Biofelsefe — Biolojik Terimler
NFA 2020 / Aziz Yardımlı

 

Biofelsefe — Terimler / BİOLOJİ


  • “Bilim Felsefesi” adlandırması “bilim bilgelik-sevgisi” demektir ve saçmadır.
  • Sevgi bir duygu sorunudur; Bilgi bir düşünce sorunudur.
  • Pozitivistler ne duyguyu düşündüler ne de düşünceyi duyumsadılar.
  • Bilim bilgiyi amaçlar. Felsefe de bilgiyi amaçlar.
  • Bilgi evrensellerin bilgisi ya da kavramsal bilgidir.
  • Bilim ussal-kavramsal realitenin insan bilincinde üretilen ussal-kavramsal idealitesidir.
Doğan bilgisi Doğanın ussal-kavramsal yapısının bilgisidir. İnsan usunun kendisi kavramsal bir dizgedir ve Bilim insan usunun Doğada kendini bulmasını amaçlar. Bilimsel etkinliği içindeki doğal usun olağan yöntemi tümevarım, tümdengelim, çıkarsama, sınıflandırma, andırım, sınama, deneme vb. gibi araçlar yoluyla Doğada kendini aramaktır. Bilim için deneyime, realiteye dayanmak gerekir demek gereksizdir, çünkü aranan şey deneyimin, realitenin kendisinin bilgisidir. Realitenin bilgisi realiteye borçludur, tıpkı yeme ediminin besine borçlu olması gibi.

Realite olarak realite ilkin soyut boş bir kavramdır. Ama realite belirlidir ve realitenin belirli biçimi kavramsaldır. Realite ya da deneyim ya da olgu ya da fenomen ya da gözlem ussal kavramlar tarafından biçimlendirilir. Biçim belirlenimdir. Sorun insan usunun kavramlarınınn kendinde realite ile bağdaşmasını sağlamaktır. Bilim insan usunun kavramlarının realitenin ussal biçimi ile birliğinin olanağı üzerine dayanır.

Bilim ya da Realitenin Bilgisi oluştadır. Ve Bilimin oluşu ereksel gelişim sürecidir. Bu yolda bilinç kendi yöntemlerini kullanarak nesnesini sürekli olarak değişim durumunda tutar, ona sürekli olarak değişen kavramsal biçimler yükler. Dogmatizm bu aşamalı gelişim sürecini herhangi bir kıpısında dondurmak demektir. Kuşku dolaysızca bulunanı olumsuzlama ve sorgulamadır ve bilimsel sürecin her kıpısı dayanıksızdır ve sorgulanmalıdır. Süreç bilim değil, bilimin oluş kipidir.
allele
archaea
axon
cell
cell biology
cell cycle
chromosome
Darwinism
Darwinism, the eclipse of
emergence
eukaryote
extremophile
extremotroph
gene
genome
homeostasis
karyotype
Lamarckism
metabolome
micelle
microorganism
metaboleme
metabolism
microbiota
mitochondrion
mutation
neural circuit
neuron
organelle
organic matter
organism
phenotype
phospholipid
phototroph
prokaryote
protist
protocell
replication, DNA
ribosome
ribozyme
species
symbiogenesis
synapse
three-domain system
translation
___
___
___
___
SİTE İÇİ ARAMA       
 
 
 
 
 


A reworked version of File:Biological_cell.svg. Diagram of a typical animal cell. Organelles are labelled as follows: Nucleolus Nucleus Ribosomes (dots on rough reticulum walls) Vesicle Rough endoplasmic reticulum Golgi apparatus (or "Golgi body") Cytoskeleton Smooth endoplasmic reticulum Mitochondrion Vacuole Cytosol Lysosome Centriole Cell membrane.
Components of a typical animal cell:
  1. Nucleolus
  2. Nucleus
  3. Ribosome (little dots)
  4. Vesicle
  5. Rough endoplasmic reticulum
  6. Golgi apparatus (or, Golgi body)
  7. Cytoskeleton
  8. Smooth endoplasmic reticulum
  9. Mitochondrion
  10. Vacuole
  11. Cytosol (fluid that contains organelles, comprising the cytoplasm)
  12. Lysosome
  13. Centrosome
  14. Cell membrane
 
 
 
a

archaea

Archaea  (singular archaeon) constitute a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), but this classification is obsolete. (W)

📂 Archaea

Archaea (W)

Archaea  (singular archaeon) constitute a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), but this classification is obsolete.

Archaeal cells have unique properties separating them from the other two domains, Bacteria and Eukaryota. Archaea are further divided into multiple recognized phyla. Classification is difficult because most have not been isolated in the laboratory and have been detected only by analysis of their nucleic acids in samples from their environment.

Archaea and bacteria are generally similar in size and shape, although 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 detection tools led to 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 microbiota, they are important in the gut, mouth, and on 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.

No clear examples of archaeal pathogens or parasites are known. Instead they are often mutualists or commensals, such as the methanogens (methane-producing strains) that inhabit the gastrointestinal tract in humans and ruminants, where their vast numbers aid digestion. Methanogens are also used in biogas production and sewage treatment, and biotechnology exploits enzymes from extremophile archaea that can endure high temperatures and organic solvents.



Archaea were found in volcanic hot springs. Pictured here is Grand Prismatic Spring of Yellowstone National Park.


The ARMAN are a group of archaea recently discovered in acid mine drainage.

 





Cluster of cells of Halobacterium sp. strain NRC-1.



allele

An allele (from Greek ἄλλος állos, "other") is a variant form of a given gene, meaning it is one of two or more versions of a known mutation at the same place on a chromosome. It can also refer to different sequence variations for a several-hundred base-pair or more region of the genome that codes for a protein. Alleles can come in different extremes of size. At the lowest possible end one can be the single base choice of a single nucleotide polymorphism (SNP). At the higher end, it can be the sequence variations for the regions of the genome that code for the same protein which can be up to several thousand base-pairs long.


Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation. A notable example of this trait of color variation is Gregor Mendel's discovery that the white and purple flower colors in pea plants were the result of "pure line" traits which could be used as a control for future experiments. However, most alleles result in little or no observable phenotypic variation.

Most multicellular organisms have two sets of chromosomes; that is, they are diploid. In this case, the chromosomes can be paired: each pair is a set of homologous chromosomes. If both alleles of a gene at the locus on the homologous chromosomes are the same, they and the organism are homozygous with respect to that gene. If the alleles are different, they and the organism are heterozygous with respect to that gene An (W)



axon

An axon (from Greek ἄξων áxōn, axis), or nerve fiber (or nerve fibre: see spelling differences), is a long, slender projection of a nerve cell, or neuron, in vertebrates, that typically conducts electrical impulses known as action potentials away from the nerve cell body. The function of the axon is to transmit information to different neurons, muscles, and glands. In certain sensory neurons (pseudounipolar neurons), such as those for touch and warmth, the axons are called afferent nerve fibers and the electrical impulse travels along these from the periphery to the cell body, and from the cell body to the spinal cord along another branch of the same axon. Axon dysfunction has caused many inherited and acquired neurological disorders which can affect both the peripheral and central neurons. Nerve fibers are classed into three types – group A nerve fibersgroup B nerve fibers, and group C nerve fibers. Groups A and B are myelinated, and group C are unmyelinated. These groups include both sensory fibers and motor fibers. Another classification groups only the sensory fibers as Type I, Type II, Type III, and Type IV.

An axon is one of two types of cytoplasmic protrusions from the cell body of a neuron; the other type is a dendrite. Axons are distinguished from dendrites by several features, including shape (dendrites often taper while axons usually maintain a constant radius), length (dendrites are restricted to a small region around the cell body while axons can be much longer), and function (dendrites receive signals whereas axons transmit them). Some types of neurons have no axon and transmit signals from their dendrites. In some species, axons can emanate from dendrites known as axon-carrying dendrites. No neuron ever has more than one axon; however in invertebrates such as insects or leeches the axon sometimes consists of several regions that function more or less independently of each other.


Axons are covered by a membrane known as an axolemma; the cytoplasm of an axon is called axoplasm. Most axons branch, in some cases very profusely. The end branches of an axon are called telodendria. The swollen end of a telodendron is known as the axon terminal which joins the dendron or cell body of another neuron forming a synaptic connection. Axons make contact with other cells—usually other neurons but sometimes muscle or gland cells—at junctions called synapses. In some circumstances, the axon of one neuron may form a synapse with the dendrites of the same neuron, resulting in an autapse. At a synapse, the membrane of the axon closely adjoins the membrane of the target cell, and special molecular structures serve to transmit electrical or electrochemical signals across the gap. Some synaptic junctions appear along the length of an axon as it extends—these are called en passant ("in passing") synapses and can be in the hundreds or even the thousands along one axon.  Other synapses appear as terminals at the ends of axonal branches.

A single axon, with all its branches taken together, can innervate multiple parts of the brain and generate thousands of synaptic terminals. A bundle of axons make a nerve tract in the central nervous system, and a fascicle in the peripheral nervous system. In placental mammals the largest white matter tract in the brain is the corpus callosum, formed of some 200 million axons in the human brain. (w)



Multipolar Neuron.



Detail showing microtubules at axon hillock and initial segment.

 




c
cell

The cell (Latin cella, meaning "small room") is the basic structural, functional, and biological unit of all known organisms. A cell is the smallest unit of life. Cells are often called the "building blocks of life". The study of cells is called cell biology, cellular biology, or cytology. (W)

📂Cell

Cell (W)

The cell (from Latin cella, meaning "small room") is the basic structural, functional, and biological unit of all known organisms. A cell is the smallest unit of life. Cells are often called the "building blocks of life". The study of cells is called cell biology, cellular biology, or cytology.

