1. DNA and the Genetic Code1

2. DNA First isolated from the nuclei of cells in 1869
Oswald Avery (1944) presented evidence that suggested that nucleic acids were involved in the storage and transfer of genetic information.
Erwin Chargaff found that the DNA always contains the same relative amounts of certain pairs of amine bases. There are always equal amounts of
adenine and thymine.
guanine and cytosine.
James Watson and Francis Crick in
1953 determined the structure of DNA
as a double helix.
Rosalind Franklin created the early X-ray diffraction pictures of DNA. 2

3. Nucleic Acids Nucleic acids fall into two classes,
-- DNA
-- RNA
RNA, or Ribonucleic Acid, is built on the ß-D-ribofuranose ring.
DNA, or deoxyribonucleic acid, is based on a modified ribofuranose ring in which the -OH group on the second carbon atom has been removed. 3

4. DNA Structure DNA is made up of three units including:
I. A ribose sugar
Ribose
Deoxyribose
Ribose and deoxyribose differ in that ribose has an OH group on carbon 2 whereas deoxyribose has only a hydrogen attached. 4

5. DNA Structure DNA is made up of three units including
I. A ribose sugar
II. A phosphate group
The phosphates are attached at carbons 3 & 5. This defines the direction of the chain. 5 3
Phosphate
Deoxyribose
The phosphate groups alternate with the ribose sugar and are attached at carbon 3 and at carbon 5 5

6. DNA Structure DNA is made up of three units including
I. A ribose sugar
II. A phosphate group
III. A nitrogen (amine) base
There are four different amine bases: adenine, thymine, cytosine, and guanine. 6

7. A Nucleotide
Cytosine
The DNA strand is made up of alternating deoxyribose and phosphate groups with a nitrogen base attached as a side chain. 7

8. DNA Structure DNA is made up of three units A ribose sugar
A phosphate group
A nitrogen (amine) base
The amine bases are side branches to a strand made
of alternating phosphate and deoxyribose sugars.
These bases are attached at carbon 1 of the deoxyribose sugar.
Adenine
Cytosine 8

9. DNA Structure DNA is made up of three units: A ribose sugar
A phosphate group
A nitrogen (amine) base
These three molecules make up a nucleotide.
A DNA strand is a sequence of nucleotides.
The phosphates are attached at carbon 3 and carbon 5.
The nitrogen bases are side chains at carbon 1.
Adenine
Cytosine 9

10. DNA Structure
DNA consists of two strands of nucleotides. These strands are wound together in a spiral known as a double helix
The amine bases hold the strand together with a
sequence
of hydrogen
bonds 10

11. Complimentary Bases
Because of their size and their ability to hydrogen bond, the amine bases exist in complimentary pairs in the DNA double helix
Adenine always bonds with Thymine and Guanine always bonds with Cytosine 11

12. Hydrogen Bond Alignment
The size and shape of the amine bases is such that hydrogen bonds can only form at specific sites
Adenine only bonds with Thymine
Guanine only bonds with Cytosine
Therefore they form complimentary base pairs 12

13. DNA Structure -- Hydrogen Bonding
Adenine and Thymine form a base pair 13

14. DNA Structure Hydrogen Bonding
Guanine and Cytosine 14

15. Base Pair Sequence
The sequences of bases appears to be random but in reality nothing is farther from the truth. The base pair sequence contains the code by which proteins are synthesized in the cell 15

16. DNA Structure
In the double helix of a DNA molecule, the two strands are not parallel, but interwoven with each other. 
The helix makes a turn every 3.4 nm, and the distance between two neighboring base pairs is 0.34 nm. 
There are about 10 pairs per turn. 
The intertwined strands make two grooves of different widths, known as the major groove and the minor groove.
These grooves may facilitate binding with specific proteins. 16

17. DNA Shape
This color enhanced image taken by the Scanning Tunneling Electron Microscope shows a double helix 17

18. DNA Replication In human beings there are 23 pairs of chromosomes
Chromosomes are effectively a very long DNA sequence. This DNA sequence replicates itself during cell division
As the DNA double helix partially unzips as the hydrogen bonds between the nitrogen bases are broken
Sugar and base units are picked up from the surrounding solution.
Since only A –T and G-C combinations can occur the new strand is a complimentary replicate of the existing DNA 18

