HUP genes.pptx
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Dr.S.KARTHIKUMAR Associate Professor Department of Biotechnology Kamaraj College of Engineering and Technology, K.Vellakulam-625701, TN, India Email: skarthikumar@gmail.com
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Why arabidopsis is a model plant
Arabidposis thaliana is commonly used as a model plant for several reasons: it has a small genome and plant size, a short generation time of 6 weeks, and the ability to easily generate many seeds and variants. It was one of the first plants to have its genome fully sequenced, furthering research on plant genetics, development, and evolution. Due to its small size and rapid life cycle, Arabidopsis thaliana provides an efficient system for studying basic plant processes that can be applied to economically important crops.
C value
The document discusses the C-value paradox, which is the lack of relationship between genome size and organism complexity. It provides data on the wide range of genome sizes across different taxonomic groups. Introns and exons are described, with exons comprising the coding sequences and introns being removed from transcripts by splicing. Alternative splicing can generate multiple protein isoforms from a single gene. Repeated sequences, including satellites, minisatellites, microsatellites, transposons, SINEs and LINEs comprise a large portion of eukaryotic genomes.
cell lineage and fate
cell lineage , cell fate - diverse class of cell fate, cell fate in plant meristem, mammalian development cell fate, nutritional effects on epigenetics, epigenetics of plants,
control of cell fate.
Complementation test
This document presents information on complementation tests. It defines complementation tests as a method used to determine if two mutations are in the same gene or different genes. It explains that if the mutations are complementary (in different genes), the offspring will show the parental phenotypes, but if they are not complementary (in the same gene), the offspring will show a new phenotype. Three examples of using complementation test results to determine the number of genes involved are provided. The document concludes by citing a reference for more information on assigning mutations to genes using complementation tests.
Second genetic code overlapping and split genes
1) Eukaryotic genes can be organized in complex ways, including overlapping genes where coding sequences partially overlap, and split genes where coding sequences are interrupted by non-coding intron sequences.
2) Overlapping genes were discovered in bacteriophage X174, where the coding sequences of genes D and E overlap but are translated in different reading frames.
3) Split genes have exons, which are the coding sequences included in mRNA, and introns, which are intervening non-coding sequences not included in mRNA. Split genes were first observed in animal viruses in 1977.
Cot curve
Cot value and Cot Curve analysis is a technique for measuring DNA complexity based on renaturation kinetics. DNA is denatured and allowed to reanneal, with larger DNA taking longer. Cot value accounts for DNA concentration, time, and buffer effects, representing repetitive sequences - lower Cot means more repeats. Examples show bacteria have nearly all single-copy DNA, while mouse has varying proportions of single-copy, middle repetitive, and highly repetitive sequences. Cot curve analysis provides information on genome size, complexity, and proportions of sequence types.
cDNA Library
This is a brief overview of the process of making a complementary DNA (cDNA) library from mRNA (messenger RNA).
chloroplast DNA
This document discusses chloroplast DNA (cpDNA). Chloroplasts contain their own circular genome of double-stranded DNA ranging from 140-200kb. The cpDNA contains genes that code for proteins involved in photosynthesis as well as rRNA and tRNA. It has a quadripartite structure containing single copy and inverted repeat regions. Tobacco and liverwort were two of the first chloroplast genomes to be sequenced. Molecular studies of cpDNA regions have been useful for plant systematics. Replication of cpDNA is independent of nuclear DNA and involves enzymes like DNA polymerase and helicase.
Recomendados
Why arabidopsis is a model plant
Arabidposis thaliana is commonly used as a model plant for several reasons: it has a small genome and plant size, a short generation time of 6 weeks, and the ability to easily generate many seeds and variants. It was one of the first plants to have its genome fully sequenced, furthering research on plant genetics, development, and evolution. Due to its small size and rapid life cycle, Arabidopsis thaliana provides an efficient system for studying basic plant processes that can be applied to economically important crops.
C value
The document discusses the C-value paradox, which is the lack of relationship between genome size and organism complexity. It provides data on the wide range of genome sizes across different taxonomic groups. Introns and exons are described, with exons comprising the coding sequences and introns being removed from transcripts by splicing. Alternative splicing can generate multiple protein isoforms from a single gene. Repeated sequences, including satellites, minisatellites, microsatellites, transposons, SINEs and LINEs comprise a large portion of eukaryotic genomes.
cell lineage and fate
cell lineage , cell fate - diverse class of cell fate, cell fate in plant meristem, mammalian development cell fate, nutritional effects on epigenetics, epigenetics of plants,
control of cell fate.
Complementation test
This document presents information on complementation tests. It defines complementation tests as a method used to determine if two mutations are in the same gene or different genes. It explains that if the mutations are complementary (in different genes), the offspring will show the parental phenotypes, but if they are not complementary (in the same gene), the offspring will show a new phenotype. Three examples of using complementation test results to determine the number of genes involved are provided. The document concludes by citing a reference for more information on assigning mutations to genes using complementation tests.
