BIOORGANIC CHEMISTRY Flashcards
In a reaction mixture we are mixing:
a filled orbital and a vacant orbital
New molecules orbital =
new bond
nucleophiles most reactive when
high energy filled orbitals used
electrophiles most reactive when
low energy unfilled orbitals used
a electronegative element is
less nucleophilic as holds onto electrons
what is allylic strain
refers to where 2 side groups have steric hinderance as they are too close together. Because of allylic strain as well as restriction of rotation, there are only a few conformations 2º structures can take.
amides are more kinetically stable than esters due to…
electron delocalization of neighbouring nitrogen atom into p* MO of adjacent C=O carbon.
Why are phosphoesters used in DNA
Very stable, suitable to store permanent genetic information as does not degrade
what is prebiotic chemistry
concerned with studying the biological chemistry of primordial earth before life.
what gases were present on primordial earth
water ammonia methane hydrogen cyanide cyanoacetylene
has a largely reducing atmosphere
What are tautomers
constitutional isomers that differ by migration of one proton.
tautomerization is acid or base catalysed.
Favoured tautomers are based on stability which is present more in aromatic structures and more resonance structures.
Outline the Miller-Urey experiment
heating produced gases present in prebiotic
electrical energy represented lightning strike
observed carbon molecules like formaldehyde and then amino acids were produced in a prebiotic environment
What is an imine
amine + carbonyl compound
produced by condensation, 2 step proton transfer
Uracil and thymine differ by:
thymine has an extra methyl group
bases are nucleophilic. Hierarchy?
G>A>T>C
explain why there are major and minor grooves in DNA
the helix is not symmetrical due to phosphoribose backbones not being oriented. This produces the grooves
explain pi stacking and intercalation
π-stacking between aromatic rings of base pairs stabilises DNA double helix by allowing pi interactions between stacked bases.
many cytotoxic drugs are DNA intercalators
what are cytotoxic drugs
drugs that kill cells or inhibit cell growth
what are the 3 ways cytotoxic drugs target DNA
Thymine biosynthesis
DNA replication
Inhibition of mitosis
explain thymine biosynthesis
inhibitors like 5-fluorouracil stop thymidylate synthase from producing thymine
explain alkylating agents
react as electrophiles to form stable covalent bonds.
bond to DNA affecting replication
what is an alfatoxin
natural products and belong to the epode alkylator class.
converted to highly electrophilic epoxide in liver
intercalates and react s with N7 nitrogen at guanidylate residues
carbohydrate functions
Structure and support
Energy and metabolism
Signalling and cellular communication
Reaction to attach a carbohydrate to other molecules
Diversity of all protein and lipid glycosylation (like a genome, this is the glycome)
ways to depict structure of monosaccharides
fischer projection
haworth projection
chain conformations
what is relative configuration
refers to not atom level and where they are relative to other atoms (e.g: cis and trans)
what is absolute configuration
D and L
D = R last chiral carbon
L = S last chiral carbon
why would equatorial positions be more thermodynamically stable?
less steric hinderance
larger substituents should be in the equatorial positions and the lighter substituents in the axial positions.
polar effects on anomer stability
axial cancel out reducing dipole
equatorial aline increase dipole
explain the anomeric effect
ring oxygen lone pair is antiperiplanar to C-O. Greater overlap of filled and unfilled orbitals
donation of the lone pair of the sigma star orbital of the anomeric C-O bond.
electrons go into lower energy hybrid orbital stabilising system
water attacks aldehyde/ketone =
hydrates
alcohol attacks aldehyde/ketone =
hemiacetals and acetals
glycosyl donor
Acts as electrophile
Has an activated leaving group on anomeric carbon
Glycosyl acceptor:
Acts as nucleophile
Has a protective group on the anomeric carbon
Has an OH taking part in reaction
Non-participating groups:
Do not donate electrons to anomeric carbon or leaving group
Give mainly alpha products
Acyl protective groups
e.g: OAc
Donate to anomeric carbon and then take back electrons when new group comes in
Give mainly beta products
Electron withdrawing protective groups
e.g: Oac, Bz
Deactivate the acceptor as they withdraw e.d from molecule stopping reactivity of oxcarbenium ion, Harder stability of intermediate
Stronger promoter needed, higher temperature for reaction
Electron donating protective groups
e.g: OBn, TBDMS
Promote acceptor as electron donating character makes intermediate more stable.
Milder promoter and lower temperature can be used
what are natural products
natural products are molecules made by living organisms
primary metabolite: essential for life “the big four”
secondary metabolite: not essential, may provide benefit
what is an alkaloid
for secondary metabolites that contain nitrogen.
