Elementary molecular biology

DNA
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The two DNA strands are also known as poly-nucleotides as they are composed of simpler monomeric units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases (cytosine [C], guanine [G], adenine [A] or thymine [T]), a sugar called deoxyribose, and a phosphate group.



DNA replication
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In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the basis for biological inheritance.

RNA
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The chemical structure of RNA is very similar to that of, but differs in three primary ways:
 * Unlike double-stranded DNA, RNA is a single-stranded molecule in many of its biological roles and consists of much shorter chains of nucleotides. However, a single RNA molecule can, by complementary base pairing, form intrastrand double helixes, as in tRNA (see "Transfer RNA" below).
 * While the sugar-phosphate "backbone" of DNA contains ', RNA contains ' instead. Ribose has a group attached to the pentose ring in the  position, whereas deoxyribose does not. The hydroxyl groups in the ribose backbone make RNA more chemically  than DNA by lowering the  of.
 * The complementary base to in DNA is, whereas in RNA, it is , which is an  form of thymine.

Transcription
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Transcription is the first step of DNA based gene expression, in which a particular segment of DNA is copied into RNA (especially mRNA) by the enzyme RNA polymerase. Only one of the two DNA strands serves as a template for transcription.

Transcription proceeds in the following general steps:
 * 1) RNA polymerase, together with one or more, binds to.
 * 2) RNA polymerase creates a, which separates the two strands of the DNA helix. This is done by breaking the s between complementary DNA nucleotides.
 * 3) RNA polymerase adds RNA nucleotides (which are complementary to the nucleotides of one DNA strand).
 * 4) RNA sugar-phosphate backbone forms with assistance from RNA polymerase to form an RNA strand.
 * 5) Hydrogen bonds of the RNA–DNA helix break, freeing the newly synthesized RNA strand.
 * 6) If the cell has a, the RNA may be further processed. This may include , , and.
 * 7) The RNA may remain in the nucleus or exit to the  through the  complex.

Genetic code
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The genetic code is the set of rules used by living cells to translate information encoded within mRNA sequences into proteins. Translation is accomplished by the ribosome, which links amino acids in an order specified by messenger RNA (mRNA).

The code defines how sequences of nucleotide triplets, called codons, specify which amino acid will be added next during protein synthesis. With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid.

Translation starts with a chain-initiation codon or start codon.

The three stop codons have names: UAG is amber, UGA is opal (sometimes also called umber), and UAA is ochre.

Transfer RNA
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A transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length, that serves as the physical link between the mRNA and the amino acid sequence of proteins. tRNA does this by carrying an amino acid to the protein synthetic machinery of a cell (ribosome).





One end of the tRNA matches the genetic code in a three-nucleotide sequence called the anticodon. The anticodon forms three complementary base pairs with a codon in mRNA during protein biosynthesis. On the other end of the tRNA is a covalent attachment to the amino acid. Each type of tRNA molecule can be attached to only one type of amino acid, so each organism has many types of tRNA. Because the genetic code contains multiple codons that specify the same amino acid, there are several tRNA molecules bearing different anticodons which carry the same amino acid.

Codons
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 * A The codon AUG both codes for methionine and serves as an initiation site: the first AUG in an 's coding region is where translation into protein begins. The other start codons listed by GenBank are rare in eukaryotes and generally codes for Met/fMet.
 * B The historical basis for designating the stop codons as amber, ochre and opal is described in an autobiography by Sydney Brenner and in a historical article by Bob Edgar.

Proteins
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Proteins are large biomolecules, or macromolecules, consisting of 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.

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, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds.

Peptide bond
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When two amino acids form a  through a peptide bond it is a type of. In this kind of condensation, two "amino" acids approach each other, with the non- (C1)  of one coming near the non-side chain (N2)  moiety of the other. One loses a hydrogen and oxygen from its carboxyl group (COOH) and the other loses a hydrogen from its amino group (NH2). This reaction produces a molecule of water (H2O) and two amino acids joined by a peptide bond (-CO-NH-). The two joined amino acids are called a dipeptide.



Cofactor
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A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme's activity as a catalyst, a substance that increases the rate of a chemical reaction. Cofactors can be considered "helper molecules" that assist in biochemical transformations.

Cofactors can be divided into two types, either inorganic ions, or complex organic molecules called coenzymes.

Metal ions are common cofactors. The study of these cofactors falls under the area of bioinorganic chemistry. In nutrition, the list of essential trace elements reflects their role as cofactors. In humans this list commonly includes iron, magnesium, manganese, cobalt, copper, zinc, and molybdenum.

