Dr. Maha Daghestani DNA structure and function Dr. Maha Daghestani November 2007.
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Transcript of Dr. Maha Daghestani DNA structure and function Dr. Maha Daghestani November 2007.
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
Dr. Maha Daghestani
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
Dr. Maha Daghestani
.Nucleotides
Dr. Maha Daghestani
This is
the five-carbon sugarfound in RNA.
Dr. Maha Daghestani
This is
the five-carbon sugarfound in DNA.
Dr. Maha Daghestani
How are they different?
Dr. Maha Daghestani
phosphate
sugar
ADENINE (A) THYMINE (T)
CYTOSINE (C)GUANINE (G)
base
4 DNA Nucleotides
Dr. Maha Daghestani
Dr. Maha Daghestani
Nitrogen bases
Dr. Maha Daghestani
Nitrogen bases
Dr. Maha Daghestani
ADENINE (A)
ADENINE (A)
Dr. Maha Daghestani
GUANINE (G)
Dr. Maha Daghestani
THYMINE (T)
Dr. Maha Daghestani
CYTOSINE (C)
Dr. Maha Daghestani
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
Dr. Maha Daghestani
Genotype and PhenotypeGenotype and Phenotype
• Genotype1. Genetic Composition of an
Organism2. Represents the Potential Properties
• Phenotype1. The Expression of the Genes2. What You See
Dr. Maha Daghestani
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
Dr. Maha Daghestani
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.
Dr. Maha Daghestani
Genes
Dr. Maha Daghestani
Dr. Maha Daghestani
ReplicationReplication
• The duplication of DNA which occurs during the S phase of Interphase.
• 1 Strand 2 Complementary Strands
• DNA Polymerase
Dr. Maha Daghestani
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
Dr. Maha Daghestani
by adding one nucleotide after
anotherto a growing daughter
strand.
the enzyme
can build long strandsof DNA
Dr. Maha Daghestani
can only add nucleotides
if they contain the sugar
deoxyribose
Dr. Maha Daghestani
Noticethe
deoxyribosesugar
in eachof these
molecules.
Dr. Maha Daghestani
andthis hydrogen
Cells removethis OH
as a moleculeof H2O
Dr. Maha Daghestani
- H2O
Dr. Maha Daghestani
Two empty bonds
remain afterthe molecule
of waterhas been removed.
- H2O
Dr. Maha Daghestani
a new
forms at this location, joining the two nucleotides.
bond
Dr. Maha Daghestani
a new
forms at this location, joining the two nucleotides.
bond
Dr. Maha Daghestani
Growing daughter strands
Dr. Maha Daghestani
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
Dr. Maha Daghestani
Step 1: Hydrogen bonds between complimentary bases break
DNA “unzips”
DNA Replication
Dr. Maha Daghestani
Step 2: DNA strandspull apart from each other
DNA Replication
Dr. Maha Daghestani
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
Dr. Maha Daghestani
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
Dr. Maha Daghestani
Central Dogma of Genetics
DNA
RNA
Protein
Replication
Transcription
Translation
Reverse Transcription
aa aa aa aa aa aa
Dr. Maha Daghestani
Replication Replication Transcription Transcription TranslationTranslation
Dr. Maha Daghestani
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.
Dr. Maha Daghestani
DNA DNA RNA RNA ProteinProtein
Dr. Maha Daghestani
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
Dr. Maha Daghestani
Question:Question:
• How does RNARNA (ribonucleic (ribonucleic acid) acid) differ from DNA DNA
(deoxyribonucleic acid)(deoxyribonucleic acid)?
Dr. Maha Daghestani
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
Dr. Maha Daghestani
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.
Dr. Maha Daghestani
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?
Dr. Maha Daghestani
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.
Dr. Maha Daghestani
1. Transcription1. Transcription
DNADNA
pre-mRNApre-mRNA
RNA PolymeraseRNA Polymerase
Dr. Maha Daghestani
Question:Question:
• What would be the complementary RNARNA strand for the following DNADNA sequence?
• DNA 5’-GCGTATG-3’DNA 5’-GCGTATG-3’
Dr. Maha Daghestani
Answer:Answer:
• DNA 5’-GCGTATG-3’DNA 5’-GCGTATG-3’
• RNA 3’-CGCAUAC-5’RNA 3’-CGCAUAC-5’
Dr. Maha Daghestani
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.
Dr. Maha Daghestani
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
Dr. Maha Daghestani
During transcription, one DNA strand, the template strand, provides a template for ordering the sequence of nucleotides
in an RNA transcript
Dr. Maha Daghestani
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!!
Dr. Maha Daghestani
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.
Dr. Maha Daghestani
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
Dr. Maha Daghestani
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.
Dr. Maha Daghestani
• 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
Dr. Maha Daghestani
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.
Dr. Maha Daghestani
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
Dr. Maha Daghestani
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
Dr. Maha Daghestani
• 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
Dr. Maha Daghestani
• 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
Dr. Maha Daghestani
• 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
Dr. Maha Daghestani
• 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
Dr. Maha Daghestani
• 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
Dr. Maha Daghestani
3. Translation3. Translation
Nuclearmembrane
TranscriptionTranscription
RNA ProcessingRNA Processing
TranslationTranslation
DNA
Pre-mRNA
mRNA
Ribosome
Protein
Eukaryotic Eukaryotic CellCell
Dr. Maha Daghestani
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
Dr. Maha Daghestani
3. Translation3. Translation• Three parts:
1. initiationinitiation: start codon (AUG)
2. elongationelongation:
3. terminationtermination: stop codon (UAG)
• Let’s make a PROTEIN!!!!PROTEIN!!!!.
Dr. Maha Daghestani
3. Translation3. Translation
PSite
ASite
Largesubunit
Small subunit
mRNAmRNA
A U G C U A C U U C G
Dr. Maha Daghestani
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
Dr. Maha Daghestani
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
Dr. Maha Daghestani
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)
Dr. Maha Daghestani
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
Dr. Maha Daghestani
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
Dr. Maha Daghestani
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
Dr. Maha Daghestani
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
Dr. Maha Daghestani
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
Dr. Maha Daghestani
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
Dr. Maha Daghestani
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
Dr. Maha Daghestani
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?
Dr. Maha Daghestani
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