The E. Coli genome includes approximately 4,000 genes

The E. Coli genome includes approximately 4,000 genes

• Chromosomes Strands of DNA that contain all of

the genes an organism needs to survive and reproduce

Chromosomes

• Genes Segments of DNA that specify

how to build a protein• genes may specify more

than one protein in eukaryotes

Chromosome maps are used to show the locus (location) of genes on a chromosome

• Genetic Variation Phenotypic variation among organisms is due to genotypic variation

(differences in the sequence of their DNA bases)

Differences exist between species and within a species• Different genes (genomes) different proteins (proteomes)

• Different versions of the same gene (alleles)

• Differences in gene expression (epigenetics)

Chromosomes

• Cell Division (mitosis) Cells must copy their chromosomes

(DNA synthesis) before they divide so that each daughter cell will have a copy

A region of the chromosome remains uncopied (centromere) in order to hold the sister chromatids together– Keeps chromatids organized to help

make sure each daughter cell gets exactly one copy

– Nondisjunction is when sister chromatids do not assort correctly and one cell ends up with both copies while the other cell ends up with none

DNA Replication

• DNA Synthesis The DNA bases on each

strand act as a template to synthesize a complementary strand• Recall that Adenine (A)

pairs with thymine (T)and guanine (G) pairs with cytosine (C)

The process is semiconservative because each new double-stranded DNA contains one old strand (template) and one newly-synthesized complementary strand

DNA Replication

AGCTG

TCGAC

AGCTG

TCGAC

AGCTG

TCGAC

AGCTG

TCGAC

TCGAC

AGCTG

DNA Replication• DNA Polymerase

Enzyme that catalyzes the covalent bond between the phosphate of one nucleotide and the deoxyribose (sugar) of the next nucleotide

DNA Polymerization

3’ end has a free deoxyribose

5’ end has a free phosphate

DNA polymerase: can only build the new strand in

the 5’ to 3’ direction Thus scans the template strand in

3’ to 5’ direction

DNA Replication

Initiation• Primase (a type of RNA polymerase) builds an RNA primer

(5-10 ribonucleotides long)

• DNA polymerase attaches onto the 3’ end of the RNA primer

DNA Replication

DNA polymerase

Elongation • DNA polymerase uses each strand as a template in the 3’ to 5’ direction to build a complementary strand in the 5’ to 3’ direction

DNA Replication

DNA polymerase

Elongation • DNA polymerase uses each strand as a template in the 3’ to 5’ direction to build a complementary strand in the 5’ to 3’ direction results in a leading strand and a lagging strand

DNA Replication

Leading Strand1. Topisomerase unwinds DNA and then Helicase breaks H-bonds2. DNA primase creates a single RNA primer to start the replication3. DNA polymerase slides along the leading strand in the 3’ to 5’ direction

synthesizing the matching strand in the 5’ to 3’ direction4. The RNA primer is degraded by RNase H and replaced with DNA nucleotides by

DNA polymerase, and then DNA ligase connects the fragment at the start of the new strand to the end of the new strand (in circular chromosomes)

DNA Replication

Lagging Strand1. Topisomerase unwinds DNA and then Helicase breaks H-bonds2. DNA primase creates RNA primers in spaced intervals3. DNA polymerase slides along the leading strand in the 3’ to 5’ direction

synthesizing the matching Okazaki fragments in the 5’ to 3’ direction4. The RNA primers are degraded by RNase H and replaced with DNA nucleotides

by DNA polymerase5. DNA ligase connects the Okazaki fragments to one another (covalently bonds the

phosphate in one nucleotide to the deoxyribose of the adjacent nucleotide)

DNA Replication

Topoisomerase - unwinds DNAHelicase – enzyme that breaks H-bonds DNA Polymerase – enzyme that catalyzes connection of nucleotides to form complementary DNA strand in 5’ to 3’ direction (reads template in 3’ to 5’ direction)Leading Strand – transcribed continuously in 5’ to 3’ directionLagging Strand – transcribed in segments in 5’ to 3’ direction (Okazaki fragments)DNA Primase – enzyme that catalyzes formation of RNA starting segment (RNA primer)DNA Ligase – enzyme that catalyzes connection of two Okazaki fragments

DNA Replication

Web ResourcesDNA Replication (synthesis)• http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter11/animation_quiz_2.html

• http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.html

• http://www.biostudio.com/d_%20DNA%20Replication%20Coordination%20Leading%20Lagging%20Strand%20Synthesis.htm

• http://www.biostudio.com/d_%20DNA%20Replication%20Nucleotide%20Polymerization.htm

• http://www.dnalc.org/resources/3d/DNAReplicationBasic_w_FX.html (download this video file from the website to view it without interruptions)

• http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/dna-rna2.swf

• http://www.bioteach.ubc.ca/TeachingResources/MolecularBiology/DNAReplication.swf

• DNA provides the instructions for how to build proteins

• Each gene dictates how to build a single protein in prokaryotes

• The sequence of nucleotides (AGCT) in DNA dictate the order of amino acids that make up a protein

