Lecture 7 - The structure of DNA

Question 1

Who was Phoebus Levene and what theory did he propose? (1909)

Answer 1

Tetranucleotide theory

Showed each building block of DNA is a nucleotide:

Phosphate group linked to a deoxyribose sugar, linked to nitrogenous base

Question 2

What sugar is used in DNA and RNA?

Answer 2

DNA: pentose (5C) deoxyribose
RNA: pentose (5C) ribose

Question 3

What is the difference in structure between ribose and deoxyribose molecular structure?

Answer 3

Hydroxyl group in ribose on 2’

Hydrogen in deoxyribose on 2’

Question 4

What bases are purines?

Answer 4

Adenine

Guanine

Question 5

What bases are pyrimidine?

Answer 5

Cytosine

Thymine

Uracil

Question 6

What are nucleosides and where/what is the bond?

Answer 6

Sugar and base

Glyosidic bond: between C-1’ and N-9 (purine) or N-1 (pyrimidine)

Question 7

What are nucleotides and where/what is the bond?

Answer 7

Phosphorylated nucleosides

Ester links: between sugar C-5’ group and the phosphate

Question 8

What forms do nucleotides come in?

Answer 8

All come in mono, di and tri phosphate form

Question 9

What kind of molecule is DNA?

Answer 9

Polynucleotide with polarity

Question 10

What is the polarity associated with DNA?

Answer 10

Phosphodiester bond links the 3’C of one nucleotide to 5’ of the next

Base sequence is written and read 5’ to 3’

Polarity at the 5’ phosphate end –> 3’ hydroxyl end

Question 11

How did Levene ‘tetranucletoide model’ not support Avery et al?

Answer 11

Showed how DNA was simple and repetitive and could not be the genetic material

Not believed to be transforming principle

Question 12

Who was Erwin Chargaff and what did he propose?

Answer 12

Nucleotides in DNA should be present in equal proportions

(If Levene was correct)

%T = %A = %G = %C

Question 13

How did Chargaff show Levene to be incorrect?

Answer 13

Measured concentrations of each of 4 nitrogenous bases in different organisms

Different organisms had different DNA constitutions

Reality: %T = %A and %G = %C

Question 14

What did Linus Pauling say about DNA? (1951)

Answer 14

Described the alpha helix

Basic structure present in many proteins

Used X-ray crystallography - so shape must be helical

Question 15

How does an X-ray crystallography indicate the helical structure of DNA?

Answer 15

Crystalline target molecule diffracts X-rays

Causes exposed patches on photographic film

Resulting diffraction pattern is unique

Question 16

What did Huygens show with the ‘Wave theory of light’?

Answer 16

When light passes through a small opening, a wave front is propagated on the other side, single spot appears on a screen

Wider slit, all points across the slit act as point source - results in single slit diffraction pattern on screen

2 slits causes interference - causes double slit interference pattern on screen

With a diffraction grating the pattern becomes much sharper

Question 17

What did Augustin Fresnel extend the ‘Wave theory of Light’ concept?

Answer 17

Showed diffraction occurred around a solid object with the same width as a slit

Replacing slit with object of same size causes the same results

Question 18

What are the spatial relationships with the light theory?

Answer 18

Features that are close produce widely separated reflections

Features that are distant produce closely separated reflections

Vertical grids = horizontal spots
Grid = cross

Question 19

What did Maurice Wilkins do?

Answer 19

Stretched DNA and air dried it

Allowing for stretching into long fibres and mounting in front of X-ray source

Question 20

What was Maurice Wilkins produce?

Answer 20

1950 - Produced X-ray diffraction of dried DNA

High resolution

Without clear model in mind - too difficult to interpret

Question 21

What was Gosling and Franklin B model of DNA?

Answer 21

1952 - Used hydrated DNA after 100 h of exposure

Cross is unmistakable - DNA must be helical

Question 22

Who proposed the triple helical model of DNA?

Answer 22

Linus Pauling

Triple helix 3-strand model, with bases pointing outwards

(supported by Watson and Crick)

Question 23

What did Watson, Crick and Wilkins propose?

Answer 23

Double helix 2-strand model, with the bases pointing inwards

Question 24

What was each turn of the DNA helix measured to be?

Answer 24

3.4nm

(Spots far apart give features that are close together)

Question 25

How many bases were there thought to be per turn of the DNA helix?

Answer 25

10 bases per turn

(More distant the spots, smaller the actual distance in the target)

Question 26

What was the measured diameter of DNA to be?

Answer 26

2nm

Calculated using degrees of rise within the ‘X’

Question 27

Why did Pauling model of DNA fail?

Answer 27

(triple helix)

The negative charges of the stacked phosphate groups would repel each other and destabilise the molecule

• Sugar phosphate backbone must be compressed together

Question 28

How did Watson’s deduction support Chargaff rule?

Answer 28

2 purines = too wide for DNA

2 pyrimidines = too narrow for DNA

= A must pair with T
= G must pair with C

Question 29

What was Watson and Crick’s model in 1953?

Answer 29

Made DNA with metal scraps, almost 2m tall

Watson: specific A/T and G/C pairing scheme

Crick: idea of antiparallel strands

Everything clicked into place beautifully

Question 30

What are 6 key features of Watson-Crick model?

Answer 30

1. Right-handed (clockwise) double helix
2. The strands are anti-parallel 5’ –> 3’ and 3’–> 5’
3. Sugar-phosphate backbones are on the outside of the helix, bases oriented towards the central axis
4. Complementary base-pairing - bound by weak hydrogen bonds
5. Base pair distance (10.5 bp per turn, helix turn = 3.6nm
6. major and minor grooves - backbone not equalling spaced causing grooves

Question 31

How many bonds does A-T have?

Answer 31

2 hydrogen bonds

Question 32

What are the other structural variants of DNA?

Answer 32

A-DNA: occurs in low hydration conditions (uncertain whether this occurs)

B-DNA: most structurally stable

Z-DNA: taken up physiologically by stretches of alternating pyrimidines and purines