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158-531: RuBisCO is important biologically because it catalyzes the primary chemical reaction by which inorganic carbon enters the biosphere . While many autotrophic bacteria and archaea fix carbon via the reductive acetyl CoA pathway , the 3-hydroxypropionate cycle , or the reverse Krebs cycle , these pathways are relatively small contributors to global carbon fixation compared to that catalyzed by RuBisCO. Phosphoenolpyruvate carboxylase , unlike RuBisCO, only temporarily fixes carbon. Reflecting its importance, RuBisCO

316-428: A C=C−OH connectivity. Deprotonation of organic carbonyls gives the enolate anion , which are a strong nucleophile . A classic example for favoring the keto form can be seen in the equilibrium between vinyl alcohol and acetaldehyde (K = [enol]/[keto] ≈ 3 × 10 ). In 1,3-diketones , such as acetylacetone (2,4-pentanedione), the enol form is favored. The acid-catalyzed conversion of an enol to

474-450: A gem-diol intermediate. Carboxylation and hydration have been proposed as either a single concerted step or as two sequential steps. Concerted mechanism is supported by the proximity of the water molecule to C3 of RuBP in multiple crystal structures. Within the spinach structure, other residues are well placed to aid in the hydration step as they are within hydrogen bonding distance of the water molecule. The gem-diol intermediate cleaves at

632-535: 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

790-440: 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

948-443: 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

1106-508: 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

1264-474: 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

1422-408: 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

1580-443: A compromise between specificity and reaction rate. It has been also suggested that the oxygenase reaction of RuBisCO prevents CO 2 depletion near its active sites and provides the maintenance of the chloroplast redox state. Since photosynthesis is the single most effective natural regulator of carbon dioxide in the Earth's atmosphere , a biochemical model of RuBisCO reaction is used as the core module of climate change models. Thus,

1738-403: A correct model of this reaction is essential to the basic understanding of the relations and interactions of environmental models. There currently are very few effective methods for expressing functional plant Rubisco in bacterial hosts for genetic manipulation studies. This is largely due to Rubisco's requirement of complex cellular machinery for its biogenesis and metabolic maintenance including

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1896-491: A diversity of plant lineages, ancestral C 3 -type RuBisCO evolved to have faster turnover of CO 2 in exchange for lower specificity as a result of the greater localization of CO 2 from the mesophyll cells into the bundle sheath cells . This was achieved through enhancement of conformational flexibility of the “open-closed” transition in the Calvin cycle . Laboratory-based phylogenetic studies have shown that this evolution

2054-417: A favorable environment for the binding of Mg . Formation of the carbamate is favored by an alkaline pH . The pH and the concentration of magnesium ions in the fluid compartment (in plants, the stroma of the chloroplast ) increases in the light. The role of changing pH and magnesium ion levels in the regulation of RuBisCO enzyme activity is discussed below . Once the carbamate is formed, His335 finalizes

2212-1233: 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

2370-403: 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

2528-404: A high optimal pH (can be >9.0, depending on the magnesium ion concentration) and, thus, becomes "activated" by the introduction of carbon dioxide and magnesium to the active sites as described above. In plants and some algae, another enzyme, RuBisCO activase (Rca, GO:0046863 , P10896 ), is required to allow the rapid formation of the critical carbamate in the active site of RuBisCO. This

2686-418: A higher affinity for CO 2 . The process first makes a 4-carbon intermediate compound, hence the name C 4 plants, which is shuttled into a site of C 3 photosynthesis then decarboxylated, releasing CO 2 to boost the concentration of CO 2 . Crassulacean acid metabolism (CAM) plants keep their stomata closed during the day, which conserves water but prevents the light-independent reactions (a.k.a.

