MGC Proteins (HI) Flashcards
What is the primary, secondary, tertiary, and quaternary structures of a protein?
Primary = sequence of amino acids in polypeptide chain
Secondary = polypeptide folding into beta sheets and alpha helices
Tertiary = Arrangement of one or more domains into a 3D structure
Quaternary structure = arrangement of multiple polypeptides into a protein complex (multiple subunits)
What is a domain in protein structure?
Different secondary structures packed together in a “bundle” of secondary structures
What type of proteins are made of basic, hydrophobic, and cysteine amino acids?
Basic = histones
Hydrophobic = membrane proteins
Cysteines = extracellular proteins, as are stable from the disulphide bonds
What are phi and psi angles?
Phi = torsion angle of N-Calpha bond
Psi = torsion angle of Calpha - CO bond
Describe the flexibility of the peptide back bone and what this depends on
Partially flexible, as N-C bond is rigid, but Calpha-C (Psi) and N-Calpha (Phi) bonds are free to rotate to a certain extend, depending on the size of the R chains involved (to avoid clashes) and are also restricted by the fact that the whole plane moves with the rotation of the one bond.
What are the 3 important non-covalent bonds involved in stabilising proteins and describe each of them
Hydrogen bonds - When a H atom bonded to an N, O, or F atom has a partial positive charge, it interacts with nearby atoms with partial negative charges to form a hydrogen bond and neutralise the partial positive charges.
Salt bridges (ionic interactions) - Interactions between oppositely charged atoms (e.g. between basic and acidic side chains). These interactions can be disrupted with pH changes.
Van der Waal’s (LDFs) - Electron clouds fluctuate, so that there are more electrons on one side of the atom, forming a temporary dipole. Temporary dipoles can induce neighbouring atoms to form oppositely charged temporary dipoles, causing a weak interaction between the 2 atoms. Need to be at a certain distance, as if too close, the dipoles will repel one another, and if too far apart then the dipoles won’t interact.
Describe an alpha helix
Polypeptide forms a right-handed spiral structure. Vertical rise per turn = pitch. Stabilised by hydrogen bonding between the NH and C=O of amino acids that are 4 residues apart (e.g. 2 and 6). Side chains of amino acids radiate outwards in a spiral. Alpha helices are amphipathic, with all of the hydrophobic groups facing inwards, away from the water outside of the protein and all of the polar groups face outwards.
What does amphipathic mean?
Has both hydrophobic and hydrophilic groups, usually with the hydrophobic groups on one side and the hydrophilic groups on the other.
What type of interaction holds alpha helices, beta-sheets and beta turns/loops together?
Hydrogen bonds
What is the hydrophobic effect and how are water molecules involved in this and how does this effect protein folding?
Where the hydrophobic groups in a FOLDED polypeptide chain are positioned inwards, away from the water.
Water molecules are repulsed by hydrophobic side chains, so when the protein is folded and the side chains are facing away from the water, the water molecules are no longer repulsed and can therefore move more freely (have increased entropy).
This increase in entropy suggests that protein folding is spontaneous (favourable, negative delta G).
What are chaperones and how do they work? (3 mechanisms)
Chaperones = proteins that enhance the rate at which other proteins fold
Assist folding via:
- Catalysing the cis/trans isomerization of X-Pro bonds
-Catalysing the interchange of disulphide bonds
- Acting as compartments in which a single polypeptide can fold, away from other polypeptide molecules
What are the 3 classes of domain structure and what do they look like?
Alpha helical domains = Coiled-coils with 2 or more helices packed together
Beta-sheet domains = Beta sandwich, where one beta-sheet is layered on top of the other, with hydrophobic residues pointing towards the centre OR Beta-barrel, with 8 beta strands form a closed barrel like structure and the hydrophobic residues are orientated towards the centre of the barrel
Alpha/Beta domains = Alpha/beta barrel, with alpha helices located on the outside of the beta barrel OR open twisted Beta-sheet, with alpha helices on both sides of the sheet
What are the 4 forces that drive protein folding?
Gibbs free energy
Entropy
Enthalpy - conformation of non-covalent bonds e.g. Hydrogen bonds
Hydrophobic effect
What are the 3 types of chemistry that proteins “recruit” and what do they do ?
-Metal ions = provide stability (ionic interactions) and enable catalytic activity
- Prosthetic groups = allow the protein to perform specific tasks (e.g. Haem groups allow O2 binding and release)
- Cofactors = perform special chemical reactions within enzyme active sites
What is an epitope/antigenic determinant?
Part of the pathogen that the antibody recognises (e.g. surface of antigen)
How do antibodies help in terms of phagocytosis?
They cross-link pathogens into aggregates (clusters) so they can be held in place, which allows phagocytes to ingest them more easily
How does the formation of an antibody-antigen complex signal to kill the antigen cell?
Binding stimulates the binding of compliment 1 (C1). C1 triggers an amplification cascade, and thousands of molecules of membrane attack complex (MAC) are formed, which all punch holes in the membrane of the pathogen cell, which kills the cell
What are the 4 key features of an antibody?
- Constant region = recognised by C1 and by the target cell receptors (where the antibody binds to on the cell)
- Variable domains = so antibody can recognise a massive range of different antigens
- Multivalency = can bind to 2 different epitopes to form immune complexes
- Flexibility = contains hinge to adjust to different spacing of epitopes
What bonds are involved in stabilising the antibody-antigen complex?
Van der Waals’ (LDFs)
Ionic interactions
Hydrogen-bonds
Hydrophobic affect
(all same as stabilising folded proteins)
