BIOC 192 – Proteins Module Learning Objectives
1. Describe the chemical properties of amino acids.
Amino acids consist of a Nitrogen, alpha Carbon, and carboxyl Carbon. They
are chiral (except for glycine) and have R, S, D, and L configurations/isomers.
The 20 naturally occurring amino acids can be divided into charged polar,
uncharged polar, and non-polar based on their side chains. They are
zwitterionic and have no overall charge at their isoelectric point, pI.
2. How do amino acids join to form peptides?
Amino acids form peptide bonds, or amide bonds, between the N-terminus of
one amino acid and the C-terminus of the other. The reaction releases water
(condensation reaction), forming a bond between the carboxyl carbon and
nitrogen atom.
3. Describe the key properties of peptide bonds.
They are planar, rigid, partial double bonds, and usually trans (180˚).
4. Differentiate between primary, secondary, tertiary, and quaternary
structures.
The primary structure consists of the amino acid sequence. This makes up
secondary structures – patterns of 3D folding that then make up the tertiary
structures – the full 3D structure of a protein. Quaternary structures are
structures that are made up of multiple tertiary structures.
5. Describe the structure and properties of alpha helices.
Alpha helices are helical, twisting structures of amino acids. These have
hydrogen bonds between n and n+4 amino acids, and each turn consists of 3.6
amino acids (1.5Å). The side chains of amino acids point out of the helix, and
the helices often have polar amino acid chains on one side and non-polar
amino acid chains on the other side.
6. Describe the structure and properties of beta sheets.
Beta sheets consist of 2-10 beta strands which can either be orientated in the
parallel or antiparallel direction. These have hydrogen bonds between amino
acids in each chain, are pleated, and have a right-hand twist. The polar side
chains tend to face one direction while the non-polar side chains tend to face
the other direction.
7. What are the three most important bond angles in peptide chains? Describe
how each of these is important.
Phi (N-C), Psi (C-C’), and Omega (N-C’). These bond angles occur so that
steric hindrance is minimised. Certain phi and psi angles determine the
secondary structure of proteins.
, 8. What is the function of a protein ultimately dictated by?
The primary amino acid sequence (and the resulting 3D structure).
9. Describe the interactions that stabilise the tertiary structure of proteins.
Non-covalent interactions (hydrogen bonds, van der Waals, ionic bonds,
electrostatic, hydrophobic, metal ion coordination), covalent interactions
(sulphide bridges), and interactions with the aqueous environment.
10. What does Anfinsen’s experiment show?
That the tertiary structure of proteins is ultimately determined by the primary
sequence of amino acids.
11. What are the roles of chaperones in protein folding?
These help complex proteins fold into their final tertiary structure by keeping
structures separated until they are meant to bond.
12. Give some examples of misfolded proteins and the diseases associated with
them.
Misfolding of the PrP protein causes Kuru disease, Creutzfeld-Jacob’s disease,
and Bovine Spongiform Encephalopathy. PrP is a prion that is very resistant to
degradation. Amyloids are proteins that are misfolded to aggregate (but not
cause) diseases such as Alzheimer’s.
13. What do post-translational modifications provide in terms of diversity,
control, and complexity?
By increasing the number of proteins formed from one gene and increasing
the possible interactions they can form, we get an increase in diversity,
control, and complexity.
14. Name the three main types of post-translational modification and provide
examples of each.
Phosphorylation, hydroxylation, and gamma carboxylation. Phosphorylation is
used to activate insulin receptors and sodium-potassium pumps.
Hydroxylation is used to tightly pack collagen (particularly by hydroxylating
lysine and proline). Gamma carboxylation is used on glutamic acid to produce
gamma carboxyglutamic acid which plays a key role in blood clotting factors.
15. Describe how oxygen binds and releases from myoglobin and haemoglobin.
Haemoglobin binds to the haem iron (sixth coordination site) of myoglobin
and haemoglobin at high oxygen partial pressures. At low partial pressures of
oxygen (and usually high concentrations of allosteric factors) the oxygen
molecule is released by breaking the bind to the haem iron.
16. How is myoglobin adapted to act as an oxygen storage molecule?
Myoglobin has a high affinity for oxygen, even at low partial pressures of
oxygen. This means that it doesn’t readily release oxygen – it stores it.
