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Biosynthesis is a multi-step,
enzyme Enzymes () are proteins that act as biological catalysts (biocatalysts). Catalysts accelerate chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates in ...

enzyme
-
catalyzed that utilizes a low-temperature oxidation catalyst to convert carbon monoxide to less toxic carbon dioxide at room temperature. It can also remove formaldehyde from the air. Catalysis () is the process of increasing the reaction rate, rate of a ...

catalyzed
process where substrates are converted into more complex
products Product may refer to: Business * Product (business), an item that serves as a solution to a specific consumer problem. * Product (project management), a deliverable or set of deliverables that contribute to a business solution Mathematics * Produc ...
in living organisms. In biosynthesis, simple
compound Compound may refer to: Architecture and built environments * Compound (enclosure), a cluster of buildings having a shared purpose, usually inside a fence or wall ** Compound (fortification), a version of the above fortified with defensive structu ...
s are modified, converted into other compounds, or joined together to form
macromolecules macromolecule A macromolecule is a very large molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neu ...
. This process often consists of
metabolic pathway In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell (biology), cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence ...
s. Some of these biosynthetic pathways are located within a single cellular
organelle In cell biology Cell biology (also cellular biology or cytology) is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, ...
, while others involve enzymes that are located within multiple cellular organelles. Examples of these biosynthetic pathways include the production of
lipid membrane 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 cell (biology), cells. The cell membranes of almost all organism ...
components and
nucleotide Nucleotides are organic molecules , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, ...

nucleotide
s. Biosynthesis is usually
synonym A synonym is a word, morpheme A morpheme is the smallest meaningful lexical item in a language. A morpheme is not a word. The difference between a morpheme and a word is that a morpheme bound and free morphemes, sometimes does not stand alone ...
ous with
anabolism Anabolism () is the set of metabolic pathway In biochemistry Biochemistry or biological chemistry, is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be d ...
. The prerequisite elements for biosynthesis include:
precursor Precursor or Precursors may refer to: *Precursor (religion), a forerunner, predecessor ** The Precursor, John the Baptist Science and technology * Precursor (bird), a hypothesized genus of fossil birds that was composed of fossilized parts of unre ...
compounds,
chemical energy Chemical energy is the energy of chemical substance A chemical substance is a form of matter In classical physics and general chemistry, matter is any substance that has mass and takes up space by having volume. All everyday objects th ...
(e.g.
ATP ATP may refer to: Companies and organizations * Association of Tennis Professionals * American Technical Publishers * ', a Danish pension * Armenia Tree Project * Association for Transpersonal Psychology * ATP architects engineers office * ATP ...

ATP
), and catalytic enzymes which may require
coenzymes A cofactor is a non-protein Proteins are large biomolecules or macromolecules that are comprised of one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including ...
(e.g.
NADH Nicotinamide adenine dinucleotide (NAD) is a Cofactor (biochemistry), coenzyme central to metabolism. Found in all living cell (biology), cells, NAD is called a dinucleotide because it consists of two nucleotides joined through their phosphate ...
,
NADPH Nicotinamide adenine dinucleotide phosphate, abbreviated NADP or, in older notation, TPN (triphosphopyridine nucleotide), is a cofactor used in anabolic reactions, such as the Calvin cycle The Calvin cycle, light-independent reactions, bio syn ...

NADPH
). These elements create
monomers In chemistry Chemistry is the scientific Science () is a systematic enterprise that builds and organizes knowledge Knowledge is a familiarity or awareness, of someone or something, such as facts A fact is an occurrence in th ...
, the building blocks for macromolecules. Some important biological macromolecules include:
proteins Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a No ...

proteins
, which are composed of
amino acid Amino acids are organic compound In , organic compounds are generally any s that contain - . Due to carbon's ability to (form chains with other carbon s), millions of organic compounds are known. The study of the properties, reactions, a ...

amino acid
monomers joined via
peptide bonds In organic chemistry Organic chemistry is a branch of chemistry that studies the structure, properties and reactions of organic compounds, which contain carbon in covalent bonding.Clayden, J.; Greeves, N. and Warren, S. (2012) ''Organic Chemistr ...
, and
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

DNA
molecules, which are composed of nucleotides joined via
phosphodiester bondsImage:Phosphodiester Bond Diagram.svg, 200px, Diagram of phosphodiester bonds (PO43−) between three nucleotides. A phosphodiester bond occurs when exactly two of the hydroxyl groups in phosphoric acid react with hydroxyl groups on other molecules ...
.


Properties of chemical reactions

Biosynthesis occurs due to a series of chemical reactions. For these reactions to take place, the following elements are necessary: * Precursor compounds: these compounds are the starting molecules or substrates in a reaction. These may also be viewed as the
reactants Image:SulfurReagent.jpg, 200px, Reactants, such as sulfur (''pictured''), are the starting materials that are used in chemical reactions. A reagent is a substance or compound added to a system to cause a chemical reaction, or added to test if a ...
in a given chemical process. *
Chemical energy Chemical energy is the energy of chemical substance A chemical substance is a form of matter In classical physics and general chemistry, matter is any substance that has mass and takes up space by having volume. All everyday objects th ...
: chemical energy can be found in the form of high energy molecules. These molecules are required for energetically unfavorable reactions. Furthermore, the
hydrolysis Hydrolysis (; ) is any chemical reaction in which a molecule of water breaks one or more chemical bonds. The term is used broadly for substitution Substitution may refer to: Arts and media *Chord substitution, in music, swapping one chord fo ...

hydrolysis
of these compounds drives a reaction forward. High energy molecules, such as
ATP ATP may refer to: Companies and organizations * Association of Tennis Professionals * American Technical Publishers * ', a Danish pension * Armenia Tree Project * Association for Transpersonal Psychology * ATP architects engineers office * ATP ...

