DNA stands for DeoxyriboNucleic Acid and carries genetic information in cells. In eukaryotic cells most DNA is found in the nucleus as linear chromosomes, with some circular chromosomes in organelles. This extranuclear DNA includes mitochondrial DNA and plastid DNA. In prokaryotic cells chromosomal DNA is circular and is found in a nucleoid consisting of DNA, RNA and protein. Most prokaryotic cells have plasmids, circular DNA which replicates independently from the chromosomal DNA and can sometimes be passed between organisms during conjugation. Information in DNA includes not only genes to be transcribed but also binding regions for inhibitor or promoter proteins which regulate the amount and timing of gene expression.
The building blocks of DNA are four nucleotides; the purines Adenine (A) and Guanine (G) and the pyrimidines Cytosine (C) and Thymine (T). These are joined together in long strange by covalent phosphodiester bones. In DNA two strand join non-covalently through hydrogen bonds between complimentary base pairs (A+T and C+G) to form two stranded DNA. This coils into a right handed helix with ten nucleotides per turn of the helix. The bases point into the center of the helix with a phosphate backbone around the outside which gives DNA a negative charge. The helix contains major and minor grooves due to the way it twists. Major grooves have more H bond acceptors and donors (O and N, and H respectively) exposed than minor grooves.
Two strands will only pair if they are complementary, meaning that the complimentary base pairs line up. For example the sequence AAAA is complimentary to TTTT but not to itself or GGGG. Strands are in an antiparallel orientation; 5' carbon of one nucleotide binds to 3' carbon of adjacent nucleotide - this is oppositely orientated on each opposing strand, 5' -> 3' and 3' -> 5' directions.
To sequence genomes, Allan Maxam and Walter Gilbert made the Maxam-Gilbert method, or chemical method. This involves chemicals cleaving DNA at specific base sequences.
Another method, called the Sanger or chain termination method, involves dideoxynucleotides interfering with DNA enzymatic synthesis.
Genomes differ from person to person commonly by SNPs or single nucleotide polymorphisms. If SNPs occur close together on a chromosome, they usually become inherited together in haplotypes. Genomes also differ by DNA duplications, deletions, and rearrangements.
Eukaryotic genomes contain lots of repeated sections of DNA. This property makes eukaryotic genomes very large. For instance, the human genome is 3200 Mb (mega base) long.
One type of repeat includes tandem repeats. These account for about 10 - 15% of mammalian genomes which includes many types of sequences of DNA. One repeated unit can vary 1 - 2000 bp (base pairs) in length. Most units are 10 bp or less - simple-sequence DNA repeats.
These types of sequences will not usually be transcribed (made into RNA) but may account for creating certain physical properties at particular regions on a chromosome - they are usually found at the centromere. Telomeres also contain simple-sequence repeats.
Another type of repeat includes interspersed repeats. These repeats are spread across the genome. Different kinds include transposable elements, LINEs, and SINEs.
Different Types of DNA
B-DNA = right handed - most common type in the cell
Z-DNA = left handed - long, thin, biological significance relatively unknown
A-DNA = also right handed but shorter and thicker than B-DNA - created by dehydrating the B-DNA
Centromere = region that holds together sister chromatids before anaphase
Chromatin = DNA-protein complex fibres that chromosomes are made up of
Chromosome = a single molecule of DNA found in eukaryotes
col (colicinogenic) factor = enable bacteria to secrete compounds (colicins) which kill col factor-lacking bacteria
Cryptic plasmid = unknown function
Euchromatin = in interphase, a type of loose and uncondensed DNA-containing chromatin
F (fertility) factor = involved in conjugation
Genome = the DNA which is a complete copy of total genetic information of an organism/virus. To sequence a genome, a number of methods can be used
Haplotype = SNP group positioned near each other on a chromosome, usually inherited together
Heterochromatin = in interphase, a type of compact DNA-containing chromatin
LINEs = long interspersed nuclear elements - 6000 - 8000 bp long repeated DNA sequence
Metabolic plasmid = allow metabolic reactions to take place by producing certain enzymes
Purines = nitrogen-containing, two-ringed molecule
Pyrimidines = nitrogen-containing, one-ringed molecule
R (resistance) factor = drug resistant gene carriers
SINEs = short interspersed nuclear elements - > 500 bp long & relies on enzymes for movement
Single nucleotide polymorphisms = change in a single base in DNA which takes place between individuals of a particular species
Supercoiled = when DNA twists upon itself
Telomere = sequences of DNA at the end of a eukaryotic chromosome which can be broken down by telomerase
Telomerase = enzyme which carries out catalysis of forming extra copies of telomeric repeat sequences
Transposable elements = or transposon, sequence of DNA that can move to different chromosome locations
Virulence factor = allow bacteria to enter the host cells by enabling bacteria to produce toxic proteins, leading to disease
W. M. Becker, L. J Kleinsmith, J. Hardin, G. P. Bertoni (2009) The World of the Cell (7th ed.) San Fransisco : Pearson Education, Inc., chap. 18 ; pg 513 - 538
H. R. Horton, L. A. Moran, K. G. Scrimgeour, M. D. Perry, J. D. Rawn (2006) Principles of Biochemistry (4th ed.) New Jersey : Pearson Education, Inc., chap 19 ; pg 583 -604
Human Chromosomes Picture from University of Leicester (n/a) DNA, genes, and chromosomes [online] http://www2.le.ac.uk/departments/genetics/vgec/education/under18/topics/dnageneschromosomes Creative Commons Licence [Accessed on 02/04/2012]
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