DNAStructure

&Replication

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DNADNA• DNA DNA is often

called the blueprint of life..

• In simple terms, DNA contains the instructions for making proteins within the cell.

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Why do we study DNADNA?

We study DNA for many reasons, e.g.,

• its central importance to all life on Earth,

• medical benefits such as cures for diseases,

• better food crops.

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Chromosomes and Chromosomes and DNADNA

• Our genes are on our chromosomes.

• Chromosomes are made up of a chemical called DNA.

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The Shape of the The Shape of the MoleculeMolecule

•DNA is a very long polymer.

•The basic shape is like a twisted ladder or zipper.

•This is called a double helix.

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The Double Helix The Double Helix MoleculeMolecule

•Discovered by James Watson & Francis Crick

•The DNA double helix has two strands twisted together.

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One Strand of DNAOne Strand of DNA• The backbone

of the molecule is alternating phosphates and deoxyribose sugar

• The teeth are nitrogenous bases.

phosphate

deoxyribose

bases

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NucleotidesNucleotides

C C

C

OPhosphate

O

CC

O -P OO

O

O -P OO

O

O -P OO

O One deoxyribose together with its phosphate and

base make a nucleotide.

Nitrogenous base

Deoxyribose

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One Strand of DNAOne Strand of DNA

• One strand of DNA is a polymer of nucleotides.

• One strand of DNA has many millions of nucleotides.

nucleotide

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Four nitrogenous Four nitrogenous basesbases

• Cytosine C• Thymine T

• Adenine A

• Guanine G

DNA has four different bases:

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Two Stranded DNATwo Stranded DNA• Remember,

DNA has two strands that fit together something like a zipper.

• The teeth are the nitrogenous bases but why do they stick together?

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C

C

C

C

N

N

OO

N

C

C

C

C

N N

OO

N

N

N C

Hydrogen BondsHydrogen Bonds• The bases attract each

other because of hydrogen bonds.

• Hydrogen bonds are weak but there are millions and millions of them in a single molecule of DNA.

• The bonds between cytosine and guanine are shown here with dotted lines

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Hydrogen Bonds, Hydrogen Bonds, cont.

• When making hydrogen bonds, cytosine always pairs up with guanine

• Adenine always pairs up with thymine

• Adenine is bonded to thymine here

C

C

CC

N

N

N

N

N

C

C

C

C

C

N

N

OO

OO

C

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Chargaff’s Rule:Chargaff’s Rule:• Adenine and Thymine

always join togetherA T

• Cytosine and Guanine always join together

C G

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DNA by the DNA by the NumbersNumbers

• Each cell has about 2 m of DNA.

• The average human has 75 trillion cells.

• The average human has enough DNA to go from the earth to the sun more than 400 times.

• DNA has a diameter of only 0.000000002 m.

The earth is 150 billion mor 93 million miles from the sun.

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DNA DNA ReplicatiReplicati

onon

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Replication FactsReplication Facts

• DNA has to be copied DNA has to be copied before a cell dividesbefore a cell divides

• DNA is copied during DNA is copied during the the SS or synthesis phase or synthesis phase of of interphaseinterphase

• New cells will need New cells will need identical identical DNA strandsDNA strands

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Synthesis Phase (S Synthesis Phase (S phase)phase)

• S phase during interphase of the cell cycle

• Nucleus of eukaryotes

Mitosis-prophase-metaphase-anaphase-telophase

G1 G2

Sphase

interphase

DNA replication takesDNA replication takesplace in the S phase.place in the S phase.

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DNA ReplicationDNA Replication

• Begins atBegins at Origins of ReplicationOrigins of Replication• Two strands open forming Two strands open forming

Replication Forks (Y-shaped Replication Forks (Y-shaped region)region)

• New strands grow at the forksNew strands grow at the forks

ReplicationReplicationForkFork

Parental DNA MoleculeParental DNA Molecule

3’

5’

3’

5’

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DNA ReplicationDNA Replication• As the 2 DNA strands open at As the 2 DNA strands open at

the origin, the origin, Replication Replication BubblesBubbles form form

• Prokaryotes (bacteria) have a single bubble

• Eukaryotic chromosomes have MANY bubbles

Bubbles Bubbles

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DNA ReplicationDNA Replication

• Enzyme Enzyme HelicaseHelicase unwinds and unwinds and separates the 2 DNA separates the 2 DNA strands by breaking strands by breaking the the weak hydrogen weak hydrogen bondsbonds

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Question:Question:

•What would be the complementary DNA strand for the following DNA sequence?

