Conservapedia - User contributions [en]

Intron

2008-07-23T22:58:37Z

JohnDavis: expand

An '''Intron''' is a non-protein-coding sequence of [[DNA]] that is initially copied into [[RNA]] but is cut out of the final RNA transcript (mature mRNA). They are found in most multicellular eukaryotes, but are rare in housekeeping genes and RNA-coding genes. They are also rare or absent in most unicellular eukaryotes and prokaryotes, but present in the DNA or RNA of viruses that infect eukaryotic cells. In contrast to introns, the protein-coding segments of DNA are called [[exon]]s. The presence of introns in many genes can cause problems with protein purification when bacteria are used to propagate a protein, as they lack the machinery to excise introns from genes. The presence of these foreign structures causes the bacteria to recognize and degrade the protein, in a specific reaction that may be part of the bacterial defense against bacteriophage infection. The gene containing the protein to be purified must therefore have its introns excised before being subcloned into a suitable plasmid. This is often done using a [[cDNA library]].

== Sources ==
http://www.genome.gov/glossary.cfm?key=intron

Molecular Cell Biology, 5th ed. Lodish et al. New York: W. H. Freeman and Co, 2004. pp 111-112.

[[Category:Genetics]]

Prokaryote

2008-07-23T22:52:03Z

JohnDavis: expand

The structure of a '''prokaryote''' is very much simpler than that of a [[eukaryote]]. There are no endomembranes, endosymbionts, nucleus or cytoskeleton. The [[DNA]] is carried on the genophore, a circular chromosome, in a ill defined area of the cytosol called the nucleoid. The chromosome is attached to the cell membrane during cell division (fission), frequently at a point called the mesosome.

#πρό-καρυον (pro-karyon) - before kernel.
#No nucleus - free circular genophore.
#'Simple' rotating motor-type flagellum.
#Cell division by fission, genophore attached to plasmalemma by mesosome.
#Few membrane-bound organelles, no double-membrane bound organelles.
#They are 'small' because diffusion limits the rate of transport across the cell - 1 μm.
[[Image:Bacterial_cell.png|center||Prokaryotes are characterised by the lack of a nucleus and membranes bound organelles.]]
The cytosol contains oil droplets, food reserves and the 70S ribosomes, and is surrounded by a plasmalemma. In Gram negative bacteria, a further outer membrane surrounds the plasmalemma, with a thin cell wall and periplasmic space trapped between them. In Gram positive bacteria, there is no outer membrane, and the cell wall is thicker. The cell wall is composed of peptidoglycan and various organic acids in Eubacteria. Bacteria have flagella, but they are simple proteinaceous strands attached to a rotary motor, completely dissimilar to the complex eukaryotic undulipodium. Membranes may be present in the cell, as in the thylakoids of the Cyanobacteria. In gram-positive bacteria the mambrane may form [[mesosome]]s, which are invaginations in the cell membrane that may be involved in DNA replication and oxidative phosphorylation. The cytosol may also contain various episomes (small circular chromosomes), some called plasmids, and others called (bacterio)phages, which are bacterial viruses.

Prokaryotes are extraordinarily diverse:

''Proteobacteria'' - Gram-negative, two cell membranes, hugely diverse, ''[[Escherichia coli]]''.

''Firmicutes'' and ''Actinobacteria'' - Gram-positive, thick peptidoglycan cell wall.

''Spirochaetes'' - helical bacteria.

Prokaryotic DNA lacks histones (packaging [[protein]]s), although other packaging proteins are present, and molecules have easier access to DNA compared with eukaryotes. They generally have efficient genomes, with little sequence other than coding sequence or regulatory sequence. Transcription leads to translation with no intermediate processing, which allows several genes to be encoded in a single transcriptional unit (a polycistron). No bacterial [[intron]]s exist. They have small (70S) ribosomes.

[[Category:Molecular Biology]]
[[Category:microbiology]]

Prokaryote

2008-07-23T22:48:08Z

JohnDavis: correct, multiple classes exist eg in archaea

The structure of a '''prokaryote''' is very much simpler than that of a [[eukaryote]]. There are no endomembranes, endosymbionts, nucleus or cytoskeleton. The [[DNA]] is carried on the genophore, a circular chromosome, in a ill defined area of the cytosol called the nucleoid. The chromosome is attached to the cell membrane during cell division (fission), frequently at a point called the mesosome.

