Biosynthesis, i.e., chemical synthesis occurring in biological contexts, is a term most often referring to multi-step, enzyme-Catalysis processes where chemical substances absorbed as nutrients (or previously converted through biosynthesis) serve as enzyme substrates, with conversion by the living organism either into simpler or more complex products. Examples of biosynthetic pathways include those for the production of amino acids, lipid membrane components, and , but also for the production of all classes of biological macromolecules, and of acetyl-coenzyme A, adenosine triphosphate, nicotinamide adenine dinucleotide and other key intermediate and transactional molecules needed for metabolism. Thus, in biosynthesis, any of an array of compounds, from simple to complex, are converted into other compounds, and so it includes both the catabolism and anabolism (building up and breaking down) of complex molecules (including macromolecules). Biosynthetic processes are often represented via charts of metabolic pathways. A particular biosynthetic pathway may be located within a single cellular organelle (e.g., mitochondrial fatty acid synthesis pathways), while others involve enzymes that are located across an array of cellular organelles and structures (e.g., the biosynthesis of glycosylated cell surface proteins).
Elements of biosynthesis
Elements of biosynthesis include: precursor compounds,
chemical energy (e.g. ATP), and catalytic enzymes which may need
coenzymes (e.g.
NADH,
NADPH). These elements create
monomers, the building blocks for macromolecules. Some important biological macromolecules include:
proteins, which are composed of
amino acid monomers joined via
peptide bonds, and
DNA molecules, which are composed of nucleotides joined via phosphodiester bonds.
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 in a given chemical process.
-
Chemical energy: chemical energy can be found in the form of high energy molecules. These molecules are required for energetically unfavourable reactions. Furthermore, the hydrolysis of these compounds drives a reaction forward. High energy molecules, such as ATP, have three phosphates. Often, the terminal phosphate is split off during hydrolysis and transferred to another molecule.
-
Catalysis: these may be for example metal ions or coenzymes and they catalyze a reaction by increasing the Reaction rate and lowering the activation energy.
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 and the charging of tRNA prior to translation. For some of these steps, chemical energy is required:
-
::{Precursor\ molecule}+ATP <=> {product\ AMP} + PP_i
-
Simple compounds that are converted into other compounds with the assistance of cofactors. For example, the synthesis of requires acetyl CoA, while the synthesis of another membrane component, , requires NADH and FADH for the formation the sphingosine backbone. The general equation for these examples is:
-
::{Precursor\ molecule} + {Cofactor} ->enzyme {macromolecule}
-
Simple compounds that join to create a macromolecule. For example, join to form phospholipids. In turn, phospholipids and cholesterol interact noncovalently in order to form the lipid bilayer. This reaction may be depicted as follows:
-
::{Molecule\ 1} + {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. Fatty acids are
hydrocarbon derivatives; they contain a
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 and
sphingolipids. A third major membrane component,
cholesterol, does not contain these fatty acid units.
Eukaryotic phospholipids
The foundation of all
consists of a
bilayer structure of phospholipids.
The phospholipid molecule is
amphipathic; it contains a
hydrophilic polar head and a
hydrophobic 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 phosphatidate or diacylglycerol 3-phosphate at the endoplasmic reticulum and outer mitochondrial membrane.
Sphingolipids
Like phospholipids, these fatty acid derivatives have a polar head and nonpolar tails.
Unlike phospholipids, sphingolipids have a
sphingosine backbone.
Sphingolipids exist in
eukaryotic cells and are particularly abundant in the central nervous system.
For example,
sphingomyelin is part of the
myelin sheath of nerve fibers.
Sphingolipids are formed from that consist of a fatty acid chain attached to the amino group of a sphingosine backbone. These ceramides are synthesized from the acylation of sphingosine.
Cholesterol
This
lipid belongs to a class of molecules called
sterols.
Sterols have four fused rings and a
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 hormones, including
cortisol,
testosterone, and
estrogen.
Cholesterol is synthesized from acetyl CoA.
- :1. The synthesis of isopentenyl pyrophosphate, the "building block" of cholesterol
- :2. The formation of 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
involves enzyme-
Catalyst reactions that convert substrates into more complex products.
Nucleotides are the building blocks of
DNA and
RNA. Nucleotides are composed of a five-membered ring formed from
ribose sugar in RNA, and
deoxyribose sugar in DNA; these sugars are linked to a
purine or
pyrimidine base with a
glycosidic bond and a
phosphate group at the
Ribonucleotide of the sugar.
Purine nucleotides
The DNA nucleotides
adenosine and
guanosine consist of a purine base attached to a ribose sugar with a glycosidic bond. In the case of RNA nucleotides
deoxyadenosine and
deoxyguanosine, 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 employ a similar reaction mechanism in ten reaction steps. Purine bases are synthesized by converting phosphoribosyl pyrophosphate (PRPP) to inosine monophosphate (IMP), which is the first key intermediate in purine base biosynthesis.
Further enzymatic modification of IMP produces the adenosine and guanosine bases of nucleotides.
-
The first step in purine biosynthesis is a condensation reaction, performed by glutamine-PRPP amidotransferase. This enzyme transfers the amino group from glutamine to PRPP, forming 5-phosphoribosylamine. The following step requires the activation of glycine by the addition of a phosphate group from ATP.
-
GAR synthetase
-
GAR transformylase adds a formyl group onto the amino group of GAR, forming formylglycinamide ribonucleotide (FGAR).
-
FGAR amidotransferase
-
FGAM cyclase catalyzes ring closure, which involves removal of a water molecule, forming the 5-membered imidazole ring 5-aminoimidazole ribonucleotide (AIR).
-
N5-CAIR synthetase transfers a carboxyl group, forming the intermediate N5-carboxyaminoimidazole ribonucleotide (N5-CAIR).