DNA 5’-CGTATG-3’DNA 5’-CGTATG-3’

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Answer:Answer:

DNA 5’-CGTATG-3’DNA 5’-CGTATG-3’

DNA 3’-GCATAC-5’DNA 3’-GCATAC-5’

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PROTEIN PROTEIN SYNTHESISSYNTHESIS

DNA DNA and and

GeneGeness

DNADNA

•DNA contains genes, sequences of nucleotide bases

•These Genes code for polypeptides (proteins)

•Proteins are used to build cells and do much of the work inside cells

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Genes & ProteinsGenes & Proteins

Proteins are made of amino acids linked together by peptide bonds

20 different amino acids exist

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Amino Acid Amino Acid StructureStructure

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PolypeptidesPolypeptides

•Amino acid chains are called polypeptides

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DNA Begins the DNA Begins the ProcessProcess

• DNA is found inside the nucleus

• Proteins, however, are made in the cytoplasm of cells by organelles called ribosomes

• Ribosomes may be free in the cytosol or attached to the surface of rough ER

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Starting with DNAStarting with DNA• DNA ‘s codeDNA ‘s code must be must be copiedcopied

and taken to the cytosoland taken to the cytosol• In the cytoplasm, this In the cytoplasm, this code code

must be readmust be read so so amino acidsamino acids can be assembled to make can be assembled to make polypeptides (proteins)polypeptides (proteins)

• This process is called This process is called PROTEIN SYNTHESISPROTEIN SYNTHESIS

RNARNA

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Roles of RNA and DNA

•DNA is the MASTER PLAN

•RNA is the BLUEPRINT of the

Master Plan

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RNA Differs from DNARNA Differs from DNA

• RNA has a sugar RNA has a sugar riboseribose

DNA has a sugar DNA has a sugar deoxyribosedeoxyribose

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Other DifferencesOther Differences

• RNA contains RNA contains the base the base uracil uracil (U(U))DNA has DNA has thymine (T)thymine (T)

• RNA molecule is RNA molecule is single-strandedsingle-strandedDNA is DNA is double-double-strandedstranded

DNA

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Structure of RNAStructure of RNA

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. Three Types of Three Types of RNARNA

• Messenger RNA (mRNA)Messenger RNA (mRNA) copies DNA’s code & carries copies DNA’s code & carries the genetic information to the the genetic information to the ribosomesribosomes

• Ribosomal RNA (rRNA)Ribosomal RNA (rRNA), along , along with protein, makes up the with protein, makes up the ribosomesribosomes

• Transfer RNA (tRNA)Transfer RNA (tRNA) transfers transfers amino acids to the ribosomes amino acids to the ribosomes where proteins are where proteins are synthesizedsynthesized

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Messenger RNA• Long Straight

chain of Nucleotides

• Made in the Nucleus

• Copies DNA & leaves through nuclear pores

• Contains the Nitrogen Bases A, G, C, U ( no T )

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Messenger RNA (mRNA)Messenger RNA (mRNA)• Carries the information for a Carries the information for a

specific proteinspecific protein• Made up of Made up of 500 to 1000 500 to 1000

nucleotides longnucleotides long• Sequence of 3 bases called Sequence of 3 bases called

codoncodon• AUGAUG – methionine or – methionine or start codonstart codon• UAA, UAG, or UGAUAA, UAG, or UGA – – stop codonsstop codons

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Ribosomal RNA (rRNA)Ribosomal RNA (rRNA)

• rRNA is a single rRNA is a single strand strand 100 to 100 to 3000 nucleotides3000 nucleotides longlong

• GlobularGlobular in shape in shape• Made inside the Made inside the

nucleusnucleus of a cell of a cell• Associates with Associates with

proteins to form proteins to form ribosomesribosomes

• Site of Site of protein protein SynthesisSynthesis

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The Genetic Code

• A codon designates an amino acid

• An amino acid may have more than one codon

• There are 20 amino acids, but 64 possible codons

• Some codons tell the ribosome to stop translating

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The Genetic Code

•Use the code by reading from the center to the outside•Example: AUG codes for Methionine

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Name the Amino Acids

•GGG?•UCA?•CAU?•GCA?•AAA?

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Remember the Remember the Complementary Complementary

BasesBasesOn DNA: A-T C-GOn RNA: A-U C-G

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Transfer RNA Transfer RNA (tRNA)(tRNA)

• Clover-leaf shape• Single stranded molecule

with attachment site at one end for an amino acid

• Opposite end has three nucleotide bases called the anticodon

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Transfer RNATransfer RNAamino acidamino acid

attachment siteattachment site

U A C

anticodonanticodon

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Codons and Anticodons

• The 3 bases of an anticodon are complementary to the 3 bases of a codon

• Example: Codon ACU

Anticodon UGA

UGA

ACU

TranscriptiTranscription and on and

TranslationTranslation

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Pathway to Making a Pathway to Making a ProteinProtein

DNADNA

mRNAmRNA

tRNA (ribosomes)tRNA (ribosomes)

ProteinProtein

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Protein SynthesisProtein Synthesis The production or synthesis of

polypeptide chains (proteins) Two phases:

Transcription & Translation mRNA must be processed

before it leaves the nucleus of eukaryotic cells

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DNADNA RNARNA ProteinProtein

Nuclearmembrane

TranscriptionTranscription

RNA ProcessingRNA Processing

TranslationTranslation

DNA

Pre-mRNA

mRNA

Ribosome

Protein

EukaryotEukaryotic Cellic Cell

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TranscriptionTranscription

• The process of copying the sequence of one strand of DNA, the template strand

• mRNA copies the template strand

• Requires the enzyme RNA Polymerase

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Template Strand

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Question:Question: What would be the What would be the

complementary RNA complementary RNA strand for the following strand for the following DNA sequence?DNA sequence?

