1. DNA Structure
The deoxyribonucleic acid, DNA, is a long chain of nucleotides which consist of
Deoxyribose (a pentose = sugar with 5 carbons)
Phosphoric Acid
Organic (nitrogenous) bases (Purines - Adenine and Guanine, or Pyrimidines -Cytosine and Thymine)

2. Bases
Purine (A+G)
Pyrimidine (T+C)

3. a nucleotide, a building block of DNA
a nucleotide, a building block of DNA. It is a phosphate ester of a nucleoside Nucleotide Nucleoside

4. a nucleotide, a building block of DNA

5. Note numbering system for carbons in ring
Also note the difference between a ribose used for building DNA and one used for RNA

6. DNA and RNA chains are made by connecting nucleotides together via chemical bonds
What is this chain RNA or DNA?

7. four different types of nucleotide possible in a DNA sequence, adenine, cytosine, guanine and thymine (ATCG)
Nucleotides are situated in adjacent pairs in the double helix.
Thymine and adenine can only make up a base pair
Guanine and cytosine can only make up a base pair

9. Double-stranded DNA is simply two chains of single- stranded DNA, positioned so their "bases" can interact with each other.
The sugar-and-phosphate 'backbone' is red, and the bases are blue.
the two strands travel in opposite directions; "anti-parallel".
The bases in the middle "pair up" with bases on the opposite strand, A+T, G+C
Hydrogen bonds hold stucture together

12. Genome- entire complement of genetic information.
Includes coding and non coding
Genes (exons and introns)
Alleles are different gene forms
Useful DNA for doing genome analysis

14. Plasmid- extra chromosomal DNA, found naturally mainly in bacteria
covalent closed circle, double stranded DNA
Non essential
Replicates independently
Occurs naturally in bacteria,
Molecular biologists recognise use and made them their own
Used as cloning vectors i.e. to transfer DNA between bacteria
Recombinant plasmids made by molecular biologists have been designed to carry foreign DNA into bacterial cells.
They have
unique restriction enzyme sites. Usually many different ones in a polylinker site
origin of replication for bacteria
selectable marker (often antibiotic resistance)

16. DNA isolation and purification
Important to obtain clean intact DNA in sufficient quantities to work with
Always do on ice
Most purification procedures include many of the following steps
Lysis of cells to release contents including DNA
Treatment with EDTA to bind divalent cations
Proteinase K treatment to digest proteins and tissue away from DNA
Separation of DNA from other contaminants in cellular soup using chemical and physical differences e.g. differential solubilities, precipitation, binding to columns and centrifugation

17. Cloning a Restriction Fragment into a Plasmid
                                                                                                                                                                                                               

18. Restriction endonucleases molecular scissors – they cut DNA
restriction enzymes are highly specific. They cut DNA only within very precise recognition sequences.
Pst 1 EcoR1 Sma1
The red line shows where the enzymes will cut the DNA. Notice that all of these recognition sites are symmetrical, or what is called "palindromic." This means that the recognition sequence on one DNA strand reads in the opposite direction on the complementary strand.

20. Examples of Restriction Enzymes
Organism from which derived
Target sequence (cut at *) 5' -->3'
Ava I
Anabaena variabilis
C* C/T C G A/G G
Bam HI
Bacillus amyloliquefaciens
G* G A T C C
Bgl II
Bacillus globigii
A* G A T C T
Eco RI
Escherichia coli RY 13
G* A A T T C
Eco RII
Escherichia coli R245
* C C A/T G G
Hae III
Haemophilus aegyptius
G G * C C
Hha I
Haemophilus haemolyticus
G C G * C
Hind III
Haemophilus inflenzae Rd
A* A G C T T
Hpa I
Haemophilus parainflenzae
G T T * A A C
Kpn I
Klebsiella pneumoniae
G G T A C * C
Sma I
Serratia marcescens
C C C * G G G
Sal I
Streptomyces albus G
G * T C G A C
Xma I
Xanthamonas malvacearum
C * C C G G G

21. DNA ligase
Enzyme
is molecular glue- sticks DNA together
H bonds are not enough to hold sticky ends together. A means of reforming the internucleotide linkage between 3’OH and 5’phosphate groups is required and ligase does this