ATP
, have three
phosphates In chemistry Chemistry is the scientific discipline involved with Chemical element, elements and chemical compound, compounds composed of atoms, molecules and ions: their composition, structure, properties, behavior and the changes they un ...
. Often, the terminal phosphate is split off during hydrolysis and transferred to another molecule. * : these molecules are special
proteins Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a No ...

proteins
that catalyze a reaction by increasing the rate of the reaction and lowering the
activation energy In chemistry Chemistry is the study of the properties and behavior of . It is a that covers the that make up matter to the composed of s, s and s: their composition, structure, properties, behavior and the changes they undergo during ...
. *
Coenzymes A cofactor is a non-protein Proteins are large biomolecules or macromolecules that are comprised of one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including ...
or cofactors: cofactors are molecules that assist in chemical reactions. These may be
metal ions A metal (from Greek Greek may refer to: Greece Anything of, from, or related to Greece Greece ( el, Ελλάδα, , ), officially the Hellenic Republic, is a country located in Southeast Europe. Its population is approximately 10.7 mil ...
, vitamin derivatives such as
NADH Nicotinamide adenine dinucleotide (NAD) is a Cofactor (biochemistry), coenzyme central to metabolism. Found in all living cell (biology), cells, NAD is called a dinucleotide because it consists of two nucleotides joined through their phosphate ...
and
acetyl CoA Acetyl-CoA (acetyl coenzyme A) is a molecule that participates in many biochemical reaction Biochemistry or biological chemistry, is the study of chemical processes within and relating to living organism In biology, an organism (from ...

acetyl CoA
, or non-vitamin derivatives such as ATP. In the case of NADH, the molecule transfers a hydrogen, whereas acetyl CoA transfers an
acetyl group In organic chemistry Organic chemistry is a branch of chemistry that studies the structure, properties and reactions of organic compounds, which contain carbon in covalent bonding.Clayden, J.; Greeves, N. and Warren, S. (2012) ''Organic Chemis ...

acetyl group
, and ATP transfers a phosphate. In the simplest sense, the reactions that occur in biosynthesis have the following format: :: Reactant ->[][enzyme] Product Some variations of this basic equation which will be discussed later in more detail are: # Simple compounds which are converted into other compounds, usually as part of a multiple step reaction pathway. Two examples of this type of reaction occur during the formation of
nucleic acid Nucleic acids are biopolymer Biopolymers are natural polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large molecules, or macromolecule ...

nucleic acid
s and the charging of
tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an e ...

tRNA
prior to
translation Translation is the communication of the meaning Meaning most commonly refers to: * Meaning (linguistics), meaning which is communicated through the use of language * Meaning (philosophy), definition, elements, and types of meaning discusse ...

translation
. For some of these steps, chemical energy is required: #:: + ATP <=> + PP_i # Simple compounds that are converted into other compounds with the assistance of cofactors. For example, the synthesis of
phospholipid Phospholipids, also known as phosphatides, are a class of lipid In and , a lipid is a macro that is soluble in solvents. are typically s used to dissolve other naturally occurring hydrocarbon lipid s that do not (or do not easily) disso ...

phospholipid
s requires acetyl CoA, while the synthesis of another membrane component,
sphingolipid Sphingolipids are a class of lipid In and , a lipid is a macro that is soluble in solvents. are typically s used to dissolve other naturally occurring hydrocarbon lipid s that do not (or do not easily) dissolve in water, including s, es, ...

sphingolipid
s, requires NADH and FADH for the formation the
sphingosine Sphingosine (2-amino-4-trans-octadecene-1,3-diol) is an 18-carbon amino alcohol with an unsaturated hydrocarbon chain, which forms a primary part of sphingolipids, a class of cell membrane lipids that include sphingomyelin, an important phospholipi ...

sphingosine
backbone. The general equation for these examples is: #:: + Cofactor ->[][enzyme] macromolecule # Simple compounds that join together to create a macromolecule. For example, fatty acids join together to form phospholipids. In turn, phospholipids and
cholesterol Cholesterol is any of a class of certain organic compound, organic molecules. A cholesterol is a sterol (or chemical modification, modified steroid), a type of lipid. Cholesterol is biosynthesis, biosynthesized by all animal Cell (biology)#Euk ...

cholesterol
interact Noncovalent bonding, noncovalently in order to form the
lipid bilayer The lipid bilayer (or phospholipid bilayer) is a thin polar membrane A polarized membrane is a lipid bilayer, lipid membrane that has a positive electrical charge on one side and a negative charge on another side, which produces the resting pot ...
. This reaction may be depicted as follows: #:: + Molecule~2 -> macromolecule


Lipid

Many intricate macromolecules are synthesized in a pattern of simple, repeated structures. For example, the simplest structures of lipids are
fatty acids In chemistry Chemistry is the scientific Science () is a systematic enterprise that builds and organizes knowledge Knowledge is a familiarity or awareness, of someone or something, such as facts A fact is an occurrence in ...
. Fatty acids are
hydrocarbon In organic chemistry Organic chemistry is a branch of chemistry Chemistry is the study of the properties and behavior of . It is a that covers the that make up matter to the composed of s, s and s: their composition, structure, prop ...
derivatives; they contain a
carboxyl group A carboxylic acid is an organic acid that contains a carboxyl group (C(=O)OH) attached to an R-group. The general formula of a carboxylic acid is R−COOH or R−CO2H, with substituent, R referring to the alkyl, alkenyl, aryl, or other group. ...

carboxyl group
"head" and a hydrocarbon chain "tail". These fatty acids create larger components, which in turn incorporate noncovalent interactions to form the lipid bilayer. Fatty acid chains are found in two major components of membrane lipids:
phospholipids Phospholipids, also known as phosphatides, are a class of lipids whose molecule has a hydrophile, hydrophilic "head" containing a phosphate group and two hydrophobic "tails" derived from fatty acids, joined by an alcohol residue (usually a glyce ...

phospholipids
and
sphingolipids Sphingolipids are a class of lipids containing a backbone of sphingoid bases, a set of aliphatic amino alcohols that includes sphingosine. They were discovered in brain extracts in the 1870s and were named after the mythological sphinx because ...
. A third major membrane component,
cholesterol Cholesterol is any of a class of certain organic compound, organic molecules. A cholesterol is a sterol (or chemical modification, modified steroid), a type of lipid. Cholesterol is biosynthesis, biosynthesized by all animal Cell (biology)#Euk ...

cholesterol
, does not contain these fatty acid units.


