A gene family is a set of several similar genes, formed by duplication of a single original gene , and generally with similar biochemical functions. One such family are the genes for human hemoglobin subunits; the ten genes are in two clusters on different chromosomes, called the α-globin and β-globin loci. These two gene clusters are thought to have arisen as a result of a precursor gene being duplicated approximately 500 million years ago.
167-775: In biology , a mutation is an alteration in the nucleic acid sequence of the genome of an organism , virus , or extrachromosomal DNA . Viral genomes contain either DNA or RNA . Mutations result from errors during DNA or viral replication , mitosis , or meiosis or other types of damage to DNA (such as pyrimidine dimers caused by exposure to ultraviolet radiation), which then may undergo error-prone repair (especially microhomology-mediated end joining ), cause an error during other forms of repair, or cause an error during replication ( translesion synthesis ). Mutations may also result from substitution , insertion or deletion of segments of DNA due to mobile genetic elements . Mutations may or may not produce detectable changes in
334-433: A butterfly may produce offspring with new mutations. The majority of these mutations will have no effect; but one might change the colour of one of the butterfly's offspring, making it harder (or easier) for predators to see. If this color change is advantageous, the chances of this butterfly's surviving and producing its own offspring are a little better, and over time the number of butterflies with this mutation may form
501-535: A last universal common ancestor that lived about 3.5 billion years ago . Geologists have developed a geologic time scale that divides the history of the Earth into major divisions, starting with four eons ( Hadean , Archean , Proterozoic , and Phanerozoic ), the first three of which are collectively known as the Precambrian , which lasted approximately 4 billion years. Each eon can be divided into eras, with
668-440: A lipid bilayer , including cholesterols that sit between phospholipids to maintain their fluidity at various temperatures. Cell membranes are semipermeable , allowing small molecules such as oxygen, carbon dioxide, and water to pass through while restricting the movement of larger molecules and charged particles such as ions . Cell membranes also contain membrane proteins , including integral membrane proteins that go across
835-443: A nucleus , and prokaryotic cells, which do not. Prokaryotes are single-celled organisms such as bacteria , whereas eukaryotes can be single-celled or multicellular. In multicellular organisms , every cell in the organism's body is derived ultimately from a single cell in a fertilized egg . Every cell is enclosed within a cell membrane that separates its cytoplasm from the extracellular space . A cell membrane consists of
1002-508: A number of shapes , ranging from spheres to rods and spirals . Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats . Bacteria inhabit soil, water, acidic hot springs , radioactive waste , and the deep biosphere of the Earth's crust . Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about 27 percent of
1169-477: A "stem" (or "root") symbol for members of a gene family (by homology or function), with a hierarchical numbering system to distinguish the individual members. For example, for the peroxiredoxin family, PRDX is the root symbol, and the family members are PRDX1 , PRDX2 , PRDX3 , PRDX4 , PRDX5 , and PRDX6 . One level of genome organization is the grouping of genes into several gene families. Gene families are groups of related genes that share
1336-474: A cell's size, shape, membrane potential , metabolic activity , and responsiveness to signals, which are largely due to highly controlled modifications in gene expression and epigenetics . With a few exceptions, cellular differentiation almost never involves a change in the DNA sequence itself. Thus, different cells can have very different physical characteristics despite having the same genome . Morphogenesis, or
1503-408: A chemical (e.g., nitrous acid , benzopyrene ) or radiation (e.g., x-ray , gamma ray , ultraviolet radiation , particles emitted by unstable isotopes). Mutations can lead to phenotypic effects such as loss-of-function, gain-of-function , and conditional mutations. Some mutations are beneficial, as they are a source of genetic variation for evolution. Others are harmful if they were to result in
1670-544: A common ancestor. Members of gene families may be paralogs or orthologs. Gene paralogs are genes with similar sequences from within the same species while gene orthologs are genes with similar sequences in different species. Gene families are highly variable in size, sequence diversity, and arrangement. Depending on the diversity and functions of the genes within the family, families can be classified as multigene families or superfamilies. Multigene families typically consist of members with similar sequences and functions, though
1837-577: A family duplicating and diversifying into new genes, and genes being lost. An entire gene family may also be lost, or gained through de novo gene birth , by such extensive divergence such that a gene is considered part of a new family, or by horizontal gene transfer . When the number of genes per genome remains relatively constant, this implies that genes are gained and lost at relatively same rates. There are some patterns in which genes are more likely to be lost vs. which are more likely to duplicate and diversify into multiple copies. An adaptive expansion of
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#17327937025982004-1233: A few archaea have very different shapes, such as the flat and square cells of Haloquadratum walsbyi . Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation . Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes , including archaeols . Archaea use more energy sources than eukaryotes: these range from organic compounds , such as sugars, to ammonia , metal ions or even hydrogen gas . Salt-tolerant archaea (the Haloarchaea ) use sunlight as an energy source, and other species of archaea fix carbon , but unlike plants and cyanobacteria , no known species of archaea does both. Archaea reproduce asexually by binary fission , fragmentation , or budding ; unlike bacteria, no known species of Archaea form endospores . The first observed archaea were extremophiles , living in extreme environments, such as hot springs and salt lakes with no other organisms. Improved molecular detection tools led to
2171-403: A final electron acceptor, which is usually the oxidized form of NADP , which is reduced to NADPH, a process that takes place in a protein complex called photosystem I (PSI). The transport of electrons is coupled to the movement of protons (or hydrogen) from the stroma to the thylakoid membrane, which forms a pH gradient across the membrane as hydrogen becomes more concentrated in the lumen than in
2338-411: A healthy, uncontaminated cell. Naturally occurring oxidative DNA damage is estimated to occur 10,000 times per cell per day in humans and 100,000 times per cell per day in rats . Spontaneous mutations can be characterized by the specific change: There is increasing evidence that the majority of spontaneously arising mutations are due to error-prone replication ( translesion synthesis ) past DNA damage in
2505-577: A high degree of divergence (at the sequence and/or functional level) does not lead to the removal of a gene from a gene family. Individual genes in the family may be arranged close together on the same chromosome or dispersed throughout the genome on different chromosomes. Due to the similarity of their sequences and their overlapping functions, individual genes in the family often share regulatory control elements. In some instances, gene members have identical (or nearly identical) sequences. Such families allow for massive amounts of gene product to be expressed in
2672-514: A hollow sphere of cells , the blastula , during embryonic development . Over 1.5 million living animal species have been described —of which around 1 million are insects —but it has been estimated there are over 7 million animal species in total. They have complex interactions with each other and their environments, forming intricate food webs . Gene family Genes are categorized into families based on shared nucleotide or protein sequences . Phylogenetic techniques can be used as
2839-1012: A larger percentage of the population. Neutral mutations are defined as mutations whose effects do not influence the fitness of an individual. These can increase in frequency over time due to genetic drift . It is believed that the overwhelming majority of mutations have no significant effect on an organism's fitness. Also, DNA repair mechanisms are able to mend most changes before they become permanent mutations, and many organisms have mechanisms, such as apoptotic pathways , for eliminating otherwise-permanently mutated somatic cells . Beneficial mutations can improve reproductive success. Four classes of mutations are (1) spontaneous mutations (molecular decay), (2) mutations due to error-prone replication bypass of naturally occurring DNA damage (also called error-prone translesion synthesis), (3) errors introduced during DNA repair, and (4) induced mutations caused by mutagens . Scientists may sometimes deliberately introduce mutations into cells or research organisms for
3006-769: A loss of function of genes needed for survival. Gene expression is the molecular process by which a genotype encoded in DNA gives rise to an observable phenotype in the proteins of an organism's body. This process is summarized by the central dogma of molecular biology , which was formulated by Francis Crick in 1958. According to the Central Dogma, genetic information flows from DNA to RNA to protein. There are two gene expression processes: transcription (DNA to RNA) and translation (RNA to protein). The regulation of gene expression by environmental factors and during different stages of development can occur at each step of
