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105-564: Many authors have incorrectly assumed that the 'C' in "C-value" refers to "characteristic", "content", or "complement". Even among authors who have attempted to trace the origin of the term, there had been some confusion because Hewson Swift did not define it explicitly when he coined it in 1950. In his original paper, Swift appeared to use the designation "1C value", "2C value", etc., in reference to "classes" of DNA content (e.g., Gregory 2001, 2002); however, Swift explained in personal correspondence to Prof. Michael D. Bennett in 1975 that "I am afraid

210-405: A Mendelian pattern. These laws of inheritance were described extensively by Gregor Mendel , who performed experiments with pea plants to determine how traits were passed on from generation to generation. He studied phenotypes that were easily observed, such as plant height, petal color, or seed shape. He was able to observe that if he crossed two true-breeding plants with distinct phenotypes, all

315-516: A carboxyl group, and a variable side chain are bonded . Only proline differs from this basic structure as it contains an unusual ring to the N-end amine group, which forces the CO–NH amide moiety into a fixed conformation. The side chains of the standard amino acids, detailed in the list of standard amino acids , have a great variety of chemical structures and properties; it is the combined effect of all of

420-470: A gene may be duplicated before it can mutate freely. However, this can also lead to complete loss of gene function and thus pseudo-genes . More commonly, single amino acid changes have limited consequences although some can change protein function substantially, especially in enzymes . For instance, many enzymes can change their substrate specificity by one or a few mutations. Changes in substrate specificity are facilitated by substrate promiscuity , i.e.

525-448: A Mendelian fashion, but have more complex patterns of inheritance. For some traits, neither allele is completely dominant. Heterozygotes often have an appearance somewhere in between those of homozygotes. For example, a cross between true-breeding red and white Mirabilis jalapa results in pink flowers. Codominance refers to traits in which both alleles are expressed in the offspring in approximately equal amounts. A classic example

630-402: A Y chromosome from their father. X-linked dominant conditions can be distinguished from autosomal dominant conditions in pedigrees by the lack of transmission from fathers to sons, since affected fathers only pass their X chromosome to their daughters. In X-linked recessive conditions, males are typically affected more commonly because they are hemizygous, with only one X chromosome. In females,

735-552: A combination of sequence, structure and function, and they can be combined in many different ways. In an early study of 170,000 proteins, about two-thirds were assigned at least one domain, with larger proteins containing more domains (e.g. proteins larger than 600 amino acids having an average of more than 5 domains). Most proteins consist of linear polymers built from series of up to 20 different L -α- amino acids. All proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group,

840-423: A complete understanding of genome size evolution is to be achieved (Gregory 2005). Moreover, the term paradox implies a lack of understanding of one of the most basic features of eukaryotic genomes: namely that they are composed primarily of non-coding DNA . Some have claimed that the term paradox also has the unfortunate tendency to lead authors to seek simple one-dimensional solutions to what is, in actuality,

945-461: A copy of the recessive allele in order to have an affected offspring, the parents are referred to as carriers of the condition. In autosomal conditions, the sex of the offspring does not play a role in their risk of being affected. In sex-linked conditions, the sex of the offspring affects their chances of having the condition. In humans, females inherit two X chromosomes , one from each parent, while males inherit an X chromosome from their mother and

1050-403: A defined conformation . Proteins can interact with many types of molecules, including with other proteins , with lipids , with carbohydrates , and with DNA . It has been estimated that average-sized bacteria contain about 2 million proteins per cell (e.g. E. coli and Staphylococcus aureus ). Smaller bacteria, such as Mycoplasma or spirochetes contain fewer molecules, on

1155-834: A detailed review of the vegetable proteins at the Connecticut Agricultural Experiment Station . Then, working with Lafayette Mendel and applying Liebig's law of the minimum , which states that growth is limited by the scarcest resource, to the feeding of laboratory rats, the nutritionally essential amino acids were established. The work was continued and communicated by William Cumming Rose . The difficulty in purifying proteins in large quantities made them very difficult for early protein biochemists to study. Hence, early studies focused on proteins that could be purified in large quantities, including those of blood, egg whites, and various toxins, as well as digestive and metabolic enzymes obtained from slaughterhouses. In

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1260-460: A dominant "A" allele codes for brown hair, and a recessive "a" allele codes for blonde hair, but a separate "B" gene controls hair growth, and a recessive "b" allele causes baldness. If the individual has the BB or Bb genotype, then they produce hair and the hair color phenotype can be observed, but if the individual has a bb genotype, then the person is bald which masks the A gene entirely. A polygenic trait

1365-411: A genotype of Bb. The offspring can inherit a dominant allele from each parent, making them homozygous with a genotype of BB. The offspring can inherit a dominant allele from one parent and a recessive allele from the other parent, making them heterozygous with a genotype of Bb. Finally, the offspring could inherit a recessive allele from each parent, making them homozygous with a genotype of bb. Plants with