19. DNA Replication When cells divide the DNA must is replicated exactly
As the DNA unzips new complimentary strands are formed.
These new strands are exact replicas of the previously existing strands 19

20. DNA and the Genetic Code
Genes are long sequences of DNA that code for the formation of proteins
Typical genes are often thousands of base pairs long
Not all of the DNA strand appears to have genetic information
The sequence for a particular gene is very specific. 20

21. Gene Correspondance for Neuropilin-1
Species bp NP-1 Sense Primer Macaque ACCCGCACCTCATTCCTACATCAATGAGTGGCTCCAAATAGACCTGGGGG Human ACCCGCACCTCATTCCTACATCAATGAGTGGCTCCAAATAGACCTGGGGG Rat ACCCTCACCCCACCCATACATCAATGAATGGCTCCAAGTGGACCTGGGAG Macaque AGGAGAAGATCGTGAGGGGCATCATCATTCAGGGTGGGAAGCACCGAGAG Human AGGAGAAGATCGTGAGGGGCATCATCATTCAGGGTGGGAAGCACCGAGAG Rat ATGAGAAGATAGTAAGAGGTGTCATCATTCAAGGTGGGAAGCACCGAGAA Macaque AACAAGGTATTCATGAGGAAGTTCAAGATCGGGTACAGCAACAACGGCTC Human AACAAGGTGTTCATGAGGAAGTTCAAGATCGGGTACAGCAACAACGGCTC Rat AACAAAGTGTTCATGAGGAAGTTCAAGATCGCCTACAGTAACAATGGTTC
Macaque CGACTGGAAGATGATCATGGACGACAGCAAACGCAAGGCAAAGTCTTTTG Human GGACTGGAAGATGATCATGGATGACAGCAAACGCAAGGCGAAGTCTTTTG Rat TGACTGGAAAATGATCATGGATGACAGCAAGCGCAAGGCTAAGTCTTTTG Macaque AGGGCAACAACAACTATGACACACCTGAGCTGCGGACTTTTCCAGCTCTC Human AGGGCAACAACAACTATGATACACCTGAGCTGCGGACTTTTCCAGCTCTC Rat AAGGCAACAACAACTATGACACACCTGAGCTCCGGGCCTTTACACCTCTC Macaque TCCACGCGATTCATCAGGATCTACCCCGAGAGAGCCACTCATGGCGGACT Human TCCACGCGATTCATCAGGATCTACCCCGAGAGAGCCACTCATGGCGGACT Rat TCCACAAGATTCATCAGGATCTACCCCGAGAGAGCCACACATAGTGGGCT NP-1 Anti-sense Primer (reverse)
Macaque GGGGCCCCGAATGGAGCTGCTGGGCTGTGAAGTGGAA Human GGGGCTCAGAATGGAGCTGCTGGGCTGTGAAGTGGAA Rat CGGACTGAGGATGGAGCTACTGGGCTGTGAAGTAGAA 21

22. Protein Synthesis
DNA is found in the chromosomes which are found in the nucleus of the cell
DNA stores the genetic code for an organism through its sequence of the nitrogen bases
The genetic code is transferred via RNA to the ribosomes in the cytoplasm outside of the cell nucleus where protein in synthesized
The information required for protein synthesis is passed through a similar unzipping and replication process 22

23. RNA and Protein Synthesis
The transfer of information for building proteins is then accomplished by the RNA.
RNA is similar to DNA but there are some important differences
RNA is a single strand rather than a double helix
Deoxyribose is replaced with ribose
The nitrogen base thymine is replaced with uracil 23

24. RNA Structure
Ribose has a slightly different structure from deoxyribose.
Ribose has an –OH group on carbon 2 rather than a H as in deoxyribose. 24

25. RNA v DNA The structure of Uracil differs only slightly from Thymine
Thymine has a methyl side group
Uracil
Thymine 25