Second genetic code overlapping and split genes
1) Eukaryotic genes can be organized in complex ways, including overlapping genes where coding sequences partially overlap, and split genes where coding sequences are interrupted by non-coding intron sequences.
2) Overlapping genes were discovered in bacteriophage X174, where the coding sequences of genes D and E overlap but are translated in different reading frames.
3) Split genes have exons, which are the coding sequences included in mRNA, and introns, which are intervening non-coding sequences not included in mRNA. Split genes were first observed in animal viruses in 1977.
Cot curve
Cot value and Cot Curve analysis is a technique for measuring DNA complexity based on renaturation kinetics. DNA is denatured and allowed to reanneal, with larger DNA taking longer. Cot value accounts for DNA concentration, time, and buffer effects, representing repetitive sequences - lower Cot means more repeats. Examples show bacteria have nearly all single-copy DNA, while mouse has varying proportions of single-copy, middle repetitive, and highly repetitive sequences. Cot curve analysis provides information on genome size, complexity, and proportions of sequence types.
cDNA Library
This is a brief overview of the process of making a complementary DNA (cDNA) library from mRNA (messenger RNA).
chloroplast DNA
This document discusses chloroplast DNA (cpDNA). Chloroplasts contain their own circular genome of double-stranded DNA ranging from 140-200kb. The cpDNA contains genes that code for proteins involved in photosynthesis as well as rRNA and tRNA. It has a quadripartite structure containing single copy and inverted repeat regions. Tobacco and liverwort were two of the first chloroplast genomes to be sequenced. Molecular studies of cpDNA regions have been useful for plant systematics. Replication of cpDNA is independent of nuclear DNA and involves enzymes like DNA polymerase and helicase.
Complementation test; AC-DS System in Maize
The document discusses the Ac-Ds transposable element system in maize and complementation testing. It notes that Ac is an autonomous transposable element that enables the movement of Ds elements. McClintock discovered that Ac, Ds, and the C gene are responsible for color instability in maize seeds. Complementation testing determines if two recessive mutations represent alleles of the same gene or different genes.
Mitochondrial genome and its manipulation
Mitochondria contain their own DNA and play an essential role in cellular respiration by generating ATP. While small, the mitochondrial genome encodes components of the electron transport chain. Manipulation of the mitochondrial genome holds promise for crop improvement due to maternal inheritance and absence of position effects. However, transforming the mitochondrial genome remains challenging due to difficulties incorporating foreign DNA and a lack of selectable markers. Successful manipulation could generate cytoplasmic male sterility for hybrid seed production.
Transposable elements in Maize And Drosophila
Transposable elements are mobile DNA sequences found in genomes of all organisms. Barbara McClintock discovered transposable elements called Ac and Ds in maize that cause color patterns in corn kernels. Her discovery showed that genes can move within genomes. Experiments with Drosophila revealed another transposable element called P elements that cause hybrid dysgenesis. Transposable elements can provide genetic variation and flexibility that influences evolution.
chloroplast genome ppt.
Chloroplasts are organelles found in plant cells and algae that conduct photosynthesis. They contain their own DNA known as the chloroplast genome, which is typically 100-200kb in size and encodes genes for photosynthesis. The chloroplast genome is highly conserved and maternally inherited. It has been used for phylogenetic studies and shows potential for genetic engineering due to high transgene expression and maternal inheritance that prevents gene flow to other species.
Transposons ppt
Transposons are DNA sequences that can change position within a genome. Barbara McClintock first discovered transposons in corn in the 1940s. There are two classes of transposons: class I (retrotransposons) move via an RNA intermediate, while class II (DNA transposons) move directly via a cut-and-paste mechanism. Transposons make up a large percentage of many genomes and can cause mutations when they insert into genes, which has implications for genetic disease and genome evolution.
Cosmid Vectors, YAC and BAC Expression Vectors
1. Cosmid vectors are hybrid vectors derived from plasmids that contain the cos site from bacteriophage lambda, allowing them to clone DNA fragments up to 40 kb in size.
2. Yeast artificial chromosomes (YACs) are engineered yeast chromosomes that can clone very large DNA fragments, averaging 200-500 kb but up to 1 MB, taking advantage of yeast cell machinery.
3. Bacterial artificial chromosomes (BACs) are DNA constructs based on fertility plasmids that can clone up to 300 kb fragments and address issues with YAC stability and recombination.