1470-478: A little ambiguous and can overlap in meaning. Protein is generally used to refer to the complete biological molecule in a stable conformation , whereas peptide is generally reserved for a short amino acid oligomers often lacking a stable 3D structure. But the boundary between the two is not well defined and usually lies near 20–30 residues. Polypeptide can refer to any single linear chain of amino acids, usually regardless of length, but often implies an absence of

1575-519: A loss of one H 2 O molecule. Further, phosphates of nucleotides in the DNA chain are acidic, so at physiologic pH the H ion is dissociated. Provided the ratio of A/T to G/C pairs is 1:1 (the GC-content is 50%), the mean relative mass of one nucleotide pair is 615.8771. The relative molecular mass may be converted to an absolute value by multiplying it by the atomic mass unit (1 u) in picograms. Thus, 615.8771

1680-552: A multi-faceted puzzle. For these reasons, in 2003 the term "C-value enigma" was endorsed in preference to "C-value paradox" at the Second Plant Genome Size Discussion Meeting and Workshop at the Royal Botanic Gardens, Kew , UK , and an increasing number of authors have begun adopting this term. In 1948, Roger and Colette Vendrely reported a "remarkable constancy in the nuclear DNA content of all

1785-410: A particular cell or cell type is known as its proteome . The chief characteristic of proteins that also allows their diverse set of functions is their ability to bind other molecules specifically and tightly. The region of the protein responsible for binding another molecule is known as the binding site and is often a depression or "pocket" on the molecular surface. This binding ability is mediated by

1890-500: A protein carries out its function: for example, enzyme kinetics studies explore the chemical mechanism of an enzyme's catalytic activity and its relative affinity for various possible substrate molecules. By contrast, in vivo experiments can provide information about the physiological role of a protein in the context of a cell or even a whole organism . In silico studies use computational methods to study proteins. Proteins may be purified from other cellular components using

1995-411: A protein is defined by the sequence of a gene, which is encoded in the genetic code . In general, the genetic code specifies 20 standard amino acids; but in certain organisms the genetic code can include selenocysteine and—in certain archaea — pyrrolysine . Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification , which alters

2100-539: A protein that fold into distinct structural units. Domains usually also have specific functions, such as enzymatic activities (e.g. kinase ) or they serve as binding modules (e.g. the SH3 domain binds to proline-rich sequences in other proteins). Short amino acid sequences within proteins often act as recognition sites for other proteins. For instance, SH3 domains typically bind to short PxxP motifs (i.e. 2 prolines [P], separated by two unspecified amino acids [x], although

2205-486: A role in biological recognition phenomena involving cells and proteins. Receptors and hormones are highly specific binding proteins. Transmembrane proteins can also serve as ligand transport proteins that alter the permeability of the cell membrane to small molecules and ions. The membrane alone has a hydrophobic core through which polar or charged molecules cannot diffuse . Membrane proteins contain internal channels that allow such molecules to enter and exit

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2310-406: A series of purification steps may be necessary to obtain protein sufficiently pure for laboratory applications. To simplify this process, genetic engineering is often used to add chemical features to proteins that make them easier to purify without affecting their structure or activity. Here, a "tag" consisting of a specific amino acid sequence, often a series of histidine residues (a " His-tag "),

2415-432: A solution known as a crude lysate . The resulting mixture can be purified using ultracentrifugation , which fractionates the various cellular components into fractions containing soluble proteins; membrane lipids and proteins; cellular organelles , and nucleic acids . Precipitation by a method known as salting out can concentrate the proteins from this lysate. Various types of chromatography are then used to isolate

2520-441: A variety of techniques such as ultracentrifugation , precipitation , electrophoresis , and chromatography ; the advent of genetic engineering has made possible a number of methods to facilitate purification. To perform in vitro analysis, a protein must be purified away from other cellular components. This process usually begins with cell lysis , in which a cell's membrane is disrupted and its internal contents released into

2625-441: Is a carrier for a particular condition. This can be done via a variety of techniques, including allele specific oligonucleotide (ASO) probes or DNA sequencing . Tools such as multiplex ligation-dependent probe amplification can also be used to look for duplications or deletions of genes or gene sections. Other techniques are meant to assess a large number of SNPs across the genome, such as SNP arrays . This type of technology

2730-449: Is an autosomal dominant condition, but up to 25% of individuals with the affected genotype will not develop symptoms until after age 50. Another factor that can complicate Mendelian inheritance patterns is variable expressivity , in which individuals with the same genotype show different signs or symptoms of disease. For example, individuals with polydactyly can have a variable number of extra digits. Many traits are not inherited in

2835-431: Is commonly used for genome-wide association studies . Large-scale techniques to assess the entire genome are also available. This includes karyotyping to determine the number of chromosomes an individual has and chromosomal microarrays to assess for large duplications or deletions in the chromosome. More detailed information can be determined using exome sequencing , which provides the specific sequence of all DNA in

