1.
Genetics
–
Genetics is the study of genes, genetic variation, and heredity in living organisms. It is generally considered a field of biology, but intersects frequently with other life sciences and is strongly linked with the study of information systems. The father of genetics is Gregor Mendel, a late 19th-century scientist, Mendel studied trait inheritance, patterns in the way traits are handed down from parents to offspring. He observed that organisms inherit traits by way of discrete units of inheritance and this term, still used today, is a somewhat ambiguous definition of what is referred to as a gene. Gene structure and function, variation, and distribution are studied within the context of the cell, the organism, genetics has given rise to a number of subfields, including epigenetics and population genetics. Organisms studied within the broad field span the domain of life, including bacteria, plants, animals, genetic processes work in combination with an organisms environment and experiences to influence development and behavior, often referred to as nature versus nurture. The intracellular or extracellular environment of a cell or organism may switch gene transcription on or off, a classic example is two seeds of genetically identical corn, one placed in a temperate climate and one in an arid climate. The word genetics stems from the ancient Greek γενετικός genetikos meaning genitive/generative, the observation that living things inherit traits from their parents has been used since prehistoric times to improve crop plants and animals through selective breeding. The modern science of genetics, seeking to understand this process, prior to Mendel, Imre Festetics, a Hungarian noble, who lived in Kőszeg before Mendel, was the first who used the word genetics. He described several rules of inheritance in his work The genetic law of the Nature. His second law is the same as what Mendel published, in his third law, he developed the basic principles of mutation. Other theories of inheritance preceded his work, a popular theory during Mendels time was the concept of blending inheritance, the idea that individuals inherit a smooth blend of traits from their parents. Mendels work provided examples where traits were not blended after hybridization. Blending of traits in the progeny is now explained by the action of genes with quantitative effects. Another theory that had some support at that time was the inheritance of acquired characteristics, other theories included the pangenesis of Charles Darwin and Francis Galtons reformulation of pangenesis as both particulate and inherited. Modern genetics started with Gregor Johann Mendel, a scientist and Augustinian friar who studied the nature of inheritance in plants, the importance of Mendels work did not gain wide understanding until the 1890s, after his death, when other scientists working on similar problems re-discovered his research. William Bateson, a proponent of Mendels work, coined the word genetics in 1905, Bateson popularized the usage of the word genetics to describe the study of inheritance in his inaugural address to the Third International Conference on Plant Hybridization in London in 1906. After the rediscovery of Mendels work, scientists tried to determine which molecules in the cell were responsible for inheritance, in 1911, Thomas Hunt Morgan argued that genes are on chromosomes, based on observations of a sex-linked white eye mutation in fruit flies
Genetics
–
Morgan's observation of
sex-linked inheritance of a mutation causing white eyes in
Drosophila led him to the hypothesis that genes are located upon chromosomes.
Genetics
–
Walther Flemming 's 1882 diagram of eukaryotic cell division. Chromosomes are copied, condensed, and organized. Then, as the cell divides, chromosome copies separate into the daughter cells.
Genetics
–
Siamese cats have a temperature-sensitive pigment-production mutation.
2.
Chromosome
–
A chromosome is a DNA molecule with part or all of the genetic material of an organism. Prokaryotes usually have one single circular chromosome, whereas most eukaryotes are diploid, chromosomes in eukaryotes are composed of chromatin fiber. Chromatin fiber is made of nucleosomes, a nucleosome is a histone octamer with part of a longer DNA strand attached to and wrapped around it. Chromatin fiber, together with associated proteins is known as chromatin, chromatin is present in most cells, with a few exceptions, for example, red blood cells. Occurring only in the nucleus of cells, chromatin contains the vast majority of DNA, except for a small amount inherited maternally. Chromosomes are normally visible under a microscope only when the cell is undergoing the metaphase of cell division. Before this happens every chromosome is copied once, and the copy is joined to the original by a centromere resulting in an X-shaped structure, the original chromosome and the copy are now called sister chromatids. During metaphase, when a chromosome is in its most condensed state, in this highly condensed form chromosomes are easiest to distinguish and study. In prokaryotic cells, chromatin occurs free-floating in cytoplasm, as these cells lack organelles, the main information-carrying macromolecule is a single piece of coiled double-helix DNA, containing many genes, regulatory elements and other noncoding DNA. The DNA-bound macromolecules are proteins that serve to package the DNA, chromosomes vary widely between different organisms. Some species such as certain bacteria also contain plasmids or other extrachromosomal DNA and these are circular structures in the cytoplasm that contain cellular DNA and play a role in horizontal gene transfer. Chromosomal recombination during meiosis and subsequent sexual reproduction plays a significant role in genetic diversity. In prokaryotes and viruses, the DNA is often densely packed and organized, in the case of archaea, by homologs to eukaryotic histones, small circular genomes called plasmids are often found in bacteria and also in mitochondria and chloroplasts, reflecting their bacterial origins. Some use the term chromosome in a sense, to refer to the individualized portions of chromatin in cells. However, others use the concept in a sense, to refer to the individualized portions of chromatin during cell division. The word chromosome comes from the Greek χρῶμα and σῶμα, describing their strong staining by particular dyes, schleiden, Virchow and Bütschli were among the first scientists who recognized the structures now so familiar to everyone as chromosomes. The term was coined by von Waldeyer-Hartz, referring to the term chromatin, in a series of experiments beginning in the mid-1880s, Theodor Boveri gave the definitive demonstration that chromosomes are the vectors of heredity. His two principles were the continuity of chromosomes and the individuality of chromosomes and it is the second of these principles that was so original
Chromosome
–
Walter Sutton (left) and
Theodor Boveri (right) independently developed the chromosome theory of inheritance in 1902.
Chromosome
–
Diagram of a replicated and condensed
metaphase eukaryotic chromosome. (1)
Chromatid – one of the two identical parts of the chromosome after
S phase. (2)
Centromere – the point where the two chromatids touch. (3) Short arm. (4) Long arm.
Chromosome
Chromosome
–
Human chromosomes during
metaphase
3.
DNA
–
Deoxyribonucleic acid is a molecule that carries the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. DNA and RNA are nucleic acids, alongside proteins, lipids and complex carbohydrates, most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA strands are termed polynucleotides since they are composed of simpler units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases—cytosine, guanine, adenine, or thymine —a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. The nitrogenous bases of the two polynucleotide strands are bound together, according to base pairing rules, with hydrogen bonds to make double-stranded DNA. The total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037, in comparison the total mass of the biosphere has been estimated to be as much as 4 trillion tons of carbon. The DNA backbone is resistant to cleavage, and both strands of the double-stranded structure store the same biological information and this information is replicated as and when the two strands separate. A large part of DNA is non-coding, meaning that these sections do not serve as patterns for protein sequences, the two strands of DNA run in opposite directions to each other and are thus antiparallel. Attached to each sugar is one of four types of nucleobases and it is the sequence of these four nucleobases along the backbone that encodes biological information. RNA strands are created using DNA strands as a template in a process called transcription, under the genetic code, these RNA strands are translated to specify the sequence of amino acids within proteins in a process called translation. Within eukaryotic cells DNA is organized into structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, eukaryotic organisms store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast prokaryotes store their DNA only in the cytoplasm, within the eukaryotic chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed, DNA was first isolated by Friedrich Miescher in 1869. DNA is used by researchers as a tool to explore physical laws and theories, such as the ergodic theorem. The unique material properties of DNA have made it an attractive molecule for material scientists and engineers interested in micro-, among notable advances in this field are DNA origami and DNA-based hybrid materials. DNA is a polymer made from repeating units called nucleotides
DNA
–
T7 RNA polymerase (blue) producing a mRNA (green) from a DNA template (orange).
DNA
–
The structure of the DNA
double helix. The
atoms in the structure are colour-coded by
element and the detailed structure of two base pairs are shown in the bottom right.
DNA
–
Sculpture of DNA made out of shopping carts
DNA
–
James Watson and
Francis Crick (right), co-originators of the double-helix model, with Maclyn McCarty (left).
4.
RNA
–
Ribonucleic acid is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes. RNA and DNA are nucleic acids, and, along with proteins and carbohydrates, like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more often found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA to convey information that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome, some RNA molecules play an active role within cells by catalyzing biological reactions, controlling gene expression, or sensing and communicating responses to cellular signals. One of these processes is protein synthesis, a universal function where RNA molecules direct the assembly of proteins on ribosomes. This process uses transfer RNA molecules to deliver amino acids to the ribosome, analysis of these RNAs has revealed that they are highly structured. Unlike DNA, their structures do not consist of long double helices, in this fashion, RNAs can achieve chemical catalysis. For instance, determination of the structure of the enzyme that catalyzes peptide bond formation—revealed that its active site is composed entirely of RNA. Each nucleotide in RNA contains a sugar, with carbons numbered 1 through 5. A base is attached to the 1 position, in general, adenine, cytosine, guanine, adenine and guanine are purines, cytosine and uracil are pyrimidines. A phosphate group is attached to the 3 position of one ribose, the phosphate groups have a negative charge each, making RNA a charged molecule. The bases form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil, however, other interactions are possible, such as a group of adenine bases binding to each other in a bulge, or the GNRA tetraloop that has a guanine–adenine base-pair. An important structural feature of RNA that distinguishes it from DNA is the presence of a group at the 2 position of the ribose sugar. The A-form geometry results in a deep and narrow major groove. RNA is transcribed with only four bases, but these bases, pseudouridine, in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, and ribothymidine are found in various places. Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine, inosine plays a key role in the wobble hypothesis of the genetic code. The specific roles of many of these modifications in RNA are not fully understood, the functional form of single-stranded RNA molecules, just like proteins, frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule and this leads to several recognizable domains of secondary structure like hairpin loops, bulges, and internal loops
RNA
–
Secondary structure of a
telomerase RNA.
