Biochem: 3D protein structure Flashcards
dG separating the folded and unfolded states
20-50 kJ/mol
What bonds/forces stabilise the folded state of the protein and counteract interaction of solvent with polypeptide chains?
covalent (disulphide bonds) and weak hydrogen bonds and hydrophobic and ionic interactions - in extracellular proteins disulphide bonds are more common, and in intracellular its mainly weak interactions.
What is the protein conformation with the smallest amount of free energy?
the protein with the highest amount of weak interactions (specifically hydrophobic interactions)
What are the 3 defining angles that define peptide conformation?
torsion angles: phi, psi, omega
peptide backbone: phi - C—N—Calpha—C (bond at N—Calpha)
psi - N—Calpha—C—N
both between +- 180 polypeptide is fully extended
omega: Calpha—C—N—Calpha (bond at C—N, the peptide bond, which is constrained)
Describe the alpha helix structure
- A polypeptide backbone tightly wound around an imaginary axis drawn longitudinally.
- R groups of the AA residues point away from the helical backbone.
- The repeating unit is a single turn of the helix, which extends about 5.4 Å along the long axis
- Each helical turn includes 3.6
amino acid residues
True or false: proteins include mostly left extended aloha helices
False. they include only right extended helices, as left extended helices are far less stable and have not been observed so far in proteins
Why does the $ helix form more readily than many other possible conformations
Stability.
The structure is stabilized by a hydrogen bond between the hydrogen atom attached to the electronegative N atom of a peptide linkage and the electronegative COO atom of the fourth AA on the N-terminal side of that peptide bond.
which AA has the greatest tendency to form alpha helices and which AA has the lowest tendency?
Alanine (greatest) Proline (lowest)
what is the structural difference between a parallel and antiparallel ß sheet?
the repeat period (parallel 6.5 Å, vs. 7 Å antiparallel), and hydrogen bonding pattern
How can one describe/recognise the type of protein structure?
by the dihedral angles phi and psi, using a Ramachandran plot
summarise the key points on secondary structure
- Secondary structure is the local spatial
arrangement of the main-chain atoms in a selected segment of a polypeptide chain. - The most common regular secondary structures are the alpha helix, the ß conformation, and ß turns.
- The secondary structure of a polypeptide segment can be completely defined if the phi and psi angles are known for all amino acid residues in that segment.
- Circular dichroism spectroscopy is a method for assessing common secondary structure and monitoring folding in proteins.
In protein denaturation what will be the effect of the following factors:
1. pH
2. Temperature
3. Organis solvents
- pH changes result in electrostatic rejection
- Temp affects H+ bonds
- Organic solvents infiltrate the protein and disrupt the hydrophobic protein core
discard
What can one test using circular dichorism spectroscopy?
Assess common secondary structure and monitor protein folding
What is the difference between AA interaction on secondary and tertiary strucure?
AAs interacting in a secondary strucure form a polypeptide of a type of secondary strucure, whereas in tertiary the Aas interacting with each other belong to different polypeptide chains in differenc sec. structures. The interaction is enabled thanks to protein folding that brings structures close together.
what is the structural characteristic of fibrous proteins?
chains of polypeptides together arranged in long strands or sheets- a simple repeating element of secondary
structure
How is the strucutre of fibrous proteins help their biological function?
Fibrous proteins help provide the shape to the structures they occour in. Their long repeated strands of secondary structure gives them flexibility and strength that allow their function.
True/False: All fibrous proteins are soluble in water because they interact with aqueous environment all the time
False. Fibrous proteins are insoluble because of theur high number of hydrophobic AAs.
what stereoisomer is the alphahelix of alpha keratins ?
right handed. The 2 alpha helices are arranged parallel to each other and foem a supertwisted coiled coil that increases its strength
Why is the direction of the helical supertwiist (superhelix) is opposoite to the direction of lpha keratin’s alpha helices?
The surfaces
where the two $ helices touch are made up of hydrophobic
amino acid residues, their R groups meshed together in a
regular interlocking pattern. This permits a close packing
of the polypeptide chains within the left-handed supertwist
In which tissue can you expect to fins collagen?
tendons, cartilage, the organic matrix of bone, and the cornea of the eye.
Why does the aging tussue appear brittle and wrinkled?
due to accumulated covalent crosslinks in collagen fibrils, these covalent fibrils are unusual bonds involving lysin residue (hylys) such as dehydrohydroxylysinonorleucine.
