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11. Nucleic Acids / Genes. Chapter 18. Nucleic Acids – the Master Molecules. Nucleotide:Phosphate + Sugar + Heterocycle;nucleoside: No phosphate. DNA - DeoxyriboNucleic Acid RNA - RiboNucleic Acid. A denosine. T hymidine. G uanidine. C ytidine. A Sequence of DNA.

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11. Nucleic Acids / Genes

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11. Nucleic Acids / Genes

Chapter 18


Nucleic Acids – the Master Molecules

Nucleotide:Phosphate + Sugar + Heterocycle;nucleoside: No phosphate

DNA - DeoxyriboNucleic AcidRNA - RiboNucleic Acid


Adenosine

Thymidine

Guanidine

Cytidine

A Sequence of DNA


Base-Pairing - the ‘Glue’ of the Double Helix

Thymine Adenine

Cytosine Guanine

to ‘backbone’

The DNA of each human cell contains ~6 billion of these base-pairs


DNA - Storehouse of the Genetic Code

The Double Helix


Chromosomes - chains of DNA contained in the nucleus of every cell. Arranged in 23 pairs (of each pair, 1 set comes from sperm and 1 from egg). 

Total length of these molecular threads in each cell = ~2 meters !

When cells divide one strand from each ‘double thread/helix ’ goes to each new cell thus carrying the identical sequence/information.


The sequence of bases A, C, T & G contains the information to direct the synthesis of all the proteins in the body and is called the Genetic Code.

The sequence of bases, somewhere on a chromosome, that is responsible for each protein is called a gene.

If there are only 4 ‘bases/letters’ which must uniquely code for 20 different amino acids then the relationship cannot be 1:1 or 2:1 but must be 3:1, ie. a triplet code.


Why is this so?

  • we need to code for 20 different amino acids using 4 different Bases (A,T,G,C)

  • If only 2 bases used in the code, the number of possibilities is 4x4=16

  • Thus if we use a sequence of 3 bases , we can code for 4x4x4=64 amino acids


RNA transforms genetic info into action

  • Messenger RNA (mRNA) –carries info from DNA out of the nucleus into the cytoplasm

  • Transfer RNA (tRNA) –finds and transports each amino acid to the protein synthesis site


Thymine(T) in DNA is replaced by Uracil (U) in RNA

  • Thymine Uracil


But base pairing still OK

  • A-U base pairs in RNA


Can you spot the error in this?


RNA contains U in place of T

  • Thus, whenever U is present, must be a ribose unit (not deoxy ribose)


Codons and anticodons!

  • m-RNA sends its information to t-RNA via complementary interactions between base pairs

  • Thus G in m-RNA codon becomes the complementary base C in the t-RNA anticodon (and vice versa)

  • A in m-RNA codon becomes U in t-RNA anticodon (and vice versa)


Lots of Possibilities!

  • With 4 different bases in RNA arranged in codons of 3 bases each, total number of codons possible=4x4x4=64

  • Some redundancy: ie GCA and GCC both code for the amino acid lysine

  • Signal to terminate the protein chain is given by UAA, UAG or UGA


Building a new DNA Chain (Replication)


The GENETIC CODE - a Proposal and a Nobel Prize

First published by James Watson* and Francis Crick in 1953. Nobel prize awarded in 1962 to Watson,Crick and M. Wilkens (based on X-ray results by Rosemary Carter). 

* head of the World Genome Project, ~1990 -2001.

 Bedtime reading: The Double Helix (J. Watson)


The Genetic Code

AUG also = start


The Human Genome contains more than 100,000 genes each of which can be 1000 - 100,000 units (base-pairs) long ......... but ..........

this is only ~3 - 5% of the total number of units available!

Why? - maybe safety How to find? - start/stop signals


transfer RNA: withanticodonand related amino acid

anticodon

a.a. binding site

valine


The human body can repair DNA/RNA by cutting, splicing, inserting, but mutations can occur !

Mutation - any chemical or physical change that alters the nucleic acid sequence in the DNA.

May be by chemical means, radiation, etc. May be by substitution, insertion, deletion.

Every time a cell divides ~6 billion NA are matched and ~ 2000 errors occur (most are repaired).

'Aging' is thought to be due to an increased breakdown of RNA.


Intercalation into DNA

  • Planar molecules such as Polynuclear Aromatic Hydrocarbons (PNAH’s) can slide into the “grooves” in the DNA double helix, potentially causing mutations, and cancer induction


Most mutations are detrimental. If at a crucial position the defective protein will lack biological activity, the cell/organism dies and the DNA will not be reproduced.

Non-lethal mutations often lead to metabolic abnormalities or hereditary/genetic diseases,

eg. sickle-cell anemia, hemophilia or PKU (phenylketonuria) - cannot convert Phe to Tyr (precursor of neurotransmitters); can cause severe mental retardation.(~1 in 12,000). But can be cured/controlled if detected within 3 weeks of birth.


Cloning

  • First remove the nucleus of an egg cell

  • Replace it in the cell by a nucleus from body cell of a mature adult, thus producing a cell which has a full complement of chromosomes

  • Induce cell division and implant into the reproductive system of a surrogate mother


CLONING


Cloned mammals

  • Dolly (1st cloned mammal) UK


What about meat and milk from cloned animals?

  • Is it safe to eat/drink?

  • What do you think?


The US FDA thinks so!

  • Jan 15, 2008 announcement

  • But cloned animals are very expensive at present, thus not likely to be a major issue……yet!


Human Cloning??

  • Technically possible


Cloning and Stem Cells

  • Cloning of human embryonic cells is being considered for production of stem cells to treat many diseases

  • Also controversial –When does life start??


Genetically Modified Food

  • Selective breeding-started with Gregor Mendel’s work on peas in 1800’s

  • Cross pollination or fertilization will change genetic makeup of “new organism”

  • Ie. Cattle cross breeding


Santa Gertrudis cattle

  • Cross breed Brahman (poor quality meat) but high resistance to heat and humidity with English shorthorn (good meat but low resistance to heat and humidity) : outcome was a new breed (Santa Gertrudis) with good quality meat and good resistance to heat and humidity


Cross breeding of Cattle

  • English shorthorn (LHS)+ Brahma =

  • Santa Gertrudis (RHS)


Disadvantages to selective breeding

  • Relatively slow and imprecise (also got cattle with poor meat and poor resistance to heat/humidity!)

  • Trial and error !


Genetic Modification by DNA manipulation

  • Recombinant DNA technology

  • Isolate the segment of DNA that encodes for a protein conferring desirable traits

  • Extract the DNA segment using DNA restriction enzymes

  • Copy the DNA segment using PCR (polymerase chain reaction)


Kary Mullis (1993 Chem Nobel Prize)

  • PCR!


Raw materials for PCR

  • Add oligonucleotide “Primers” which hybridize to the complementary DNA strands in the region of interest

  • Then DNA polymerase enzyme extends each DNA strand


DNA amplification by PCR

  • Tiny amounts of DNA can be made into enough to permit analysis of the sequence

  • Up to 1 million x more DNA in an hour

  • Valuable in forensics

  • A few nanograms is sufficient

  • GMO impossible without it!


DNA manipulation cont’d

  • Then splice copies of this DNA into the cells of the organism lacking the desired trait

  • New “modified DNA” then causes the organism to build the protein of interest

  • Many successful and useful applications of this and some “exploitations”


Tomato plants growing in salty soil

  • Traditionally tomatoes would not tolerate salty soil

  • Recombinant DNA technology inserted a gene for salt tolerance, thus permitting the use of soil for agriculture that was otherwise a wasteland


Other useful modifications

  • Soybeans and canola have been genetically modified to increase their content of “heart healthy” monounsaturated fatty acids

  • GMO animals: 98% of GMO animals are mice:used for research


The Harvard Mouse

  • The oncomouse (develops cancer)

  • US supreme court; it cannot be patented!


Exploitation of the technology

  • “Roundup ready” corn (Monsanto)

  • Corn has been genetically modified to be resistant to the herbicide “Roundup”

  • Thus crops can be sprayed with Roundup and only the weeds are harmed

  • Monsanto has monopoly on seed


Signs of the times in Agriculture


What do you think?

  • Relative benefits vs. harm of GMO foods


On balance…….

  • Concerns: seeds and pollen from GMO crops disrupt others through cross pollination

  • Effects on animals/insects who consume them or use them for their habitat

  • Effects on humans! Unknown allergies

  • Products of GMO should be labelled


Labelling GE foods in Europe


Canadian “Policy”

  • 2004: Feds adopted a “voluntary labelling”: result: zero labelled products!

  • 2007: NDP private member’s bill calling for mandatory labelling of all GMO products in Canada

  • USA: 17 states currently considering it


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