Organic cofactors are often vitamins or made from vitamins. Many contain the nucleotide adenosine monophosphate (AMP) as part of their structures, such as ATP, coenzyme A, FAD, and NAD+.

ATP
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Adenosine triphosphate (ATP) is a complex organic chemical that provides energy to drive many processes in living cells, e.g. muscle contraction, nerve impulse propagation, and chemical synthesis. Found in all forms of life, ATP is often referred to as the "molecular unit of currency" of intracellular energy transfer. When consumed in metabolic processes, it converts either to adenosine diphosphate (ADP) or to adenosine monophosphate (AMP). Other processes regenerate ATP so that the human body recycles its own body weight equivalent in ATP each day.

In terms of its structure, ATP consists of an adenine attached by the 9-nitrogen atom to the 1′ carbon atom of a sugar (ribose), which in turn is attached at the 5′ carbon atom of the sugar to a triphosphate group. In its many reactions related to metabolism, the adenine and sugar groups remain unchanged, but the triphosphate is converted to di- and monophosphate, giving respectively the derivatives ADP and AMP.



Carbohydrates
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Glucose (also called dextrose) is a simple with the. Glucose is the most abundant, a subcategory of. Glucose is mainly made by and most  during  from water and carbon dioxide, using energy from sunlight. There it is used to make in s, which is the most abundant carbohydrate. In, glucose is the most important source of energy in all s. Glucose for metabolism is partially stored as a , in plants mainly as and  and in animals as. Glucose circulates in the blood of animals as. The naturally occurring form of glucose is -glucose, while is produced synthetically in comparatively small amounts and is of lesser importance. Approximately 4 grams of glucose are present in the blood of humans at all times.



The structural formula of amylose (a starch) is pictured below. The number of repeated glucose subunits (n) is usually in the range of 300 to 3000, but can be many thousands:



Cellulose is an with the , a  consisting of a linear chain of several hundred to many thousands of   units.



Glycogen is a multibranched polysaccharide of glucose that serves as a form of energy storage in animals, fungi, and bacteria. In humans, glycogen is made and stored primarily in the cells of the liver and skeletal muscle. Glycogen forms an energy reserve that can be quickly mobilized to meet a sudden need for glucose, but one that is less compact than the energy reserves of triglycerides (lipids).



Lipids
From : A triglyceride (TG, triacylglycerol, TAG, or triacylglyceride) is an derived from  and three  (from ' and '). Triglycerides are the main constituents of in humans and other vertebrates, as well as. There are many different types of triglyceride, with the main division between types. s are "saturated" with hydrogen — all available places where hydrogen atoms could be bonded to carbon atoms are occupied. These have a higher melting point and are more likely to be solid at room temperature. s have double bonds between some of the carbon atoms, reducing the number of places where hydrogen atoms can bond to carbon atoms. These have a lower melting point and are more likely to be liquid at room temperature.





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Phospholipids are a class of lipids that are a major component of all cell membranes. They can form lipid bilayers because of their amphiphilic characteristic. The structure of the phospholipid molecule generally consists of two hydrophobic fatty acid "tails" and a hydrophilic "head" consisting of a phosphate group. The two components are joined together by a glycerol molecule.

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The lipid bilayer (or phospholipid bilayer) is a thin polar membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around all cells. The cell membranes of almost all organisms and many viruses are made of a lipid bilayer, as are the nuclear membrane surrounding the cell nucleus, and other membranes surrounding sub-cellular structures. The lipid bilayer is the barrier that keeps ions, proteins and other molecules where they are needed and prevents them from diffusing into areas where they should not be. Lipid bilayers are ideally suited to this role, even though they are only a few nanometers in width, they are impermeable to most water-soluble (hydrophilic) molecules. Bilayers are particularly impermeable to ions, which allows cells to regulate salt concentrations and pH by transporting ions across their membranes using proteins called ion pumps.

Proton pump
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A proton pump is an integral membrane protein pump that builds up a proton gradient across a biological membrane. The energy required for the proton pumping reaction may come from light (light energy; ), electron transfer (electrical energy; electron transport complexes, and ) or energy-rich metabolites (chemical energy) such as  (PPi; ) or  (ATP; ).

F-ATPase
Proton pumps also work in reverse to create ATP.

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F-ATPase, also known as F-Type ATPase, is an found in bacterial s, in  (in, where it is known as Complex V), and in. It uses a gradient to drive ATP synthesis by allowing the passive flux of protons across the membrane down their electrochemical gradient and using the energy released by the transport reaction to release newly formed  from the active site of F-ATPase.

Ribozyme
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Ribozymes (ribonucleic acid enzymes) are RNA molecules that are capable of catalyzing specific biochemical reactions, similar to the action of protein enzymes.

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