1. Describe the chemical properties of amino acids.
Amino acids consist of a Nitrogen, alpha Carbon, and carboxyl Carbon. They
are chiral (except for glycine) and have R, S, D, and L configurations/isomers.
The 20 naturally occurring amino acids can be divided into charged polar,
uncharged polar, and non-polar based on their side chains. They are
zwitterionic and have no overall charge at their isoelectric point, pI.
2. How do amino acids join to form peptides?
Amino acids form peptide bonds, or amide bonds, between the N-terminus of
one amino acid and the C-terminus of the other. The reaction releases water
(condensation reaction), forming a bond between the carboxyl carbon and
nitrogen atom.
3. Describe the key properties of peptide bonds.
They are planar, rigid, partial double bonds, and usually trans (180˚).
4. Differentiate between primary, secondary, tertiary, and quaternary
structures.
The primary structure consists of the amino acid sequence. This makes up
secondary structures – patterns of 3D folding that then make up the tertiary
structures – the full 3D structure of a protein. Quaternary structures are
structures that are made up of multiple tertiary structures.
5. Describe the structure and properties of alpha helices.
Alpha helices are helical, twisting structures of amino acids. These have
hydrogen bonds between n and n+4 amino acids, and each turn consists of 3.6
amino acids (1.5Å). The side chains of amino acids point out of the helix, and
the helices often have polar amino acid chains on one side and non-polar
amino acid chains on the other side.
6. Describe the structure and properties of beta sheets.
Beta sheets consist of 2-10 beta strands which can either be orientated in the
parallel or antiparallel direction. These have hydrogen bonds between amino
acids in each chain, are pleated, and have a right-hand twist. The polar side
chains tend to face one direction while the non-polar side chains tend to face
the other direction.
7. What are the three most important bond angles in peptide chains? Describe
how each of these is important.
Phi (N-C), Psi (C-C’), and Omega (N-C’). These bond angles occur so that
steric hindrance is minimised. Certain phi and psi angles determine the
secondary structure of proteins.
, 8. What is the function of a protein ultimately dictated by?
The primary amino acid sequence (and the resulting 3D structure).
9. Describe the interactions that stabilise the tertiary structure of proteins.
Non-covalent interactions (hydrogen bonds, van der Waals, ionic bonds,
electrostatic, hydrophobic, metal ion coordination), covalent interactions
(sulphide bridges), and interactions with the aqueous environment.
10. What does Anfinsen’s experiment show?
That the tertiary structure of proteins is ultimately determined by the primary
sequence of amino acids.
11. What are the roles of chaperones in protein folding?
These help complex proteins fold into their final tertiary structure by keeping
structures separated until they are meant to bond.
12. Give some examples of misfolded proteins and the diseases associated with
them.
Misfolding of the PrP protein causes Kuru disease, Creutzfeld-Jacob’s disease,
and Bovine Spongiform Encephalopathy. PrP is a prion that is very resistant to
degradation. Amyloids are proteins that are misfolded to aggregate (but not
cause) diseases such as Alzheimer’s.
13. What do post-translational modifications provide in terms of diversity,
control, and complexity?
By increasing the number of proteins formed from one gene and increasing
the possible interactions they can form, we get an increase in diversity,
control, and complexity.
14. Name the three main types of post-translational modification and provide
examples of each.
Phosphorylation, hydroxylation, and gamma carboxylation. Phosphorylation is
used to activate insulin receptors and sodium-potassium pumps.
Hydroxylation is used to tightly pack collagen (particularly by hydroxylating
lysine and proline). Gamma carboxylation is used on glutamic acid to produce
gamma carboxyglutamic acid which plays a key role in blood clotting factors.
15. Describe how oxygen binds and releases from myoglobin and haemoglobin.
Haemoglobin binds to the haem iron (sixth coordination site) of myoglobin
and haemoglobin at high oxygen partial pressures. At low partial pressures of
oxygen (and usually high concentrations of allosteric factors) the oxygen
molecule is released by breaking the bind to the haem iron.
16. How is myoglobin adapted to act as an oxygen storage molecule?
Myoglobin has a high affinity for oxygen, even at low partial pressures of
oxygen. This means that it doesn’t readily release oxygen – it stores it.