RNA
RNA
–
Robert W. Holley, left, poses with his research team.
5.
Genome
–
In modern molecular biology and genetics, a genome is the genetic material of an organism. The genome includes both the genes, the noncoding DNA and the material of the mitochondria and chloroplasts. The term genome was created in 1920 by Hans Winkler, professor of botany at the University of Hamburg, the Oxford Dictionary suggests the name is a blend of the words gene and chromosome. However, see omics for a thorough discussion. A few related -ome words already existed—such as biome, rhizome, Some organisms have multiple copies of chromosomes, diploid, triploid, tetraploid and so on. In classical genetics, in a sexually reproducing organism the gamete has half the number of chromosomes of the somatic cell, the halving of the genetic material in gametes is accomplished by the segregation of homologous chromosomes during meiosis. Additionally, the genome can comprise non-chromosomal genetic elements such as viruses, plasmids, even in species that exist in only one sex, what is described as a genome sequence may be a composite read from the chromosomes of various individuals. Colloquially, the genetic makeup is sometimes used to signify the genome of a particular individual or organism. Both the number of pairs and the number of genes vary widely from one species to another. The only exception in humans is found in red blood cells which become enucleated during development. In 1976, Walter Fiers at the University of Ghent was the first to establish the complete sequence of a viral RNA-genome. The next year Fred Sanger completed the first DNA-genome sequence, Phage Φ-X174, the first genome sequence for an archaeon, Methanococcus jannaschii, was completed in 1996, again by The Institute for Genomic Research. The development of new technologies has made it easier and cheaper to do sequencing. The US National Institutes of Health maintains one of several databases of genomic information. Among the thousands of completed genome sequencing projects include those for rice, a mouse, the plant Arabidopsis thaliana, the fish. In December 2013, scientists first sequenced the genome of a Neanderthal. The genome was extracted from the toe bone of a 130, new sequencing technologies, such as massive parallel sequencing have also opened up the prospect of personal genome sequencing as a diagnostic tool, as pioneered by Manteia Predictive Medicine. A major step toward that goal was the completion in 2007 of the genome of James D. Watson
Genome
–
An image of the 46 chromosomes making up the diploid genome of a human male. (The
mitochondrial chromosome is not shown.)
6.
Mutation
–
In biology, a mutation is the permanent alteration of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal DNA or other genetic elements. Mutations may also result from insertion or deletion of segments of DNA due to mobile genetic elements, mutations may or may not produce discernible changes in the observable characteristics of an organism. Mutations play a part in normal and abnormal biological processes including, evolution, cancer, and the development of the immune system. The genomes of RNA viruses are based on RNA rather than DNA, the RNA viral genome can be double stranded or single stranded. In some of these viruses replication occurs quickly and there are no mechanisms to check the genome for accuracy and this error-prone process often results in mutations. Mutation can result in different types of change in sequences. Mutations in genes can either have no effect, alter the product of a gene, mutations can also occur in nongenic regions. Mutations can involve the duplication of large sections of DNA, usually through genetic recombination and these duplications are a major source of raw material for evolving new genes, with tens to hundreds of genes duplicated in animal genomes every million years. Most genes belong to larger families of shared ancestry, known as homology. Here, protein domains act as modules, each with a particular and independent function, that can be mixed together to produce genes encoding new proteins with novel properties. For example, the eye uses four genes to make structures that sense light. Another advantage of duplicating a gene is that this increases engineering redundancy, other types of mutation occasionally create new genes from previously noncoding DNA. Changes in chromosome number may involve even larger mutations, where segments of the DNA within chromosomes break and then rearrange. For example, in the Homininae, two fused to produce human chromosome 2, this fusion did not occur in the lineage of the other apes. Sequences of DNA that can move about the genome, such as transposons, make up a fraction of the genetic material of plants and animals. For example, more than a million copies of the Alu sequence are present in the genome. Another effect of these mobile DNA sequences is that when they move within a genome, they can mutate or delete existing genes, nonlethal mutations accumulate within the gene pool and increase the amount of genetic variation. The abundance of some changes within the gene pool can be reduced by natural selection, while other more favorable mutations may accumulate
Mutation
–
A mutation has caused this garden
moss rose to produce flowers of different colors. This is a
somatic mutation that may also be passed on in the
germline.
Mutation
–
Diagrammatic representation of the
divergence of modern
taxonomic groups from their
common ancestor
7.
Nucleotide
–
Nucleotides are organic molecules that serve as the monomer units for forming the nucleic acid polymers DNA and RNA, both of which are essential biomolecules in all life-forms on Earth. Nucleotides are the blocks of nucleic acids, they are composed of three subunit molecules, a nitrogenous base, a five-carbon sugar, and at least one phosphate group. They are also known as phosphate nucleotides, a nucleoside is a nitrogenuous base and a 5-carbon sugar. Thus a nucleoside plus a group yields a nucleotide. Nucleotides also play a role in life-form metabolism at the fundamental. In addition, nucleotides participate in signaling, and are incorporated into important cofactors of enzymatic reactions. In experimental biochemistry, nucleotides can be radiolabeled with radionuclides to yield radionucleotides, a nucleotide is composed of three distinctive chemical sub-units, a five-carbon sugar molecule, a nitrogenous base—which two together are called a nucleoside—and one phosphate group. With all three joined, a nucleotide is also termed a nucleoside monophosphate, thus, the terms nucleoside diphosphate or nucleoside triphosphate may also indicate nucleotides. Nucleotides contain either a purine or a pyrimidine base—i. e, the nitrogenous base molecule, also known as a nucleobase—and are termed ribonucleotides if the sugar is ribose, or deoxyribonucleotides if the sugar is deoxyribose. These chain-joins of sugar and phosphate molecules create a backbone strand for a single- or double helix, in any one strand, the chemical orientation of the chain-joins runs from the 5-end to the 3-end —referring to the five carbon sites on sugar molecules in adjacent nucleotides. Unlike in nucleic acid nucleotides, singular cyclic nucleotides are formed when the group is bound twice to the same sugar molecule. These individual nucleotides function in cell metabolism rather than the nucleic acid structures of long-chain molecules, nucleic acids then are polymeric macromolecules assembled from nucleotides, the monomer-units of nucleic acids. The purine bases adenine and guanine and pyrimidine base cytosine occur in both DNA and RNA, while the pyrimidine bases thymine and uracil in just one, adenine forms a base pair with thymine with two hydrogen bonds, while guanine pairs with cytosine with three hydrogen bonds. Nucleotides can be synthesized by a variety of both in vitro and in vivo. In vivo, nucleotides can be synthesized de novo or recycled through salvage pathways, the components used in de novo nucleotide synthesis are derived from biosynthetic precursors of carbohydrate and amino acid metabolism, and from ammonia and carbon dioxide. The liver is the organ of de novo synthesis of all four nucleotides. De novo synthesis of pyrimidines and purines follows two different pathways, purines, however, are first synthesized from the sugar template onto which the ring synthesis occurs. For reference, the syntheses of the purine and pyrimidine nucleotides are carried out by several enzymes in the cytoplasm of the cell, nucleotides undergo breakdown such that useful parts can be reused in synthesis reactions to create new nucleotides
Nucleotide
–
The structure of nucleotide monomers.
Nucleotide
–
This nucleotide contains the five-carbon sugar
deoxyribose, a
nitrogenous base called
adenine, and one
phosphate group. Together, the deoxyribose and adenine make up a
nucleoside (specifically, a
deoxyribonucleoside) called
deoxyadenosine. With the one phosphate group included, whole structure is considered a
deoxyribonucleotide (a nucleotide constituent of DNA) with the name
deoxyadenosine monophosphate.
8.
