Misplaced Pages

#278721

95-601: KaiC is a gene belonging to the KaiABC gene cluster (with KaiA , and KaiB ) that, together, regulate bacterial circadian rhythms , specifically in cyanobacteria . KaiC encodes the KaiC protein, which interacts with the KaiA and KaiB proteins in a post-translational oscillator (PTO). The PTO is cyanobacteria master clock that is controlled by sequences of phosphorylation of KaiC protein. Regulation of KaiABC expression and KaiABC phosphorylation

190-584: A promoter sequence. The promoter is recognized and bound by transcription factors that recruit and help RNA polymerase bind to the region to initiate transcription. The recognition typically occurs as a consensus sequence like the TATA box . A gene can have more than one promoter, resulting in messenger RNAs ( mRNA ) that differ in how far they extend in the 5' end. Highly transcribed genes have "strong" promoter sequences that form strong associations with transcription factors, thereby initiating transcription at

285-521: A " start codon ", and three " stop codons " indicate the beginning and end of the protein coding region . There are 64 possible codons (four possible nucleotides at each of three positions, hence 4  possible codons) and only 20 standard amino acids; hence the code is redundant and multiple codons can specify the same amino acid. The correspondence between codons and amino acids is nearly universal among all known living organisms. Lysis Many species of bacteria are subject to lysis by

380-548: A bacterial luciferase reporter to monitor the expression of clock-controlled gene psbAI in Synechococcus, they investigated and reported on the rescue to normal rhythmicity of long-period clock mutant C44a (with a period of 44 hours) by kaiABC. They inserted wild-type DNA through a pNIBB7942 plasmid vector into the C44a mutant, and generated clones that restored normal period (a period of 25 hours). They were eventually able to localize

475-474: A change in the period of their circadian rhythms. Gene In biology , the word gene has two meanings. The Mendelian gene is a basic unit of heredity . The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA . There are two types of molecular genes: protein-coding genes and non-coding genes. During gene expression (the synthesis of RNA or protein from

570-424: A circadian oscillator in vitro in the presence of only KaiA, KaiB, KaiC, and ATP has sparked interest in the relationship between cellular biochemical oscillators and their associated transcription-translation feedback loops (TTFLs). TTFLs have long been assumed to be the core of circadian rhythmicity, but that claim is now being tested again due to the possibility that the biochemical oscillators could constitute

665-445: A continuous messenger RNA , referred to as a polycistronic mRNA . The term cistron in this context is equivalent to gene. The transcription of an operon's mRNA is often controlled by a repressor that can occur in an active or inactive state depending on the presence of specific metabolites. When active, the repressor binds to a DNA sequence at the beginning of the operon, called the operator region , and represses transcription of

760-569: A double-domain structure and sequence that classifies it as part of the RecA gene family of ATP-dependent recombinases . Based on a number of single-domain homologous genes in other species, KaiC is hypothesized to have horizontally transferred from Bacteria to Archaea, eventually forming the double-domain KaiC through duplication and fusion . KaiC' s key role in circadian control and homology to RecA suggest its individual evolution before its presence in

855-652: A double-doughnut structure and a central pore which is open at the N-terminal ends and partially sealed at the C-terminal ends due to the presence of six arginine residues. The hexamer has twelve ATP molecules between the N- (CI) and C-terminal (CII) domains, which demonstrate ATPase activity. The CI and CII domains are linked by the N-terminal region of the CII domain. The last 20 residues from

950-495: A double-helix run in opposite directions. Nucleic acid synthesis, including DNA replication and transcription occurs in the 5'→3' direction, because new nucleotides are added via a dehydration reaction that uses the exposed 3' hydroxyl as a nucleophile . The expression of genes encoded in DNA begins by transcribing the gene into RNA , a second type of nucleic acid that is very similar to DNA, but whose monomers contain

1045-488: A few genes and are transferable between individuals. For example, the genes for antibiotic resistance are usually encoded on bacterial plasmids and can be passed between individual cells, even those of different species, via horizontal gene transfer . Whereas the chromosomes of prokaryotes are relatively gene-dense, those of eukaryotes often contain regions of DNA that serve no obvious function. Simple single-celled eukaryotes have relatively small amounts of such DNA, whereas

SECTION 10

#1733085501279

1140-434: A gene - surprisingly, there is no definition that is entirely satisfactory. A gene is a DNA sequence that codes for a diffusible product. This product may be protein (as is the case in the majority of genes) or may be RNA (as is the case of genes that code for tRNA and rRNA). The crucial feature is that the product diffuses away from its site of synthesis to act elsewhere. The important parts of such definitions are: (1) that