2940-562: Is dictated by the nucleotide sequence of their genes , and which usually results in protein folding into a specific 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide . A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides . The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in

3045-628: Is found in hard or filamentous structures such as hair , nails , feathers , hooves , and some animal shells . Some globular proteins can also play structural functions, for example, actin and tubulin are globular and soluble as monomers, but polymerize to form long, stiff fibers that make up the cytoskeleton , which allows the cell to maintain its shape and size. Other proteins that serve structural functions are motor proteins such as myosin , kinesin , and dynein , which are capable of generating mechanical forces. These proteins are crucial for cellular motility of single celled organisms and

3150-469: Is higher in prokaryotes than eukaryotes and can reach up to 20 amino acids per second. The process of synthesizing a protein from an mRNA template is known as translation . The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its base pairing anticodon located on a transfer RNA molecule, which carries the amino acid corresponding to the codon it recognizes. The enzyme aminoacyl tRNA synthetase "charges"

3255-461: Is inefficient for polypeptides longer than about 300 amino acids, and the synthesized proteins may not readily assume their native tertiary structure . Most chemical synthesis methods proceed from C-terminus to N-terminus, opposite the biological reaction. Most proteins fold into unique 3D structures. The shape into which a protein naturally folds is known as its native conformation . Although many proteins can fold unassisted, simply through

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3360-494: Is its complete set of genetic material. Genotype can also be used to refer to the alleles or variants an individual carries in a particular gene or genetic location. The number of alleles an individual can have in a specific gene depends on the number of copies of each chromosome found in that species, also referred to as ploidy . In diploid species like humans, two full sets of chromosomes are present, meaning each individual has two alleles for any given gene. If both alleles are

3465-456: Is multiplied by 1.660539 × 10 pg. Consequently, the mean mass per nucleotide pair would be 1.023 × 10 pg, and 1 pg of DNA would represent 0.978 × 10 base pairs (978 Mbp). No species has a GC-content of exactly 50% (equal amounts of A/T and G/C nucleotide bases) as assumed by Doležel et al. However, as a G/C pair is only heavier than an A/T pair by about 1/6 of 1%, the effect of variations in GC content

3570-404: Is often enormous—as much as 10 -fold increase in rate over the uncatalysed reaction in the case of orotate decarboxylase (78 million years without the enzyme, 18 milliseconds with the enzyme). The molecules bound and acted upon by enzymes are called substrates . Although enzymes can consist of hundreds of amino acids, it is usually only a small fraction of the residues that come in contact with

3675-408: Is one whose phenotype is dependent on the additive effects of multiple genes. The contributions of each of these genes are typically small and add up to a final phenotype with a large amount of variation. A well studied example of this is the number of sensory bristles on a fly. These types of additive effects is also the explanation for the amount of variation in human eye color. Genotyping refers to

3780-632: Is responsible for the difference in the size of the two gametes. When the gametes are combined, the XX female zygote has a size of 6,062,084,834 bp while the XY male zygote has a size 5,963,271,354 bp. However, the base pairs of the XX female zygote are distributed among 2 homologous groups of 23 heterologous chromosomes each, while the base pairs of the XY male zygote are distributed among 2 homologous groups of 22 heterologous chromosomes each plus 2 heterologous chromosomes. Although each zygote has 46 chromosomes, 23 chromosomes of

3885-476: Is small. The actual GC content varies between species, between chromosomes, and between isochores (sections of a chromosome with like GC content). Adjusting Doležel's calculation for GC content, the theoretical variation in base pairs per picogram ranges from 977.0317 Mbp/pg for 100% GC content to 978.6005 Mbp/pg for 0% GC content (A/T being lighter, has more Mbp/pg), with a midpoint of 977.8155 Mbp/pg for 50% GC content. The human genome varies in size; however,

3990-510: Is the ABO blood group system in humans, where both the A and B alleles are expressed when they are present. Individuals with the AB genotype have both A and B proteins expressed on their red blood cells. Epistasis is when the phenotype of one gene is affected by one or more other genes. This is often through some sort of masking effect of one gene on the other. For example, the "A" gene codes for hair color,

4095-486: Is the code for methionine . Because DNA contains four nucleotides, the total number of possible codons is 64; hence, there is some redundancy in the genetic code, with some amino acids specified by more than one codon. Genes encoded in DNA are first transcribed into pre- messenger RNA (mRNA) by proteins such as RNA polymerase . Most organisms then process the pre-mRNA (also known as a primary transcript ) using various forms of post-transcriptional modification to form

4200-493: Is the complex puzzle surrounding the extensive variation in nuclear genome size among eukaryotic species. At the center of the C-value enigma is the observation that genome size does not correlate with organismal complexity; for example, some single-celled protists have genomes much larger than that of humans . Some prefer the term C-value enigma because it explicitly includes all of the questions that will need to be answered if

