Perpetuation of Life PDF

Perpetuation of Life  Perpetuation of species- continuation of species Reproduction ensures the continuation of species How do organisms create exact copies of themselves? Cell is known as a basic unit of life which consists of a nucleus. Nucleus carries the genetic information for...

Perpetuation of Life  Perpetuation of species- continuation of species Reproduction ensures the continuation of species How do organisms create exact copies of themselves? Cell is known as a basic unit of life which consists of a nucleus. Nucleus carries the genetic information for the future generation within the DNA (genetic material). How to create a Cat? A list of information! Genome (cat DNA) is the complete set of genetic information to create a cat. It provides all of the information the organism requires to function. Genes Proteins Organism  Whether the kittens will be same as their parent ? Newly produced cell/organisms- although are not 100% identical they are broadly similar to their parents. Hence organisms creates a clone which not identical (variations)but consists of similar body designs. Importance of Variation Better adaptation to the environment- Survival of the fittest- Natural selection- Evolution  Flow of information: the capability of life to continue to exist Parents ✔ One of the amazing aspects of Flow of information living things is that they transmit the information for building themselves from one Offsprings generation to the next. Information flow in biological systems (expression of genetic information) Gene: A sequence of DNA in the nucleus specifies a sequence of RNA, which acts as a messenger (messenger RNA or mRNA) to direct the synthesis of polypeptide chains. Proteins are the effectors Genetic information flow is unidirectional!  Generations are linked by the flow of information Parents Flow of information Offsprings ✔ Organisms' capability of reproduction leads to self-perpetuation of the species (if not to the individual), via passing (perpetuating) information from one generation to the next. ✔ Parents produce similar organisms (offsprings) through reproduction, which allows the maintenance of the species. ✔ Thus, generations are linked by the flow of information from one to another.  Genetic information What is the Nature of this information? Much of what an organism is made of depends on the linear sequence information in its genome. ✔ Genes in the DNA carry the coding information required to produce specific proteins, and these proteins in turn carries out unique functions within the cell. ✔ All characteristics/traits that an organism possess are encoded in its genome. ✔ Genotype Vs Phenotype ✔ Gene Vs Allele In other words a cell holds information in the DNA sequence that is replicated during cell divisions and passed to next generation during reproduction. This strategy allows for retention through out development of largely the same sequence in every cell that forms a continuous lineage from one generation to the next.  How information is encoded in genes? DNA contains the instructions needed for an organism to develop, survive and reproduce. To carry out these functions, DNA sequences must be converted into messages that can be used to produce proteins, which are the complex molecules that do most of the work in our bodies. Proteins are needed for the body to function properly. They are the basis of body structures, such as skin and hair, and of other substances such as enzymes, cytokines, and antibodies. There are seven types of proteins: antibodies, contractile proteins, enzymes, hormonal proteins, structural proteins, storage proteins, and transport proteins.  Any other source of information for the perpetuation of life? Yes- Epigenetics! The DNA bases and/or histones can have chemical modifications (addition or deletion of chemical groups) that change the degrees to which genes are turned on and off (change activity status) Transgenerational epigenetic inheritance is the transmission of epigenetic markers from one organism to the next (i.e., from parent to child). This affects the traits of offspring without altering the nucleotide sequence of DNA in other words, epigenetically Note: Chemical modifications of either Parents DNA (e.g. cytosine methylation & Flow of information hydroxymethylation) or of histone proteins (e.g. lysine acetylation, lysine & arginine methylation, serine & threonine Offsprings phosphorylation, lysine ubiquitination and sumoylation) play central role in many types of epigenetic inheritance. These reversable changes play essential roles in development, aging and disease  Modulation of Gene Expression Without Changing the Genome ✔ It means that linear sequence of DNA is not the only store of information that is transmitted across generations. ✔ We can see evidence for the transmission of extra-genomic information in cases where changes that do not alter DNA sequence nevertheless persist for many generations Note Beyond genetics: Epigenetic information Epigenetics is the study of heritable changes in gene expression (active versus inactive genes) that do not involve