Genetic variation
–
Genetic variation means that biological systems – individuals and populations – are different over space. Each gene pool includes various alleles of genes, the variation occurs both within and among populations, supported by individual carriers of the variant genes. Genetic variation is brought about, fundamentally, by mutation, which is a permanent change in the structure of chromosomes. Genetic recombination also produces changes within alleles, Genetic variation among individuals within a population can be identified at a variety of levels. It is possible to identify genetic variation from observations of variation in either quantitative traits or discrete traits. Genetic variation can also be identified by examining variation at the level of enzymes using the process of protein electrophoresis, polymorphic genes have more than one allele at each locus. Half of the genes code for enzymes in insects and plants may be polymorphic. Ultimately, genetic variation is caused by variation in the order of bases in the nucleotides in genes, New technology now allows scientists to directly sequence DNA which has identified even more genetic variation than was previously detected by protein electrophoresis. Examination of DNA has shown variation in both coding regions and in the non-coding intron region of genes. Geographic variation means genetic differences in populations from different locations and this is caused by natural selection or genetic drift. Genetic variation within a population is measured as the percentage of gene loci that are polymorphic or the percentage of gene loci in individuals that are heterozygous. Random mutations are the source of genetic variation. Mutations are likely to be rare and most mutations are neutral or deleterious, polyploidy is an example of chromosomal mutation. Polyploidy is a condition wherein organisms have three or more sets of genetic variation, crossing over and random segregation during meiosis can result in the production of new alleles or new combinations of alleles. Furthermore, random fertilization also contributes to variation, Variation and recombination can be facilitated by transposable genetic elements, endogenous retroviruses, LINEs, SINEs, etc. For a given genome of an organism, genetic variation may be acquired in somatic cells or inherited through the germline. Genetic variation can be divided into different forms according to the size, small-scale sequence variation includes base-pair substitution and indels. Large-scale Structural variation can be either copy number variation, or chromosomal rearrangement, numerical variation in whole chromosomes or genomes can be either polyploidy or aneuploidy
Genetic variation
–
Darwin's finches or Galapagos finches.
Genetic variation
–
Diagrammatic representation of the
divergence of modern
taxonomic groups from their
common ancestor
Genetic variation
–
A range of variability in the mussel Donax variabilis
Genetic variation
–
Variability of walnuts
9.
Introduction to genetics
–
Genetics is the study of genes—what they are, what they do, and how they work. Genes inside the nucleus of a cell are strung together in such a way that the sequence carries information, for example, offspring produced by sexual reproduction usually look similar to each of their parents because they have inherited some of each of their parents genes. Genetics identifies which features are inherited, and explains how these features pass from generation to generation, in addition to inheritance, genetics studies how genes are turned on and off to control what substances are made in a cell—gene expression, and how a cell divides—mitosis or meiosis. Some phenotypic traits can be seen, such as eye color while others can only be detected, another example is a persons height, it is determined by both genetics and nutrition. Chromosomes are tiny packages which contain one DNA molecule and its associated proteins and this number varies between species—for example, many primates have 24 pairs. Meiosis creates special cells, sperm in males and eggs in females and these two cells merge into one during the fertilization stage of sexual reproduction, creating a zygote. In a zygote, a nucleic acid double helix divides, with each single helix occupying one of the daughter cells, by the time the zygote divides again, genetic recombination has created a new embryo with 23 pairs of chromosomes, half from each parent. Mating and resultant mate choice result in sexual selection, chromosomes all contain DNA made up of four nucleotides, abbreviated C, G, A, or T, which line up in a particular sequence and make a long string. There are two strings of nucleotides coiled around one another in each chromosome, a double helix, C on one string is always opposite from G on the other string, A is always opposite T. There are about 3.2 billion nucleotide pairs on all the human chromosomes, the order of the nucleotides carries genetic information, whose rules are defined by the genetic code, similar to how the order of letters on a page of text carries information. Three nucleotides in a row—a triplet—carry one unit of information, a codon and this series of exposed triplets carries the information to allow machinery in the cell to read the codons on the exposed DNA, which results in the making of RNA molecules. Closing the uncoiled segment turns off the gene, each unique form of a single gene is called an allele, different forms are collectively called polymorphisms. Genes are pieces of DNA that contain information for synthesis of ribonucleic acids or polypeptides, genes are inherited as units, with two parents dividing out copies of their genes to their offspring. This process can be compared with mixing two hands of cards, shuffling them, and then dealing them out again. Humans have two copies of each of their genes, and make copies that are found in eggs or sperm—but they only include one copy of each type of gene, an egg and sperm join to form a complete set of genes. The eventually resulting offspring has the number of genes as their parents. The effects of this mixing depend on the types of the gene, the hair color of these children depends on how these alleles work together. If one allele dominates the instructions from another, it is called the dominant allele, in the case of a daughter with alleles for both red and brown hair, brown is dominant and she ends up with brown hair
Introduction to genetics
–
Red hair is a
recessive trait.
Introduction to genetics
–
Mice with different coat colors.
10.
Evolution
–
Evolution is change in the heritable characteristics of biological populations over successive generations. Evolutionary processes give rise to biodiversity at every level of organisation, including the levels of species, individual organisms. In July 2016, scientists reported identifying a set of 355 genes from the LUCA of all living on Earth. The fossil record includes a progression from early biogenic graphite, to microbial mat fossils, existing patterns of biodiversity have been shaped both by speciation and by extinction. More than 99 percent of all species that lived on Earth are estimated to be extinct. Estimates of Earths current species range from 10 to 14 million, more recently, in May 2016, scientists reported that 1 trillion species are estimated to be on Earth currently with only one-thousandth of one percent described. In the mid-19th century, Charles Darwin formulated the theory of evolution by natural selection. This teleonomy is the quality whereby the process of natural selection creates and preserves traits that are fitted for the functional roles they perform. The processes by which the changes occur, from one generation to another, are called evolutionary processes or mechanisms, the four most widely recognized evolutionary processes are natural selection, genetic drift, mutation and gene migration. Natural selection and genetic drift sort variation, mutation and gene migration create variation, consequences of selection can include meiotic drive, nonrandom mating and genetic hitchhiking. In the early 20th century the modern evolutionary synthesis integrated classical genetics with Darwins theory of evolution by natural selection through the discipline of population genetics, the importance of natural selection as a cause of evolution was accepted into other branches of biology. Moreover, previously held notions about evolution, such as orthogenesis, evolutionism, evolutionary computation, a sub-field of artificial intelligence, involves the application of Darwinian principles to problems in computer science. The proposal that one type of organism could descend from another type goes back to some of the first pre-Socratic Greek philosophers, such as Anaximander, such proposals survived into Roman times. The poet and philosopher Lucretius followed Empedocles in his masterwork De rerum natura, in contrast to these materialistic views, Aristotelianism considered all natural things as actualisations of fixed natural possibilities, known as forms. This was part of a teleological understanding of nature in which all things have an intended role to play in a divine cosmic order. In the 17th century, the new method of modern science rejected the Aristotelian approach, however, this new approach was slow to take root in the biological sciences, the last bastion of the concept of fixed natural types. The biological classification introduced by Carl Linnaeus in 1735 explicitly recognized the nature of species relationships. Other naturalists of this time speculated on the change of species over time according to natural laws
Evolution
–
Lucretius
Evolution
Evolution
–
Alfred Russel Wallace
Evolution
–
Thomas Robert Malthus
11.
Molecular evolution
–
Molecular evolution is the process of change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of biology and population genetics to explain patterns in these changes. Major topics in molecular evolution concern the rates and impacts of single nucleotide changes, the field of molecular evolution came into its own in the 1960s and 1970s, following the rise of molecular biology. The content and structure of a genome is the product of the molecular, novel genetic variants will arise through mutation and will spread and be maintained in populations due to genetic drift or natural selection. Mutations are permanent, transmissible changes to the material of a cell or virus. Mutations result from errors in DNA replication during cell division and by exposure to radiation, chemicals, most mutations that occur are single nucleotide polymorphisms which modify single bases of the DNA sequence, resulting in point mutations. Other types of mutations modify larger segments of DNA and can cause duplications, insertions, deletions, inversions, most organisms display a strong bias in the types of mutations that occur with strong influence in GC-content. Transitions are more common than transversions ↔ pyrimidine ) and are likely to alter amino acid sequences of proteins. Mutations are stochastic and typically occur randomly across genes, because mutations are extremely rare, they accumulate very slowly across generations. While the number of mutations which appears in any single generation may vary, using the mutation rate per generation and the number of nucleotide differences between two sequences, divergence times can be estimated effectively via the molecular clock. Recombination is a process results in genetic exchange between chromosomes or chromosomal regions. Recombination counteracts physical linkage between adjacent genes, thereby reducing genetic hitchhiking, recombination can also generate particular types of mutations if chromosomes are misaligned. Gene conversion is a type of recombination that is the product of DNA repair where nucleotide damage is corrected using a genomic region as a template. Damaged bases are first excised, the strand is then aligned with an undamaged homolog. Gene conversion is often responsible for homogenizing sequences of genes over long time periods. Genetic drift is the change of allele frequencies from one generation to the due to stochastic effects of random sampling in finite populations. Some existing variants have no effect on fitness and may increase or decrease in frequency due to chance. Nearly neutral variants whose selection coefficient is close to a value of 1 / the effective population size will also be affected by chance as well as by selection and mutation
Molecular evolution
–
Diagrammatic representation of the
divergence of modern
taxonomic groups from their
common ancestor
12.
