Module 1 PPT.pdf

 Unit: 1 Chromosomal organisation of Genes: Genome structure, Chromosomal organization and function, C value Cells structure, Function & Signalling Gene families, clusters, mobile DNA C value paradox, Cot curves, repetitive and non-repetitive DNA sequences, Cot 1⁄2 and Rot 1⁄2 values,...

 Unit: 1 Chromosomal organisation of Genes: Genome structure, Chromosomal organization and function, C value Cells structure, Function & Signalling Gene families, clusters, mobile DNA C value paradox, Cot curves, repetitive and non-repetitive DNA sequences, Cot 1⁄2 and Rot 1⁄2 values, satellite DNA, DNA melting and buoyant density.  Molecular cell biology Molecular cell biology is a rich, integrative science that brings together biochemistry, biophysics, molecular biology, microscopy, genetics, physiology, computer science, and developmental biology.  Unit 2: Cell structure and function: Prokaryotic and eukaryotic cell structure, cytoplasmic membrane system - structure and functions of organelles and membrane trafficking. Transport across plasma membrane and intra-cellular transport (vesicular and membrane transport) at molecular level. Cell to cell signalling: hormones & receptors, second messengers in signalling pathways. Cytoskeleton Structure- assembly and disassembly of cytoskeletal elements, role in cell division  Unit: 3 Cell interactions in development Mitosis, meiosis; Control & regulation of cell cycle, Genes involved in cell cycle. Cell death & its regulation- apoptosis, programmed cell death, cell transformation and etiology of cancer. Integrating cells into tissues- cell-cell adhesion, extracellular matrix components.  Unit 4: DNA Replication, Repair & Recombination DNA replication machinery: Replication in prokaryotes and eukaryotes DNA replication models. DNA damage & repair & their role in carcinogenesis: Types of DNA damage, DNA repair mechanisms nucleotide excision repair, base excision repair, mismatch repair. Homologous and site- specific recombination, Holliday junction, Proteins involved in recombination- RecA, RuvA, B, C, Gene conversion.  Unit 5: Transcription and translation Transcription: General principles in bacterial & eukaryotic gene control, Molecular mechanism of eukaryotic transcription. Post- transcriptional modifications. Processing of eukaryotic mRNA, rRNA, tRNA Translation: Genetic code, Translation, Components & mechanism of protein synthesis. Regulation of protein synthesis, Post translational modifications. Transport of proteins, Protein turnover and degradation Specialised proteins & their mechanism of action.  What is Cell Like ourselves, the individual cells that form our bodies can grow, reproduce, process information, respond to stimuli, and carry out an amazing array of chemical reactions. These abilities define life. The smallest functional unit of life is cell, discovered by Robert Hooke in 1665. A cell can independently perform all necessary activities to sustain life. Hence cell is the basic unit of life. There are two types of cells → plant cell and animal cell. Cells have different organelles, each one with a distinct function. Size of cells vary greatly Generally small and seen only with microscope  Module 1 Chromosomal organisation of Genes: Genome structure, Chromosomal organization and function  Genetic material in a cell: All cells have the capability to give rise to new cells and the encoded information in a living cell is passed from one generation to another. The information encoding material is the genetic or hereditary material of the cell. The prokaryotic (bacterial) genetic material is usually concentrated in a specific clear region of the cytoplasm called nucleiod. The bacterial chromosome is a single, circular, double stranded DNA molecule mostly attached to the plasma membrane at one point. Virus genetic material: The chromosomal material of viruses is DNA or RNA which adopts different structures. It is circular when packaged inside the virus particle. Eukaryotic genetic material: A Eukaryotic cell has genetic material in the form of genomic DNA enclosed within the nucleus. Genes or the hereditary units are located on the chromosomes which exist as chromatin network in the non dividing cell/interphase. This will be discussed in detail in the coming sections. DNA of higher eukaryotes consists of unique and repeated sequences. Only ~5% of human DNA encodes proteins and functional RNAs and the regulatory sequences that control their expression; the remainder is merely spacer DNA between genes and introns within genes. Much of this DNA, ~50% in humans, is derived from mobile DNA elements, genetic symbiots that have contributed to the evolution of contemporary genomes. Each chromosome consists of a single, long molecule of DNA up to ~280 Mb in humans, organized into increasing levels of condensation by the histone and nonhistone proteins with which it is intricately complexed. Much smaller DNA molecules are localized in mitochondria and chloroplasts.  Chromosome The term chromosome was coined by W. Waldeyer in 1888. Chrome is coloured and soma is body, hence they mean “colored bodies” and can be defined as higher order organized arrangement of DNA and proteins.  Eukaryotic chromosome Chromosome number: There are normally two copies of each chromosome present in every somatic cell. The number of unique chromosomes (N) in such a cell is known as its haploid number, and the total number of chromosomes (2N) is its diploid number. The suffix ‘ploid’ refers to chromosome ‘sets’. The haploid set of the chromosome is also known as the genome. Structurally, eukaryotes possess large linear chromosomes unlike prokaryotes which have circular chromosomes. In Eukaryotes other than the nucleus chromosomes are present in mitochondria and chloroplast too. The number of chromosomes in each somatic cell is same for all members of a given species. The organism with lowest number of chromosome is the nematode, Ascaris megalocephalusunivalens which has only two chromosomes in the somatic cells (2n=2).  