Elementary molecular biology

## Nucleotide

From Nucleotide:

A nucleotide is composed of three distinctive chemical sub-units: a five-carbon sugar molecule, a nitrogenous base and one phosphate group.

Nucleotides contain either a purine or a pyrimidine base—i.e., the nitrogenous base molecule, also known as a nucleobase—and are termed *ribo*nucleotides if the sugar is ribose, or *deoxyribo*nucleotides if the sugar is deoxyribose.

## DNA

From DNA:

DNA is a molecule composed of two chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organisms.

The two DNA strands are also known as poly-nucleotides as they are composed of simpler monomeric units called nucleotides. The nucleotides of each individual strand are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone.

The nitrogenous bases of the two separate polynucleotide strands are bound together, according to base pairing rules (A with T and C with G), with hydrogen bonds to make double-stranded DNA.

Hydrogen bonds are much weaker than covalent bonds.

## Base pair

From Base pair:

A **base pair** (**bp**) is a unit consisting of two nucleobases bound to each other by weak hydrogen bonds.

* Top, a **G-C** base pair with three hydrogen bonds.
* Bottom, an **A-T** base pair with two hydrogen bonds.
* Non-covalent hydrogen bonds between the bases are shown as dashed lines.
* The wiggly lines stand for the connection to the sugar-phosphate backbone.

## DNA replication

See also: DNA clamp
From DNA replication:

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

Phosphodiester (intra-strand) bonds are stronger than hydrogen (inter-strand) bonds. This allows the two strands to be separated from one another. The nucleotide sequence on each single strand can then be used to reconstruct the nucleotide sequence of the missing strand.

## RNA

From RNA:

The chemical structure of RNA is very similar to that of DNA, but differs in three primary ways:

* Unlike double-stranded DNA, RNA is a single-stranded molecule in many of its biological roles and consists of much shorter chains of nucleotides. However, a single RNA molecule can, by complementary base pairing, form intrastrand double helixes, as in tRNA (see "Transfer RNA" below).

* While the sugar-phosphate "backbone" of DNA contains *deoxyribose*, RNA contains *ribose* instead. Ribose has a hydroxyl group attached to the pentose ring in the 2' position, whereas deoxyribose does not. The hydroxyl groups in the ribose backbone make RNA more chemically labile than DNA by lowering the activation energy of hydrolysis.

* The complementary base to adenine in RNA is uracil, whereas in DNA it is thymine, which is a methylated form of uracil.

## Transcription

From Transcription (biology):

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

Transcription proceeds in the following general steps:

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

## Genetic code

From Genetic code:

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

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

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

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

## Ribosome

From Ribosome:

**Ribosomes** comprise a complex macromolecular machine, found within all living cells, that serves as the site of biological protein synthesis (translation). Ribosomes link amino acids together in the order specified by messenger RNA (mRNA) molecules.

Ribosomes consist of two major components:

* The small ribosomal subunits, which read the RNA.
* The large subunits, which join amino acids to form a polypeptide chain.

Each subunit consists of one or more ribosomal RNA (rRNA) molecules and a variety of ribosomal proteins (r-protein or rProtein). The ribosomes and associated molecules are also known as the *translational apparatus*.

* Prokaryotic ribosomes (plastoribosomes) are around 20 nm (200 Å) in diameter and are composed of 65% rRNA and 35% ribosomal proteins.
* Eukaryotic ribosomes (cytoribosomes) are between 25 and 30 nm (250–300 Å) in diameter and are composed of 50% rRNA and 50% ribosomal proteins.

Ribosomes are classified as being either "free" or "membrane-bound".

## Transfer RNA

From Transfer RNA:

A transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length, that carryies an amino acid to a ribosome (protein synthetic machinery of a cell).

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

## Codons

From Template:Codon table:

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

## Peptide bond

From Peptide bond:

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

## Proteins

From Protein:

Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions (see also: Catalytic triad), DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids.

A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds.

### Protein folding

From Wikipedia:Protein folding

Folding is a spontaneous process that is mainly guided by hydrophobic interactions, formation of intramolecular hydrogen bonds, van der Waals forces, and it is opposed by conformational entropy. The process of folding often begins co-translationally, so that the N-terminus of the protein begins to fold while the C-terminal portion of the protein is still being synthesized by the ribosome; however, a protein molecule may fold spontaneously during or after biosynthesis. While these macromolecules may be regarded as "folding themselves", the process also depends on the solvent (water or lipid bilayer), the concentration of salts, the pH, the temperature, the possible presence of cofactors and of molecular chaperones.

