DNA and Related Topics

A hairpin loop from a pre-mRNA. Highlighted are the nucleobases (green) and the ribose-phosphate backbone (blue). This is a single strand of RNA that folds back upon itself.

RNA

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Polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes.

Three-dimensional representation of the 50S ribosomal subunit. Ribosomal RNA is in ochre, proteins in blue. The active site is a small segment of rRNA, indicated in red.

Watson-Crick base pairs in a siRNA (hydrogen atoms are not shown)

Structure of a fragment of an RNA, showing a guanosyl subunit.

Secondary structure of a telomerase RNA.

Structure of a hammerhead ribozyme, a ribozyme that cuts RNA

Uridine to pseudouridine is a common RNA modification.

Robert W. Holley, left, poses with his research team.

RNA and deoxyribonucleic acid (DNA) are nucleic acids.

In biology, a gene (from γένος, ; meaning generation or birth or gender) is a basic unit of heredity and a sequence of nucleotides in DNA that encodes the synthesis of a gene product, either RNA or protein.

Protein

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Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues.

John Kendrew with model of myoglobin in progress

Chemical structure of the peptide bond (bottom) and the three-dimensional structure of a peptide bond between an alanine and an adjacent amino acid (top/inset). The bond itself is made of the CHON elements.

Resonance structures of the peptide bond that links individual amino acids to form a protein polymer

A ribosome produces a protein using mRNA as template

The DNA sequence of a gene encodes the amino acid sequence of a protein

The crystal structure of the chaperonin, a huge protein complex. A single protein subunit is highlighted. Chaperonins assist protein folding.

Three possible representations of the three-dimensional structure of the protein triose phosphate isomerase. Left: All-atom representation colored by atom type. Middle: Simplified representation illustrating the backbone conformation, colored by secondary structure. Right: Solvent-accessible surface representation colored by residue type (acidic residues red, basic residues blue, polar residues green, nonpolar residues white).

Molecular surface of several proteins showing their comparative sizes. From left to right are: immunoglobulin G (IgG, an antibody), hemoglobin, insulin (a hormone), adenylate kinase (an enzyme), and glutamine synthetase (an enzyme).

The enzyme hexokinase is shown as a conventional ball-and-stick molecular model. To scale in the top right-hand corner are two of its substrates, ATP and glucose.

Ribbon diagram of a mouse antibody against cholera that binds a carbohydrate antigen

Proteins in different cellular compartments and structures tagged with green fluorescent protein (here, white)

Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure, in this case hemoglobin containing heme units

Because DNA contains four nucleotides, the total number of possible codons is 64; hence, there is some redundancy in the genetic code, with some amino acids specified by more than one codon.

Base pair

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Fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds.

They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA.

Nucleic acid

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Nucleic acids are biopolymers, macromolecules, essential to all known forms of life.

The Swiss scientist Friedrich Miescher discovered nucleic acid first naming it as nuclein, in 1868. Later, he raised the idea that it could be involved in heredity.

The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

Nucleotide

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Nucleotides are organic molecules consisting of a nucleoside and a phosphate.

Showing the arrangement of nucleotides within the structure of nucleic acids: At lower left, a monophosphate nucleotide; its nitrogenous base represents one side of a base-pair. At the upper right, four nucleotides form two base-pairs: thymine and adenine (connected by double hydrogen bonds) and guanine and cytosine (connected by triple hydrogen bonds). The individual nucleotide monomers are chain-joined at their sugar and phosphate molecules, forming two 'backbones' (a double helix) of nucleic acid, shown at upper left.

Structural elements of three nucleo tides —where one-, two- or three-phosphates are attached to the nucleo side (in yellow, blue, green) at center: 1st, the nucleotide termed as a nucleoside mono phosphate is formed by adding a phosphate (in red); 2nd, adding a second phosphate forms a nucleoside di phosphate; 3rd, adding a third phosphate results in a nucleoside tri phosphate. + The nitrogenous base (nucleobase) is indicated by "Base" and "glycosidic bond" (sugar bond). All five primary, or canonical, bases—the purines and pyrimidines—are sketched at right (in blue).

