Doug RaifordLesson 2

Material of life Heritable traits

The job of DNA is to produce proteins Involved in virtually every

chemical reaction ▪ Enzymes catalyze reactions

Structure ▪ muscle, cellulose, etc.

Every cell has the same DNA Yet not all cells perform

same job2Background

Double stranded Sequence of nucleotides

Named for their nitrogenous bases▪ Adenine▪ Guanine▪ Cytosine▪ Thymine

Strands are complementary Gs with Cs, As with Ts Called base-pairs

3Background

Article: molecular structure of nucleic acids Published in Nature in

April of 1953 http://www.nature.com/natur

e/dna50/watsoncrick.pdf One page Possibly the most

famous passage in all of science

“It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”

“It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”

4Background

Carbons numbered

Synthesis 5’ to 3’

Strands are antiparallel

Reverse complement

Deoxyribonucleic acid

5Background

Can be represented as a string of characters

1 aataaatact tacaggtatt ccacctgaaa ctctttctat gaatgacttt caagtctata 61 tcctatattt atcctcaata aaatatgcac aatagatctc tactgagaaa actttatatt121 ttagaagcaa ttcatctccc ttttaaaata caaacttgca taggattgcc ataaattaat181 gcacctaaaa ttaagtcgtt tctatgaaat ttattttagg tgtgaaatta tatattaggt241 gtacaattag ccataccatt ccgacaatat cgacatagga atattgagta gaacaagatg301 taccattatt agcttctggg ttggcataag ggaatacagg caaagactta aacctattcg361 gactctgtag agctggctca atattcaaaa gaataatgtc cctcgataca agcatcagaa421 tagagatcgc gctctttaca cctattaaat acatcatcta aaacaactgc atattgttct481 atgctcaagc tgtaagcatc aatatctagg caagctcatt gactaaaaca gtctctatcg541 aaatgttcca gctcaattca aggtcgagat agtacaccta ttaaattaat ttcataccta601 taaattcgag attcccagta gtctattggt gactacatca atcgggcaac accaccatgg

6Background

DNA strand: chromosomeGenome: all chromosomes combined

7Background

Gene is a sub-region of DNA As mentioned: job of a gene is to produce protein

Each gene is associated with a particular protein

8Background

Two step process Transcription Translation

Central dogma

DNA RNA Proteintranscription translation

9Background

RNA polymerase Protein complex

Free-floating nucleotides stitches together

Result is single strand of RNA Messenger RNA mRNA

Exact copy Hence transcription

10Background

Strand of amino acids20 common aa’sFolds into shapeShape dictates

function

11Background

mRNA: 4 nucleotide alphabetProtein: 20 amino acid alphabetHow translate?

Triplet nucleotides “code” for amino acid Codon

atg Methionineatg Methionine

12Background

64 combinations of 3 nucleotidesBut only 20 amino acidsSome amino acids are coded for by

multiple codons

CTACTCCTGCTTTTATTG

Leucine

13Background

Ribosome Protein and RNA

complexAAs delivered

by Transfer RNA (tRNA)

14Background

TranslationDNA Replication

15Background

Central dogma

DNA RNA Proteintranscriptiontranslation

RNA Polymerase

Free-floating nt’s

Ribosome

tRNAs

16Background

Use the cell’s own machinery for replicating DNA

Polymerase chain reaction (PCR) Free-floating nucleotides DNA Polymerase

Amplifies a single or small number of strands into millions

17Background

Instead of free floating ATP, CTP, TTP, and GTP Small percentage is

dideoxy variant Stops transcription if

encounters one of these

All fragments end with A, C, T, or G depending on test tube

18Background

Dye-labeled chain terminators: can do all in one chamber

Capillary electrophoresis instead of gel

19Background

Sequence termination techniques Only 700-900 base-pairs at a time Very time consuming and labor intensive

Slow: human genome would take 8,000 years

20Background

Breakup into random sized fragments

Determine sequences of fragments

Reassemble algorithmically

High-throughput

Look for regions of overlap

21Background

How the polymerase knows where to attach The term expression: phenotypical expression Now equated to protein production rate

Promoter Region

Coding regionTerminator

Region

RNA polymerase

Start Codon‘ATG’ = Methionine

Stop Codon: non coding‘TAA’, ‘TAG’,

or ‘TGA’ 22Background

23Background