Cells consist of cytoplasm enclosed within a membrane, which contains many biomolecules such as proteins and nucleic acids. Most plant and animal cells are only visible under a microscope, with dimensions between 1 and 100 micrometres. Organisms can be classified as unicellular (consisting of a single cell such as bacteria) or multicellular (including plants and animals). Most unicellular organisms are classed as microorganisms.

The number of cells in plants and animals varies from species to species; it has been estimated that humans contain somewhere around 40 trillion (4×1013) cells. The human brain accounts for around 80 billion of these cells.

Cells were discovered by Robert Hooke in 1665, who named them for their resemblance to cells inhabited by Christian monks in a monastery. Cell theory, first developed in 1839 by Matthias Jakob Schleiden and Theodor Schwann, states that all organisms are composed of one or more cells, that cells are the fundamental unit of structure and function in all living organisms, and that all cells come from pre-existing cells. Cells emerged on Earth at least 3.5 billion years ago.

 



 
The cells of eukaryotes (left) and prokaryotes (right).
 



Structure of a typical plant cell.

📂 Plant cell

Plant cell (W)

Plant cells are quite different from the cells of the other eukaryotic organisms. Their distinctive features are:

 



 


Structure of a typical animal cell.

All animals are eukaryotic. Animal cells are distinct from those of other eukaryotes, most notably plants, as they lack cell walls and chloroplasts and have smaller vacuoles. Due to the lack of a cell wall, animal cells can transform into a variety of shapes. A phagocytic cell can even engulf other structures.

📹📹📹 CELL (VİDEO)

📹 Cell Structure (Nucleus Medical Media) (VİDEO)

📹 Cell Structure / Nucleus Medical Media (LINK)

This animation by Nucleus shows you the function of plant and animal cells for middle school and high school biology, including organelles like the nucleus, nucleolus, DNA (chromosomes), ribosomes, mitochondria, etc. Also included are ATP molecules, cytoskeleton, cytoplasm, microtubules, proteins, chloroplasts, chlorophyll, cell walls, cell membrane, cilia, flagellae, etc.

 



📹 Parts of a cell / Khan Academy (VİDEO)

📹 Parts of a cell / Khan Academy (LINK)

Parts of a cell: nucleus, ribosomes, endoplasmic reticulum, Golgi bodies, mitochondria, chloroplasts, vacuoles, and vesicles.

 



📹 Organelles of the Cell / Beverly (VİDEO)

📹 Organelles of the Cell / Beverly (LINK)

This video is taught at the high school level. I use this PowerPoint in my biology classes at Beverly Hills High School.
Topics:
- 3 Main sections
- Cytoplasm
- Cell membrane
- Nucleus
- Nucleolus
- Ribosomes
- Rough ER
- Smooth ER
- Golgi body
- Vesicles
- Mitochondria
- Endosymbiosis
- Lysosomes
- Cilia
- Flagella
- Chloroplasts
- Vacuole
- Cell wall

 



📹 A Tour of the Cell / Bozeman (VİDEO)

📹 A Tour of the Cell / Bozeman (LINK)

Paul Andersen takes you on a tour of the cell. He starts by explaining the difference between prokaryotic and eukaryotic cells. He also explains why cells are small but not infinitely small. He also explains how the organelles work together in a similar fashion.

 



📹 Ten Craziest Things Cells Do / Wallace Marshall (UCSF) (VİDEO)

📹 Ten Craziest Things Cells Do / Wallace Marshall (UCSF) (LINK)

Dr. Marshall refutes the commonly held idea that cells are just bags of watery enzymes. He runs through his “Top 10 List” of unexpected and amazing things that individual cells can do. These including growing to be huge, navigating mazes, and performing feats that seem to belong in science fiction.

 



 





cell biology

Cell biology is a branch of biology studying the structure and function of the cell, also known as the basic unit of life. Cell biology encompasses both prokaryotic and eukaryotic cells and can be divided into many sub-topics which may include the study of cell metabolism, cell communication, cell cycle, and cell composition. The study of cells is performed using several techniques such as cell culture, various types of microscopy, and cell fractionation. These have allowed for and are currently being used for discoveries and research pertaining to how cells function, ultimately giving insight into understanding larger organisms. Knowing the components of cells and how cells work is fundamental to all biological sciences while also being essential for research in biomedical fields such as cancer, and other diseases. Research in cell biology is interconnected to other fields such as genetics, molecular genetics, biochemistry, molecular biology, medical microbiology, immunology, and cytochemistry. (W

📂 Plant cell

Plant cell (W)

Plant cells are quite different from the cells of the other eukaryotic organisms. Their distinctive features are:

 



📥 Outline of cell biology (W)

 






cell cycle

The cell cycle, or cell-division cycle, is the series of events that take place in a cell that cause it to divide into two daughter cells. These events include the duplication of its DNA (DNA replication) and some of its organelles, and subsequently the partitioning of its cytoplasm and other components into two daughter cells in a process called cell division.


In cells with nuclei (eukaryotes), (i.e., animal, plant, fungal, and protist cells), the cell cycle is divided into two main stages: interphase and the mitotic (M) phase (including mitosis and cytokinesis). During interphase, the cell grows, accumulating nutrients needed for mitosis, and replicates its DNA and some of its organelles. During the mitotic phase, the replicated chromosomes, organelles, and cytoplasm separate into two new daughter cells. To ensure the proper replication of cellular components and division, there are control mechanisms known as cell cycle checkpoints after each of the key steps of the cycle that determine if the cell can progress to the next phase.

In cells without nuclei (prokaryotes), (i.e., bacteria and archaea), the cell cycle is divided into the B, C, and D periods. The B period extends from the end of cell division to the beginning of DNA replication. DNA replication occurs during the C period. The D period refers to the stage between the end of DNA replication and the splitting of the bacterial cell into two daughter cells.


The cell-division 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 a new cycle. Although the various stages of interphase are not usually morphologically distinguishable, each phase of the cell cycle has a distinct set of specialized biochemical processes that prepare the cell for initiation of the cell division. (W)



Life cycle of the cell (L)
🔎
Diagram of the animal cell cycle. (L)
🔎



chromosome

chromosome is a DNA (deoxyribonucleic acid) molecule with part or all of the genetic material (genome) of an organism. Most eukaryotic chromosomes include packaging proteins which, aided by chaperone proteins, bind to and condense the DNA molecule to prevent it from becoming an unmanageable tangle. This three-dimensional genome structure plays a significant role in transcriptional regulation.


Chromosomes are normally visible under a light microscope only when the cell is undergoing the metaphase of cell division (where all chromosomes are aligned in the center of the cell in their condensed form). Before this happens, every chromosome is copied once (S phase), and the copy is joined to the original by a centromere, resulting either in an X-shaped structure (pictured here) if the centromere is located in the middle of the chromosome or a two-arm structure if the centromere is located near one of the ends. The original chromosome and the copy are now called sister chromatids. During metaphase the X-shape structure is called a metaphase chromosome. In this highly condensed form chromosomes are easiest to distinguish and study. In animal cells, chromosomes reach their highest compaction level in anaphase during chromosome segregation.


Chromosomal recombination during meiosis and subsequent sexual reproduction play a significant role in genetic diversity. If these structures are manipulated incorrectly, through processes known as chromosomal instability and translocation, the cell may undergo mitotic catastrophe. Usually, this will make the cell initiate apoptosis leading to its own death, but sometimes mutations in the cell hamper this process and thus cause progression of cancer.


Some use the term chromosome in a wider sense, to refer to the individualized portions of chromatin in cells, either visible or not under light microscopy. Others use the concept in a narrower sense, to refer to the individualized portions of chromatin during cell division, visible under light microscopy due to high condensation. (W)



The major structures in DNA compaction
🔎

 
The major structures in DNA compaction: DNA, the nucleosome, the 10 nm "beads-on-a-string" fibre, the 30 nm fibre and the metaphase chromosome.

 




d
Darwinism

Darwinism is a theory of biological evolution developed by the English naturalist Charles Darwin (1809–1882) and others, stating that all species of organisms arise and develop through the natural selection of small, inherited variations that increase the individual's ability to compete, survive, and reproduce. Also called Darwinian theory, it originally included the broad concepts of transmutation of species or of evolution which gained general scientific acceptance after Darwin published On the Origin of Species in 1859, including concepts which predated Darwin's theories. English biologist Thomas Henry Huxley coined the term Darwinism in April 1860. (W)



Darwinism, the eclipse of

Julian Huxley used the phrase “the eclipse of Darwinism” to describe the state of affairs prior to what he called the modern synthesis, when evolution was widely accepted in scientific circles but relatively few biologists believed that natural selection was its primary mechanism. Historians of science such as Peter J. Bowler have used the same phrase as a label for the period within the history of evolutionary thought from the 1880s to around 1920, when alternatives to natural selection were developed and explored—as many biologists considered natural selection to have been a wrong guess on Charles Darwin's part, or at least as of relatively minor importance.An alternative term, the interphase of Darwinism, has been proposed to avoid the largely incorrect implication that the putative eclipse was preceded by a period of vigorous Darwinian research.


While there had been multiple explanations of evolution including vitalismcatastrophism, and structuralism through the 19th century, four major alternatives to natural selection were in play at the turn of the 20th century:

  • Theistic evolution was the belief that God directly guided evolution.
  • Neo-Lamarckism was the idea that evolution was driven by the inheritance of characteristics acquired during the life of the organism.
  • Orthogenesis was the belief that organisms were affected by internal forces or laws of development that drove evolution in particular directions
  • Mutationism was the idea that evolution was largely the product of mutations that created new forms or species in a single step.


