17. 3D structure of proteins

Question 1

Describe the folding of the polypeptide chain? (2pts)

Answer 1

1. Functionality of a protein is dependant upon the 3D arrangement of the polypeptide chain.
2. Folding of a polypeptide chain is determined by:
3. The amino acid sequence
4. The molecular structure and properties of its amino acid.
5. The molecular environment

Question 2

Describe Amino acid categories?

Answer 2

Amino acids fall into categories defined by:

1. Structural and chemical properties
2. Classification is hierarchal
3. The nomenclature and classification will vary in different text books but are fundamentally similar and broadly consistent based upon logical rules.

Question 3

Describe charged amino acids (3pts)

Answer 3

1. Charged amino acids contain charged groups in their variable side chains.
2. e.g aspartic acid, lysine
3. Charged molecules can be subdivided into acids or bases and are polar in nature.

Question 4

Describe the difference between polar and non-polar amino acids ?

Answer 4

The difference between polar and non-polar amino acids is that they contain nitrogen and oxygen as part of carbonyl and amine groups.

Question 5

Describe the variable side chain? (2pts)

Answer 5

1. The variable side chain contains amino acids that confer acidic, basic hydrophobic or polar properties.
2. e.g aparagine is a polar molecule and the side chain contains groups that have an uneven charged distribution.

Question 6

Describe a polypeptide chain? (3pts)

Answer 6

1. Amino acid residues are arranged in a trans conformation- alternating arrangement.
2. Each repeating unit of the polypeptide chain is joined by a peptide bond.
3. The variable side chain R is usually arranged in a trans conformation.

Question 7

Describe the peptide bond? (5pts)

Answer 7

1. Delocalised electrons of the N-Co makes the bond ridged with the oxygen and hydrogen atoms on opposite sides.
2. Peptide bond is a planar structure
3. Rotational freedom within a polypeptide is found around the alpha carbon.
4. Amide C-N bond is rigid due to its partial double-bond characteristic.
5. Adjacent C-C and N-C bonds can undergo torsional-rotational motions resulting in the folding of the chain.

Question 8

Describe rotational freedom? (2pts)

Answer 8

1. Rotational freedom of the bonds allows huge variation in the conformation of the peptide chain.
2. This freedom favours the formation of structural arrangements such as alpha helices and beta sheets.

Question 9

Describe energy minimisation? (3pts)

Answer 9

1. Each molecule has a specific energetic state.
2. (G) The free energy of a molecule= The minimisation of the energetic state. This determines the most favourable arrangement of the atoms.
3. △G= the change in free energy upon folding. If it is negative then the molecule will spontaneously fold.

Question 10

How is the free energy of any conformation affected? (3pts)

Answer 10

1. The molecular environment. If it is aqueous or a lipid.
2. Other proteins or molecules including salts and their iconic state.
3. Changes in this environment can induce a further conformational change for example association with cofactors or binding a ligand.

Question 11

Describe structural stability? (2pts)

Answer 11

1. Bonds determine structural stability
2. Covalent bonds are stronger than non-covalent bonds however the significance of non-covalent bonds is greater because they are larger in number.

Question 12

Describe non-covalent bonds? (4pts)

Answer 12

1. Electrostatic forces of attraction- occurs between oppositely charged ions.
2. Hydrogen bonds- occurs between hydrogen atoms.
3. VDW forces- occurs between two atoms.
4. Hydrophobic interactions- in polar molecules such as water.

Question 13

Describe Van der Waal forces of attraction? (3pts)

Answer 13

1. Attraction at a close distance is balanced by repulsion due to proximity that is determined by the van der waals radius of an atom.
2. Van der waals forces are induced by proximity of molecules.
3. Repulsion= attraction

Question 14

Describe Disulphide bonds? (5pts)

Answer 14

1. Disulphide bonds form between the side chains of 2 cytesine residues
2. Bonds form in an oxidative reaction.
3. The SH groups from each cysteine cross link.
4. Usually occurs in distant parts of the primary sequence but adjacent in the 3rd structure.
5. Can form on the same (intra-chain) or different (iter-chain).

Question 15

Why does Folding occur?

Answer 15

Folding occurs in order to minimise the energy of a molecule and form the structure with the lowest free energy

Question 16

Describe Protein misfolding? (3pts)

Answer 16

1. The function of the mis-folded protein is always lost or reduced.
2. Mis-folded proteins have a tendency to self-associate and form aggregates.
3. e.g.
   - Huntingtons disease= Huntington hill self aggregates
   - Alzheimers disease- Amyloid beta protein self aggregates

Question 17

Describe the 6 misfolding reasons? (6pts)

Answer 17

1. Somatic mutations- in the gene sequence leading to the production of a protein unable to adopt the native folding.
2. Errors in transcription or translation- leading to the production of modified proteins unable to properly fold.
3. Failure of the folding machinery
4. Mistakes of the post-translational modifications or in trafficking of proteins.
5. Structural modifications produced by environmental changes.
6. Induction protein mis-folding.

Question 18

Describe the Amyloid precursor protein (APP) ? (4pts)

Answer 18

1. In Alzheimers disease proteolytic cleavage of APP is observed.
2. APP has multiple functions but is involved in G-protein signalling.
3. Cleavage of APP results in a 40 residue peptide beta amyloid being released.
4. In the intact molecule this anchors the protein in the membrane, APP accumulates and mis-folds to form beta sheets.

Question 19

Describe Alzheimers disease? (4pts)

Answer 19

1. In Alzheimers disease the B-amyloid peptide accumulates.
2. Mis folding of this proteins results in a planar arrangement and polymerisation.
3. This forms amyloid fibres
4. B-Amyloid fibres are formed from stacked beta sheets in which the side chains interdigitate.

Question 20

Describe cystic Fibrosis? (4pts)

Answer 20

1. In CF the most common mutation is a deletion of Phenylaline at residue 508 of the CFTR.
2. F508del leads to mis-folding of the protein whilst it is still in the ER.
3. This is recognised by the cellular machinery that identifies and processes misfolded proteins.
4. This results in ubiquination, trafficking to the proteasome and degradation.

Question 21

Describe induced Protein mis-folding? (5pts)

Answer 21

1. Mis folded proteins interact with other normal proteins
2. Through this interaction they induce mis-folding of the normal protein and polymerisation.
3. Oligomers form fibrils of the mis folded protein.
4. This process is reliant upon the concept of energy minimisation.
5. It is a dynamic process brought about by the interaction of molecules resulting in a more stable aggregated structure.