changes to the underlying DNA sequence- a change in phenotype without a change in genotype These are manifested through patterns of chemical 'marks' on or around (via histones) our DNA that are hypothesized to be passed down the generations Both the environment and individual lifestyle can also directly interact with the genome to influence epigenetic change. Some epigenetic tags remain in place as genetic information passes from generation to generation, a process called epigenetic inheritance Evidence has been building in recent Studies have shown that children born during the years that our diet, our habits or period of the Dutch famine from 1944-1945 have traumatic experiences can have increased rates of coronary heart disease and consequences for the health of our obesity after maternal exposure to famine during children -- and even our early pregnancy compared to those not exposed to grandchildren. famine. Other studies suggest that mechanism of non-genetic inheritance is likely to be very rare!!  Reprogramming Between each generation the epigenetic marks are erased in cells called primordial gene cells (PGC), the precursors to sperm and eggs. This ‘reprogramming’ allows all genes to be read afresh for each new person. Non-coding RNA Your DNA is used as instructions for making coding and non-coding RNA. Coding RNA is used to make proteins. Non-coding RNA helps control gene expression by attaching to coding RNA, along with certain proteins, to break down the coding RNA so that it cannot be used to make proteins. Non-coding RNA may also recruit proteins to modify histones to turn genes “on” or “off.”  Beyond genetics: extra-genomic information ✔ The non-genetic information encoded in molecular assemblies independent of DNA sequence, Cell also holds information in, ✔the three-dimensional arrangement of molecules that can change during development but is recreated at th start of each generation. ✔ This include the spatial arrangement of various pre-existing molecules, including RNAs, proteins, sugars, lipids, etc inside the cell. ✔ Unlike the genome sequence, the arrangement of these molecules inside the cell and how this information is passed are not well understood.  Concept of minimal information What is the minimum information required to perpetuate an organism? ✔ The information needed to perpetuate an organism, must be present even in the life stage that has the least number of cells. ✔ This stage acts as a bottleneck for the transmission of information from one generation to the next and is minimally a single cell. Information encoded in the Gametes Therefore, all the molecules and their arrangement that is reproduced in the gametes of an organism is the minimal information required for the perpetuation of that organism.  Passing information: early thoughts! The question of “likeness” had preoccupied scientists and philosophers for centuries Pythagoras (530 BC)- proposed that hereditary information is carried in the male sperm It acts as a mobile library of every part of the body- a condensed distillate of the self! Plato (380 BC) argued that if children were the arithmetic derivatives of their parents, then atleast in principle the formula could be hacked – to make perfect children! Aristotle (350BC): observed that children can inherit features from both parents and even from grandparents. ✔ Features can skip generations! ✔ He proposed perhaps, females like males also contribute information to the fetus! ✔ What passed is not matter but message! But what is this message/information passed!  Beginning of modern biology? ✔ Science is an endless search for truth. Science is impelled by two main factors, technological advance and a guiding vision ✔ Since the beginning, scientists had wrestled with Two problems, 1) Creation of life from nonlife- genesis ex nihilo? 2) Once created- what generated the diversity of the natural world? Did new species arise from another species? What is the mechanism driving variation? ✔ In the winter of 1831, Charles Darwin, boarded the HMS Beagle ✔ The struggle for survival seems to act as the shaping hand! (but not published) ✔ In the summer of 1855, Alfred Russel Wallace published a paper proposing more or less the same idea- the best fitted (variants) live..! ✔ In 1859 Darwin published (on the origin of species by means of natural selection) the general theory of evolution by natural selection Birth of Genetics! Heredity is the passing on of traits from parents to their offspring Mendel's scientific biography thus provides an example of the failure of obscure, highly original, innovators to receive the attention they deserve  Theory of heredity Hereditary theory is the idea that physical traits can be passed from one generation to the next, by passing on the set of instructions. Evolution- creation of new traits Theory of heredity is crucial to the theory of evolution: without any means of ✔generate variation, and ✔fix it across generations -there would be no mechanism for an organism to evolve new characteristics! In that sense, ✔All of evolution could be perceived as the vertical transfer of germplasm (hereditary material) from one generation to the next. ✔But what is the material nature of germplasm? Is the information in germplasm discrete and carried in packets-like unbroken, unbreakable message? Is it a protein? RNA? Or something else?  