Restriction Mapping
Restriction enzymes cut DNA molecules at specific recognition sites. Restriction mapping involves digesting an unknown DNA segment with restriction enzymes and analyzing the fragment sizes to determine the locations of restriction sites. One method involves single and double digestions with two enzymes followed by gel electrophoresis to separate the fragments by size. By comparing the fragment patterns between single and double digestions, the positions of each restriction site can be mapped, generating a restriction map of the DNA segment. Restriction mapping was previously important for characterizing cloned DNA but is now easier using DNA sequencing, though analysis of restriction sites remains useful for comparing chromosomal organization between strains.
Linkage mapping
This document discusses linkage mapping, which involves determining the relative positions of genes on chromosomes based on how often they are inherited together through analysis of recombination frequencies during meiosis. It provides background on the history of linkage mapping and definitions of key terms like linkage, linkage mapping, linkage groups, and types of linkage (complete and incomplete). Examples are also given to illustrate linkage analysis through test crosses and calculation of recombination frequencies.
Chloroplast genome organisation
Chloroplasts are double-membrane organelles found in plant cells that contain chlorophyll and are the site of photosynthesis. Chloroplast DNA is circular and ranges in size from 120,000 to 170,000 base pairs. It contains approximately 120 genes, including genes that encode proteins involved in photosynthesis and the transcription and translation machinery. Chloroplast DNA replication is semi-conservative and there are typically multiple copies of the chloroplast genome within each chloroplast.
Complementation of defined mutations
A complementation test (sometimes called a "cis-trans" test) can be used to test whether the mutations in two strains are in different genes. By taking an example of Benzer's work, complementation has been explained.
Plant expression vectors
What are an expression vector? Detailed description of plant gene structure. Plant expression vector systems are generally consists of Ri and Ti plasmids.
The other vectors which are generally used are DNA and RNA viruses.
Molecular probes
This document discusses molecular probes, including their definition, types, preparation, and labeling. It describes the three main types of probes - oligonucleotide probes, DNA probes, and RNA probes. It explains how to prepare probes from genomic DNA, cDNA, synthetic oligonucleotides, and RNA. Methods of radioactive labeling including nick translation and oligonucleotide labeling are covered. Non-radioactive labeling using biotin and digoxigenin is also discussed. Finally, applications of molecular probes in identification of recombinant clones, fingerprinting, in situ hybridization, and medical research are summarized.
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This document discusses somatic embryogenesis and its consequences in cereals. It begins with an introduction to somatic embryogenesis, noting that it is a process where embryos are derived from somatic cells rather than gametes. It then covers factors that affect somatic embryogenesis like the explant source, plant growth regulators, and genotype. It also describes the stages of somatic embryogenesis and different types. The document discusses the role of somatic embryogenesis in improving cereals through somaclonal variation and disease resistance. It concludes that somatic embryogenesis is a model for plant breeding and genetic improvement.
C value paradox
This document discusses the C-Value Paradox, which is the observation that there is no correlation between the complexity of an organism and the amount of DNA (C-value) in its genome. The document provides examples showing that C-values, or the amount of DNA per haploid cell, can vary widely both within and across species, from 105 base pairs in mycoplasma to over 109 base pairs in mammals. While complexity tends to increase with higher C-values, exceptions exist, demonstrating there is no direct linear relationship between genome size and organism complexity. The term "C-value" refers to the haploid DNA content of a species.
Various model of DNA replication
1. There are four main models of DNA replication: rolling circle replication, theta replication, bidirectional replication of linear DNA, and telomere replication.
2. Rolling circle replication involves nicking circular DNA and using one strand as a template to produce multiple copies of the original circular DNA.
3. Theta replication occurs in prokaryotes and involves unwinding circular DNA at an origin of replication and replicating bi-directionally to form a theta-shaped structure.
4. Bidirectional replication of linear DNA involves unwinding DNA at origins of replication and using leading and lagging strand synthesis to replicate in both directions until the ends of the linear genome are reached.
Somatic cell genetics
Somatic cell hybridization allows genetic analysis using cell culture rather than sexual reproduction. It involves fusing somatic cells from two different species or tissues to form hybrid cells. Gene mapping can be done by selecting hybrids that retain specific genes as parental chromosomes are lost. Chromosomal rearrangements like deletions, duplications, and translocations also help map genes to specific chromosome regions. A case study describes using somatic cell selection in potato cultures with a herbicide to recover resistant variants with mutations in the AHAS gene.
1. ABCDE flower model
The document discusses the ABCDE model of flower development and its utility. It begins by describing the original ABC model proposed in 1991 to explain floral organ development. It then provides details on the classical ABCDE model, including the gene classes that specify the identity of each floral whorl. The document discusses modifications to the model in different plant species. It also summarizes several case studies on using mutations in floral organ identity genes to develop traits like male sterility and novel flower forms with commercial value.