#πρό-καρυον (pro-karyon) - before kernel.
#No nucleus - free circular genophore.
#'Simple' rotating motor-type flagellum.
#Cell division by fission, genophore attached to plasmalemma by mesosome.
#Few membrane-bound organelles, no double-membrane bound organelles.
#They are 'small' because diffusion limits the rate of transport across the cell - 1 μm.
[[Image:Bacterial_cell.png|center||Prokaryotes are characterised by the lack of a nucleus and membranes bound organelles.]]
The cytosol contains oil droplets, food reserves and the 70S ribosomes, and is surrounded by a plasmalemma. In Gram negative bacteria, a further outer membrane surrounds the plasmalemma, with a thin cell wall and periplasmic space trapped between them. In Gram positive bacteria, there is no outer membrane, and the cell wall is thicker. The cell wall is composed of peptidoglycan and various organic acids in Eubacteria. Bacteria have flagella, but they are simple proteinaceous strands attached to a rotary motor, completely dissimilar to the complex eukaryotic undulipodium. Membranes may be present in the cell, as in the thylakoids of the Cyanobacteria. The cytosol may also contain various episomes (small circular chromosomes), some called plasmids, and others called (bacterio)phages, which are bacterial viruses.

Prokaryotes are extraordinarily diverse:

''Proteobacteria'' - Gram-negative, two cell membranes, hugely diverse, ''[[Escherichia coli]]''.

''Firmicutes'' and ''Actinobacteria'' - Gram-positive, thick peptidoglycan cell wall.

''Spirochaetes'' - helical bacteria.

Prokaryotic DNA lacks histones (packaging [[protein]]s), although other packaging proteins are present, and molecules have easier access to DNA compared with eukaryotes. They generally have efficient genomes, with little sequence other than coding sequence or regulatory sequence. Transcription leads to translation with no intermediate processing, which allows several genes to be encoded in a single transcriptional unit (a polycistron). They have small (70S) ribosomes.

[[Category:Molecular Biology]]
[[Category:microbiology]]

Transcription (biology)

2008-07-23T22:46:47Z

JohnDavis: expand

'''Transcription''' is the biological process by which [[prokaryotic]] and [[eukaryotic]] cells generate single stranded [[RNA]]
through the enzymatic action of a specific isoform of [[RNA polymerase]]. It is the intermediary step in the production of [[protein|proteins]], and the final step for non-protein coding RNAs. Protein-coding genes are transcribed into mRNA which are then translated by the [[ribosome]] to create a nascent [[polypeptides|polypetide]] chain.

In virally-infected cells, both RNA and DNA can be transcribed, and the resulting double-stranded RNA is an alarm signal for infection, as it is captured by the [[RNA interference]] pathway, imported into the [[endplasmic reticulum]] and then displayed on the cell surface in a specific subtype of MHC class II molecules. These short interfering RNAs (siRNAs) cause the production of [[interferon]]s, and the activation of the immune system.

Non-protein coding RNAs are transcribed from [[DNA]] for the production of ribosomal RNA, transfer RNA, and small nuclear RNAs which serve various other functions in the cell. The biochemical process for transcription is similar to [[DNA replication]] in that it requires the action of multiple enzymes to unravel double-stranded genomic DNA, which allows an enzyme ([[polymerase]]) to processively catalyze the formation of a complementary strand based on proper [[nucleotide]] base pairing.

[[Category:Biology]]

Gene

2008-07-23T22:40:44Z

JohnDavis: /* History */ ref

The '''gene''' is the fundamental unit of [[heredity]].

A section of [[DNA]] that codes for the production of an [[RNA]] molecule. In most cases that RNA molecule codes for the production of a [[protein]], but in some cases (most notably the transfer RNA ([[tRNA]]) and ribosomal RNA ([[rRNA]]) genes) the RNA molecule is the end product.

