DNA and the DNA and the Genetic CodeGenetic Code

Larry J. SchefflerLarry J. Scheffler

Lincoln High SchoolLincoln High School20092009

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DNADNA• 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

Nucleic AcidsNucleic 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.

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DNA StructureDNA StructureDNA is made up of three units including:I. A ribose sugar

Ribose and deoxyribose differ in that ribose has an OH group on carbon 2 whereas deoxyribose has only a hydrogen attached.

RiboseDeoxyribose

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DNA StructureDNA StructureDNA is made up of three units includingI. A ribose sugarII. A phosphate group

The phosphate groups alternate with the ribose sugar and are attached at carbon 3 and at carbon 5

Phosphate

Deoxyribose

The phosphates are attached at carbons 3 & 5. This defines the direction of the chain.

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3

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DNA StructureDNA StructureDNA is made up of three units including

I. A ribose sugarII. A phosphate groupIII. A nitrogen (amine) base

There are four different amine bases: adenine, thymine, cytosine, and guanine.

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A NucleotideA Nucleotide

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

Cytosine

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DNA StructureDNA StructureDNA is made up of three

units1. A ribose sugar2. A phosphate group3. A nitrogen (amine) base

The amine bases are side branches to a strand madeof alternating phosphate and deoxyribose sugars.

These bases are attached at carbon 1 of the deoxyribose sugar.

Adenine

Cytosine

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DNA StructureDNA StructureDNA is made up of three units:

1. A ribose sugar2. A phosphate group3. 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. Cytosine

Adenine

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DNA StructureDNA 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

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Complimentary BasesComplimentary 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

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Hydrogen Bond Hydrogen Bond AlignmentAlignment

• 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

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DNA Structure -- Hydrogen DNA Structure -- Hydrogen BondingBonding

• Adenine and Thymine form a base pair

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DNA Structure Hydrogen DNA Structure Hydrogen BondingBonding

• Guanine and Cytosine

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Base Pair SequenceBase 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

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DNA StructureDNA 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

DNA ShapeDNA Shape

• This color enhanced image taken by the Scanning Tunneling Electron Microscope shows a double helix

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DNA ReplicationDNA 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

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DNA ReplicationDNA 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

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DNA and the Genetic CodeDNA 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.

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Species bp NP-1 Sense Primer Macaque -- ACCCGCACCTCATTCCTACATCAATGAGTGGCTCCAAATAGACCTGGGGGHuman 1422 ACCCGCACCTCATTCCTACATCAATGAGTGGCTCCAAATAGACCTGGGGGRat 1419 ACCCTCACCCCACCCATACATCAATGAATGGCTCCAAGTGGACCTGGGAG

Macaque AGGAGAAGATCGTGAGGGGCATCATCATTCAGGGTGGGAAGCACCGAGAGHuman 1472 AGGAGAAGATCGTGAGGGGCATCATCATTCAGGGTGGGAAGCACCGAGAGRat 1469 ATGAGAAGATAGTAAGAGGTGTCATCATTCAAGGTGGGAAGCACCGAGAA

Macaque AACAAGGTATTCATGAGGAAGTTCAAGATCGGGTACAGCAACAACGGCTCHuman 1522 AACAAGGTGTTCATGAGGAAGTTCAAGATCGGGTACAGCAACAACGGCTCRat 1519 AACAAAGTGTTCATGAGGAAGTTCAAGATCGCCTACAGTAACAATGGTTC

Macaque CGACTGGAAGATGATCATGGACGACAGCAAACGCAAGGCAAAGTCTTTTGHuman 1572 GGACTGGAAGATGATCATGGATGACAGCAAACGCAAGGCGAAGTCTTTTGRat 1569 TGACTGGAAAATGATCATGGATGACAGCAAGCGCAAGGCTAAGTCTTTTG

Macaque AGGGCAACAACAACTATGACACACCTGAGCTGCGGACTTTTCCAGCTCTCHuman 1622 AGGGCAACAACAACTATGATACACCTGAGCTGCGGACTTTTCCAGCTCTCRat 1619 AAGGCAACAACAACTATGACACACCTGAGCTCCGGGCCTTTACACCTCTC

Macaque TCCACGCGATTCATCAGGATCTACCCCGAGAGAGCCACTCATGGCGGACTHuman 1672 TCCACGCGATTCATCAGGATCTACCCCGAGAGAGCCACTCATGGCGGACTRat 1669 TCCACAAGATTCATCAGGATCTACCCCGAGAGAGCCACACATAGTGGGCT

-NP-1 Anti-sense Primer (reverse) Macaque GGGGCCCCGAATGGAGCTGCTGGGCTGTGAAGTGGAAHuman 1722 GGGGCTCAGAATGGAGCTGCTGGGCTGTGAAGTGGAARat 1719 CGGACTGAGGATGGAGCTACTGGGCTGTGAAGTAGAA

Gene Correspondance for Gene Correspondance for Neuropilin-1Neuropilin-1

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Protein SynthesisProtein 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

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RNA and Protein SynthesisRNA 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 differences1. RNA is a single strand rather than a

double helix2. Deoxyribose is replaced with ribose3. The nitrogen base thymine is

replaced with uracil

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RNA StructureRNA Structure

• Ribose has a slightly different structure from deoxyribose.

