Lecture 1 protein structure Flashcards
What are characteristics of a typical protein?
Size ~5 nm, roughly globular
Molecular mass: 40000
Consists of ~300 Amino acid residues
Describe the different protein structure levels
Primary Structure: Linear sequence of amino acids in polypeptide
Secondary Structure: Mainly beta-sheet
(strands) or alpha-helix
Tertiary structure: 3-D Arrangement of sheets, helices, etc..
Quarternary Structure: Association of several polypeptides
What are the bonds each atom can have?
(H,C,N,O) What is the order of electronegativity?
Hydrogen (H): one bond
Carbon (C): four bonds
Nitrogen (N): three bonds
Oxygen (O): two bonds
Order of electronegativity:
O>N>C>H
What does the backbone of a protein look like? How many amino acid residues does a protein typically have?
Backbone (NH-C-CO)
Side-chains (R1,2….)
Proteins are polypeptides of >typically 100 amino acid residues.
What is an example of a sec. structure? Characteristics?
Alpha helix
Stabilized by
H-bonds of
peptide back-
bone
What is another example of a secondary structure? Characteristics?
Secondary structure: beta sheet.
Flat sheet stabilized by backbone H-bonds. Residues alternatingly point up or down
How is a tertiary structure built?
Polar residues interact with
water (and with each other)
(H-bonds, electrostatic)
Non-polar residues interact
with each other
(van der Waals)
Polar residues at surface
Non-polar residues interior
What can a stretch of hydrophobic residues do?
Stretch of hydrophobic residues (>20) can form transmembrane helix. No water to compete Helix H-bonds crucial. Prediction of transmembrane helices possible
How can a quarternary structure be formed? How is the assembly caused?
Proteins (monomers) assemble
into larger structures (oligomers)
Monomers can be identical
(homo-oligomer) or not identical
(hetero-oligomer).
Assembly caused by
hydrophobic forces, salt bridges,
hydrogen bonds.
The energy difference between a properly folded (native) and completely unfolded state is small (20-30 kJ/mol, corresponding to energy of ~5 H-bonds. (Covalent bond = >200 kJ/mol) What are important consequences of this?
Interactions within the protein and with water nearly compensate each other.
Very important consequences:
1. Proteins quite instable, not easy to handle!
2. One or two additional interactions can lead to small
structure change
Many factors (temperature, solvent composition, pH) influence protein stability
At what pH do what proteins get ionized?
At pH lower then 4 and higher then 10, groups which were neutral at physiological pH become ionized
