Dr. Maha Daghestani

DNA structure and function

Dr. Maha Daghestani

November 2007

Dr. Maha Daghestani

Dr. Maha Daghestani

DNA Structure: Double Helix

• 1953 - Watson and Crick 3-D structure of DNA

• DNA is a double helix (ll-stranded)

• Polymer of nucleotides (phosphate, sugar, base)

• DNA has 4 base types (adenine, thymine, guanine, cytosine)

Dr. Maha Daghestani

DNA

1. Double Stranded Helix

2. Hydrogen Bonds between Nitrogenous Base Pairs

3. Adenine-Thymine and Guanine-Cytosine

Dr. Maha Daghestani

DNA in a cell1. Which organelles contain DNA ?

• Eukaryotic cells contain several organelles. • The nucleus contains most of the DNA in a cell and

this DNA is called the chromosomal DNA. It is separated from the rest of the cell (cytoplasm) by a double layer of membrane.

• The mitochondria, which have a role in the oxidative degradation of nutrient molecules, also contain DNA, called the mitochondrial DNA.

• Eucariotic cells that are capable of photosynthesis contain chloroplasts with chloroplast DNA.

Dr. Maha Daghestani

Dr. Maha Daghestani

Dr. Maha Daghestani

DNA StructureDNA Structure

DNA compositionDNA compositionPhosphatePhosphate

SugarSugarNucleic acids (bases)Nucleic acids (bases)

DNA StructureDNA Structure

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1-Basic chemical units

1-Basic chemical units

A 5 carbon sugar - deoxyribose phosphate - link between sugars

bases: purines = adenine and guaninepyrimidines = thymine and cytosine

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.Nucleotides

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This is

the five-carbon sugarfound in RNA.

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This is

the five-carbon sugarfound in DNA.

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How are they different?

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phosphate

sugar

ADENINE (A) THYMINE (T)

CYTOSINE (C)GUANINE (G)

base

4 DNA Nucleotides

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Dr. Maha Daghestani

Nitrogen bases

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Nitrogen bases

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ADENINE (A)

ADENINE (A)

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GUANINE (G)

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THYMINE (T)

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CYTOSINE (C)

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Dr. Maha Daghestani

• Gene:- segment of DNA that contains all the information needed for regulated synthesis of an RNA or protein product.

• Genome:- the entire DNA sequence content of an organism (nuclear DNA)

Some Important Definitions

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Genotype and PhenotypeGenotype and Phenotype

• Genotype1. Genetic Composition of an

Organism2. Represents the Potential Properties

• Phenotype1. The Expression of the Genes2. What You See

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Gene Expression

• DNA codes for genes

• Genes are expressed as proteins

• Gene expression is regulated

• The genome of every cell in your body is identical

• Cell type is determined by the genes the cells express

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What are genes

• Genes are working subunits of DNA. • Genes, which are made up of DNA, act as

instructions to make molecules called proteins

• In humans, genes vary in size from a few hundred DNA bases to more than 2 million bases.

• The Human Genome Project has estimated that humans have between 20,000 and 25,000 genes. Every person has two copies of each gene, one inherited from each parent.

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Genes

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Dr. Maha Daghestani

ReplicationReplication

• The duplication of DNA which occurs during the S phase of Interphase.

• 1 Strand 2 Complementary Strands

• DNA Polymerase

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DNA Replication

• Must be completed prior to cell division

• Helicase enzymes open the DNA

• Polymerase enzymes generate a new DNA strand on each old template

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by adding one nucleotide after

anotherto a growing daughter

strand.

the enzyme

can build long strandsof DNA

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can only add nucleotides

if they contain the sugar

deoxyribose

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Noticethe

deoxyribosesugar

in eachof these

molecules.

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andthis hydrogen

Cells removethis OH

as a moleculeof H2O

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- H2O

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Two empty bonds

remain afterthe molecule

of waterhas been removed.

- H2O

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a new

forms at this location, joining the two nucleotides.

bond

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a new

forms at this location, joining the two nucleotides.

bond

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Growing daughter strands

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Dr. Maha Daghestani

Dr. Maha Daghestani

One More Time!