Phospholipids

The foundation of all biomembranes consists of a
bilayer :''For bilayers in biology, see lipid bilayer 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 cell (biology), ce ...

bilayer
structure of phospholipids. The phospholipid molecule is
amphipathic 250px, Cross-section view of the structures that can be formed by phospholipids, biological amphiphiles in aqueous solutions. Unlike this illustration, micelles are usually formed by non-biological, single-chain, amphiphiles, soaps or detergents, ...
; it contains a
hydrophilic A hydrophile is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral group of two or more atoms ...
polar head and a
hydrophobic In chemistry Chemistry is the scientific Science () is a systematic enterprise that builds and organizes knowledge Knowledge is a familiarity or awareness, of someone or something, such as facts A fact is an occurrence ...
nonpolar tail. The phospholipid heads interact with each other and aqueous media, while the hydrocarbon tails orient themselves in the center, away from water. These latter interactions drive the bilayer structure that acts as a barrier for ions and molecules. There are various types of phospholipids; consequently, their synthesis pathways differ. However, the first step in phospholipid synthesis involves the formation of
phosphatidatePhosphatidic acids are anionic phospholipids important to cell signaling and direct activation of lipid-gated ion channels Lipid-gated ion channels are a class of ion channel s (typically four per channel), 2 - outer vestibule, 3 - selectivity fi ...
or diacylglycerol 3-phosphate at the
endoplasmic reticulum The endoplasmic reticulum (ER) is, in essence, the transportation system of the eukaryotic cell, and has many other important functions such as protein folding. It is a type of organelle made up of two subunits – rough endoplasmic reticulum ( ...
and
outer mitochondrial membrane A mitochondrion (, plural mitochondria) is a double membrane-bound organelle found in most eukaryotic organisms. Some cells in some multicellular organisms lack mitochondria (for example, mature mammalian red blood cells). A number of unice ...
. The synthesis pathway is found below: The pathway starts with glycerol 3-phosphate, which gets converted to lysophosphatidate via the addition of a fatty acid chain provided by acyl coenzyme A. Then, lysophosphatidate is converted to phosphatidate via the addition of another fatty acid chain contributed by a second acyl CoA; all of these steps are catalyzed by the glycerol phosphate
acyltransferase Acyl Acyltransferase is a type of transferase enzyme Enzymes () are proteins that act as biological catalysts (biocatalysts). Catalysts accelerate chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), ...
enzyme. Phospholipid synthesis continues in the endoplasmic reticulum, and the biosynthesis pathway diverges depending on the components of the particular phospholipid.


Sphingolipids

Like phospholipids, these fatty acid derivatives have a polar head and nonpolar tails. Unlike phospholipids, sphingolipids have a
sphingosine Sphingosine (2-amino-4-trans-octadecene-1,3-diol) is an 18-carbon amino alcohol with an unsaturated hydrocarbon chain, which forms a primary part of sphingolipids, a class of cell membrane lipids that include sphingomyelin, an important phospholipi ...

sphingosine
backbone. Sphingolipids exist in
eukaryotic Eukaryotes () are organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interact ...
cells and are particularly abundant in the
central nervous system The central nervous system (CNS) is the part of the nervous system In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecu ...

central nervous system
. For example, sphingomyelin is part of the
myelin sheath Myelin is a lipid In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, phys ...
of nerve fibers. Sphingolipids are formed from
ceramide Ceramide. R represents the alkyl portion of a fatty acid. Ceramides are a family of wax , a typical wax ester. Image:Beeswax foundation.jpg, Commercial honeycomb foundation, made by pressing beeswax between patterned metal rollers. Waxes are a ...
s that consist of a fatty acid chain attached to the amino group of a sphingosine backbone. These ceramides are synthesized from the
acylationIn chemistry Chemistry is the scientific discipline involved with Chemical element, elements and chemical compound, compounds composed of atoms, molecules and ions: their composition, structure, properties, behavior and the changes they undergo ...

acylation
of sphingosine. The biosynthetic pathway for sphingosine is found below: As the image denotes, during sphingosine synthesis, palmitoyl CoA and serine undergo a
condensation reaction In organic chemistry Organic chemistry is a branch of chemistry Chemistry is the study of the properties and behavior of . It is a that covers the that make up matter to the composed of s, s and s: their composition, structure, prop ...
which results in the formation of dehydrosphingosine. This product is then reduced to form dihydrospingosine, which is converted to sphingosine via the
oxidation reaction (mild reducing agent) are added to powdered potassium permanganate Potassium permanganate is an inorganic compound with the chemical formula KMnO4 and composed of potassium ion, K+ and permanganate, . It is a purplish-black crystalline salt, th ...
by
FAD A fad is any form of collective behavior The expression collective behavior was first used by Franklin Henry Giddings Franklin Henry Giddings (March 23, 1855 – June 11, 1931) was an American sociologist and economist An econ ...

FAD
.


Cholesterol

This
lipid In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanis ...
belongs to a class of molecules called
sterols Sterol is an organic compound with formula , whose molecule is derived from that of gonane by replacement of a hydrogen atom in position 3 by a hydroxyl group. It is therefore an alcohol (chemistry), alcohol of gonane. More generally, any compounds ...

sterols
. Sterols have four fused rings and a
hydroxyl group A hydroxy or hydroxyl group is a functional group with the chemical formula -OH and composed of one oxygen Oxygen is the chemical element Image:Simple Periodic Table Chart-blocks.svg, 400px, Periodic table, The periodic table of the ...

hydroxyl group
. Cholesterol is a particularly important molecule. Not only does it serve as a component of lipid membranes, it is also a precursor to several
steroid A steroid is a biologically active organic compound In chemistry Chemistry is the study of the properties and behavior of . It is a that covers the that make up matter to the composed of s, s and s: their composition, structure, ...

steroid
hormones, including
cortisol Cortisol is a steroid hormone, in the glucocorticoid class of hormones. When used as a medication, it is known as hydrocortisone. It is produced in many animals, mainly by the ''zona fasciculata'' of the adrenal cortex in the adrenal gland. ...

cortisol
,
testosterone Testosterone is the primary sex hormone and anabolic steroid in males. In humans, testosterone plays a key role in the development of Male reproductive system, male reproductive tissues such as testes and prostate, as well as promoting secondar ...
, and
estrogen Estrogens or oestrogens, are a class of natural or synthetic sex hormone Sex hormones, also known as sex steroids, gonadocorticoids and gonadal steroids, are steroid hormone A steroid hormone is a steroid that acts as a hormone. Steroid ho ...

estrogen
. Cholesterol is synthesized from
acetyl CoA Acetyl-CoA (acetyl coenzyme A) is a molecule that participates in many biochemical reaction Biochemistry or biological chemistry, is the study of chemical processes within and relating to living organism In biology, an organism (from ...

acetyl CoA
. The pathway is shown below: More generally, this synthesis occurs in three stages, with the first stage taking place in the
cytoplasm In cell biology Cell biology (also cellular biology or cytology) is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes ...
and the second and third stages occurring in the endoplasmic reticulum. The stages are as follows: ::1. The synthesis of
isopentenyl pyrophosphate Isopentenyl pyrophosphate (IPP, isopentenyl diphosphate, or IDP) is an isoprenoid precursor. IPP is an intermediate in the classical, HMG-CoA reductase pathway (commonly called the mevalonate pathway) and in the ''non-mevalonate'' MEP pathway of i ...