-
N5-CAIR mutase rearranges the carboxyl functional group and transfers it onto the imidazole ring, forming 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,
-
SAICAR synthetase forms a peptide bond between aspartate and the added carboxyl group of the imidazole ring, forming N-succinyl-5-aminoimidazole-4-carboxamide ribonucleotide (SAICAR).
-
SAICAR lyase removes the carbon skeleton of the added aspartate, leaving the amino group and forming 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR).
-
AICAR transformylase transfers a carbonyl group to AICAR, forming N-formylaminoimidazole- 4-carboxamide ribonucleotide (FAICAR).
-
The final step involves the enzyme 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 mitochondrial inner membrane and multifunctional enzymes that are located in the
cytosol.
-
The first step involves the enzyme carbamoyl phosphate synthase combining glutamine with CO2 in an ATP dependent reaction to form carbamoyl phosphate.
-
Aspartate carbamoyltransferase condenses carbamoyl phosphate with aspartate to form uridosuccinate.
-
Dihydroorotase performs ring closure, a reaction that loses water, to form dihydroorotate.
-
Dihydroorotate dehydrogenase, located within the mitochondrial inner membrane,
-
Orotate phosphoribosyl hydrolase (OMP pyrophosphorylase) condenses orotate with PRPP to form orotidine-5'-phosphate.
-
OMP decarboxylase catalyzes the conversion of orotidine-5'-phosphate to 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 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 CTP by transferring an amino group from glutamine to uridine; this forms the cytosine base of CTP.
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. 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.
DNA
Although there are differences between
eukaryotic and
prokaryotic DNA synthesis, the following section denotes key characteristics of DNA replication shared by both organisms.
DNA is composed of that are joined by phosphodiester bonds.
In order for DNA replication to occur, a replication fork is created by enzymes called which unwind the DNA helix.
DNA synthesis is initiated by the RNA polymerase primase, which makes an RNA primer with a free 3'OH.
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 bridge that attaches a new nucleotide and releases pyrophosphate.
Two types of strands are created simultaneously during replication: the leading strand, which is synthesized continuously and grows towards the replication fork, and the lagging strand, which is made discontinuously in Okazaki fragments and grows away from the replication fork.
Amino acids
A protein is a polymer that is composed from
that are linked by
. There are more than 300 amino acids found in nature of which only twenty two, known as the proteinogenic amino acids, are the building blocks for protein.
Only
green plants and most
microbes are able to synthesize all of the 20 standard amino acids that are needed by all living species.
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
general structure of the standard amino acids includes a
Amine, a
carboxyl group and the
functional group attached to the
Alpha-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 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 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 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,
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 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 pyrroline-5-carboxylate synthase (P5CS), which catalyzes the reduction of the 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 N-acetylglutamate kinase, N-acetyl-gamma-glutamyl-phosphate reductase, and acetylornithine/succinyldiamino pimelate aminotransferase and yield the N-acetyl-L-ornithine. The acetyl group of acetylornithine is removed by the enzyme acetylornithinase (AO) or 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 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 catalyzes the NADPH-dependent reduction of aspartyl phosphate to yield aspartate semialdehyde.
-
4-hydroxy-tetrahydrodipicolinate synthase adds a Pyruvic acid group to the β-aspartyl-4-semialdehyde, and a water molecule is removed. This causes Cyclic compound and gives rise to (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate.
-
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 acyltransferase catalyzes the acetylation reaction that results in ring opening and yields N-acetyl α-amino-ε-ketopimelate.
-
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.
-
N-acyldiaminopimelate deacylase catalyzes the deacylation of N-succinyl-L-diaminopimelate to yield L,L-diaminopimelate.
-
DAP epimerase catalyzes the conversion of L,L-diaminopimelate to the Meso form form of L,L-diaminopimelate.
-
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,
There are two known pathways for the biosynthesis of glycine. Organisms that use ethanol and acetate as the major carbon source utilize the Glyconeogenesis 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-methylene-tetrahydrofolate.
Cysteine biosynthesis is a two-step reaction that involves the incorporation of inorganic sulfur. In microorganisms and plants, the enzyme serine acetyltransferase catalyzes the transfer of acetyl group from acetyl-CoA onto L-serine to yield O-acetyl-L-serine.
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.
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.
-
Dihydrodipicolinate synthase catalyzes the condensation reaction of aspartate-β-semialdehyde with pyruvate to yield dihydrodipicolinic acid.
-
4-hydroxy-tetrahydrodipicolinate reductase catalyzes the reduction of dihydrodipicolinic acid to yield tetrahydrodipicolinic acid.
-
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.
-
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.
During translation, genetic material called
mRNA is read by
ribosomes to generate a protein
polypeptide chain.
This process requires
TRNA (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 and 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:
- {Amino\ acid} + ATP <=> {aminoacyl-AMP} + 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:
- {Aminoacyl-AMP} + tRNA <=> {aminoacyl-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 that with specific nucleotide triplets on the mRNA called codons; codons encode a specific amino acid.
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.
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. 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 , which causes the 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:
| +
! Key players in Translation | Purpose |
| Responsible for tRNA charging |
| Template for protein synthesis; contains regions named codons which encode amino acids |
| Binds ribosomes sites A, P, E; anticodon base pairs with mRNA codon to ensure that the correct amino acid is incorporated into the growing polypeptide chain |
| Directs protein synthesis and catalyzes the formation of the peptide bond |
|
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 receptors for LDL.
-
Lesch–Nyhan syndrome: this genetic disease is characterized by Self mutilation, mental deficiency, and gout.
-
Severe combined immunodeficiency (SCID): SCID is characterized by a loss of T cells.
-
Huntington's disease: this neurological disease is caused from errors that occur during DNA synthesis.
See also