2844-430: 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 . Keto-enol tautomerism In organic chemistry , enols are

3002-456: A hydroxyl group on each carbon of the C=C double bond. Normally such compounds are disfavored components in equilibria with acyloins . One special case is catechol , where the C=C subunit is part of an aromatic ring. In some other cases however, enediols are stabilized by flanking carbonyl groups. These stabilized enediols are called reductones . Such species are important in glycochemistry, e.g.,

3160-769: 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

3318-417: 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

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3476-457: 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

3634-409: 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

3792-408: 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

3950-541: 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

4108-436: 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

4266-400: A similar way to how RuBisCO activase functions in higher plants. Since carbon dioxide and oxygen compete at the active site of RuBisCO, carbon fixation by RuBisCO can be enhanced by increasing the carbon dioxide level in the compartment containing RuBisCO ( chloroplast stroma ). Several times during the evolution of plants, mechanisms have evolved for increasing the level of carbon dioxide in

4424-423: 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

4582-446: 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

4740-446: A strategy to increase crop yields. Approaches under investigation include transferring RuBisCO genes from one organism into another organism, engineering Rubisco activase from thermophilic cyanobacteria into temperature sensitive plants, increasing the level of expression of RuBisCO subunits, expressing RuBisCO small chains from the chloroplast DNA , and altering RuBisCO genes to increase specificity for carbon dioxide or otherwise increase

4898-454: A type of Functional group or intermediate in organic chemistry containing a group with the formula C=C(OH) (R = many substituents). The term enol is an abbreviation of alkenol , a portmanteau deriving from "-ene"/"alkene" and the "-ol". Many kinds of enols are known. Keto–enol tautomerism refers to a chemical equilibrium between a "keto" form (a carbonyl , named for the common ketone case) and an enol. The interconversion of

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5056-399: 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

5214-421: 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

5372-492: 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,

5530-536: 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

5688-553: Is nucleophilic . Its reactions with electrophilic organic compounds is important in biochemistry as well as synthetic organic chemistry . In the former area, the fixation of carbon dioxide involves addition of CO 2 to an enol. Deprotonation of enolizable ketones, aldehydes, and esters gives enolates . Enolates can be trapped by the addition of electrophiles at oxygen. Silylation gives silyl enol ether . Acylation gives esters such as vinyl acetate . In general, enols are less stable than their keto equivalents because of

5846-420: Is "trapped" in the less thermodynamically favorable enol form, whereas after dephosphorylation it can assume the keto form. The enzyme enolase catalyzes the dehydration of 2-phosphoglyceric acid to the enol phosphate ester. Metabolism of PEP to pyruvic acid by pyruvate kinase (PK) generates adenosine triphosphate (ATP) via substrate-level phosphorylation . The terminus of the double bond in enols

6004-444: 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

6162-641: 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,

6320-480: 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

6478-918: 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

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6636-403: 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

6794-430: Is inhibited (or protected from hydrolysis) by a competitive inhibitor synthesized by these plants, a substrate analog 2-carboxy-D-arabitinol 1-phosphate (CA1P). CA1P binds tightly to the active site of carbamylated RuBisCO and inhibits catalytic activity to an even greater extent. CA1P has also been shown to keep RuBisCO in a conformation that is protected from proteolysis . In the light, RuBisCO activase also promotes

6952-471: Is inhibited by the presence of ADP , and, thus, activase activity depends on the ratio of these compounds in the chloroplast stroma. Furthermore, in most plants, the sensitivity of activase to the ratio of ATP/ADP is modified by the stromal reduction/oxidation ( redox ) state through another small regulatory protein, thioredoxin . In this manner, the activity of activase and the activation state of RuBisCO can be modulated in response to light intensity and, thus,

7110-441: 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

7268-535: 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

7426-526: 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

7584-399: 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

7742-407: 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

7900-399: 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

8058-412: 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

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8216-426: Is required because ribulose 1,5-bisphosphate (RuBP) binds more strongly to the active sites of RuBisCO when excess carbamate is present, preventing processes from moving forward. In the light, RuBisCO activase promotes the release of the inhibitory (or — in some views — storage) RuBP from the catalytic sites of RuBisCO. Activase is also required in some plants (e.g., tobacco and many beans) because, in darkness, RuBisCO

