Chau-Ti Ting
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Chapter 2
Genes, Genetic Codes, and Mutation
DNA
Neucleotides{Phosphate
Deoxyribose sugar
Nitrogen base AdenineGuanineCytosineThymine
Purine
Pyrimidine
S
S
P
S
P
T
T
G
S
S
P
S
P
A
A
C
3‘
5‘
5‘
3‘
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Source: National Institute of General Medical Sciences (NIGMS)http://images.nigms.nih.gov/index.cfm?event=viewDetail&imageID=2542
One-letter abbreviations for the DNA alphabet
A
T
G
C
SW
R
Y
KM
B x
x D
Hx
x V
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RNA
Single-stranded nucleotides
Ribose sugar in its nucleotides, rather than deoxyribose
Four nitrogenous bases: A, C, G, U (uracil)
A:UG:C
DNA replication: semiconservative replication
The polymerization processDNA polymerase 5' to 3'DNA polymerase acts at the replication forkLeading strand Lagging strand1. RNA oligonucleotides (primer) copied from DNA2. DNA polymerase elongates with new DNA Okazaki fragment3. DNA polymerase moves 5' RNA at the end of neighboring fragment and fills gap4. DNA ligase joins adjacent fragments
http://en.wikipedia.org/wiki/DNA_replication
The nature of genes (Fig. 2-4)
Prokaryotesgene = regulatory region + coding region +
transcription termination signals
Eukaryotesgene = regulatory region + exons + introns +
transcription termination signals
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Exon Exon Exon
Intron Intron
5’ 3’
Flanking region Flanking region
GC box
CAAT boxTATA box
Transcription initiation
Initiation codon
Stop codon
AATAAA box
Transcription termination
Poly(A) site
Promoter region
GT AG
Intron
19-27 bp upstream of the transcription startpoint
TACTAAC box
30 bp upstream of the 3’ end of the intron
GT-AG rule
5’ 3’
PseudogenesA pseudogene is a nongenic DNA segment that exhibits
a high degree of similarity to a functional gene but which contains defects, such as nonsense and frameshift mutations, that prevent it from being expressed properly.
Source: Dan Graur and Wen-Hsiung Li2000. Fundamentals of Molecular Evolution., p. 14. Sinauer Associates, Inc. Sunderland, MA, USA.
Amino AcidsThe basic building blocks of proteins. There are 20
different amino acid types. Each protein consists of a different sequence of amino acids linked together according to the genetic information encoded in DNA.
-NH2 (amine) group-COOH (carboxyl) groupside chain (-R group)
Source: Howard Hughes Medical Institutehttp://www.hhmi.org/genetictrail/glossary.html
ProteinsA molecule composed of amino acids linked together in
a particular order specified by a gene's DNA sequence. Proteins perform a wide variety of functions in the cell; these include serving as enzymes, structural components, or signaling molecules.
Peptide two or more amino acids linked together
Residue each amino acid in a polypeptide
N terminus terminated with free amine group
C terminus terminated by a free carboxyl group
Source: Howard Hughes Medical Institutehttp://www.hhmi.org/genetictrail/glossary.html
Source: Howard Hughes Medical Institutehttp://www.hhmi.org/genetictrail/glossary.html
http://en.wikipedia.org/wiki/N-terminus
http://en.wikipedia.org/wiki/C-terminus
http://en.wikibooks.org/wiki/Structural_Biochemistry/Proteins/Structures
Genetic Code• Codon: a section of DNA (3 nucleotide pairs in length) that
encodes a single amino acid.
• Genetic code: The set of correspondences between nucleotide pair triplets in DNA and amino acid in protein.
• Stop codons (termination codons) can be recognized by release factors.
ATA TGT ATA AAG GCA Ile Cys Ile Lys Ala
http://en.wikipedia.org/wiki/Stop_codon#cite_note-0
Source: A. J. F. Griffiths, J. H. Miller, D. T. Suzuki, R. C. Lewontin, and W. M. Gelbart.2000. An Introduction to Genetic Analysis, 7th edition. W. H. Freeman and Company. New York, USA.http://www.ncbi.nlm.nih.gov/books/NBK21878/
(a) AGGCAAACCTACTGGTCTTAT original sequence(b) AGGCAAATCTACTGGTCTTAT C to T transition(c) AGGCAAACCTACTGCTCTTAT G to C transversion(d) AGGCAAACCTACTGCAAACAT recombination
GTCTT
ACCTA
(e) AGGCAACTGGTCTTAT deletion of ACCTA
(f) AGGCAAACCTACTAAAGCGGTCTTAT insertion of AAAGC
(g) AGGTTTGCCTACTGGTCTTAT inversion of GCAAAC
Source: Dan Graur and Wen-Hsiung Li2000. Fundamentals of Molecular Evolution., p. 26. Sinauer Associates, Inc. Sunderland, MA, USA.