Molecular definition of gene In molecular terms, a gene commonly is defined as the entire nucleic acid sequence that is necessary for the synthesis of a functional gene product (polypeptide or RNA).  Chromatin Chemical composition of chromatin Chromatin consists of DNA, RNA and protein. The protein of chromatin could be of two types: histones and non histones. DNA: DNA is the most important chemical component of chromatin, since it plays central role of controlling heredity and is most conveniently measured in picograms. In addition to describing the genome of an organism by its number of chromosomes, it is also described by the amount of DNA in a haploid cell.  Centromers Centromeres are those condensed regions within the chromosome that are responsible for the accurate segregation of the replicated chromosome during mitosis and meiosis. When chromosomes are stained they typically show a dark-stained region that is the centromere. The actual location where the attachments of spindle fibres occur is called the kinetochore and is composed of both DNA and protein.  In molecular terms, a gene is the entire DNA sequence required for synthesis of a functional protein or RNA molecule. In addition to the coding regions (exons), a gene includes control regions and sometimes introns. Most bacterial and yeast genes lack introns, whereas most genes in multicellular organisms contain introns. The total length of intron sequences often is much longer than that of exon sequences. A simple eukaryotic transcription unit produces a single monocistronic mRNA, which is translated into a single protein. A complex eukaryotic transcription unit is transcribed into a primary transcript that can be processed into two or more different monocistronic mRNAs depending on the choice of splice sites or polyadenylation sites. Many complex transcription units (e.g., the fibronectin gene) express one mRNA in one cell type and an alternative mRNA in a different cell type.  Telomeres: Telomeres are the region of DNA at the end of the linear eukaryotic chromosome that are required for the replication and stability of the chromosome. McClintock recognized their special features when she noticed, that if two chromosomes were broken in a cell, the ends were sticky and end of one could attach to the other and vice versa. However she never observed the attachment of the broken end to the end of an unbroken chromosome suggesting that the end of chromosomes have unique features. Telomere sequences remain conserved throughout vertebrates and they form caps that protect the chromosomes from nucleases and other destabilizing influences; and they prevent the ends of chromosomes from fusing with one another.  Telomere replication Telomere replication is an important aspect in DNA replication. The primary difficulty with telomeres is the replication of the lagging strand. Because DNA synthesis requires a RNA template (that provides the free 3'-OH group) to prime DNA replication, and this template is eventually degraded, a short single-stranded region would be left at the end of the chromosome. This region would be susceptible to enzymes that degrade single-stranded DNA. Telomerase replication. Telomerase contains an RNA primer that is complementary to the end of the G-rich strand, which extends past the C-rich strand. The telomerase RNA binds to the protruding end of the G-rich strand in step 1 and then serves as a template for the addition of nucleotides onto the 3’ terminus of the strand in step 2. After a segment of DNA is synthesized, the telomerase RNA slides to the new end of the strand being elongated in step 3 and serves as the template for the incorporation of additional nucleotides in step 4. The gap in the complementary strand is filled by the replication enzymes polymerase α- primase. This figure has been adapted from Cell and Molecular Biology Concepts and Experiments by Karp, 2010. Importance of DNA Packeging  THE COMPLEXITY OF EUKARYOTIC GENOMES Introns and Exons: Most eukaryotic genes have a split structure in which segments of coding sequence (exons) are interrupted by noncoding sequences (introns). In complex eukaryotes, introns account for more than ten times as much DNA as exons. Repetitive DNA Sequences: Over 50% of mammalian DNA consists of highly repetitive DNA sequences, some of which are present in l05 to 106 copies per genome. These sequences include simple-sequence repeats as well as repetitive elements that have moved throughout the genome by either RNA or DNA intermediates.  Gene Duplications and Pseudogenes: Many eukaryotic genes are present in multiple copies, called gene families, which have arisen by duplication of ancestral genes. Some members of gene families function in different tissues or at different stages of development. Other members of gene families (pseudogenes) have been inactivated by mutations and no longer represent functional genes. Gene duplications can occur either by duplication of a segment of DNA or by reverse transcription of an mRNA, giving rise to a processed pseudogene. Approximately 5% of the human genome consists of duplicated DNA segments. ln addition, there are more than 10,000 processed pseudogenes in the human genome.  