3173-493: 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 gene families of shared ancestry, detectable by their sequence homology . Novel genes are produced by several methods, commonly through the duplication and mutation of an ancestral gene, or by recombining parts of different genes to form new combinations with new functions. Here, protein domains act as modules, each with
3340-501: A minor effect. For instance, human height is determined by hundreds of genetic variants ("mutations") but each of them has a very minor effect on height, apart from the impact of nutrition . Height (or size) itself may be more or less beneficial as the huge range of sizes in animal or plant groups shows. Attempts have been made to infer the distribution of fitness effects (DFE) using mutagenesis experiments and theoretical models applied to molecular sequence data. DFE, as used to determine
3507-414: A more rigorous test. The positions of exons within the coding sequence can be used to infer common ancestry. Knowing the sequence of the protein encoded by a gene can allow researchers to apply methods that find similarities among protein sequences that provide more information than similarities or differences among DNA sequences. If the genes of a gene family encode proteins, the term protein family
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#17327937025983674-417: A more successful evolutionary theory based on natural selection ; similar reasoning and evidence led Alfred Russel Wallace to independently reach the same conclusions. The basis for modern genetics began with the work of Gregor Mendel in 1865. This outlined the principles of biological inheritance. However, the significance of his work was not realized until the early 20th century when evolution became
3841-457: A new cycle. In contrast to mitosis, meiosis results in four haploid daughter cells by undergoing one round of DNA replication followed by two divisions. Homologous chromosomes are separated in the first division ( meiosis I ), and sister chromatids are separated in the second division ( meiosis II ). Both of these cell division cycles are used in the process of sexual reproduction at some point in their life cycle. Both are believed to be present in
4008-571: A number of beneficial mutations as well. For instance, in a screen of all gene deletions in E. coli , 80% of mutations were negative, but 20% were positive, even though many had a very small effect on growth (depending on condition). Gene deletions involve removal of whole genes, so that point mutations almost always have a much smaller effect. In a similar screen in Streptococcus pneumoniae , but this time with transposon insertions, 76% of insertion mutants were classified as neutral, 16% had
4175-402: A particular and independent function, that can be mixed together to produce genes encoding new proteins with novel properties. For example, the human eye uses four genes to make structures that sense light: three for cone cell or colour vision and one for rod cell or night vision; all four arose from a single ancestral gene. Another advantage of duplicating a gene (or even an entire genome)
4342-409: A process known as allopatric speciation . A phylogeny is an evolutionary history of a specific group of organisms or their genes. It can be represented using a phylogenetic tree , a diagram showing lines of descent among organisms or their genes. Each line drawn on the time axis of a tree represents a lineage of descendants of a particular species or population. When a lineage divides into two, it
4509-408: A region of deoxyribonucleic acid (DNA) that carries genetic information that controls form or function of an organism. DNA is composed of two polynucleotide chains that coil around each other to form a double helix . It is found as linear chromosomes in eukaryotes , and circular chromosomes in prokaryotes . The set of chromosomes in a cell is collectively known as its genome . In eukaryotes, DNA
4676-541: A role in the synthesis and packaging of proteins, respectively. Biomolecules such as proteins can be engulfed by lysosomes , another specialized organelle. Plant cells have additional organelles that distinguish them from animal cells such as a cell wall that provides support for the plant cell, chloroplasts that harvest sunlight energy to produce sugar, and vacuoles that provide storage and structural support as well as being involved in reproduction and breakdown of plant seeds. Eukaryotic cells also have cytoskeleton that
4843-436: A separate clade as some protists may be more closely related to plants, fungi, or animals than they are to other protists. Like groupings such as algae , invertebrates , or protozoans , the protist grouping is not a formal taxonomic group but is used for convenience. Most protists are unicellular; these are called microbial eukaryotes. Plants are mainly multicellular organisms , predominantly photosynthetic eukaryotes of
5010-975: A short time as needed. Other families allow for similar but specific products to be expressed in different cell types or at different stages of an organism's development. Superfamilies are much larger than single multigene families. Superfamilies contain up to hundreds of genes, including multiple multigene families as well as single, individual gene members. The large number of members allows superfamilies to be widely dispersed with some genes clustered and some spread far apart. The genes are diverse in sequence and function displaying various levels of expression and separate regulation controls. Some gene families also contain pseudogenes , sequences of DNA that closely resemble established gene sequences but are non-functional. Different types of pseudogenes exist. Non-processed pseudogenes are genes that acquired mutations over time becoming non-functional. Processed pseudogenes are genes that have lost their function after being moved around
5177-485: A significantly reduced fitness, but 6% were advantageous. This classification is obviously relative and somewhat artificial: a harmful mutation can quickly turn into a beneficial mutations when conditions change. Also, there is a gradient from harmful/beneficial to neutral, as many mutations may have small and mostly neglectable effects but under certain conditions will become relevant. Also, many traits are determined by hundreds of genes (or loci), so that each locus has only
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5344-423: A single carbon atom can form four single covalent bonds such as in methane , two double covalent bonds such as in carbon dioxide (CO 2 ), or a triple covalent bond such as in carbon monoxide (CO). Moreover, carbon can form very long chains of interconnecting carbon–carbon bonds such as octane or ring-like structures such as glucose . The simplest form of an organic molecule is the hydrocarbon , which
5511-701: A single gene in the ancestor of humans and chimpanzees now occurs in both species and can be thought of as having been 'duplicated' via speciation. As a result of duplication by speciation, a gene family might include 15 genes, one copy in each of 15 different species. In the formation of gene families, four levels of duplication exist: 1) exon duplication and shuffling , 2) entire gene duplication , 3) multigene family duplication, and 4) whole genome duplication . Exon duplication and shuffling gives rise to variation and new genes. Genes are then duplicated to form multigene families which duplicate to form superfamilies spanning multiple chromosomes. Whole genome duplication doubles
5678-436: A single gene into many initially identical copies occurs when natural selection would favour additional gene copies. This is the case when an environmental stressor acts on a species. Gene amplification is more common in bacteria and is a reversible process. Contraction of gene families commonly results from accumulation of loss of function mutations. A nonsense mutation which prematurely halts gene transcription becomes fixed in
5845-446: A specific enzyme. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts —they allow a reaction to proceed more rapidly without being consumed by it—by reducing the amount of activation energy needed to convert reactants into products . Enzymes also allow
6012-399: A unified theory as the modern synthesis reconciled Darwinian evolution with classical genetics . In the 1940s and early 1950s, a series of experiments by Alfred Hershey and Martha Chase pointed to DNA as the component of chromosomes that held the trait-carrying units that had become known as genes . A focus on new kinds of model organisms such as viruses and bacteria, along with
6179-421: A varied mix of traits, and reproduction is able to increase any population, Darwin argued that in the natural world, it was nature that played the role of humans in selecting for specific traits. Darwin inferred that individuals who possessed heritable traits better adapted to their environments are more likely to survive and produce more offspring than other individuals. He further inferred that this would lead to
6346-492: A water molecule again. In pure water , the number of hydrogen ions balances (or equals) the number of hydroxyl ions, resulting in a pH that is neutral. Organic compounds are molecules that contain carbon bonded to another element such as hydrogen. With the exception of water, nearly all the molecules that make up each organism contain carbon. Carbon can form covalent bonds with up to four other atoms, enabling it to form diverse, large, and complex molecules. For example,
6513-421: A whole. Changes in DNA caused by mutation in a coding region of DNA can cause errors in protein sequence that may result in partially or completely non-functional proteins. Each cell, in order to function correctly, depends on thousands of proteins to function in the right places at the right times. When a mutation alters a protein that plays a critical role in the body, a medical condition can result. One study on