isopentenyl pyrophosphate
, the "building block" of cholesterol ::2. The formation of
squalene Squalene is an organic compound. With the formula (C5H8)6, it is a triterpene. It is a colourless oil although impure samples appear yellow. It was originally obtained from shark liver oil (hence its name, as ''Squalus'' is a genus of sharks). Al ...

squalene
via the condensation of six molecules of isopentenyl phosphate ::3. The conversion of squalene into cholesterol via several enzymatic reactions


Nucleotides

The biosynthesis of
nucleotides Nucleotides are organic molecules , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, ...

nucleotides
involves enzyme-
catalyzed that utilizes a low-temperature oxidation catalyst to convert carbon monoxide to less toxic carbon dioxide at room temperature. It can also remove formaldehyde from the air. Catalysis () is the process of increasing the reaction rate, rate of a ...

catalyzed
reactions that convert substrates into more complex products. Nucleotides are the building blocks of
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

DNA
and
RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large molecules, or macromolecules, composed of many Re ...

RNA
. Nucleotides are composed of a five-membered ring formed from
ribose Ribose is a simple sugar and carbohydrate with molecular formula C5H10O5 and the linear-form composition H−(C=O)−(CHOH)4−H. The naturally-occurring form, , is a component of the ribonucleotides from which RNA is built, and so this compoun ...

ribose
sugar in RNA, and
deoxyribose Deoxyribose, or more precisely 2-deoxyribose, is a monosaccharide Monosaccharides (from Greek#REDIRECT Greek Greek may refer to: Greece Anything of, from, or related to Greece Greece ( el, Ελλάδα, , ), officially the Hellenic Rep ...

deoxyribose
sugar in DNA; these sugars are linked to a
purine Purine is a heterocyclic 125px, Pyridine, a heterocyclic compound A heterocyclic compound or ring structure is a cyclic compound that has atoms of at least two different chemical element, elements as members of its ring(s). Heterocyclic chemi ...

purine
or
pyrimidine Pyrimidine is an aromatic In chemistry Chemistry is the scientific Science () is a systematic enterprise that builds and organizes knowledge Knowledge is a familiarity or awareness, of someone or something, such as facts ...

pyrimidine
base with a
glycosidic bond A glycosidic bond or glycosidic linkage is a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate. A glycosidic bond is formed between the hemiacetal or hemiketal group ...
and a
phosphate In chemistry, a phosphate is an anion, salt (chemistry), salt, functional group or ester derived from a phosphoric acids and phosphates, phosphoric acid. It most commonly means orthophosphate, a derivative of phosphoric acid, orthophosphoric a ...

phosphate
group at the 5' location of the sugar.


Purine nucleotides

The DNA nucleotides
adenosine Adenosine is an organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, cate ...

adenosine
and
guanosine Guanosine (symbol A symbol is a mark, sign, or that indicates, signifies, or is understood as representing an , , or . Symbols allow people to go beyond what is n or seen by creating linkages between otherwise very different s and s. All ...
consist of a purine base attached to a ribose sugar with a glycosidic bond. In the case of RNA nucleotides
deoxyadenosine Deoxyadenosine (symbol dA or dAdo) is a deoxyribonucleoside A deoxyribonucleoside is a type of nucleoside including deoxyribose as a component. An example is deoxycytidine. References {{organic-compound-stub Nucleosides, * .... It is a deriva ...
and
deoxyguanosine Deoxyguanosine is composed of the purine nucleobase guanine linked by its N9 nitrogen to the C1 carbon of deoxyribose. It is similar to guanosine, but with one hydroxyl group removed from the 2' position of the ribose sugar (making it deoxyribose) ...
, the purine bases are attached to a deoxyribose sugar with a glycosidic bond. The purine bases on DNA and RNA nucleotides are synthesized in a twelve-step reaction mechanism present in most single-celled organisms. Higher
eukaryotes Eukaryotes () are organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system that embodies the Life#Biology, properties of life. It is a synonym for "Outline ...
employ a similar
reaction mechanism In chemistry Chemistry is the scientific Science () is a systematic enterprise that builds and organizes knowledge Knowledge is a familiarity or awareness, of someone or something, such as facts A fact is an occurrence in t ...

reaction mechanism
in ten reaction steps. Purine bases are synthesized by converting
phosphoribosyl pyrophosphate Phosphoribosyl pyrophosphate (PRPP) is a pentosephosphate. It is formed from ribose 5-phosphate by the enzyme ribose-phosphate diphosphokinase. It plays a role in transferring phospho-ribose groups in several reactions: In ''de novo In ge ...

phosphoribosyl pyrophosphate
(PRPP) to
inosine monophosphate Inosinic acid or inosine monophosphate (IMP) is a nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers deoxyribonucleic acid (DNA) and ribonucleic a ...

inosine monophosphate
(IMP), which is the first key intermediate in purine base biosynthesis. Further enzymatic modification of
IMP An imp is a European European, or Europeans, may refer to: In general * ''European'', an adjective referring to something of, from, or related to Europe ** Ethnic groups in Europe ** Demographics of Europe ** European cuisine, the cuisines of E ...

IMP
produces the adenosine and guanosine bases of nucleotides. # The first step in purine biosynthesis is a
condensation reaction In organic chemistry Organic chemistry is a branch of chemistry Chemistry is the study of the properties and behavior of . It is a that covers the that make up matter to the composed of s, s and s: their composition, structure, prop ...
, performed by glutamine-PRPP amidotransferase. This enzyme transfers the
amino group In organic chemistry, amines (, ) are organic compound, compounds and functional groups that contain a base (chemistry), basic nitrogen atom with a lone pair. Amines are formally derivative (chemistry), derivatives of ammonia, wherein one or ...
from
glutamine Glutamine (symbol Gln or Q) is an α-amino acid Amino acids are organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical b ...

glutamine
to PRPP, forming 5-phosphoribosylamine. The following step requires the activation of glycine by the addition of a
phosphate In chemistry, a phosphate is an anion, salt (chemistry), salt, functional group or ester derived from a phosphoric acids and phosphates, phosphoric acid. It most commonly means orthophosphate, a derivative of phosphoric acid, orthophosphoric a ...

phosphate
group from
ATP ATP may refer to: Companies and organizations * Association of Tennis Professionals * American Technical Publishers * ', a Danish pension * Armenia Tree Project * Association for Transpersonal Psychology * ATP architects engineers office * ATP ...