Theistic evolution largely disappeared from the scientific literature by the end of the 19th century as direct appeals to supernatural causes came to be seen as unscientific. The other alternatives had significant followings well into the 20th century; mainstream biology largely abandoned them only when developments in genetics made them seem increasingly untenable, and when the development of population genetics and the modern synthesis demonstrated the explanatory power of natural selectionErnst Mayr wrote that as late as 1930 most textbooks still emphasized such non-Darwinian mechanisms. (W)



Alternatives to evolution by natural selection included directed evolution (orthogenesis), sometimes invoking divine control directly or indirectly.



e
emergence

In philosophysystems theoryscience, and artemergence occurs when an entity is observed to have properties its parts do not have on their own. These properties or behaviors emerge only when the parts interact in a wider whole. For example, smooth forward motion emerges when a bicycle and its rider interoperate, but neither part can produce the behavior on their own.


Emergence plays a central role in theories of integrative levels and of complex systems. For instance, the phenomenon of life as studied in biology is an emergent property of chemistry, and psychological phenomena emerge from the neurobiological phenomena of living things.


In philosophy, theories that emphasize emergent properties have been called emergentism. Almost all accounts of emergentism include a form of epistemic or ontological irreducibility to the lower levels. (w)



emergent evolution

Emergent evolution was the hypothesis that, in the course of evolution, some entirely new properties, such as mind and consciousness, appear at certain critical points, usually because of an unpredictable rearrangement of the already existing entities. The term was originated by the psychologist C. Lloyd Morgan in 1922 in his Gifford Lectures at St. Andrews, which would later be published as the 1923 book Emergent Evolution.

The hypothesis was widely criticized for providing no mechanism to how entirely new properties emerge, and for its historical roots in teleology. (w)



emergentism

In philosophyemergentism is the belief in emergence, particularly as it involves consciousness and the philosophy of mind, and as it contrasts with and also does not contrast with reductionism. A property of a system is said to be emergent if it is a new outcome of some other properties of the system and their interaction, while it is itself different from them. Emergent properties are not identical with, reducible to, or deducible from the other properties. The different ways in which this independence requirement can be satisfied lead to variant types of emergence. (W)



Af.


eukaryote

 

Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, unlike prokaryotes (Bacteria and Archaea), which have no membrane-bound organelles. Eukaryotes belong to the domain Eukaryota or Eukarya. Their name comes from the Greek εὖ (eu, "well" or "good") and κάρυον (karyon, "nut" or "kernel"). Eukaryotic cells typically contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, and in addition, some cells of plants and algae contain chloroplasts. Unlike unicellular archaea and bacteria, eukaryotes may also be multicellular and include organisms consisting of many cell types forming different kinds of tissue. Animals and plants are the most familiar eukaryotes. (W)

Eukaryotic cells are typically much larger than those of prokaryotes, having a volume of around 10,000 times greater than the prokaryotic cell. (W)

📂Eukaryote

Eukaryote (W)

Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, unlike prokaryotes (Bacteria and Archaea), which have no membrane-bound organelles.Eukaryotes belong to the domain Eukaryota or Eukarya. Their name comes from the Greek εὖ (eu, "well" or "good") and κάρυον (karyon, "nut" or "kernel"). Eukaryotic cells typically contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, and in addition, some cells of plants and algae contain chloroplasts. Unlike unicellular archaea and bacteria, eukaryotes may also be multicellular and include organisms consisting of many cell types forming different kinds of tissue. Animals and plants are the most familiar eukaryotes.

Eukaryotes can reproduce both asexually through mitosis and sexually through meiosis and gamete fusion. In mitosis, one cell divides to produce two genetically identical cells. In meiosis, DNA replication is followed by two rounds of cell division to produce four haploid daughter cells. These act as sex cells (gametes). Each gamete has just one set of chromosomes, each a unique mix of the corresponding pair of parental chromosomes resulting from genetic recombination during meiosis.

The domain Eukaryota is monophyletic and makes up one of the domains of life in the three-domain system. The two other domains, Bacteria and Archaea, are prokaryotes and have none of the above features. Eukaryotes represent a tiny minority of all living things. However, due to their generally much larger size, their collective worldwide biomass is estimated to be about equal to that of prokaryotes. Eukaryotes evolved approximately 1.6–2.1 billion years ago, during the Proterozoic eon.

 





Phylogenetic and symbiogenetic tree of living organisms, showing a view of the origins of eukaryotes and prokaryotes
 
File:Collapsed tree labels simplified.png
 
   
Evolutionary tree showing the divergence of modern species from their common ancestor in the centre. The three domains are coloured, with bacteria blue, archaea green and eukaryotes red.  


The endomembrane system and its components.
 


Structure of a typical animal cell.

All animals are eukaryotic. Animal cells are distinct from those of other eukaryotes, most notably plants, as they lack cell walls and chloroplasts and have smaller vacuoles. Due to the lack of a cell wall, animal cells can transform into a variety of shapes. A phagocytic cell can even engulf other structures.


Structure of a typical plant cell.



extremophile


An extremophile (from Latin extremus meaning "extreme" and Greek philiā (φιλία) meaning "love") is an organism with optimal growth in environmental conditions considered extreme in that it is challenging for a carbon-based life form with water as a solvent, such as all life on Earth, to survive.


This is not the same as a more anthropocentric and non-scientific view which considers an extremophile to be an organism that lives in environments uncomfortable to humans. In contrast, organisms that live in more moderate environmental conditions, according to an anthropocentric view, may be termed mesophiles or neutrophiles. (W)



The bright colors of Grand Prismatic SpringYellowstone National Park, are produced by Thermophiles, a type of extremophile.


The limits of known life on Earth.
Factor Environment / source Limits Examples
High temperature Submarine hydrothermal vents 110 °C to 121 °C Pyrolobus fumariiPyrococcus furiosus
Low temperature Ice -20 °C to -25 °C Synechococcus lividus
Alkaline systems Soda lakes pH > 11 PsychrobacterVibrioArthrobacterNatronobacterium
Acidic systems Volcanic springs, acid mine drainage pH -0.06 to 1.0 BacillusClostridium paradoxum
Ionizing radiation Cosmic raysX-raysradioactive decay 1,500 to 6,000 Gy Deinococcus radioduransRubrobacterThermococcus gammatolerans
UV radiation Sunlight 5,000 J/m2 Deinococcus radioduransRubrobacterThermococcus gammatolerans
High pressure Mariana Trench 1,100 bar Pyrococcus sp.
Salinity High salt concentration aw ~ 0.6 HalobacteriaceaeDunaliella salina
Desiccation Atacama Desert (Chile), McMurdo Dry Valleys (Antarctica) ~60% relative humidity Chroococcidiopsis
Deep crust accessed at some gold mines Halicephalobus mephistoMylonchulus brachyurus, unidentified arthropods




extremotroph


An extremotroph (from Latin extremus meaning "extreme" and Greek troph (τροφ) meaning "food") is an organism that feeds on matter that is not typically considered to be food to most life on Earth. "These anthropocentric definitions that we make of extremophily and extremotrophy focus on a single environmental extreme but many extremophiles may fall into multiple categories, for example, organisms living inside hot rocks deep under the Earth's surface." (W)




g
gene

In biology, a gene is a sequence of nucleotides in DNA or RNA that encodes the synthesis of a gene product, either RNA or protein.


During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic trait. These genes make up different DNA sequences called genotypes. Genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes (many different genes) as well as gene–environment interactions. Some genetic traits are instantly visible, such as eye color or the number of limbs, and some are not, such as blood type, risk for specific diseases, or the thousands of basic biochemical processes that constitute life.


Genes can acquire mutations in their sequence, leading to different variants, known as alleles, in the population. These alleles encode slightly different versions of a protein, which cause different phenotypical traits. Usage of the term "having a gene" (e.g., "good genes," "hair colour gene") typically refers to containing a different allele of the same, shared gene. Genes evolve due to natural selection / survival of the fittest and genetic drift of the alleles.


The concept of gene continues to be refined as new phenomena are discovered. For example, regulatory regions of a gene can be far removed from its coding regions, and coding regions can be split into several exons. Some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. Therefore, a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product or by regulation of gene expression.


The term gene was introduced by Danish botanist, plant physiologist and geneticist Wilhelm Johannsen in 1909. It is inspired by the ancient Greek: γόνος, gonos, that means offspring and procreation. (W)




Fluorescent microscopy image of a human female karyotype, showing 23 pairs of chromosomes . The DNA is stained red, with regions rich in housekeeping genes further stained in green. The largest chromosomes are around 10 times the size of the smallest.