4305-407: Is using a Punnett square . In a Punnett square, the genotypes of the parents are placed on the outside. An uppercase letter is typically used to represent the dominant allele, and a lowercase letter is used to represent the recessive allele. The possible genotypes of the offspring can then be determined by combining the parent genotypes. In the example on the right, both parents are heterozygous, with

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4410-486: The amino acid leucine for which he found a (nearly correct) molecular weight of 131 Da . Early nutritional scientists such as the German Carl von Voit believed that protein was the most important nutrient for maintaining the structure of the body, because it was generally believed that "flesh makes flesh." Around 1862, Karl Heinrich Ritthausen isolated the amino acid glutamic acid . Thomas Burr Osborne compiled

4515-464: The complexity of the organism ). For example, the cells of some salamanders may contain 40 times more DNA than those of humans. Given that C-values were assumed to be constant because genetic information is encoded by DNA, and yet bore no relationship to presumed gene number, this was understandably considered paradoxical ; the term "C-value paradox" was used to describe this situation by C.A. Thomas Jr. in 1971. The discovery of repetitive DNA in

4620-607: The genomes of different eukaryotes. The C-value enigma, unlike the older C-value paradox, is explicitly defined as a series of independent but equally important component questions, including: †Source of table: Doležel et al. , 2003 The formulas for converting the number of nucleotide pairs (or base pairs) to picograms of DNA and vice versa are: By using the data in Table 1, relative masses of nucleotide pairs can be calculated as follows: A/T = 615.383 and G/C = 616.3711, bearing in mind that formation of one phosphodiester linkage involves

4725-644: The muscle sarcomere , with a molecular mass of almost 3,000 kDa and a total length of almost 27,000 amino acids. Short proteins can also be synthesized chemically by a family of methods known as peptide synthesis , which rely on organic synthesis techniques such as chemical ligation to produce peptides in high yield. Chemical synthesis allows for the introduction of non-natural amino acids into polypeptide chains, such as attachment of fluorescent probes to amino acid side chains. These methods are useful in laboratory biochemistry and cell biology , though generally not for commercial applications. Chemical synthesis

4830-645: The sperm of many multicellular organisms which reproduce sexually . They also generate the forces exerted by contracting muscles and play essential roles in intracellular transport. A key question in molecular biology is how proteins evolve, i.e. how can mutations (or rather changes in amino acid sequence) lead to new structures and functions? Most amino acids in a protein can be changed without disrupting activity or function, as can be seen from numerous homologous proteins across species (as collected in specialized databases for protein families , e.g. PFAM ). In order to prevent dramatic consequences of mutations,

4935-493: The 1700s by Antoine Fourcroy and others, who often collectively called them " albumins ", or "albuminous materials" ( Eiweisskörper , in German). Gluten , for example, was first separated from wheat in published research around 1747, and later determined to exist in many plants. In 1789, Antoine Fourcroy recognized three distinct varieties of animal proteins: albumin , fibrin , and gelatin . Vegetable (plant) proteins studied in

5040-562: The 1950s, the Armour Hot Dog Company purified 1 kg of pure bovine pancreatic ribonuclease A and made it freely available to scientists; this gesture helped ribonuclease A become a major target for biochemical study for the following decades. The understanding of proteins as polypeptides , or chains of amino acids, came through the work of Franz Hofmeister and Hermann Emil Fischer in 1902. The central role of proteins as enzymes in living organisms that catalyzed reactions

5145-498: The 20,000 or so proteins encoded by the human genome, only 6,000 are detected in lymphoblastoid cells. Proteins are assembled from amino acids using information encoded in genes. Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein. The genetic code is a set of three-nucleotide sets called codons and each three-nucleotide combination designates an amino acid, for example AUG ( adenine – uracil – guanine )

5250-671: The BB and Bb genotypes will look the same, since the B allele is dominant. The plant with the bb genotype will have the recessive trait. These inheritance patterns can also be applied to hereditary diseases or conditions in humans or animals. Some conditions are inherited in an autosomal dominant pattern, meaning individuals with the condition typically have an affected parent as well. A classic pedigree for an autosomal dominant condition shows affected individuals in every generation. Other conditions are inherited in an autosomal recessive pattern, where affected individuals do not typically have an affected parent. Since each parent must have

5355-516: The EC number system provides a functional classification scheme. Similarly, the gene ontology classifies both genes and proteins by their biological and biochemical function, but also by their intracellular location. Sequence similarity is used to classify proteins both in terms of evolutionary and functional similarity. This may use either whole proteins or protein domains , especially in multi-domain proteins . Protein domains allow protein classification by

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5460-477: The XX female zygote are heterologous while 24 chromosomes of the XY male zygote are heterologous. As a result, the C-value for the XX female zygote is 3.099361 while the C-value for the XY male zygote is 3.157877. The human genome's GC content is about 41%. Accounting for the autosomal, X, and Y chromosomes, human haploid GC contents are 40.97460% for X gametes, and 41.01724% for Y gametes. Summarizing these numbers: Genotype The genotype of an organism