Southern hybridization
Southern blotting is a technique used to detect specific DNA sequences in a DNA sample. It involves extracting DNA from cells, cutting the DNA into fragments using restriction enzymes, separating the fragments via gel electrophoresis, transferring the DNA fragments to a membrane, and using a labeled probe to detect fragments that are complementary to the probe through hybridization. Southern blotting is useful for identifying mutations, DNA fingerprinting, and detecting DNA in applications like prenatal screening and forensics. While effective for detecting specific DNA sequences, it is a complex, time-consuming, and labor-intensive technique.
Tetrad analysis
Tetrad analysis is a technique used to study genetics in lower eukaryotes like fungi and algae. These organisms undergo meiosis and form haploid spores called tetrads. Analyzing the patterns of genes in the tetrads can determine if genes are linked and calculate the distance between them. Examples given are yeast and Neurospora fungi. Neurospora ordered tetrads allow direct mapping of genes by examining the patterns of alleles in ascus spores. The document provides examples of analyzing unordered and ordered tetrads to determine linkage and map distance between genes.
Flower development
Flower development is controlled by floral developmental genes that are induced in response to environmental signals like photoperiod and temperature. The ABC model describes how MADS-box transcription factors encoded by ABC genes control floral organ identity in four whorls. Class A genes specify sepals, Class B genes specify petals, Class C genes specify stamens, and the combination of B and C genes specify carpels. Mutations in these ABC genes result in homeotic transformations of floral organs. The ABC model was later expanded to the ABCDE model with the addition of SEPALLATA genes that act redundantly with ABC genes.
pentosephosphate.ppt
This document provides information about the pentose phosphate pathway (PPP), including its role in generating the reducing agent NADPH and producing ribose-5-phosphate. The PPP occurs in the cytosol and begins with the intermediate glucose-6-phosphate from glycolysis. It produces NADPH through glucose-6-phosphate dehydrogenase and provides pentoses to build nucleic acids. The PPP is especially important in red blood cells for maintaining glutathione levels and preventing oxidative damage through NADPH production. Deficiencies in glucose-6-phosphate dehydrogenase can lead to hemolytic anemia upon exposure to oxidative drugs or foods like fava beans.
My work at OHSU
A presentation of my work on peptidyl-hydroxylating monooxygenase conducted at Oregon Health and Science University.
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Complementation test; AC-DS System in Maize
The document discusses the Ac-Ds transposable element system in maize and complementation testing. It notes that Ac is an autonomous transposable element that enables the movement of Ds elements. McClintock discovered that Ac, Ds, and the C gene are responsible for color instability in maize seeds. Complementation testing determines if two recessive mutations represent alleles of the same gene or different genes.
Mitochondrial genome and its manipulation
Mitochondria contain their own DNA and play an essential role in cellular respiration by generating ATP. While small, the mitochondrial genome encodes components of the electron transport chain. Manipulation of the mitochondrial genome holds promise for crop improvement due to maternal inheritance and absence of position effects. However, transforming the mitochondrial genome remains challenging due to difficulties incorporating foreign DNA and a lack of selectable markers. Successful manipulation could generate cytoplasmic male sterility for hybrid seed production.
Transposable elements in Maize And Drosophila
Transposable elements are mobile DNA sequences found in genomes of all organisms. Barbara McClintock discovered transposable elements called Ac and Ds in maize that cause color patterns in corn kernels. Her discovery showed that genes can move within genomes. Experiments with Drosophila revealed another transposable element called P elements that cause hybrid dysgenesis. Transposable elements can provide genetic variation and flexibility that influences evolution.
chloroplast genome ppt.
Chloroplasts are organelles found in plant cells and algae that conduct photosynthesis. They contain their own DNA known as the chloroplast genome, which is typically 100-200kb in size and encodes genes for photosynthesis. The chloroplast genome is highly conserved and maternally inherited. It has been used for phylogenetic studies and shows potential for genetic engineering due to high transgene expression and maternal inheritance that prevents gene flow to other species.
Transposons ppt
Transposons are DNA sequences that can change position within a genome. Barbara McClintock first discovered transposons in corn in the 1940s. There are two classes of transposons: class I (retrotransposons) move via an RNA intermediate, while class II (DNA transposons) move directly via a cut-and-paste mechanism. Transposons make up a large percentage of many genomes and can cause mutations when they insert into genes, which has implications for genetic disease and genome evolution.
Cosmid Vectors, YAC and BAC Expression Vectors
1. Cosmid vectors are hybrid vectors derived from plasmids that contain the cos site from bacteriophage lambda, allowing them to clone DNA fragments up to 40 kb in size.
2. Yeast artificial chromosomes (YACs) are engineered yeast chromosomes that can clone very large DNA fragments, averaging 200-500 kb but up to 1 MB, taking advantage of yeast cell machinery.
3. Bacterial artificial chromosomes (BACs) are DNA constructs based on fertility plasmids that can clone up to 300 kb fragments and address issues with YAC stability and recombination.