6680-601: Is Concerted evolution . Concerted evolution occurs through repeated cycles of unequal crossing over events and repeated cycles of gene transfer and conversion. Unequal crossing over leads to the expansion and contraction of gene families. Gene families have an optimal size range that natural selection acts towards. Contraction deletes divergent gene copies and keeps gene families from becoming too large. Expansion replaces lost gene copies and prevents gene families from becoming too small. Repeat cycles of gene transfer and conversion increasingly make gene family members more similar. In
6847-536: Is evolution , which explains the unity and diversity of life. Energy processing is also important to life as it allows organisms to move , grow, and reproduce . Finally, all organisms are able to regulate their own internal environments . Biologists are able to study life at multiple levels of organization , from the molecular biology of a cell to the anatomy and physiology of plants and animals, and evolution of populations. Hence, there are multiple subdisciplines within biology , each defined by
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7014-444: Is a central feature of sexual reproduction in eukaryotes, and the most fundamental function of meiosis appears to be conservation of the integrity of the genome that is passed on to progeny by parents. Two aspects of sexual reproduction , meiotic recombination and outcrossing , are likely maintained respectively by the adaptive advantages of recombinational repair of genomic DNA damage and genetic complementation which masks
7181-641: Is a large family of organic compounds that are composed of hydrogen atoms bonded to a chain of carbon atoms. A hydrocarbon backbone can be substituted by other elements such as oxygen (O), hydrogen (H), phosphorus (P), and sulfur (S), which can change the chemical behavior of that compound. Groups of atoms that contain these elements (O-, H-, P-, and S-) and are bonded to a central carbon atom or skeleton are called functional groups . There are six prominent functional groups that can be found in organisms: amino group , carboxyl group , carbonyl group , hydroxyl group , phosphate group , and sulfhydryl group . In 1953,
7348-414: Is a major pathway for repairing double-strand breaks. NHEJ involves removal of a few nucleotides to allow somewhat inaccurate alignment of the two ends for rejoining followed by addition of nucleotides to fill in gaps. As a consequence, NHEJ often introduces mutations. Induced mutations are alterations in the gene after it has come in contact with mutagens and environmental causes. Induced mutations on
7515-480: Is a small polar molecule with a bent shape formed by the polar covalent bonds of two hydrogen (H) atoms to one oxygen (O) atom (H 2 O). Because the O–H bonds are polar, the oxygen atom has a slight negative charge and the two hydrogen atoms have a slight positive charge. This polar property of water allows it to attract other water molecules via hydrogen bonds, which makes water cohesive . Surface tension results from
7682-918: Is a term of convenience as not all algae are closely related. Algae comprise several distinct clades such as glaucophytes , which are microscopic freshwater algae that may have resembled in form to the early unicellular ancestor of Plantae. Unlike glaucophytes, the other algal clades such as red and green algae are multicellular. Green algae comprise three major clades: chlorophytes , coleochaetophytes , and stoneworts . Fungi are eukaryotes that digest foods outside their bodies, secreting digestive enzymes that break down large food molecules before absorbing them through their cell membranes. Many fungi are also saprobes , feeding on dead organic matter, making them important decomposers in ecological systems. Animals are multicellular eukaryotes. With few exceptions, animals consume organic material , breathe oxygen , are able to move , can reproduce sexually , and grow from
7849-467: Is accepted that the majority of mutations are neutral or deleterious, with advantageous mutations being rare; however, the proportion of types of mutations varies between species. This indicates two important points: first, the proportion of effectively neutral mutations is likely to vary between species, resulting from dependence on effective population size ; second, the average effect of deleterious mutations varies dramatically between species. In addition,
8016-443: Is called a de novo mutation . A change in the genetic structure that is not inherited from a parent, and also not passed to offspring, is called a somatic mutation . Somatic mutations are not inherited by an organism's offspring because they do not affect the germline . However, they are passed down to all the progeny of a mutated cell within the same organism during mitosis. A major section of an organism therefore might carry
8183-403: Is catalyzed by lactate dehydrogenase in a reversible reaction. Lactate can also be used as an indirect precursor for liver glycogen. During recovery, when oxygen becomes available, NAD attaches to hydrogen from lactate to form ATP. In yeast, the waste products are ethanol and carbon dioxide. This type of fermentation is known as alcoholic or ethanol fermentation . The ATP generated in this process
8350-478: Is important in animals that have a dedicated germline to produce reproductive cells. However, it is of little value in understanding the effects of mutations in plants, which lack a dedicated germline. The distinction is also blurred in those animals that reproduce asexually through mechanisms such as budding , because the cells that give rise to the daughter organisms also give rise to that organism's germline. A new germline mutation not inherited from either parent
8517-445: Is in a coding or non-coding region . Mutations in the non-coding regulatory sequences of a gene, such as promoters, enhancers, and silencers, can alter levels of gene expression, but are less likely to alter the protein sequence. Mutations within introns and in regions with no known biological function (e.g. pseudogenes , retrotransposons ) are generally neutral , having no effect on phenotype – though intron mutations could alter
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#17327937025988684-441: Is made by substrate-level phosphorylation , which does not require oxygen. Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that can later be released to fuel the organism's metabolic activities via cellular respiration. This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water. In most cases, oxygen
8851-535: Is made up of microtubules , intermediate filaments , and microfilaments , all of which provide support for the cell and are involved in the movement of the cell and its organelles. In terms of their structural composition, the microtubules are made up of tubulin (e.g., α-tubulin and β-tubulin ) whereas intermediate filaments are made up of fibrous proteins. Microfilaments are made up of actin molecules that interact with other strands of proteins. All cells require energy to sustain cellular processes. Metabolism
9018-526: Is mainly in the cell nucleus . In prokaryotes, the DNA is held within the nucleoid . The genetic information is held within genes, and the complete assemblage in an organism is called its genotype . DNA replication is a semiconservative process whereby each strand serves as a template for a new strand of DNA. Mutations are heritable changes in DNA. They can arise spontaneously as a result of replication errors that were not corrected by proofreading or can be induced by an environmental mutagen such as
9185-501: Is often used in an analogous manner to gene family . The expansion or contraction of gene families along a specific lineage can be due to chance, or can be the result of natural selection. To distinguish between these two cases is often difficult in practice. Recent work uses a combination of statistical models and algorithmic techniques to detect gene families that are under the effect of natural selection. The HUGO Gene Nomenclature Committee (HGNC) creates nomenclature schemes using
9352-399: Is one of the key ways a cell releases chemical energy to fuel cellular activity. The overall reaction occurs in a series of biochemical steps, some of which are redox reactions. Although cellular respiration is technically a combustion reaction , it clearly does not resemble one when it occurs in a cell because of the slow, controlled release of energy from the series of reactions. Sugar in
9519-407: Is pulled to the separate poles of the bacterium as it increases the size to prepare for splitting. Growth of a new cell wall begins to separate the bacterium (triggered by FtsZ polymerization and "Z-ring" formation). The new cell wall ( septum ) fully develops, resulting in the complete split of the bacterium. The new daughter cells have tightly coiled DNA rods, ribosomes , and plasmids . Meiosis
9686-399: Is released as a waste product. Most plants, algae , and cyanobacteria perform photosynthesis, which is largely responsible for producing and maintaining the oxygen content of the Earth's atmosphere, and supplies most of the energy necessary for life on Earth. Photosynthesis has four stages: Light absorption , electron transport, ATP synthesis, and carbon fixation . Light absorption is
9853-412: Is represented as a fork or split on the phylogenetic tree. Phylogenetic trees are the basis for comparing and grouping different species. Different species that share a feature inherited from a common ancestor are described as having homologous features (or synapomorphy ). Phylogeny provides the basis of biological classification. This classification system is rank-based, with the highest rank being
10020-402: Is that this increases engineering redundancy ; this allows one gene in the pair to acquire a new function while the other copy performs the original function. 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