5565-709: The ability of many enzymes to bind and process multiple substrates . When mutations occur, the specificity of an enzyme can increase (or decrease) and thus its enzymatic activity. Thus, bacteria (or other organisms) can adapt to different food sources, including unnatural substrates such as plastic. Methods commonly used to study protein structure and function include immunohistochemistry , site-directed mutagenesis , X-ray crystallography , nuclear magnetic resonance and mass spectrometry . The activities and structures of proteins may be examined in vitro , in vivo , and in silico . In vitro studies of purified proteins in controlled environments are useful for learning how

5670-405: The addition of a single methyl group to a binding partner can sometimes suffice to nearly eliminate binding; for example, the aminoacyl tRNA synthetase specific to the amino acid valine discriminates against the very similar side chain of the amino acid isoleucine . Proteins can bind to other proteins as well as to small-molecule substrates. When proteins bind specifically to other copies of

5775-464: The alleles present in the pea plant. However, other traits are only partially influenced by genotype. These traits are often called complex traits because they are influenced by additional factors, such as environmental and epigenetic factors. Not all individuals with the same genotype look or act the same way because appearance and behavior are modified by environmental and growing conditions. Likewise, not all organisms that look alike necessarily have

5880-595: The alpha carbons are roughly coplanar . The other two dihedral angles in the peptide bond determine the local shape assumed by the protein backbone. The end with a free amino group is known as the N-terminus or amino terminus, whereas the end of the protein with a free carboxyl group is known as the C-terminus or carboxy terminus (the sequence of the protein is written from N-terminus to C-terminus, from left to right). The words protein , polypeptide, and peptide are

5985-531: The amino acid side chains in a protein that ultimately determines its three-dimensional structure and its chemical reactivity. The amino acids in a polypeptide chain are linked by peptide bonds . Once linked in the protein chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen, and oxygen atoms are known as the main chain or protein backbone. The peptide bond has two resonance forms that contribute some double-bond character and inhibit rotation around its axis, so that

6090-574: The binding of a substrate molecule to an enzyme's active site , or the physical region of the protein that participates in chemical catalysis. In solution, proteins also undergo variation in structure through thermal vibration and the collision with other molecules. Proteins can be informally divided into three main classes, which correlate with typical tertiary structures: globular proteins , fibrous proteins , and membrane proteins . Almost all globular proteins are soluble and many are enzymes. Fibrous proteins are often structural, such as collagen ,

6195-570: The body of a multicellular organism. These proteins must have a high binding affinity when their ligand is present in high concentrations, but must also release the ligand when it is present at low concentrations in the target tissues. The canonical example of a ligand-binding protein is haemoglobin , which transports oxygen from the lungs to other organs and tissues in all vertebrates and has close homologs in every biological kingdom . Lectins are sugar-binding proteins which are highly specific for their sugar moieties. Lectins typically play

6300-558: The cell is as enzymes , which catalyse chemical reactions. Enzymes are usually highly specific and accelerate only one or a few chemical reactions. Enzymes carry out most of the reactions involved in metabolism , as well as manipulating DNA in processes such as DNA replication , DNA repair , and transcription . Some enzymes act on other proteins to add or remove chemical groups in a process known as posttranslational modification. About 4,000 reactions are known to be catalysed by enzymes. The rate acceleration conferred by enzymatic catalysis

6405-436: The cell surface and an effector domain within the cell, which may have enzymatic activity or may undergo a conformational change detected by other proteins within the cell. Antibodies are protein components of an adaptive immune system whose main function is to bind antigens , or foreign substances in the body, and target them for destruction. Antibodies can be secreted into the extracellular environment or anchored in

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6510-752: The cell's machinery through the process of protein turnover . A protein's lifespan is measured in terms of its half-life and covers a wide range. They can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal or misfolded proteins are degraded more rapidly either due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids , proteins are essential parts of organisms and participate in virtually every process within cells . Many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism . Proteins also have structural or mechanical functions, such as actin and myosin in muscle and

6615-450: The cell. Many ion channel proteins are specialized to select for only a particular ion; for example, potassium and sodium channels often discriminate for only one of the two ions. Structural proteins confer stiffness and rigidity to otherwise-fluid biological components. Most structural proteins are fibrous proteins ; for example, collagen and elastin are critical components of connective tissue such as cartilage , and keratin

6720-403: The cells in all the individuals within a given animal species", which they took as evidence that DNA , rather than protein , was the substance of which genes are composed. The term C-value reflects this observed constancy. However, it was soon found that C-values ( genome sizes ) vary enormously among species and that this bears no relationship to the presumed number of genes ( as reflected by

6825-621: The chemical properties of their amino acids, others require the aid of molecular chaperones to fold into their native states. Biochemists often refer to four distinct aspects of a protein's structure: Proteins are not entirely rigid molecules. In addition to these levels of structure, proteins may shift between several related structures while they perform their functions. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as " conformations ", and transitions between them are called conformational changes. Such changes are often induced by

