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Lecture 16

BIOC 2580 Lecture Notes - Lecture 16: The Double Helix, Erwin Chargaff, Fritz Albert Lipmann


Department
Biochemistry
Course Code
BIOC 2580
Professor
John Dawson
Lecture
16

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BIOC2580 Lecture 16
November 7, 2017
Secondary Structures of DNA
Erwin Chargaff and his colleagues (later 1940’s) found that in all cellular DNAs the number of
adenosine residues were equal to the number of thiamine residues and the number of guanosine
residues were equal to the number of cytidine residues
Known as “Chargaffs Rule”
A = T, G = C
However, % of GC and AT varied among different organisms
Rosalind Franklin and Maurice Wilkins
Use X-ray diffraction to identify the secondary structure of DNA
Chromosomes are extremely long DNA molecules and they tend to shear and fragment during
isolation
Each fragment is similar but not identical and it is impossible to form well ordered crystals with them
Instead, DNA can be drawn into hair like fibres that can still diffract and give valuable insights
Franklin’s X-Ray Diffraction Studies of DNA
Rosalind Franklin obtained the first useful X-ray diffraction images of DNA “Photo 51”
It showed that DNA molecules are helical
It revealed periodicities along the axis
A primary one of 3.4 Å
And a secondary one of 34Å
Francis Crick and James Watson
Relying on these accumulated data on DNA structure, Watson and Crick were able to come up with a
model for DNA secondary structure in 1953
The Double Helix: Geometry
Two helical DNA chains wind around a single axis forming a right handed double helix
The hydrophilic sugar phosphate backbone is on the outside of the helix facing the surrounding water
The hydrophobic bases are stacked inside the double helix perpendicular to helix axis
Each base of one strand is paired in the same plane with a base of the other strand, A with T and C
with G
Two strands of DNA are antiparallel to each other: the 3’,5’ phoshpodiester bonds run in opposite
directions
The vertically stacked base pairs are 3.4 Å apart
Each turn of the helix contained ~ 10 base pairs (34Å)
The diameter of the double helix is 20Å (2nm)
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Self Complementarity: The Essential Feature of the Watson-Crick Model
Self-complementarity allows each pre-existing strand of a double helix to sere as a template to guide
the synthesis of new daughter strands
This explained how a cell or an organism could reproduce - mitosis, and meiosis and heredity and
genetics
It also explained in principle how the cell can repair damaged DNA
Watson-Crick Base Pairs are Held Together by sets of Hydrogen Bonds
Three hydrogen bonds form between C and G
Two hydrogen bonds form between A and T
Higher the ratio of GC to AT the more difficult it is to separate to DNA strands
The two strands of the double helix are wrapped around each other (plectonemically coiled)
Strands cannot be separated except by unwinding form the end
Much like a phone cord, DNA can undergo “supercoiling” to give very compact structures
Double Helical DNA Contains Two Grooves: Major Groove and Minor Groove
The glycosylic bonds of a base pair are not collinear they are at an angle
So there is a short angle (minor groove) and a large angle (major groove) between them
Major and Minor Groove
When the two strands wind around each other, it leads to a wider gap between the backbone on one
side of the helix and a narrower gap on the opposite side
As the double helix winds up, major and minor grooves alternate on the surface of the duplex
Each group is lined by potential hydrogen bond donor and acceptor atoms of the bases that enable
specific interactions with proteins
The larger size of the major groove makes it more accessible of interactions with protein that
Recognize specific DNA sequences
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DNA: Secondary Structure is Largely Independent of Sequence
This is because the two kinds of base pairs have very similar shapes and properties
What forces stabilize the double helix?
Hydrophobic effect (the hydrophobic bases are hidden in the core)
Van Der Waals stacking of bases
H-bonding within base pairs
The “Central Dogma”of Molecular Biology
Adenosine Triphosphate (ATP): The Ubiquitous Cellular “Energy Currency”
Was discovered by Fritz Lipmann (also discovered coenzyme A)
ATP is a nucleotide it comprises of a base (adenine), a sugar (ribose) and three phosphate groups
which are labeled alpha, beta, gamma
A 70 kg person used about 40 kg of ATP during a restful day (assuming a ~50% of converting food
energy (8400kJ/2000kcal/day into ATP)
ATP is not a Store of Chemical Energy; Rather its a Link Between Catabolism and Anabolism
Cells breakdown nutrient molecules (catabolism) and use the available free energy to synthesize ATP
from ADP
ATP then donates its energy to endergonic processes that require energy (synthesis of metabolic
intermediates and macromolecules (anabolism), active transport across membranes, mechanical
motion etc)
ATP turns over (broken down and synthesized) very rapidly in cells; the typical lifetime of an ATP
molecule is measured in seconds to minutes
The Free Energy Change for Hydrolysis of ATP is Large and Negative
Most hydrolysis reactions are energetically favourable but the ΔG value (free energy released by
hydrolysis) depends on the nature of the bond being hydrolyzed
Typical values for amides, esters, and phophoesters are about 15-20kJ/mol
The ΔGhydrolysis = -30.5 kJ/mol
It is the phosphates that the energy requiring/releasing processes take place
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