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Principles of Biochemistry

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1 Principles of Biochemistry
Horton • Moran • Scrimgeour • Perry • Rawn Principles of Biochemistry Fourth Edition Chapter 23 Recombinant DNA Technology Copyright © 2006 Pearson Prentice Hall, Inc.

2 Chapter 23 - Recombinant DNA Technology
23.1 Making Recombinant DNA Recombinant DNA molecules are constructed with DNA from different sources Recombinant DNA molecules are created often in nature Bacteriophage or eukaryotic virus infects a host cell and integrates its DNA into the host creating a recombinant DNA molecule

3 Fig 23.1 Basic steps in the generation of a recombinant DNA molecule

4 Fig 23.1 Basic steps in the generation of a recombinant DNA molecule

5 Fig 23.1 (cont)

6 Six Basic Steps in a Recombinant DNA Experiment
1. Preparation of DNA. Vector and target DNA 2. Cleavage of DNA at particular sequences. Insert DNA can be added at specific points that have been cleaved 3. Ligation of DNA fragments. Joining of the fragments (continued)

7 Six Basic Steps (cont) 4. Introduction of recombinant DNA into compatible host cells. Genetic transformation is the uptake of foreign DNA by a host cell 5. Replication and expression of recombinant DNA in host cells. Cloning vectors allow insert DNA to be replicated in host cells 6. Identification of host cells that contain recombinant DNA of interest. Screening a large number of DNA clones for desired fragment

8 23.2 Cloning Vectors Cloning vectors can be: plasmids, bacterio-phages, viruses, small artificial chromosomes Some vectors can be replicated autonomously in a host cell, other vectors can be integrated into the host chromosome Vectors have at least one unique cloning site: a sequence cut by a restriction endonuclease to allow site-specific insertion of foreign DNA

9 Fig 23.2 Restriction enzymes can generate recombinant DNA

10 A. Plasmid(質體) Vectors Plasmids are small, circular DNA molecules used as vectors for DNA fragments to 20 kb Replicate autonomously within a host cell Carry genes conferring antibiotic resistance, used as marker genes for cells carrying vectors pBR322 was one of the first plasmid vectors

11 Fig 23.3 Plasmid vector pBR322 pBR322 has 4361 base pairs
Origin of replication (ori) Antibiotic resistance genes amp and tet Rop gene regulates replication for ~20 copies of the plasmid per cell

12 B. Bacteriophage l Vectors
Efficient, commonly used vector for delivering DNA into a bacterial cell Advantage over plasmid vectors is that transfection(轉染作用) is more efficient than transformation(轉形作用) Disadvantage: DNA must be packaged into phage particles in vitro

13 Fig 23.4 Preparation and use of phage l vector

14 Fig 23.4 Preparation and use of phage l vector

15 Fig 23.4 (cont) (From previous slide)

16 Fig 23.4 (cont)

17 Cosmids Cosmids combine the advantages of plasmid and phage vectors
Cosmids can accommodate large DNA fragments and allow efficient transfection Recombinant DNA molecule can be propagated as a plasmid in the host cell

18 C. Shuttle Vectors Shuttle vectors can replicate in either prokaryotic or eukaryotic cells They can be used to transfer recombinant DNA between prokaryotes and eukaryotes Useful for cloning eukaryotic DNA in bacteria, and then expressing the gene products in a eukaryotic cell

19 D. Yeast Artificial Chromosomes as Vectors
Large DNA fragments can be inserted into artificial chromosomes that are replicated in eukaryotic cells Such chromosomes must be linear and contain a eukaryotic replication origin Yeast artificial chromosome (YAC) is a shuttle vector

20 Fig 23.5 Yeast artificial chromosome (YAC)

21 23.3 Identification of Host Cells Containing Recombinant DNA
After a cloning vector and insert DNA have been joined in vitro, recombinant DNA is introduced into a host cell such as E. coli (transformation) Only a small percentage of cells take up the DNA Selection -cells are grown under conditions in which only transformed cells survive Screening - transformed cells are tested for the presence of the recombinant DNA

22 A. Selection Strategies Use Marker Genes
Bacterial plasmid vectors can carry a b-lactamase marker gene (marker genes allow detection of cells) b-Lactamase hydrolyzes b-lactam antibiotics (e.g. ampicillin) Only cells transformed with plasmids expressing the b-lactamase gene are ampicillin resistant and can grow in media containing ampicillin (ampR)