The First Piece of the Puzzle: Miescher Discovers DNA In the winter of 1868/9 the young Swiss doctor Friedrich Miescher, performed experiments on the chemical composition of white blood cells that lead to the discovery of DNA. In his experiments, Miescher noticed a precipitate of an unknown substance, which he characterized further. Its properties during the isolation procedure and its resistance to protease digestion indicated that the novel substance was not a protein or lipid. Later Miescher recognized that he had discovered a novel molecule. Since he had isolated it from the cells' nuclei he named it nuclein, a name preserved in today's designation deoxyribonucleic acid. In subsequent work Miescher showed that nuclein was a characteristic component of all nuclei and hypothesised that it would prove to be inextricably linked to the function of this organelle. He suggested that its abundance in tissues might be related to their physiological status with increases in "nuclear substances" preceding cell division. Miescher even speculated that it might have a role in the transmission of hereditary traits, but subsequently rejected the idea. In 1900, three European botanists independently rediscovered the work of Gregor Mendel. A gene is the basic physical and functional unit of heredity. Genes are made up of DNA (a stretch of DNA) Sutton & Boveri, proposed that (hereditary units) genes resided in chromosomes: (chromosome theory of inheritance-1903) Morgan demonstrated that genes are carried on chromosomes and are the mechanical basis of heredity. Gene linkage: some genes acted as if they are linked- they moved in packs!  Griffith's experiment-1928 Transformation phenomenon: Described the conversion of a non-pathogenic pneumococcal bacteria to a virulent strain. In this experiment, Frederick Griffith mixed the living non-virulent bacteria with a heat inactivated virulent form. The first experiment suggesting that bacteria are capable of transferring genetic information through a process known as transformation. In this experiment Griffith concluded that the type rough strain had been "transformed" into the lethal smooth strain by a "transforming principle" that was somehow part of the dead smooth strain bacteria. But what is this transforming principle- Proteins ??  DNA is the transforming principle! Protein- and RNA-degrading enzymes had little effect on the transforming principle, but enzymes able to degrade DNA eliminated the transforming activity.  Composition of DNA The total amount of purines (A + G) and the total amount of pyrimidines (C + T) are usually nearly equal (Chargaff's rule) Deoxyribonucleic acid: is a polymer composed of two polynucleotide chains (made up of simpler monomeric units called nucleotides) nucleotide  The information in DNA is stored as a code made up of four chemical bases: ✔The order, or sequence, of these bases determines the information available for building and maintaining an organism, similar to the way in which letters of the alphabet appear in a certain order to form words and sentences in a rule book ✔ Chemical bases are divided into two groups ✔ The phosphoryl groups starting with that on AMP are referred to as the alpha, beta, and gamma phosphates.  The phosphodiester bond Chemical structure of DNA strand The phosphodiester bond is the linkage (bond) between the 3' carbon atom of one sugar molecule and the 5' carbon atom of another. The double helix model Watson strand or sense strand (5′-to-3′) Crick strand or antisense strand (3′ ←5′) Note: The structure of the double helix is somewhat like a ladder, with the base pairs forming the ladder’s steps and the sugar and phosphate molecules forming the vertical sidepieces of the ladder. Photo 51: DNA X-ray image First picture of DNA The diffraction pattern determined the helical nature of the double helix strands. A DNA molecule has the following dimensions in Angstroms: Width: A single DNA molecule is approximately 20 Angstroms (1.9 nanometers (nm)) wide/ diameter Length: A DNA molecule is approximately 34 Angstroms long per turn Distance between base pairs: The distance between two successive base pairs is 3.4 Angstroms (0.34 nm) 1 nanometer = 10 angstrom. Each human cell contains around 6 feet of DNA. Nucleus of a human cell is only about 6 micrometers in diameter. This is similar to packing 40 kilometers of thread into a tennis ball. Has approximately 3 billion base pairs and contains 20,000 to 25,000 genes If a human has around 10 trillion cells, then they have around 60 trillion feet or 10 billion miles of DNA (575 billion kilometer). 1 billion = 10000 lakhs The smallest known genome of a living organism is in the bacterium Carsonella ruddii, which has a genome of 159,662 base pairs of DNA and 182 protein-coding genes. This is less than half the size of what was previously thought to be the minimum necessary for life.  