Restriction Mapping
Restriction enzymes cut DNA molecules at specific recognition sites. Restriction mapping involves digesting an unknown DNA segment with restriction enzymes and analyzing the fragment sizes to determine the locations of restriction sites. One method involves single and double digestions with two enzymes followed by gel electrophoresis to separate the fragments by size. By comparing the fragment patterns between single and double digestions, the positions of each restriction site can be mapped, generating a restriction map of the DNA segment. Restriction mapping was previously important for characterizing cloned DNA but is now easier using DNA sequencing, though analysis of restriction sites remains useful for comparing chromosomal organization between strains.
Linkage mapping
This document discusses linkage mapping, which involves determining the relative positions of genes on chromosomes based on how often they are inherited together through analysis of recombination frequencies during meiosis. It provides background on the history of linkage mapping and definitions of key terms like linkage, linkage mapping, linkage groups, and types of linkage (complete and incomplete). Examples are also given to illustrate linkage analysis through test crosses and calculation of recombination frequencies.
Chloroplast genome organisation
Chloroplasts are double-membrane organelles found in plant cells that contain chlorophyll and are the site of photosynthesis. Chloroplast DNA is circular and ranges in size from 120,000 to 170,000 base pairs. It contains approximately 120 genes, including genes that encode proteins involved in photosynthesis and the transcription and translation machinery. Chloroplast DNA replication is semi-conservative and there are typically multiple copies of the chloroplast genome within each chloroplast.
Complementation of defined mutations
A complementation test (sometimes called a "cis-trans" test) can be used to test whether the mutations in two strains are in different genes. By taking an example of Benzer's work, complementation has been explained.
Plant expression vectors
What are an expression vector? Detailed description of plant gene structure. Plant expression vector systems are generally consists of Ri and Ti plasmids.
The other vectors which are generally used are DNA and RNA viruses.
Molecular probes
This document discusses molecular probes, including their definition, types, preparation, and labeling. It describes the three main types of probes - oligonucleotide probes, DNA probes, and RNA probes. It explains how to prepare probes from genomic DNA, cDNA, synthetic oligonucleotides, and RNA. Methods of radioactive labeling including nick translation and oligonucleotide labeling are covered. Non-radioactive labeling using biotin and digoxigenin is also discussed. Finally, applications of molecular probes in identification of recombinant clones, fingerprinting, in situ hybridization, and medical research are summarized.
Somatic embryogenesis .pptx 1
This document discusses somatic embryogenesis and its consequences in cereals. It begins with an introduction to somatic embryogenesis, noting that it is a process where embryos are derived from somatic cells rather than gametes. It then covers factors that affect somatic embryogenesis like the explant source, plant growth regulators, and genotype. It also describes the stages of somatic embryogenesis and different types. The document discusses the role of somatic embryogenesis in improving cereals through somaclonal variation and disease resistance. It concludes that somatic embryogenesis is a model for plant breeding and genetic improvement.
C value paradox
This document discusses the C-Value Paradox, which is the observation that there is no correlation between the complexity of an organism and the amount of DNA (C-value) in its genome. The document provides examples showing that C-values, or the amount of DNA per haploid cell, can vary widely both within and across species, from 105 base pairs in mycoplasma to over 109 base pairs in mammals. While complexity tends to increase with higher C-values, exceptions exist, demonstrating there is no direct linear relationship between genome size and organism complexity. The term "C-value" refers to the haploid DNA content of a species.
Various model of DNA replication
1. There are four main models of DNA replication: rolling circle replication, theta replication, bidirectional replication of linear DNA, and telomere replication.
2. Rolling circle replication involves nicking circular DNA and using one strand as a template to produce multiple copies of the original circular DNA.
3. Theta replication occurs in prokaryotes and involves unwinding circular DNA at an origin of replication and replicating bi-directionally to form a theta-shaped structure.
4. Bidirectional replication of linear DNA involves unwinding DNA at origins of replication and using leading and lagging strand synthesis to replicate in both directions until the ends of the linear genome are reached.
Somatic cell genetics
Somatic cell hybridization allows genetic analysis using cell culture rather than sexual reproduction. It involves fusing somatic cells from two different species or tissues to form hybrid cells. Gene mapping can be done by selecting hybrids that retain specific genes as parental chromosomes are lost. Chromosomal rearrangements like deletions, duplications, and translocations also help map genes to specific chromosome regions. A case study describes using somatic cell selection in potato cultures with a herbicide to recover resistant variants with mutations in the AHAS gene.
1. ABCDE flower model
The document discusses the ABCDE model of flower development and its utility. It begins by describing the original ABC model proposed in 1991 to explain floral organ development. It then provides details on the classical ABCDE model, including the gene classes that specify the identity of each floral whorl. The document discusses modifications to the model in different plant species. It also summarizes several case studies on using mutations in floral organ identity genes to develop traits like male sterility and novel flower forms with commercial value.