The synthesis of UMP. The color scheme is as follows: enzymes, <span style="color: rgb(219,155,36);">coenzymes, <span style="color: rgb(151,149,45);">substrate names , <span style="color: rgb(128,0,0);">inorganic molecules

The synthesis of IMP. The color scheme is as follows: enzymes, <span style="color: rgb(219,155,36);">coenzymes, <span style="color: rgb(151,149,45);">substrate names , <span style="color: rgb(227,13,196);">metal ions , <span style="color: rgb(128,0,0);">inorganic molecules

They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth.

DNA replication

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DNA polymerases adds nucleotides to the 3′ end of a strand of DNA. If a mismatch is accidentally incorporated, the polymerase is inhibited from further extension. Proofreading removes the mismatched nucleotide and extension continues.

Overview of the steps in DNA replication

Role of initiators for initiation of DNA replication.

Scheme of the replication fork.
a: template, b: leading strand, c: lagging strand, d: replication fork, e: primer, f: Okazaki fragments

Many enzymes are involved in the DNA replication fork.

The assembled human DNA clamp, a trimer of the protein PCNA.

E. coli Replisome. Notably, the DNA on lagging strand forms a loop. The exact structure of replisome is not well understood.

Dam methylates adenine of GATC sites after replication.

Replication fork restarts by homologous recombination following replication stress

Epigenetic consequences of nucleosome reassembly defects at stalled replication forks

In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule.

Bacteria

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Bacteria (singular bacterium, common noun bacteria) are ubiquitous, mostly free-living organisms often consisting of one biological cell.

Phylogenetic tree of Bacteria, Archaea and Eucarya. The vertical line at bottom represents the last universal common ancestor.

Bacteria display many cell morphologies and arrangements

The range of sizes shown by prokaryotes (Bacteria), relative to those of other organisms and biomolecules.

Structure and contents of a typical Gram-positive bacterial cell (seen by the fact that only one cell membrane is present).

An electron micrograph of Halothiobacillus neapolitanus cells with carboxysomes inside, with arrows highlighting visible carboxysomes. Scale bars indicate 100 nm.

Helicobacter pylori electron micrograph, showing multiple flagella on the cell surface

Bacillus anthracis (stained purple) growing in cerebrospinal fluid

Many bacteria reproduce through binary fission, which is compared to mitosis and meiosis in this image.

Helium ion microscopy image showing T4 phage infecting E. coli. Some of the attached phage have contracted tails indicating that they have injected their DNA into the host. The bacterial cells are ~ 0.5 µm wide.

Transmission electron micrograph of Desulfovibrio vulgaris showing a single flagellum at one end of the cell. Scale bar is 0.5 micrometers long.

The different arrangements of bacterial flagella: A-Monotrichous; B-Lophotrichous; C-Amphitrichous; D-Peritrichous

Streptococcus mutans visualised with a Gram stain.

Phylogenetic tree showing the diversity of bacteria, compared to other organisms. Here bacteria are represented by three main supergroups: the CPR ultramicrobacterias, Terrabacteria and Gracilicutes according to recent genomic analyzes (2019).

Overview of bacterial infections and main species involved.

Colour-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells

In bacterial vaginosis, beneficial bacteria in the vagina (top) are displaced by pathogens (bottom). Gram stain.

Antonie van Leeuwenhoek, the first microbiologist and the first person to observe bacteria using a microscope.

Bacteria do not have a membrane-bound nucleus, and their genetic material is typically a single circular bacterial chromosome of DNA located in the cytoplasm in an irregularly shaped body called the nucleoid.

Martinus Beijerinck in his laboratory in 1921

Virus

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Submicroscopic infectious agent that replicates only inside the living cells of an organism.

Antigenic shift, or reassortment, can result in novel and highly pathogenic strains of human flu

Some bacteriophages inject their genomes into bacterial cells (not to scale)

The Baltimore Classification of viruses is based on the method of viral mRNA synthesis

Overview of the main types of viral infection and the most notable species involved

Transmission electron microscope image of a recreated 1918 influenza virus

Two rotaviruses: the one on the right is coated with antibodies that prevent its attachment to cells and infecting them.

The structure of the DNA base guanosine and the antiviral drug acyclovir

Transmission electron micrograph of multiple bacteriophages attached to a bacterial cell wall

Scientist studying the H5N1 influenza virus

When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent particles, or virions, consisting of (i) the genetic material, i.e., long molecules of DNA or RNA that encode the structure of the proteins by which the virus acts; (ii) a protein coat, the capsid, which surrounds and protects the genetic material; and in some cases (iii) an outside envelope of lipids.