Gene expression refers to all the processes involved in converting [[gene]]tic information from a [[DNA]] sequence, or [[protein]]. In [[prokaryote]]s, there are just two processes required: [[transcription]] and [[translation]]. In [[eukaryote]]s, there is an additional step [[RNA]] processing (splicing), which intervenes.
The synthesis of a single-stranded RNA molecule using DNA as a template is referred to as transcription. The enzyme that catalyzes this reaction is known as RNA polymerase. Although the subunit structure and details of the process differ significantly in prokaryotes and eukaryotes, the chemical reaction is identical.

==History==

By 1900 scientists knew that cells were the building blocks of living things. All living things start as a single fertilized cell which keeps dividing. Scientists identified tiny threads in the nucleus of the cells. Because they could stain the threads with colored dyes to study them under a microscope, they called the threads [[chromosome]]s, from the [[Greek]] words for colored bodies. They could see that chromosomes came in pairs, and that human cells all contained 23 matching pairs. American biologist [[Walter Sutton]] knew [[Mendel's principles of genetics|Mendel's]] work on peas, and suggested that chromosomes held the secret of inheritance.

Another American biologist, [[Thomas Hunt Morgan]], developed the idea that chromosomes were made up of linked groups of factors called [[genes]]. He experimented with red-eyed [[fruit fly|fruit flies]] and found that sometimes a white-eyed fly appeared. When he mated them, he found that as he expected there were three red-eyed flies to every white-eyed fly, but that all the white-eyed flies were male. He concluded that the gene for white eyes must be on a chromosome that was related to being male. Later workers found that this is why some hereditary diseases such as [[hemophilia]] and [[muscular dystrophy]] only show in males, though women can carry the gene for the disease without showing it.

Once Crick and Watson had unraveled the structure of [[DNA]], the function of genes became clearer.

One strand of [[DNA]] contains many genes. DNA is made of four [[nucleotide]]s, [[guanine]], [[adenine]], [[thymine]] and [[cytosine]]. G always pairs with C, and A with T. Different combinations of GC and AT join together in different orders along the strands of DNA coiled up along our [[chromosome]]s to give our cells instructions for making the different kind of protein of which our bodies are made. These groups of instructions are called genes. Our bodies are made up of about 100 trillion cells, each of which is responsible for a specific function. The thousands of different proteins in the cells work together like a machine to make the [[cell]] function as it should. If the genes are normal, the body part will function well. If a change (mutation) has happened in a gene, the protein may be faulty, as for example in sickle cell anemia where the instructions for making [[blood]] cells are abnormal.

In 2005 it was shown that genes were not the only way that genetic information could be inherited. Scientists working at Purdue University discovered that Arabidopsis plants could remember what genes they had in the past, and correct mistakes in their current genes. This non-mendelian inheritance probably involves a RNA cache of past messenger RNA transcripts.<ref>[http://www.ncbi.nlm.nih.gov/pubmed/15785770?ordinalpos=15&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 2005 study]</ref>

==Mutation==

Changes of a species from its normal state are called [[mutation]]s. Sometimes they happen on their own, but they can also happen when a parent is exposed to something that will affect the way they reproduce. High doses of [[X-rays]] can produce mutations, and so can some chemicals. According to the [[theory of evolution]], most mutations are neutral, some are deleterious (harmful), and a very small proportion are beneficial such that they improve the individual's chance of survival and reproduction, thus passing on to the next generation. Some mutations can be both helpful and harmful. For example, people from some [[Africa]]n countries carry a gene for an illness called [[sickle-cell anemia]]. This illness causes health problems, but people who have the gene for sickle-cell anemia are also less likely to catch [[malaria]], a serious illness common in Africa.

==References==
<references/>

[[Category:Genetics]]

Gene

2008-07-23T22:39:27Z

JohnDavis: /* History */ add new study

The '''gene''' is the fundamental unit of [[heredity]].

A section of [[DNA]] that codes for the production of an [[RNA]] molecule. In most cases that RNA molecule codes for the production of a [[protein]], but in some cases (most notably the transfer RNA ([[tRNA]]) and ribosomal RNA ([[rRNA]]) genes) the RNA molecule is the end product.

