DNA Structure Flashcards
Describe the history of the discovery of DNA
James Watson and Francis Crick worked out the structure of DNA in 1953. By using data from other scientists (Rosalind Franklin and Maurice Wilkins) they were able to build a model of DNA. Watson and Crick got additional information from an unpublished report by Franklin, which discussed the dimensions of the helix and the orientations of the two strands, details that proved crucial to their model. Franklin’s report also included her conclusion that the nitrogenous bases were hidden on the inside of the DNA molecule. The X-ray crystallography data they used showed that DNA consists of two strands coiled into a double helix.
Describe the general points about the structure of DNA
- DNA acts as a store for genetic information, this was first shown in studies of pneumococcal transformation and of bacteriophage infection of E. Coli
- DNA has a double helix structure, made of complementary polynucleotide chains, minor and major grooves form receptors for drugs
- The DNA bases encode genetic information, the central dogma = “DNA makes RNA makes protein”
- DNA is present as chromatin in the nucleus, it is not “free”
- DNA can be damaged by radiation and chemicals, which means DNA has to repair itself.
- DNA is conformationally mobile and can form many different states
- DNA is made up of repeating units of nucleotides – sugar (deoxyribose), phosphate, base (ATGC).
- Each strand has a polarity.
- DNA is acidic as the phosphates are negative and are acidic as they lose their protons. When DNA is packaged in chromatin due to the DNA being negative and the protein (histone) is positive, this causes attraction.
- Pyrimidines (single ringed/smaller bases)- Thymine (T) and Cytosine (C).
- Purines (double ringed/larger bases) – Adenine (A) and Guanine (G).
- A and T, two hydrogen bonds. G and C, three hydrogen bonds.
- As the distance between both pairs are similar size this provides for a regular helix.
- DNA strand are held together by AT and GC base pairs, bases held together by hydrogen bonds. Distance between G and C is 1.08 nm. A and T is 1.11nm.
- Bases on inside of the helix- phosphate and sugars on outside.
Describe the history of DNA (part 2)
Double helix is stabilised by hydrogen bonds and Van der Waals interactions. Maurice Wilkins and Rosalind Franklin obtained x-ray diffraction photographs of fibers of DNA. This shows that DNA is formed of two strands that wind in a regular helical structure. From this data and others James Watson and Francis Crick deduced a structural model for DNA that accounted for the diffraction pattern.
Describe the structure of the Watson-Crick model (4)
Two helical polynucleotide strands are coiled around a common axis. The stands are antiparallel, mean that they have opposite directionality.
- The sugar-phosphate backbones are on the outside and the purine and pyrimidine bases lie on the inside of the helix.
- The bases are nearly perpendicular to the helix axis, and adjacent bases are separated by approximately 3.4 Å. The helical structure repeats on the order of every 34 Å, with about 10.4 bases per turn of helix. There is a rotation of nearly 36 degrees per base (360 degrees per full turn/10.4 bases per turn).
- The diameter of the helix is about 20 Å
Describe syn and anti
Syn and anti refer to the orientation of the N-glycosidic bond between the base and deoxyribose. In the anti orientation, the base extends away from the deoxyribose. In the syn orientation, the base is above the deoxyribose. Pyrimidines can be in anti orientations only, whereas purines can be anti or syn.
Describe Unusual DNA structures (4)
- Left-handed/Z DNA formed by 5’…GCGCGCGCGC… or 5’GTGTGTGTGTG…
- Four-stranded junction – Holliday junction
- Forms during normal chromosome replication. Two DNA strands, if the strands are complementary they can exchange strands and can get base pairs. Four-way junction involving strand exchange, forms when two chromosomes join, allows the exchange of genetic information. It is important in repairing damage.
- Higher order complex chromosomes for example, tetraplex DNA, is formed at the telomeres (which protect the chromosomes). Tetraplex DNA is formed by the DNA folding back in itself, it is found at the end of chromosomes. Involves G-rich sequences.
Describe the levels of DNA structure
Primary – Sequence of bases (found by DNA sequencing)
Can be useful when developing drugs/vaccines to target specific enzymes.
Secondary – Helical structure [e.g. A,B,Z] (X –ray crystallography and chemistry)
Tertiary – DNA supercoiling (electron microscopy)
DNA is the nucleus is 2m long, needs to coil to fit.
Quaternary – Interlocked chromosomes [e.g. when bacteria replicate and chromosomes interlock initially]
Describe the structure of DNA in bacteria (3)
E. coli DNA is circular and comprises of 3 x 106 base pairs (around 3 million).
Is supercoiled – The DNA ribbon itself is twisted in space (it has to be supercoiled in bacteria to replicate, supercoil stores energy).
Supercoiling is caused by the enzyme DNA gyrase (which uses ATP to twist up the DNA like a rubber band which is reversible).
E. coli chromosome is circular and organised into around 50 independently supercoiled domains, with a central domain.
Describe DNA in eukaryotic cells (7)
Humans have 3 billion base-pairs of DNA, organized into 23 pairs of linear chromosomes.
DNA is complexed with histones and made into a fibre, this is called chromatin.
The nucleosome is the basic building block of chromatin.
Nucleosomes were first in electron microscopy as “beads on a string”
DNA has to be tightly packed up in order to fit into the nucleus.
The DNA double helix is wound around 8 histone subunits (two molecules each of 2A, 2B, 3 and 4 known as histone octate). Histones have tails which are positively charged amino acids, this interacts with the negative phosphate groups in DNA, this electrostatic attraction allows the DNA to store around the outside/wrap around the histone octate. This keeps the DNA in place compacting the DNA by a factor of 6 (otherwise DNA would be 2m long) still not enough. Histone 1 binds to the outside and to linker DNA. The combined loop of DNA around the histones is the nucleosome.
Multiple nucleosomes are coiled together, which then stack on top of each other. This results in a fibre of nucleosomes called chromatin, which is then condensed to a 30nm chromatin fibre, this is then looped and coiled more, using other proteins to form chromosomes, only form when cells are dividing
Describe how DNA damage causes mutations to DNA (3)
Spontaneous - e.g. loss of bases, or hydrolysis of C to U
Chemicals–change base structure - (but also cyclophosphamide)-insert between bases - (intercalators such as doxorubicin widely used as anticancer drugs)
Radiation-UV light produces thymine dimers-Ionising radiation (X-ray, gamma-ray) break DNA chromosomes to cause leukemia
Describe the importance of DNA base repair (4)
Maintains genome stability
50-100 different enzymes/proteins involved – large investment for the cell
Patients with xeroderma pigmentosum- have a defect in excision repair that deals with UV damage to DNA. Very prone to skin cancer.
Other cancer-prone families have DNA repair defects