Southern hybridization
Southern blotting is a technique used to detect specific DNA sequences in a DNA sample. It involves extracting DNA from cells, cutting the DNA into fragments using restriction enzymes, separating the fragments via gel electrophoresis, transferring the DNA fragments to a membrane, and using a labeled probe to detect fragments that are complementary to the probe through hybridization. Southern blotting is useful for identifying mutations, DNA fingerprinting, and detecting DNA in applications like prenatal screening and forensics. While effective for detecting specific DNA sequences, it is a complex, time-consuming, and labor-intensive technique.
Tetrad analysis
Tetrad analysis is a technique used to study genetics in lower eukaryotes like fungi and algae. These organisms undergo meiosis and form haploid spores called tetrads. Analyzing the patterns of genes in the tetrads can determine if genes are linked and calculate the distance between them. Examples given are yeast and Neurospora fungi. Neurospora ordered tetrads allow direct mapping of genes by examining the patterns of alleles in ascus spores. The document provides examples of analyzing unordered and ordered tetrads to determine linkage and map distance between genes.
Flower development
Flower development is controlled by floral developmental genes that are induced in response to environmental signals like photoperiod and temperature. The ABC model describes how MADS-box transcription factors encoded by ABC genes control floral organ identity in four whorls. Class A genes specify sepals, Class B genes specify petals, Class C genes specify stamens, and the combination of B and C genes specify carpels. Mutations in these ABC genes result in homeotic transformations of floral organs. The ABC model was later expanded to the ABCDE model with the addition of SEPALLATA genes that act redundantly with ABC genes.
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Phage Gene Regulation.pptx
Phage Gene Regulation.pptxDepartment of Biotechnology, Kamaraj college of engineering and technology
A bacteriophage is a virus that infects bacteria. Lambda phage is a temperate bacteriophage that has two life cycle choices: lytic and lysogenic. During lysogeny, the lambda repressor binds to the operator region (OR) on the phage DNA and represses transcription of lytic genes, allowing the phage genome to remain dormant as a prophage integrated into the bacterial chromosome.Trp Operon.pptx
The trp operon controls the biosynthesis of tryptophan in E. coli. It contains 5 genes that encode enzymes for tryptophan production. The operon uses attenuation to regulate expression based on tryptophan levels. When tryptophan is low, transcription proceeds through the leader sequence. When tryptophan is high, translation is rapid and a stem loop structure forms, terminating transcription. The trp operon is a repressible system, where the effector molecule allows the repressor to bind the operator and shut down expression.
Lac operon.pptx
The document summarizes the lac operon in E. coli, which controls the breakdown of lactose. The lac operon contains 3 genes - lacZ, lacY, and lacA - that code for enzymes involved in lactose catabolism. In the absence of lactose, a repressor protein binds to the operator region and prevents transcription. In the presence of lactose, it binds to the repressor and induces transcription of the structural genes. The lac operon demonstrates both negative control by the repressor and positive control through induction by lactose binding. Glucose also regulates the operon through catabolite repression involving cAMP levels.
post translational modification.pptx
post translational modification.pptxDepartment of Biotechnology, Kamaraj college of engineering and technology
Post-translational modifications (PTMs) are chemical changes that occur to proteins after translation. PTMs regulate protein activity, localization, and interactions. The main types of PTMs are phosphorylation, glycosylation, ubiquitination, and methylation. Phosphorylation involves the addition of phosphate groups and is important for cell signaling. Glycosylation adds carbohydrate groups and affects protein structure. Ubiquitination tags proteins for destruction, and methylation adds methyl groups, regulating processes like gene expression. PTMs are identified through techniques like mass spectrometry and chromatographic analysis.Inhibitors of protein synthesis.pptx
Inhibitors of protein synthesis.pptxDepartment of Biotechnology, Kamaraj college of engineering and technology
Aminoglycosides like streptomycin bind to the 30S ribosomal subunit and interfere with initiation complex formation, inducing misreading of mRNA and breaking polysomes into monosomes. Chloramphenicol inhibits protein synthesis by binding reversibly to the 50S ribosomal subunit and preventing the binding of aminoacyl tRNA to the acceptor site. Tetracyclines also bind to the 30S ribosomal subunit but prevent the binding of aminoacyl tRNA to the mRNA ribosome complex. Macrolides inhibit protein synthesis by reversibly binding to the 50S ribosomal subunit and suppressing translocation of mRNA.Protein Synthesis.pptx
Protein synthesis involves three main steps - initiation, elongation, and termination. In initiation, the small and large ribosomal subunits assemble along with mRNA and tRNA to form the initiation complex. In elongation, amino acids are added one by one to the growing polypeptide chain. Termination occurs when a stop codon is reached, causing the release of the completed protein. While the overall process is similar between prokaryotes and eukaryotes, there are some key differences like the number of initiation factors and whether mRNA is polycistronic or monocistronic.