8374-485: Is should all be in lower case (rubisco), similar to other terms like scuba or laser. 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

8532-471: Is slow, fixing only 3-10 carbon dioxide molecules each second per molecule of enzyme. The reaction catalyzed by RuBisCO is, thus, the primary rate-limiting factor of the Calvin cycle during the day. Nevertheless, under most conditions, and when light is not otherwise limiting photosynthesis, the speed of RuBisCO responds positively to increasing carbon dioxide concentration. RuBisCO is usually only active during

8690-472: Is the most abundant protein in leaves , accounting for 50% of soluble leaf protein in C 3 plants (20–30% of total leaf nitrogen) and 30% of soluble leaf protein in C 4 plants (5–9% of total leaf nitrogen). Given its important role in the biosphere, the genetic engineering of RuBisCO in crops is of continuing interest (see below ). In plants, algae , cyanobacteria , and phototrophic and chemoautotrophic Pseudomonadota (formerly proteobacteria),

8848-468: 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

9006-485: 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,

9164-410: 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

9322-476: Is the substrate, the products of the oxygenase reaction are phosphoglycolate and 3-phosphoglycerate. Phosphoglycolate is recycled through a sequence of reactions called photorespiration , which involves enzymes and cytochromes located in the mitochondria and peroxisomes (this is a case of metabolite repair ). In this process, two molecules of phosphoglycolate are converted to one molecule of carbon dioxide and one molecule of 3-phosphoglycerate, which can reenter

9480-493: 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

9638-546: The Calvin Cycle ) from taking place, since these reactions require CO 2 to pass by gas exchange through these openings. Evaporation through the upper side of a leaf is prevented by a layer of wax . Since RuBisCO is often rate-limiting for photosynthesis in plants, it may be possible to improve photosynthetic efficiency by modifying RuBisCO genes in plants to increase catalytic activity and/or decrease oxygenation rates. This could improve sequestration of CO 2 and be

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9796-644: 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

9954-495: 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

10112-497: The Lobry de Bruyn-van Ekenstein transformation . Ribulose-1,5-bisphosphate is a key substrate in the Calvin cycle of photosynthesis . In the Calvin cycle, the ribulose equilibrates with the enediol, which then binds carbon dioxide . The same enediol is also susceptible to attack by oxygen (O 2 ) in the (undesirable) process called photorespiration . Phenols represent a kind of enol. For some phenols and related compounds,

10270-535: 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

10428-492: 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

10586-727: 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

10744-515: The active site of the enzyme involves addition of an "activating" carbon dioxide molecule ( CO 2 ) to a lysine in the active site (forming a carbamate ). Mg operates by driving deprotonation of the Lys210 residue, causing the Lys residue to rotate by 120 degrees to the trans conformer, decreasing the distance between the nitrogen of Lys and the carbon of CO 2 . The close proximity allows for

10902-592: 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

11060-404: 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

11218-403: 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,

11376-416: 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

11534-597: The cytosol by crossing the outer chloroplast membrane . The enzymatically active substrate ( ribulose 1,5-bisphosphate) binding sites are located in the large chains that form dimers in which amino acids from each large chain contribute to the binding sites. A total of eight large chains (= four dimers) and eight small chains assemble into a larger complex of about 540,000 Da. In some Pseudomonadota and dinoflagellates , enzymes consisting of only large subunits have been found. Magnesium ions ( Mg ) are needed for enzymatic activity. Correct positioning of Mg in

11692-528: 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

11850-481: 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

12008-403: 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

12166-420: The methionine salvage pathway . Later identifications found functionally divergent examples dispersed all over bacteria and archaea, as well as transitionary enzymes performing both RLP-type enolase and RuBisCO functions. It is now believed that the current RuBisCO evolved from a dimeric RLP ancestor, acquiring its carboxylase function first before further oligomerizing and then recruiting the small subunit to form