 



genome

In the fields of molecular biology and genetics, a genome is the genetic material of an organism. It consists of DNA (or RNA in RNA viruses). The genome includes both the genes (the coding regions) and the noncoding DNA, as well as mitochondrial DNA and chloroplast DNA. The study of the genome is called genomics. (w)

📂 A table of some significant or representative genomes

A table of some significant or representative genomes (W)

Organism type Organism Genome size
(base pairs)
Approx. no. of genes Note
Virus Porcine circovirus type 1 1,759 1.8kb Smallest viruses replicating autonomously in eukaryotic cells.
Virus Bacteriophage MS2 3,569 3.5kb First sequenced RNA-genome
Virus SV40 5,224 5.2kb  
Virus Phage Φ-X174 5,386 5.4kb First sequenced DNA-genome
Virus HIV 9,749 9.7kb [47]
Virus Phage λ 48,502 48.5kb Often used as a vector for the cloning of recombinant DNA.
Virus Megavirus 1,259,197 1.3Mb Until 2013 the largest known viral genome.
Virus Pandoravirus salinus 2,470,000 2.47Mb Largest known viral genome.
Bacterium Nasuia deltocephalinicola (strain NAS-ALF) 112,091 112kb Smallest non-viral genome.
Bacterium Carsonella ruddii 159,662 160kb
Bacterium Buchnera aphidicola 600,000 600kb  
Bacterium Wigglesworthia glossinidia 700,000 700Kb
Bacterium Haemophilus influenzae 1,830,000 1.8Mb First genome of a living organism sequenced, July 1995
Bacterium Escherichia coli 4,600,000 4.6Mb 4,288  
Bacterium Solibacter usitatus (strain Ellin 6076) 9,970,000 10Mb  
Bacterium – cyanobacterium Prochlorococcus spp. (1.7 Mb) 1,700,000 1.7Mb 1,884 Smallest known cyanobacterium genome
Bacterium – cyanobacterium Nostoc punctiforme 9,000,000 9Mb 7,432 7432 open reading frames
Amoeboid Polychaos dubium ("Amoeba" dubia) 670,000,000,000 670Gb Largest known genome. (Disputed)
Eukaryotic organelle Human mitochondrion 16,569 16.6kb  
Plant Genlisea tuberosa 61,000,000 61Mb Smallest recorded flowering plant genome, 2014.
Plant Arabidopsis thaliana 135,000,000[65] 135 Mb 27,655[66] First plant genome sequenced, December 2000.
Plant Populus trichocarpa 480,000,000 480Mb 73,013 First tree genome sequenced, September 2006
Plant Fritillaria assyriaca 130,000,000,000 130Gb
Plant Paris japonica (Japanese-native, pale-petal) 150,000,000,000 150Gb Largest plant genome known
Plant – moss Physcomitrella patens 480,000,000 480Mb First genome of a bryophyte sequenced, January 2008.
Fungus – yeast Saccharomyces cerevisiae 12,100,000 12.1Mb 6,294 First eukaryotic genome sequenced, 1996
Fungus Aspergillus nidulans 30,000,000 30Mb 9,541  
Nematode Pratylenchus coffeae 20,000,000 20Mb Smallest animal genome known
Nematode Caenorhabditis elegans 100,300,000 100Mb 19,000 First multicellular animal genome sequenced, December 1998
Insect Drosophila melanogaster (fruit fly) 175,000,000 175Mb 13,600 Size variation based on strain (175-180Mb; standard y w strain is 175Mb)
Insect Apis mellifera (honey bee) 236,000,000 236Mb 10,157  
Insect Bombyx mori (silk moth) 432,000,000 432Mb 14,623 14,623 predicted genes
Insect Solenopsis invicta (fire ant) 480,000,000 480Mb 16,569  
Mammal Mus musculus 2,700,000,000 2.7Gb 20,210  
Mammal Homo sapiens 3,289,000,000 3.3Gb 20,000 Homo sapiens estimated genome size 3.2 billion bp

Initial sequencing and analysis of the human genome

Mammal Pan paniscus 3,286,640,000 3.3Gb 20,000 Bonobo - estimated genome size 3.29 billion bp
Bird Gallus gallus 1,043,000,000 1.0Gb 20,000  
Fish Tetraodon nigroviridis (type of puffer fish) 385,000,000 390Mb Smallest vertebrate genome known estimated to be 340 Mb  – 385 Mb.
Fish Protopterus aethiopicus (marbled lungfish) 130,000,000,000 130Gb Largest vertebrate genome known

 





 

A label diagram explaining the different parts of a prokaryotic genome
🔎




H

homeostasis


In biologyhomeostasis is the state of steady internal, physical, and chemical conditions maintained by living systems. This is the condition of optimal functioning for the organism and includes many variables, such as body temperature and fluid balance, being kept within certain pre-set limits (homeostatic range). Other variables include the pH of extracellular fluid, the concentrations of sodiumpotassium and calcium ions, as well as that of the blood sugar level, and these need to be regulated despite changes in the environment, diet, or level of activity. Each of these variables is controlled by one or more regulators or homeostatic mechanisms, which together maintain life. (W)




k
karyotype

Karyotyping is the process by which photographs of chromosomes are taken in order to determine the chromosome complement of an individual, including the number of chromosomes and any abnormalities. The term is also used for the complete set of chromosomes in a species or in an individual organism and for a test that detects this complement or measures the number.


Karyotypes describe the chromosome count of an organism and what these chromosomes look like under a light microscope. Attention is paid to their length, the position of the centromeres, banding pattern, any differences between the sex chromosomes, and any other physical characteristics. The preparation and study of karyotypes is part of cytogenetics.


The study of whole sets of chromosomes is sometimes known as karyology. The chromosomes are depicted (by rearranging a photomicrograph) in a standard format known as a karyogram or idiogram: in pairs, ordered by size and position of centromere for chromosomes of the same size.


The basic number of chromosomes in the somatic cells of an individual or a species is called the somatic number and is designated 2n. In the germ-line (the sex cells) the chromosome number is n (humans: n = 23). Thus, in humans 2n = 46.


So, in normal diploid organisms, autosomal chromosomes are present in two copies. There may, or may not, be sex chromosomesPolyploid cells have multiple copies of chromosomes and haploid cells have single copies.


Karyotypes can be used for many purposes; such as to study chromosomal aberrationscellular function, taxonomic relationships, medicine and to gather information about past evolutionary events.(karyosystematics). (W)

 




L
Lamarckism

Lamarckism, or Lamarckian inheritance, also known as "Neo-Lamarckism", is the notion that an organism can pass on to its offspring physical characteristics that the parent organism acquired through use or disuse during its lifetime. This idea is also called the inheritance of acquired characteristics or soft inheritance. It is inaccurately named after the French biologist Jean-Baptiste Lamarck (1744-1829), who incorporated the action of soft inheritance into his evolutionary theories as a supplement to his concept of orthogenesis, a drive towards complexity. The theory is cited in textbooks to contrast with Darwinism. This paints a false picture of the history of biology, as Lamarck did not originate the idea of soft inheritance, which was known from the classical era onwards, and it was not the primary focus of Lamarck's theory of evolution. Further, in On the Origin of Species (1859), Charles Darwin supported the idea of "use and disuse inheritance", though rejecting other aspects of Lamarck's theory. Darwin's own concept of pangenesis implied soft inheritance.


Many researchers from the 1860s onwards attempted to find evidence for Lamarckian inheritance, but these have all been explained away, either by other mechanisms such as genetic contamination or as fraud. On the other hand, August Weismann's experiment is now considered to have failed to disprove Lamarckism as it did not address use and disuse. Later, Mendelian genetics supplanted the notion of inheritance of acquired traits, eventually leading to the development of the modern synthesis, and the general abandonment of Lamarckism in biology. Despite this, interest in Lamarckism has continued.


Studies in the fields of epigeneticsgenetics, and somatic hypermutation have highlighted the possible inheritance of traits acquired by the previous generation. The characterization of these findings as Lamarckism has been disputed. The inheritance of the hologenome, consisting of the genomes of all an organism's symbiotic microbes as well as its own genome, is also somewhat Lamarckian in effect, though entirely Darwinian in its mechanisms. (W)



Lamarck's two-factor theory involves 1) a complexifying force that drives animal body plans towards higher levels (orthogenesis) creating a ladder of phyla, and 2) an adaptive force that causes animals with a given body plan to adapt to circumstances (use and disuse, inheritance of acquired characteristics), creating a diversity of species and genera. Popular views of Lamarckism only consider an aspect of the adaptive force.



m
metaboleme
The metabolome refers to the complete set of small-molecule chemicals found within a biological sample. The biological sample can be a cell, a cellular organelle, an organ, a tissue, a tissue extract, a biofluid or an entire organism. The small molecule chemicals found in a given metabolome may include both endogenous metabolites that are naturally produced by an organism (such as amino acidsorganic acidsnucleic acidsfatty acidsaminessugarsvitaminsco-factorspigmentsantibiotics, etc.) as well as exogenous chemicals (such as drugs, environmental contaminantsfood additivestoxins and other xenobiotics) that are not naturally produced by an organism.

In other words, there is both an endogenous metabolome and an exogenous metabolome. The endogenous metabolome can be further subdivided to include a "primary" and a "secondary" metabolome (particularly when referring to plant or microbial metabolomes). A primary metabolite is directly involved in the normal growth, development, and reproduction. A secondary metabolite is not directly involved in those processes, but usually has important ecological function. Secondary metabolites may include pigmentsantibiotics or waste products derived from partially metabolized xenobiotics. The study of the metabolome is called metabolomics. (W)



General schema showing the relationships of the genometranscriptomeproteome, and metabolome (lipidome).

 



metabolism


Metabolism (from Greek: μεταβολή metabolē, "change") is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: the conversion of food to energy to run cellular processes; the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of nitrogenous wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. (The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including digestion and the transport of substances into and between different cells, in which case the above described set of reactions within the cells is called intermediary metabolism or intermediate metabolism).


Metabolic reactions may be categorized as catabolic – the breaking down of compounds (for example, 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. (W)



Simplified view of the cellular metabolism.

A diagram depicting a large set of human metabolic pathways (L)
🔎



microbiota

Microbiota are "ecological communities of commensal, symbiotic and pathogenic microorganisms" found in and on all multicellular organisms studied to date from plants to animals. Microbiota includes bacteria, archaea, protists, fungi and viruses. Microbiota have been found to be crucial for immunologic, hormonal and metabolic homeostasis of their host. The synonymous term microbiome describes either the collective genomes of the microorganisms that reside in an environmental niche or the microorganisms themselves.

The microbiome and host emerged during evolution as a synergistic unit from epigenetics and genetic characteristics, sometimes collectively referred to as a holobiont.

All plants and animals, from simple life forms to humans, live in close association with microbial organisms. Several advances have driven the perception of microbiomes, including:

  • the ability to perform genomic and gene expression analyses of single cells and of entire microbial communities in the disciplines of metagenomics and metatranscriptomics
  • databases accessible to researchers across multiple disciplines
  • methods of mathematical analysis suitable for complex data sets


Biologists have come to appreciate that microbes make up an important part of an organism's phenotype, far beyond the occasional symbiotic case study. (W)

📘 Campbell Essential Biology-Pearson Education Limited (2016) p. 17

 






The predominant bacteria on human skin.