What is double helix? Helix is a type of smooth space curve, i.e. a curve in three-dimensional space Double helix ✔ The two strands are held together by hydrogen bonds between the bases, with adenine forming a base pair with thymine, and cytosine forming a base pair with guanine  Hydrogen bonds A hydrogen bond is a primarily electrostatic force of attraction between a hydrogen atom which is covalently bound to a more electronegative atom Cytosine and Guanine are held together by three hydrogen bonds. The pairing of adenine and thymine share two hydrogen bonds, thus the bond is slightly weaker The discovery of DNA's double helix structure in the 1950s by James Watson and Francis Crick is considered one of the most significant biological accomplishments of the 20th century.  3’ to 5′ direction 5′-to-3′ direction DNA directionality Next NT Next NT  Relaxed Coiled ✔Refers to the winding/coiling of a DNA strand  DNA Supercoiling If you stretched the DNA in one cell all the way out, it would be about 2m long and all the DNA in all your cells (37.2 trillion) put together would be about twice the diameter of the Solar System (287.46 billion km) The average size of a human cell is about 100 μm in diameter.  Nucleosome A nucleosome is basically DNA segments surrounded by histone protein octamers. Histones are highly basic proteins- provides structural support to a chromosomes. A Histone octamer, consists of 2 copies each of the core histones H2A, H2B, H3, and H4. The nucleosome core particle consists of approximately 146bp of DNA. Linker DNA is 38-80bp long in between two nucleosomes Technically, a nucleosome is defined as the core particle (DNA + Octamer) plus one of these linker regions ✔ Linker histones such as H1 are involved in chromatin compaction and sit at the base of the nucleosome near the DNA entry and exit binding to the linker region of the DNA. ✔ Nucleosome positions in the genome are not random, and it is important to know where each nucleosome is located because this determines the accessibility of the DNA to regulatory proteins.  Chromosome Chromosome Structure Chromosome is made up of DNA tightly coiled many times around histones that support its structure. Chromatin ✔ The "p" comes from the French "petit" meaning small q stands for queue meaning tail (long) in French Chromatin is a complex of DNA and protein. Its primary function is packaging long DNA ✔ A chromatid is one-half of two identical copies of a replicated molecules into more compact, denser structures chromosome. ✔ The centromere is the specialized DNA sequence of a Chromatin undergoes further condensation to form chromosome that links a pair of sister chromatids. the chromosome. ✔ A telomere is a region of repetitive nucleotide sequences at each end of a chromosome. Notes Chromosome Vs Chromatid A chromosome is nothing more than a discrete (and large) molecule of DNA with associated histones. A chromatid, on the other hand, is an identical half of a duplicated chromosome. After duplication of a chromosome, two identical halves are formed, each of which is called a chromatid. A chromosome can consist of either one or two chromatids depending on the cell cycle stage (Chromatids are less condensed than chromosomes and temporary structures that only exist to aid the process of chromosome duplication and separation) The pericentromere and centromere regions of the genome have previously been considered tightly compacted and transcriptionally inert. However, there is mounting evidence that these regions not only actively produce transcripts but that these pericentric and centromeric transcripts are also vital to maintaining genome stability and proper cell division.  Constitutive heterochromatin contains no genes in the genome AND Facultative heterochromatin contains the inactive genes in the genome (may be inactive either in some cells or during some periods) Heterochromatin is highly condensed, gene-poor, and transcriptionally silent, whereas euchromatin is less condensed, gene-rich, and more easily transcribed. Nucleosome modifications distinguish heterochromatin from euchromatin. The centromere is a DNA sequence that binds to a protein complex called the kinetochore. The kinetochore is connected to spindle fibers, which pull the chromatids to opposite ends of the cell. The centromere's role is to ensure that chromosomes reach their correct destinations during cell division. Without centromeres, cells can't divide properly The position of a centromere in a chromosome can vary and is not always in the middle of the chromosome. Homologous chromosomes are chromosomes within a diploid organism which carry the same genes, one from each parental source (eg: in humans, chromosome #1 from father and mother) Non-homologous chromosomes are chromosomes that do not belong to the same pair. (eg: in humans, chromosome #1 & #2) Generally, the length of the arms and the position of the centromere, is different in non-homologous chromosomes. Therefore, non-homologous chromosomes do not pair at the time recombination.  