DNA Structure

Question 1

Describe the structure of a nucleotide

Answer 1

• Composed of a Pentose sugar, a phosphate moiety that can vary in nucleotides and an organic (aromatic) nitrogenous base
• The nitrogenous base can accept protons

Question 2

Contrast primary structure of rna and dna

Answer 2

• In RNA the Penrose sugar is ribose, in DNA it is deoxyribose
• Very chemically similar
• Linear polymers composed of varying sequences of 4 different building blocks called nucleotides
• Ribose is arranged as a 5 membered ring with 1’C linked to oxygen by 4’C
• 5’C is attached as a side chain to 4’C
• In DNA the Penrose sugar is 2’-deoxyribose with a H group rather than an OH group attached to 2’C
• Absence of a 2’ OH group in dna further increases its resistance to hydrolysis

Question 3

Why does dna form a helix

Answer 3

The planar ring is subject to steric strain, relieved by puckering so that the 2’ or 3’ carbon is out of the plane
• Puckering induced by every C atom trying to arrange as a tetrahedral
• DNA double helix is because of the sugars. Twist comes from structure of the sugars as puckering causes a subtle twist

Question 4

Purine vs pyrimidine bases

Answer 4

• Purines have a double ring structure of a 5 membered ring fused with a six membered ring
• Adenine and guanine are purines
• Pyrimidines have a single six membered ring structure
• Cytosine, thymine and uracil are pyrimidines

Question 5

Keto vs amino bases

Answer 5

• The groups at position 4 of pyrimidines and position 6 of purines determine whether the base is a keto base or an amino base
• Keto bases have a c=o group
• Amino bases have a -NH2 group
• Only difference between thymine and uracil is the presence of -ch3 at c2
• N-9 of a purine or N-1 of a pyramiding is attached to C-1’ of the sugar by an N-beta-glycosidic linkage
• Base lies above plane of the sugar i.e. configuration of the glycosidic linkage is beta

Question 6

nucleoside vs nucleotide

Answer 6

• Nucleoside = sugar + base
• Nucleotide = sugar + base + phosphate
• Adenine -> adenosine/ deoxyadenosine
• Guanine -> guanosine/deoxyguanosine
• Cytosine-> cytidine/ deoxycitidine
• Uracil-> uridine
• Thymine -> thymidine

Question 7

What type of nucleotides make up dna

Answer 7

Nucleotide monophosphates

Question 8

Bases

Answer 8

• In a base the 1’C is joined by a beta glycosidic linkage to the base, which is in the plane above the sugar ring
• A glycosidic linkage is any bond between a sugar and another compound where you lose the OH group of the sugar in a condensation reaction
• Bases form planar rings
• Bases have pi orbital systems
• Bases can be purines or pyrimadines

Question 9

How do nucleic acids interact with proteins

Answer 9

VDW interactions

Question 10

What holds nucleic acids together

Answer 10

VDW interactions

Question 11

How is a nucleotide added to the 3’ end

Answer 11

• During polymerisation the alpha phosphoryl group of a free nucleotide triphosphate undergoes nucleophilic attack by the 3’C-OH group of the nucleotide at the 3’ end of the growing chain
• The strand attacks the nucleotide
• The alpha phosphoryl is the most electro positive phosphoryl group of the 3, it is the one closest to the carbon of the sugar
• This results in the addition of a nucleotide to the 3’C via a phosphodiester bond (c-o-p-o-c) with the elimination of pyrophosphate
• 3’C linked by phosphate group to 5’C of new sugar
• Polymerisation is catalysed by polymerase enzymes and is fuelled by the energy-rich phosphoanhydride bonds (p-o-p)
• Hydrolysis of phosphoester linkages highly enthalpically favourable as you lose beta and gamma phosphate

Question 12

Why do nucleic acids have direction

Answer 12

• Phosphodiester bonds link the 3’ and 5’C of all the sugars within the chain
• At one end there will be a free 5’ phosphate group
• At the other end there will be a free 3’ OH group
• We write nucleic acid sequences in the 5’ to 3’ direction

Question 13

Why is rna susceptible to base catalysed hydrolysis

Answer 13

• The presence of the 2’ OH group in RNA makes it susceptible to base-catalysed hydrolysis
• Free hydroxyl group can be deprotonated if you use a base
• Therefore DNA is much more stable than RNA so is better suited to being the hereditary material
Base attacks 2’ OH group
E- pair move to phosphate
Hydrolysis of phosphodiester bond

Question 14

Describe the structure of duplex dna

Answer 14

• 2 right handed helices
• Strands run in anti parallel direction
• Purine and pyrimidines always facing each other- gives constant width and allows for constant symmetry of double helix
• Complementary bases on each strand form hydrogen bonds with each other
• Bases project perpendicular to the helical axis
• Bases are parallel to one another and stack, partially overlapping as they are partially rotated