26. Messenger RNA
Messenger RNA or mRNA copies and carries the genetic code from the DNA template within the cell nucleus to the ribosomes where proteins are synthesized.
It essentially aligns itself with the DNA and produces a complimentary copy 26

27. Messenger RNA
Messenger RNA (mRNA) acts as a template for protein synthesis
It has the same sequence of bases (in the 5' to the 3' direction) as the DNA strand that holds the gene sequence.
mRNA strands can range from 300 to as many as 7000 nucleotides.
The length depends on the size and the number of proteins related to the code. 27

28. Transfer RNA
Transfer RNA acts as an amino acid carrier in the formation of proteins.
Through a decoding mechanism it facilitates the addition of an amino acid to a peptide chain forming a protein.
It directs the insertion of amino acids in the proper sequence in the poly peptide chain through sets of three nitrogen bases known as codons. 28

29. Transfer RNA
tRNA molecules are covalently attached to the corresponding amino-acid at one end, and at the other end they have a triplet sequence (called the anti-codon) that is complementary to the triplet codon on the mRNA.
All tRNA molecules are in the range ~70-90 nucleotides. They have a molecular weight of ~25,000 29

30. RNA Codons U C A G 30 UUU Phe UCU Ser UAU Tyr UGU Cys UUC UCC UAC UGC
UUA
Leu
UCA
UAA
Term.
UGA
UUG
UCG
UAG
UGG
Trp
CUU
CCU
Pro
CAU
His
CGU
Arg
CUC
CCC
CAC
CGC
CUA
CCA
CAA
Gln
CGA
CUG
CCG
CAG
CGG
AUU
Ile
ACU
Thr
AAU
Asn
AGU
AUC
ACC
AAC
AGC
AUA
ACA
AAA
Lys
AGA
AUG
Met
ACG
AAG
AGG
GUU
Val
GCU
Ala
GAU
Asp
GGU
Gly
GUC
GCC
GAC
GGC
GUA
GCA
GAA
Glu
GGA
GUG
GCG
GAG
GGG 30

31. Ribosomal RNA
Ribosomal RNA (rRNA) is one of the structural components of a cell structure known as a Ribosome.
Ribosomes structurally support and catalyze protein synthesis. 31

32. DNA Replication During Cell Division
During cell replication the DNA unwinds and each strand builds a new complimentary strand. 32

33. RT-PCR or Reverse Transcriptase Polymerase Chain Reactions
RT-PCR was first developed by Cary Mullis for which he was awarded the Nobel Prize in Chemistry
Replicated DNA can be then separated and classified
This process allows the DNA from very small amounts of
cellular material to be replicated
DNA is extracted and broken down into smaller fragments
using restriction enzymes
The DNA is then replicated and separated using gel
electrophoresis 33

34. RT-PCR and DNA Replication
NP-1
Cyclo
Primers bp bp bp bp
Semi-quantitative RT-PCR was used to ascertain the relative presence of neuropilin-1 in assays from various stages of the menstrual cycle. Cyclophilin was used as an internal standard.
The NP-1 band confirms the presence of neuropilin-1 at all luteal phases. The relative intensity of the NP-1 band relative to cyclophilin appears to be elevated at thre midlate stage.
EARLY
MID
LATE
MENSE
CTRL
RT-PCR gel showing relative amounts of NP-1 using cyclophilin as an internal standard. 34

35. DNA Sequencing
Dr. Lee Hood (Univ. of Washington) invented a device that can sequence the bases for a DNA fragment. 35

36. Forensic DNA Analysis
The DNA fragment contains codons that code for proteins
It also contains regions where there is no coded message in the base sequence
The application of a restriction enzyme cuts this part of
the DNA into fragments.
The sequence and hence the fragment sizes are unique
for each individual (Except for Identical Twins) 36

37. DNA Fingerprinting Process
DNA fingerprinting is a multistep process. 37

38. Forensic DNA Analysis Used to identify people in criminal cases.
Used to establish identity, paternity and ancestry.
Used to study evolutionary changes in species. 38

39. Forensic DNA Analysis
DNA evidence is only as good as the person performing the tests. Care must be taken to guard against contamination for legal evidence to stand.
Chain of evidence rules 39