• Ribose has an –OH group on carbon 2 rather than a H as in deoxyribose.

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RNA v DNARNA v DNA• The structure of Uracil differs only

slightly from Thymine

Uracil ThymineThymine has a methyl side group

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Messenger RNAMessenger 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

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Messenger RNAMessenger 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.

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Transfer RNATransfer 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.

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Transfer RNATransfer 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

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RNA CodonsRNA CodonsU C A G

U

UUUPhe

UCU

Ser

UAUTyr

UGUCys

UUC UCC UAC UGC

UUALeu

UCA UAATerm.

UGA Term.

UUG UCG UAG UGG Trp

C

CUU

Leu

CCU

Pro

CAUHis

CGU

ArgCUC CCC CAC CGC

CUA CCA CAAGln

CGA

CUG CCG CAG CGG

A

AUU

Ile

ACU

Thr

AAUAsn

AGUSer

AUC ACC AAC AGC

AUA ACA AAALys

AGAArg

AUG Met ACG AAG AGG

G

GUU

Val

GCU

Ala

GAUAsp

GGU

GlyGUC GCC GAC GGC

GUA GCA GAAGlu

GGA

GUG GCG GAG GGG 30

Ribosomal RNARibosomal 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.

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DNA Replication During Cell DNA Replication During Cell DivisionDivision

• During cell replication the DNA unwinds and each strand builds a new complimentary strand.

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RT-PCR or Reverse RT-PCR or Reverse Transcriptase Polymerase Transcriptase Polymerase

Chain ReactionsChain Reactions• RT-PCR was first developed RT-PCR was first developed

by Cary Mullis for which he by Cary Mullis for which he was awarded the Nobel was awarded the Nobel Prize in ChemistryPrize in Chemistry

• Replicated DNA can be then Replicated DNA can be then separated and classifiedseparated and classified

•This process allows the DNA from very small amounts of This process allows the DNA from very small amounts of cellular material to be replicatedcellular material to be replicated•DNA is extracted and broken down into smaller fragments DNA is extracted and broken down into smaller fragments using restriction enzymesusing restriction enzymes•The DNA is then replicated and separated using gelThe DNA is then replicated and separated using gel electrophoresiselectrophoresis 33

400 bp300 bp

200 bp

100 bp

RT-PCR and DNA ReplicationRT-PCR and DNA Replication

EARLY MID MIDLATE

LATE MENSECTRL

RT-PCR gel showing relative amounts of NP-1 RT-PCR gel showing relative amounts of NP-1 using cyclophilin as an internal standard.using cyclophilin as an internal standard.

NP-1

Cyclo

Primers

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DNA SequencingDNA Sequencing

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

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Forensic DNA AnalysisForensic DNA Analysis

• The DNA fragment The DNA fragment contains codons that contains codons that code for proteinscode for proteins

• It also contains regions It also contains regions where there is no coded where there is no coded message in the base message in the base sequencesequence

•The application of a restriction enzyme cuts this part of The application of a restriction enzyme cuts this part of the DNA into fragments.the DNA into fragments.•The sequence and hence the fragment sizes are uniqueThe sequence and hence the fragment sizes are unique for each individual (Except for Identical Twins)for each individual (Except for Identical Twins)

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DNA Fingerprinting ProcessDNA Fingerprinting Process

DNA fingerprinting is a multistep process.37

Forensic DNA AnalysisForensic DNA Analysis

• Used to identify Used to identify people in criminal people in criminal cases.cases.

• Used to establish Used to establish identity, paternity identity, paternity and ancestry.and ancestry.

• Used to study Used to study evolutionary evolutionary changes in species.changes in species.

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Forensic DNA AnalysisForensic DNA Analysis• DNA evidence is only DNA evidence is only

as good as the person as good as the person performing the tests. performing the tests. Care must be taken to Care must be taken to guard against guard against contamination for legal contamination for legal evidence to stand.evidence to stand.

• Chain of evidence rulesChain of evidence rules

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