Bacteria

Rod-shaped Bacillus subtilis
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.
A culture of ''Salmonella
A colony of Escherichia coli
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 (singular bacterium, common noun bacteria) are ubiquitous, mostly free-living organisms often consisting of one biological cell.

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A Gram stain of mixed Staphylococcus aureus (S. aureus ATCC 25923, Gram-positive cocci, in purple) and Escherichia coli (E. coli ATCC 11775, Gram-negative bacilli, in red), the most common Gram stain reference bacteria

Gram stain

A Gram stain of mixed Staphylococcus aureus (S. aureus ATCC 25923, Gram-positive cocci, in purple) and Escherichia coli (E. coli ATCC 11775, Gram-negative bacilli, in red), the most common Gram stain reference bacteria
Gram stain of Candida albicans from a vaginal swab. The small oval chlamydospores are 2–4 µm in diameter.
Purple-stained gram-positive (left) and pink-stained gram-negative (right)

Gram stain or Gram staining, also called Gram's method, is a method of staining used to classify bacterial species into two large groups: gram-positive bacteria and gram-negative bacteria.

A red tulip exhibiting a partially yellow petal due to a mutation in its genes

Mutation

Alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA.

Alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA.

A red tulip exhibiting a partially yellow petal due to a mutation in its genes
Mutation with double bloom in the Langheck Nature Reserve near Nittel, Germany
Prodryas persephone, a Late Eocene butterfly
A covalent adduct between the metabolite of benzo[a]pyrene, the major mutagen in tobacco smoke, and DNA
Five types of chromosomal mutations
Selection of disease-causing mutations, in a standard table of the genetic code of amino acids
The structure of a eukaryotic protein-coding gene. A mutation in the protein coding region (red) can result in a change in the amino acid sequence. Mutations in other areas of the gene can have diverse effects. Changes within regulatory sequences (yellow and blue) can effect transcriptional and translational regulation of gene expression.
The distribution of fitness effects (DFE) of mutations in vesicular stomatitis virus. In this experiment, random mutations were introduced into the virus by site-directed mutagenesis, and the fitness of each mutant was compared with the ancestral type. A fitness of zero, less than one, one, more than one, respectively, indicates that mutations are lethal, deleterious, neutral, and advantageous.
A mutation has caused this moss rose plant to produce flowers of different colors. This is a somatic mutation that may also be passed on in the germline.
Dutch botanist Hugo de Vries making a painting of an evening primrose, the plant which had apparently produced new forms by large mutations in his experiments, by Thérèse Schwartze, 1918

Mutagenesis experiment: The direct method to investigate the DFE is to induce mutations and then measure the mutational fitness effects, which has already been done in viruses, bacteria, yeast, and Drosophila. For example, most studies of the DFE in viruses used site-directed mutagenesis to create point mutations and measure relative fitness of each mutant. In Escherichia coli, one study used transposon mutagenesis to directly measure the fitness of a random insertion of a derivative of Tn10. In yeast, a combined mutagenesis and deep sequencing approach has been developed to generate high-quality systematic mutant libraries and measure fitness in high throughput. However, given that many mutations have effects too small to be detected and that mutagenesis experiments can detect only mutations of moderately large effect; DNA sequence analysis can provide valuable information about these mutations.

In a cleaning symbiosis the clownfish feeds on small invertebrates, that otherwise have potential to harm the sea anemone, and the fecal matter from the clownfish provides nutrients to the sea anemone. The clownfish is protected from predators by the anemone's stinging cells, to which the clownfish is immune, and the clownfish emits a high pitched sound that deters butterfly fish, which would otherwise eat the anemone. The relationship is therefore classified as mutualistic.

Symbiosis

Any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or parasitic.

Any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or parasitic.

In a cleaning symbiosis the clownfish feeds on small invertebrates, that otherwise have potential to harm the sea anemone, and the fecal matter from the clownfish provides nutrients to the sea anemone. The clownfish is protected from predators by the anemone's stinging cells, to which the clownfish is immune, and the clownfish emits a high pitched sound that deters butterfly fish, which would otherwise eat the anemone. The relationship is therefore classified as mutualistic.
Diagram of the six possible types of symbiotic relationship, from mutual benefit to mutual harm.
Alder tree root nodule houses endosymbiotic nitrogen-fixing bacteria.
Male-male interference competition in red deer
Hermit crab, Calcinus laevimanus, with sea anemone.
Bryoliths document a mutualistic symbiosis between a hermit crab and encrusting bryozoans.
Commensal mites travelling (phoresy) on a fly (Pseudolynchia canariensis)
Head (scolex) of tapeworm Taenia solium is adapted to parasitism with hooks and suckers to attach to its host.
The black walnut secretes a chemical from its roots that harms neighboring plants, an example of antagonism.
Leafhoppers protected by meat ants
Pollination is a mutualism between flowering plants and their animal pollinators.
A fig is pollinated by the fig wasp, Blastophaga psenes.
Pseudomyrmex ant on bull thorn acacia (Vachellia cornigera) with Beltian bodies that provide the ants with protein