10187-420: Is that when they move within a genome, they can mutate or delete existing genes and thereby produce genetic diversity. Nonlethal mutations accumulate within the gene pool and increase the amount of genetic variation. The abundance of some genetic changes within the gene pool can be reduced by natural selection , while other "more favorable" mutations may accumulate and result in adaptive changes. For example,
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#173279370259810354-468: Is the process by which genes and traits are passed on from parents to offspring. It has several principles. The first is that genetic characteristics, alleles , are discrete and have alternate forms (e.g., purple vs. white or tall vs. dwarf), each inherited from one of two parents. Based on the law of dominance and uniformity , which states that some alleles are dominant while others are recessive ; an organism with at least one dominant allele will display
10521-485: Is the set of chemical reactions in an organism. The three main purposes of metabolism are: the conversion of food to energy to run cellular processes; the conversion of food/fuel to monomer building blocks; and the elimination of metabolic wastes . These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolic reactions may be categorized as catabolic —the breaking down of compounds (for example,
10688-410: Is the study of chemical processes within and relating to living organisms . Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including molecular synthesis, modification, mechanisms, and interactions. Life arose from the Earth's first ocean, which formed some 3.8 billion years ago. Since then, water continues to be
10855-493: Is to store, transmit, and express hereditary information. Cell theory states that cells are the fundamental units of life, that all living things are composed of one or more cells, and that all cells arise from preexisting cells through cell division . Most cells are very small, with diameters ranging from 1 to 100 micrometers and are therefore only visible under a light or electron microscope . There are generally two types of cells: eukaryotic cells, which contain
11022-644: The Cambrian explosion . During the Permian period, synapsids , including the ancestors of mammals , dominated the land, but most of this group became extinct in the Permian–Triassic extinction event 252 million years ago. During the recovery from this catastrophe, archosaurs became the most abundant land vertebrates; one archosaur group, the dinosaurs, dominated the Jurassic and Cretaceous periods. After
11189-495: The Cretaceous–Paleogene extinction event 66 million years ago killed off the non-avian dinosaurs, mammals increased rapidly in size and diversity . Such mass extinctions may have accelerated evolution by providing opportunities for new groups of organisms to diversify. Bacteria are a type of cell that constitute a large domain of prokaryotic microorganisms . Typically a few micrometers in length, bacteria have
11356-533: The Homininae , two chromosomes fused to produce human chromosome 2 ; this fusion did not occur in the lineage of the other apes , and they retain these separate chromosomes. In evolution, the most important role of such chromosomal rearrangements may be to accelerate the divergence of a population into new species by making populations less likely to interbreed, thereby preserving genetic differences between these populations. Sequences of DNA that can move about
11523-535: The Miller–Urey experiment showed that organic compounds could be synthesized abiotically within a closed system mimicking the conditions of early Earth , thus suggesting that complex organic molecules could have arisen spontaneously in early Earth (see abiogenesis ). Macromolecules are large molecules made up of smaller subunits or monomers . Monomers include sugars, amino acids, and nucleotides. Carbohydrates include monomers and polymers of sugars. Lipids are
11690-492: The Precambrian about 1.5 billion years ago and can be classified into eight major clades : alveolates , excavates , stramenopiles , plants, rhizarians , amoebozoans , fungi , and animals. Five of these clades are collectively known as protists , which are mostly microscopic eukaryotic organisms that are not plants, fungi, or animals. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor ), protists by themselves do not constitute
11857-727: The activator is the transcription factor that stimulates transcription when it binds to the sequence near or at the promoter. Negative regulation occurs when another transcription factor called a repressor binds to a DNA sequence called an operator , which is part of an operon, to prevent transcription. Repressors can be inhibited by compounds called inducers (e.g., allolactose ), thereby allowing transcription to occur. Specific genes that can be activated by inducers are called inducible genes , in contrast to constitutive genes that are almost constantly active. In contrast to both, structural genes encode proteins that are not involved in gene regulation. In addition to regulatory events involving
12024-592: The bacterial phyla have species that can be grown in the laboratory. Archaea constitute the other domain of prokaryotic cells and were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom ), a term that has fallen out of use. Archaeal cells have unique properties separating them from the other two domains , Bacteria and Eukaryota . Archaea are further divided into multiple recognized phyla . Archaea and bacteria are generally similar in size and shape, although
12191-404: The cell . In 1838, Schleiden and Schwann began promoting the now universal ideas that (1) the basic unit of organisms is the cell and (2) that individual cells have all the characteristics of life, although they opposed the idea that (3) all cells come from the division of other cells, continuing to support spontaneous generation . However, Robert Remak and Rudolf Virchow were able to reify
12358-403: The cell membrane of another cell or located deep inside a cell. There are generally four types of chemical signals: autocrine , paracrine , juxtacrine , and hormones . In autocrine signaling, the ligand affects the same cell that releases it. Tumor cells, for example, can reproduce uncontrollably because they release signals that initiate their own self-division. In paracrine signaling,
12525-416: The circulatory systems of animals or vascular systems of plants to reach their target cells. Once a ligand binds with a receptor, it can influence the behavior of another cell, depending on the type of receptor. For instance, neurotransmitters that bind with an inotropic receptor can alter the excitability of a target cell. Other types of receptors include protein kinase receptors (e.g., receptor for
12692-528: The domain followed by kingdom , phylum , class , order , family , genus , and species . All organisms can be classified as belonging to one of three domains : Archaea (originally Archaebacteria), bacteria (originally eubacteria), or eukarya (includes the fungi, plant, and animal kingdoms). The history of life on Earth traces how organisms have evolved from the earliest emergence of life to present day. Earth formed about 4.5 billion years ago and all life on Earth, both living and extinct, descended from
12859-481: The duplication of its DNA and some of its organelles , and the subsequent partitioning of its cytoplasm into two daughter cells in a process called cell division . In eukaryotes (i.e., animal, plant, fungal , and protist cells), there are two distinct types of cell division: mitosis and meiosis . Mitosis is part of the cell cycle, in which replicated chromosomes are separated into two new nuclei. Cell division gives rise to genetically identical cells in which
13026-403: The kingdom Plantae, which would exclude fungi and some algae . Plant cells were derived by endosymbiosis of a cyanobacterium into an early eukaryote about one billion years ago, which gave rise to chloroplasts. The first several clades that emerged following primary endosymbiosis were aquatic and most of the aquatic photosynthetic eukaryotic organisms are collectively described as algae, which
13193-423: The microscope . It was then that scholars discovered spermatozoa , bacteria, infusoria and the diversity of microscopic life. Investigations by Jan Swammerdam led to new interest in entomology and helped to develop techniques of microscopic dissection and staining . Advances in microscopy had a profound impact on biological thinking. In the early 19th century, biologists pointed to the central importance of
13360-412: The mitochondrial cristae . Oxidative phosphorylation comprises the electron transport chain, which is a series of four protein complexes that transfer electrons from one complex to another, thereby releasing energy from NADH and FADH 2 that is coupled to the pumping of protons (hydrogen ions) across the inner mitochondrial membrane ( chemiosmosis ), which generates a proton motive force . Energy from
13527-546: The phenotype of that dominant allele. During gamete formation, the alleles for each gene segregate, so that each gamete carries only one allele for each gene. Heterozygotic individuals produce gametes with an equal frequency of two alleles. Finally, the law of independent assortment , states that genes of different traits can segregate independently during the formation of gametes, i.e., genes are unlinked. An exception to this rule would include traits that are sex-linked . Test crosses can be performed to experimentally determine
13694-409: The product of a gene , or prevent the gene from functioning properly or completely. Mutations can also occur in non-genic regions . A 2007 study on genetic variations between different species of Drosophila suggested that, if a mutation changes a protein produced by a gene, the result is likely to be harmful, with an estimated 70% of amino acid polymorphisms that have damaging effects, and