12324-423: 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

12482-412: 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

12640-546: 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

12798-497: 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

12956-423: The thylakoid membrane. The movement of protons into thylakoids is driven by light and is fundamental to ATP synthesis in chloroplasts (Further reading: Photosynthetic reaction centre ; Light-dependent reactions ) . To balance ion potential across the membrane, magnesium ions ( Mg ) move out of the thylakoids in response, increasing the concentration of magnesium in the stroma of the chloroplasts. RuBisCO has

13114-403: The "activating" carbon dioxide). RuBisCO also catalyses a reaction of ribulose-1,5-bisphosphate and molecular oxygen (O 2 ) instead of carbon dioxide (CO 2 ). Discriminating between the substrates CO 2 and O 2 is attributed to the differing interactions of the substrate's quadrupole moments and a high electrostatic field gradient . This gradient is established by the dimer form of

13272-421: The C 3 cycle was shown to be possible, and it was first achieved in 2019 through a synthetic biology approach. One avenue is to introduce RuBisCO variants with naturally high specificity values such as the ones from the red alga Galdieria partita into plants. This may improve the photosynthetic efficiency of crop plants, although possible negative impacts have yet to be studied. Advances in this area include

13430-734: The C2-C3 bond to form one molecule of glycerate-3-phosphate and a negatively charged carboxylate. Stereo specific protonation of C2 of this carbanion results in another molecule of glycerate-3-phosphate. This step is thought to be facilitated by Lys175 or potentially the carbamylated Lys210. When carbon dioxide is the substrate, the product of the carboxylase reaction is an unstable six-carbon phosphorylated intermediate known as 3-keto-2-carboxyarabinitol-1,5-bisphosphate, which decays rapidly into two molecules of glycerate-3-phosphate . This product, also known as 3-phosphoglycerate, can be used to produce larger molecules such as glucose . When molecular oxygen

13588-549: The C3 carbon of RuBP to form a 2,3-enediolate. Carboxylation of the 2,3-enediolate results in the intermediate 3-keto-2-carboxyarabinitol-1,5-bisphosphate and Lys334 is positioned to facilitate the addition of the CO 2 substrate as it replaces the third Mg -coordinated water molecule and add directly to the enediol. No Michaelis complex is formed in this process. Hydration of this ketone results in an additional hydroxy group on C3, forming

13746-535: The Calvin cycle. Some of the phosphoglycolate entering this pathway can be retained by plants to produce other molecules such as glycine . At ambient levels of carbon dioxide and oxygen, the ratio of the reactions is about 4 to 1, which results in a net carbon dioxide fixation of only 3.5. Thus, the inability of the enzyme to prevent the reaction with oxygen greatly reduces the photosynthetic capacity of many plants. Some plants, many algae, and photosynthetic bacteria have overcome this limitation by devising means to increase

13904-481: 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

14062-696: 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,

14220-579: The activation by returning to its initial position through thermal fluctuation. RuBisCO is one of many enzymes in the Calvin cycle . When Rubisco facilitates the attack of CO 2 at the C2 carbon of RuBP and subsequent bond cleavage between the C3 and C2 carbon, 2 molecules of glycerate-3-phosphate are formed. The conversion involves these steps: enolisation , carboxylation , hydration , C-C bond cleavage, and protonation . Substrates for RuBisCO are ribulose-1,5-bisphosphate and carbon dioxide (distinct from

14378-589: 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

14536-450: 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

14694-410: 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

14852-433: 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

15010-686: The concentration of carbon dioxide around the enzyme, including C 4 carbon fixation , crassulacean acid metabolism , and the use of pyrenoid . Rubisco side activities can lead to useless or inhibitory by-products. Important inhibitory by-products include xylulose 1,5-bisphosphate and glycero-2,3-pentodiulose 1,5-bisphosphate , both caused by "misfires" halfway in the enolisation-carboxylation reaction. In higher plants, this process causes RuBisCO self-inhibition, which can be triggered by saturating CO 2 and RuBP concentrations and solved by Rubisco activase (see below). Some enzymes can carry out thousands of chemical reactions each second. However, RuBisCO