Ribosomes.pptx
Ribosomes are organelles found in all cells that synthesize proteins. They consist of RNA and proteins and exist as two subunits - a smaller 30S subunit in prokaryotes and 40S in eukaryotes, and a larger 50S subunit in prokaryotes and 60S in eukaryotes. Ribosomes translate mRNA into proteins through initiation, elongation, and termination steps. Errors in ribosome functioning can lead to improper protein folding and diseases.
Translation Basics.ppt
This document discusses genetic code, tRNA, and translation. It provides definitions of key terms like codon, anticodon, wobble hypothesis. It describes the structure and function of tRNA, including how it is charged with specific amino acids by aminoacyl tRNA synthetases. The document also discusses characteristics of the genetic code, including that it is degenerate, uses triplet codons, and has start and stop signals. It provides information on ribosomes, including their composition in prokaryotes and eukaryotes. In summary, the document provides an overview of the mechanisms and key components involved in translating genetic code into proteins.
Mutation and DNA repair.pdf
Mutation and DNA repair.pdfDepartment of Biotechnology, Kamaraj college of engineering and technology
Mutation is a change in genetic material that can be caused by errors during DNA replication or DNA repair. There are several types of mutations including point mutations, insertions, deletions, and chromosomal mutations. Point mutations include transitions, transversions, missense mutations, and nonsense mutations. Insertions and deletions can disrupt the genetic code. Spontaneous mutations arise naturally while induced mutations are caused by mutagens like radiation, chemicals, or viruses. Mutations can be germline or somatic and can have different effects on protein function and the phenotype. The document provides examples of specific mutations and their effects.TELOMERE AND TELOMERASE.pdf
TELOMERE AND TELOMERASE.pdfDepartment of Biotechnology, Kamaraj college of engineering and technology
Telomeres are repetitive DNA sequences at the ends of chromosomes that protect them from degradation. Telomeres naturally shorten each time a cell divides until they reach a critical shortness that causes cell senescence. Telomerase is an enzyme that adds telomere repeats to chromosome ends and counteracts shortening. It is active in 90% of cancer cells, allowing unlimited cell division by maintaining telomere length, but is not generally active in most adult somatic cells.DNA Replication.pdf
This document discusses DNA replication and the central dogma. It covers the basic requirements for DNA replication including substrates, templates, enzymes, and primers. The stages of replication - initiation, elongation, and termination - are described. Key aspects of the replication process are explained, such as semi-conservative mechanism, unwinding of DNA, formation of replication forks, and bidirectional replication. Differences between prokaryotic and eukaryotic DNA replication are highlighted. Finally, various inhibitors of DNA replication are listed.
Structure and function of RNA.pptx
Structure and function of RNA.pptxDepartment of Biotechnology, Kamaraj college of engineering and technology
RNA differs from DNA in several key ways. RNA is typically single-stranded, contains ribose sugar instead of deoxyribose, and contains uracil instead of thymine. There are multiple types of RNA that serve different cellular functions, including messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). mRNA carries coding information from DNA to the ribosome for protein synthesis. tRNA transfers amino acids to the ribosome during protein assembly according to the mRNA codon sequence. rRNA is a core component of ribosomes and facilitates protein translation.Regulatory elements of transcription.pptx
Regulatory elements of transcription.pptxDepartment of Biotechnology, Kamaraj college of engineering and technology
Transcriptional regulatory elements such as promoters, enhancers, silencers, and insulators help control gene expression. Promoters initiate transcription and contain core and proximal elements. Enhancers can activate transcription from farther distances by binding activator proteins. Silencers negatively regulate genes by binding repressor proteins. Insulators block interactions between genes to prevent neighboring transcriptional effects. These cis-acting elements help precisely regulate protein levels through transcriptional mechanisms.ribozyme.pptx
Ribozymes are RNA molecules that act as enzymes and catalyze biochemical reactions. They were first discovered in 1982 by Thomas Czech and Sidney Altman, who later won the Nobel Prize in Chemistry for their discovery. Ribozymes increase the rate and specificity of reactions like phosphodiester bond cleavage and peptide bond synthesis. Common types of ribozymes include self-splicing introns, RNase P, hammerhead ribozymes, and hairpin ribozymes. Artificial ribozymes can also be synthesized in the laboratory by mutating natural ribozymes.