13861-497: The regulation of the rate of a metabolic reaction, for example in response to changes in the cell's environment or to signals from other cells. Cellular respiration is a set of metabolic reactions and processes that take place in cells to convert chemical energy from nutrients into adenosine triphosphate (ATP), and then release waste products. The reactions involved in respiration are catabolic reactions , which break large molecules into smaller ones, releasing energy. Respiration
14028-428: The "Delicious" apple and the "Washington" navel orange . Human and mouse somatic cells have a mutation rate more than ten times higher than the germline mutation rate for both species; mice have a higher rate of both somatic and germline mutations per cell division than humans. The disparity in mutation rate between the germline and somatic tissues likely reflects the greater importance of genome maintenance in
14195-471: The DFE also differs between coding regions and noncoding regions , with the DFE of noncoding DNA containing more weakly selected mutations. In multicellular organisms with dedicated reproductive cells , mutations can be subdivided into germline mutations , which can be passed on to descendants through their reproductive cells, and somatic mutations (also called acquired mutations), which involve cells outside
14362-469: The DFE of advantageous mutations may lead to increased ability to predict the evolutionary dynamics. Theoretical work on the DFE for advantageous mutations has been done by John H. Gillespie and H. Allen Orr . They proposed that the distribution for advantageous mutations should be exponential under a wide range of conditions, which, in general, has been supported by experimental studies, at least for strongly selected advantageous mutations. In general, it
14529-422: The DNA. Ordinarily, a mutation cannot be recognized by enzymes once the base change is present in both DNA strands, and thus a mutation is not ordinarily repaired. At the cellular level, mutations can alter protein function and regulation. Unlike DNA damages, mutations are replicated when the cell replicates. At the level of cell populations, cells with mutations will increase or decrease in frequency according to
14696-481: The Phanerozoic eon that began 539 million years ago being subdivided into Paleozoic , Mesozoic , and Cenozoic eras. These three eras together comprise eleven periods ( Cambrian , Ordovician , Silurian , Devonian , Carboniferous , Permian , Triassic , Jurassic , Cretaceous , Tertiary , and Quaternary ). The similarities among all known present-day species indicate that they have diverged through
14863-696: The accumulation of favorable traits over successive generations, thereby increasing the match between the organisms and their environment. A species is a group of organisms that mate with one another and speciation is the process by which one lineage splits into two lineages as a result of having evolved independently from each other. For speciation to occur, there has to be reproductive isolation . Reproductive isolation can result from incompatibilities between genes as described by Bateson–Dobzhansky–Muller model . Reproductive isolation also tends to increase with genetic divergence . Speciation can occur when there are physical barriers that divide an ancestral species,
15030-491: The adaptation rate of organisms, they have some times been named as adaptive mutagenesis mechanisms, and include the SOS response in bacteria, ectopic intrachromosomal recombination and other chromosomal events such as duplications. The sequence of a gene can be altered in a number of ways. Gene mutations have varying effects on health depending on where they occur and whether they alter the function of essential proteins. Mutations in
15197-442: The ancestral gene. Transposable elements play a role in the movement of genes. Transposable elements are recognized by inverted repeats at their 5' and 3' ends. When two transposable elements are close enough in the same region on a chromosome, they can form a composite transposon. The protein transposase recognizes the outermost inverted repeats, cutting the DNA segment. Any genes between the two transposable elements are relocated as
15364-517: The appearance of skin cancer during one's lifetime is induced by overexposure to UV radiation that causes mutations in the cellular and skin genome. There is a widespread assumption that mutations are (entirely) "random" with respect to their consequences (in terms of probability). This was shown to be wrong as mutation frequency can vary across regions of the genome, with such DNA repair - and mutation-biases being associated with various factors. For instance, Monroe and colleagues demonstrated that—in
15531-589: The body plan and the number, identity, and pattern of body parts. Among the most important toolkit genes are the Hox genes . Hox genes determine where repeating parts, such as the many vertebrae of snakes, will grow in a developing embryo or larva. Evolution is a central organizing concept in biology. It is the change in heritable characteristics of populations over successive generations . In artificial selection , animals were selectively bred for specific traits. Given that traits are inherited, populations contain
15698-450: The breaking down of glucose to pyruvate by cellular respiration ); or anabolic —the building up ( synthesis ) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy. The chemical reactions of metabolism are organized into metabolic pathways , in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by
15865-438: The category of by effect on function, but depending on the specificity of the change the mutations listed below will occur. In genetics , it is sometimes useful to classify mutations as either harmful or beneficial (or neutral ): Large-scale quantitative mutagenesis screens , in which thousands of millions of mutations are tested, invariably find that a larger fraction of mutations has harmful effects but always returns
16032-410: The cohesive force due to the attraction between molecules at the surface of the liquid. Water is also adhesive as it is able to adhere to the surface of any polar or charged non-water molecules. Water is denser as a liquid than it is as a solid (or ice). This unique property of water allows ice to float above liquid water such as ponds, lakes, and oceans, thereby insulating the liquid below from
16199-433: The cold air above. Water has the capacity to absorb energy, giving it a higher specific heat capacity than other solvents such as ethanol . Thus, a large amount of energy is needed to break the hydrogen bonds between water molecules to convert liquid water into water vapor . As a molecule, water is not completely stable as each water molecule continuously dissociates into hydrogen and hydroxyl ions before reforming into
16366-437: The comparatively higher frequency of cell divisions in the parental sperm donor germline drive conclusions that rates of de novo mutation can be tracked along a common basis. The frequency of error during the DNA replication process of gametogenesis , especially amplified in the rapid production of sperm cells, can promote more opportunities for de novo mutations to replicate unregulated by DNA repair machinery. This claim combines
16533-543: The comparison of genes between different species of Drosophila suggests that if a mutation does change a protein, the mutation will most likely be harmful, with an estimated 70 per cent of amino acid polymorphisms having damaging effects, and the remainder being either neutral or weakly beneficial. Some mutations alter a gene's DNA base sequence but do not change the protein made by the gene. Studies have shown that only 7% of point mutations in noncoding DNA of yeast are deleterious and 12% in coding DNA are deleterious. The rest of
16700-407: The complementary undamaged strand in DNA as a template or an undamaged sequence in a homologous chromosome if it is available. If DNA damage remains in a cell, transcription of a gene may be prevented and thus translation into a protein may also be blocked. DNA replication may also be blocked and/or the cell may die. In contrast to a DNA damage, a mutation is an alteration of the base sequence of
16867-593: The composite transposon jumps to a new area of the genome. Reverse transcription is another method of gene movement. An mRNA transcript of a gene is reversed transcribed, or copied, back into DNA. This new DNA copy of the mRNA is integrated into another part of the genome, resulting in gene family members being dispersed. A special type of multigene family is implicated in the movement of gene families and gene family members. LINE ( L ong IN terspersed E lements) and SINE ( S hort IN terspersed E lements) families are highly repetitive DNA sequences spread all throughout
17034-501: The cytoplasm of a cell, there are many biomolecules such as proteins and nucleic acids . In addition to biomolecules, eukaryotic cells have specialized structures called organelles that have their own lipid bilayers or are spatially units. These organelles include the cell nucleus , which contains most of the cell's DNA, or mitochondria , which generate adenosine triphosphate (ATP) to power cellular processes. Other organelles such as endoplasmic reticulum and Golgi apparatus play
17201-455: The cytoplasm, where it is converted to waste products that may be removed from the cell. This serves the purpose of oxidizing the electron carriers so that they can perform glycolysis again and removing the excess pyruvate. Fermentation oxidizes NADH to NAD so it can be re-used in glycolysis. In the absence of oxygen, fermentation prevents the buildup of NADH in the cytoplasm and provides NAD for glycolysis. This waste product varies depending on
17368-404: The dedicated reproductive group and which are not usually transmitted to descendants. Diploid organisms (e.g., humans) contain two copies of each gene—a paternal and a maternal allele. Based on the occurrence of mutation on each chromosome, we may classify mutations into three types. A wild type or homozygous non-mutated organism is one in which neither allele is mutated. A germline mutation in