15168-417: The conversion is called a keto-enol tautomerism, although this name is often more generally applied to all such tautomerizations. Usually the equilibrium constant is so small that the enol is undetectable spectroscopically. In some compounds with two (or more) carbonyls, the enol form becomes dominant. The behavior of 2,4-pentanedione illustrates this effect: Enols are derivatives of vinyl alcohol , with

15326-501: 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

15484-455: 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

15642-427: The day, as ribulose 1,5-bisphosphate is not regenerated in the dark. This is due to the regulation of several other enzymes in the Calvin cycle. In addition, the activity of RuBisCO is coordinated with that of the other enzymes of the Calvin cycle in several other ways: Upon illumination of the chloroplasts, the pH of the stroma rises from 7.0 to 8.0 because of the proton (hydrogen ion, H ) gradient created across

15800-677: 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

15958-418: 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

16116-440: 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

16274-411: 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

16432-420: 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

16590-634: 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

16748-503: The enzyme must be closed off, allowing the active site to be isolated from the solvent and lowering the dielectric constant . This isolation has a significant entropic cost, and results in the poor turnover rate. Carbamylation of the ε-amino group of Lys210 is stabilized by coordination with the Mg . This reaction involves binding of the carboxylate termini of Asp203 and Glu204 to the Mg ion. The substrate RuBP binds Mg displacing two of

16906-404: The enzyme usually consists of two types of protein subunit, called the large chain ( L , about 55,000 Da ) and the small chain ( S , about 13,000 Da). The large-chain gene ( rbcL ) is encoded by the chloroplast DNA in plants. There are typically several related small-chain genes in the nucleus of plant cells, and the small chains are imported to the stromal compartment of chloroplasts from

17064-481: 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

17222-499: The familiar modern enzyme. The small subunit probably first evolved in anaerobic and thermophilic organisms, where it enabled RuBisCO to catalyze its reaction at higher temperatures. In addition to its effect on stabilizing catalysis, it enabled the evolution of higher specificities for CO 2 over O 2 by modulating the effect that substitutions within RuBisCO have on enzymatic function. Substitutions that do not have an effect without

17380-472: The favorability of the C=O double bond over C=C double bond. However, enols can be stabilized kinetically or thermodynamically. Some enols are sufficiently stabilized kinetically so that they can be characterized. Delocalization can stabilize the enol tautomer. Thus, very stable enols are phenols . Another stabilizing factor in 1,3-dicarbonyls is intramolecular hydrogen bonding. Both of these factors influence

17538-455: 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

17696-474: The formation of a covalent bond, resulting in the carbamate. Mg is first enabled to bind to the active site by the rotation of His335 to an alternate conformation. Mg is then coordinated by the His residues of the active site (His300, His302, His335), and is partially neutralized by the coordination of three water molecules and their conversion to OH. This coordination results in an unstable complex, but produces

17854-426: 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

18012-414: 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

18170-494: The keto form proceeds by proton transfer from O to carbon. The process does not occur intramolecularly, but requires participation of solvent or other mediators. If R and R (note equation at top of page) are different substituents, there is a new stereocenter formed at the alpha position when an enol converts to its keto form. Depending on the nature of the three R groups, the resulting products in this situation would be diastereomers or enantiomers . Enediols are alkenes with

18328-421: The keto tautomer plays an important role. Many of the reactions of resorcinol involve the keto tautomer, for example. Naphthalene-1,4-diol exists in observable equilibrium with the diketone tetrahydronaphthalene-1,4-dione. Keto–enol tautomerism is important in several areas of biochemistry . The high phosphate-transfer potential of phosphoenolpyruvate results from the fact that the phosphorylated compound