ATP
. # GAR synthetase performs the condensation of activated glycine onto PRPP, forming glycineamide ribonucleotide (GAR). # GAR transformylase adds a formyl group onto the amino group of GAR, forming formylglycinamide ribonucleotide (FGAR). # FGAR amidotransferase catalyzes the addition of a nitrogen group to FGAR, forming formylglycinamidine ribonucleotide (FGAM). # AIR synthetase (FGAM cyclase), FGAM cyclase catalyzes ring closure, which involves removal of a water molecule, forming the 5-membered imidazole ring 5-Aminoimidazole ribotide, 5-aminoimidazole ribonucleotide (AIR). # N5-CAIR synthetase transfers a carboxyl group, forming the intermediate N5-carboxyaminoimidazole ribonucleotide (N5-CAIR). # 5-(carboxyamino)imidazole ribonucleotide mutase, N5-CAIR mutase rearranges the carboxyl functional group and transfers it onto the imidazole ring, forming 5'-phosphoribosyl-4-carboxy-5-aminoimidazole, carboxyamino- imidazole ribonucleotide (CAIR). The two step mechanism of CAIR formation from AIR is mostly found in single celled organisms. Higher eukaryotes contain the enzyme AIR carboxylase, which transfers a carboxyl group directly to AIR imidazole ring, forming CAIR. # Phosphoribosylaminoimidazolesuccinocarboxamide synthase, SAICAR synthetase forms a peptide bond between aspartate and the added carboxyl group of the imidazole ring, forming phosphoribosylaminoimidazolesuccinocarboxamide, N-succinyl-5-aminoimidazole-4-carboxamide ribonucleotide (SAICAR). # Adenylosuccinate lyase, SAICAR lyase removes the carbon skeleton of the added aspartate, leaving the amino group and forming AICA ribonucleotide, 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR). # AICAR transformylase transfers a carbonyl group to AICAR, forming 5-Formamidoimidazole-4-carboxamide ribotide, N-formylaminoimidazole- 4-carboxamide ribonucleotide (FAICAR). # The final step involves the enzyme inosine monophosphate synthase, IMP synthase, which performs the purine ring closure and forms the inosine monophosphate intermediate.


Pyrimidine nucleotides

Other DNA and RNA nucleotide bases that are linked to the ribose sugar via a glycosidic bond are thymine, cytosine and uracil (which is only found in RNA). Uridine monophosphate biosynthesis involves an enzyme that is located in the Inner mitochondrial membrane, mitochondrial inner membrane and multifunctional enzymes that are located in the cytosol. # The first step involves the enzyme carbamoyl phosphate synthase combining
glutamine Glutamine (symbol Gln or Q) is an α-amino acid Amino acids are organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical b ...

glutamine
with CO2, CO2 in an ATP dependent reaction to form carbamoyl phosphate. # Aspartate carbamoyltransferase Condensation reaction, condenses carbamoyl phosphate with aspartate to form uridosuccinate. # Dihydroorotase performs Ring-closure reaction, ring closure, a reaction that loses water, to form dihydroorotate. # Dihydroorotate dehydrogenase, located within the mitochondrial inner membrane, oxidizes dihydroorotate to orotate. # Orotate phosphoribosyl hydrolase (OMP pyrophosphorylase) condenses orotate with PRPP to form orotidine 5'-monophosphate, orotidine-5'-phosphate. # OMP decarboxylase catalyzes the conversion of orotidine-5'-phosphate to Uridine monophosphate, UMP. After the uridine nucleotide base is synthesized, the other bases, cytosine and thymine are synthesized. Cytosine biosynthesis is a two-step reaction which involves the conversion of UMP to Uridine triphosphate, UTP. Phosphate addition to UMP is catalyzed by a kinase enzyme. The enzyme CTP synthase catalyzes the next reaction step: the conversion of UTP to cytidine triphosphate, CTP by transferring an
amino group In organic chemistry, amines (, ) are organic compound, compounds and functional groups that contain a base (chemistry), basic nitrogen atom with a lone pair. Amines are formally derivative (chemistry), derivatives of ammonia, wherein one or ...
from glutamine to uridine; this forms the cytosine base of CTP. The mechanism, which depicts the reaction UTP + ATP + glutamine ⇔ CTP + ADP + glutamate, is below: Cytosine is a nucleotide that is present in both DNA and RNA. However, uracil is only found in RNA. Therefore, after UTP is synthesized, it is must be converted into a deoxy form to be incorporated into DNA. This conversion involves the enzyme Ribonucleoside-triphosphate reductase, ribonucleoside triphosphate reductase. This reaction that removes the 2'-OH of the ribose sugar to generate deoxyribose is not affected by the bases attached to the sugar. This non-specificity allows ribonucleoside triphosphate reductase to convert all nucleotide triphosphates to deoxyribonucleotide by a similar mechanism. In contrast to uracil, thymine bases are found mostly in DNA, not RNA. Cells do not normally contain thymine bases that are linked to ribose sugars in RNA, thus indicating that cells only synthesize deoxyribose-linked thymine. The enzyme thymidylate synthetase is responsible for synthesizing thymine residues from dUMP to dTMP. This reaction transfers a methyl group onto the uracil base of dUMP to generate dTMP. The thymidylate synthase reaction, dUMP + 5,10-methylenetetrahydrofolate ⇔ dTMP + dihydrofolate, is shown to the right.


DNA

Although there are differences between
eukaryotic Eukaryotes () are organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interact ...
and prokaryotic DNA synthesis, the following section denotes key characteristics of DNA replication shared by both organisms.
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

DNA
is composed of
nucleotide Nucleotides are organic molecules , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, ...

