L5&6 - Protein Structure Flashcards
Four classes of amino acids:
- Polar
- Hydrophobic
- Basic
- Acidic
Peptide bond:
Name from end terminus (N) so residue 1 from amine group.
Peptide bond forms between Cα - planar so reduces rotation.
In trans configuration and not cis as side chains may be charged so if same charge they would repel. Opposite charges would attract.
So cis dont form due to steric hindrance.
Phi ϕ bond between N(in peptide) and Cα
Psi Ψ bond between Cα and C (in peptide).
Ramachandra Plot:
Determins the structure of protein if ϕ and Ψ values are acceptable.
Shows how restricted confirmation of polypeptide chain is. Only 15% values are allowed.
Steric hindrance prevents other confirmations. So ϕ and Ψ values are affected by side chains. Glycine can have any ϕ and Ψ values.
Determines structure of protein e.g. if amino acids have ϕ and Ψ in α region then it shows α-helix present.
Organisation of protein structure:
(Primary, Secondary, Supersecondary, Tertiary, Quaternary):
Primary Structure:
Amino acid Sequence
Secondary Structure:
α-helix, β-sheets, β-turn
Supersecondary Structure:
α-bundle and β-barrel
Tertiary Structure:
Overall 3D folded structure (one polypeptide chain so one subunit)
Quaternary Structure:
Arrangement of domains/subunits (many subunits and more than one polypeptide chain)
Secondary Structure: α-helix
(Where H bonds are, why they are needed, Myoglobin, α-keratin)
N-H point down and C=O point up forming H bond. 0.28nm.
Right handed helix stabilised by H bonds. Not left handed as not superimposable. Made of L-amino acids so more stable as right handed.
Single polypeptide chain wound into helix held by H bonds. e.g. myoglobin.
α-Keratin: many right handed helices wound around each other giving tough rigid structure. Main single strand is left handed (superhelix).
Secondary Strucutre: β-sheets
(Definition, Types, Why H bonds are useful)
Single chain stretched out in most entended confirmation.
Two types:
- Parallel β-sheet (parallel strands and H bonds not parallel)
- Antiparallel β-sheet (antiparallel strands and H bonds are parallel so perpendicular to strands)
H bonds make β-sheet flexible and strong. H bonds present between chains.
Secondary Structure: β turn
(H bonds, Two types, No. of residues per turn)
This commonly occurs. Stabilised by H bonds.
Two types:
- Type I (C=O points up and N-H point down in peptide bond)
- Type II (C=O points down and N-H point up in peptide bond)
It folds chains back on itself. 4 AA per turn. H bond between C=O of reside 1 and H-N of residue 4.Stabilises strucutre.
Collagen:
(Structure, where its found, superhelix and helices)
- Triple helix: 3 chains wound around each other
- Most abundant protein in humans
- Helical but not α-helix
- Superhelix is right handed so the 3 chains are right handed.
- Strands in each chain is left handed wound around each other forming a single chain.
Alpha helix vs. Collagen
Supersecondary Structure: β-barrel
β-sheet flexible so can be twisted to form barrel - uses at least 8 chains. Held together by H bonds making barrel more stable than sheets. e.g. pyruvate kinase. Barrel structure more thermodynamically stable.
Supersecondary structure: α-bundle
- Have similar elements to each other (polypeptide chain) so can bundle together
- Pack 4 at a time (right handed helices)
- side chains sit side by side
- more thermodynamically stable as a bundle of 4
- e.g. cytochrome C and B
Rossmann Fold:
2 proteins can have different sequences and function but have similar structure - can defer by number of crevices.
Similar structure but different functions. Have seven mostly parallel β-sheets. Connected by α helices.
Pyruvate Kinase:
Some proteins have 2 or more domains linked together e.g. pyruvate kinase.
Pack together forming 1 continuous polypeptide chain with 3 different domains:
- β-barrel
- β-sandwich
- Rossmann Fold
Motifs used to span membrane:
- α helix (bundle)
- β-barrel
Both are hydrophobic outside so can pass through membrane. β-barrel can be used to create bacterial porin.
Single polypeptide chains and β-sheets can’t pass through membrane as hydrophilic side chains on outside. Membrane is hydrophobic so don’t allow hydrophilic substances to pass through.
Teriary Structure:
(definition, covalent and non-covalent bonds, example, two types)
- 3D structure held by various bonds
- Has α-helices and β-sheets
- disulphide bonds can form. Covalent bond stabilises structure.
- Held by non-covalent forces:
- H bonds - reversible and weak
- Electrostatic interactions
- VDW’s - dipole-dipole interactions
- Hydrophobic effect (aggregate together)
- e.g. lysozyme (single chain, hydrophilic outside and globular)
- Tertiary structure is the folding of a single chain (only one subunit)
- 2 Types:
- Globular (water soluble)
- Fibrous (water insoluble)