18486-406: The large subunit of RuBisCO has been widely used as an appropriate locus for analysis of phylogenetics in plant taxonomy . Non-carbon-fixing proteins similar to RuBisCO, termed RuBisCO-like proteins (RLPs), are also found in the wild in organisms as common as Bacillus subtilis . This bacterium has a rbcL-like protein with a 2,3-diketo-5-methylthiopentyl-1-phosphate enolase function, part of

18644-406: 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

18802-405: 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

18960-444: 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

19118-525: The minimally active RuBisCO, which with its two components provides a combination of oppositely charged domains required for the enzyme's interaction with O 2 and CO 2 . These conditions help explain the low turnover rate found in RuBisCO: In order to increase the strength of the electric field necessary for sufficient interaction with the substrates’ quadrupole moments , the C- and N- terminal segments of

19276-403: 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

19434-437: 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

19592-499: The mutant plants grew more slowly than wild-type. A recent theory explores the trade-off between the relative specificity (i.e., ability to favour CO 2 fixation over O 2 incorporation, which leads to the energy-wasteful process of photorespiration ) and the rate at which product is formed. The authors conclude that RuBisCO may actually have evolved to reach a point of 'near-perfection' in many plants (with widely varying substrate availabilities and environmental conditions), reaching

19750-403: 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

19908-463: The newly-evolved enzyme was found to have further developed a series of stabilizing mutations. While RuBisCO has always been accumulating new mutations, most of these mutations that have survived have not had significant effects on protein stability. The destabilizing C 4 mutations on RuBisCO has been sustained by environmental pressures such as low CO 2 concentrations, requiring a sacrifice of stability for new adaptive functions. The term "RuBisCO"

20066-460: The nuclear-encoded RbcS subunits, which are typically imported into chloroplasts as unfolded proteins. Furthermore, sufficient expression and interaction with Rubisco activase are major challenges as well. One successful method for expression of Rubisco in E. coli involves the co-expression of multiple chloroplast chaperones, though this has only been shown for Arabidopsis thaliana Rubisco. Due to its high abundance in plants (generally 40% of

20224-441: 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,

20382-517: 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

20540-404: 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

20698-428: 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

20856-907: 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

21014-539: 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,

21172-517: 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

21330-406: 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

21488-402: The rate of carbon fixation. In general, site-directed mutagenesis of RuBisCO has been mostly unsuccessful, though mutated forms of the protein have been achieved in tobacco plants with subunit C 4 species, and a RuBisCO with more C 4 -like kinetic characteristics have been attained in rice via nuclear transformation. Robust and reliable engineering for yield of RuBisCO and other enzymes in

21646-487: The rate of formation of the ribulose 1,5-bisphosphate substrate. In cyanobacteria, inorganic phosphate (P i ) also participates in the co-ordinated regulation of photosynthesis: P i binds to the RuBisCO active site and to another site on the large chain where it can influence transitions between activated and less active conformations of the enzyme. In this way, activation of bacterial RuBisCO might be particularly sensitive to P i levels, which might cause it to act in

21804-448: The ratio of O 2 to CO 2 available to RuBisCO shifts too far towards oxygen. This phenomenon is primarily temperature-dependent: high temperatures can decrease the concentration of CO 2 dissolved in the moisture of leaf tissues. This phenomenon is also related to water stress : since plant leaves are evaporatively cooled, limited water causes high leaf temperatures. C 4 plants use the enzyme PEP carboxylase initially, which has

21962-486: The release of CA1P from the catalytic sites. After the CA1P is released from RuBisCO, it is rapidly converted to a non-inhibitory form by a light-activated CA1P-phosphatase . Even without these strong inhibitors, once every several hundred reactions, the normal reactions with carbon dioxide or oxygen are not completed; other inhibitory substrate analogs are still formed in the active site. Once again, RuBisCO activase can promote

22120-438: The release of these analogs from the catalytic sites and maintain the enzyme in a catalytically active form. However, at high temperatures, RuBisCO activase aggregates and can no longer activate RuBisCO. This contributes to the decreased carboxylating capacity observed during heat stress. The removal of the inhibitory RuBP, CA1P, and the other inhibitory substrate analogs by activase requires the consumption of ATP . This reaction