Population genetics
–
Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, population genetics was a vital ingredient in the emergence of the modern evolutionary synthesis. Its primary founders were Sewall Wright, J. B. S. Haldane and Ronald Fisher, traditionally a highly mathematical discipline, modern population genetics encompasses theoretical, lab, and field work. Population genetic models are used both for statistical inference from DNA sequence data and for proof/disproof of concept and this makes it appropriate for comparison to population genomics data. Population genetics began as a reconciliation of Mendelian inheritance and biostatistics models, natural selection will only cause evolution if there is enough genetic variation in a population. Before the discovery of Mendelian genetics, one hypothesis was blending inheritance. But with blending inheritance, genetic variance would be rapidly lost, the Hardy–Weinberg principle provides the solution to how variation is maintained in a population with Mendelian inheritance. According to this principle, the frequencies of alleles will remain constant in the absence of selection, mutation, migration, the next key step was the work of the British biologist and statistician Ronald Fisher. In a series of papers beginning in 1924, another British geneticist, Haldane worked out the mathematics of allele frequency change at a single gene locus under a broad range of conditions. The work of Fisher, Haldane and Wright founded the discipline of population genetics and this integrated natural selection with Mendelian genetics, which was the critical first step in developing a unified theory of how evolution worked. John Maynard Smith was Haldanes pupil, whilst W. D. Hamilton was heavily influenced by the writings of Fisher, the American George R. Price worked with both Hamilton and Maynard Smith. American Richard Lewontin and Japanese Motoo Kimura were heavily influenced by Wright, the mathematics of population genetics were originally developed as the beginning of the modern synthesis. According to Beatty, population genetics defines the core of the modern synthesis, however, as the field of genetics continued to develop, those views became less tenable. During the modern synthesis, these ideas were purged, and only evolutionary causes that could be expressed in the framework of population genetics were retained. Consensus was reached as to which evolutionary factors might influence evolution, theodosius Dobzhansky, a postdoctoral worker in T. H. Morgans lab, had been influenced by the work on genetic diversity by Russian geneticists such as Sergei Chetverikov. The book also took the highly mathematical work of the population geneticists, many more biologists were influenced by population genetics via Dobzhansky than were able to read the highly mathematical works in the original. Fords work, in collaboration with Fisher, contributed to a shift in emphasis during the course of the synthesis towards natural selection as the dominant force. During the modern synthesis, these ideas were purged
Population genetics
–
Ronald Fisher
Population genetics
–
Diagrammatic representation of the
divergence of modern
taxonomic groups from their
common ancestor
Population genetics
–
J.B.S.Haldane
Population genetics
–
E B Ford
13.
Mendelian inheritance
–
Mendelian inheritance is a type of biological inheritance that follows the laws originally proposed by Gregor Mendel in 1865 and 1866 and re-discovered in 1900. These laws were very controversial. When Mendels theories were integrated with the Boveri–Sutton chromosome theory of inheritance by Thomas Hunt Morgan in 1915, between 1856 and 1863, Mendel cultivated and tested some 5,000 pea plants. From these experiments, he induced two generalizations which later known as Mendels Principles of Heredity or Mendelian inheritance. In 1900, however, his work was re-discovered by three European scientists, Hugo de Vries, Carl Correns, and Erich von Tschermak. De Vries may not have acknowledged truthfully how much of his knowledge of the came from his own work. Later scholars have accused Von Tschermak of not truly understanding the results at all, regardless, the re-discovery made Mendelism an important but controversial theory. Its most vigorous promoter in Europe was William Bateson, who coined the terms genetics, the model of heredity was highly contested by other biologists because it implied that heredity was discontinuous, in opposition to the apparently continuous variation observable for many traits. Many biologists also dismissed the theory because they were not sure it would apply to all species, Mendels findings allowed scientists such as Fisher and J. B. S. Haldane to predict the expression of traits on the basis of mathematical probabilities, an important aspect of Mendels success can be traced to his decision to start his crosses only with plants he demonstrated were true-breeding. He also only measured absolute characteristics, such as color, shape and he expressed his results numerically and subjected them to statistical analysis. His method of analysis and his large sample size gave credibility to his data. He also had the foresight to follow several successive generations of pea plants, finally, he performed test crosses to reveal the presence and proportions of recessive characters. Without his diligence and careful attention to procedure and detail, Mendels work would have had a smaller impact on the world of genetics. Mendel discovered that, when he crossed purebred white flower and purple flower pea plants, rather than being a mix of the two, the offspring was purple-flowered. When Mendel self-fertilized the F1 generation pea plants, he obtained a purple flower to white flower ratio in the F2 generation of 3 to 1, the results of this cross are tabulated in the Punnett square to the right. He then conceived the idea of heredity units, which he called factors, Mendel found that there are alternative forms of factors—now called genes—that account for variations in inherited characteristics. For example, the gene for color in pea plants exists in two forms, one for purple and the other for white
Mendelian inheritance
–
Gregor Mendel, the German-speaking Augustinian monk who founded the modern science of genetics.
14.
Quantitative genetics
–
Quantitative genetics is a branch of population genetics that deals with phenotypes that vary continuously —as opposed to discretely identifiable phenotypes and gene-products. Due to the distribution of phenotypic values, quantitative genetics must employ many other statistical methods to link phenotypes to genotypes. Some phenotypes may be analyzed either as discrete categories or as continuous phenotypes, depending on the definition of cut-off points, mendel himself had to discuss this matter in his famous paper, especially with respect to his peas attribute tall/dwarf, which actually was length of stem. Analysis of quantitative trait loci, or QTL, is a recent addition to quantitative genetics. In diploid organisms, the average value may be defined by the allele effect together with a dominance effect. The founder of quantitative genetics - Sir Ronald Fisher - perceived much of this when he proposed the first mathematics of this branch of genetics. Being a statistician, he defined the gene effects as deviations from a central value—enabling the use of concepts such as mean and variance. The central value he chose for the gene was the midpoint between the two opposing homozygotes at the one locus, the deviation from there to the greater homozygous genotype can be named +a, and therefore it is -a from that same midpoint to the lesser homozygote genotype. This is the effect mentioned above. The heterozygote deviation from the same midpoint can be named d, however, in reality we measure phenotypes, and the figure also shows how observed phenotypes relate to the gene effects. Formal definitions of these effects recognize this phenotypic focus, epistasis has been approached statistically as interaction, but epigenetics suggests a new approach may be needed. If 0<d<a, the dominance is regarded as partial or incomplete—while d=a indicates full or classical dominance, previously, d>a was known as over-dominance. Mendels pea attribute length of stem provides us with a good example, mendel stated that the tall true-breeding parents ranged from 6–7 feet in stem length, giving a median of 198 cm. The short parents ranged from 0.75 -1.25 feet in length, with a rounded median of 34 cm. Their hybrid ranged from 6–7.5 feet in length, with a median of 206 cm, the mean of P1 and P2 is 116 cm, this being the phenotypic value of the homozygotes midpoint. The allele affect is =82 cm = -, the dominance effect is =90 cm. This historical example illustrates clearly how phenotype values and gene effects are linked, to obtain means, variances and other statistics, both quantities and their occurrences are required. The gene effects provide the framework for quantities, and the frequencies of the alleles in the fertilization gamete-pool provide the information on occurrences
Quantitative genetics
–
Gene effects and Phenotype values.
Quantitative genetics
–
Analysis of Sexual reproduction.
Quantitative genetics
–
Population mean across all values of p, for various d effects.
15.
DNA sequencing
–
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. It includes any method or technology that is used to determine the order of the four bases—adenine, guanine, cytosine, the advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery. The first DNA sequences were obtained in the early 1970s by academic researchers using laborious methods based on two-dimensional chromatography, following the development of fluorescence-based sequencing methods with a DNA sequencer, DNA sequencing has become easier and orders of magnitude faster. DNA sequencing may be used to determine the sequence of genes, larger genetic regions, full chromosomes or entire genomes. DNA sequencing is also the most efficient way to sequence RNA or proteins, in fact, DNA sequencing has become a key technology in many areas of biology and other sciences such as medicine, forensics, or anthropology. Sequencing is used in biology to study genomes and the proteins they encode. Information obtained using sequencing allows researchers to identify changes in genes, associations with diseases and phenotypes, the field of metagenomics involves identification of organisms present in a body of water, sewage, dirt, debris filtered from the air, or swab samples from organisms. Knowing which organisms are present in an environment is critical to research in ecology, epidemiology, microbiology. Sequencing enables researchers to determine which types of microbes may be present in a microbiome, medical technicians may sequence genes from patients to determine if there is risk of genetic diseases. This is a form of testing, though some genetic tests may not involve DNA sequencing. DNA sequencing may be used along with DNA profiling methods for forensic identification, the canonical structure of DNA has four bases, thymine, adenine, cytosine, and guanine. DNA sequencing is the determination of the order of these bases in a molecule of DNA. However, there are other bases that may be present in a molecule. In some viruses, cytosine may be replaced by hydroxy methyl or hydroxy methyl glucose cytosine, in mammalian DNA, variant bases with methyl groups or phosphosulfate may be found. Depending on the technique, a particular modification, e. g. the 5mC common in humans. This situation changed after 1944 as a result of experiments by Oswald Avery, Colin MacLeod. This was the first time that DNA was shown capable of transforming the properties of cells, in 1953, James Watson and Francis Crick put forward their double-helix model of DNA, based on crystallized X-ray structures being studied by Rosalind Franklin. According to the model, DNA is composed of two strands of nucleotides coiled around each other, linked together by bonds and running in opposite directions
DNA sequencing
–
An example of the results of automated chain-termination DNA sequencing.