Question 15

Role of VDW and hydrophobic interactions in stabilising dna

Answer 15

• VDW and hydrophobic interactions between the planar base rings stabilise the DNA structure
• VDW is the largest force holding DNA together
• Can’t fit water between bases as they are stacked - gives enormous hydrophobic effect as aromatic bases are hydrophobic

Question 16

Major and minor groove of dna

Answer 16

• Due to hydrogen bonding, base paired nucleotides are not directly opposite each other
• This results in two grooves of different widths, major groove and minor groove
• Major groove is formed by large arc and minor by small arc
• The major groove is large enough to allow intimate protein binding to the double stranded DNA molecule

Question 17

Chargaff’s rules

Answer 17

• Chargraff’s rules explain base composition of DNA
• %A=%T and %G=%C
• %keto bases = %amino bases
• % purine bases = % pyrimidine bases
• GC compared to AT varies between species but constant within a species, provides evidence that dna is the heritable material

Question 18

Wilkin and franklin x ray diffraction

Answer 18

• DNA is a helical molecule
• Bases form a stack of parallel rings parallel to the fibre axis
• X like image proved DNA must be helical as X shows rotational symmetry
• Major periodic distances could be inferred from image- distance between bases and between turns
• Used fibre diffraction
• Conc solution of dna, decrease water to increase conc, gives viscous solution
• Can dip in glass rod and pull out fibres that can be stretched out so molecules line up
• Used fibres with high humidity, this is most common form of DNA as in most aqueous conditions
• If you lower humidity there are many more spots on the image as dna changes conformation from B form to A form
• Spot missing shows double helix, as you go around the P of each strand line up and cause destructible interference
•

Question 19

Watson crick base pairing

Answer 19

• A-T 2H bonds
• C-G 3 H bonds
• Key component of DNAs function, key in replication, transcription and translation as it provides specificity

Question 20

B form dna

Answer 20

• Right handed helices
• Rise between adjacent bases is 0.34nm
• Helical repeat is 3.4 nm
• 10.4 bases per turn
• Helix is 2nm wide
• B DNA has C-2’ endo puckering

Question 21

A form dna

Answer 21

• A form DNA is usually found in viruses as there is no water in the viral capsid
• A form DNA is a more compact right hand helix with 11 base pairs per turn, large tilt of base pairs and a central hole
• A DNA has C-3’ endo puckering that leads to 11 degree tilting of base pairs away from perpendicular to the helix
• RNA helices further induced to take A form because of steric hindrance from the 2’-OH group as it would be too close to 3 atoms of the adjoining phosphoryl group and to one atom in the next base
• Phosphorylation and other groups in the a form bind fewer H2O molecules than those in B DNA so dehydration favours the A form

Question 22

Z form dna

Answer 22

• Z form DNA is a left handed helix with 12 base pairs per turn and a zig-zag appearance
• You can make antibodies against Z form DNA that will stay in chromatin so it is thought to be naturally occurring
• Existence of Z form dna shows DNA is a flexible, dynamic molecule
• Biochemical conditions within the cell, and particularly protein-dna interactions can locally alter dna secondary structure
• Usually determined by water, protein binding occludes presence of water

Question 23

How does ssRNA adopt secondary structure

Answer 23

• RNA is flexible and unstructured but with pockets of structure where complementary base pairing forms hairpin or stem-loop structures
• More flexible than DNA
• Nucleotides have same properties as in DNA so will be helical due to orientation of 3’ and 5’ carbons, bases will stack
• Non complementary regions of RNA give bulges
• As single strand of RNA is more flexible, non Watson-Crick base pairing can also form
• Similar folding to proteins
• There is also 3D folding due to Watson-crick base pairing
• RNA catalysts can also exist with enzymatic activity

Question 24

Examples of rna secondary structure

Answer 24

• Hairpins form when complementary sequences of bases are close together
• Stem loop structures form where the complementary sequences are more distant
• Complementary sequences within a single stand come together to form a double-helical structure
• May include mismatched base pairs that bulge out from helix
• Mismatches destabilise local structure but may intriduce deviations from standard double helical structure that are important for higher order folding and function
• Metal ions assist in stabilisation of more elaborate structures
• Well-defined RNA secondary structures containing hairpin and stem-loop structures are important for ribosomal RNA (rRNA) and transfer RNA (tRNA)
• Thermodynamically stable as there is a large hydrophobic effect as hydrophobic bases are hidden from the environment

Question 25

Duplex RNA

Answer 25

• Duplex RNA in these regions resembles A DNA
• Hybrid DNA-RNA duplexes can form and also have an A DNA – like conformation
• This occurs during transcription when mRNA is synthesised on a DNA template and replication when RNA primers are synthesised to initiate DNA synthesis.