22278-631: The replacement of the tobacco enzyme with that of the purple photosynthetic bacterium Rhodospirillum rubrum . In 2014, two transplastomic tobacco lines with functional RuBisCO from the cyanobacterium Synechococcus elongatus PCC7942 (Se7942) were created by replacing the RuBisCO with the large and small subunit genes of the Se7942 enzyme, in combination with either the corresponding Se7942 assembly chaperone, RbcX, or an internal carboxysomal protein, CcmM35. Both mutants had increased CO 2 fixation rates when measured as carbon molecules per RuBisCO. However,

22436-449: 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

22594-628: 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

22752-553: 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

22910-399: The small subunit suddenly become beneficial when it is bound. Furthermore, the small subunit enabled the accumulation of substitutions that are only tolerated in its presence. Accumulation of such substitutions leads to a strict dependence on the small subunit, which is observed in extant Rubiscos that bind a small subunit. With the mass convergent evolution of the C 4 -fixation pathway in

23068-402: The stroma (see C 4 carbon fixation ). The use of oxygen as a substrate appears to be a puzzling process, since it seems to throw away captured energy. However, it may be a mechanism for preventing carbohydrate overload during periods of high light flux. This weakness in the enzyme is the cause of photorespiration , such that healthy leaves in bright light may have zero net carbon fixation when

23226-479: 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

23384-471: 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

23542-458: The three aquo ligands. Enolisation of RuBP is the conversion of the keto tautomer of RuBP to an enediol(ate). Enolisation is initiated by deprotonation at C3. The enzyme base in this step has been debated, but the steric constraints observed in crystal structures have made Lys210 the most likely candidate. Specifically, the carbamate oxygen on Lys210 that is not coordinated with the Mg ion deprotonates

23700-439: 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

23858-467: The total protein content), RuBisCO often impedes analysis of important signaling proteins such as transcription factors , kinases , and regulatory proteins found in lower abundance (10-100 molecules per cell) within plants. For example, using mass spectrometry on plant protein mixtures would result in multiple intense RuBisCO subunit peaks that interfere and hide those of other proteins. Recently, one efficient method for precipitating out RuBisCO involves

24016-400: The two forms involves the transfer of an alpha hydrogen atom and the reorganisation of bonding electrons . The keto and enol forms are tautomers of each other. Organic esters , ketones , and aldehydes with an α-hydrogen ( C−H bond adjacent to the carbonyl group ) often form enols. The reaction involves migration of a proton ( H ) from carbon to oxygen: In the case of ketones,

24174-431: 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

24332-451: The usage of protamine sulfate solution. Other existing methods for depleting RuBisCO and studying lower abundance proteins include fractionation techniques with calcium and phytate, gel electrophoresis with polyethylene glycol, affinity chromatography , and aggregation using DTT , though these methods are more time-consuming and less efficient when compared to protamine sulfate precipitation. The chloroplast gene rbcL , which codes for

24490-656: 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

24648-506: Was coined humorously in 1979, by David Eisenberg at a seminar honouring the retirement of the early, prominent RuBisCO researcher, Sam Wildman , and also alluded to the snack food trade name " Nabisco " in reference to Wildman's attempts to create an edible protein supplement from tobacco leaves. The capitalization of the name has been long debated. It can be capitalized for each letter of the full name ( R ib u lose-1,5 bis phosphate c arboxylase/ o xygenase), but it has also been argued that

24806-439: Was constrained by the trade-off between stability and activity brought about by the series of necessary mutations for C 4 RuBisCO. Moreover, in order to sustain the destabilizing mutations, the evolution to C 4 RuBisCO was preceded by a period in which mutations granted the enzyme increased stability, establishing a buffer to sustain and maintain the mutations required for C 4 RuBisCO. To assist with this buffering process,

24964-434: 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

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