Dr. Maha Daghestani

thymine

adenine

cytosine

guanine

phosphate

deoxyribose sugar

DNA nucleotide

Deoxyribose sugar

phosphate

Nitrogenous base (guanine)

RNA nucleotide

ribose sugar

phosphate

Nitrogenous base (uracil)

Sugar / phosphate “strand”Nitrogenous base “rung”

Hydrogen bond(H-bonds)

DNA Replication

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Step 1: Hydrogen bonds between complimentary bases break

DNA “unzips”

DNA Replication

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Step 2: DNA strandspull apart from each other

DNA Replication

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Step 3: DNA nucleotides in the cellmatch up with each side of the “unzipped” DNA

each “unzipped’ strands forms a template for a new strand

DNA Replication

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Step 4: Each “old’ strandforms a template for a “new” strand

two identical DNA molecules form

“old” (original) strand

“new” strand, identicalsequence to the original

DNA Replication

Dr. Maha Daghestani

Central Dogma

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Central Dogma of Genetics

DNA

RNA

Protein

Replication

Transcription

Translation

Reverse Transcription

aa aa aa aa aa aa

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Replication Replication Transcription Transcription TranslationTranslation

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protein• For a cell to make protein, the information from

a gene is copied, base by base, from DNA into new strands of messenger RNA (mRNA).

• Then mRNA travels out of the nucleus into the cytoplasm, to cell organelles called ribosomes. There, mRNA directs the assembly of amino acids that fold into completed protein molecule.

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DNA DNA RNA RNA ProteinProtein

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Protein SynthesisProtein Synthesis

• The production (synthesis) of proteinsproteins.

• 3 phases3 phases:

1.1. TranscriptionTranscription

2.2. RNA processingRNA processing

3.3. TranslationTranslation

• RememberRemember:: DNA DNA RNA RNA ProteinProtein

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Question:Question:

• How does RNARNA (ribonucleic (ribonucleic acid) acid) differ from DNA DNA

(deoxyribonucleic acid)(deoxyribonucleic acid)?

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RNARNA differs from DNADNA

1. RNARNA has a sugar ribosesugar ribose

DNADNA has a sugar deoxyribosesugar deoxyribose

2. RNARNA contains uracil (U)uracil (U)

DNADNA has thymine (T)thymine (T)

3. RNARNA molecule is single-single-strandedstranded

DNADNA is double-strandeddouble-stranded

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1. Transcription1. Transcription

• The transfer of information in the nucleusnucleus from a DNADNA molecule to an RNARNA molecule.

• Only 1 1 DNADNA strand serves as the templatetemplate

• Starts at promoter DNADNA (TATA box)

• Ends at terminator DNADNA (stop)

• When complete, pre-RNApre-RNA molecule is released.

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Question:Question:

• What is the What is the enzymeenzyme responsible for responsible for the production of the RNA the production of the RNA molecule?molecule?

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Answer:Answer: RNA PolymeraseRNA Polymerase

• Separates the DNADNA molecule by breaking the H-bonds between the bases.

• Then moves along one of the DNA DNA strandsstrands and links RNARNA nucleotides together.

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1. Transcription1. Transcription

DNADNA

pre-mRNApre-mRNA

RNA PolymeraseRNA Polymerase

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Question:Question:

• What would be the complementary RNARNA strand for the following DNADNA sequence?

• DNA 5’-GCGTATG-3’DNA 5’-GCGTATG-3’

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Answer:Answer:

• DNA 5’-GCGTATG-3’DNA 5’-GCGTATG-3’

• RNA 3’-CGCAUAC-5’RNA 3’-CGCAUAC-5’

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2. RNA Processing2. RNA Processing

• Maturation of pre-RNApre-RNA molecules.

• Also occurs in the nucleus.nucleus.

• IntronsIntrons spliced out by splicesome-enzymesplicesome-enzyme and exonsexons come together.

• End product is a mature RNA moleculemature RNA molecule that leaves the nucleusnucleus to the cytoplasm.cytoplasm.

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2. RNA Processing2. RNA Processing

pre-RNA molecule

intron

intronexon exon exon

exon exon exon

Mature RNA moleculeMature RNA molecule

exon exon exon

intron intron

splicesome splicesome

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During transcription, one DNA strand, the template strand, provides a template for ordering the sequence of nucleotides

in an RNA transcript

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Types of RNATypes of RNA

• Three types ofThree types of RNARNA:

A.A. messenger RNA (mRNA)messenger RNA (mRNA)

B.B. transfer RNA (tRNA)transfer RNA (tRNA)

C.C. ribosome RNA (rRNA)ribosome RNA (rRNA)

• Remember: all produced in theRemember: all produced in the nucleusnucleus!!

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A. Messenger RNA (mRNA)A. Messenger RNA (mRNA)

• Carries the information for a specific proteinprotein.

• Made up of 500 to 1000 nucleotides nucleotides long.

• Made up of codons codons (sequence of three bases: AUG - methionine).

• Each codoncodon, is specific for an amino acidamino acid.

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A. Messenger RNA (mRNA)A. Messenger RNA (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

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B. Transfer RNA (tRNA)B. Transfer RNA (tRNA)

• Made up of 75 to 80 nucleotides long.