DNA sequencing
–
Genomic DNA is fragmented into random pieces and cloned as a bacterial library. DNA from individual bacterial clones is sequenced and the sequence is assembled by using overlapping DNA regions.(click to expand)
DNA sequencing
–
An Illumina HiSeq 2500 sequencer
16.
Genetic engineering
–
Genetic engineering, also called genetic modification, is the direct manipulation of an organisms genome using biotechnology. It is a set of used to change the genetic makeup of cells, including the transfer of genes within. Genes may be removed, or knocked out, using a nuclease, gene targeting is a different technique that uses homologous recombination to change an endogenous gene, and can be used to delete a gene, remove exons, add a gene, or introduce point mutations. An organism that is generated through genetic engineering is considered to be a modified organism. The first GMOs were bacteria generated in 1973 and GM mice in 1974, insulin-producing bacteria were commercialized in 1982 and genetically modified food has been sold since 1994. GloFish, the first GMO designed as a pet, was first sold in the United States in December 2003, Genetic engineering techniques have been applied in numerous fields including research, agriculture, industrial biotechnology, and medicine. However the European Commission has also defined genetic engineering broadly as including selective breeding, cloning and stem cell research, although not considered genetic engineering, are closely related and genetic engineering can be used within them. Synthetic biology is a discipline that takes genetic engineering a step further by introducing artificially synthesized material from raw materials into an organism. If genetic material from another species is added to the host, if genetic material from the same species or a species that can naturally breed with the host is used the resulting organism is called cisgenic. Genetic engineering can also be used to remove material from the target organism. In Europe genetic modification is synonymous with genetic engineering while within the United States of America it can refer to conventional breeding methods. The Canadian regulatory system is based on whether a product has novel features regardless of method of origin, within the scientific community, the term genetic engineering is not commonly used, more specific terms such as transgenic are preferred. Plants, animals or micro organisms that have changed through genetic engineering are termed genetically modified organisms or GMOs, bacteria were the first organisms to be genetically modified. Plasmid DNA containing new genes can be inserted into the bacterial cell and these genes can code for medicines or enzymes that process food and other substrates. Plants have been modified for insect protection, herbicide resistance, virus resistance, enhanced nutrition, tolerance to environmental pressures, most commercialised GMOs are insect resistant and/or herbicide tolerant crop plants. Genetically modified animals have used for research, model animals. The genetically modified animals include animals with genes knocked out, increased susceptibility to disease, hormones for extra growth, humans have altered the genomes of species for thousands of years through selective breeding, or artificial selection as contrasted with natural selection, and more recently through mutagenesis. Genetic engineering as the manipulation of DNA by humans outside breeding
Genetic engineering
–
In 1974
Rudolf Jaenisch created the first
GM animal.
Genetic engineering
–
Knockout mice
17.
Genomics
–
Genomics is an interdisciplinary field of science focusing on genomes. A genome is a set of DNA within a single cell of an organism, and as such genomics is a branch of molecular biology concerned with the structure, function, evolution. Genomics aims at the collective characterization and quantification of genes, which direct the production of proteins with the assistance of enzymes, proteins in turn make up body structures like organs and tissues as well as control chemical reactions and carry signals between cells. If a cells DNA is mutated, a protein may be produced. Advances in genomics have triggered a revolution in discovery-based research to understand even the most complex systems such as the brain. The field includes efforts to determine the entire DNA sequence of organisms, the field also includes studies of intragenomic phenomena such as heterosis, epistasis, pleiotropy and other interactions between loci and alleles within the genome. From the Greek ΓΕΝ gen, gene meaning become, create, creation, birth, following Rosalind Franklins confirmation of the helical structure of DNA, James D. In 1964, Robert W. Holley and colleagues published the first nucleic acid sequence ever determined, extending this work, Marshall Nirenberg and Philip Leder revealed the triplet nature of the genetic code and were able to determine the sequences of 54 out of 64 codons in their experiments. In 1972, Walter Fiers and his team at the Laboratory of Molecular Biology of the University of Ghent were the first to determine the sequence of a gene, the gene for Bacteriophage MS2 coat protein. Fiers group expanded on their MS2 coat protein work, determining the complete nucleotide-sequence of bacteriophage MS2-RNA and Simian virus 40 in 1976 and 1978, in 1975, he and Alan Coulson published a sequencing procedure using DNA polymerase with radiolabelled nucleotides that he called the Plus and Minus technique. This involved two closely related methods that generated short oligonucleotides with defined 3 termini and these could be fractionated by electrophoresis on a polyacrylamide gel and visualised using autoradiography. The procedure could sequence up to 80 nucleotides in one go and was a big improvement, nevertheless, in 1977 his group was able to sequence most of the 5,386 nucleotides of the single-stranded bacteriophage φX174, completing the first fully sequenced DNA-based genome. For their groundbreaking work in the sequencing of nucleic acids, Gilbert, the advent of these technologies resulted in a rapid intensification in the scope and speed of completion of genome sequencing projects. The first complete genome sequence of an organelle, the human mitochondrion, was reported in 1981. In 1992, the first eukaryotic chromosome, chromosome III of brewers yeast Saccharomyces cerevisiae was sequenced, the first free-living organism to be sequenced was that of Haemophilus influenzae in 1995. As of October 2011, the sequences are available for,2,719 viruses,1,115 archaea and bacteria. Of the other sequenced species, most were chosen because they were well-studied model organisms or promised to become good models, yeast has long been an important model organism for the eukaryotic cell, while the fruit fly Drosophila melanogaster has been a very important tool. The worm Caenorhabditis elegans is an often used model for multicellular organisms
Genomics
–
Frederick Sanger
Genomics
–
Walter Gilbert
Genomics
–
An ABI PRISM 3100 Genetic Analyzer. Such capillary sequencers automated early large-scale genome sequencing efforts.
18.
Medical genetics
–
Medical genetics is the branch of medicine that involves the diagnosis and management of hereditary disorders. In contrast, the study of typically non-medical phenotypes such as the genetics of eye color would be considered part of human genetics, but not necessarily relevant to medical genetics. Genetic medicine is a term for medical genetics and incorporates areas such as gene therapy, personalized medicine. Medical genetics is becoming relevant to many common diseases. In some ways, many of the fields within medical genetics are hybrids between clinical care and research. This is due in part to recent advances in science and technology that have enabled an unprecedented understanding of genetic disorders, Clinical genetics is the practice of clinical medicine with particular attention to hereditary disorders. Referrals are made to genetics clinics for a variety of reasons, including birth defects, developmental delay, autism, epilepsy, short stature, in the United States, physicians who practice clinical genetics are accredited by the American Board of Medical Genetics and Genomics. In order to become a practitioner of Clinical Genetics, a physician must complete a minimum of 24 months of training in a program accredited by the ABMGG. Examples of metabolic disorders include galactosemia, glycogen storage disease, lysosomal storage disorders, metabolic acidosis, peroxisomal disorders, phenylketonuria, cytogenetics is the study of chromosomes and chromosome abnormalities. While cytogenetics historically relied on microscopy to analyze chromosomes, new technologies such as array comparative genomic hybridization are now becoming widely used. Examples of chromosome abnormalities include aneuploidy, chromosomal rearrangements, and genomic deletion/duplication disorders, molecular genetics involves the discovery of and laboratory testing for DNA mutations that underlie many single gene disorders. Molecular tests are used in the diagnosis of syndromes involving epigenetic abnormalities, such as Angelman syndrome, Beckwith-Wiedemann syndrome, Prader-willi syndrome. Mitochondrial genetics concerns the diagnosis and management of mitochondrial disorders, which have a molecular basis, there exists some overlap between medical genetic diagnostic laboratories and molecular pathology. Genetic counseling is the process of providing information about conditions, diagnostic testing. Genetic counselors are non-physician members of the medical team who specialize in family risk assessment. The precise role of the genetic counselor varies somewhat depending on the disorder, although genetics has its roots back in the 19th century with the work of the Bohemian monk Gregor Mendel and other pioneering scientists, human genetics emerged later. It started to develop, albeit slowly, during the first half of the 20th century, mendelian inheritance was studied in a number of important disorders such as albinism, brachydactyly, and hemophilia. Mathematical approaches were devised and applied to human genetics
Medical genetics
–
Geneticist working with a pedigree
19.