Pathogenic microbiota causing inflammation in the lung.
(W)

📂Commensals vs pathogens mechanism.

Commensals vs pathogens mechanism. Mechanisms underlaying the inflammation in COPD. Airway epithelium has complex structure: consists of at least seven diverse cell types interacting with each other by means of tight junctions. Moreover, epithelial calls can deliver the signals into the underlying tissues taking part in the mechanisms of innate and adaptive immune defence. The key transmitters of the signals are dendritic cells. Once pathogenic bacterium (e.g., S. pneumoniae, P. aeruginosa) has activated particular pattern recognition receptors on/in epithelial cells, the proinflammatory signaling pathways are activated. This results mainly in IL-1, IL-6 and IL-8 production. These cytokines induce the chemotaxis to the site of infection in its target cells (e.g., neutrophils, dendritic cells and macrophages). On the other hand, representatives of standard microbiota cause only weak signaling preventing the inflammation. The mechanism of distinguishing between harmless and harmful bacteria on the molecular as well as on physiological levels is not completely understood.

 





Tryptophan metabolism by human gastrointestinal microbiota. (W)

📂Tryptophan metabolism by human gastrointestinal microbiota

This diagram shows the biosynthesis of bioactive compounds (indole and certain other derivatives) from tryptophan by bacteria in the gut. Indole is produced from tryptophan by bacteria that express tryptophanase. Clostridium sporogenes metabolizes tryptophan into indole and subsequently 3-indolepropionic acid (IPA), a highly potent neuroprotective antioxidant that scavenges hydroxyl radicals. IPA binds to the pregnane X receptor (PXR) in intestinal cells, thereby facilitating mucosal homeostasis and barrier function. Following absorption from the intestine and distribution to the brain, IPA confers a neuroprotective effect against cerebral ischemia and Alzheimer's disease. Lactobacillus species metabolize tryptophan into indole-3-aldehyde (I3A) which acts on the aryl hydrocarbon receptor (AhR) in intestinal immune cells, in turn increasing interleukin-22 (IL-22) production. Indole itself triggers the secretion of glucagon-like peptide-1 (GLP-1) in intestinal L cells and acts as a ligand for AhR. Indole can also be metabolized by the liver into indoxyl sulfate, a compound that is toxic in high concentrations and associated with vascular disease and renal dysfunction. AST-120 (activated charcoal), an intestinal sorbent that is taken by mouth, adsorbs indole, in turn decreasing the concentration of indoxyl sulfate in blood plasma.

 





micelle

micelle or micella  (plural micelles or micellae, respectively) is an aggregate (or supramolecular assembly) of surfactant molecules dispersed in a liquid colloid. A typical micelle in aqueous solution forms an aggregate with the hydrophilic "head" regions in contact with surrounding solvent, sequestering the hydrophobic single-tail regions in the micelle centre.


This phase is caused by the packing behavior of single-tail lipids in a bilayer. The difficulty filling all the volume of the interior of a bilayer, while accommodating the area per head group forced on the molecule by the hydration of the lipid head group, leads to the formation of the micelle. This type of micelle is known as a normal-phase micelle (oil-in-water micelle). Inverse micelles have the head groups at the centre with the tails extending out (water-in-oil micelle).


Micelles are approximately spherical in shape. Other phases, including shapes such as ellipsoids, cylinders, and bilayers, are also possible. The shape and size of a micelle are a function of the molecular geometry of its surfactant molecules and solution conditions such as surfactant concentration, temperaturepH, and ionic strength. The process of forming micelles is known as micellisation and forms part of the phase behaviour of many lipids according to their polymorphism. (W)

.
Scheme of a micelle formed by phospholipids in an aqueous solution.



microorganism

microorganism, or microbe, is a microscopic organism, which may exist in its single-celled form or in a colony of cells.


The possible existence of unseen microbial life was suspected from ancient times, such as in Jain scriptures from 6th century BC India and the 1st century BC book On Agriculture by Marcus Terentius Varro. The scientific study of microorganisms began with their observation under the microscope in the 1670s by Antonie van Leeuwenhoek. In the 1850s, Louis Pasteur found that microorganisms caused food spoilage, debunking the theory of spontaneous generation. In the 1880s, Robert Koch discovered that microorganisms caused the diseases tuberculosis, cholera and anthrax.


Microorganisms include all unicellular organisms and so are extremely diverse. Of the three domains of life identified by Carl Woese, all of the Archaea and Bacteria are microorganisms. These were previously grouped together in the two domain system as Prokaryotes, the other being the eukaryotes. The third domain Eukaryota includes all multicellular organisms and many unicellular protists and protozoans. Some protists are related to animals and some to green plants. Many of the multicellular organisms are microscopic, namely micro-animals, some fungi and some algae, but these are not discussed here.


They live in almost every habitat from the poles to the equator, deserts, geysers, rocks and the deep sea. Some are adapted to extremes such as very hot or very cold conditions, others to high pressure and a few such as Deinococcus radiodurans to high radiation environments. Microorganisms also make up the microbiota found in and on all multicellular organisms. There is evidence that 3.45-billion-year-old Australian rocks once contained microorganisms, the earliest direct evidence of life on Earth.


Microbes are important in human culture
 and health in many ways, serving to ferment foods, treat sewage, produce fuel, enzymes and other bioactive compounds. They are essential tools in biology as model organisms and have been put to use in biological warfare and bioterrorism. They are a vital component of fertile soils. In the human body microorganisms make up the human microbiota including the essential gut flora. They are the pathogens responsible for many infectious diseases and as such are the target of hygiene measures.

(W)



cluster of Escherichia coli bacteria magnified 10,000 times.


mitochondrion




Components of a typical animal cell:
  1. Nucleolus
  2. Nucleus
  3. Ribosome (little dots)
  4. Vesicle
  5. Rough endoplasmic reticulum
  6. Golgi apparatus (or, Golgi body)
  7. Cytoskeleton
  8. Smooth endoplasmic reticulum
  9. Mitochondrion
  10. Vacuole
  11. Cytosol (fluid that contains organelles, comprising the cytoplasm)
  12. Lysosome
  13. Centrosome
  14. Cell membrane


The mitochondrion (plural mitochondria) is a semi autonomous double-membrane-bound organelle found in most eukaryotic organisms. Some cells in some multicellular organisms may, however, lack mitochondria (for example, mature mammalian red blood cells). A number of unicellular organisms, such as microsporidia, parabasalids, and diplomonads, have also reduced or transformed their mitochondria into other structures. To date, only one eukaryote, Monocercomonoides, is known to have completely lost its mitochondria, and one multicellular organism, Henneguya salminicola, is known to have retained mitochondrion-related organelles in association with a complete loss of their mitochondrial genome.

The word mitochondrion comes from the Greek μίτοςmitos, "thread", and χονδρίονchondrion, "granule" or "grain-like". Mitochondria generate most of the cell's supply of adenosine triphosphate (ATP), used as a source of chemical energy. A mitochondrion is thus termed the powerhouse of the cell.

Mitochondria are commonly between 0.75 and 3 μm² in area but vary considerably in size and structure. Unless specifically stained, they are not visible. In addition to supplying cellular energy, mitochondria are involved in other tasks, such as signaling, cellular differentiation, and cell death, as well as maintaining control of the cell cycle and cell growth. Mitochondrial biogenesis is in turn temporally coordinated with these cellular processes. Mitochondria have been implicated in several human diseases, including mitochondrial disorders,[13] cardiac dysfunction, heart failure and autism.

The number of mitochondria in a cell can vary widely by organism, tissue, and cell type. For instance, red blood cells have no mitochondria, whereas liver cells can have more than 2000. The organelle is composed of compartments that carry out specialized functions. These compartments or regions include the outer membrane, the intermembrane space, the inner membrane, and the cristae and matrix.

Although most of a cell's DNA is contained in the cell nucleus, the mitochondrion has its own independent genome ("mitogenome") that shows substantial similarity to bacterial genomes. Mitochondrial proteins (proteins transcribed from mitochondrial DNA) vary depending on the tissue and the species. In humans, 615 distinct types of proteins have been identified from cardiac mitochondria, whereas in rats, 940 proteins have been reported. The mitochondrial proteome is thought to be dynamically regulated. (W)




Diagramtic structural features of a mitochondrion



Mitochondrion ultrastructure (interactive diagram) A mitochondrion has a double membrane; the inner one contains its chemiosmotic apparatus and has deep grooves which increase its surface area. While commonly depicted as an "orange sausage with a blob inside of it" (like it is here), mitochondria can take many shapes[47] and their intermembrane space is quite thin.

One model for the origin of mitochondria and plastids (L)
🔎


📹📹📹 Mitochondria (VİDEO)

📹 Mitochondria (VİDEO)

📹 Mitochondria (LINK)

 



📹 How Mitochondria Produce Energy? (VİDEO)

📹 How Mitochondria Produce Energy? (LINK)

Explaining the complex process of oxidative phosphorylation. Excerpt from a Mode of Action animation.

 



📹 Powering the Cell — Mitochondria (VİDEO)

📹 Powering the Cell — Mitochondria (LINK)

Together Harvard University and XVIVO developed this 3D animation journey for Harvard's undergraduate Molecular and Cellular Biology students about the microscopic world of mitochondria. The animation highlights the creation of Adenosine Triphosphate (ATP) -- mobile molecules which store chemical energy derived from the breakdown of carbon-based food. ATP molecules act as a kind of currency, imparting chemical energy to power all the functional components of cellular activity. This piece is the second in a series of award winning animations XVIVO is creating for Harvard's educational website BioVisions at Harvard. The first program, Inner Life of the Cell, received international acclaim and can be seen both on our website and the BioVisions site.