nucleotide
s that are joined by
phosphodiester bondsImage:Phosphodiester Bond Diagram.svg, 200px, Diagram of phosphodiester bonds (PO43−) between three nucleotides. A phosphodiester bond occurs when exactly two of the hydroxyl groups in phosphoric acid react with hydroxyl groups on other molecules ...
. DNA replication, DNA synthesis, which takes place in the Cell nucleus, nucleus, is a Semiconservative replication, semiconservative process, which means that the resulting DNA molecule contains an original strand from the parent structure and a new strand. DNA synthesis is catalyzed by a family of DNA polymerases that require four deoxynucleoside triphosphates, a Template strand#Elongation, template strand, and a Rna primer, primer with a free 3'OH in which to incorporate nucleotides. In order for DNA replication to occur, a Replication fork#Replication fork, replication fork is created by enzymes called helicases which unwind the DNA helix. Topoisomerases at the replication fork remove DNA supercoil, supercoils caused by DNA unwinding, and Single-strand binding protein, single-stranded DNA binding proteins maintain the two single-stranded DNA templates stabilized prior to replication. DNA synthesis is initiated by the RNA polymerase primase, which makes an RNA primer with a free 3'OH. This primer is attached to the single-stranded DNA template, and DNA polymerase elongates the chain by incorporating nucleotides; DNA polymerase also proofreads the newly synthesized DNA strand. During the polymerization reaction catalyzed by DNA polymerase, a nucleophilic attack occurs by the 3'OH of the growing chain on the innermost phosphorus atom of a deoxynucleoside triphosphate; this yields the formation of a Phosphodiester bridges, phosphodiester bridge that attaches a new nucleotide and releases pyrophosphate. Two types of strands are created simultaneously during replication: the Leading strand#Replication fork, leading strand, which is synthesized continuously and grows towards the replication fork, and the Lagging strand#Replication fork, lagging strand, which is made discontinuously in Okazaki fragments and grows away from the replication fork. Okazaki fragments are covalently joined by DNA ligase to form a continuous strand. Then, to complete DNA replication, RNA primers are removed, and the resulting gaps are replaced with DNA and joined via DNA ligase.


Amino acids

A protein is a polymer that is composed from
amino acid Amino acids are organic compound In , organic compounds are generally any s that contain - . Due to carbon's ability to (form chains with other carbon s), millions of organic compounds are known. The study of the properties, reactions, a ...

amino acid
s that are linked by peptide bonds. There are more than Amino acid#Non-standard amino acids, 300 amino acids found in nature of which only twenty, known as the Amino acid#Essential amino acids, standard amino acids, are the building blocks for protein. Only green plants and most microbes are able to Amino acid synthesis, synthesize all of the 20 standard amino acids that are needed by all living species. Mammals can only synthesize ten of the twenty standard amino acids. The other amino acids, valine, methionine, leucine, isoleucine, phenylalanine, lysine, threonine and tryptophan for adults and histidine, and arginine for babies are obtained through diet.


Amino acid basic structure

The general structure of the standard amino acids includes a Amine, primary amino group, a
carboxyl group A carboxylic acid is an organic acid that contains a carboxyl group (C(=O)OH) attached to an R-group. The general formula of a carboxylic acid is R−COOH or R−CO2H, with substituent, R referring to the alkyl, alkenyl, aryl, or other group. ...

carboxyl group
and the functional group attached to the Alpha-carbon, α-carbon. The different amino acids are identified by the functional group. As a result of the three different groups attached to the α-carbon, amino acids are Chirality (chemistry)#Definition, asymmetrical molecules. For all standard amino acids, except glycine, the α-carbon is a chiral center. In the case of glycine, the α-carbon has two hydrogen atoms, thus adding symmetry to this molecule. With the exception of proline, all of the amino acids found in life have the Chirality (chemistry)#By configuration: D- and L-, L-isoform conformation. Proline has a functional group on the α-carbon that forms a ring with the amino group.


Nitrogen source

One major step in amino acid biosynthesis involves incorporating a nitrogen group onto the α-carbon. In cells, there are two major pathways of incorporating nitrogen groups. One pathway involves the enzyme glutamine oxoglutarate aminotransferase (GOGAT) which removes the amide amino group of
glutamine Glutamine (symbol Gln or Q) is an α-amino acid Amino acids are organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical b ...

glutamine
and transfers it onto 2-oxoglutarate, producing two glutamate molecules. In this catalysis reaction, glutamine serves as the nitrogen source. An image illustrating this reaction is found to the right. The other pathway for incorporating nitrogen onto the α-carbon of amino acids involves the enzyme glutamate dehydrogenase (GDH). GDH is able to transfer ammonia onto 2-oxoglutarate and form glutamate. Furthermore, the enzyme glutamine synthetase (GS) is able to transfer ammonia onto glutamate and synthesize glutamine, replenishing glutamine.


The glutamate family of amino acids

The glutamate family of amino acids includes the amino acids that derive from the amino acid glutamate. This family includes: glutamate,
glutamine Glutamine (symbol Gln or Q) is an α-amino acid Amino acids are organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical b ...

glutamine
, proline, and arginine. This family also includes the amino acid lysine, which is derived from α-ketoglutarate. The biosynthesis of glutamate and glutamine is a key step in the nitrogen assimilation discussed above. The enzymes GOGAT and Glutamate dehydrogenase, GDH catalyze the nitrogen assimilation reactions. In bacteria, the enzyme glutamate 5-kinase initiates the biosynthesis of proline by transferring a phosphate group from ATP onto glutamate. The next reaction is catalyzed by the enzyme Glutamate-5-semialdehyde dehydrogenase, pyrroline-5-carboxylate synthase (P5CS), which catalyzes the reduction of the Gamma-carboxylation, ϒ-carboxyl group of L-glutamate 5-phosphate. This results in the formation of glutamate semialdehyde, which spontaneously cyclizes to pyrroline-5-carboxylate. Pyrroline-5-carboxylate is further reduced by the enzyme pyrroline-5-carboxylate reductase (P5CR) to yield a proline amino acid. In the first step of arginine biosynthesis in bacteria, glutamate is acetylated by transferring the acetyl group from acetyl-CoA at the N-α position; this prevents spontaneous cyclization. The enzyme N-acetylglutamate synthase (glutamate N-acetyltransferase) is responsible for catalyzing the acetylation step. Subsequent steps are catalyzed by the enzymes acetylglutamate kinase, N-acetylglutamate kinase, N-acetyl-gamma-glutamyl-phosphate reductase, and acetylornithine transaminase, acetylornithine/succinyldiamino pimelate aminotransferase and yield the N-acetyl-L-ornithine. The acetyl group of acetylornithine is removed by the enzyme Acetylornithine deacetylase, acetylornithinase (AO) or Glutamate N-acetyltransferase, ornithine acetyltransferase (OAT), and this yields ornithine. Then, the enzymes citrulline and argininosuccinate convert ornithine to arginine. There are two distinct lysine biosynthetic pathways: the diaminopimelic acid pathway and the Alpha-aminoadipate pathway, α-aminoadipate pathway. The most common of the two synthetic pathways is the diaminopimelic acid pathway; it consists of several enzymatic reactions that add carbon groups to aspartate to yield lysine: # Aspartate kinase initiates the diaminopimelic acid pathway by phosphorylating aspartate and producing aspartyl phosphate. # Aspartate-semialdehyde dehydrogenase, Aspartate semialdehyde dehydrogenase catalyzes the
NADPH Nicotinamide adenine dinucleotide phosphate, abbreviated NADP or, in older notation, TPN (triphosphopyridine nucleotide), is a cofactor used in anabolic reactions, such as the Calvin cycle The Calvin cycle, light-independent reactions, bio syn ...