17535-677: The development of biological knowledge. He explored biological causation and the diversity of life. His successor, Theophrastus , began the scientific study of plants. Scholars of the medieval Islamic world who wrote on biology included al-Jahiz (781–869), Al-Dīnawarī (828–896), who wrote on botany, and Rhazes (865–925) who wrote on anatomy and physiology . Medicine was especially well studied by Islamic scholars working in Greek philosopher traditions, while natural history drew heavily on Aristotelian thought. Biology began to quickly develop with Anton van Leeuwenhoek 's dramatic improvement of
17702-418: The development of body form, is the result of spatial differences in gene expression. A small fraction of the genes in an organism's genome called the developmental-genetic toolkit control the development of that organism. These toolkit genes are highly conserved among phyla , meaning that they are ancient and very similar in widely separated groups of animals. Differences in deployment of toolkit genes affect
17869-440: The developmental fate of a cell, which becomes more restrictive during development. Differentiation is the process by which specialized cells arise from less specialized cells such as stem cells . Stem cells are undifferentiated or partially differentiated cells that can differentiate into various types of cells and proliferate indefinitely to produce more of the same stem cell. Cellular differentiation dramatically changes
18036-411: The discovery of archaea in almost every habitat , including soil, oceans, and marshlands . Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are a major part of Earth's life . They are part of the microbiota of all organisms. In the human microbiome , they are important in the gut , mouth, and on
18203-420: The discovery of the double-helical structure of DNA by James Watson and Francis Crick in 1953, marked the transition to the era of molecular genetics . From the 1950s onwards, biology has been vastly extended in the molecular domain. The genetic code was cracked by Har Gobind Khorana , Robert W. Holley and Marshall Warren Nirenberg after DNA was understood to contain codons . The Human Genome Project
18370-428: The distribution of fitness effects was done by Motoo Kimura , an influential theoretical population geneticist . His neutral theory of molecular evolution proposes that most novel mutations will be highly deleterious, with a small fraction being neutral. A later proposal by Hiroshi Akashi proposed a bimodal model for the DFE, with modes centered around highly deleterious and neutral mutations. Both theories agree that
18537-634: The earliest terrestrial ecosystems , at least 2.7 billion years ago. Microorganisms are thought to have paved the way for the inception of land plants in the Ordovician period. Land plants were so successful that they are thought to have contributed to the Late Devonian extinction event . Ediacara biota appear during the Ediacaran period, while vertebrates , along with most other modern phyla originated about 525 million years ago during
18704-433: The effects of the mutations on the ability of the cell to survive and reproduce. Although distinctly different from each other, DNA damages and mutations are related because DNA damages often cause errors of DNA synthesis during replication or repair and these errors are a major source of mutation. Mutations can involve the duplication of large sections of DNA, usually through genetic recombination . These duplications are
18871-414: The exchange of gene alleles - results in one chromosome expanding or increasing in gene number and the other contracting or decreasing in gene number. The expansion of a gene cluster is the duplication of genes that leads to larger gene families. Gene members of a multigene family or multigene families within superfamilies exist on different chromosomes due to relocation of those genes after duplication of
19038-481: The expression of deleterious recessive mutations . The beneficial effect of genetic complementation, derived from outcrossing (cross-fertilization) is also referred to as hybrid vigor or heterosis. Charles Darwin in his 1878 book The Effects of Cross and Self-Fertilization in the Vegetable Kingdom at the start of chapter XII noted “The first and most important of the conclusions which may be drawn from
19205-455: The form of glucose is the main nutrient used by animal and plant cells in respiration. Cellular respiration involving oxygen is called aerobic respiration, which has four stages: glycolysis , citric acid cycle (or Krebs cycle), electron transport chain , and oxidative phosphorylation . Glycolysis is a metabolic process that occurs in the cytoplasm whereby glucose is converted into two pyruvates , with two net molecules of ATP being produced at
19372-661: The formation of gene families. Non-synonymous mutations resulting in the substitution of amino acids, increase in duplicate gene copies. Duplication gives rise to multiple copies of the same gene, giving a level of redundancy where mutations are tolerated. With one functioning copy of the gene, other copies are able to acquire mutations without being extremely detrimental to the organisms. Mutations allow duplicate genes to acquire new or different functions. Some multigene families are extremely homogenous, with individual genes members sharing identical or almost identical sequences. The process by which gene families maintain high homogeneity
19539-431: The genome by retrotransposition. Pseudogenes that have become isolated from the gene family they originated in, are referred to as orphans . Gene families arose from multiple duplications of an ancestral gene, followed by mutation and divergence. Duplications can occur within a lineage (e.g., humans might have two copies of a gene that is found only once in chimpanzees) or they are the result of speciation. For example,
19706-456: The genome, such as transposons , make up a major fraction of the genetic material of plants and animals, and may have been important in the evolution of genomes. For example, more than a million copies of the Alu sequence are present in the human genome , and these sequences have now been recruited to perform functions such as regulating gene expression . Another effect of these mobile DNA sequences
19873-512: The genome. The LINEs contain a sequence that encodes a reverse transcriptase protein. This protein aids in copying the RNA transcripts of LINEs and SINEs back into DNA, and integrates them into different areas of the genome. This self-perpetuates the growth of LINE and SINE families. Due to the highly repetitive nature of these elements, LINEs and SINEs when close together also trigger unequal crossing over events which result in single-gene duplications and
20040-455: The germline than in the soma. In order to categorize a mutation as such, the "normal" sequence must be obtained from the DNA of a "normal" or "healthy" organism (as opposed to a "mutant" or "sick" one), it should be identified and reported; ideally, it should be made publicly available for a straightforward nucleotide-by-nucleotide comparison, and agreed upon by the scientific community or by a group of expert geneticists and biologists , who have
20207-426: The hormone insulin ) and G protein-coupled receptors . Activation of G protein-coupled receptors can initiate second messenger cascades. The process by which a chemical or physical signal is transmitted through a cell as a series of molecular events is called signal transduction . The cell cycle is a series of events that take place in a cell that cause it to divide into two daughter cells. These events include
20374-414: The initial step of photosynthesis whereby light energy is absorbed by chlorophyll pigments attached to proteins in the thylakoid membranes . The absorbed light energy is used to remove electrons from a donor (water) to a primary electron acceptor, a quinone designated as Q. In the second stage, electrons move from the quinone primary electron acceptor through a series of electron carriers until they reach
20541-406: The last eukaryotic common ancestor. Prokaryotes (i.e., archaea and bacteria) can also undergo cell division (or binary fission ). Unlike the processes of mitosis and meiosis in eukaryotes, binary fission in prokaryotes takes place without the formation of a spindle apparatus on the cell. Before binary fission, DNA in the bacterium is tightly coiled. After it has uncoiled and duplicated, it
20708-405: The ligand diffuses to nearby cells and affects them. For example, brain cells called neurons release ligands called neurotransmitters that diffuse across a synaptic cleft to bind with a receptor on an adjacent cell such as another neuron or muscle cell . In juxtacrine signaling, there is direct contact between the signaling and responding cells. Finally, hormones are ligands that travel through
20875-444: The membrane serving as membrane transporters , and peripheral proteins that loosely attach to the outer side of the cell membrane, acting as enzymes shaping the cell. Cell membranes are involved in various cellular processes such as cell adhesion , storing electrical energy , and cell signalling and serve as the attachment surface for several extracellular structures such as a cell wall , glycocalyx , and cytoskeleton . Within
21042-403: The mitotic phase of an animal cell cycle—the division of the mother cell into two genetically identical daughter cells. The cell cycle is a vital process by which a single-celled fertilized egg develops into a mature organism, as well as the process by which hair, skin, blood cells , and some internal organs are renewed. After cell division, each of the daughter cells begin the interphase of