 



 





mutation

In biology,mutation is an alteration in the nucleotide sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes can be of either DNA or RNA. Mutations result from errors during DNA replication, mitosis, and meiosis or other types of damage to DNA (such as pyrimidine dimers that may be caused by exposure to radiation or carcinogens), which then may undergo error-prone repair (especially microhomology-mediated end joining) or cause an error during other forms of repair or else may cause an error during replication (translesion synthesis). Mutations may also result from insertion or deletion of segments of DNA due to mobile genetic elements.

Mutations may or may not produce discernible changes in the observable characteristics (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. (W)




n
neural circuit

neural circuit is a population of neurons interconnected by synapses to carry out a specific function when activated. Neural circuits interconnect to one another to form large scale brain networks. Biological neural networks have inspired the design of artificial neural networks, but artificial neural networks are usually not strict copies of their biological counterparts. (W)



neuron

neuronneurone or nerve cell, is an electrically excitable cell[ that communicates with other cells via specialized connections called synapses. It is the main component of nervous tissue in all animals except sponges and placozoaPlants and fungi do not have nerve cells.


Neurons are typically classified into three types based on their function. Sensory neurons respond to stimuli such as touch, sound, or light that affect the cells of the sensory organs, and they send signals to the spinal cord or brain. Motor neurons receive signals from the brain and spinal cord to control everything from muscle contractions to glandular outputInterneurons connect neurons to other neurons within the same region of the brain or spinal cord. A group of connected neurons is called a neural circuit.


A typical neuron consists of a cell body (soma), dendrites, and a single axon. The soma is usually compact. The axon and dendrites are filaments that extrude from it. Dendrites typically branch profusely and extend a few hundred micrometers from the soma. The axon leaves the soma at a swelling called the axon hillock, and travels for as far as 1 meter in humans or more in other species. It branches but usually maintains a constant diameter. At the farthest tip of the axon's branches are axon terminals, where the neuron can transmit a signal across the synapse to another cell. Neurons may lack dendrites or have no axon. The term neurite is used to describe either a dendrite or an axon, particularly when the cell is undifferentiated.


Most neurons receive signals via the dendrites and soma and send out signals down the axon. At the majority of synapses, signals cross from the axon of one neuron to a dendrite of another. However, synapses can connect an axon to another axon or a dendrite to another dendrite.


The signaling process is partly electrical and partly chemical. Neurons are electrically excitable, due to maintenance of voltage gradients across their membranes. If the voltage changes by a large enough amount over a short interval, the neuron generates an all-or-nothing electrochemical pulse called an action potential. This potential travels rapidly along the axon, and activates synaptic connections as it reaches them. Synaptic signals may be excitatory or inhibitory, increasing or reducing the net voltage that reaches the soma.

In most cases, neurons are generated by neural stem cells during brain development and childhood. Neurogenesis largely ceases during adulthood in most areas of the brain. However, strong evidence supports generation of substantial numbers of new neurons in the hippocampus and olfactory bulb. (w)



Multipolar Neuron.



Diagram of the human nervous system. The relationship between the brain, spinal cord, and rest of the nerves in the body is demonstrated.



SMI32-stained pyramidal neurons in cerebral cortex.



Synaptic vesicles containing neurotransmitters.



Chemical synapse.



Guillain–Barré syndrome – demyelination.

 




o
organ

An organ is a group of tissues with similar functions. Plant life and animal life rely on many organs that coexist in organ systems.


A given organ's tissues can be broadly categorized as parenchyma, the tissue peculiar to (or at least archetypal of) the organ and that does the organ's specialized job, and stroma, the tissues with supportive, structural, connective, or ancillary functions. For example, in a gland, the tissue that makes the hormones is the parenchyma, whereas the stroma includes the nerves that innervate the parenchyma, the blood vessels that oxygenate and nourish it and carry away its metabolic wastes, and the connective tissues that provide a suitable place for it to be situated and anchored. The main tissues that make up an organ tend to have common embryologic origins, such as arising from the same germ layer. Functionally related organs often cooperate to form whole organ systems. Organs exist in most multicellular organisms. In single-celled organisms such as bacteria, the functional analogue of an organ is known as an organelle. In plants, there are three main organs. A hollow organ is an internal organ that forms a hollow tube, or pouch such as the stomachintestine, or bladder.


In the study of anatomy, the term viscus refers to an internal organ. Viscera is the plural form.


The number of organs in any organism depends on which precise definition of the term one uses. By one widely used definition, 79 organs have been identified in the human body. (W)



General schema showing the relationships of the genometranscriptomeproteome, and metabolome (lipidome).

 



organelle

Components of a typical animal cell:
  1. Nucleolus
  2. Nucleus
  3. Ribosome (little dots)
  4. Vesicle
  5. Rough endoplasmic reticulum
  6. Golgi apparatus (or, Golgi body)
  7. Cytoskeleton
  8. Smooth endoplasmic reticulum
  9. Mitochondrion
  10. Vacuole
  11. Cytosol (fluid that contains organelles, comprising the cytoplasm)
  12. Lysosome
  13. Centrosome
  14. Cell membrane
 
   

In cell biology, an organelle is a specialized subunit, usually within a cell, that has a specific function. Organelles are either separately enclosed within their own lipid bilayers (also called membrane-bound organelles) or are spatially distinct functional units without a surrounding lipid bilayer (non-membrane bound organelles). Although most organelles are functional units within cells, some functional units that extend outside of cells are often termed organelles, such as cilia, the flagellum and archaellum, and the trichocyst.


The name organelle comes from the idea that these structures are parts of cells, as organs are to the body, hence organelle, the suffix -elle being a diminutive. Organelles are identified by microscopy, and can also be purified by cell fractionation. There are many types of organelles, particularly in eukaryotic cells. While prokaryotes do not possess intracellular organelles per se, some do contain protein-based bacterial microcompartments, which are thought to act as primitive prokaryotic organelles. Also, the prokaryotic flagellum which protrudes outside the cell, and its motor, as well as the largely extracellular pilus, are often spoken of as organelles. (W)

Eukaryotic organelles

Eukaryotic cells are structurally complex, and by definition are organized, in part, by interior compartments that are themselves enclosed by lipid membranes that resemble the outermost cell membrane. The larger organelles, such as the nucleus and vacuoles, are easily visible with the light microscope. They were among the first biological discoveries made after the invention of the microscope.


Not all eukaryotic cells have each of the organelles listed below. Exceptional organisms have cells that do not include some organelles that might otherwise be considered universal to eukaryotes (such as mitochondria). There are also occasional exceptions to the number of membranes surrounding organelles, listed in the tables below (e.g., some that are listed as double-membrane are sometimes found with single or triple membranes). In addition, the number of individual organelles of each type found in a given cell varies depending upon the function of that cell. (W)


Prokaryotic organelles

Prokaryotes are not as structurally complex as eukaryotes, and were once thought not to have any internal structures enclosed by lipid membranes. In the past, they were often viewed as having little internal organization, but slowly, details are emerging about prokaryotic internal structures. An early false turn was the idea developed in the 1970s that bacteria might contain membrane folds termed mesosomes, but these were later shown to be artifacts produced by the chemicals used to prepare the cells for electron microscopy.


However, more recent research has revealed that at least some prokaryotes have microcompartments such as carboxysomes. These subcellular compartments are 100–200 nm in diameter and are enclosed by a shell of proteins. Even more striking is the description of membrane-bound magnetosomes in bacteria, reported in 2006, as well as the nucleus-like structures of the Planctomycetes that are surrounded by lipid membranes, reported in 2005. (W)



organic matter

Organic matterorganic material, or natural organic matter refers to the large source of carbon-based compounds found within natural and engineered, terrestrial and aquatic environments. It is matter composed of organic compounds that have come from the remains of organisms such as plants and animals and their waste products in the environment. Organic molecules can also be made by chemical reactions that don't involve life. Basic structures are created from cellulosetannincutin, and lignin, along with other various proteinslipids, and carbohydrates. Organic matter is very important in the movement of nutrients in the environment and plays a role in water retention on the surface of the planet. (W)



organism





Amoebae are single-celled eukaryotes.
 
   

In biology, an organism (from Greek: ὀργανισμός, organismos) is any individual entity that embodies the properties of life. It is a synonym for "life form".


Organisms are classified by taxonomy into groups such as multicellular animalsplants, and fungi; or unicellular microorganisms such as protistsbacteria, and archaeaAll types of organisms are capable of reproductiongrowth and developmentmaintenance, and some degree of response to stimuli. Humanssquidsmushrooms, and vascular plants are examples of multicellular organisms that differentiate specialized tissues and organs during development.


An organism may be either a prokaryote or a eukaryote. Prokaryotes are represented by two separate domains – bacteria and archaea. Eukaryotic organisms are characterized by the presence of a membrane-bound cell nucleus and contain additional membrane-bound compartments called organelles (such as mitochondria in animals and plants and plastids in plants and algae, all generally considered to be derived from endosymbiotic bacteria). Fungi, animals and plants are examples of kingdoms of organisms within the eukaryotes.

Estimates on the number of Earth's current species range from 2 million to 1 trillion, of which over 1.7 million have been documented. More than 99% of all species, amounting to over five billion species, that ever lived are estimated to be extinct.