Inhibitors of transcription.pptx
Inhibitors of transcription.pptxDepartment of Biotechnology, Kamaraj college of engineering and technology
Rifampicin binds to the beta subunit of prokaryotic RNA polymerase, inhibiting prokaryotic transcription initiation. It selectively binds bacterial RNA polymerase without affecting eukaryotic polymerases. This allows rifampicin to be an effective treatment for bacterial infections like tuberculosis and leprosy. Alpha amanitin from death cap mushrooms potently inhibits RNA polymerase II during both transcription initiation and elongation, potentially causing death in 10 days from just one mushroom due to failure of gene expression.RNA processing and Splicing.pptx
RNA processing and Splicing.pptxDepartment of Biotechnology, Kamaraj college of engineering and technology
Eukaryotic pre-mRNA undergoes processing in the nucleus before being exported to the cytoplasm for protein synthesis. This involves adding a 5' cap and poly-A tail to increase stability and facilitate export. Introns are also spliced out by the spliceosome, a complex of small nuclear RNAs and proteins that cuts out introns and joins exons to form mature mRNA. Capping occurs at the 5' end shortly after transcription, while polyadenylation adds around 200 adenine nucleotides to the 3' end. Splicing removes intervening intron sequences by cutting and religating exons. These processing steps produce translation-competent mRNA from initial pre-mRNA transcripts.Transcription in Eukaryotes.pptx
Transcription in Eukaryotes.pptxDepartment of Biotechnology, Kamaraj college of engineering and technology
Transcription is the first step in gene expression for eukaryotic organisms where DNA is copied into RNA. This process involves RNA polymerase binding to promoter regions on DNA and synthesizing a complementary RNA strand. Transcription results in RNA transcripts that can then undergo further processing and modification before being translated into proteins.Transcription in Prokaryotes.pptx
Transcription in Prokaryotes.pptxDepartment of Biotechnology, Kamaraj college of engineering and technology
The document summarizes transcription in prokaryotes. It discusses the key components including the template strand, coding strand, and RNA polymerase. RNA polymerase is made up of multiple subunits and recognizes promoter sequences to initiate transcription. The process of transcription involves three phases - initiation when RNA polymerase binds to the promoter, elongation as the RNA strand continuously grows, and termination when RNA polymerase stops synthesis.denaturation and renaturation of dna.pptx
denaturation and renaturation of dna.pptxDepartment of Biotechnology, Kamaraj college of engineering and technology
DNA is a double-helix molecule that carries genetic instructions. It is composed of two strands called polynucleotides made up of nucleotides, each containing a nucleobase (A, T, C, or G), sugar, and phosphate. The strands are stabilized by hydrogen bonds between nucleotides and base stacking. DNA can be denatured by heat, pH extremes, or chemicals, breaking the hydrogen bonds and separating the strands. Denaturation temperature depends on factors like composition, length, and environment. Renaturation occurs when strands reconnect under appropriate conditions.Forces That Stabilize the DNA structure.pptx
Forces That Stabilize the DNA structure.pptxDepartment of Biotechnology, Kamaraj college of engineering and technology
DNA's double helical structure is stabilized by several weak forces that collectively provide strong stabilization. Hydrogen bonding between complementary base pairs provides some stability, while base stacking interactions between the hydrophobic bases, including hydrophobic and van der Waals forces, provide additional stability by burying the bases in the interior. Ionic interactions between the negatively charged phosphate backbone and positive ions like magnesium also contribute to stability. Though each individual interaction is weak, the collective effects of all of these forces interacting along the entire DNA molecule strongly stabilize its double helical structure.Más de Department of Biotechnology, Kamaraj college of engineering and technology (20)
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HUP genes.pptx
- 1. HUP genes Hydrogen uptake genes
- 2. • An undesirable side reaction of nitrogen fixation is the reduction of H+ to H2 gas. • Energy in form of ATP is wasted on production of hydrogen which is eventually lost to atmosphere • This lower the efficiency of nitrogen fixing process. • Theoretically if H2 would be recycled to H+ the extend of energy loss could be minimized and the nitrogen fixation process could become more effective
- 3. ROLE OF HUP GENES
- 5. • Energy is wasted • Hydrogen is eventually lost in to atmosphere • Lower the efficiency of nitrogen fixation • Bradyrhizobium japonicum • In Bradyrhizobium japonicum hydrogen is used as a energy source for growth in microaerophillic conditions. • They possess an enzyme hydrogenase which takes H2 from atmosphere and convert to H+ • The gene is approsimately 60Kda, organized in one to three transcriptional unit covering 15Kb of genome.
- 6. • The first hydrogenase gene to be isolated (E.coli membrane bound hydrogenase) was selected by complementation of an E.coli mutant that no longer expressed this activity with a clone bank of wild type E.coli DNA in plasmid pBR322. • The mutants were unable to grow on minimal medium containing formate • The transformants that were able to grow on this medium were assayed for the presence of hydrogenase activity
- 7. • Similarly, hup genes from B.japonicum using a clone bank of wild type DNA in broad host range vector pLAFR 1 to complement B.japonicum Hup- mutants. • The transformants were selected by their capacity to reduce methylene blue dye in hydrogen atmosphere. • Thus the isolated hup genes would be used as hybridization probe to select homologous genes from the clone bank.