A biomolecule is any molecule that
is produced by a living organism, including large macromolecules
such as proteins,
polysaccharides,
lipids, and nucleic
acids, as well as small molecules such as primary metabolites,
secondary metabolites, and natural
products. A more general name for this class of molecules is biogenic substances.
Types of biomolecules
A diverse range of biomolecules exist, including:
Nucleosides and nucleotides
Main articles: Nucleosides
and Nucleotides
Nucleosides are molecules formed by attaching a nucleobase
to a ribose or
deoxyribose ring. Examples of these include cytidine (C), uridine (U), adenosine
(A), guanosine
(G), thymidine
(T) and inosine
(I).
Nucleosides can be phosphorylated
by specific kinases
in the cell, producing nucleotides. Both DNA and RNA are polymers,
consisting of long, linear molecules assembled by polymerase
enzymes from repeating structural units, or monomers, of mononucleotides. DNA
uses the deoxynucleotides C, G, A, and T, while RNA uses the ribomucleotides
(which have an extra hydroxyl(OH) group on the pentose ring) C, G, A, and U.
Modified bases are fairly common (such as with methyl groups on the base ring),
as found in ribosomal
RNA or transfer
RNAs or for discriminating the new from old strands of DNA after
replication.
Each nucleotide is made of an acyclic nitrogenous
base, a pentose
and one to three phosphate groups. They contain carbon, nitrogen, oxygen,
hydrogen and phosphorus. They serve as sources of chemical energy (adenosine triphosphate and guanosine triphosphate), participate in cellular
signaling (cyclic guanosine monophosphate and cyclic adenosine monophosphate), and
are incorporated into important cofactors of enzymatic reactions (coenzyme A,
flavin adenine dinucleotide,
flavin mononucleotide, and nicotinamide adenine
dinucleotide phosphate).
DNA and RNA structure
DNA structure is dominated by the well-known double
helix formed by Watson-Crick base-pairing
of C with G and A with T. This is known as B-form DNA, and is
overwhelmingly the most favorable and common state of DNA; its highly specific
and stable base-pairing is the basis of reliable genetic information storage.
DNA can sometimes occur as single strands (often needing to be stabilized by
single-strand binding proteins) or as A-form or Z-form helices, and
occasionally in more complex 3D structures such as the crossover at Holliday
junctions during DNA replication.
Stereo 3D image of a group I intron ribozyme (PDB file
1Y0Q); gray lines show base pairs; ribbon arrows show double-helix regions,
blue to red from 5' to 3' end; white ribbon is an RNA product.
RNA, in contrast, forms large and complex 3D tertiary
structures reminiscent of proteins, as well as the loose single strands with
locally folded regions that constitute messenger
RNA molecules. Those RNA structures contain many stretches of A-form double
helix, connected into definite 3D arrangements by single-stranded loops,
bulges, and junctions. Examples are tRNA, ribosomes, ribozymes, and riboswitches.
These complex structures are facilitated by the fact that RNA backbone has less
local flexibility than DNA but a large set of distinct conformations,
apparently because of both positive and negative interactions of the extra OH
on the ribose.Structured RNA molecules can do highly specific binding of other
molecules and can themselves be recognized specifically; in addition, they can
perform enzymatic catalysis (when they are known as "ribozymes",
as initially discovered by Tom Cech and colleagues.
Saccharides
Monosaccharides are the simplest form of carbohydrates
with only one simple sugar.
They essentially contain an aldehyde or ketone group in their structure. The presence of an aldehyde
group in a monosaccharide is indicated by the prefix aldo-. Similarly, a
ketone group is denoted by the prefix keto-. Examples of monosaccharides
are the hexoses glucose, fructose, and galactose and
pentoses,
ribose, and deoxyribose Consumed fructose and glucose have
different rates of gastric emptying, are differentially absorbed and have
different metabolic fates, providing multiple opportunities for 2 different
saccharides to differentially affect food intake. Most saccharides eventually
provide fuel for cellular respiration.
Disaccharides are formed when two
monosaccharides, or two single simple sugars, form a bond with removal of
water. They can be hydrolyzed to yield their saccharin building blocks by
boiling with dilute acid or reacting them with appropriate enzymes. Examples of
disaccharides include sucrose, maltose, and lactose.
Polysaccharides are polymerized monosaccharides, or complex
carbohydrates. They have multiple simple sugars. Examples are starch, cellulose,
and glycogen.
They are generally large and often have a complex branched connectivity.
Because of their size, polysaccharides are not water-soluble, but their many
hydroxy groups become hydrated individually when exposed to water, and some
polysaccharides form thick colloidal dispersions when heated in water. Shorter
polysaccharides, with 3 - 10 monomers, are called oligosaccharides.
A fluorescent indicator-displacement molecular imprinting sensor was developed
for discriminating saccharides. It successfully discriminated three brands of
orange juice beverage. The change in fluorescence intensity of the sensing
films resulting is directly related to the saccharide concentration.
Lignin
Lignin
is a complex polyphenolic macromolecule composed mainly of beta-O4-aryl
linkages. After cellulose, lignin is the second most abundant biopolymer and is
one of the primary structural components of most plants. It contains subunits
derived from p-coumaryl alcohol, coniferyl
alcohol, and sinapyl alcohol and is unusual among biomolecules
in that it is racemic.
The lack of optical activity is due to the polymerization of lignin which
occurs via free radical coupling reactions in which there
is no preference for either configuration at a chiral center.