In 2016, a set of 355 genes from the last universal common ancestor (LUCA) of all organisms was identified. (W)




p
phenotype

Phenotype (from Greek pheno-, meaning 'showing', and type, meaning 'type') is the term used in genetics for the composite observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological properties, its behavior, and the products of behavior. An organism's phenotype results from two basic factors: the expression of an organism's genetic code, or its genotype, and the influence of environmental factors. Both factors may interact, further affecting phenotype. When two or more clearly different phenotypes exist in the same population of a species, the species is called polymorphic. A well-documented example of polymorphism is Labrador Retriever coloring; while the coat color depends on many genes, it is clearly seen in the environment as yellow, black, and brown. Richard Dawkins in 1978 and then again in his 1982 book The Extended Phenotype suggested that one can regard bird nests and other built structures such as caddis-fly larvae cases and beaver dams as "extended phenotypes".


Wilhelm Johannsen
 proposed the genotype-phenotype distinction in 1911 to make clear the difference between an organism's heredity and what that heredity produces. The distinction resembles that proposed by August Weismann (1834-1914), who distinguished between germ plasm (heredity) and somatic cells (the body).


The genotype-phenotype distinction should not be confused with Francis Crick's central dogma of molecular biology, a statement about the directionality of molecular sequential information flowing from DNA to protein, and not the reverse. (W)



The shells of individuals within the bivalve mollusk species Donax variabilis show diverse coloration and patterning in their phenotypes.

 



phospholipid

Phospholipids (PL) are a class of lipids that are a major component of all cell membranes. They can form lipid bilayers because of their amphiphilic characteristic. The structure of the phospholipid molecule generally consists of two hydrophobic fatty acid "tails" and a hydrophilic "head" consisting of a phosphate group. The two components are usually joined together by a glycerol molecule. The phosphate groups can be modified with simple organic molecules such as cholineethanolamine or serine.


The first phospholipid identified in 1847 as such in biological tissues was lecithin, or phosphatidylcholine, in the egg yolk of chickens by the French chemist and pharmacist Theodore Nicolas GobleyBiological membranes in eukaryotes also contain another class of lipid, sterol, interspersed among the phospholipids and together they provide membrane fluidity and mechanical strength. Purified phospholipids are produced commercially and have found applications in nanotechnology and materials science. (W)




phototroph

Phototrophs (Gr: φῶς, φωτός = light, τροϕή = nourishment) are organisms that carry out photon capture to produce complex organic compounds (such as carbohydrates) and acquire energy. They use the energy from light to carry out various cellular metabolic processes. It is a common misconception that phototrophs are obligatorily photosynthetic. Many, but not all, phototrophs often photosynthesize: they anabolically convert carbon dioxide into organic material to be utilized structurally, functionally, or as a source for later catabolic processes (e.g. in the form of starches, sugars and fats). All phototrophs either use electron transport chains or direct proton pumping to establish an electrochemical gradient which is utilized by ATP synthase, to provide the molecular energy currency for the cell. Phototrophs can be either autotrophs or heterotrophs. If their electron and hydrogen donors are inorganic compounds (e.g. Na2S2O3, as in some purple sulfur bacteria, or H2S, as in some green sulfur bacteria) they can be also called lithotrophs, and so, some photoautotrophs are also called photolithoautotrophs. Examples of phototroph organisms are: Rhodobacter capsulatusChromatiumChlorobium etc. (W)

📂 Phototroph

Phototroph (W)

Originally used with a different meaning, the term took its current definition after Lwoff and collaborators (1946).

Photoautotroph

Most of the well-recognized phototrophs are autotrophic, also known as photoautotrophs, and can fix carbon. They can be contrasted with chemotrophs that obtain their energy by the oxidation of electron donors in their environments. Photoautotrophs are capable of synthesizing their own food from inorganic substances using light as an energy source. Green plants and photosynthetic bacteria are photoautotrophs. Photoautotrophic organisms are sometimes referred to as holophytic. Such organisms derive their energy for food synthesis from light and are capable of using carbon dioxide as their principal source of carbon.

Oxygenic photosynthetic organisms use chlorophyll for light-energy capture and oxidize water, "splitting" it into molecular oxygen. In contrast, anoxygenic photosynthetic bacteria have a substance called bacteriochlorophyll – which absorbs predominantly at non-optical wavelengths – for light-energy capture, live in aquatic environments, and will, using light, oxidize chemical substances such as hydrogen sulfide rather than water.


Ecology

In an ecological context, phototrophs are often the food source for neighboring heterotrophic life. In terrestrial environments, plants are the predominant variety, while aquatic environments include a range of phototrophic organisms such as algae (e.g., kelp), other protists (such as euglena), phytoplankton, and bacteria (such as cyanobacteria). The depth to which sunlight or artificial light can penetrate into water, so that photosynthesis may occur, is known as the photic zone.

Cyanobacteria, which are prokaryotic organisms which carry out oxygenic photosynthesis, occupy many environmental conditions, including fresh water, seas, soil, and lichen. Cyanobacteria carry out plant-like photosynthesis because the organelle in plants that carries out photosynthesis is derived from an endosymbiotic cyanobacterium. This bacterium can use water as a source of electrons in order to perform CO2 reduction reactions. Evolutionarily, cyanobacteria's ability to survive in oxygenic conditions, which are considered toxic to most anaerobic bacteria, might have given the bacteria an adaptive advantage which could have allowed the cyanobacteria to populate more efficiently.

photolithoautotroph is an autotrophic organism that uses light energy, and an inorganic electron donor (e.g., H2O, H2, H2S), and CO2 as its carbon source. Examples include plants.


Photoheterotroph

Main article: Photoheterotroph

In contrast to photoautotrophs, photoheterotrophs are organisms that depend solely on light for their energy and principally on organic compounds for their carbon. Photoheterotrophs produce ATP through photophosphorylation but use environmentally obtained organic compounds to build structures and other bio-molecules.

 





Terrestrial and aquatic phototrophs: plants grow on a fallen log floating in algae-rich water.


prokaryote

prokaryote is a unicellular organism that lacks a membrane-bound nucleus, mitochondria, or any other membrane-bound organelle. The word prokaryote comes from the Greek πρό (pro, 'before') and κάρυον (karyon, 'nut' or 'kernel'). Prokaryotes are divided into two domains, Archaea and Bacteria. Organisms with nuclei and other organelles are placed in a third domain, Eukaryota. Prokaryotes are asexual, reproducing without fusion of gametes. The first organisms are thought to have been prokaryotes. (W)



Phylogenetic and symbiogenetic tree of living organisms, showing a view of the origins of eukaryotes and prokaryotes
 
File:Collapsed tree labels simplified.png
 
   
Evolutionary tree showing the divergence of modern species from their common ancestor in the centre. The three domains are coloured, with bacteria blue, archaea green and eukaryotes red.  



Diagram of a typical prokaryotic cell.
 


Comparison of eukaryotes vs. prokaryotes.
 


Phylogenetic ring showing the diversity of prokaryotes, and symbiogenetic origins of eukaryotes.
 


Phylogenetic and symbiogenetic tree of living organisms, showing the origins of eukaryotes and prokaryotes.
 


Diagram of the origin of life with the Eukaryotes appearing early, not derived from Prokaryotes, as proposed by Richard Egel in 2012. This view, one of many on the relative positions of Prokaryotes and Eukaryotes, implies that the universal common ancestor was relatively large and complex.

📂 Prokaryote

Prokaryote

prokaryote is unicellular organism that lacks a membrane-bound nucleus, mitochondria, or any other membrane-bound organelle. The word prokaryote comes from the Greek πρό (pro, 'before') and κάρυον (karyon, 'nut' or 'kernel'). Prokaryotes are divided into two domains, Archaea and Bacteria. Organisms with nuclei and other organelles are placed in a third domain, Eukaryota. Prokaryotes are asexual, reproducing without fusion of gametes. The first organisms are thought to have been prokaryotes.

In prokaryotes, all of the intracellular water-soluble components – proteins, DNA and metabolites – are located in the cytoplasm enclosed by the cell membrane, rather than in separate cellular compartments. Bacteria, however, do possess protein-based microcompartments, which are thought to act as primitive organelles enclosed in protein shells. Some prokaryotes, such as cyanobacteria, may form large colonies. Others, such as myxobacteria, have multicellular stages in their life cycles.

Molecular studies have provided insight into the evolution and interrelationships of the three domains of life. Eukaryotic cells have a well-defined membrane-bound nucleus that contains chromosomal DNA and other membrane-bound organelles including mitochondria. The division between prokaryotes and eukaryotes reflects the existence of two very different levels of cellular organization. Distinctive types of prokaryotes include extremophiles and methanogens; these are common in some extreme environments.

 





protist
protist  is any eukaryotic organism (one with cells containing a nucleus) that is not an animal, plant, or fungus. The protists do not form a natural group, or clade, since they exclude certain eukaryotes with whom they share a common ancestor, i.e. some protists are more closely related to plants or animals than they are to other protists. However, like algae or invertebrates, the grouping is used for convenience. In some systems of biological classification, such as the popular five-kingdom scheme proposed by Robert Whittaker in 1969, the protists make up a kingdom called Protista, composed of eukaryotic "organisms which are unicellular or unicellular-colonial and which form no tissues." (W)


protocell

protocell (or protobiont) is a self-organized, endogenously ordered, spherical collection of lipids proposed as a stepping-stone toward the origin of life. A central question in evolution is how simple protocells first arose and how they could differ in reproductive output, thus enabling the accumulation of novel biological emergences over time, i.e. biological evolution. Although a functional protocell has not yet been achieved in a laboratory setting, the goal to understand the process appears well within reach. (W)



The three main structures phospholipids form in solution; the liposome (a closed bilayer), the micelle and the bilayer.



Scheme of a micelle spontaneously formed by phospholipids in an aqueous solution.

📥 Protocell (W)

 







r
replication, DNA

In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritance. The cell possesses the distinctive property of division, which makes replication of DNA essential.