RNA has hydroxyl group (OH) present on the 2’ carbon. This hydroxyl group invites hydrolysis reaction and so not possible to maintain long length RNA molecule RNA hydrolysis is a reaction in which a phosphodiester bond in the sugar-phosphate backbone of RNA is broken, cleaving the RNA molecule.  Ribozymes RNA that can act as an enzyme Ribozymes are RNA molecules that accelerate chemical reactions (mostly phosphoryl transfer reactions), enzymes that happen to be made of RNA rather than protein. RNA world hypothesis The RNA world hypothesis is a theory that RNA came before DNA and proteins in the evolution of life on Earth The RNA world is a hypothetical stage in the evolutionary history of life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins. Proposed by Crick, Orgel, and others that potentially solves a massive chicken-and-egg problem that results from the requirement for the coincident emergence of nucleic acids and proteins with a division of labor between genetic encoding and catalysis. The discovery of the peptidyl transferase ribozyme is the closest we get to a “smoking gun” proof of this concept.  Requirement of a template and a catalyst to perform the replication ✔ Polynucleotides (DNA or RNA) have one property that contrasts with those of polypeptides (proteins): they can directly guide the formation of exact copies of their own sequence. ✔ This capacity depends on complementary base pairing of nucleotide subunits, which enables one polynucleotide to act as a template for the formation of another. But the efficient synthesis of polynucleotides by such complementary templating mechanisms requires catalysts to promote (usually proteins) the polymerization reaction: without catalysts, polymer formation is slow, error-prone, and inefficient. The beginnings of an answer to this question were obtained in 1982, when it was that molecules themselves can act as catalysts RNA therefore has all the properties required of a molecule that could catalyze its own synthesis. Although self-replicating systems of RNA molecules have not been found in nature!  However… Two of the cell's most important reactions are catalyzed by RNA. ✔The condensation of amino acids (Amino acids can be linked by a condensation reaction in which an ―OH is lost from the carboxyl group of one amino acid along with a hydrogen from the amino group of a second, forming a molecule of water and leaving the two amino acids linked via an amide—called, in this case, a peptide bond) in the peptidyl transferase center (P site) of the ribosome (arguably THE most important reaction in the cell!) is catalyzed not by protein, but by the major RNA component of the large subunit (28S RNA (e), 23S (P)). ✔Similarly, the splicing of mRNA in eukaryotes is catalyzed by the U2-U6 snRNA. So mechanistically both the ribosome and the spliceosome are ribozymes. It seems probable that chemically-diverse ribozymes existed during an RNA-world era, but whether or not any remnants of these species still exist in contemporary cells is not known at present.  Why is DNA preferred over RNA as genetic material? RNA was the first genetic material RNA was the first molecule of heredity, so it evolved all the essential methods for storing and expressing genetic information before DNA came onto the scene. DNA offer several advantages over RNA so was chosen by natural selection to represent higher beings: 1)DNA is chemically more stable than RNA so it is possible to maintain greater length of DNA in comparison to RNA. (RNA has hydroxyl group (OH) present on the 2’ carbon. This hydroxyl group invites hydrolysis reaction and so not possible to maintain long length RNA molecule. This hydroxyl group was absent in DNA leading to stability of DNA molecule) 2) DNA is more capable in handling self-repair during replication process due to the presence of Thymine instead of Uracil. (It is due to the fact that often cytosine is changed into uracil due to the deamination reaction (removal of an amino group from a molecule). Now in case of RNA it is impossible for cell to know if uracil should be present there or not but in DNA since Uracil is not all present so it is quite easy to identify the error and rectify that) 3) DNA also offers more information security because of the double helical structure (two copies of information)  Is DNA a good choice as genetic material? Base substitutions, deamination reactions, etc  Expression of information Stored information to >>>>>> action Expression of information: Gene expression  Why to express genes? Genes control phenotypic traits mostly through the synthesis of proteins Gene products dictate the characteristics of the organism ✔Determine the types of metabolic pathways the organism can have ✔Determine what other molecules the organism can make: carbohydrates, lipids, cholesterol, amino acids, nucleotides, nucleic acids, special chemicals like caffeine, chlorophyll, lignin (wood), and a whole lot more stuff ! Thus, DNA specifies traits by dictating protein synthesis. ✔Proteins are the links between genotype and phenotype. ✔Enzymes (proteins) determine what metabolism (chemical reactions) the organism can have. Metabolism = traits / characteristics of the