BIOC 192 – Proteins Worksheet Answers
1. Describe the main differences between primary, secondary, tertiary, and
quaternary protein structures.
Primary structure describes the amino acid sequence of a protein. Secondary
structure describes patterns of 3D folding in proteins. Tertiary structures are the
complete 3D structures of a single sequence – the combination of secondary
structures. Quaternary structures are a combination of tertiary proteins.
2. Name some ways in which interactions between a molecule and a protein can be
prevented.
Decrease concentration of the molecule or degrade it.
Introduce a molecule with higher binding affinity for the active site.
Change the environment (pH, temperature)
Bind something to the substrate.
Change the shape of the binding site by adding functional groups.
Bind a regulatory molecule that changes the protein’s shape.
3. What is the effect of lowering pH on protein interactions?
Lower pH means higher H+ concentration. The hydrogen ions will neutralise negative
charges, therefore decreasing interactions with positively charged molecules.
4. Why are prolines ‘imino acids’ rather than ‘amino acids’?
The side chain of proline ‘folds back on itself’ and binds to the amine group of the
molecule in a ring structure, so it doesn’t have a free amino group.
5. What is the isoelectric point?
The isoelectric point is the point at which the molecule is zwitterionic – the amine
group is positively charged and the carboxyl group is negatively charged, giving an
overall neutral charge.
6. Name some post-translational modifications:
Phosphorylation
Gamma carboxylation
Glycosylation
Hydroxylation
7. Peptide bonds are: planar/pyramidal, cis/trans, and single/partial double bonds.
,8. State which atoms each of the following bond angles exist between:
Phi: N - Calpha
Psi: Calpha – C’
Omega: N – C’
Chi: Carbons of side chains.
9. What does the Ramachandran plot show?
The possible combinations of psi and phi bonds in an amino acid.
10. Label the following diagram with the angles that exist for: antiparallel beta sheets,
parallel beta sheets, right alpha helices, and left alpha helices.
11. What is the usual angle for the omega bond? 180˚.
12. Describe the interactions found in alpha helices that stabilise the helix.
Hydrogen bonds between n and n+4 amino acids stabilise the alpha helix, between
the partially negative O atom and partially positive H atom.
13. Which amino acids are not usually found in alpha helices? Why is this?
Proline and glycine tend not to occur in alpha helices. Glycine molecules tend to
introduce turns that are too sharp and proline is too large.
14. Describe the structure of beta sheets.
Beta sheets consist of 2-10 beta strands joined together with turns or loops. They
can occur in the parallel or antiparallel direction and are stabilised by hydrogen
bonds between opposite strands. They are pleated and have a right-hand twist.
15. What are supersecondary structures?
Structures made up of multiple elements secondary structures with a distinct
pattern, for example helix-turn-helix or strand-helix-strand.
, 16. What are domains/motifs?
Domains and motifs are made up by supersecondary structures to give a distinct
structure with a specific function.
17. Name and give examples of the three main types of domain.
Alpha domains: four helix bundles, globin folds.
Alpha/beta domains: alpha/beta barrel or open twisted sheet.
Antiparallel beta domains: antiparallel beta barrels.
18. What is the function of chaperones and chaperonins?
Chaperones are important in preventing misfolding of proteins. They keep segments
of proteins from binding while they’re being produced until it is the correct time to
bind. Chaperonins are larger, more complex structures that assist folding of larger
and more complex proteins.
19. Name some conditions under which denaturation can occur.
Denaturation occurs at extremely high/low pH and high temperatures. Adding
detergents, urea, and organic solvents also causes denaturation.
20. What is the difference between prions and amyloids?
Prions are misfolded proteins that directly cause disease, while amyloids are
misfolded proteins that aggregate the disease but do not cause it.
21. What are the two main categories of post-translational modifications?
Addition of a chemical group and covalent hydrolysis of a peptide bond.
22. Describe how phosphorylation occurs.
Phosphorylation is the process of adding a phosphate to change the conformation of
a protein to switch it on/off, often Ser, Thr, and Tyr. This is catalysed by kinase, while
dephosphorylation is catalysed by phosphatase.
23. Give an example of where phosphorylation is used in the body.
In Na+/K+ ATPase.
24. Where in the body is gamma carboxylation used as a PTM?
In clotting proteins in the blood.
25. What co-factor does gamma carboxylation require for Gla->Glu conversion?
Vitamin K.
26. Where in the body is hydroxylation most commonly used?
In connective tissue proteins, particularly collagen.
