Higher order structure(AA, peptides, proteins) Flashcards
How are beta strands different to alpha strands along the polypeptide backbone?
In beta strands the amino acids zig-zag along the polypeptide backbone whereas AA in alpha helix they sprial.
Describe the conformation of the beta conformation in the beta sheet?
- In a b-sheet, carbonyl oxygens and amides form hydrogen bonds.
- These secondary structures can be either antiparallel (as shown) or parallel and need not be planar (like here) but can be twisted.
- The propensity of a peptide for forming b-sheet also depends on its sequence.
how do you correct strands in antiparallel sheets?
beta turns
How do you connect strands in all parallel sheets?
Loops
How does a beta turn work?
It allows the protein backbone to make abrupt turns, the propensity for forming b-turns depends on its sequence.
How is an amyloid fibril formed?
Abnormal prion proteins propagate and aggregate to form amyloid fibrils which leads to amyloid disease
Give an example of a protein with mostly beta sheet stucture?
Immunoglobin
What is the secondary stucture of a protein defined by?
The peptide backbone repeated structure.
It comprises regions of alpha helical structures, beta sheet structures as well as bends and turns in the shape.
When a polypeptide chain has a folded conformation and in aqueous environment what can for between the water and polar side chains?
Hydrogen bonds
Aqueous vs non aqueous environment for membrane protein hydrophobic and hydrophilic components
non aqueous= hydrophobic components internalised and buried.
Aqueous= folding rules reversed and hydrophobic components face outwards.
What are the 3 “special amino acids” that can have “special” influence on tertiary stucture?
Cysteine(Cys, C)
Glycine(Gly, G)
Proline(Pro, P)
How does the special AA Glycine affect tertiary structure?
Small side chain- a single H.
Non-chiral
Allows for very tight turns in a polypeptide chain making it looser too.
**PROVIDES HINGE to allow protein stuctures and domains to change orientation relative to each other
Which amino acid will be rich in a hinge region of a polypeptide chain?
Gly rich
(glycine)
How does the special AA Proline affect tertiary structure?
Very rigid, opposite to the flexibility of glycine.
Side chain is incorporated that is quite bulky.
**LIMITS FLEXIBILITY due to side chain and rigid nature.
Produces a more open helix.
How does the special AA Cysteine affect tertiary structure?
Ability to cross-link to other cys residues.
Happens under oxidising conditions.
Cross links INCREASE PROTEIN STABILITY.
Common in extracellular proteins, absent in cytoplasmic proteins.
How does a ‘heptad’ 7 residue motif help polypeptide chains in aqueous environments?
Means that the helices wrap around each other to minimise exposure of hydrophobic amino acid side chains to aqueous environment. Increased stability of the coiled coil.
What are the characteristics of alpha helix, cross linked by disulfide bonds?
Tough, insoluble protective structures of varying hardness and flexibility.
Give an example of an alpha helix structure?
a-keratin of hair and nails.
What are the characteristics of beta conformation?
Soft and flexible filaments
Give an example of beta conformation?
Silk fibroin
Give the characteristics of collagen triple helix?
High tensile strength, without stretch
How do vertebrates fight infections with soluble antibodies that specifically bind antigens?
The soluble antibodies are stimulated from antigens.
They coat proteins of bacteria and viruses.
They surface carbohydrates of cells or viruses to help identification of foreign content.
Give an example of occurrence for the collagen triple helix?
Collagen of tendons, bone matrix.
What is an epitope?
A small region of an antigen.
(Commonly binded to by an antibody)
Describe the structure of immunoglobulin G…?
Two heavy chains and two light chains.
Composed of constant domains and variable domains.
What is a protein domain?
independently folded units of tertiary structure along a polypetide chain
C= constant
V=Variable
How many variable domains does an antigen binding site require?
2 variable domains per antibody, making it hypervariable. Confers antigen specificity.
What domains are in a light chain?
One constant and one variable domain
What domains are in a heavy chain?
Three constant and 1 variable domain.
Give a few factors that help to activate a protein aside from simple folding and assembly of its component polypeptides?
Covalent modification:
- Side chains
- Attachment of macromolecules
- Proteolytic activation
- Crosslinkling
Non-covalent binding of prosthetic groups:
- Functional groups
- Activation signals
