Week 2 - Structure and Properties of Nucleic Acids

Question 1

A-form adaptations

Answer 1

• dsRNA

- dehydrated crystals

Question 2

Z-form adaptations

Answer 2

• dsDNA

- dehydrated crystals

Question 3

Z-form DNA in cells

Answer 3

proved through immunofluorescence during germination

Question 4

evidence for function in Z-form DNA

Answer 4

1. purine/pyrimidine tracts
2. dynamic observation of Z-form DNA in cells with immunofluorescence
3. proteins that specifically bind to DNA

Question 5

poxvirus

Answer 5

protein forms complex with Z-DNA

Question 6

vaccination

Answer 6

cow pox was injected to form immunization against poxvirus

Question 7

cruciform structures

Answer 7

• depends on palindromes and self-complementarity
• formed when palindromic sequences are exposed too much during replication and transcription (DNA unwinds in these processes)

Question 8

staggered palindrome

Answer 8

• a gap in palindromic structures

- more common

Question 9

overlapping palindrome

Answer 9

• no gap in palindromic structures

- less common

Question 10

hairpin bends

Answer 10

staggered palindromic sequences that enables formation of cruciform structure

Question 11

negative consequences of cruciform structures

Answer 11

• leads to an extra chromosome, leading to Trisomy syndrome (bits of 11 and 22 incorporated)
• rate of swapping is proportional to length of palindrome
• longer palindrome results in a larger chance to form cruciform

Question 12

three-stranded structures in nucleic acids

Answer 12

• requires extra hydrogen bond (non-WC bonds)
• triple helix
• H-form DNA

Question 13

Hoogsten pairs

Answer 13

non Watson and Crick pairs

Question 14

triple helix

Answer 14

• 3 nucleic acid molecules

- third strand runs parallel instead

Question 15

mirror repeat

Answer 15

• reflection on a single strand.

- most do not have a gap

Question 16

H-DNA

Answer 16

• only in ds DNA
• folding back must be a mirror sequence
• homopyrimidine and homopurine sequences favour the formation of H-form DNA

Question 17

H-DNA biological role

Answer 17

1. does it occur in the cell? not sure
2. distribution of homopurine:homopyrimidine sequence in genome? statistical over-representation in genome; found at specific locations
3. are there H-form DNA binding proteins? some proteins have been found to bind these special regions

Question 18

quadruple helix

Answer 18

steric hindrance

Question 19

bulge

Answer 19

a single nucleotide with nothing to pair with

Question 20

internal loop

Answer 20

region that loops out because it is not base paired

Question 21

hairpin bends

Answer 21

single stranded (4-6) nucleotide with 180 degree turn to form intrastrand double helix

Question 22

complex secondary structures of RNA molecules

Answer 22

single strand parts will stack up to 3D shape

Question 23

factors that affect the folding of secondary structure of nucleic acids

Answer 23

• changes in pH
• changes in temp
• addition of polar substances
• changes in salt concentration

Question 24

melting temperature of DNA in relation to GC content

Answer 24

• proportional relationship
• CG bp makes 3 H-bonds
• CG base stacking interactions are greater

Question 25

AT base pairs

Answer 25

regions rich in AT base pairs denature most readily

Question 26

hybridization

Answer 26

- annealing/rewinding of double stranded helix between complementary nucleic acids (DNA and RNA) - spontaneous, therefore occurs under favourable, non denaturing conditions (lower temperature, high salt concentration, no extreme pH)

Question 27

ideal conditions in a hybridization experiment

Answer 27

- dependent on the % complementarity to look for | - example: if the melting temp is 72 degrees and 75% complementarity is desired, temperature should be lower

Question 28

electrophoresis

Answer 28

- nucleic acids contain a net negative charge therefore they will migrate in an electric field. - conducted in agarose or acrylamide gel

Question 29

speed of nucleic acids

Answer 29

- proportional to voltage - proportional to charge on molecule - inversely proportional to MW - inversely proportional to friction/length - speed = E x q/length x MW

Question 30

intercalating fluorescent dyes

Answer 30

complex, aromatic organic molecules that intercalate in between bases due to hydrophobic effect

Question 31

unresolved zone

Answer 31

too clustered and too long as they have no run long enough

Question 32

resolution zone

Answer 32

- can be used for analysis as it had run long enough | - distance migrated is proportional to length of bp

Question 33

overresolved zone

Answer 33

have run for too long and is not visible for analysis

Question 34

using lines to determine fragment length

Answer 34

line of best fit must go through data point or it will introduce error