Gene expression refers to all the processes involved in converting [[gene]]tic information from a [[DNA]] sequence, or [[protein]]. In [[prokaryote]]s, there are just two processes required: [[transcription]] and [[translation]]. In [[eukaryote]]s, there is an additional step [[RNA]] processing (splicing), which intervenes.
The synthesis of a single-stranded RNA molecule using DNA as a template is referred to as transcription. The enzyme that catalyzes this reaction is known as RNA polymerase. Although the subunit structure and details of the process differ significantly in prokaryotes and eukaryotes, the chemical reaction is identical.

==History==

By 1900 scientists knew that cells were the building blocks of living things. All living things start as a single fertilized cell which keeps dividing. Scientists identified tiny threads in the nucleus of the cells. Because they could stain the threads with colored dyes to study them under a microscope, they called the threads [[chromosome]]s, from the [[Greek]] words for colored bodies. They could see that chromosomes came in pairs, and that human cells all contained 23 matching pairs. American biologist [[Walter Sutton]] knew [[Mendel's principles of genetics|Mendel's]] work on peas, and suggested that chromosomes held the secret of inheritance.

Another American biologist, [[Thomas Hunt Morgan]], developed the idea that chromosomes were made up of linked groups of factors called [[genes]]. He experimented with red-eyed [[fruit fly|fruit flies]] and found that sometimes a white-eyed fly appeared. When he mated them, he found that as he expected there were three red-eyed flies to every white-eyed fly, but that all the white-eyed flies were male. He concluded that the gene for white eyes must be on a chromosome that was related to being male. Later workers found that this is why some hereditary diseases such as [[hemophilia]] and [[muscular dystrophy]] only show in males, though women can carry the gene for the disease without showing it.

Once Crick and Watson had unraveled the structure of [[DNA]], the function of genes became clearer.

One strand of [[DNA]] contains many genes. DNA is made of four [[nucleotide]]s, [[guanine]], [[adenine]], [[thymine]] and [[cytosine]]. G always pairs with C, and A with T. Different combinations of GC and AT join together in different orders along the strands of DNA coiled up along our [[chromosome]]s to give our cells instructions for making the different kind of protein of which our bodies are made. These groups of instructions are called genes. Our bodies are made up of about 100 trillion cells, each of which is responsible for a specific function. The thousands of different proteins in the cells work together like a machine to make the [[cell]] function as it should. If the genes are normal, the body part will function well. If a change (mutation) has happened in a gene, the protein may be faulty, as for example in sickle cell anemia where the instructions for making [[blood]] cells are abnormal.

In 2005 it was shown that genes were not the only way that genetic information could be inherited. Scientists working at Purdue University discovered that Arabidopsis plants could remember what genes they had in the past, and correct mistakes in their current genes. This non-mendelian inheritance probably involves a RNA cache of past messenger RNA transcripts.

==Mutation==

Changes of a species from its normal state are called [[mutation]]s. Sometimes they happen on their own, but they can also happen when a parent is exposed to something that will affect the way they reproduce. High doses of [[X-rays]] can produce mutations, and so can some chemicals. According to the [[theory of evolution]], most mutations are neutral, some are deleterious (harmful), and a very small proportion are beneficial such that they improve the individual's chance of survival and reproduction, thus passing on to the next generation. Some mutations can be both helpful and harmful. For example, people from some [[Africa]]n countries carry a gene for an illness called [[sickle-cell anemia]]. This illness causes health problems, but people who have the gene for sickle-cell anemia are also less likely to catch [[malaria]], a serious illness common in Africa.