1235-443: A gene can be found in the articles Genetics and Gene-centered view of evolution . The molecular gene definition is more commonly used across biochemistry, molecular biology, and most of genetics — the gene that is described in terms of DNA sequence. There are many different definitions of this gene — some of which are misleading or incorrect. Very early work in the field that became molecular genetics suggested

1330-565: A gene corresponds to a transcription unit; (2) that genes produce both mRNA and noncoding RNAs; and (3) regulatory sequences control gene expression but are not part of the gene itself. However, there's one other important part of the definition and it is emphasized in Kostas Kampourakis' book Making Sense of Genes . Therefore in this book I will consider genes as DNA sequences encoding information for functional products, be it proteins or RNA molecules. With 'encoding information', I mean that

1425-410: A gene may be split across chromosomes but those transcripts are concatenated back together into a functional sequence by trans-splicing . It is also possible for overlapping genes to share some of their DNA sequence, either on opposite strands or the same strand (in a different reading frame, or even the same reading frame). In all organisms, two steps are required to read the information encoded in

1520-404: A gene's DNA and produce the protein it specifies. First, the gene's DNA is transcribed to messenger RNA ( mRNA ). Second, that mRNA is translated to protein. RNA-coding genes must still go through the first step, but are not translated into protein. The process of producing a biologically functional molecule of either RNA or protein is called gene expression , and the resulting molecule

1615-411: A gene), DNA is first copied into RNA . RNA can be directly functional or be the intermediate template for the synthesis of a protein. The transmission of genes to an organism's offspring , is the basis of the inheritance of phenotypic traits from one generation to the next. These genes make up different DNA sequences, together called a genotype , that is specific to every given individual, within

1710-565: A gene: that of bacteriophage MS2 coat protein. The subsequent development of chain-termination DNA sequencing in 1977 by Frederick Sanger improved the efficiency of sequencing and turned it into a routine laboratory tool. An automated version of the Sanger method was used in early phases of the Human Genome Project . The theories developed in the early 20th century to integrate Mendelian genetics with Darwinian evolution are called

1805-439: A gene; however, members of a population may have different alleles at the locus, each with a slightly different gene sequence. The majority of eukaryotic genes are stored on a set of large, linear chromosomes. The chromosomes are packed within the nucleus in complex with storage proteins called histones to form a unit called a nucleosome . DNA packaged and condensed in this way is called chromatin . The manner in which DNA

1900-448: A high rate. Others genes have "weak" promoters that form weak associations with transcription factors and initiate transcription less frequently. Eukaryotic promoter regions are much more complex and difficult to identify than prokaryotic promoters. Additionally, genes can have regulatory regions many kilobases upstream or downstream of the gene that alter expression. These act by binding to transcription factors which then cause

1995-572: A new expanded definition that includes noncoding genes. However, some modern writers still do not acknowledge noncoding genes although this so-called "new" definition has been recognised for more than half a century. Although some definitions can be more broadly applicable than others, the fundamental complexity of biology means that no definition of a gene can capture all aspects perfectly. Not all genomes are DNA (e.g. RNA viruses ), bacterial operons are multiple protein-coding regions transcribed into single large mRNAs, alternative splicing enables

SECTION 20

#1733085501279

2090-408: A period of approximately 24 hours when placed in vitro with the three recombinant Kai proteins, incubated with ATP. The circadian rhythm of KaiC phosphorylation persists in constant darkness, regardless of Synechococcus transcription rates . This oscillation rate is thought to be controlled by the ratio of phosphorylated to unphosphorylated KaiC protein. KaiC phosphorylation ratio is a main factor in

2185-606: A phase-dependent shift in the phase of the KaiC phosphorylation rhythms. The period of the circadian clock was not changed, reinforcing the temperature compensation of the clock mechanism. A 2012 study out of Vanderbilt University shows evidence that KaiC acts as a phospho-transferase that hands back phosphates to ADP on the T432 (threonine residue at position 432) and S431 (serine residue 431) indicating that KaiC effectively serves as an ATP synthase . Various KaiC mutants have been identified and their phenotypes studied. Many mutants show

2280-400: A process known as RNA splicing . Finally, the ends of gene transcripts are defined by cleavage and polyadenylation (CPA) sites , where newly produced pre-mRNA gets cleaved and a string of ~200 adenosine monophosphates is added at the 3' end. The poly(A) tail protects mature mRNA from degradation and has other functions, affecting translation, localization, and transport of the transcript from