6930-441: The chief actors within the cell, said to be carrying out the duties specified by the information encoded in genes. With the exception of certain types of RNA , most other biological molecules are relatively inert elements upon which proteins act. Proteins make up half the dry weight of an Escherichia coli cell, whereas other macromolecules such as DNA and RNA make up only 3% and 20%, respectively. The set of proteins expressed in

7035-442: The coding region of the genome, or whole genome sequencing , which sequences the entire genome including non-coding regions. In linear models, the genotypes can be encoded in different manners. Let us consider a biallelic locus with two possible alleles, encoded by A {\textstyle A} and a {\displaystyle a} . We consider a {\displaystyle a} to correspond to

7140-502: The complexity of the organism or the number of genes contained in its genome; for example, some single-celled protists have genomes much larger than that of humans . This observation was deemed counterintuitive before the discovery of repetitive DNA . It became known as the C-value paradox as a result. However, although there is no longer any paradoxical aspect to the discrepancy between C-value and gene number, this term remains in common usage. For reasons of conceptual clarification,

7245-490: The construction of enormously complex signaling networks. As interactions between proteins are reversible, and depend heavily on the availability of different groups of partner proteins to form aggregates that are capable to carry out discrete sets of function, study of the interactions between specific proteins is a key to understand important aspects of cellular function, and ultimately the properties that distinguish particular cell types. The best-known role of proteins in

7350-407: The current estimate of the nuclear haploid size of the reference human genome is 3,031,042,417 bp for the X gamete and 2,932,228,937 bp for the Y gamete. The X gamete and Y gamete both contain 22 autosomes whose combined lengths comprise the majority of the genome in both gametes. The X gamete contains an X chromosome , while the Y gamete contains a Y chromosome . The larger size of the X chromosome

7455-408: The derivative unit kilodalton (kDa). The average size of a protein increases from Archaea to Bacteria to Eukaryote (283, 311, 438 residues and 31, 34, 49 kDa respectively) due to a bigger number of protein domains constituting proteins in higher organisms. For instance, yeast proteins are on average 466 amino acids long and 53 kDa in mass. The largest known proteins are the titins , a component of

7560-669: The dominant allele to the reference allele A {\textstyle A} . The following table details the different encoding. Protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues . Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions , DNA replication , responding to stimuli , providing structure to cells and organisms , and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which

7665-447: The erroneous conclusion that they might be composed of a single type of (very large) molecule. The term "protein" to describe these molecules was proposed by Mulder's associate Berzelius; protein is derived from the Greek word πρώτειος ( proteios ), meaning "primary", "in the lead", or "standing in front", + -in . Mulder went on to identify the products of protein degradation such as

7770-411: The example above, the three genotypes would be CC, CT and TT. Other types of genetic marker , such as microsatellites , can have more than two alleles, and thus many different genotypes. Penetrance is the proportion of individuals showing a specified genotype in their phenotype under a given set of environmental conditions. Traits that are determined exclusively by genotype are typically inherited in

7875-459: The first two have the same phenotype (purple) as distinct from the third (white). A more technical example to illustrate genotype is the single-nucleotide polymorphism or SNP. A SNP occurs when corresponding sequences of DNA from different individuals differ at one DNA base, for example where the sequence AAGCCTA changes to AAGCTTA. This contains two alleles : C and T. SNPs typically have three genotypes, denoted generically AA Aa and aa. In

7980-471: The haploid DNA content of individual species and retains this usage today. C-values vary enormously among species. In animals they range more than 3,300-fold, and in land plants they differ by a factor of about 1,000. Protist genomes have been reported to vary more than 300,000-fold in size, but the high end of this range ( Amoeba ) has been called into question. Variation in C-values bears no relationship to

8085-525: The late 1700s and early 1800s included gluten , plant albumin , gliadin , and legumin . Proteins were first described by the Dutch chemist Gerardus Johannes Mulder and named by the Swedish chemist Jöns Jacob Berzelius in 1838. Mulder carried out elemental analysis of common proteins and found that nearly all proteins had the same empirical formula , C 400 H 620 N 100 O 120 P 1 S 1 . He came to

8190-450: The late 1960s resolved the main question of the C-value paradox: genome size does not reflect gene number in eukaryotes since most of the excess DNA in many species appears to be Junk DNA . The human genome , for example, contains about 10% functional elements and the remaining 90% is thought to be junk. Species with larger genomes are thought to contain a higher proportion of junk DNA. The term "C-value enigma" represents an update of

8295-663: The letter C stood for nothing more glamorous than 'constant', i.e., the amount of DNA that was characteristic of a particular genotype " (quoted in Bennett and Leitch 2005). This is in reference to the report in 1948 by Vendrely and Vendrely of a "remarkable constancy in the nuclear DNA content of all the cells in all the individuals within a given animal species" (translated from the original French ). Swift's study of this topic related specifically to variation (or lack thereof) among chromosome sets in different cell types within individuals, but his notation evolved into "C-value" in reference to