Phenotypic trait
–
For example, eye color is a character of an organism, while blue, brown and hazel are traits. A phenotypic trait is an obvious, observable, and measurable trait, it is the expression of genes in an observable way. An example of a trait is hair color, underlying genes, which make up the genotype, control the hair color, but the actual hair color. The inheritable unit that may influence a trait is called a gene, a gene is a portion of a chromosome, which is a very long and compacted string of DNA and proteins. An important reference point along a chromosome is the centromere, the distance from a gene to the centromere is referred to as the locus or map location. The nucleus of a cell contains two of each chromosome, with homologous pairs of chromosomes having the same genes at the same loci. Different phenotypic traits are caused by different forms of genes, or alleles, a gene is only a DNA code sequence, the slightly different variations of that sequence are called alleles. Alleles can be different and produce different product RNAs. Combinations of different alleles thus go on to different traits through the information flow charted above. For example, if the alleles on homologous chromosomes exhibit a simple dominance relationship and his most famous analyses were based on clear-cut traits with simple dominance. He determined that the units, what we now call genes. His tool was statistics The biochemistry of the intermediate proteins determines how they interact in the cell, therefore, biochemistry predicts how different combinations of alleles will produce varying traits. Extended expression patterns seen in diploid organisms include facets of incomplete dominance, codominance, incomplete dominance is the condition in which neither allele dominates the other in one heterozygote. Instead the phenotype is intermediate in heterozygotes, thus you can tell that each allele is present in the heterozygote. Codominance refers to the relationship that occurs when two alleles are both expressed in the heterozygote, and both phenotypes are seen simultaneously. Multiple alleles refers to the situation there are more than 2 common alleles of a particular gene. Blood groups in humans is a classic example, the ABO blood group proteins are important in determining blood type in humans, and this is determined by different alleles of the one locus. Schizotypy is an example of a phenotypic trait found in schizophrenia-spectrum disorders
Phenotypic trait
–
Blue
human eye.
20.
Asexual reproduction
–
Asexual reproduction is the primary form of reproduction for single-celled organisms such as the Archaea and bacteria. Many plants and fungi reproduce asexually as well, a complete lack of sexual reproduction is relatively rare among multicellular organisms, particularly animals. It is not entirely understood why the ability to reproduce sexually is so common among them, developmental constraints may underlie why few animals have relinquished sexual reproduction completely in their life-cycles. An important form of fission is binary fission, in binary fission, the parent/adult organism is replaced by two daughter organisms, because it literally divides in two. Only prokaryotes reproduce asexually through binary fission, eukaryotes may reproduce in a functionally similar manner by mitosis, most of these are also capable of sexual reproduction. Another type of fission is multiple fission, multiple fission at the cellular level occurs in many protists, e. g. sporozoans and algae. The nucleus of the parent cell divides several times by mitosis, the cytoplasm then separates, creating multiple daughter cells. In apicomplexans, multiple fission, or schizogony, is manifested either as merogony, sporogony or gametogony, merogony results in merozoites, which are multiple daughter cells, that originate within the same cell membrane, sporogony results in sporozoites, and gametogony results in microgametes. Some cells split via budding, resulting in a mother and daughter cell, the offspring organism is smaller than the parent. Budding is also known on a level, an animal example is the hydra. The buds grow into fully matured individuals which break away from the parent organism. Internal budding is a process of reproduction, favoured by parasites such as Toxoplasma gondii. It involves a process in which two or more daughter cells are produced inside a mother cell, which is then consumed by the offspring prior to their separation. Also, budding is present in some worm like Taenia or Echinococci, vegetative propagation is a type of asexual reproduction found in plants where new individuals are formed without the production of seeds or spores by meiosis or syngamy. Examples of vegetative reproduction include the formation of miniaturized plants called plantlets on specialized leaves, other plants reproduce by forming bulbs or tubers. Some plants produce adventitious shoots and may form a colony, where all the individuals are clones. Many multicellular organisms form spores during their life cycle in a process called sporogenesis. Exceptions are animals and some protists, who undergo meiosis immediately followed by fertilization, plants and many algae on the other hand undergo sporic meiosis where meiosis leads to the formation of haploid spores rather than gametes
Asexual reproduction
–
Asexual reproduction in
liverworts: a
caducous phylloid germinating
Asexual reproduction
–
Closeup of a
Bryophyllum daigremontianum
21.
Cell (biology)
–
The cell is the basic structural, functional, and biological unit of all known living organisms. A cell is the smallest unit of life that can replicate independently, the study of cells is called cell biology. Cells consist of cytoplasm enclosed within a membrane, which contains many such as proteins. Organisms can be classified as unicellular or multicellular, while the number of cells in plants and animals varies from species to species, humans contain more than 10 trillion cells. Most plant and animal cells are only under a microscope. The cell was discovered by Robert Hooke in 1665, who named the unit for its resemblance to cells inhabited by Christian monks in a monastery. Cells emerged on Earth at least 3.5 billion years ago, Cells are of two types, eukaryotic, which contain a nucleus, and prokaryotic, which do not. Prokaryotes are single-celled organisms, while eukaryotes can be either single-celled or multicellular, prokaryotic cells were the first form of life on Earth, characterised by having vital biological processes including cell signaling and being self-sustaining. They are simpler and smaller than eukaryotic cells, and lack membrane-bound organelles such as the nucleus, prokaryotes include two of the domains of life, bacteria and archaea. The DNA of a prokaryotic cell consists of a chromosome that is in direct contact with the cytoplasm. The nuclear region in the cytoplasm is called the nucleoid, most prokaryotes are the smallest of all organisms ranging from 0.5 to 2.0 µm in diameter. Though most prokaryotes have both a cell membrane and a wall, there are exceptions such as Mycoplasma and Thermoplasma which only possess the cell membrane layer. The envelope gives rigidity to the cell and separates the interior of the cell from its environment, the cell wall consists of peptidoglycan in bacteria, and acts as an additional barrier against exterior forces. It also prevents the cell from expanding and bursting from osmotic pressure due to a hypotonic environment, some eukaryotic cells also have a cell wall. Inside the cell is the region that contains the genome, ribosomes. The genetic material is found in the cytoplasm. Prokaryotes can carry extrachromosomal DNA elements called plasmids, which are usually circular, linear bacterial plasmids have been identified in several species of spirochete bacteria, including members of the genus Borrelia notably Borrelia burgdorferi, which causes Lyme disease. Though not forming a nucleus, the DNA is condensed in a nucleoid, plasmids encode additional genes, such as antibiotic resistance genes
Cell (biology)
–
Onion (
Allium) cells in different phases of the cell cycle
Cell (biology)
–
Structure of an animal cell
Cell (biology)
–
A fluorescent image of an endothelial cell. Nuclei are stained blue,
mitochondria are stained red, and microfilaments are stained green.
Cell (biology)
–
Human cancer cells with nuclei (specifically the DNA) stained blue. The central and rightmost cell are in
interphase, so the entire nuclei are labeled. The cell on the left is going through
mitosis and its DNA has condensed.
22.
Organisms
–
In biology, an organism is any contiguous living system, such as an animal, plant, fungus, protist, archaeon, or bacterium. All known types of organisms are capable of some degree of response to stimuli, reproduction, growth and development and homeostasis. An organism consists of one or more cells, when it has one cell it is known as an organism. Most unicellular organisms are of microscopic scale and are thus described as microorganisms. Humans are multicellular organisms composed of trillions of cells grouped into specialized tissues. An organism may be either a prokaryote or a eukaryote, prokaryotes are represented by two separate domains—bacteria and archaea. Eukaryotic organisms are characterized by the presence of a cell nucleus. Fungi, animals and plants are examples of kingdoms of organisms within the eukaryotes, estimates on the number of Earths current species range from 10 million to 14 million, of which only about 1.2 million have been documented. More than 99% of all species, amounting to five billion species. In 2016, a set of 355 genes from the last universal ancestor of all living organisms living was identified. The term organism first appeared in the English language in 1703 and it is directly related to the term organization. There is a tradition of defining organisms as self-organizing beings. An organism may be defined as an assembly of molecules functioning as a more or less stable whole that exhibits the properties of life. Dictionary definitions can be broad, using such as any living structure, such as a plant, animal, fungus or bacterium, capable of growth. Many definitions exclude viruses and possible man-made non-organic life forms, as viruses are dependent on the machinery of a host cell for reproduction. A superorganism is an organism consisting of individuals working together as a single functional or social unit. There has been controversy about the best way to define the organism, several contributions are responses to the suggestion that the category of organism may well not be adequate in biology. Viruses are not typically considered to be organisms because they are incapable of autonomous reproduction and this controversy is problematic because some cellular organisms are also incapable of independent survival and live as obligatory intracellular parasites
Organisms
–
These
Escherichia coli cells provide an example of a
prokaryotic microorganism.
Organisms
–
A
polypore mushroom has a
parasitic relationship with its
host.
Organisms
–
An
ericoid mycorrhizal fungus
Organisms
23.
Genetic information
–
A nucleic acid sequence is a succession of letters that indicate the order of nucleotides within a DNA or RNA molecule. By convention, sequences are presented from the 5 end to the 3 end. For DNA, the strand is used. Because nucleic acids are linear polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is also termed the primary structure, the sequence has capacity to represent information. Biological deoxyribonucleic acid represents the information which directs the functions of a living thing, nucleic acids also have a secondary structure and tertiary structure. Primary structure is sometimes referred to as primary sequence. Conversely, there is no concept of secondary or tertiary sequence. Nucleic acids consist of a chain of linked units called nucleotides, each nucleotide consists of three subunits, a phosphate group and a sugar make up the backbone of the nucleic acid strand, and attached to the sugar is one of a set of nucleobases. The nucleobases are important in base pairing of strands to form secondary and tertiary structure such as the famed double helix. The possible letters are A, C, G, and T, in the typical case, the sequences are printed abutting one another without gaps, as in the sequence AAAGTCTGAC, read left to right in the 5 to 3 direction. With regards to transcription, a sequence is on the strand if it has the same order as the transcribed RNA. One sequence can be complementary to sequence, meaning that they have the base on each position in the complementary. For example, the sequence to TTAC is GTAA. If one strand of the double-stranded DNA is considered the sense strand, then the other strand, considered the antisense strand, will have the complementary sequence to the sense strand. Apart from adenine, cytosine, guanine, thymine and uracil, in DNA, the most common modified base is 5-methylcytidine. In RNA, there are many modified bases, including pseudouridine, dihydrouridine, inosine, ribothymidine and 7-methylguanosine, hypoxanthine and xanthine are two of the many bases created through mutagen presence, both of them through deamination. Hypoxanthine is produced from adenine, xanthine from guanine, similarly, deamination of cytosine results in uracil
Genetic information
–
A series of codons in part of a
mRNA molecule. Each codon consists of three
nucleotides, usually representing a single
amino acid.