The Composition of Higher Eukaryotic Genomes: Only a small fraction of the genome in complex eukaryotes corresponds to protein-coding sequences. The human genome is estimated to contain 20,000-25,000 genes, with protein- coding sequence corresponding to only about 1.2% of the DNA. Approximately 20% of the human genome consists of introns, and more than 60% is composed of repetitive and duplicated DNA sequences. Prokaryotic Genomes: The genomes of more than 100 different bacteria, including E. coli, have been completely sequenced. The E. coli genome contains 4288 genes, w ith protein-coding sequences accounting for nearly 90% of the DNA.  The Yeast Genome: The first eukaryotic genome to be sequenced was that of the yeast S. cerevisiae. The S. cerevisiae genome contains about 6000 genes, and protein-coding sequences account for approximately 70% of the genome. The genome of the fission yeast S. pombe contains fewer genes (about 5000) and more introns than S. cerevisiae, with proteincoding sequence corresponding to about 60% of the S. pombe genome.  The Genomes of Caenorhabditis elegans and Drosophila melanogaster: The genome of C. elegans was the first sequenced genome of a multicellular organism. The C. elegans genome contains about 19,000 protein-coding sequences, which account for only about 25% of the genome. The genome of Drosophila contains approximately 14,000 genes, with proteincoding sequences accounting for about 13% of the genome. Although Drosophila contains fewer genes than C. elegans, many genes in both species are duplicated, and it appears that both species contain 10,000- 15,000 unique genes. Some of these genes are shared between Drosophila, C. elegans, and yeast- these genes may encode proteins with common functions in all eukaryotic cells.  Plant Genomes: The genome of the small flowering plant Arabidopsis thaliana contains approximately 26,000 genes-surprisingly more genes than were found in either Drosophila or C. elegans. However, many of these genes are the result of duplications of large segments of the Arabidopsis genome, so the number of unique genes in Arabidopsis is about 15,000. Many of these genes are unique to plants, including genes involved in plant physiology, development, and defense.  The Human Genome: The human genome appears to contain 20,000-25,000 genes-not much more than the number of genes found in simpler animals like Drosophila and C. elegans. Over 40% of the predicted human proteins are related to proteins found in other sequenced organisms, including Drosophila and C. elegans. In addition, the human genome contains expanded numbers of genes involved in the nervous system, the immune system, blood clotting, development, cell signaling, and the regulation of gene expression.  Human Chromosome Human Chromosome: The human genome is 3 x 109 base pairs of DNA and the smallest human chromosome is several times larger than the entire yeast genome; and the extended length of DNA that makes up the human genome is about 1 m long. The human genome is distributed among 24 chromosomes (22 autosomes and the 2 sex chromosomes), each containing between 45 and 280 Mb of DNA  When they are stained, the mitotic chromosomes have a banded structure that unambiguously identifies each chromosome of a karyotype. Each band contains millions of DNA nucleotide pairs which do not correspond to any functional structure. G-banding is obtained with Giemsa stain yielding a series of lightly and darkly stained bands. The dark regions tend to be heterochromatic and AT rich. The light regions tend to be euchromatic and GC rich. R-banding is the reverse of G-banding where the dark regions are euchromatic and the bright regions are heterochromatic.  Human Chromosome Karyotype Eukaryotic species have several chromosomes and are detected only during mitosis or meiosis. They are best observed during the metaphase stage of cell division as they are found in the most condensed state. Thus each eukaryotic species is characterized by a karyotype which is the numerical description (number and size) of chromosomes in the normal diploid cell. For example, the Homo sapiens possess 46 chromosome i,e., 23 pairs. The karyotype is important because genetic research can correlate changes in the karyotype with changes in the phenotype of the individual. For example, Down's syndrome is caused by duplication of the human chromosome number 21. Insertions, deletions and changes in chromosome number can be detected by the skilled cytogeneticist, but correlating these with specific phenotypes is difficult.  The Complexity of Eukaryotic Genomes The genomes of most eukaryotes are larger and more complex than those of prokaryotes. This larger size of eukaryotic genomes is not inherently surprising, since one would expect to find more genes in organisms that are more complex. However, the genome size of many eukaryotes does not appear to be related to genetic complexity The structure of eukaryotic genes Most eukaryotic genes contain segments of coding se-quences (exons) interrupted by non- coding sequences (introns). Both exons and introns are transcribed to yield a long primary RNA transcript. The introns are then removed by splicing to form the mature mRNA. The presence of large amounts of noncoding sequences is a general property of the genomes of complex eukaryotes. The gene illustrated contains six exons, separated by five introns. Alternative splicing allows these exons to be joined in different combinations, resulting in the formation of three distinct mRNAs and proteins from the single primary transcript  The C-value is the amount of DNA in the haploid genome of an organism. C-value is the amount of DNA in one haploid set of chromosomes. The C-value paradox arises from the fact that different organisms having the same general level of complexity and even organisms belonging to the same genus often have widely different C-values.