tightly coiled backbone h. B pleated sheet - formed by hydrogen bonds between parallel or antiparallel chains. i. B strand - a fully extended polypeptide chain. j. secondary structure - regular repeating 3D structures

17. MATCHING a. tertiary structure b. supersecondary structure c. domain d. subunit e. quaternary structure f. folding funnel g. molten globule h. metamorphin protein i. intrisically unstructured protein j. prion 1. basic component of quaternary structure 2. an energy landscape 3. structure characterized by dynamic hydrophobic interactions 4. proteins that in whole or in part lack discrete 3D structure under physiological conditions 5. refers to the spacial arrangement of amino acid residues that are far apart in sequence 6. proteins that exist in an ensemble of structures of approximately equal energy that are in equilibrium 7. compact regions that may be connected by a flexible segment of polypeptide side chain 8. refers to the arrangement of subunits and the nature of their interactions 9. cause of spongiform encephalopathies 10. combinations of secondary structure are present in many proteins.

a. tertiary structure - refers to the spacial arrangement of amino acid residues that are far apart in sequence b. supersecondary structure - combination of secondary structure that are present in many proteins c. domain - compact regions that may be connected by a flexible segment of polypeptide side chain. d. subunit - basic component of quaternary structure e. quaternary structure - refers to the arrangement of subunits and the nature of their interactions f. folding funnel - an energy landscape g. molten globule - structure characterized by dynamic hydrophobic interactions h. metamorphin protein - proteins that exist in an ensemble of structures of approximately equal energy that are in equilibrium i. intrisically unstructured protein - proteins that lack discrete 3D structures under physiological conditions j. prion - causes of spongiform encephalopathies

14. List some of the benefits of knowing the primary structure of the protein

knowing primary structure reveals the function of the protein. knowledge of the primary structure of mutated proteins enables an understanding of the biochemical basis of some diseases. can reveal evolutionary history of a protein

5. Table 3.1 gives typical pKa values for ionizable groups in proteins. However, more than 500p Ka values have been determined for individual groups in proteins. Account of the discrepancy.

pKa values are affected by the environment. A given amino acid can have a variety of pKa values, depending on the chemical environment inside of the protein.

29. Osteogensis imperfecta displays a wide range of symptoms, from the mild to the severe. On the basis of your knowledge of amino acids and collagen structure, propose a biochemical basis for the variety of symptoms.

severity of symptoms probably corresponds to degree of structural disruption. subbing alanine for glycine might result in mild symptoms, but the substitution of a larger tryptophan might prevent little or no collagen triple helix formation

26. Most proteins have hydrophillic exteriors and hydrophobic interiors. Would you expect this structure to apply to proteins embedded in the hydrophobic interior of a membrane? Explain.

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