23 Selection or Screening by Insertional Inactivation
Insertional inactivation - insertion of a DNA fragment within the coding region of a gene on a vector results in inactivation of that gene If the gene product can be detected, this can be used for selection and screening pBR322 gene for tetracycline resistance (tetR) can be inactivated by DNA insertion making them tetracycline sensitive (tetS)

24 Fig 23.3 Plasmid vector pBR322 pBR322 has 4361 base pairs
Origin of replication (ori) Antibiotic resistance genes amp and tet Rop gene regulates replication for ~20 copies of the plasmid per cell

25 B. Selection in Eukaryotes
Yeast shuttle vectors may contain prokaryotic genes for antibiotic resistance and yeast genes for metabolite biosynthesis Yeast gene LEU2 encodes the enzyme b-isopropylmalate dehydrogenase, (leucine biosynthesis pathway) Cells transformed with a Leu2-containing plasmid can grow in the absence of leucine

26 Fig 23.6 Yeast shuttle vector is propagated, selected in both E. coli and S. cerevisiae

27 C. Visual Markers: Insertional Inactivation of the b-Galactosidase Gene
The lacZ gene of E. coli encodes b-galactosidase and cleavage of an artificial substrate produces a blue dye (X-gal) Vectors without inserts in the lacZ gene give rise to blue colonies in the presence of X-gal Vectors with DNA inserted in the lacZ gene do not produce the enzyme and yields colonies which are white

28 Fig Blue/white screen Blue colonies: cells transformed with cloning vectors not containing inserts (b-galactosidase is active) White colonies: cells transformed with recombinants. b-Galactosidase gene disrupted by insert

29 23.4 Genomic Libraries A method for isolating large quantities of specific DNA fragments from organisms DNA library consists of all the recombinant DNA molecules generated by ligating all the fragments of a particular DNA into vectors Recombinant DNA molecules are then introduced into cells for replication

30 Genomic Library Properties
Genomic libraries represent all the DNA from an organism’s genome (基因組) Partial (rather than total) restriction digestion is used to ensure that every gene is represented Cosmid, YAC and BAC vectors used Genomic libraries include both expressed and non-expressed DNA from the organism

31 23.5 cDNA Libraries Are Made from Messenger RNA
cDNA libraries represent all the mRNAs made in a given cell or tissue cDNA (complementary DNA) is double-stranded DNA made with reverse transcriptase Purification of mRNA relies on the polyA tails on mature eukaryotic mRNA The more abundant rRNA and tRNA lack tails

32 Fig 23.8 Preparation of cDNA
RNase H: a ribonuclease that cleaves the 3'-O-P-bond of RNA in a DNA/RNA duplex to produce 3'-hydroxyl and 5'-phosphate terminated products.

33 Fig 23.8 Preparation of cDNA

34 Fig 23.8 (continued)

35 Properties of cDNA libraries
Using a cDNA library from a specific tissue with abundant protein of interest increases the chances of successfully cloning the gene for that protein Specialized phage l vectors and plasmids are used in constructing cDNA libraries cDNA libraries from mRNA do not include introns or flanking sequences (much less complex than genomic libraries)

36 23.6 Screening a Library Isolation of the desired recombinant DNA is difficult (probability that a library of a given size contains the particular clone of interest is): P = 1 - (1-n)N or N = ln(1-P)/ln(1-n) N = number of recombinant clones in library P = probability of finding a particular clone n = frequency of occurrence of the clone

37 Finding a Clone in a cDNA Library
Probability of finding desired clone depends on the abundance of the original DNA molecule and not on the genome size n Represents the abundance of the relevant mRNA molecule General procedure for screening a DNA library with a probe (next slide)

38 Fig 23.9 General procedure for screening DNA library

39 Fig 23.9 General procedure for screening DNA library

40 Fig 23.9 (cont) Hybridization

41 Chromosome Walking A recombinant DNA fragment from a nearby region of the chromosome can be used as a starting point for a chromosome walk to the desired gene (Fig , next slide) Overlapping DNA fragments are isolated in successive screenings Larger and larger regions of DNA are cloned in a “walk” along the chromosome

42 Fig 23.4 Preparation and use of phage l vector


44 23.8 Expression of Proteins Using Recombinant DNA Technology
Cloned or amplified DNA can be purified and sequenced or used to produce RNA and protein Such DNA can also be introduced into organisms to change their phenotype Purification of proteins begins with overproduction of the protein in a cell containing the expression vector