Protein Synthesis

Nucleotide sequence of His gene

Protein Synthesis

Nucleotide sequence of His geneAmino acid sequence of

His protein

• DNA provides the instructions for how to build proteins

• Each gene dictates how to build a single protein in prokaryotes

• The sequence of nucleotides (AGCT) in DNA dictate the order of amino acids that make up a protein

• Protein synthesis occurs in two primary steps

Protein Synthesis

mRNA (messenger RNA) copy of a gene is synthesized

Cytoplasm of prokaryotesNucleus of eukaryotes

1

mRNA is used by ribosome to build protein

(Ribosomes attach to the mRNA and use its sequence of nucleotides to determine the order of amino acids in the protein)

Cytoplasm of prokaryotes and eukaryotes

Some proteins feed directly into rough ER in eukaryotes

2

(eukaryotes)

Protein Synthesis1) INITIATION

• Transcription Initiation RNA polymerase binds to a region on DNA known as the promoter, which signals the start of a gene

Promoters are specific to genes

RNA polymerase does not need a primer

Transcription factors assemble

at the promoter forming a transcription initiation complex – activator proteins help stabilize the complex

Gene expression can be regulated (turned on/off or up/down) by controlling the amount of each transcription factor


• Transcription Elongation RNA polymerase unwinds the DNA and breaks the H-bonds between the bases of the two strands, separating them from one another

Base pairing occurs between incoming RNA nucleotides and the DNA nucleotides of the gene (template)•recall RNA uses uracil instead of thymine

AGTCAT

UCA GUA

Protein Synthesis• Transcription

Elongation RNA polymerase unwinds the DNA and breaks the H-bonds between the bases of the two strands, separating them from one another.

Base pairing occurs between incoming RNA nucleotides and the DNA nucleotides of the gene (template)•recall RNA uses uracil instead of thymine

RNA polymerase catalyzes bond to form between ribose of 3’ nucleotide of mRNA and phosphate of incoming RNA nucleotide

3’

5’

3’

5’

+ ATP

+ ADP

Protein Synthesis• Transcription

ElongationThe gene occurs on only one of the DNA strands; each strand possesses a separate set of genes


• Transcription Termination A region on DNA known as the terminator signals the stop of a gene

RNA polymerase disengages the mRNA and the DNA

Exons are “coding” regions

Introns are removed different combinations

of exons form different mRNA resulting in multiple proteins from the same gene

Humans have 30,000 genes but are capable of producing 100,000 proteins

Protein Synthesis• Alternative Splicing (eukaryotes only)

Web ResourcesTranscription• http://www.biostudio.com/d_%20Transcription.htm• http://www.youtube.com/watch?v=WsofH466lqk• http://www.dnalc.org/resources/3d/TranscriptionBasic_withFX.html

Alternative Splicing• http://www.youtube.com/watch?v=FVuAwBGw_pQ&feature=related

mRNA copy of a gene is synthesized

Cytoplasm of prokaryotesNucleus of eukaryotes

1

Protein Synthesis

mRNA is used by ribosome to build protein

(Ribosomes attach to the mRNA and use its sequence of nucleotides to determine the order of amino acids in the protein)

Cytoplasm of prokaryotes and eukaryotes

Some proteins feed directly into rough ER in eukaryotes

2mRNA

Transcription

Translation

mRNA

tRNA synthesis

Transcription

Translation

mRNA

tRNA synthesis

Protein Synthesis• Translation

Every three mRNA nucleotides (codon) specify an amino acid


tRNA have an anticodon region that specifically binds to its codon

Transcription

Translation

mRNA

tRNA synthesis


Each tRNA carries a specific amino acid

Transcription

Translation

mRNA

tRNA synthesis

Protein Synthesis

Aminoacyl tRNA synthetases attach amino acids to their specific tRNA

Protein Synthesis• TranslationInitiation Start codon signals where the gene begins (at 5’ end of mRNA)

AUGGACAUUGAACCG…5’ 3’

start codon

Translation

mRNA

Protein Synthesis• TranslationInitiation Start codon signals where the gene begins (at 5’ end of mRNA)

Ribosome binding site (Shine Dalgarno sequence) upstream from the start codon binds to small ribosomal subunit–then this complex recruits the large ribosomal subunit

Small ribosomal subunit

Small ribosomal subunit

Ribosome

Large ribosomal subunit

Protein Synthesis• TranslationScanningThe ribosome moves in 5’ to 3’ direction “reading” the mRNA and assembling amino acids into the correct protein

large ribosome subunit

small ribosome subunit

Protein Synthesis• TranslationScanningThe ribosome moves in 5’ to 3’ direction “reading” the mRNA and assembling amino acids into the correct protein

Protein Synthesis• TranslationTerminationRibosome disengages from the mRNA when it encounters a stop codon

Web ResourcesTranslation• Eukaryotic: http://www.youtube.com/watch?v=5bLEDd-PSTQ&feature=related

