synthetic approaches

Question 1

what do DNA and RNA do

Answer 1

DNA - store genetic info
RNA - forms protein, messenger, transfer and ribosomal RNA

Question 2

difference in structure between DNA and RNA

Answer 2

DNA doesn’t have a hydroxyl group on the 2’ position

Question 3

explain the DNA structure

Answer 3

• two strands run opposite, anti parallel
• A=T and G—C
• bases on the inside and has a phosphate backbone
• stabilised by aromatic stacking and H bonding

Question 4

what is the problem in the synthesis of DNA

Answer 4

there are too many nucleophile in the structure to attack the desired electrophile

Question 5

name and explain the two types of protecting groups

Answer 5

permanent protecting group
- it stay during the whole reaction
- must be removed so DNA stays intact

temporary protecting group
- removed to elongate polymer
- removed so other PPG can stay intact

Question 6

what is the problem with the DCC protecting group for peptide synthesis

Answer 6

DCC can rearrange and become unreactive

Question 7

what is DNA polymerase and brief explanation on how it works

Answer 7

catalyst for DNA replication
- binds to DNA template
- primer intiates DNA synthesis
- matches bases to the template

Question 8

what are the two types of nucleases and describe how they work

Answer 8

exonuclease - starts at 3’ to 5’
endonuclease - hydrolyses at internal site of DNA strand

Question 9

how does ligase work

Answer 9

catalyses the synthesis of phosphate diesters from the DNA 5’ phosphate monoester with 3’ OH group
requires coenzyme NAD+ and Mg2+

Question 10

what are introns and exons

Answer 10

introns - non coding sections of RNA transcript
exons - section that codes for the protein

Question 11

what is splicing

Answer 11

The process by which introns, the noncoding regions of genes, are excised out of the primary messenger RNA transcript,

Question 12

what are the basic steps to cloning

Answer 12

1. DNA inserted in vector
2. forms a recombinant
3. binds recombinant with bacterial cell
4. multiplication of recombinant DNA inside the cell
5. multiplication of host cell

Question 13

what is the most common host and cloning vector

Answer 13

e.coli is the most common host
plasmid is the most common vector

Question 14

how is the recombinant formed in cloning

Answer 14

• target DNA is “cut” at two sites with endonuclease
• the plasmid is cut with the same endonuclease
• both are mixed and hybridised with DNA ligase

Question 15

how does tRNA work in protein synthesis

Answer 15

• tRNA binds to amino acid (3’ OH to O- on acid)
• then the N terminal binds to the C terminal on the peptide chain and the tRNA is removed simultanously

Question 16

what is mutagensis

Answer 16

process where the genetic information (DNA sequence) of an organism is altered by a mutation

Question 17

what is mutagensis

Answer 17

process where the genetic information (DNA sequence) of an organism is altered by a mutation

Question 18

what is point mutation and frame shift mutation

Answer 18

point mutation is a change in a base pair

frame shift is a insertion or deletion of nucleotides

Question 19

impact of point mutation

Answer 19

• silent degeneracy
• minimal changes
• possibly beneficial (rare)
• possibly very bad

Question 20

impact of frame mutation

Answer 20

• a different polypeptide is formed
• effects depend on where the change occurs

Question 21

what is bioconjugation

Answer 21

a biomolecule is modified by another molecule and ligated by a covalent bond

Question 22

how does antisense therapy work

Answer 22

• antisense strand complementary in base sequence to mRNA of protein of interest
• blocks translation of mRNA
• no protein synthesis

Question 23

steps in solid phase synthesis

Answer 23

1. detritylation (deprotection)
2. coupling with another nucleotide
3. oxidation (I_2 and aq pyridine
4. repeat cycle

Question 24

RNA synthesis cycle

Answer 24

1. deprotection
2. condensation (coupling)
3. capping
4. oxidation