Substitution mutations
Transition changes beween A and G, or between T and CTransversion changes between a purine and a pyrimidine
Synonymous (silent mutations) Nucleotide changes in the encoding part of a gene that do not
result in a change in the amino acid sequence of the encoded protein.
Nonsynonymous (replacement mutations) Nucleotide changes in the encoding part of a gene that result in
a change in the amino acid sequence of the encoded protein.
DNA CCG CTG CTCmRNA CCG CUG CUCAmino acid Proline Leucine Leucine
Source: Marjorie A. Hoy2003. Insect molecular genetics: an introduction to principles and applications, 2nd edition, p. 23. Academic Press. USA.
Source: A. J. F. Griffiths, J. H. Miller, D. T. Suzuki, R. C. Lewontin, and W. M. Gelbart.2000. An Introduction to Genetic Analysis, 7th edition. W. H. Freeman and Company. New York, USA.
Source: A. J. F. Griffiths, J. H. Miller, D. T. Suzuki, R. C. Lewontin, and W. M. Gelbart.2000. An Introduction to Genetic Analysis, 7th edition. W. H. Freeman and Company. New York, USA.
Types of Mutation
Nucleotide substitution Replacement mutations: Nucleotide changes in the encoding part of a gene that result in a change in the amino acid sequence of the encoded protein. Silent mutations: Nucleotide changes in the encoding part of a gene that do not result in a change in the amino acid sequence of the encoded protein.
DNA CCG CTG CTCmRNA CCG CUG CUCAmino acid Proline Leucine Leucine
Addition or deletion (frameshift mutations) Deletion
Wild type UUG CUG AGG CCC GAG U….Deletion UUG CGA GGC CCG AGU ……
Source: A. J. F. Griffiths, J. H. Miller, D. T. Suzuki, R. C. Lewontin, and W. M. Gelbart.2000. An Introduction to Genetic Analysis, 7th edition. W. H. Freeman and Company. New York, USA.
(a) synonymousIle Cys Ile Lys Ala Leu Val Leu Leu ThrATA TGT ATA AAG GCA CTG GTC CTG TTA ACA
ATA TGT ATA AAG GCA CTG GTA CTG TTA ACAIle Cys Ile Lys Ala Leu Val Leu Leu Thr
(b) missenseIle Cys Ile Lys Ala Leu Val Leu Leu ThrATA TGT ATA AAG GCA CTG GTC CTG TTA ACA
ATA TGT ATA AAG GCA CTG TTA CTG TTA ACAIle Cys Ile Lys Ala Leu Phe Leu Leu Thr
(c) nonsense Ile Cys Ile Lys Ala Leu Val Leu Leu Thr
ATA TGT ATA AAG GCA CTG GTC CTG TTA ACA
ATA TGT ATA TAG GCACTGGTACTGTTAACAIle Cys Ile Stop Source: Dan Graur and Wen-Hsiung Li
2000. Fundamentals of Molecular Evolution., p. 27. Sinauer Associates, Inc. Sunderland, MA, USA.
RecombinationCrossing over (reciprocal recombination)Gene conversion (non-reciprocal recombination)
Deletions and insertionsmechanisms unequal crossing over
intrastrand deletionreplication slippage
indel = insertion-or-deletionframeshift mutation
Deletion
Wild type UUG CUG AGG CCC GAG U….Deletion UUG CGA GGC CCG AGU ……
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National Institute of General Medical Sciences (NIGMS)http://images.nigms.nih.gov/index.cfm?event=viewDetail&imageID=25422012/02/24 visitedThis work is used subject to the fair use doctrine of :•Article 46, 52 & 65 Taiwan Copyright Act.•Permission for Use NIGMS Image Gallery http://images.nigms.nih.gov/
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Wikipedia Madprimehttp://en.wikipedia.org/wiki/File:DNA_replication_split.svg2012/02/22 visited
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P. 11. “A pseudogene is a nongenic DNA segment that exhibits a high degree of … that prevent it from being expressed properly.”
Dan Graur and Wen-Hsiung Li2000. Fundamentals of Molecular Evolution., p. 14. Sinauer Associates, Inc. Sunderland, MA, USA.It is used subject to fair use doctrine in accordance with Articles 52 & 65 of Taiwan Copyright Act
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Wikipedia Dhorspool http://en.wikipedia.org/wiki/File:Central_Dogma_of_Molecular_Biochemistry_with_Enzymes.jpg2012/02/22 visited
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P. 13. “The basic building blocks of proteins … linked together according to the genetic information encoded in DNA.”