2375-419: A protein-coding gene consists of many elements of which the actual protein coding sequence is often only a small part. These include introns and untranslated regions of the mature mRNA. Noncoding genes can also contain introns that are removed during processing to produce the mature functional RNA. All genes are associated with regulatory sequences that are required for their expression. First, genes require

2470-520: A role for KaiC in transcription regulation. Further, the diameter of the rings in KaiC are suitable to accommodate single stranded DNA . Additionally, the surface potential at the CII ring and the C-terminal channel opening is mostly positive. The compatibility of the diameter as well as the surface potential charge suggests that DNA may be able to bind to the C-terminal channel opening. Kai proteins regulate genome-wide gene expression. Protein KaiA enhances

2565-412: A single genomic region to encode multiple district products and trans-splicing concatenates mRNAs from shorter coding sequence across the genome. Since molecular definitions exclude elements such as introns, promotors, and other regulatory regions , these are instead thought of as "associated" with the gene and affect its function. An even broader operational definition is sometimes used to encompass

2660-521: A slightly smaller amplitude than in vivo oscillation, proving that the KaiABC proteins are sufficient for circadian rhythm solely in the presence of ATP. Combined with the TTFL model, KaiABC as a circadian PTO was shown to be the fundamental clock regulator in S. elongatus On Synechococcus elongatus' singular circular chromosome, the protein-coding gene kaiC is located at position 380696-382255 (its locus tag

2755-472: A strict definition of the word "gene" with which nearly every expert can agree. First, in order for a nucleotide sequence to be considered a true gene, an open reading frame (ORF) must be present. The ORF can be thought of as the "gene itself"; it begins with a starting mark common for every gene and ends with one of three possible finish line signals. One of the key enzymes in this process, the RNA polymerase, zips along

2850-409: A true gene, by this definition, one has to prove that the transcript has a biological function. Early speculations on the size of a typical gene were based on high-resolution genetic mapping and on the size of proteins and RNA molecules. A length of 1500 base pairs seemed reasonable at the time (1965). This was based on the idea that the gene was the DNA that was directly responsible for production of

2945-456: Is called a gene product . The nucleotide sequence of a gene's DNA specifies the amino acid sequence of a protein through the genetic code . Sets of three nucleotides, known as codons , each correspond to a specific amino acid. The principle that three sequential bases of DNA code for each amino acid was demonstrated in 1961 using frameshift mutations in the rIIB gene of bacteriophage T4 (see Crick, Brenner et al. experiment ). Additionally,

KaiC - Misplaced Pages Continue

3040-498: Is crucial for Synechococcus circadian oscillation. The phosphorylation status of KaiC has been correlated with Synechococcus clock speed in vivo . Additionally, overexpression of KaiC has been shown to strongly repress the kaiBC promoter, while kaiA overexpression has experimentally enhanced the kaiBC promoter. These positive and negative binding elements mirror a feedback mechanism of rhythm generation conserved across many different species. KaiC phosphorylation oscillates with

3135-509: Is essential for cyanobacteria circadian rhythmicity , and is particularly important for regulating cyanobacteria processes such as nitrogen fixation , photosynthesis , and cell division . Studies have shown similarities to Drosophila , Neurospora , and mammalian clock models in that the kaiABC regulation of the cyanobacteria slave circadian clock is also based on a transcription translation feedback loop (TTFL). KaiC protein has both auto-kinase and auto-phosphatase activity and functions as

3230-400: Is nearly the same for all known organisms. The total complement of genes in an organism or cell is known as its genome , which may be stored on one or more chromosomes . A chromosome consists of a single, very long DNA helix on which thousands of genes are encoded. The region of the chromosome at which a particular gene is located is called its locus . Each locus contains one allele of

3325-403: Is still part of the definition of a gene in most textbooks. For example, The primary function of the genome is to produce RNA molecules. Selected portions of the DNA nucleotide sequence are copied into a corresponding RNA nucleotide sequence, which either encodes a protein (if it is an mRNA) or forms a 'structural' RNA, such as a transfer RNA (tRNA) or ribosomal RNA (rRNA) molecule. Each region of

3420-399: Is stored on the histones, as well as chemical modifications of the histone itself, regulate whether a particular region of DNA is accessible for gene expression . In addition to genes, eukaryotic chromosomes contain sequences involved in ensuring that the DNA is copied without degradation of end regions and sorted into daughter cells during cell division: replication origins , telomeres , and

