Nucleic acids

Question 1

Components of nucleic acids

Answer 1

• Double helix structure
• Made up of three different segments - base pair, phosphate and ribose/deoxyribose
• Sugar units form a chain - the backbone
• Phosphates link the sugar units on the outside of the double helix
• Antiparallel duplex (strands in opposition directions) - always gives sequences from carbon 5 to carbon 3

Question 2

Nucleobases - two different classes

Answer 2

Two classes:
1. Pyrimidines (partial double bond character around the ring) - Thymine, Uricil, cytosine
2. Purines - Adenine and Guanine
* Adenine and Thymine/Uricil bond with two hydrogen bonds
* Cytosine and Guanine bond with 3 hydrogen bonds

Question 3

Phosphates/phosphodiesters

Answer 3

• They link up the bases from carbon 5 to carbon 3
• Deprotonated really easily
• Allows DNA to be controlled, packed, stabilised or destabilised
• Asymmetric linkage gives DNA strands ‘direction’

Question 4

Primary structure of DNA

Answer 4

• Primary stucture = sequence of nucleotides
• Duplex formed with strand complementary sequence = complementary bases in opposite order
• C is complement to G
• A complement to T or U
• Longer duplex with higher GC content = more stable due to more hydrogen bonds

Question 5

Hybridisation
What is the complementary sequence for:
ATGTCTTGAACA

Answer 5

1. Split strand into three base units for clarity: ATG TCT TGA ACA
2. Write down the complementary bases: TAC AGA ACT TGT
3. Reverse the order to give strand in 5’ to 3’ format: TGT TCA AGA CAT

Question 6

Double helix

Why does duplex DNA have a helical strutcural?

Answer 6

• Negatively charged phosphate groups repel each other
• Base pairs hydrogen bond
• Stacking nucleobases through hydrophobic / Van der Waals interactions compacts duplex vertically

Question 7

A, Z and B form DNA

Answer 7

• B-DNA is the most common (right handed)
• A-DNA is similar to B-DNA but is more twisted so the major groove become huge and the minor groove become small (right handed)
• Z-DNA is much less common, it is left handed

Question 8

Nucleosomes

Definition

Answer 8

Two coils of DNA around 8 histones

Question 9

Replication of DNA

Answer 9

1. Two strands separate as the hydrogen bonds break between the base pairs due to DNA helicase
2. Free nucleotides are attracted to their complementary base pairs
3. DNA polymerase joins the base pairs and they form hydrogen bonds
4. Now two identical strands have formed

Question 10

Transcription

DNA to mRNA

Answer 10

• DNA strand splits into two and one strand is used as a template
• Transcription factors signals to RNA polymerase where to begin transcription
• RNA polymerase brings in new base pairs that are complementary to the DNA sequence
• The resulting strand is mRNA which is then used to code specific peptide sequences (proteins)

Question 11

Translation

Answer 11

1. Initiation: the ribosome binds to the mRNA and then the tRNA attaches to the start codon
2. Elongation: a specific order of amino acids are brought to the ribosomal site by the tRNAs according to the sequence of codons in the mRNA, they then form peptide bonds
3. Termination: the stop codon stops any more translation and a newly formed protein is formed