Howard Hughes Medical Institutehttp://www.hhmi.org/genetictrail/glossary.html2012/02/22 visitedIt is used subject to fair use doctrine in accordance with Articles 52 & 65 of Taiwan Copyright Act and copyright notice of HHMI (http://www.hhmi.org/popups/copyright.html)
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P. 14. “A molecule composed of amino acids linked together in … structural components, or signaling molecules.”
Howard Hughes Medical Institutehttp://www.hhmi.org/genetictrail/glossary.html2012/02/22 visitedIt is used subject to fair use doctrine in accordance with Articles 52 & 65 of Taiwan Copyright Act and copyright notice of HHMI (http://www.hhmi.org/popups/copyright.html)
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P. 14. “Peptide two or more amino acids linked together”
Howard Hughes Medical Institutehttp://www.hhmi.org/genetictrail/glossary.html2012/02/22 visitedIt is used subject to fair use doctrine in accordance with Articles 52 & 65 of Taiwan Copyright Act and copyright notice of HHMI (http://www.hhmi.org/popups/copyright.html)
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Wikipedia National Human Genome Research Institute (NHGRI)http://en.wikipedia.org/wiki/File:Protein-primary-structure.png2012/02/22 visited
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Wikipedia LadyofHatshttp://en.wikipedia.org/wiki/File:Main_protein_structure_levels_en.svg2012/02/22 visited
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P. 17. “Codon: a section of DNA (3 nucleotide pairs in length) that encodes a single amino acid.”
A. J. F. Griffiths, J. H. Miller, D. T. Suzuki, R. C. Lewontin, and W. M. Gelbart.2000. An Introduction to Genetic Analysis, 7th edition. W. H. Freeman and Company. New York, USA.http://www.ncbi.nlm.nih.gov/books/NBK21878/2012/02/22 visitedIt is used subject to fair use doctrine in accordance with Articles 52 & 65 of Taiwan Copyright Act
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Work Licensing Author/Source Page
P. 17. “Genetic code: The set of correspondences between nucleotide pair triplets in DNA and amino acid in protein.”
A. J. F. Griffiths, J. H. Miller, D. T. Suzuki, R. C. Lewontin, and W. M. Gelbart.2000. An Introduction to Genetic Analysis. 7th edition. W. H. Freeman and Company. New York, USA.http://www.ncbi.nlm.nih.gov/books/NBK21878/2012/02/22 visitedIt is used subject to fair use doctrine in accordance with Articles 52 & 65 of Taiwan Copyright Act .
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Dan Graur and Wen-Hsiung Li2000. Fundamentals of Molecular Evolution., p. 26. Sinauer Associates, Inc. Sunderland, MA, USA.It is used subject to fair use doctrine in accordance with Articles 52 & 65 of Taiwan Copyright Act
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P. 19. “Transition changes beween A and G, or between T and CTransversion changes between a purine and a pyrimidine”
Marjorie A. Hoy2003. Insect molecular genetics: an introduction to principles and applications, 2nd edition, p. 23. Academic Press. USA.http://books.google.com.tw/books?id=MPkwi-i33zYC&printsec=frontcover&hl=zh-TW#v=onepage&q&f=false2012/02/22 visitedIt is used subject to fair use doctrine in accordance with Articles 52 & 65 of Taiwan Copyright Act
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P. 19, 20. “Nucleotide changes in the encoding part of a gene that do not result in a change in the amino acid sequence of the encoded protein.”
A. J. F. Griffiths, J. H. Miller, D. T. Suzuki, R. C. Lewontin, and W. M. Gelbart.2000. An Introduction to Genetic Analysis, 7th edition. W. H. Freeman and Company. New York, USA.http://www.ncbi.nlm.nih.gov/books/NBK21878/2012/02/22 visitedIt is used subject to fair use doctrine in accordance with Articles 52 & 65 of Taiwan Copyright Act
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P. 19, 20. “Nucleotide changes in the encoding part of a gene that result in a change in the amino acid sequence of the encoded protein.”
A. J. F. Griffiths, J. H. Miller, D. T. Suzuki, R. C. Lewontin, and W. M. Gelbart.2000. An Introduction to Genetic Analysis, 7th edition. W. H. Freeman and Company. New York, USA.http://www.ncbi.nlm.nih.gov/books/NBK21878/2012/02/22 visitedIt is used subject to fair use doctrine in accordance with Articles 52 & 65 of Taiwan Copyright Act
P19,20
Dan Graur and Wen-Hsiung Li2000. Fundamentals of Molecular Evolution., p. 27. Sinauer Associates, Inc. Sunderland, MA, USA.It is used subject to fair use doctrine in accordance with Articles 52 & 65 of Taiwan Copyright Act
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