Exam Questions Flashcards
What is the difference between an atomic orbital and a molecular orbital?
An atomic orbital describes the electron distribution around an atom, a molecular orbital
describes the electron distribution in a molecule. Molecular orbitals are formed from the
combination/overlap of atomic orbitals.
How many electrons are shared in a covalent bond?
Two
What is a polar covalent bond?
A bond formed between two atoms of different electronegativity- e.g. O-H
What geometry does a sp3 hybridised carbon have?
Tetrahedral
What geometry does a sp2 hybridised carbon have?
Trigonal planar
What geometry does a sp orbital have?
Linear
What are the similarities and differences between a sigma bond and a pi bond?
Both are types of covalent bonds, both have 2 electrons. A sigma bond lies between the atomic centres, a pi bond (formed from p orbital overlap) has electron density above and below the plane of the two atoms (double bond has 1 sigma and 1 pie bond, single bond has 1 sigma bond)
Why is the H-O-H bond angle in water 104.5˚ rather than the 109.5˚ tetrahedral angle of
the H-C-H bond angles in methane?
In methane, each of the four sp3 hybrid orbitals on carbon overlaps with a 1s orbital from a hydrogen atom, forming four sigma bonds. This results in a perfect tetrahedral shape with bond angles of 109.5
In water, two of the four sp3 hybrid orbitals on oxygen overlap with 1s orbitals from hydrogen atoms, forming two sigma bonds. The remaining two sp3 hybrid orbitals each hold a lone pair of electrons
lone pairs exert a stronger repulsion than bonding pairs. The two lone pairs on oxygen push the bonding pairs closer together, reducing the H-O-H bond angle to 104.5°.
Why are protein sequences always drawn from the N to the C-terminus?
This is the order in which the polypeptide exits the ribosome.
Draw two amino acids in a bi-peptide, joined by a peptide bond. Which atoms are in the
peptide bond? Identify those with sp2 hybridisation.
N,H,C,O sp2 N,C,O
Explain the difference between a bond angle (e.g H-O-H) and a torsion angle about a bond
(e.g. Calpha-N).
A bond angle is the angle between three linked atoms e.g. H-O- H or C-O-H or C1-C2-C3
(depending on the angle concerned and molecule). A torsion angle defines the rotation
around a sigma bond between two atoms.
Why are certain areas of the Ramachandran plot disallowed?
Unfavourable steric overlap between groups of the polypeptide (side chains, main chain C=O)
This means that certain combinations of phi and psi angles would cause atoms within the amino acid or neighboring amino acids to come too close together, leading to unfavorable interactions and clashes.
Would you expect to find lysine residue in the core of a protein? Explain why?
No, as the lysine amino group will be positively charged at pH values around 7 and the core of the protein is hydrophobic.