8400-478: The major component of connective tissue, or keratin , the protein component of hair and nails. Membrane proteins often serve as receptors or provide channels for polar or charged molecules to pass through the cell membrane . A special case of intramolecular hydrogen bonds within proteins, poorly shielded from water attack and hence promoting their own dehydration , are called dehydrons . Many proteins are composed of several protein domains , i.e. segments of

8505-443: The mature mRNA, which is then used as a template for protein synthesis by the ribosome . In prokaryotes the mRNA may either be used as soon as it is produced, or be bound by a ribosome after having moved away from the nucleoid . In contrast, eukaryotes make mRNA in the cell nucleus and then translocate it across the nuclear membrane into the cytoplasm , where protein synthesis then takes place. The rate of protein synthesis

8610-405: The membranes of specialized B cells known as plasma cells . Whereas enzymes are limited in their binding affinity for their substrates by the necessity of conducting their reaction, antibodies have no such constraints. An antibody's binding affinity to its target is extraordinarily high. Many ligand transport proteins bind particular small biomolecules and transport them to other locations in

8715-444: The method used to determine an individual's genotype. There are a variety of techniques that can be used to assess genotype. The genotyping method typically depends on what information is being sought. Many techniques initially require amplification of the DNA sample, which is commonly done using PCR . Some techniques are designed to investigate specific SNPs or alleles in a particular gene or set of genes, such as whether an individual

8820-458: The more common but outdated term "C-value paradox" (Thomas 1971), being ultimately derived from the term "C-value" (Swift 1950) in reference to haploid nuclear DNA contents. The term was coined by Canadian biologist Dr. T. Ryan Gregory of the University of Guelph in 2000/2001. In general terms, the C-value enigma relates to the issue of variation in the amount of non-coding DNA found within

8925-496: The nobel prize in 1972, solidified the thermodynamic hypothesis of protein folding, according to which the folded form of a protein represents its free energy minimum. With the development of X-ray crystallography , it became possible to determine protein structures as well as their sequences. The first protein structures to be solved were hemoglobin by Max Perutz and myoglobin by John Kendrew , in 1958. The use of computers and increasing computing power also supported

9030-401: The offspring would have the same phenotype. For example, when he crossed a tall plant with a short plant, all the resulting plants would be tall. However, when he self-fertilized the plants that resulted, about 1/4 of the second generation would be short. He concluded that some traits were dominant , such as tall height, and others were recessive, like short height. Though Mendel was not aware at

9135-500: The order of 50,000 to 1 million. By contrast, eukaryotic cells are larger and thus contain much more protein. For instance, yeast cells have been estimated to contain about 50 million proteins and human cells on the order of 1 to 3 billion. The concentration of individual protein copies ranges from a few molecules per cell up to 20 million. Not all genes coding proteins are expressed in most cells and their number depends on, for example, cell type and external stimuli. For instance, of

9240-440: The physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Some proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors . Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes . Once formed, proteins only exist for a certain period and are then degraded and recycled by

9345-543: The presence of a second X chromosome will prevent the condition from appearing. Females are therefore carriers of the condition and can pass the trait on to their sons. Mendelian patterns of inheritance can be complicated by additional factors. Some diseases show incomplete penetrance , meaning not all individuals with the disease-causing allele develop signs or symptoms of the disease. Penetrance can also be age-dependent, meaning signs or symptoms of disease are not visible until later in life. For example, Huntington disease

9450-424: The process of cell signaling and signal transduction . Some proteins, such as insulin , are extracellular proteins that transmit a signal from the cell in which they were synthesized to other cells in distant tissues . Others are membrane proteins that act as receptors whose main function is to bind a signaling molecule and induce a biochemical response in the cell. Many receptors have a binding site exposed on

9555-534: The protein or proteins of interest based on properties such as molecular weight, net charge and binding affinity. The level of purification can be monitored using various types of gel electrophoresis if the desired protein's molecular weight and isoelectric point are known, by spectroscopy if the protein has distinguishable spectroscopic features, or by enzyme assays if the protein has enzymatic activity. Additionally, proteins can be isolated according to their charge using electrofocusing . For natural proteins,

9660-427: The proteins in the cytoskeleton , which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses , cell adhesion , and the cell cycle . In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized . Digestion breaks the proteins down for metabolic use. Proteins have been studied and recognized since

9765-609: The same genotype. The term genotype was coined by the Danish botanist Wilhelm Johannsen in 1903. Any given gene will usually cause an observable change in an organism, known as the phenotype. The terms genotype and phenotype are distinct for at least two reasons: A simple example to illustrate genotype as distinct from phenotype is the flower colour in pea plants (see Gregor Mendel ). There are three available genotypes, PP ( homozygous dominant ), Pp (heterozygous), and pp (homozygous recessive). All three have different genotypes but