3515-399: Is syc0334_d). The gene kaiC has paralogs kaiB (located 380338..380646) and kaiA (located 379394..380248). kaiC encodes the protein KaiC (519 amino acids ). KaiC acts as a non-specific transcription regulator that represses transcription of the kaiBC promoter. Its crystal structure has been solved at 2.8 Å resolution; it is a homohexameric complex (approximately 360 kDa ) with

3610-656: Is the most popular and simple approach. Chemical lysis chemically deteriorates/solubilizes the proteins and lipids present within the membrane of targeted cells. Common lysis buffers contain sodium hydroxide (NaOH) and sodium dodecyl sulfate (SDS). Cell lysis is best done at a pH range of 11.5-12.5. Although simple, it is a slow process, taking anywhere from 6 to 12 hours. This method uses ultrasonic waves to generate areas of high and low pressure which causes cavitation and in turn, cell lysis. Though this method usually comes out clean, it fails to be cost effective and consistent. This method uses physical penetration to pierce or cut

3705-549: Is thought to be the mechanism for basic circadian timing in Synechococcus . ∆kaiABC individuals, one of the more common mutants, grow just as well as wild type individuals but they lack rhythmicity. This is evidence that the kaiABC gene cluster is not necessary for growth. In addition to the PTO regulating the autokinase and autophosphatase activities of KaiC, there is also evidence for a TTFL, similar to other eukaryotes, that governs

3800-471: The GTPase super-family. KaiC shares structural similarities to several other proteins with hexameric rings, including RecA , DnaB and ATPases . The hexameric rings of KaiC closely resembles RecA, with 8 α-helices surrounding a twisted β-sheet made up of 7 strands. This structure favours the binding of a nucleotide at the carboxy-end of the β-sheet. KaiC’s structural similarities to these proteins suggests

3895-463: The KaiABC gene cluster. Masahiro Ishiura, Takao Kondo , Susan S. Golden , Carl H. Johnson , and their colleagues discovered the gene cluster in 1998 and named the gene cluster kaiABC, as "kai" means “cycle” in Japanese. They generated 19 different clock mutants that were mapped to kaiA, kaiB, and kaiC genes, and successfully cloned the gene cluster in the cyanobacteria Synechococcus elongatus . Using

KaiC - Misplaced Pages Continue

3990-511: The aging process. The centromere is required for binding spindle fibres to separate sister chromatids into daughter cells during cell division . Prokaryotes ( bacteria and archaea ) typically store their genomes on a single, large, circular chromosome . Similarly, some eukaryotic organelles contain a remnant circular chromosome with a small number of genes. Prokaryotes sometimes supplement their chromosome with additional small circles of DNA called plasmids , which usually encode only

4085-401: The central dogma of molecular biology , which states that proteins are translated from RNA , which is transcribed from DNA . This dogma has since been shown to have exceptions, such as reverse transcription in retroviruses . The modern study of genetics at the level of DNA is known as molecular genetics . In 1972, Walter Fiers and his team were the first to determine the sequence of

4180-419: The centromere . Replication origins are the sequence regions where DNA replication is initiated to make two copies of the chromosome. Telomeres are long stretches of repetitive sequences that cap the ends of the linear chromosomes and prevent degradation of coding and regulatory regions during DNA replication . The length of the telomeres decreases each time the genome is replicated and has been implicated in

4275-420: The contractile vacuole that exists in some paramecia , which rapidly pump water out of the cell. Cytolysis does not occur under normal conditions in plant cells because plant cells have a strong cell wall that contains the osmotic pressure, or turgor pressure , that would otherwise cause cytolysis to occur. Oncolysis is the destruction of neoplastic cells or of a tumour . The term is also used to refer to

4370-444: The gene pool of the population of a given species . The genotype, along with environmental and developmental factors, ultimately determines the phenotype of the individual. Most biological traits occur under the combined influence of polygenes (a set of different genes) and gene–environment interactions . Some genetic traits are instantly visible, such as eye color or the number of limbs, others are not, such as blood type ,

4465-549: The modern synthesis , a term introduced by Julian Huxley . This view of evolution was emphasized by George C. Williams ' gene-centric view of evolution . He proposed that the Mendelian gene is a unit of natural selection with the definition: "that which segregates and recombines with appreciable frequency." Related ideas emphasizing the centrality of Mendelian genes and the importance of natural selection in evolution were popularized by Richard Dawkins . The development of

4560-475: The neutral theory of evolution in the late 1960s led to the recognition that random genetic drift is a major player in evolution and that neutral theory should be the null hypothesis of molecular evolution. This led to the construction of phylogenetic trees and the development of the molecular clock , which is the basis of all dating techniques using DNA sequences. These techniques are not confined to molecular gene sequences but can be used on all DNA segments in