A spectacular example of obligate mutualism is the relationship between the siboglinid tube worms and symbiotic bacteria that live at hydrothermal vents and cold seeps.

An endospore stain of the cell Bacillus subtilis showing endospores as green and the vegetative cell as red

Endospore

An endospore stain of the cell Bacillus subtilis showing endospores as green and the vegetative cell as red
Phase-bright endospores of Paenibacillus alvei imaged with phase-contrast microscopy
Formation of an endospore through the process of sporulation.
Variations in endospore morphology: (1, 4) central endospore; (2, 3, 5) terminal endospore; (6) lateral endospore
Endospore formation and cycle

An endospore is a dormant, tough, and non-reproductive structure produced by some bacteria in the phylum Bacillota.

Internal symbiont: mitochondrion has a matrix and membranes, like a free-living alphaproteobacterial cell, from which it may derive.

Symbiogenesis

Leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms.

Leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms.

Internal symbiont: mitochondrion has a matrix and membranes, like a free-living alphaproteobacterial cell, from which it may derive.
Konstantin Mereschkowski's 1905 tree-of-life diagram, showing the origin of complex life-forms by two episodes of symbiogenesis, the incorporation of symbiotic bacteria to form successively nuclei and chloroplasts.
One model for the origin of mitochondria and plastids
Modern endosymbiotic theory posits that simple life forms merged, forming cell organelles, like mitochondria.
Kwang Jeon's experiment: [I] Amoebae infected by x-bacteria [II] Many amoebae become sick and die [III] Survivors have x-bacteria living in their cytoplasm [IV] Antibiotics kill x-bacteria: host amoebae die as now dependent on x-bacteria.
Mitochondria of a mammal lung cell visualized using Transmission Electron Microscopy
Diagram of endomembrane system in eukaryotic cell
The human mitochondrial genome has retained genes encoding 2 rRNAs, 22 tRNAs, and 13 redox proteins.
Simplified chart showing the three main mergers of the endosymbiotic theory

The theory holds that mitochondria, plastids such as chloroplasts, and possibly other organelles of eukaryotic cells are descended from formerly free-living prokaryotes (more closely related to bacteria than to archaea) taken one inside the other in endosymbiosis.

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Gene expression

Process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect.

Process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect.

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The process of transcription is carried out by RNA polymerase (RNAP), which uses DNA (black) as a template and produces RNA (blue).
Illustration of exons and introns in pre-mRNA and the formation of mature mRNA by splicing. The UTRs (in green) are non-coding parts of exons at the ends of the mRNA.
During the translation, tRNA charged with amino acid enters the ribosome and aligns with the correct mRNA triplet. Ribosome then adds amino acid to growing protein chain.
Protein before (left) and after (right) folding
The patchy colours of a tortoiseshell cat are the result of different levels of expression of pigmentation genes in different areas of the skin.
When lactose is present in a prokaryote, it acts as an inducer and inactivates the repressor so that the genes for lactose metabolism can be transcribed.
The lambda repressor transcription factor (green) binds as a dimer to major groove of DNA target (red and blue) and disables initiation of transcription. From.
In eukaryotes, DNA is organized in form of nucleosomes. Note how the DNA (blue and green) is tightly wrapped around the protein core made of histone octamer (ribbon coils), restricting access to the DNA. From.
Regulation of transcription in mammals. An active enhancer regulatory region is enabled to interact with the promoter region of its target gene by formation of a chromosome loop. This can initiate messenger RNA (mRNA) synthesis by RNA polymerase II (RNAP II) bound to the promoter at the transcription start site of the gene. The loop is stabilized by one architectural protein anchored to the enhancer and one anchored to the promoter and these proteins are joined to form a dimer (red zigzags). Specific regulatory transcription factors bind to DNA sequence motifs on the enhancer. General transcription factors bind to the promoter. When a transcription factor is activated by a signal (here indicated as phosphorylation shown by a small red star on a transcription factor on the enhancer) the enhancer is activated and can now activate its target promoter. The active enhancer is transcribed on each strand of DNA in opposite directions by bound RNAP IIs. Mediator (a complex consisting of about 26 proteins in an interacting structure) communicates regulatory signals from the enhancer DNA-bound transcription factors to the promoter.
DNA methylation is the addition of a methyl group to the DNA that happens at cytosine. The image shows a cytosine single ring base and a methyl group added on to the 5 carbon. In mammals, DNA methylation occurs almost exclusively at a cytosine that is followed by a guanine.
The identified areas of the human brain are involved in memory formation.
Neomycin is an example of a small molecule that reduces expression of all protein genes inevitably leading to cell death; it thus acts as an antibiotic.
The RNA expression profile of the GLUT4 Transporter (one of the main glucose transporters found in the human body)
In situ-hybridization of Drosophila embryos at different developmental stages for the mRNA responsible for the expression of hunchback. High intensity of blue color marks places with high hunchback mRNA quantity.
The three-dimensional structure of green fluorescent protein. The residues in the centre of the "barrel" are responsible for production of green light after exposing to higher energetic blue light. From.
Tet-ON inducible shRNA system