• Picks up the appropriate amino acidamino acid floating in the cytoplasm (amino amino acid activating enzymeacid activating enzyme)

• Transports amino acids amino acids to the mRNAmRNA.

• Have anticodonsanticodons that are complementary to mRNAmRNA codonscodons.

• Recognizes the appropriate codonscodons on the mRNAmRNA and bonds to them with H-bonds.

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• A tRNA molecule consists of a strand of about 80 nucleotides that folds back on itself to form a three-dimensional structure.– It includes a loop containing the anticodon and an

attachment site at the 3’ end for an amino acid.

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin CummingsFig. 17.13

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C. Ribosomal RNA (rRNA)C. Ribosomal RNA (rRNA)

• Made up of rRNrRNAA is 100 to 3000 nucleotides long.

• Important structural component of a ribosomeribosome..

• Associates with proteins proteins to form ribosomes.ribosomes.

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RibosomesRibosomes• Large and small subunits.Large and small subunits.• Composed of rRNA (40%) rRNA (40%) and proteins (60%).proteins (60%).

• Both units come together and help bind the mRNAmRNA and tRNA.tRNA.

• Two sites forTwo sites for tRNAtRNA

a. P siteP site (first and last tRNA will attachtRNA will attach)

b. A siteA site

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Dr. Maha Daghestani

• Each ribosome has a binding site for mRNA and three binding sites for tRNA molecules.

– The P site holds the tRNA carrying the growing polypeptide chain.

– The A site carries the tRNA with the next amino acid.

– Discharged tRNAs leave the ribosome at the E site.

Fig. 17.15b &c

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• Translation can be divided into three stages: initiation elongation termination

• All three phase require protein “factors” that aid in the translation process.

• Both initiation and chain elongation require

energy provided by the hydrolysis of GTP.

Translation

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• Initiation brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits.

– First, a small ribosomal subunit binds with mRNA and a special initiator tRNA, which carries methionine and attaches to the start codon.

– Initiation factors bring in the large subunit such that the initiator tRNA occupies the P site.

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin CummingsFig. 17.17

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• Elongation consists of a series of three stepcycles as each amino acid is added to the proceeding one.

• During codon recognition, an elongation factor assists hydrogen bonding between the mRNA codon under the A site with the corresonding anticodon of tRNA carrying the appropriateamino acid.

– This step requires the hydrolysis of two GTP.

Elongation

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• The three steps of elongation continue codon by codon to add amino acids until the polypeptide chain is completed.

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin CummingsFig. 17.18

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• Termination occurs when one of the three stop codons reaches the A site.

• A release factor binds to the stop codon and hydrolyzes the bond between the polypeptide and its tRNA in the P site.

• This frees the polypeptide and the translation complex

disassembles.

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 17.19

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3. Translation3. Translation

Nuclearmembrane

TranscriptionTranscription

RNA ProcessingRNA Processing

TranslationTranslation

DNA

Pre-mRNA

mRNA

Ribosome

Protein

Eukaryotic Eukaryotic CellCell

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3. Translation3. Translation

• Synthesis of proteinsproteins in the cytoplasmcytoplasm

• Involves the following:Involves the following:

1. mRNA (codons)mRNA (codons)

2. tRNA (anticodons)tRNA (anticodons)

3. rRNArRNA

4. ribosomesribosomes

5. amino acidsamino acids

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3. Translation3. Translation• Three parts:

1. initiationinitiation: start codon (AUG)

2. elongationelongation:

3. terminationtermination: stop codon (UAG)

• Let’s make a PROTEIN!!!!PROTEIN!!!!.

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3. Translation3. Translation

PSite

ASite

Largesubunit

Small subunit

mRNAmRNA

A U G C U A C U U C G

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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 ProductEnd Product

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

• A sequence of amino acid amino acid bonded together by peptide bondspeptide bonds.

aa1

aa2 aa3 aa4aa5

aa200

aa199

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PolyribosomePolyribosome

• Groups of ribosomes reading same mRNA mRNA simultaneously producing many proteins proteins (polypeptides).(polypeptides).

incominglargesubunit

incomingsmall subunit polypeptidepolypeptide

mRNAmRNA1 2 3 4 5 6 7

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Question:Question:

• The anticodon The anticodon UACUAC belongs to a tRNA belongs to a tRNA that recognizes and binds to a that recognizes and binds to a particular particular amino acid.amino acid.

• What would be theWhat would be the DNA base code DNA base code for for thisthis amino acid?amino acid?

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Answer:Answer:

• tRNA tRNA - UAC (anticodon)- UAC (anticodon)

• mRNAmRNA - AUG (codon)- AUG (codon)

• DNA DNA - TAC- TAC

Dr. Maha Daghestani

Dr. Maha Daghestani

Thank youThank you