21209-548: The molecular level can be caused by: Whereas in former times mutations were assumed to occur by chance, or induced by mutagens, molecular mechanisms of mutation have been discovered in bacteria and across the tree of life. As S. Rosenberg states, "These mechanisms reveal a picture of highly regulated mutagenesis, up-regulated temporally by stress responses and activated when cells/organisms are maladapted to their environments—when stressed—potentially accelerating adaptation." Since they are self-induced mutagenic mechanisms that increase
21376-437: The most abundant molecule in every organism. Water is important to life because it is an effective solvent , capable of dissolving solutes such as sodium and chloride ions or other small molecules to form an aqueous solution . Once dissolved in water, these solutes are more likely to come in contact with one another and therefore take part in chemical reactions that sustain life. In terms of its molecular structure , water
21543-445: The mutations are either neutral or slightly beneficial. Biology Biology is the scientific study of life . It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of at least one cell that processes hereditary information encoded in genes , which can be transmitted to future generations. Another major theme
21710-403: The nature of their research questions and the tools that they use. Like other scientists, biologists use the scientific method to make observations , pose questions, generate hypotheses , perform experiments, and form conclusions about the world around them. Life on Earth, which emerged more than 3.7 billion years ago, is immensely diverse. Biologists have sought to study and classify
21877-484: The number of copies of every gene and gene family. Whole genome duplication or polyploidization can be either autopolyploidization or alloploidization. Autopolyploidization is the duplication of the same genome and allopolyploidization is the duplication of two closely related genomes or hybridized genomes from different species. Duplication occurs primarily through uneven crossing over events in meiosis of germ cells. (1,2) When two chromosomes misalign, crossing over -
22044-513: The observable characteristics ( phenotype ) of an organism. Mutations play a part in both normal and abnormal biological processes including: evolution , cancer , and the development of the immune system , including junctional diversity . Mutation is the ultimate source of all genetic variation , providing the raw material on which evolutionary forces such as natural selection can act. Mutation can result in many different types of change in sequences. Mutations in genes can have no effect, alter
22211-441: The observations given in this volume, is that generally cross-fertilisation is beneficial and self-fertilisation often injurious, at least with the plants on which I experimented.” Genetic variation , often produced as a byproduct of sexual reproduction, may provide long-term advantages to those sexual lineages that engage in outcrossing . Genetics is the scientific study of inheritance. Mendelian inheritance , specifically,
22378-469: The observed effects of increased probability for mutation in rapid spermatogenesis with short periods of time between cellular divisions that limit the efficiency of repair machinery. Rates of de novo mutations that affect an organism during its development can also increase with certain environmental factors. For example, certain intensities of exposure to radioactive elements can inflict damage to an organism's genome, heightening rates of mutation. In humans,
22545-517: The only class of macromolecules that are not made up of polymers. They include steroids , phospholipids , and fats, largely nonpolar and hydrophobic (water-repelling) substances. Proteins are the most diverse of the macromolecules. They include enzymes , transport proteins , large signaling molecules, antibodies , and structural proteins . The basic unit (or monomer) of a protein is an amino acid . Twenty amino acids are used in proteins. Nucleic acids are polymers of nucleotides . Their function
22712-404: The organism. In skeletal muscles, the waste product is lactic acid . This type of fermentation is called lactic acid fermentation . In strenuous exercise, when energy demands exceed energy supply, the respiratory chain cannot process all of the hydrogen atoms joined by NADH. During anaerobic glycolysis, NAD regenerates when pairs of hydrogen combine with pyruvate to form lactate. Lactate formation
22879-616: The population, leading to the loss of genes. This process occurs when changes in the environment render a gene redundant. In addition to classification by evolution (structural gene family), the HGNC also makes "gene families" by function in their stem nomenclature. As a result, a stem can also refer to genes that have the same function, often part of the same protein complex . For example, BRCA1 and BRCA2 are unrelated genes that are both named for their role in breast cancer and RPS2 and RPS3 are unrelated ribosomal proteins found in
23046-428: The possibility of common descent . Serious evolutionary thinking originated with the works of Jean-Baptiste Lamarck , who presented a coherent theory of evolution. The British naturalist Charles Darwin , combining the biogeographical approach of Humboldt , the uniformitarian geology of Lyell , Malthus's writings on population growth, and his own morphological expertise and extensive natural observations, forged
23213-907: The process of evolution from their common ancestor. Biologists regard the ubiquity of the genetic code as evidence of universal common descent for all bacteria , archaea , and eukaryotes . Microbial mats of coexisting bacteria and archaea were the dominant form of life in the early Archean eon and many of the major steps in early evolution are thought to have taken place in this environment. The earliest evidence of eukaryotes dates from 1.85 billion years ago, and while they may have been present earlier, their diversification accelerated when they started using oxygen in their metabolism . Later, around 1.7 billion years ago, multicellular organisms began to appear, with differentiated cells performing specialised functions. Algae-like multicellular land plants are dated back to about 1 billion years ago, although evidence suggests that microorganisms formed
23380-594: The process of gene transfer, allelic gene conversion is biased. Mutant alleles spreading in a gene family towards homogeneity is the same process of an advantageous allele spreading in a population towards fixation. Gene conversion also aids in creating genetic variation in some cases. Gene families, part of a hierarchy of information storage in a genome, play a large role in the evolution and diversity of multicellular organisms. Gene families are large units of information and genetic variability. Over evolutionary time, gene families have expanded and contracted with genes within
23547-539: The process such as transcription , RNA splicing , translation , and post-translational modification of a protein. Gene expression can be influenced by positive or negative regulation, depending on which of the two types of regulatory proteins called transcription factors bind to the DNA sequence close to or at a promoter. A cluster of genes that share the same promoter is called an operon , found mainly in prokaryotes and some lower eukaryotes (e.g., Caenorhabditis elegans ). In positive regulation of gene expression,
23714-517: The promoter, gene expression can also be regulated by epigenetic changes to chromatin , which is a complex of DNA and protein found in eukaryotic cells. Development is the process by which a multicellular organism (plant or animal) goes through a series of changes, starting from a single cell, and taking on various forms that are characteristic of its life cycle. There are four key processes that underlie development: Determination , differentiation , morphogenesis , and growth. Determination sets
23881-479: The protein product if they affect mRNA splicing. Mutations that occur in coding regions of the genome are more likely to alter the protein product, and can be categorized by their effect on amino acid sequence: A mutation becomes an effect on function mutation when the exactitude of functions between a mutated protein and its direct interactor undergoes change. The interactors can be other proteins, molecules, nucleic acids, etc. There are many mutations that fall under
24048-406: The proton motive force drives the enzyme ATP synthase to synthesize more ATPs by phosphorylating ADPs . The transfer of electrons terminates with molecular oxygen being the final electron acceptor . If oxygen were not present, pyruvate would not be metabolized by cellular respiration but undergoes a process of fermentation . The pyruvate is not transported into the mitochondrion but remains in
24215-411: The relative abundance of different types of mutations (i.e., strongly deleterious, nearly neutral or advantageous), is relevant to many evolutionary questions, such as the maintenance of genetic variation , the rate of genomic decay , the maintenance of outcrossing sexual reproduction as opposed to inbreeding and the evolution of sex and genetic recombination . DFE can also be tracked by tracking
24382-486: The remainder being either neutral or marginally beneficial. Mutation and DNA damage are the two major types of errors that occur in DNA, but they are fundamentally different. DNA damage is a physical alteration in the DNA structure, such as a single or double strand break, a modified guanosine residue in DNA such as 8-hydroxydeoxyguanosine , or a polycyclic aromatic hydrocarbon adduct. DNA damages can be recognized by enzymes, and therefore can be correctly repaired using
24549-430: The reproductive cells of an individual gives rise to a constitutional mutation in the offspring, that is, a mutation that is present in every cell. A constitutional mutation can also occur very soon after fertilization , or continue from a previous constitutional mutation in a parent. A germline mutation can be passed down through subsequent generations of organisms. The distinction between germline and somatic mutations