4655-750: The operon ; when the repressor is inactive transcription of the operon can occur (see e.g. Lac operon ). The products of operon genes typically have related functions and are involved in the same regulatory network . Though many genes have simple structures, as with much of biology, others can be quite complex or represent unusual edge-cases. Eukaryotic genes often have introns that are much larger than their exons, and those introns can even have other genes nested inside them . Associated enhancers may be many kilobase away, or even on entirely different chromosomes operating via physical contact between two chromosomes. A single gene can encode multiple different functional products by alternative splicing , and conversely

4750-413: The phosphorylation of KaiC proved to oscillate with daily rhythms in the absence of light. In addition to the TTFL model, the PTO model was hypothesized for the KaiABC phosphorylation cycle. Also in 2005, Nakajima et al. lysed S. elongatus and isolated KaiABC proteins. In test tubes containing only KaiABC proteins and ATP , in vitro phosphorylation of KaiC oscillated with a near 24 hour period with

4845-525: The C-terminal of the CII domain protrude from the doughnut to form what is called the A-loop. [1] Interfaces on KaiC's CII domain are sites for both auto-kinase and auto-phosphatase activity, both in vitro and in vivo . KaiC has two P loops or Walker’s motif As ( ATP -/ GTP -binding motifs) in the CI and CII domains; the CI domain also contains two DXXG (X represents any amino acid) motifs that are highly conserved among

SECTION 50

#1733085501279

4940-522: The CII domain of KaiC and sequesters KaiA from the C-terminals during subjective night, which inhibits phosphorylation and stimulates auto-phosphatase activity. [2] Dephosphorylation of T432 occurs followed by S431, returning KaiC to its original state. Disruption of KaiC’s CI domain results both in arrhythmia of kaiBC expression and a reduction of ATP-binding activity; this, along with in vitro autophosphorylation of KaiC indicate that ATP binding to KaiC

5035-404: The DNA helix that produces a functional RNA molecule constitutes a gene. We define a gene as a DNA sequence that is transcribed. This definition includes genes that do not encode proteins (not all transcripts are messenger RNA). The definition normally excludes regions of the genome that control transcription but are not themselves transcribed. We will encounter some exceptions to our definition of

5130-450: The DNA sequence is used as a template for the production of an RNA molecule or a protein that performs some function. The emphasis on function is essential because there are stretches of DNA that produce non-functional transcripts and they do not qualify as genes. These include obvious examples such as transcribed pseudogenes as well as less obvious examples such as junk RNA produced as noise due to transcription errors. In order to qualify as

5225-766: The DNA to loop so that the regulatory sequence (and bound transcription factor) become close to the RNA polymerase binding site. For example, enhancers increase transcription by binding an activator protein which then helps to recruit the RNA polymerase to the promoter; conversely silencers bind repressor proteins and make the DNA less available for RNA polymerase. The mature messenger RNA produced from protein-coding genes contains untranslated regions at both ends which contain binding sites for ribosomes , RNA-binding proteins , miRNA , as well as terminator , and start and stop codons . In addition, most eukaryotic open reading frames contain untranslated introns , which are removed and exons , which are connected together in

5320-510: The activation of kaiBC promoter as well. The kaiBC operon is transcribed in a circadian fashion and precedes KaiC build up by about 6 hours, a lag thought to play a role in feedback loops. kaiA , kaiB , and kaiC have been shown to be essential genetic components in Synechococcus elongatus for circadian rhythms. Experiments have also shown that KaiC enhances the KaiA-KaiB interaction in yeast cells and in vitro. This implies that there may be

5415-433: The adenines of one strand are paired with the thymines of the other strand, and so on. Due to the chemical composition of the pentose residues of the bases, DNA strands have directionality. One end of a DNA polymer contains an exposed hydroxyl group on the deoxyribose ; this is known as the 3' end of the molecule. The other end contains an exposed phosphate group; this is the 5' end . The two strands of

5510-521: The alleles. There are many different ways to use the term "gene" based on different aspects of their inheritance, selection, biological function, or molecular structure but most of these definitions fall into two categories, the Mendelian gene or the molecular gene. The Mendelian gene is the classical gene of genetics and it refers to any heritable trait. This is the gene described in The Selfish Gene . More thorough discussions of this version of