24.
Species
–
In biology, a species is the basic unit of biological classification and a taxonomic rank. A species is defined as the largest group of organisms in which two individuals can produce fertile offspring, typically by sexual reproduction. While this definition is often adequate, looked at more closely it is problematic, for example, with hybridisation, in a species complex of hundreds of similar microspecies, or in a ring species, the boundaries between closely related species become unclear. Other ways of defining species include similarity of DNA, morphology, all species are given a two-part name, a binomial. The first part of a binomial is the genus to which the species belongs, the second part is called the specific name or the specific epithet. For example, Boa constrictor is one of four species of the Boa genus, Species were seen from the time of Aristotle until the 18th century as fixed kinds that could be arranged in a hierarchy, the great chain of being. In the 19th century, biologists grasped that species could evolve given sufficient time, Charles Darwins 1859 book The Origin of Species explained how species could arise by natural selection. Genes can sometimes be exchanged between species by horizontal transfer, and species may become extinct for a variety of reasons. In his biology, Aristotle used the term γένος to mean a kind, such as a bird or fish, a kind was distinguished by its attributes, for instance, a bird has feathers, a beak, wings, a hard-shelled egg, and warm blood. A form was distinguished by being shared by all its members, Aristotle believed all kinds and forms to be distinct and unchanging. His approach remained influential until the Renaissance, when observers in the Early Modern period began to develop systems of organization for living things, they placed each kind of animal or plant into a context. Many of these early delineation schemes would now be considered whimsical, animals likewise that differ specifically preserve their distinct species permanently, one species never springs from the seed of another nor vice versa. In the 18th century, the Swedish scientist Carl Linnaeus classified organisms according to shared physical characteristics and he established the idea of a taxonomic hierarchy of classification based upon observable characteristics and intended to reflect natural relationships. At the time, however, it was widely believed that there was no organic connection between species, no matter how similar they appeared. However, whether or not it was supposed to be fixed, by the 19th century, naturalists understood that species could change form over time, and that the history of the planet provided enough time for major changes. Jean-Baptiste Lamarck, in his 1809 Zoological Philosophy, described the transmutation of species, proposing that a species could change over time, in 1859, Charles Darwin and Alfred Russel Wallace provided a compelling account of evolution and the formation of new species. Darwin argued that it was populations that evolved, not individuals and this required a new definition of species. Darwin concluded that species are what appear to be, ideas
Species
–
John Ray
Species
–
Carl Linnaeus believed in the fixity of species.
25.
Natural selection
–
Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is a key mechanism of evolution, the change in heritable traits of a population over time, Charles Darwin popularised the term natural selection, and compared it with artificial selection. Variation exists within all populations of organisms and this occurs partly because random mutations arise in the genome of an individual organism, and offspring can inherit such mutations. Throughout the lives of the individuals, their genomes interact with their environments to cause variations in traits, the environment of a genome includes the molecular biology in the cell, other cells, other individuals, populations, species, as well as the abiotic environment. Individuals with certain variants of the trait may survive and reproduce more than individuals with other, less successful, variants, therefore, factors that affect reproductive success are also important, including sexual selection and fecundity selection. Over time, this process can result in populations that specialise for particular ecological niches, in other words, natural selection is a key process in the evolution of a population. Natural selection can be contrasted with artificial selection, in which humans intentionally choose specific traits, Natural selection is one of the cornerstones of modern biology. The concept of natural selection originally developed in the absence of a theory of heredity, at the time of Darwins writing. The union of traditional Darwinian evolution with subsequent discoveries in classical genetics formed the synthesis of the mid-20th century. The addition of molecular genetics has led to developmental biology. While genotypes can slowly change by random genetic drift, natural selection remains the primary explanation for adaptive evolution, empedocles idea that organisms arose entirely by the incidental workings of causes such as heat and cold was criticised by Aristotle in Book II of Physics. He posited natural teleology in its place, and believed that form was achieved for a purpose, nevertheless, he accepted in his biology that new types of animals, monstrosities, can occur in very rare instances. And in like manner as to the parts in which there appears to exist an adaptation to an end. Yet it is impossible that this should be the true view, for teeth and all other natural things either invariably or normally come about in a given way, but of not one of the results of chance or spontaneity is this true. We do not ascribe to chance or mere coincidence the frequency of rain in winter, but frequent rain in summer we do, nor heat in the dog-days, therefore action for an end is present in things which come to be and are by nature. The struggle for existence was later described by the Islamic writer Al-Jahiz in the 9th century, the classical arguments were reintroduced in the 18th century by Pierre Louis Maupertuis and others, including Darwins grandfather, Erasmus Darwin. Until the early 19th century, the view in Western societies was that differences between individuals of a species were uninteresting departures from their Platonic ideals of created kinds. However, the theory of uniformitarianism in geology promoted the idea that simple and this theory, Lamarckism, was an influence on the Soviet biologist Trofim Lysenkos antagonism to mainstream genetic theory as late as the mid 20th century
Natural selection
–
Morpha typica and morpha carbonaria,
morphs of the
peppered moth resting on the same tree. The light-coloured morpha typica (below the bark's scar) is hard to see on this pollution-free tree,
camouflaging it from
predators.
Natural selection
–
Diagrammatic representation of the
divergence of modern
taxonomic groups from their
common ancestor
Natural selection
–
Male peppered moth
Natural selection
–
Charles Darwin 's illustrations of beak variation in the
finches of the
Galápagos Islands, which hold 13 closely related
species that differ most markedly in the shape of their beaks. The beak of each species is suited to its preferred food, suggesting that beak shapes evolved by natural selection.
26.
Biology
–
Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, evolution, distribution, identification and taxonomy. Modern biology is a vast and eclectic field, composed of branches and subdisciplines. However, despite the broad scope of biology, there are certain unifying concepts within it that consolidate it into single, coherent field. In general, biology recognizes the cell as the unit of life, genes as the basic unit of heredity. It is also understood today that all organisms survive by consuming and transforming energy and by regulating their internal environment to maintain a stable, the term biology is derived from the Greek word βίος, bios, life and the suffix -λογία, -logia, study of. The Latin-language form of the term first appeared in 1736 when Swedish scientist Carl Linnaeus used biologi in his Bibliotheca botanica, the first German use, Biologie, was in a 1771 translation of Linnaeus work. In 1797, Theodor Georg August Roose used the term in the preface of a book, karl Friedrich Burdach used the term in 1800 in a more restricted sense of the study of human beings from a morphological, physiological and psychological perspective. The science that concerns itself with these objects we will indicate by the biology or the doctrine of life. Although modern biology is a recent development, sciences related to. Natural philosophy was studied as early as the ancient civilizations of Mesopotamia, Egypt, the Indian subcontinent, however, the origins of modern biology and its approach to the study of nature are most often traced back to ancient Greece. While the formal study of medicine back to Hippocrates, it was Aristotle who contributed most extensively to the development of biology. Especially important are his History of Animals and other works where he showed naturalist leanings, and later more empirical works that focused on biological causation and the diversity of life. Aristotles successor at the Lyceum, Theophrastus, wrote a series of books on botany that survived as the most important contribution of antiquity to the plant sciences, even into the Middle Ages. Scholars of the medieval Islamic world who wrote on biology included al-Jahiz, Al-Dīnawarī, who wrote on botany, biology began to quickly develop and grow with Anton van Leeuwenhoeks dramatic improvement of the microscope. It was then that scholars discovered spermatozoa, bacteria, infusoria, investigations by Jan Swammerdam led to new interest in entomology and helped to develop the basic techniques of microscopic dissection and staining. Advances in microscopy also had a impact on biological thinking. In the early 19th century, a number of biologists pointed to the importance of the cell. Thanks to the work of Robert Remak and Rudolf Virchow, however, meanwhile, taxonomy and classification became the focus of natural historians
Biology
Biology
Biology
Biology
27.