24716-683: The responsibility of establishing the standard or so-called "consensus" sequence. This step requires a tremendous scientific effort. Once the consensus sequence is known, the mutations in a genome can be pinpointed, described, and classified. The committee of the Human Genome Variation Society (HGVS) has developed the standard human sequence variant nomenclature, which should be used by researchers and DNA diagnostic centers to generate unambiguous mutation descriptions. In principle, this nomenclature can also be used to describe mutations in other organisms. The nomenclature specifies
24883-450: The sake of scientific experimentation. One 2017 study claimed that 66% of cancer-causing mutations are random, 29% are due to the environment (the studied population spanned 69 countries), and 5% are inherited. Humans on average pass 60 new mutations to their children but fathers pass more mutations depending on their age with every year adding two new mutations to a child. Spontaneous mutations occur with non-zero probability even given
25050-412: The same mutation. These types of mutations are usually prompted by environmental causes, such as ultraviolet radiation or any exposure to certain harmful chemicals, and can cause diseases including cancer. With plants, some somatic mutations can be propagated without the need for seed production, for example, by grafting and stem cuttings. These type of mutation have led to new types of fruits, such as
25217-449: The same time. Each pyruvate is then oxidized into acetyl-CoA by the pyruvate dehydrogenase complex , which also generates NADH and carbon dioxide. Acetyl-CoA enters the citric acid cycle, which takes places inside the mitochondrial matrix. At the end of the cycle, the total yield from 1 glucose (or 2 pyruvates) is 6 NADH, 2 FADH 2 , and 2 ATP molecules. Finally, the next stage is oxidative phosphorylation, which in eukaryotes, occurs in
25384-680: The second and third stages, respectively, provide the energy and electrons to drive the synthesis of glucose by fixing atmospheric carbon dioxide into existing organic carbon compounds, such as ribulose bisphosphate (RuBP) in a sequence of light-independent (or dark) reactions called the Calvin cycle . Cell signaling (or communication) is the ability of cells to receive, process, and transmit signals with its environment and with itself. Signals can be non-chemical such as light, electrical impulses , and heat, or chemical signals (or ligands ) that interact with receptors , which can be found embedded in
25551-654: The single-stranded human immunodeficiency virus ), replication occurs quickly, and there are no mechanisms to check the genome for accuracy. This error-prone process often results in mutations. The rate of de novo mutations, whether germline or somatic, vary among organisms. Individuals within the same species can even express varying rates of mutation. Overall, rates of de novo mutations are low compared to those of inherited mutations, which categorizes them as rare forms of genetic variation . Many observations of de novo mutation rates have associated higher rates of mutation correlated to paternal age. In sexually reproducing organisms,
25718-405: The skewness of the distribution of mutations with putatively severe effects as compared to the distribution of mutations with putatively mild or absent effect. In summary, the DFE plays an important role in predicting evolutionary dynamics . A variety of approaches have been used to study the DFE, including theoretical, experimental and analytical methods. One of the earliest theoretical studies of
25885-553: The skin. Their morphological, metabolic, and geographical diversity permits them to play multiple ecological roles: carbon fixation; nitrogen cycling; organic compound turnover; and maintaining microbial symbiotic and syntrophic communities, for example. Eukaryotes are hypothesized to have split from archaea, which was followed by their endosymbioses with bacteria (or symbiogenesis ) that gave rise to mitochondria and chloroplasts, both of which are now part of modern-day eukaryotic cells. The major lineages of eukaryotes diversified in
26052-479: The stroma. This is analogous to the proton-motive force generated across the inner mitochondrial membrane in aerobic respiration. During the third stage of photosynthesis, the movement of protons down their concentration gradients from the thylakoid lumen to the stroma through the ATP synthase is coupled to the synthesis of ATP by that same ATP synthase. The NADPH and ATPs generated by the light-dependent reactions in
26219-415: The structure of genes can be classified into several types. Large-scale mutations in chromosomal structure include: Small-scale mutations affect a gene in one or a few nucleotides. (If only a single nucleotide is affected, they are called point mutations .) Small-scale mutations include: The effect of a mutation on protein sequence depends in part on where in the genome it occurs, especially whether it
26386-571: The studied plant ( Arabidopsis thaliana )—more important genes mutate less frequently than less important ones. They demonstrated that mutation is "non-random in a way that benefits the plant". Additionally, previous experiments typically used to demonstrate mutations being random with respect to fitness (such as the Fluctuation Test and Replica plating ) have been shown to only support the weaker claim that those mutations are random with respect to external selective constraints, not fitness as
26553-423: The template strand. In mice , the majority of mutations are caused by translesion synthesis. Likewise, in yeast , Kunz et al. found that more than 60% of the spontaneous single base pair substitutions and deletions were caused by translesion synthesis. Although naturally occurring double-strand breaks occur at a relatively low frequency in DNA, their repair often causes mutation. Non-homologous end joining (NHEJ)
26720-471: The third tenet, and by the 1860s most biologists accepted all three tenets which consolidated into cell theory . Meanwhile, taxonomy and classification became the focus of natural historians. Carl Linnaeus published a basic taxonomy for the natural world in 1735, and in the 1750s introduced scientific names for all his species. Georges-Louis Leclerc, Comte de Buffon , treated species as artificial categories and living forms as malleable—even suggesting
26887-439: The total number of chromosomes is maintained. In general, mitosis (division of the nucleus) is preceded by the S stage of interphase (during which the DNA is replicated) and is often followed by telophase and cytokinesis ; which divides the cytoplasm , organelles and cell membrane of one cell into two new cells containing roughly equal shares of these cellular components. The different stages of mitosis all together define
27054-758: The type of mutation and base or amino acid changes. Mutation rates vary substantially across species, and the evolutionary forces that generally determine mutation are the subject of ongoing investigation. In humans , the mutation rate is about 50–90 de novo mutations per genome per generation, that is, each human accumulates about 50–90 novel mutations that were not present in his or her parents. This number has been established by sequencing thousands of human trios, that is, two parents and at least one child. The genomes of RNA viruses are based on RNA rather than DNA. The RNA viral genome can be double-stranded (as in DNA) or single-stranded. In some of these viruses (such as
27221-431: The underlying genotype of an organism with a dominant phenotype. A Punnett square can be used to predict the results of a test cross. The chromosome theory of inheritance , which states that genes are found on chromosomes, was supported by Thomas Morgans 's experiments with fruit flies , which established the sex linkage between eye color and sex in these insects. A gene is a unit of heredity that corresponds to
27388-656: The various forms of life, from prokaryotic organisms such as archaea and bacteria to eukaryotic organisms such as protists , fungi, plants, and animals. These various organisms contribute to the biodiversity of an ecosystem , where they play specialized roles in the cycling of nutrients and energy through their biophysical environment . The earliest of roots of science, which included medicine, can be traced to ancient Egypt and Mesopotamia in around 3000 to 1200 BCE . Their contributions shaped ancient Greek natural philosophy . Ancient Greek philosophers such as Aristotle (384–322 BCE) contributed extensively to
27555-449: The vast majority of novel mutations are neutral or deleterious and that advantageous mutations are rare, which has been supported by experimental results. One example is a study done on the DFE of random mutations in vesicular stomatitis virus . Out of all mutations, 39.6% were lethal, 31.2% were non-lethal deleterious, and 27.1% were neutral. Another example comes from a high throughput mutagenesis experiment with yeast. In this experiment it
27722-434: Was launched in 1990 to map the human genome . All organisms are made up of chemical elements ; oxygen , carbon , hydrogen , and nitrogen account for most (96%) of the mass of all organisms, with calcium , phosphorus , sulfur , sodium , chlorine , and magnesium constituting essentially all the remainder. Different elements can combine to form compounds such as water, which is fundamental to life. Biochemistry
27889-431: Was shown that the overall DFE is bimodal, with a cluster of neutral mutations, and a broad distribution of deleterious mutations. Though relatively few mutations are advantageous, those that are play an important role in evolutionary changes. Like neutral mutations, weakly selected advantageous mutations can be lost due to random genetic drift, but strongly selected advantageous mutations are more likely to be fixed. Knowing
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