organism The molecular “information flow” is from DNA in the nucleus to mRNA, then mRNA in the cytoplasm to protein. A genotype refers to the genetic characteristics (gene details) of an organism. A phenotype refers to the physical characteristics (visible features). For example, having blue eyes (an autosomal recessive trait) is a phenotype; lacking the gene for brown eyes is a genotype  One gene- one protein hypothesis ✔ The theory that each gene is responsible for the synthesis of a single polypeptide. It was originally stated as the one gene-one enzyme hypothesis by George Beadle and Edward Tatum in 1945 but later modified when it was realized that genes also encoded non-enzyme proteins. Neurospora crassa : is used as a model organism because it is easy to grow and has a haploid life cycle that makes genetic analysis simple since recessive traits will show up in the offspring. One gene- one polypeptide  Gene Expression occurs in two steps: 1. Transcription is the synthesis of RNA under the direction of DNA. Most genes encode proteins, So, those genes make a messenger RNA (mRNA) intermediary molecule = copies of the DNA code specifying the type and position of the amino acids in the protein and instructions for ribosomes. 2. Translation is the synthesis of proteins under the direction of mRNA that’s made by step 1. Most genes encode proteins. Translation changes the nucleic acid code into a polymer of amino acids. Nucleotide sequence to Amino acid sequence RNA polymerase is an enzyme that is responsible for copying a DNA sequence into an RNA sequence, during the process of transcription  Information flow DNA Transcription mRNA NUCLEUS CYTOPLASM Translation RIBOSOME Protein The flow of genetic information in the cell is DNA → RNA → protein  Coding Vs Regulatory sequence Regulatory sequence Coding = base sequences that specify the gene product itself (amino acids in the protein or the nucleotides in an RNA other than mRNA (rRNA, tRNA, snRNA, etc.), and Regulatory = base sequences that identify the locus of the gene and whether it is expressed or not expressed. The regulatory sequences determine whether the coding sequence expressed or not. cis-acting sequences/factors (sequence-motifs/factors contained/present in the same strand of DNA or RNA such as regulatory genomic regions, (like enhancers, epigenetic marks etc)) and trans-acting sequences/factors (Transcription factors and long noncoding RNAs are best examples) Cis-acting factors are mechanisms that affect gene expression only on the same chromosomal allele, while trans-factors act equally on both alleles. Coding genes Vs non-coding genes Types of Genes Inducible genes are normally off, but can be turned on when substrate is present Common for biosynthesis genes The lac operon is inducible (often called housekeeping genes) Genes for ribosomes  Gene expression: General points ✔Proteins not made at random ✔Specific purposes ✔Appropriate times Selective expression of genes All genes are not expressed at the same time Expressed at different times All cells in an organism have the same genes BUT, Some genes turned on Others remain off Leads to development of specialized cells Cellular differentiation Control or regulation of gene expression Gene expression responds (internal & external signals), To environmental conditions Type of nutrients Amounts of nutrients Developmental stage,  Cell differentiation Specifically, gene expression is controlled on two levels. First, transcription is controlled by limiting the amount of mRNA that is produced from a particular gene. The second level of control is through post-transcriptional events that regulate the translation of mRNA into proteins Control of gene expression  Mutations can affect genes & Information! A mutation is any change in the nucleotide sequence of DNA. Mutations can involve – large chromosomal regions (chromosome level) or – just a single nucleotide pair (gene level). Mutations occur when DNA is damaged and left unrepaired, creating a new variation Mutations are often discussed as part of evolutionary mechanisms. In this sense, mutations may be considered a part of a creative process. The dual nature of mutations, potentially deadly yet potentially Mutations are Random Vs Non-random We always thought of mutation as basically random (mutations can arise anywhere in a genome with equal probability) across the genome, However, It turns out that mutation is very non-random and it's non-random in a way that benefits the plant (found patches of the genome with low mutation rates. In those patches, they were surprised to discover an over-representation of essential genes, such as those involved in cell growth and gene expression) The areas are also sensitive to the harmful effects of new mutations. “DNA damage repair seems therefore to be particularly effective in these regions. The scientists found that the way DNA was wrapped around different types of proteins was a good predictor of whether a gene would mutate or not. “It means we can predict which genes are more likely to mutate than others The Gene: An Intimate History by Siddhartha Mukherjee