Lipids
Lipids
(oleaginous) are chiefly fatty acid esters, and
are the basic building blocks of biological
membranes. Another biological role is energy storage (e.g., triglycerides).
Most lipids consist of a polar or hydrophilic
head (typically glycerol) and one to three nonpolar or hydrophobic
fatty acid tails, and therefore they are amphiphilic.
Fatty acids consist of unbranched chains of carbon atoms that are connected by
single bonds alone (saturated fatty acids) or by both single and double
bonds (unsaturated fatty acids). The chains are
usually 14-24 carbon groups long, but it is always an even number.
For lipids present in biological membranes, the hydrophilic
head is from one of three classes:
- Glycolipids, whose heads contain an oligosaccharide with 1-15 saccharide residues.
- Phospholipids, whose heads contain a positively charged group that is linked to the tail by a negatively charged phosphate group.
- Sterols, whose heads contain a planar steroid ring, for example, cholesterol.
Other lipids include prostaglandins
and leukotrienes
which are both 20-carbon fatty acyl units synthesized from arachidonic
acid. They are also known as fatty acids
Amino acids
Amino acids contain both amino and carboxylic
acid functional groups. (In biochemistry,
the term amino acid is used when referring to those amino acids in which the
amino and carboxylate functionalities are attached to the same carbon, plus proline which is
not actually an amino acid).
Modified amino acids are sometimes observed in proteins;
this is usually the result of enzymatic modification after translation (protein
synthesis). For example, phosphorylation of serine by kinases and
dephosphorylation by phosphatases is an important control mechanism in the cell cycle.
Only two amino acids other than the standard twenty are known to be
incorporated into proteins during translation, in certain organisms:
- Selenocysteine is incorporated into some proteins at a UGA codon, which is normally a stop codon.
- Pyrrolysine is incorporated into some proteins at a UAG codon. For instance, in some methanogens in enzymes that are used to produce methane.
Besides those used in protein
synthesis, other biologically important amino acids include carnitine
(used in lipid transport within a cell), ornithine, GABA and taurine.
Protein structure
The particular series of amino acids that form a protein is
known as that protein's primary structure. This sequence is determined by
the genetic makeup of the individual. It specifies the order of side-chain
groups along the linear polypeptide "backbone".
Proteins have two types of well-classified, frequently
occurring elements of local structure defined by a particular pattern of hydrogen
bonds along the backbone: alpha helix and beta sheet.
Their number and arrangement is called the secondary structure of the protein. Alpha
helices are regular spirals stabilized by hydrogen bonds between the backbone
CO group (carbonyl)
of one amino acid residue and the backbone NH group (amide) of the i+4
residue. The spiral has about 3.6 amino acids per turn, and the amino acid side
chains stick out from the cylinder of the helix. Beta pleated sheets are formed
by backbone hydrogen bonds between individual beta strands each of which is in
an "extended", or fully stretched-out, conformation. The strands may
lie parallel or antiparallel to each other, and the side-chain direction
alternates above and below the sheet. Hemoglobin contains only helices, natural
silk is formed of beta pleated sheets, and many enzymes have a pattern of
alternating helices and beta-strands. The secondary-structure elements are
connected by "loop" or "coil" regions of non-repetitive
conformation, which are sometimes quite mobile or disordered but usually adopt
a well-defined, stable arrangement.
The overall, compact, 3D structure
of a protein is termed its tertiary structure or its "fold". It
is formed as result of various attractive forces like hydrogen
bonding, disulfide bridges, hydrophobic interactions, hydrophilic
interactions, van der Waals force etc.
When two or more polypeptide
chains (either of identical or of different sequence) cluster to form a
protein, quaternary structure of protein is formed.
Quaternary structure is an attribute of polymeric
(same-sequence chains) or heteromeric (different-sequence chains) proteins like hemoglobin,
which consists of two "alpha" and two "beta" polypeptide
chains.
Apoenzymes
An apoenzyme (or, generally, an apoprotein) is the protein
without any small-molecule cofactors, substrates, or inhibitors bound. It is
often important as an inactive storage, transport, or secretory form of a
protein. This is required, for instance, to protect the secretory cell from the
activity of that protein. Apoenzymes becomes active enzymes on addition of a cofactor. Cofactors can be either inorganic
(e.g., metal ions and iron-sulfur clusters) or organic compounds,
(e.g., flavin
and heme). Organic
cofactors can be either prosthetic groups, which are tightly bound to an
enzyme, or coenzymes,
which are released from the enzyme's active site during the reaction.
Isoenzymes
Isoenzymes, or isozymes, are multiple forms of an enzyme,
with slightly different protein sequence and closely similar but usually
not identical functions. They are either products of different genes, or else
different products of alternative splicing. They may either be
produced in different organs or cell types to perform the same function, or
several isoenzymes may be produced in the same cell type under differential
regulation to suit the needs of changing development or environment. LDH (lactate dehydrogenase) has multiple isozymes,
while fetal hemoglobin is an example of a
developmentally regulated isoform of a non-enzymatic protein. The relative
levels of isoenzymes in blood can be used to diagnose problems in the organ of
secretion.
Vitamins
A vitamin is a compound that is generally not synthesized by a
given organism but is nonetheless vital to its survival or health (for example coenzymes).
These compounds must be absorbed, or eaten, but typically only in trace
quantities. When originally proposed by Casimir
Funk, a Polish biochemist, he believed them to all be basic and therefore
named them vital amines.
The "al" was later dropped to form the word vitamines.
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