5605-544: The biochemical oscillator and an equally weighted coupled oscillator system in which both oscillators synchronize and influence the other oscillator. Both are coupled oscillator models that account for the high stability of the timing mechanism within Synechococcus . The biochemical oscillator relies on redundant molecular interactions based on the law of mass action , whereas the TTFL relies on cellular machinery that mediates translation, transcription, and degradation of mRNA and proteins. The different types of interactions driving

5700-423: The cell wall is completely lost and the penicillin was used on gram-positive bacteria , then the bacterium is referred to as a protoplast , but if penicillin was used on gram-negative bacteria , then it is called a spheroplast . Cytolysis occurs when a cell bursts due to an osmotic imbalance that has caused excess water to move into the cell. Cytolysis can be prevented by several different mechanisms, including

5795-458: The central mechanism of the clock system, regulating and operating within TTFLs that control output and restore proteins essential to the oscillators in organisms, such as the KaiABC system in Synechococcus . Two models have been proposed to describe the relationship between the biochemical and TTFL regulation of circadian rhythms: a master/slave oscillator system with the TTFL oscillator synchronizing to

SECTION 60

#1733085501279

5890-448: The choice of lysis mechanism; often it is desirable to avoid mechanical shear forces that would denature or degrade sensitive macromolecules, such as proteins and DNA , and different types of detergents can yield different results. The unprocessed solution immediately after lysis but before any further extraction steps is often referred to as a crude lysate . For example, lysis is used in western and Southern blotting to analyze

5985-509: The circadian regulator in both the PTO and the TTFL. KaiC has been found to not only suppress kaiBC when overexpressed, but also suppress circadian expression of all genes in the cyanobacterial genome . Though the KaiABC gene cluster has been found to exist only in cyanobacteria, evolutionarily KaiC contains homologs that occur in Archaea and Pseudomonadota . It is the oldest circadian gene that has been discovered in prokaryotes. KaiC has

6080-464: The circadian rhythm in outputs of the clock. By studying the structure and the activities of KaiC, several roles of KaiC in the TTFL were suggested. The similar structures of KaiC to the RecA/DnaB superfamily suggested a possible role for KaiC in direct DNA binding and promoting of transcription. KaiC knock-out(KO) experiments determined KaiC to be a negative regulator of the kaiBC promoter sequence but it

6175-402: The complexity of these diverse phenomena, where a gene is defined as a union of genomic sequences encoding a coherent set of potentially overlapping functional products. This definition categorizes genes by their functional products (proteins or RNA) rather than their specific DNA loci, with regulatory elements classified as gene-associated regions. The existence of discrete inheritable units

6270-434: The composition of specific proteins , lipids , and nucleic acids individually or as complexes . Depending on the detergent used, either all or some membranes are lysed. For example, if only the cell membrane is lysed then gradient centrifugation can be used to collect certain organelles . Lysis is also used for protein purification , DNA extraction , and RNA extraction . This method uses chemical disruption. It

6365-399: The concept that one gene makes one protein (originally 'one gene - one enzyme'). However, genes that produce repressor RNAs were proposed in the 1950s and by the 1960s, textbooks were using molecular gene definitions that included those that specified functional RNA molecules such as ribosomal RNA and tRNA (noncoding genes) as well as protein-coding genes. This idea of two kinds of genes

6460-524: The distinction between a heterozygote and homozygote , and the phenomenon of discontinuous inheritance. Prior to Mendel's work, the dominant theory of heredity was one of blending inheritance , which suggested that each parent contributed fluids to the fertilization process and that the traits of the parents blended and mixed to produce the offspring. Charles Darwin developed a theory of inheritance he termed pangenesis , from Greek pan ("all, whole") and genesis ("birth") / genos ("origin"). Darwin used

6555-410: The early 1950s the prevailing view was that the genes in a chromosome acted like discrete entities arranged like beads on a string. The experiments of Benzer using mutants defective in the rII region of bacteriophage T4 (1955–1959) showed that individual genes have a simple linear structure and are likely to be equivalent to a linear section of DNA. Collectively, this body of research established

6650-427: The enzyme lysozyme , found in animal saliva , egg white , and other secretions . Phage lytic enzymes ( lysins ) produced during bacteriophage infection are responsible for the ability of these viruses to lyse bacterial cells. Penicillin and related β-lactam antibiotics cause the death of bacteria through enzyme-mediated lysis that occurs after the drug causes the bacterium to form a defective cell wall . If

6745-514: The fact that both protein-coding genes and noncoding genes have been known for more than 50 years, there are still a number of textbooks, websites, and scientific publications that define a gene as a DNA sequence that specifies a protein. In other words, the definition is restricted to protein-coding genes. Here is an example from a recent article in American Scientist. ... to truly assess the potential significance of de novo genes, we relied on