45 A. Prokaryotic Expression Vectors
Expression vectors - plasmids that have been engineered to contain regulatory sequences for transcription and translation Eukaryotic genes can be expressed in prokaryotes Examples of sequences: strong promoters, ribosome-binding sites, transcription terminators

46 Fig 23.11 Expression of a eukaryotic protein in E. coli

47 Fig 23.11

48 Fig (cont)

49 B. Expression of Proteins in Eukaryotes
Prokaryotic cells may be unable to produce functional eukaryotic genes Some expression vectors are for eukaryotes Recombinant DNA molecules can also be integrated into the genomes of large multicellular organisms Creates transgenic organisms

50 Fig 23.12 Technique for creating a transgenic mouse

51 Fig 23.13 Effect of an extra growth hormone gene in mice
Transgenic mouse (left) carries a gene for rat growth hormone Normal mouse (right)

52 Transgenic oriental fruit fly
larvae pupae adults eggs

53 The Belgian Blue

54 Scaleless Chicken

55 23.9 Applications of Recombinant DNA Technology
Somatic changes in tissues are not passed on to subsequent generations Genome changes - germ cells are altered so that changes are passed to descendents Agricultural genetic engineering: to produce increased yield, resistance to insects, disease or frost, altered ripening Introduction of nitrogen fixation into plants

56 A. Genetic Engineering of Plants
Bacterial plasmid Ti can transform many kinds of plants Transforming DNA (T-DNA) of the Ti plasmid can be incorporated into E. coli-compatible vector to yield plant-E. coli shuttle vectors Insertion of foreign DNA (firefly lucerferase) into plants is shown on the next slide (Figure 23.14)


58 Fig 23.15 Insect-resistant tomato plants
Insect-resistant plant (left) contains a gene that encodes a protein that is toxic to certain insects that feed on tomato plants

59 B. Genetic Engineering in Prokaryotes
Bacterial genomics research is important in: Combating bacterial resistance to antibiotics Studying how genome determines function Understanding microbial biochemistry and pathology Developing drugs effective against pathogens

60 23.10 Applications to Human Diseases
Proteins are now produced commercially from cloned genes: insulin, interleukins, interferons, growth hormones, coagulation factors etc Proteins are produced in bacteria, or transgenic animals (blood, tissues, or milk) Mapping diseases to specific chromosomes

61 Restriction Fragment Length Polymorphisms (RFLPs)
RFLPs - genetic analysis based on variations in length of genomic restriction fragments Patterns of disease inheritance can be traced through a family RFLPs are detected by by incubating fragmented DNA of many individuals with a cloned DNA probe Hybridization pattern (Fig next slide)


63 RFLPs Studies The difference of even one nucleotide can introduce or abolish a restriction site The pattern of hybridizing fragments can be markedly changed Variations in a region of the genome near the affected gene provide good screening Individuals can be screened for potential diseases

64 RFLPs Uses in Forensic Medicine
RFLP analysis can distinguish one person from millions of others DNA samples from blood, hair, other tissues Restriction pattern is characteristic of each individual (except identical twins) Comparisons of patterns can be used in solving crimes

65 Fig 19.34 DNA Fingerprinting

66 Fingerprinting ( fingerprinting.jpg)

67 Fingerprinting (

68 23.11 The Polymerase Chain Reaction Amplifies Selected DNA Sequences
The polymerase chain reaction (PCR) is used for amplifying a small amount of DNA Also can increase the proportion of a particular DNA sequence in a mixed DNA population PCR technique is illustrated on the next 3 slides (Figure 23.17, three cycles of the PCR reaction)

69 Polymerase Chain Reaction (PCR)
Dr. Kary B. Mullis - the person who invented the polymerase chain reaction (PCR) method in the early 1980’s. Dr. Kary B. Mullis earned the Nobel Prize for Chemistry in 1993.





74 Identification of Codling Moth with Specific DNA Markers (1)

75 Identification of Codling Moth with Specific DNA Markers (2)

76 23.12 Site-Directed Mutagenesis of Cloned DNA
Powerful technique to introduce a desired mutation directly into a gene Oligonucleotide is synthesized containing mutation and flanking sequences of gene From oligonucleotide primer, DNA replication produces a new copy of the mutated gene Important in structure-function studies of genes and their protein products

77 Fig 23.19 Oligonucleotide-directed, site-specific mutagenesis

78 Fig 23.19 Oligonucleotide-directed, site-specific mutagenesis

79 Fig (cont)

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