Lecture 1 An introduction to DNA Topology

 The human cell contains 23 pairs of chromosomes  If we scale the cell nucleus to the size of Basketball then the DNA scales to 200km in length.  The cell nucleus is only 10 micrometres in diameter  The bacteria is made up of only one DNA molecule (which is a closed loop)

 DNA stands for Deoxyribonucleic acid  DNA.  DNA is often called the blueprint of life (the secret of life).  In simple terms, DNA contains the instructions for making proteins within the cell.  Its double helix structure was discovered by Crick and Watson 1953 (Nobel prize)

Mainly because of: its central importance to all life on Earth (it contains all genetic information) genetic tests medical benefits such as cures for diseases, genetically modified Food 5

 The DNA consists of two long molecules arranged into a ladder like structure called the double Helix  The two Backbones (strands) are bonded together by ladder rungs which are made up of pairs of bases.  Structure(video) Structure(video)

Each strand consists of: 2) Four Base Chemicals (Attached in Pairs) 1) A Sugar Phosphate Backbone

 DNA-Works DNA-Works  DNA packing DNA packing

 DNA of Bacteria consists of closed loop  It is made up of two circular strands which wrap around each other  The backbones are circular and the base pairs are the same as in the case of linear DNA (human)

 Bacteria and viruses are often made up of a single DNA circular molecule!

 Supercoil Supercoil (Animation)  Super coiling means coiling of a coil

 Circular DNA, has one helical turn every 10.5 bp in “relaxed”, form  Super coiling appears when two points are twisted in opposite directions

An electron micrograph of The DNA molecule in Relaxed and super-coiled States

 For a cell to divide, it must first replicate its DNA  Each strand of the original double-stranded DNA serves as template for the reproduction of the complementary strand.  DNA in Cell (replication 1) DNA in Cell  Replication2(Youtube) Replication2(Youtube)  Replication(circular) (DNA Tube) Replication(circular)

What is DNA topology about? An electron micrograph  Corresponding mathematical object

Circular DNA molecules can be knotted as Knotting may lead to cell Death. Certain Enzymes are responsible of that phenomena (topoinsomerase)

 Enzymes are proteins that catalyze (i.e., increase or decrease the rates of) chemical reactions  In enzymatic reactions, the molecules at the beginning of the process are called substrates, after the transformation they are called the products  Almost all processes in a biological cell need enzymes to occur at significant rates  Topoisomerase (video 1) Topoisomerase  Topoisomerase (video 2) Topoisomerase

 Mathematics: Deduce enzyme binding and mechanism from observed products

 Molecular basis of heredity. It is a complex giant molecule that contains, in chemically coded form, the information needed for a cell to make proteins. In other words it determines the order in which amino acids are joined to make a specific protein in a cell. DNA is a ladder-like double- stranded nucleic acid, which forms the basis of genetic inheritance in all organisms, except for a few viruses that have only RNA. DNA is organized into chromosomes and, in organisms other than bacteria, it is found only in the cell nucleus.proteinsnucleic acidRNAchromosomes  DNA is a ladder-like molecule, which means that it is made up of two halves (the ladder sides), formed of chains of nucleotide subunits. Each nucleotide contains a deoxyribose sugar, a phosphate, and a base. A set of three bases – known as a codon – acts as a blueprint for the incorporation of a particular amino acid, the subunit of a protein molecule. The two halves are joined together by the bases – a purine (adenine or guanine) or pyrimidine (cytosine or thymine) – forming pairs (the rungs). The bases form into two specific base pairs: adenine with thymine and guanine with cytosine. The sequence of base pairs along the DNA acts as a code carrying information about the sequence of amino acids in proteins. Three base pairs in sequence (triplet) name an amino acid and the next three name the next amino acid that needs to be joined and so on, to make a specific protein. The specific way in which the pairs form means that the base sequence is preserved from generation to generation. Hereditary information is stored as a specific sequence of bases.nucleotideamino acidbase pairs  Reference: