BIOORGANIC CHEMISTRY

Question 1

In a reaction mixture we are mixing:

Answer 1

a filled orbital and a vacant orbital

Question 2

New molecules orbital =

Answer 2

new bond

Question 3

nucleophiles most reactive when

Answer 3

high energy filled orbitals used

Question 4

electrophiles most reactive when

Answer 4

low energy unfilled orbitals used

Question 5

a electronegative element is

Answer 5

less nucleophilic as holds onto electrons

Question 6

what is allylic strain

Answer 6

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.

Question 7

amides are more kinetically stable than esters due to…

Answer 7

electron delocalization of neighbouring nitrogen atom into p* MO of adjacent C=O carbon.

Question 8

Why are phosphoesters used in DNA

Answer 8

Very stable, suitable to store permanent genetic information as does not degrade

Question 9

what is prebiotic chemistry

Answer 9

concerned with studying the biological chemistry of primordial earth before life.

Question 10

what gases were present on primordial earth

Answer 10

water
ammonia 
methane 
hydrogen cyanide
cyanoacetylene 

has a largely reducing atmosphere

Question 11

What are tautomers

Answer 11

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.

Question 12

Outline the Miller-Urey experiment

Answer 12

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

Question 13

What is an imine

Answer 13

amine + carbonyl compound

produced by condensation, 2 step proton transfer

Question 14

Uracil and thymine differ by:

Answer 14

thymine has an extra methyl group

Question 15

bases are nucleophilic. Hierarchy?

Answer 15

G>A>T>C

Question 16

explain why there are major and minor grooves in DNA

Answer 16

the helix is not symmetrical due to phosphoribose backbones not being oriented. This produces the grooves

Question 17

explain pi stacking and intercalation

Answer 17

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

Question 18

what are cytotoxic drugs

Answer 18

drugs that kill cells or inhibit cell growth

Question 19

what are the 3 ways cytotoxic drugs target DNA

Answer 19

Thymine biosynthesis

DNA replication

Inhibition of mitosis

Question 20

explain thymine biosynthesis

Answer 20

inhibitors like 5-fluorouracil stop thymidylate synthase from producing thymine

Question 21

explain alkylating agents

Answer 21

react as electrophiles to form stable covalent bonds.

bond to DNA affecting replication

Question 22

what is an alfatoxin

Answer 22

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

Question 23

carbohydrate functions

Answer 23

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)

Question 24

ways to depict structure of monosaccharides

Answer 24

fischer projection

haworth projection

chain conformations

Question 25

what is relative configuration

Answer 25

refers to not atom level and where they are relative to other atoms (e.g: cis and trans)

Question 26

what is absolute configuration

Answer 26

D and L

D = R last chiral carbon

L = S last chiral carbon

Question 27

why would equatorial positions be more thermodynamically stable?

Answer 27

less steric hinderance

larger substituents should be in the equatorial positions and the lighter substituents in the axial positions.

Question 28

polar effects on anomer stability

Answer 28

axial cancel out reducing dipole

equatorial aline increase dipole

Question 29

explain the anomeric effect

Answer 29

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

Question 30

water attacks aldehyde/ketone =

Answer 30

hydrates

Question 31

alcohol attacks aldehyde/ketone =

Answer 31

hemiacetals and acetals

Question 32

glycosyl donor

Answer 32

Acts as electrophile

Has an activated leaving group on anomeric carbon

Question 33

Glycosyl acceptor:

Answer 33

Acts as nucleophile

Has a protective group on the anomeric carbon

Has an OH taking part in reaction

Question 34

Non-participating groups:

Answer 34

Do not donate electrons to anomeric carbon or leaving group

Give mainly alpha products

Question 35

Acyl protective groups

Answer 35

e.g: OAc

Donate to anomeric carbon and then take back electrons when new group comes in

Give mainly beta products

Question 36

Electron withdrawing protective groups

Answer 36

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

Question 37

Electron donating protective groups

Answer 37

e.g: OBn, TBDMS

Promote acceptor as electron donating character makes intermediate more stable.

Milder promoter and lower temperature can be used

Question 38

what are natural products

Answer 38

natural products are molecules made by living organisms

primary metabolite: essential for life “the big four”

secondary metabolite: not essential, may provide benefit

Question 39

what is an alkaloid

Answer 39

for secondary metabolites that contain nitrogen.