9870-582: The same molecule, they can oligomerize to form fibrils; this process occurs often in structural proteins that consist of globular monomers that self-associate to form rigid fibers. Protein–protein interactions also regulate enzymatic activity, control progression through the cell cycle , and allow the assembly of large protein complexes that carry out many closely related reactions with a common biological function. Proteins can also bind to, or even be integrated into, cell membranes. The ability of binding partners to induce conformational changes in proteins allows

9975-444: The same, the genotype is referred to as homozygous . If the alleles are different, the genotype is referred to as heterozygous. Genotype contributes to phenotype , the observable traits and characteristics in an individual or organism. The degree to which genotype affects phenotype depends on the trait. For example, the petal color in a pea plant is exclusively determined by genotype. The petals can be purple or white depending on

10080-573: The sample, allowing scientists to obtain more information and analyze larger structures. Computational protein structure prediction of small protein structural domains has also helped researchers to approach atomic-level resolution of protein structures. As of April 2024 , the Protein Data Bank contains 181,018 X-ray, 19,809 EM and 12,697 NMR protein structures. Proteins are primarily classified by sequence and structure, although other classifications are commonly used. Especially for enzymes

10185-430: The sequencing of complex proteins. In 1999, Roger Kornberg succeeded in sequencing the highly complex structure of RNA polymerase using high intensity X-rays from synchrotrons . Since then, cryo-electron microscopy (cryo-EM) of large macromolecular assemblies has been developed. Cryo-EM uses protein samples that are frozen rather than crystals, and beams of electrons rather than X-rays. It causes less damage to

10290-405: The substrate, and an even smaller fraction—three to four residues on average—that are directly involved in catalysis. The region of the enzyme that binds the substrate and contains the catalytic residues is known as the active site . Dirigent proteins are members of a class of proteins that dictate the stereochemistry of a compound synthesized by other enzymes. Many proteins are involved in

10395-706: The surrounding amino acids may determine the exact binding specificity). Many such motifs has been collected in the Eukaryotic Linear Motif (ELM) database. Topology of a protein describes the entanglement of the backbone and the arrangement of contacts within the folded chain. Two theoretical frameworks of knot theory and Circuit topology have been applied to characterise protein topology. Being able to describe protein topology opens up new pathways for protein engineering and pharmaceutical development, and adds to our understanding of protein misfolding diseases such as neuromuscular disorders and cancer. Proteins are

10500-400: The tRNA molecules with the correct amino acids. The growing polypeptide is often termed the nascent chain . Proteins are always biosynthesized from N-terminus to C-terminus . The size of a synthesized protein can be measured by the number of amino acids it contains and by its total molecular mass , which is normally reported in units of daltons (synonymous with atomic mass units ), or

10605-472: The tertiary structure of the protein, which defines the binding site pocket, and by the chemical properties of the surrounding amino acids' side chains. Protein binding can be extraordinarily tight and specific; for example, the ribonuclease inhibitor protein binds to human angiogenin with a sub-femtomolar dissociation constant (<10 M) but does not bind at all to its amphibian homolog onconase (> 1 M). Extremely minor chemical changes such as

10710-413: The time, each phenotype he studied was controlled by a single gene with two alleles. In the case of plant height, one allele caused the plants to be tall, and the other caused plants to be short. When the tall allele was present, the plant would be tall, even if the plant was heterozygous. In order for the plant to be short, it had to be homozygous for the recessive allele. One way this can be illustrated

10815-578: The various puzzles that remain with regard to genome size variation instead have been suggested to more accurately comprise a complex but clearly defined puzzle known as the C-value enigma. C-values correlate with a range of features at the cell and organism levels, including cell size , cell division rate, and, depending on the taxon , body size, metabolic rate , developmental rate, organ complexity, geographical distribution, or extinction risk (for recent reviews, see Bennett and Leitch 2005; Gregory 2005). The C-value enigma or C-value paradox

10920-466: Was insulin , by Frederick Sanger , in 1949. Sanger correctly determined the amino acid sequence of insulin, thus conclusively demonstrating that proteins consisted of linear polymers of amino acids rather than branched chains, colloids , or cyclols . He won the Nobel Prize for this achievement in 1958. Christian Anfinsen 's studies of the oxidative folding process of ribonuclease A, for which he won

11025-581: Was not fully appreciated until 1926, when James B. Sumner showed that the enzyme urease was in fact a protein. Linus Pauling is credited with the successful prediction of regular protein secondary structures based on hydrogen bonding , an idea first put forth by William Astbury in 1933. Later work by Walter Kauzmann on denaturation , based partly on previous studies by Kaj Linderstrøm-Lang , contributed an understanding of protein folding and structure mediated by hydrophobic interactions . The first protein to have its amino acid chain sequenced

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