NADPH
-dependent reduction of aspartyl phosphate to yield aspartate semialdehyde. # 4-hydroxy-tetrahydrodipicolinate synthase adds a Pyruvic acid, pyruvate group to the β-aspartyl-4-semialdehyde, and a water molecule is removed. This causes Cyclic compound, cyclization and gives rise to (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate. # Dihydrodipicolinate reductase, 4-hydroxy-tetrahydrodipicolinate reductase catalyzes the reduction of (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate by NADPH to yield Δ'-piperideine-2,6-dicarboxylate (2,3,4,5-tetrahydrodipicolinate) and H2O. # Tetrahydrodipicolinate N-acetyltransferase, Tetrahydrodipicolinate acyltransferase catalyzes the acetylation reaction that results in ring opening and yields N-acetyl α-amino-ε-ketopimelate. # Succinyldiaminopimelate transaminase, N-succinyl-α-amino-ε-ketopimelate-glutamate aminotransaminase catalyzes the transamination reaction that removes the keto group of N-acetyl α-amino-ε-ketopimelate and replaces it with an amino group to yield N-succinyl-L-diaminopimelate. # succinyl-diaminopimelate desuccinylase, N-acyldiaminopimelate deacylase catalyzes the deacylation of N-succinyl-L-diaminopimelate to yield L,L-diaminopimelate. # diaminopimelate epimerase, DAP epimerase catalyzes the conversion of L,L-diaminopimelate to the Meso form, meso form of L,L-diaminopimelate. # Diaminopimelate decarboxylase, DAP decarboxylase catalyzes the removal of the carboxyl group, yielding L-lysine.


The serine family of amino acids

The serine family of amino acid includes: serine, cysteine, and glycine. Most microorganisms and plants obtain the sulfur for synthesizing methionine from the amino acid cysteine. Furthermore, the conversion of serine to glycine provides the carbons needed for the biosynthesis of the methionine and histidine. During serine biosynthesis, the enzyme phosphoglycerate dehydrogenase catalyzes the initial reaction that oxidizes 3-phospho-D-glycerate to yield Phosphohydroxypyruvic acid, 3-phosphonooxypyruvate. The following reaction is catalyzed by the enzyme phosphoserine aminotransferase, which transfers an amino group from glutamate onto 3-phosphonooxypyruvate to yield Phosphoserine, L-phosphoserine. The final step is catalyzed by the enzyme phosphoserine phosphatase, which Dephosphorylation, dephosphorylates L-phosphoserine to yield L-serine. There are two known pathways for the biosynthesis of glycine. Organisms that use ethanol and acetate as the major carbon source utilize the Glyconeogenesis, glyconeogenic pathway to synthesize glycine. The other pathway of glycine biosynthesis is known as the glycolytic pathway. This pathway converts serine synthesized from the intermediates of glycolysis to glycine. In the glycolytic pathway, the enzyme serine hydroxymethyltransferase catalyzes the cleavage of serine to yield glycine and transfers the cleaved carbon group of serine onto tetrahydrofolate, forming 5,10-Methylenetetrahydrofolate, 5,10-methylene-tetrahydrofolate. Cysteine biosynthesis is a two-step reaction that involves the incorporation of inorganic sulfur. In microorganisms and plants, the enzyme Serine O-acetyltransferase, serine acetyltransferase catalyzes the transfer of acetyl group from acetyl-CoA onto L-serine to yield O-acetyl-L-serine. The following reaction step, catalyzed by the enzyme Cysteine synthase, O-acetyl serine (thiol) lyase, replaces the acetyl group of O-acetyl-L-serine with sulfide to yield cysteine.


The aspartate family of amino acids

The aspartate family of amino acids includes: threonine, lysine, methionine, isoleucine, and aspartate. Lysine and isoleucine are considered part of the aspartate family even though part of their carbon skeleton is derived from pyruvate. In the case of methionine, the methyl carbon is derived from serine and the sulfur group, but in most organisms, it is derived from cysteine. The biosynthesis of aspartate is a one step reaction that is catalyzed by a single enzyme. The enzyme aspartate aminotransferase catalyzes the transfer of an amino group from aspartate onto α-ketoglutarate to yield glutamate and oxaloacetate. Asparagine is synthesized by an ATP-dependent addition of an amino group onto aspartate; asparagine synthetase catalyzes the addition of nitrogen from glutamine or soluble ammonia to aspartate to yield asparagine. The diaminopimelic acid biosynthetic pathway of lysine belongs to the aspartate family of amino acids. This pathway involves nine enzyme-catalyzed reactions that convert aspartate to lysine. # Aspartate kinase catalyzes the initial step in the diaminopimelic acid pathway by transferring a phosphoryl from ATP onto the carboxylate group of aspartate, which yields aspartyl-β-phosphate. # Aspartate-semialdehyde dehydrogenase catalyzes the reduction reaction by dephosphorylation of aspartyl-β-phosphate to yield aspartate-β-semialdehyde. # 4-hydroxy-tetrahydrodipicolinate synthase, Dihydrodipicolinate synthase catalyzes the Condensation reaction, condensation reaction of aspartate-β-semialdehyde with pyruvate to yield dihydrodipicolinic acid. # Dihydrodipicolinate reductase, 4-hydroxy-tetrahydrodipicolinate reductase catalyzes the reduction of dihydrodipicolinic acid to yield tetrahydrodipicolinic acid. # 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, Tetrahydrodipicolinate N-succinyltransferase catalyzes the transfer of a succinyl group from succinyl-CoA on to tetrahydrodipicolinic acid to yield N-succinyl-L-2,6-diaminoheptanedioate. # N-succinyldiaminopimelate aminotransferase catalyzes the transfer of an amino group from glutamate onto N-succinyl-L-2,6-diaminoheptanedioate to yield N-succinyl-L,L-diaminopimelic acid. # Succinyldiaminopimelate transaminase, Succinyl-diaminopimelate desuccinylase catalyzes the removal of acyl group from N-succinyl-L,L-diaminopimelic acid to yield L,L-diaminopimelic acid. # Diaminopimelate epimerase catalyzes the inversion of the α-carbon of L,L-diaminopimelic acid to yield meso-diaminopimelic acid. # Siaminopimelate decarboxylase catalyzes the final step in lysine biosynthesis that removes the carbon dioxide group from meso-diaminopimelic acid to yield L-lysine.