Epigenetics
–
Epigenetics are stable heritable traits that cannot be explained by changes in DNA sequence. The Greek prefix epi- in epigenetics implies features that are on top of or in addition to the genetic basis for inheritance. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors, the standard definition of epigenetic requires these alterations to be heritable, either in the progeny of cells or of organisms. The term also refers to the changes themselves, functionally relevant changes to the genome that do not involve a change in the nucleotide sequence. Examples of mechanisms that produce such changes are DNA methylation and histone modification, gene expression can be controlled through the action of repressor proteins that attach to silencer regions of the DNA. One example of a change in eukaryotic biology is the process of cellular differentiation. During morphogenesis, totipotent stem cells become the various pluripotent cell lines of the embryo, by activating some genes while inhibiting the expression of others. Historically, some phenomena not necessarily heritable have also described as epigenetic. For example, epigenetic has been used to describe any modification of regions, especially histone modifications. The consensus definition now requires a trait to be heritable for it to be considered epigenetic, the term epigenetics in its contemporary usage emerged in the 1990s, but for some years has been used in somewhat variable meanings. The term epigenesis has a generic meaning extra growth, taken directly from Koine Greek ἐπιγέννησις, from this, and the associated adjective epigenetic, the term epigenetics was coined by C. H. Waddington in 1942 as pertaining to epigenesis in parallel to Valentin Haeckers phenogenetics. Epigenesis in the context of biology refers to the differentiation of cells from their initial totipotent state in embryonic development, Waddington held that cell fates were established in development much like a marble rolls down to the point of lowest local elevation. Waddington suggested visualising increasing irreversibility of cell differentiation as ridges rising between the valleys where the marbles are travelling. In recent times Waddingtons notion of the landscape has been rigorously formalized in the context of the systems dynamics state approach to the study of cell-fate. Cell-fate determination is predicted to exhibit certain dynamics, such as attractor-convergence or oscillatory, the term epigenetic has also been used in developmental psychology to describe psychological development as the result of an ongoing, bi-directional interchange between heredity and the environment. Interactivist ideas of development have been discussed in various forms and under various names throughout the 19th and 20th centuries, an early version was proposed, among the founding statements in embryology, by Karl Ernst von Baer and popularized by Ernst Haeckel. A radical epigenetic view was developed by Paul Wintrebert, another variation, probabilistic epigenesis, was presented by Gilbert Gottlieb in 2003. This view encompasses all of the possible developing factors on an organism and how not only influence the organism and each other
Epigenetics
–
Epigenetic mechanisms
Epigenetics
–
DNA associates with histone proteins to form chromatin.
28.
Nucleobase
–
Nucleobases are nitrogen-containing biological compounds that form nucleosides, which in turn are components of nucleotides, all which are monomers that are the basic building blocks of nucleic acids. When a nucleobase forms a bond with a molecule of ribose or deoxyribose the compound is a nucleoside. A nucleoside joined to or more phosphate groups is a nucleotide, nucleobases are also known a nitrogenous bases. The pairing of purines and pyrimidines may result, in part, from dimensional constraints, the A-T and C-G pairings function to form double or triple hydrogen bonds between the amine and carbonyl groups on the complementary bases. There are five primary, or canonical, nucleobases, adenine, cytosine, guanine, thymine, the so-called DNA-bases are A, G, C, and T, the RNA-bases are A, G, C, and U. Thymine and uracil are identical except for the lack of a group in uracil. Biological bases that do not function as standard parts of the code are termed non-primary. At the sides of nucleic acid structure, phosphate molecules successively connect the two sugar-rings of two adjacent nucleotide monomers, thereby creating a long chain biomolecule and these chain-joins of phosphates with sugars create the backbone strands for a single- or double helix biomolecule. DNA and RNA also contain bases that have been modified after the nucleic acid chain has been formed. In DNA, the most common modified base is 5-methylcytosine, in RNA, there are many modified bases, including those contained in the nucleosides pseudouridine, dihydrouridine, inosine, and 7-methylguanosine. Hypoxanthine and xanthine are two of the many bases created through mutagen presence, both of them through deamination, hypoxanthine is produced from adenine, xanthine from guanine. and uracil results from deamination of cytosine. These are examples of modified adenosine or guanosine and these are examples of modified cytosine, thymine or uridine. A vast number of nucleobase analogues exist, the most common applications are used as fluorescent probes, either directly or indirectly, such as aminoallyl nucleotide, which are used to label cRNA or cDNA in microarrays. Several groups are working on alternative extra base pairs to extend the code, such as isoguanine and isocytosine or the fluorescent 2-amino-6-purine. In medicine, several nucleoside analogues are used as anticancer and antiviral agents, the viral polymerase incorporates these compounds with non-canonical bases. These compounds are activated in the cells by being converted into nucleotides, at least one set of new base pairs has been announced as of May 2014. Nucleoside Nucleotide Nucleic acid notation Nucleic acid sequence Base pairing in DNA Double Helix
Nucleobase
–
Base pairing in
RNA. Nucleobases in blue (C paired with G, A paired with U). Hydrogen bonds in red.
29.
Double helix
–
In molecular biology, the term double helix refers to the structure formed by double-stranded molecules of nucleic acids such as DNA. The double helical structure of a nucleic acid complex arises as a consequence of its secondary structure, the term entered popular culture with the publication in 1968 of The Double Helix, A Personal Account of the Discovery of the Structure of DNA, by James Watson. The DNA double helix polymer of nucleic acid, held together by nucleotides which base pair together, in B-DNA, the most common double helical structure found in nature, the double helix is right-handed with about 10–10.5 base pairs per turn. This translates into about 20-21 nucleotides per turn, the double helix structure of DNA contains a major groove and minor groove. In B-DNA the major groove is wider than the minor groove, given the difference in widths of the major groove and minor groove, many proteins which bind to B-DNA do so through the wider major groove. The prior model was triple-stranded DNA, Crick, Wilkins, and Watson each received one third of the 1962 Nobel Prize in Physiology or Medicine for their contributions to the discovery. Hybridization is the process of base pairs binding to form a double helix. Melting is the process by which the interactions between the strands of the helix are broken, separating the two nucleic acid strands. These bonds are weak, easily separated by gentle heating, enzymes, melting occurs preferentially at certain points in the nucleic acid. T and A rich regions are more easily melted than C and G rich regions, some base steps are also susceptible to DNA melting, such as T A and T G. These mechanical features are reflected by the use of such as TATA at the start of many genes to assist RNA polymerase in melting the DNA for transcription. Strand separation by heating, as used in polymerase chain reaction, is simple. The intertwining of the DNA strands makes long segments difficult to separate, helicases unwind the strands to facilitate the advance of sequence-reading enzymes such as DNA polymerase. The geometry of a base, or base pair step can be characterized by 6 coordinates, shift, slide, rise, tilt, roll, and twist. These values precisely define the location and orientation in space of every base or base pair in an acid molecule relative to its predecessor along the axis of the helix. Together, they characterize the structure of the molecule. In regions of DNA or RNA where the structure is disrupted. Opening Shift, displacement along an axis in the plane perpendicular to the first
Double helix
–
Base pair geometries
Double helix
–
Two
complementary regions of nucleic acid molecules will bind and form a double helical structure held together by
base pairs.
Double helix
–
The helix axis of A-, B-, and Z-DNA.
30.
Eye color
–
Neither blue nor green pigments are ever present in the human iris or ocular fluid. Eye color is thus an instance of structural color and varies depending on the lighting conditions, the brightly colored eyes of many bird species result from the presence of other pigments, such as pteridines, purines, and carotenoids. Humans and other animals have many variations in eye color. The genetics of eye color are complicated, and color is determined by multiple genes, so far, as many as 15 genes have been associated with eye color inheritance. Some of the eye-color genes include OCA2 and HERC2, the earlier belief that blue eye color is a simple recessive trait has been shown to be incorrect. The genetics of eye color are so complex that almost any combination of eye colors can occur. However, OCA2 gene polymorphism, close to proximal 5′ regulatory region, Eye color is an inherited trait influenced by more than one gene. These genes are sought using associations to small changes in the genes themselves and these changes are known as single-nucleotide polymorphisms or SNPs. The actual number of genes that contribute to eye color is currently unknown, a study in Rotterdam found that it was possible to predict eye color with more than 90% accuracy for brown and blue using just six SNPs. The gene OCA2, when in a variant form, causes the eye color. Different SNPs within OCA2 are strongly associated with blue and green eyes as well as variations in freckling, mole counts, hair, the polymorphisms may be in an OCA2 regulatory sequence, where they may influence the expression of the gene product, which in turn affects pigmentation. A specific mutation within the HERC2 gene, a gene that regulates OCA2 expression, is responsible for blue eyes. Other genes implicated in eye color variation are SLC24A4 and TYR, blue eyes with a brown spot, green eyes, and gray eyes are caused by an entirely different part of the genome. Classification systems have ranged from a light or dark description to detailed gradings employing photographic standards for comparison. Others have attempted to set standards of color comparison. Eye colors range from the darkest shades of brown to the lightest tints of blue, there are three pigment colors that determine, depending on their proportion, the outward appearance of the iris, along with structural color. Green irises, for example, have blue and some yellow, some eyes have a dark ring around the iris, called a limbal ring. Eye color in non-human animals is regulated differently, for example, instead of blue as in humans, autosomal recessive eye color in the skink species Corucia zebrata is black, and the autosomal dominant color is yellow-green
Eye color
–
Close up of a
blue human
iris.
Eye color
Eye color
–
Amber eyes in sunlight – displaying an orange color rather than brown
Eye color
–
A light blue iris
. PMID 23201126. doi:10.1016/j.molcel.2012.10.027.