#### Primary structure

The primary structure of a protein, its linear amino-acid sequence, determines its native conformation. The specific amino acid residues and their position in the polypeptide chain are the determining factors for which portions of the protein fold closely together and form its three-dimensional conformation.

#### Secondary structure

Formation of a secondary structure is the first step in the folding process that a protein takes to assume its native structure. Characteristic of secondary structure are the structures known as alpha helices and beta sheets that fold rapidly because they are stabilized by intramolecular hydrogen bonds, as was first characterized by Linus Pauling. Formation of intramolecular hydrogen bonds provides another important contribution to protein stability. α-helices are formed by hydrogen bonding of the backbone to form a spiral shape (refer to figure on the right). The β pleated sheet is a structure that forms with the backbone bending over itself to form the hydrogen bonds (as displayed in the figure to the left). The hydrogen bonds are between the amide hydrogen and carbonyl oxygen of the peptide bond. There exists anti-parallel β pleated sheets and parallel β pleated sheets where the stability of the hydrogen bonds is stronger in the anti-parallel β sheet as it hydrogen bonds with the ideal 180 degree angle compared to the slanted hydrogen bonds formed by parallel sheets.

#### Tertiary structure

The alpha helices and beta pleated sheets can be amphipathic in nature, or contain a hydrophilic portion and a hydrophobic portion. This property of secondary structures aids in the tertiary structure of a protein in which the folding occurs so that the hydrophilic sides are facing the aqueous environment surrounding the protein and the hydrophobic sides are facing the hydrophobic core of the protein. Secondary structure hierarchically gives way to tertiary structure formation. Once the protein's tertiary structure is formed and stabilized by the hydrophobic interactions, there may also be covalent bonding in the form of disulfide bridges formed between two cysteine residues. Tertiary structure of a protein involves a single polypeptide chain; however, additional interactions of folded polypeptide chains give rise to quaternary structure formation.

#### Quaternary structure

Tertiary structure may give way to the formation of quaternary structure in some proteins, which usually involves the "assembly" or "coassembly" of subunits that have already folded; in other words, multiple polypeptide chains could interact to form a fully functional quaternary protein.

## Cofactor

From Cofactor (biochemistry):

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

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

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

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

## ATP

From Adenosine triphosphate:

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

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

## Carbohydrates

From Glucose:

**Glucose** (also called **dextrose**) is a simple sugar with the molecular formula C6H12O6. Glucose is the most abundant monosaccharide, a subcategory of carbohydrates. Glucose is mainly made by plants and most algae during photosynthesis from water and carbon dioxide, using energy from sunlight. There it is used to make cellulose in cell walls, which is the most abundant carbohydrate. In energy metabolism, glucose is the most important source of energy in all organisms. Glucose for metabolism is partially stored as a polymer, in plants mainly as starch and amylopectin and in animals as glycogen. Glucose circulates in the blood of animals as blood sugar. The naturally occurring form of glucose is d-glucose, while l-glucose is produced synthetically in comparatively small amounts and is of lesser importance. Approximately 4 grams of glucose are present in the blood of humans at all times.

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

**Cellulose** is an organic compound with the formula (C
6H
10O
n, a polysaccharide consisting of a linear chain of several hundred to many thousands of β(1→4) linked D-glucose units.

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

## Lipids

From Triglyceride:

A **triglyceride** (**TG**, **triacylglycerol**, **TAG**, or **triacylglyceride**) is an ester derived from glycerol and three fatty acids (from *tri-* and *glyceride*). Triglycerides are the main constituents of body fat in humans and other vertebrates, as well as vegetable fat. There are many different types of triglyceride, with the main division between saturated and unsaturated types. Saturated fats are "saturated" with hydrogen — all available places where hydrogen atoms could be bonded to carbon atoms are occupied. These have a higher melting point and are more likely to be solid at room temperature. Unsaturated fats have double bonds between some of the carbon atoms, reducing the number of places where hydrogen atoms can bond to carbon atoms. These have a lower melting point and are more likely to be liquid at room temperature.

From Phospholipid:

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

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

## Proton pump

From Proton pump:

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

## F-ATPase

Proton pumps also work in reverse to create ATP.

From F-ATPase:

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

## Ribozyme

From Ribozyme:

Ribozymes (ribonucleic acid enzymes) are RNA molecules that are capable of catalyzing specific biochemical reactions, similar to the action of protein enzymes. Ribosomes are ribozymes, because the catalytic peptidyl transferase activity that links amino acids together is performed by the ribosomal RNA.

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