L2 - Protein folding and function Flashcards
What is the primary structure of a protein?
The linear amino acid sequence of the polypeptide chain
What is the secondary structure of a protein?
The local spatial arrangement of the polypeptide backbone - determined by hydrogen bonds between the backbone but NOT R-groups
What is the tertiary structure of a protein?
The 3D arrangement of all atoms in a polypeptide
What is the quaternary structure of a protein?
The 3D arrangement of protein subunits in multimeric proteins
Describe four features of alpha-helices
3.6aa/turn
0.54nm pitch (vertical distance per complete turn)
Right-handed helix
R-groups sit on the outside
Describe thfeatures of beta-sheets
Fully extended conformation
0.35nm between adjacent AAs
R-groups alternate between opposite side of the chain
Alternate side-chains also point in opposite directions
Which bonds can rotate in a polypeptide and how does this affect its conformation?
The peptide bond cannot rotate but the C-C bond in the backbone between peptide bonds can. The angle of these bonds determines the conformation of the backbone. Bulky R-groups can stop certain conformations occuring.
Between which atoms do the hydrogen bonds in an alpha-helix form?
Between the backbone -C=O group of one residue and the -NH group of the residue FOUR amino acids away
Which two residues are strong helix formers?
The small hydrophobic residues such as alanine and leucine
Which two residues are strong helix breakers?
Proline - because rotation around the N-C(alpha) bond is impossible
Glycine - because the tiny R-group supports other conformations (it’s very flexible)
What are the two main types of beta-sheet?
Parallel and anti-parallel
Describe fibrous proteins. What roles do they tend to have?
Long strands or sheets Little or no tertiary structure Single type of repeating secondary structure Usually insoluble Often have a structural role E.g. Collagen
Describe globular proteins. What roles do they tend to have?
Compact shape Complex tertiary structure Several types of secondary structure Usually soluble Many different roles
Describe the repeating structure of collagen alpha-chains
Glycine every 3 residues
When describing a tertiary structure, what is a motif?
A folding pattern containing one or more elements of secondary structure e.g. Beta-alpha-beta loop.
When describing a tertiary structrue, what is a domain?
Part of a polypeptide chain that folds into a distinct shape. It often has a specific functional role e.g. The calciu binding domains of tropo in C.
Describe the difference in amino acid distribution between soluble proteins such as myoglobin and membrane proteins such as porins
Soluble proteins: fold so hydrophobic amino acids are in the centre and Hydrophillic are on the outside
Membrane proteins: fold so that there is often a water-filled hydrophilic channel through their centre and a largely hydrophobic exterior
Describe the quaternary structure of haemoglobin
Adult Haemoglobin contains two alpha-subunits and two beta-subunits, held together by non-covalent interactions
What type of bonds are involved in primary protein structure?
Covalent peptide bonds
What forces are involved in secondary protein structure?
Hydrogen bonds between the polypeptide backbone
What forces are involved in tertiary and quaternary protein structure?
Hydrophobic interactions Ionic interactions Hydrogen bonds Van Der Waals forces Covalent (di-sulphide bonds)
Why do proteins which are secreted tend to have Disulphide bonds?
Disulphide bonds are very strong (214kJ/mol) therefore do not tend to break once formed. Proteins that are secreted (e.g. Into the gut), tend to enter a hostile environment and therefore need a more rigidly held protein structure to stop the protein from denaturing quickly.
List the forces involved in maintaing protein structure from strongest to weakest
Covalent/di-sulphide - 214kJ/mol
Ionic/ hydrogen bonds - 10-30kJ/mol
Hydrophobic effect - approx. 10kJ/mol
Van Der Waals - 4kJ/mol
Define denaturation
The process in which proteins or nucleic acids lose the quaternary, tertiary, secondary structure which is present in their native state.
What can cause protein Denaturation?
- Heat - increased vibration energy
- PH - alters ionisation state of AAs, changes ionic and hydrogen bonds
- Detergents/ organic solvents - disrupt hydrophobic interactions
How do proteins fold?
The information needed for folding is contained in the polypeptide sequence. Folding occurs in a step-wise manner and may proceed through localised folding.
Some proteins need chaperone proteins to assist in folding.
Describe a disease which is caused by protein misfolding and discuss its mechanism
Transmissible spongiform encephalopathies (BSE/ Kuru/ CJD) are caused by an altered conformation of normal human protein. This altered conformation converts exiting native conformations of the same proteins into a disease state. These abnormal forms then aggregate, forming relatively insoluble amyloid fibrils.
Define amyloidoses
Diseases that result form errors in normal folding which cause a build-up of misfolded proteins (amyloids).
Describe the strcuture of amyloid fibres
- Contain misfolded, insoluble form of a normally soluble protein
- Highly ordered with a high degree of beta-sheet
- Core beta-sheet forms before the rest of the protein
- Inter-chain assembly stabilised by hydrophobic interactions between aromatic amino acids
What condition or reagent could disrupt a Disulphide bond?
Reducing agents e.g. Mercado ethanol, dithiothreitol (or heat)
What condition or reagent could disrupt a hydrogen bond?
PH extremes (or heat)
What condition or reagent could disrupt a hydrophobic interaction?
Detergents/ organic solvents/ urea (or heat)
What condition or reagent could disrupt a ionic interaction?
Changes in pH or ionic strength (or heat)
Why are peptide bonds important for the secondary structure of proteins?
They contain carbonyl and amino groups which are able to hydrogen bond. These groups are a major determinant of the secondary structure of proteins e.g. Alpha-helices and beta-sheets.
What is the pitch of an alpha-helix?
0.54nm
How many amino acids per turn of an alpha-helix?
3.6 amino acids