6840-450: The formation of a heteromultimeric complex composed of the three Kai proteins with KaiC serving as a bridge between KaiA and KaiB. Alternatively, KaiC may form a heterodimer with KaiA or KaiB to induce a conformational change. Variations in the C-terminal region of each of their proteins suggest functional divergence between the Kai clock proteins, however there are critical interdependencies between

6935-413: The functional product. The discovery of introns in the 1970s meant that many eukaryotic genes were much larger than the size of the functional product would imply. Typical mammalian protein-coding genes, for example, are about 62,000 base pairs in length (transcribed region) and since there are about 20,000 of them they occupy about 35–40% of the mammalian genome (including the human genome). In spite of

7030-450: The gene region causing this rescue, and observed circadian rhythmicity in upstream promotor activity of kaiA and kaiB, as well as in the expression of kaiA and kaiBC messenger RNA . They determined abolishing any of the three kai genes would cause arrhythmicity in the circadian clock and reduce kaiBC promoter activity. KaiC was later found to have both autokinase and autophosphatase activity. These findings suggested that circadian rhythm

7125-421: The genome. The vast majority of organisms encode their genes in long strands of DNA (deoxyribonucleic acid). DNA consists of a chain made from four types of nucleotide subunits, each composed of: a five-carbon sugar ( 2-deoxyribose ), a phosphate group, and one of the four bases adenine , cytosine , guanine , and thymine . Two chains of DNA twist around each other to form a DNA double helix with

7220-421: The genomes of complex multicellular organisms , including humans, contain an absolute majority of DNA without an identified function. This DNA has often been referred to as " junk DNA ". However, more recent analyses suggest that, although protein-coding DNA makes up barely 2% of the human genome , about 80% of the bases in the genome may be expressed, so the term "junk DNA" may be a misnomer. The structure of

7315-458: The mother cell. The circadian gating of cell division may be a protective feature to prevent division at a vulnerable phase. Phases in which KaiC has high ATPase activity do not allow for cell division to take place. In mutants with constantly elevated KaiC ATPase activity, the protein CikA is absent. CikA is a major factor in the input pathway and causes KaiC-dependent cell elongation. The recreation of

7410-413: The nucleus. Splicing, followed by CPA, generate the final mature mRNA , which encodes the protein or RNA product. Many noncoding genes in eukaryotes have different transcription termination mechanisms and they do not have poly(A) tails. Many prokaryotic genes are organized into operons , with multiple protein-coding sequences that are transcribed as a unit. The genes in an operon are transcribed as

7505-408: The oscillations in the cell cycle and circadian rhythms of Synechococcus are linked together through a one way mechanism. The circadian clock gates cells division, only allowing it to proceed at certain phases. The cell cycle does not appear to have any effect on the circadian clock, though. When binary fission occurs, the daughter cells inherit the mother cell's circadian clock and are in phase with

7600-413: The pathogens. Cell lysis is used in laboratories to break open cells and purify or further study their contents. Lysis in the laboratory may be affected by enzymes or detergents or other chaotropic agents . Mechanical disruption of cell membranes, as by repeated freezing and thawing, sonication , pressure, or filtration may also be referred to as lysis. Many laboratory experiments are sensitive to

7695-431: The phosphate–sugar backbone spiralling around the outside, and the bases pointing inward with adenine base pairing to thymine and guanine to cytosine. The specificity of base pairing occurs because adenine and thymine align to form two hydrogen bonds , whereas cytosine and guanine form three hydrogen bonds. The two strands in a double helix must, therefore, be complementary , with their sequence of bases matching such that

7790-400: The phosphorylation of protein KaiC by binding to the A loop of the CII domain to promote auto-kinase activity during subjective day. Phosphorylation at subunits occurs in an ordered manner, beginning with phosphorylation of Threonine 432 (T432) followed by Serine 431 (S431) on the CII domain. This leads to tight stacking of the CII domain to the CI domain. KaiB then binds to the exposed B loop on

7885-486: The reduction of any swelling . Plasmolysis is the contraction of cells within plants due to the loss of water through osmosis . In a hypertonic environment, the cell membrane peels off the cell wall and the vacuole collapses. These cells will eventually wilt and die unless the flow of water caused by osmosis can stop the contraction of the cell membrane . Erythrocytes' hemoglobin release free radicals in response to pathogens when lysed by them. This can damage