==References==
<references/>

[[Category:Genetics]]

Protein

2008-07-23T22:33:02Z

JohnDavis: /* Synthesis */ expand and correct

'''Proteins''' are complex organic compounds whose basic structure is a primary chain of amino acids covalently bonded via [[peptide bond]]s and folded into a certain shape. This tertiary fold dictates the function of the protein within the organism. They can take on many forms and perform distinct functions including (but certainly not limited to) structural, enzymatic, information storage, intracellular signaling, and transportation roles. In terms of structure, proteins are important in the construction and integrity of different body tissues including connective and muscular, as well as endocrine/exocrine glands. <ref> http://www.hsph.harvard.edu/nutritionsource/protein.html </ref>

==Synthesis==

Proteins are synthesized by cytoplasmic structures composed of catalytic rRNA and proteins called [[ribosomes]]. A few peptides are synthesized in non-ribosomal reactions, such as glutathione. Ribosomes translate information coded in mRNA (transcribed from genomic DNA, specific regions known as [[genes]]) after editing and manipulation by nuclear and cytoplasmic [[spliceosome]]s. The nascent protein is elongated in the ribosome through addition of different amino-acyl moieties from the tRNA carrier. The start site and sequence of addition is specified by codons (sets of three nucleotides) in the mRNA molecule. The formation of the protein chain requires the codon, a molecule of transfer RNA (tRNA) charged with a particular amino acid, and the tRNA's anti-codon. A molecule of water is expelled after each peptide bond is formed, hence the name "condensation reaction".

After the protein has been generated, it is assisted by other proteins termed chaperones that aid in the formation of the proper conformation. A ribosomal protein is always synthesized in one direction so, invariably, proteins also exhibit the physical property known as stereoisomerism. All [[polypetide]]s possess free N-terminal(Amine; NH2) and C-terminal (Carboxylic Acid; COOH) ends. The protein may then be further edited post-translationally by certain enzymes, by for example a piece being cut out and the two halves re-ligated. Examples of other modifications include, [[isoprenylation]], [[palmitoylation]], [[myristoylation]], [[methylation]], [[acetylation]], N-terminal [[proteolysis]], and [[disulfide bond]] linkage. These modifications often have some bearing on the function and localization of the protein. After these processes occur, the protein can be transported to other sub-cellular organelles/locations such as the plasma membrane, golgi apparatus, endoplasmic reticulum, and vesicles where they perform their pre-programmed function. Membrane proteins are unfolded by a signal recognition particle, and then inserted into the lipid bilayer of a vesicle. Such vesicular proteins are usually shuttled to the plasma membrane, or reserved cytoplasmically for secretion at a later time.

==Nutrition==

Adult humans need a minimum of 1 gram of protein for every kilogram of body weight per day to keep from slowly breaking down their own tissues. Failure to receive enough protein can cause stunted growth, loss of muscle mass, decreased immunity, weakening of the heart and respiratory system, and eventually death. <ref> http://www.usda.gov/ </ref>

There are two types of the standard 20 amino acids embedded in the [[genetic code]]: ''essential'' and ''non-essential''.

There are 13 amino acids the body can manufacture on its own. Essential amino acids are those which cannot be made by the body and can only be obtained from the diet. There are 9 amino acids the human body cannot produce on its own. <ref> http://www.nutrition.gov/ </ref>

Protein is also classified as ''complete'' or ''incomplete''.

Complete protein foods supply all of the essential amino acids the body needs to build new proteins. Incomplete protein foods do not supply all the essential amino acids.

Complete protein food sources tend to come from meat and other animal products, fish, eggs, and milk products. Incomplete proteins come from plant sources, fruits, vegetables, grains, and nuts. Plant proteins can be combined to include all of the essential amino acids and form a complete protein, such as eating rice and beans together. Protein is only one component of a healthy diet. <ref> http://www.nlm.nih.gov/medlineplus/ency/article/002467.htm </ref>

==References==

<references/>

[[Category:Biochemistry]]
[[Category:Nutrition]]

Enzyme

2008-07-23T22:27:24Z

JohnDavis: expand

An '''enzyme''' is a [[protein]] produced by a living organism that functions as a [[catalyst]]. Enzymes increase the speed and likelihood of chemical reactions within an organism's body by lowering the activation energy necessary for a reaction to occur. This happens because the enzyme selects the particular configuration of the substrate and bends the bonds into the energetically-favorable orientation, with a consequent decrease in entropy. They are essential to all cellular functions, and most life could not exist without them, although viruses lack enzymes, but use them from their host cell.

[[Category:Reaction Kinetics]]
[[Category:Organic Chemistry]]
[[Category:Biochemistry]]