• Prokaryotic: http://www.biostudio.com/d_%20Protein%20Synthesis%20Prokaryotic.htm

• http://www.biostudio.com/d_%20Peptide%20Bond%20Formation.htm• http://www.johnkyrk.com/DNAtranslation.html• http://www.dnalc.org/resources/3d/TranslationBasic_withFX0.html• http://www.dnalc.org/resources/3d/TranslationAdvanced.html

Practice QuestionTranslate the following mRNA sequence

AGCUACCAUACGCACCCGAGUUCUUCAAGC


AGCUACCAUACGCACCCGAGUUCUUCAAGCSerine – Tyrosine – Histidine – Threonine – Histidine – Proline – Serine – Serine – Serine - Serine

Ser – Tyr – His – Thr – His – Pro – Ser – Ser – Ser - Ser


AGCUACCAUACGCACCCGAGUUCUUCAAGCSerine – Tyrosine – Histidine – Threonine – Histidine – Proline – Serine – Serine – Serine - Serine

Serine – Tyrosine – Histidine – Threonine – Histidine – Proline – Serine – Serine – Serine - Serine


AGCUACCAUACGCACCCGAGUUCUUCAAGC

S – Y –H– T – H – P – S – S – S - SSer – Tyr – His – Thr – His – Pro – Ser – Ser – Ser - Ser

Protein Synthesis• Multiple RNA polymerases can

engage a gene at one time

• Multiple ribosomes can engage a single mRNA at one time

DNA mRNAsTranscription

Translation

Protein Synthesis• Eukaryotes:

transcription occurs in the nucleus and translation occurs in the cytoplasm

• Prokaryotes: Transcription and translation occur simultaneously in the cytoplasm

• There are four main types of RNA:1. mRNA

- RNA copy of a gene used as a template for protein synthesis

2. rRNA - part of structure of ribosomes

3. tRNA- amino acid carrier that matches to mRNA codon

4. snRNA - found in nucleus where they have several important jobs

RNA

1. Why is DNA synthesis said to be “semiconservative”?2. What role do DNA polymerase, DNA primase (a type of RNA

polymerase), helicase, topoisomerase, RNase H, and ligase play in DNA replication?

3. What is the difference between how the leading strand and lagging strand are copied during DNA replication? Why do they have to be synthesized differently in this fashion?

4. What would happen if insufficient RNase H were produced by a cell? What if insufficient ligase were produced by a cell?

5. What are four key differences between DNA polymerase and RNA polymerase? (“they are difference molecules” doesn’t count as one!)

6. Compare and contrast codons and anticodons?7. What is alternative splicing? Why is it necessary in

eukaryotes?8. During translation, what amino acid sequence would the

following mRNA segment be converted into: AUGGACAUUGAACCG?9. How come there are only 20 amino acids when there are 64

different codons?10. How come prokaryotes can both transcribe and translate a gene

at the same time, but eukaryotes cannot?

Practice Questions

Web ResourcesTranscription• http://www.biostudio.com/d_%20Transcription.htm• http://www.youtube.com/watch?v=WsofH466lqk• http://www.dnalc.org/resources/3d/TranscriptionBasic_withFX.html

Translation• Eukaryotic: http://www.youtube.com/watch?v=5bLEDd-PSTQ&feature=related

• Prokaryotic: http://www.biostudio.com/d_%20Protein%20Synthesis%20Prokaryotic.htm

• http://www.biostudio.com/d_%20Peptide%20Bond%20Formation.htm• http://www.johnkyrk.com/DNAtranslation.html• http://www.dnalc.org/resources/3d/TranslationBasic_withFX0.html• http://www.dnalc.org/resources/3d/TranslationAdvanced.html

Alternative Splicing• http://www.youtube.com/watch?v=FVuAwBGw_pQ&feature=related

Insulin Example of Protein Synthesishttp://www.biotopics.co.uk/as/insulinproteinstructure.html

Hemoglobin Example of Protein Synthesishttp://www.biotopics.co.uk/as/insulinproteinstructure.html

Collagen Example of Protein Synthesishttp://www.biotopics.co.uk/JmolApplet/collagen.html

Web Resources

Images• http://www.kscience.co.uk/as/module1/pictures/bacteria.jpg• http://www.biologie.uni-hamburg.de/b-online/library/onlinebio/14_1.jpg• http://pharmamotion.com.ar/wp-content/uploads/2009/12/nrti_mechanism_action_antiretrovirals.jpg• http://biology200.gsu.edu/houghton/4564%20%2704/figures/lecture%204/AAAreverse.jpg• http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/2d8x/traces.jpg• http://www.ncbi.nlm.nih.gov• http://xarquon.jcu.cz/edu/uvod/09nucleus/092function/images/activation3.jpg• http://www.ncbi.nlm.nih.gov• http://bass.bio.uci.edu/~hudel/bs99a/lecture23/lecture4_4.html• http://selfhpvdna.diagcorlab.com/images/images/CervicalCancer.jpg

Documents

The E. Coli genome includes approximately 4,000 genes