DNA is made up of a double helix of two complementary strands. During replication, these strands are separated. Each strand of the original DNA molecule then serves as a template for the production of its counterpart, a process referred to as semiconservative replication. As a result of semi-conservative replication, the new helix will be composed of an original DNA strand as well as a newly synthesized strand. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication.

In a cell, DNA replication begins at specific locations, or origins of replication, in the genome. Unwinding of DNA at the origin and synthesis of new strands, accommodated by an enzyme known as helicase, results in replication forks growing bi-directionally from the origin. A number of proteins are associated with the replication fork to help in the initiation and continuation of DNA synthesis. Most prominently, DNA polymerase synthesizes the new strands by adding nucleotides that complement each (template) strand. DNA replication occurs during the S-stage of interphase.

DNA replication (DNA amplification) can also be performed in vitro (artificially, outside a cell). DNA polymerases isolated from cells and artificial DNA primers can be used to start DNA synthesis at known sequences in a template DNA molecule. Polymerase chain reaction (PCR), ligase chain reaction (LCR), and transcription-mediated amplification (TMA) are examples. (W)




DNA replication: The double helix is un'zipped' and unwound, then each separated strand (turquoise) acts as a template for replicating a new partner strand (green). Nucleotides (bases) are matched to synthesize the new partner strands into two new double helices..


ribosome


Ribosomes are macromolecular machines, found within all living cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to form polypeptide chains. Ribosomes consist of two major components: the small and large ribosomal subunits. Each subunit consists of one or more ribosomal RNA (rRNA) molecules and many ribosomal proteins (RPs or r-proteins). The ribosomes and associated molecules are also known as the translational apparatus. (W)



3.
Ribosome (little dots)

 



Ribosomes assemble polymeric protein molecules whose sequence is controlled by the sequence of messenger RNA molecules. This is required by all living cells and associated viruses..


ribozyme


Ribozymes (ribonucleic acid enzymes) are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes. The 1982 discovery of ribozymes demonstrated that RNA can be both genetic material (like DNA) and a biological catalyst (like protein enzymes), and contributed to the RNA world hypothesis, which suggests that RNA may have been important in the evolution of prebiotic self-replicating systems. The most common activities of natural or in vitro-evolved ribozymes are the cleavage or ligation of RNA and DNA and peptide bond formation. Within the ribosome, ribozymes function as part of the large subunit ribosomal RNA to link amino acids during protein synthesis. They also participate in a variety of RNA processing reactions, including RNA splicing, viral replication, and transfer RNA biosynthesis. Examples of ribozymes include the hammerhead ribozyme, the VS ribozyme, Leadzyme and the hairpin ribozyme.


Investigators studying the origin of life have produced ribozymes in the laboratory that are capable of catalyzing their own synthesis from activated monomers under very specific conditions, such as an RNA polymerase ribozyme. Mutagenesis and selection has been performed resulting in isolation of improved variants of the "Round-18" polymerase ribozyme from 2001. "B6.61" is able to add up to 20 nucleotides to a primer template in 24 hours, until it decomposes by cleavage of its phosphodiester bonds. The "tC19Z" ribozyme can add up to 95 nucleotides with a fidelity of 0.0083 mutations/nucleotide.


Attempts have been made to develop ribozymes as therapeutic agents, as enzymes which target defined RNA sequences for cleavage, as biosensors, and for applications in functional genomics and gene discovery. (W)



3D structure of a hammerhead ribozyme.



Schematic showing ribozyme cleavage of RNA.



Image showing the diversity of ribozyme structures. From left to right: leadzyme, hammerhead ribozyme, twister ribozyme.




s

species

 
   

In biology, a species  is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. Other ways of defining species include their karyotypeDNA sequence, morphology, behaviour or ecological niche. In addition, paleontologists use the concept of the chronospecies since fossil reproduction cannot be examined. The total number of species is estimated to be between 8 and 8.7 million. However the vast majority of them are not studied or documented and it may take over 1000 years to fully catalogue them all.


All species (except viruses) are given a two-part name, a "binomial". The first part of a binomial is the genus to which the species belongs. The second part is called the specific name or the specific epithet (in botanical nomenclature, also sometimes in zoological nomenclature). For example, Boa constrictor is one of four species of the genus Boa, with constrictor being the species’ epithet.

While the definitions given above may seem adequate, when looked at more closely they represent problematic species concepts. For example, the boundaries between closely related species become unclear with hybridisation, in a species complex of hundreds of similar microspecies, and in a ring species. Also, among organisms that reproduce only asexually, the concept of a reproductive species breaks down, and each clone is potentially a microspecies. Though none of these are entirely satisfactory definitions, scientists and conservationists need a species definition which allows them to work, regardless of the theoretical difficulties. If species were fixed and clearly distinct from one another, there would be no problem, but evolutionary processes cause species to change continually, and to grade into one another.


Species were seen from the time of Aristotle until the 18th century as fixed categories that could be arranged in a hierarchy, the great chain of being. In the 19th century, biologists grasped that species could evolve given sufficient time. Charles Darwin's 1859 book The Origin of Species explained how species could arise by natural selection. That understanding was greatly extended in the 20th century through genetics and population ecology. Genetic variability arises from mutations and recombination, while organisms themselves are mobile, leading to geographical isolation and genetic drift with varying selection pressures. Genes can sometimes be exchanged between species by horizontal gene transfer; new species can arise rapidly through hybridisation and polyploidy; and species may become extinct for a variety of reasons. Viruses are a special case, driven by a balance of mutation and selection, and can be treated as quasispecies. (W)



symbiogenesis
Symbiogenesis, or endosymbiotic theory, is an evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms, first articulated in 1905 and 1910 by the Russian botanist Konstantin Mereschkowski, and advanced and substantiated with microbiological evidence by Lynn Margulis in 1967. It holds that the organelles distinguishing eukaryote cells evolved through symbiosis of individual single-celled prokaryotes (bacteria and archaea). The theory holds that mitochondria, plastids such as chloroplasts, and possibly other organelles of eukaryotic cells are descended from formerly free-living prokaryotes taken one inside the other in endosymbiosis. Mitochondria appear to be phylogenetically related to Rickettsiales proteobacteria, and chloroplasts to nitrogen-fixing filamentous cyanobacteria. Among the many lines of evidence supporting symbiogenesis are that new mitochondria and plastids are formed only through binary fission, and that cells cannot create new ones otherwise; that the transport proteins called porins are found in the outer membranes of mitochondria, chloroplasts and bacterial cell membranes; that cardiolipin is found only in the inner mitochondrial membrane and bacterial cell membranes; and that some mitochondria and plastids contain single circular DNA molecules similar to the chromosomes of bacteria. (W)

One model for the origin of mitochondria and plastids (L)
🔎



synapse

In the nervous system, a synapse is a structure that permits a neuron (or nerve cell) to pass an electrical or chemical signal to another neuron or to the target effector cell (W)



Different types of synapses.



t
three-domain system

The three-domain system is a biological classification introduced by Carl Woese et al. in 1990 that divides cellular life forms into archaeabacteria, and eukaryote domains. The key difference from earlier classifications is the splitting of archaea from bacteria. (W)




phylogenetic tree based on rRNA data, emphasizing the separation of bacteria, archaea, and eukaryotes, as proposed by Carl Woese et al. in 1990.



translation (biology)


In molecular biology and geneticstranslation is the process in which ribosomes in the cytoplasm or ER synthesize proteins after the process of transcription of DNA to RNA in the cell's nucleus. The entire process is called gene expression.


In translation, messenger RNA (mRNA) is decoded in the ribosome decoding center to produce a specific amino acid chain, or polypeptide. The polypeptide later folds into an active protein and performs its functions in the cell. The ribosome facilitates decoding by inducing the binding of complementary tRNA anticodon sequences to mRNA codons. The tRNAs carry specific amino acids that are chained together into a polypeptide as the mRNA passes through and is read by the ribosome.


Translation proceeds in three phases:

  1. Initiation: The ribosome assembles around the target mRNA. The first tRNA is attached at the start codon.
  2. Elongation: The tRNA transfers an amino acid to the tRNA corresponding to the next codon. The ribosome then moves (translocates) to the next mRNA codon to continue the process, creating an amino acid chain.
  3. Termination: When a peptidyl tRNA encounters a stop codon, then the ribosome folds the polypeptide into its final structure.

In prokaryotes (unicellular), translation occurs in the cytosol, where the medium and small subunits of the ribosome bind to the tRNA. In eukaryotes, translation occurs in the cytosol or across the membrane of the endoplasmic reticulum in a process called co-translational translocation. In co-translational translocation, the entire ribosome/mRNA complex binds to the outer membrane of the rough endoplasmic reticulum (ER) and the new protein is synthesized and released into the ER; the newly created polypeptide can be stored inside the ER for future vesicle transport and secretion outside the cell, or immediately secreted.


Many types of transcribed RNA, such as transfer RNA, ribosomal RNA, and small nuclear RNA, do not undergo translation into proteins.

A number of antibiotics act by inhibiting translation. These include clindamycinanisomycincycloheximidechloramphenicoltetracyclinestreptomycinerythromycin, and puromycin. Prokaryotic ribosomes have a different structure from that of eukaryotic ribosomes, and thus antibiotics can specifically target bacterial infections without any harm to a eukaryotic host's cells. (W)



Diagram showing the translation of mRNA and the synthesis of proteins by a ribosome.

 



Tertiary structure of tRNA. CCA tail in yellow, Acceptor stem in purple, Variable loop in orange, D arm in red, Anticodon arm in blue with Anticodon in black, T arm in green.



Overview of the translation of eukaryotic messenger RNA


 


İdea Yayınevi Site Haritası | İdea Yayınevi Tüm Yayınlar
© Aziz Yardımlı 2020 | aziz@ideayayınevi.com