General Biological Chemistry - Johnathan Cox Flashcards
What is a Lewis structure?
All atoms are shown, as well as all covalent bonds
What are reduced structures?
All carbons omitted, hydrogens attached to Carbon omitted, hydrogens attached to heteroatoms left in
What is a heteroatom?
A non carbon/hydrogen atom
What do curly arrows indicate?
Movement of the least stable pair of electrons
What is resonance shown by?
A double headed arrow, not in equilibrium
How can a species’ stability be indicated by resonance?
The more resonance structures that a species has, the more stable it is
What can resonance be described as?
The delocalisation or ‘spreading’ of charge
What is a resonance hybrid?
Shows possible resonance structures with a dashed line
What is tautomerism?
The movement of one or ore double bonds and a small atom, usually hydrogen but could also be fluorine
What is an example of tautomerism?
The changing of adenine from amino form to imino form
What is conjugation?
Alternation of single and double bonds, to form a ‘partial’ double bond
What can conjugation be described as?
Net stabilisation of the system
What is the relationship between the change in energy and wavelength in conjugation?
As the change in energy gets smaller, the wavelength gets larger
When does the wavelength of light emitted by conjugated compounds reach the visible spectrum?
When there are 8 or more conjugated double bonds
What is the change in energy in conjugation created by?
Movement of electrons from the ground state bonding orbital to the antibonding orbital
As conjugation increases, what happens to energy change and wavelength?
Energy change decreases, wavelength increases
What is the name of the molecule which gives lobsters their colour?
Astaxanthin
How many conjugated double bonds does astaxanthin have?
13
What does astaxanthin form a complex with?
Crustacyanin
Why do lobsters change from slate blue to red?
Astaxanthin and crustacyanin form a twisted complex, and when denatured, the crustacyanin leaves the complex
What are some of the importances of acids/bases?
Proteins, enzymes, DNA (gel electrophoresis), biological interactions
What is a Bronsted acid?
Proton donor
What is a Bronsted base?
Proton acceptor
What kind of pKa do strong acids have?
Low
What kind of Ka do strong acids have?
High
Which side of an equilibrium is favoured, in terms of pKa?
The side with the weaker acid, so higher pKa
What is the equation for Ka?
[A-][H3O+] / [HA]
How can Keq be calculated?
log(Keq) = pKa(RHS) - pKa(LHS)
What factors affect acid strength?
H-A bond strength, stability of A-, inductive effect
How does H-A bond strength affect acid strength?
If the bond is weak, then the acid is strong as it will dissociate easily
How does stability of A- affect acid strength?
If it is stable, then the acid is strong as it will stay dissociated
How does inductive effect affect acid strength?
Non electron donating groups eg Methyl, can destabilise a negatively charged atom
What is the Henderson Hasselbalch equation?
pH = pKa + log([A-]/[HA])
What is the pH when [A-] and [HA] are equal?
The pKa value
What is a Lewis base?
A lone pair donor
What is a Lewis acid?
A lone pair acceptor
HA + H2O –>
A- + H3O+
HB+ + H2O –>
B: + H3O+
The more available the lone pair…
…the stronger the base
The more stable the B-H+…
…the stronger the base
What changes between Oxygen to Nitrogen?
Increasing basicity
Decreasing electronegativity
What is the availability of the lone pair governed by?
Electronegativity of the atom with the lone pair
Delocalisation of the lone pair
Inductive effects
If +B-H has a high pKa, how strong is it?
Strong
What is the barrier to rotation?
The difference in energy between two conformers
Which conformer is more energetically favoured?
Staggered
Which conformer is the highest energy conformation?
Eclipsed
Why is staggered conformation more energetically favoured?
Due to electron repulsion
Why are hydrocarbon chains drawn as zig zags?
Due to staggered confromations
Why is a chair conformation more stable than boat?
Because it is staggered
What can cyclopentane exist as?
An envelope conformation