Proteins

Protein synthesis occurs via a process called
translation Translation is the communication of the meaning Meaning most commonly refers to: * Meaning (linguistics), meaning which is communicated through the use of language * Meaning (philosophy), definition, elements, and types of meaning discusse ...

translation
. During translation, genetic material called mRNA is read by ribosomes to generate a protein polypeptide chain. This process requires TRNA, transfer RNA (tRNA) which serves as an adaptor by binding amino acids on one end and interacting with mRNA at the other end; the latter pairing between the tRNA and mRNA ensures that the correct amino acid is added to the chain. Protein synthesis occurs in three phases: initiation, elongation, and termination. Prokaryotic (Archaeal translation, archaeal and Bacterial translation, bacterial) translation differs from eukaryotic translation; however, this section will mostly focus on the commonalities between the two organisms.


Additional background

Before translation can begin, the process of binding a specific amino acid to its corresponding tRNA must occur. This reaction, called tRNA charging, is catalyzed by aminoacyl tRNA synthetase. A specific tRNA synthetase is responsible for recognizing and charging a particular amino acid. Furthermore, this enzyme has special discriminator regions to ensure the correct binding between tRNA and its cognate amino acid. The first step for joining an amino acid to its corresponding tRNA is the formation of aminoacyl-AMP: : + ATP <=> + PP_i This is followed by the transfer of the aminoacyl group from aminoacyl-AMP to a tRNA molecule. The resulting molecule is aminoacyl-tRNA: : + tRNA <=> + AMP The combination of these two steps, both of which are catalyzed by aminoacyl tRNA synthetase, produces a charged tRNA that is ready to add amino acids to the growing polypeptide chain. In addition to binding an amino acid, tRNA has a three nucleotide unit called an Anticodon#Anticodon, anticodon that Basepairing, base pairs with specific nucleotide triplets on the mRNA called codons; codons encode a specific amino acid. This interaction is possible thanks to the ribosome, which serves as the site for protein synthesis. The ribosome possesses three tRNA binding sites: the aminoacyl site (A site), the peptidyl site (P site), and the exit site (E site). There are numerous codons within an mRNA transcript, and it is very common for an amino acid to be specified by more than one codon; this phenomenon is called Codon degeneracy, degeneracy. In all, there are 64 codons, 61 of each code for one of the 20 amino acids, while the remaining codons specify chain termination.


Translation in steps

As previously mentioned, translation occurs in three phases: initiation, elongation, and termination.


Step 1: Initiation

The completion of the initiation phase is dependent on the following three events: 1. The recruitment of the ribosome to mRNA 2. The binding of a charged initiator tRNA into the P site of the ribosome 3. The proper alignment of the ribosome with mRNA's start codon


Step 2: Elongation

Following initiation, the polypeptide chain is extended via anticodon:codon interactions, with the ribosome adding amino acids to the polypeptide chain one at a time. The following steps must occur to ensure the correct addition of amino acids: 1. The binding of the correct tRNA into the A site of the ribosome 2. The formation of a peptide bond between the tRNA in the A site and the polypeptide chain attached to the tRNA in the P site 3. Protein translocation#Protein translocation, Translocation or advancement of the tRNA-mRNA complex by three nucleotides Translocation "kicks off" the tRNA at the E site and shifts the tRNA from the A site into the P site, leaving the A site free for an incoming tRNA to add another amino acid.


Step 3: Termination

The last stage of translation occurs when a stop codon enters the A site. Then, the following steps occur: 1. The recognition of codons by release factors, which causes the
hydrolysis Hydrolysis (; ) is any chemical reaction in which a molecule of water breaks one or more chemical bonds. The term is used broadly for substitution Substitution may refer to: Arts and media *Chord substitution, in music, swapping one chord fo ...

hydrolysis
of the polypeptide chain from the tRNA located in the P site 2. The release of the polypeptide chain 3. The dissociation and "recycling" of the ribosome for future translation processes A summary table of the key players in translation is found below:


Diseases associated with macromolecule deficiency

Errors in biosynthetic pathways can have deleterious consequences including the malformation of macromolecules or the underproduction of functional molecules. Below are examples that illustrate the disruptions that occur due to these inefficiencies. *Familial hypercholesterolemia: this disorder is characterized by the absence of functional Receptor (biochemistry), receptors for LDL. Deficiencies in the formation of LDL receptors may cause faulty receptors which disrupt the Endocytosis, endocytic pathway, inhibiting the entry of LDL into the liver and other cells. This causes a buildup of LDL in the blood plasma, which results in atherosclerotic plaques that narrow arteries and increase the risk of heart attacks. *Lesch–Nyhan syndrome: this genetic disease is characterized by Self mutilation, self- mutilation, mental deficiency, and gout. It is caused by the absence of hypoxanthine-guanine phosphoribosyltransferase, which is a necessary enzyme for purine nucleotide formation. The lack of enzyme reduces the level of necessary nucleotides and causes the accumulation of biosynthesis Reaction intermediate, intermediates, which results in the aforementioned unusual behavior. *Severe combined immunodeficiency, Severe combined immunodeficiency (SCID): SCID is characterized by a loss of T cells. Shortage of these immune system components increases the susceptibility to infectious agents because the affected individuals cannot develop immunological memory. This immunological disorder results from a deficiency in Adenosine deaminase, adenosine deanimase activity, which causes a buildup of dATP. These dATP molecules then inhibit ribonucleotide reductase, which prevents of DNA synthesis. *Huntington's disease: this neurological disease is caused from errors that occur during DNA synthesis. These errors or mutations lead to the expression of a mutant huntingtin protein, which contains repetitive
glutamine Glutamine (symbol Gln or Q) is an α-amino acid Amino acids are organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical b ...

glutamine
residues that are encoded by expanding Trinucleotide repeat#CAG Repeats, CAG trinucleotide repeats in the gene. Huntington's disease is characterized by neuronal loss and gliosis. Symptoms of the disease include: movement disorder, cognitive decline, and behavioral disorder.


See also

* Lipids * Phosopholipid bilayer, Phospholipid bilayer * Nucleotides *
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

DNA
* DNA replication * Proteinogenic amino acid * Codon table * Prostaglandin * Porphyrin#Synthesis, Porphyrins * Chlorophyllide, Chlorophylls and bacteriochlorophylls * Biosynthesis of cobalamin, Vitamin B12


References

{{Portal bar, Metabolism Biosynthesis, Metabolism