1. Describe the main differences between primary, secondary, tertiary, and
quaternary protein structures.
Primary structure describes the amino acid sequence of a protein. Secondary
structure describes patterns of 3D folding in proteins. Tertiary structures are the
complete 3D structures of a single sequence – the combination of secondary
structures. Quaternary structures are a combination of tertiary proteins.
2. Name some ways in which interactions between a molecule and a protein can be
prevented.
Decrease concentration of the molecule or degrade it.
Introduce a molecule with higher binding affinity for the active site.
Change the environment (pH, temperature)
Bind something to the substrate.
Change the shape of the binding site by adding functional groups.
Bind a regulatory molecule that changes the protein’s shape.
3. What is the effect of lowering pH on protein interactions?
Lower pH means higher H+ concentration. The hydrogen ions will neutralise negative
charges, therefore decreasing interactions with positively charged molecules.
4. Why are prolines ‘imino acids’ rather than ‘amino acids’?
The side chain of proline ‘folds back on itself’ and binds to the amine group of the
molecule in a ring structure, so it doesn’t have a free amino group.
5. What is the isoelectric point?
The isoelectric point is the point at which the molecule is zwitterionic – the amine
group is positively charged and the carboxyl group is negatively charged, giving an
overall neutral charge.
6. Name some post-translational modifications:
Phosphorylation
Gamma carboxylation
Glycosylation
Hydroxylation
7. Peptide bonds are: planar/pyramidal, cis/trans, and single/partial double bonds.
,8. State which atoms each of the following bond angles exist between:
Phi: N - Calpha
Psi: Calpha – C’
Omega: N – C’
Chi: Carbons of side chains.
9. What does the Ramachandran plot show?
The possible combinations of psi and phi bonds in an amino acid.
10. Label the following diagram with the angles that exist for: antiparallel beta sheets,
parallel beta sheets, right alpha helices, and left alpha helices.
11. What is the usual angle for the omega bond? 180˚.
12. Describe the interactions found in alpha helices that stabilise the helix.
Hydrogen bonds between n and n+4 amino acids stabilise the alpha helix, between
the partially negative O atom and partially positive H atom.
13. Which amino acids are not usually found in alpha helices? Why is this?
Proline and glycine tend not to occur in alpha helices. Glycine molecules tend to
introduce turns that are too sharp and proline is too large.
14. Describe the structure of beta sheets.
Beta sheets consist of 2-10 beta strands joined together with turns or loops. They
can occur in the parallel or antiparallel direction and are stabilised by hydrogen
bonds between opposite strands. They are pleated and have a right-hand twist.
15. What are supersecondary structures?
Structures made up of multiple elements secondary structures with a distinct
pattern, for example helix-turn-helix or strand-helix-strand.
, 16. What are domains/motifs?
Domains and motifs are made up by supersecondary structures to give a distinct
structure with a specific function.
17. Name and give examples of the three main types of domain.
Alpha domains: four helix bundles, globin folds.
Alpha/beta domains: alpha/beta barrel or open twisted sheet.
Antiparallel beta domains: antiparallel beta barrels.
18. What is the function of chaperones and chaperonins?
Chaperones are important in preventing misfolding of proteins. They keep segments
of proteins from binding while they’re being produced until it is the correct time to
bind. Chaperonins are larger, more complex structures that assist folding of larger
and more complex proteins.
19. Name some conditions under which denaturation can occur.
Denaturation occurs at extremely high/low pH and high temperatures. Adding
detergents, urea, and organic solvents also causes denaturation.
20. What is the difference between prions and amyloids?
Prions are misfolded proteins that directly cause disease, while amyloids are
misfolded proteins that aggregate the disease but do not cause it.
21. What are the two main categories of post-translational modifications?
Addition of a chemical group and covalent hydrolysis of a peptide bond.
22. Describe how phosphorylation occurs.
Phosphorylation is the process of adding a phosphate to change the conformation of
a protein to switch it on/off, often Ser, Thr, and Tyr. This is catalysed by kinase, while
dephosphorylation is catalysed by phosphatase.
23. Give an example of where phosphorylation is used in the body.
In Na+/K+ ATPase.
24. Where in the body is gamma carboxylation used as a PTM?
In clotting proteins in the blood.
25. What co-factor does gamma carboxylation require for Gla->Glu conversion?
Vitamin K.
26. Where in the body is hydroxylation most commonly used?
In connective tissue proteins, particularly collagen.