7980-431: The risk for specific diseases, or the thousands of basic biochemical processes that constitute life . A gene can acquire mutations in its sequence , leading to different variants, known as alleles , in the population . These alleles encode slightly different versions of a gene, which may cause different phenotypical traits. Genes evolve due to natural selection or survival of the fittest and genetic drift of

8075-467: The strand of DNA like a train on a monorail, transcribing it into its messenger RNA form. This point brings us to our second important criterion: A true gene is one that is both transcribed and translated. That is, a true gene is first used as a template to make transient messenger RNA, which is then translated into a protein. This restricted definition is so common that it has spawned many recent articles that criticize this "standard definition" and call for

8170-461: The sugar ribose rather than deoxyribose . RNA also contains the base uracil in place of thymine . RNA molecules are less stable than DNA and are typically single-stranded. Genes that encode proteins are composed of a series of three- nucleotide sequences called codons , which serve as the "words" in the genetic "language". The genetic code specifies the correspondence during protein translation between codons and amino acids . The genetic code

8265-805: The term gemmule to describe hypothetical particles that would mix during reproduction. Mendel's work went largely unnoticed after its first publication in 1866, but was rediscovered in the late 19th century by Hugo de Vries , Carl Correns , and Erich von Tschermak , who (claimed to have) reached similar conclusions in their own research. Specifically, in 1889, Hugo de Vries published his book Intracellular Pangenesis , in which he postulated that different characters have individual hereditary carriers and that inheritance of specific traits in organisms comes in particles. De Vries called these units "pangenes" ( Pangens in German), after Darwin's 1868 pangenesis theory. Twenty years later, in 1909, Wilhelm Johannsen introduced

8360-436: The term gene , he explained his results in terms of discrete inherited units that give rise to observable physical characteristics. This description prefigured Wilhelm Johannsen 's distinction between genotype (the genetic material of an organism) and phenotype (the observable traits of that organism). Mendel was also the first to demonstrate independent assortment , the distinction between dominant and recessive traits,

8455-412: The term "gene" (inspired by the ancient Greek : γόνος, gonos , meaning offspring and procreation) and, in 1906, William Bateson , that of " genetics " while Eduard Strasburger , among others, still used the term "pangene" for the fundamental physical and functional unit of heredity. Advances in understanding genes and inheritance continued throughout the 20th century. Deoxyribonucleic acid (DNA)

8550-414: The three paralogs. Cyanobacteria are the simplest organisms with a known mechanism for the generation of circadian rhythms . KaiC ATPase activity is temperature compensated from 25 to 50 degrees Celsius and has a Q10 of about 1.1 (Q10 values around 1 indicate temperature compensation). Because the period of KaiC phosphorylation is temperature compensated and agrees with in vivo circadian rhythms, KaiC

8645-525: The two oscillators allows the circadian clock to be resilient to changes within the cell, such as metabolic fluctuation, temperature changes, and cell division. Though the period of the circadian clock is temperature compensated, the phosphorylation of KaiC can be stably entrained to a temperature cycle. The phosphorylation of KaiC was successfully entrained in vitro to temperature cycles with periods between 20 and 28 hours using temperature steps from 30 °C to 45 °C and vice versa. The results reflect

8740-420: Was controlled by a TTFL mechanism, which is consistent with other known biological clocks. In 2000, S. elongatus was observed in constant dark (DD) and constant light (LL). In DD, transcription and translation halted due to the absence of light but the circadian mechanism showed no significant phase shift after transitioning to constant light. In 2005, after closer examination of the KaiABC protein interactions,

8835-446: Was first suggested by Gregor Mendel (1822–1884). From 1857 to 1864, in Brno , Austrian Empire (today's Czech Republic), he studied inheritance patterns in 8000 common edible pea plants , tracking distinct traits from parent to offspring. He described these mathematically as 2  combinations where n is the number of differing characteristics in the original peas. Although he did not use

8930-406: Was found working through a separate, SasA/RpaA pathway, as KaiC was found to be not a transcription factor. However, elimination of the PTO did not fully eliminate the rhythmicity in kaiBC promoter activities, suggesting that the PTO is not necessary in generating rhythms in the TTFL. In truth, the activities of KaiC outside of the PTO is still relatively unknown. Recent experiments have found that

9025-430: Was shown to be the molecular repository of genetic information by experiments in the 1940s to 1950s. The structure of DNA was studied by Rosalind Franklin and Maurice Wilkins using X-ray crystallography , which led James D. Watson and Francis Crick to publish a model of the double-stranded DNA molecule whose paired nucleotide bases indicated a compelling hypothesis for the mechanism of genetic replication. In

#278721