DNA 5’-DNA 5’-GCGTATGGCGTATG-3’-3’

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Answer:Answer:

•DNA 5’-GCGTATG-DNA 5’-GCGTATG-3’3’

•RNA 3’-CGCAUAC-RNA 3’-CGCAUAC-5’5’

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TranscriptionTranscription

• During transcription, RNA polymerase binds to DNA and separates the DNA strands

• RNA Polymerase then uses one strand of DNA as a template to assemble nucleotides into RNA

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TranscriptionTranscription• Promoters are regions on

DNA that show where RNA Polymerase must bind to begin the Transcription of RNA

• Called the TATA box• Specific base sequences act

as signals to stop• Called the termination signal

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RNA PolymeraseRNA Polymerase

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mRNA ProcessingmRNA Processing

• After the DNA is transcribed into RNA, editing must be done to the nucleotide chain to make the RNA functional

• Introns, non-functional segments of DNA are snipped out of the chain

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mRNA EditingmRNA Editing• Exons, segments of DNA that code for proteins, are then rejoined by the

enzyme ligase• A guanine triphosphate cap is added to the 5’ end of the newly copied mRNA• A poly A tail is added to the 3’ end of the RNA• The newly processed mRNA can then leave the nucleus

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TailNew Transcript

Result of TranscriptionResult of Transcription

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mRNA Transcript

•mRNA leaves the nucleus through its pores and goes to the ribosomes

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TranslationTranslation

•Translation is the process of decoding the mRNA into a polypeptide chain

•Ribosomes read mRNA three bases or 1 codon at a time and construct the proteins

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TranscriptioTranscriptionn

TranslatiTranslationon

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RibosomesRibosomes

•Made of a large and small subunit

•Composed of rRNA (40%) and proteins (60%)

•Have two sites for tRNA attachment --- P and A

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Step 1- InitiationStep 1- Initiation

• mRNA transcript start codon AUG attaches to the small ribosomal subunit

• Small subunit attaches to large ribosomal subunitmRNA transcript

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RibosomesRibosomes

PSite

ASite

Largesubunit

Small subunit

mRNAmRNA

A U G C U A C U U C G

Step 2 - Elongation• As ribosome moves, two tRNA

with their amino acids move into site A and P of the ribosome

• Peptide bonds join the amino acids

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InitiationInitiation

mRNAmRNA

A U G C U A C U U C G

2-tRNA

G

aa2

A U

A

1-tRNA

U A C

aa1

anticodon

hydrogenbonds codon

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mRNAmRNA

A U G C U A C U U C G

1-tRNA 2-tRNA

U A C G

aa1 aa2

A UA

anticodon

hydrogenbonds codon

peptide bond

3-tRNA

G A A

aa3

ElongationElongation

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mRNAmRNA

A U G C U A C U U C G

1-tRNA

2-tRNA

U A C

G

aa1

aa2

A UA

peptide bond

3-tRNA

G A A

aa3

Ribosomes move over one codon

(leaves)

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mRNAmRNA

A U G C U A C U U C G

2-tRNA

G

aa1

aa2

A UA

peptide bonds

3-tRNA

G A A

aa3

4-tRNA

G C U

aa4

A C U

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mRNAmRNA

A U G C U A C U U C G

2-tRNA

G

aa1aa2

A U

A

peptide bonds

3-tRNA

G A A

aa3

4-tRNA

G C U

aa4

A C U

(leaves)

Ribosomes move over one codon

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mRNAmRNA

G C U A C U U C G

aa1aa2

A

peptide bonds

3-tRNA

G A A

aa3

4-tRNA

G C U

aa4

A C U

U G A

5-tRNA

aa5

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mRNAmRNA

G C U A C U U C G

aa1aa2

A

peptide bonds

3-tRNA

G A A

aa3

4-tRNA

G C U

aa4

A C U

U G A

5-tRNA

aa5

Ribosomes move over one codon

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mRNAmRNA

A C A U G U

aa1

aa2

U

primaryprimarystructurestructureof a proteinof a protein

aa3

200-tRNA

aa4

U A G

aa5

C U

aa200

aa199

terminatorterminator or stopor stop codoncodon

TerminationTermination

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End Product –The End Product –The Protein!Protein!

• The end products of protein synthesis is a primary structure of a protein

• A sequence of amino acid bonded together by peptide bonds

aa1

aa2 aa3 aa4aa5

aa200

aa199

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Messenger RNA Messenger RNA (mRNA)(mRNA)

methionine glycine serine isoleucine glycine alanine stopcodon

proteinprotein

A U G G G C U C C A U C G G C G C A U A AmRNAmRNA

startcodon

Primary structure of a proteinPrimary structure of a protein

aa1 aa2 aa3 aa4 aa5 aa6

peptide bonds

codon 2 codon 3 codon 4 codon 5 codon 6 codon 7codon 1

Protein Synthesis

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