The process of gene expression is used by all known life—eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea), and utilized by viruses—to generate the macromolecular machinery for life.

Pseudomonas aeruginosa

Pseudomonas aeruginosa in Petri dish.
Pigment production, growth on cetrimide agar, the oxidase test, plaque formation and Gram stain.
A culture dish with Pseudomonas
Gram-stained P. aeruginosa bacteria (pink-red rods)
Phagocytosis of P. aeruginosa by neutrophil in patient with bloodstream infection (Gram stain)
Production of pyocyanin, water-soluble green pigment of P. aeruginosa (left tube)
Pseudomonas aeruginosa fluorescence under UV illumination
The antibiogram of P. aeruginosa on Mueller–Hinton agar

Pseudomonas aeruginosa is a common encapsulated, Gram-negative, strict aerobic (although can grow anaerobically in the presence of nitrate), Rod-shaped bacterium that can cause disease in plants and animals, including humans.

Structure of a generic L-amino acid in the "neutral" form needed for defining a systematic name, without implying that this form actually exists in detectable amounts either in aqueous solution or in the solid state.

Amino acid

Amino acids are organic compounds that contain amino (\sNH3+) and carboxylate (\sCO2-) functional groups, along with a side chain (R group) specific to each amino acid.

Amino acids are organic compounds that contain amino (\sNH3+) and carboxylate (\sCO2-) functional groups, along with a side chain (R group) specific to each amino acid.

Structure of a generic L-amino acid in the "neutral" form needed for defining a systematic name, without implying that this form actually exists in detectable amounts either in aqueous solution or in the solid state.
The 21 proteinogenic α-amino acids found in eukaryotes, grouped according to their side chains' pKa values and charges carried at physiological pH (7.4)
Structure of -proline
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Ionization and Brønsted character of N-terminal amino, C-terminal carboxylate, and side chains of amino acid residues
Composite of titration curves of twenty proteinogenic amino acids grouped by side chain category
Share of amino acid in various human diets and the resulting mix of amino acids in human blood serum. Glutamate and glutamine are the most frequent in food at over 10%, while alanine, glutamine, and glycine are the most common in blood.
The Strecker amino acid synthesis
The condensation of two amino acids to form a dipeptide. The two amino acid residues are linked through a peptide bond
Catabolism of proteinogenic amino acids. Amino acids can be classified according to the properties of their main degradation products: 
 * Glucogenic, with the products having the ability to form glucose by gluconeogenesis
 * Ketogenic, with the products not having the ability to form glucose. These products may still be used for ketogenesis or lipid synthesis.
 * Amino acids catabolized into both glucogenic and ketogenic products.
Composite of titration curves of twenty proteinogenic amino acids grouped by side chain category

The two nonstandard proteinogenic amino acids are selenocysteine (present in many non-eukaryotes as well as most eukaryotes, but not coded directly by DNA) and pyrrolysine (found only in some archaea and at least one bacterium).

DNA replication: The double helix is un'zipped' and unwound, then each separated strand (turquoise) acts as a template for replicating a new partner strand (green). Nucleotides (bases) are matched to synthesize the new partner strands into two new double helices.

DNA replication

Biological process of producing two identical replicas of DNA from one original DNA molecule.

Biological process of producing two identical replicas of DNA from one original DNA molecule.

DNA replication: The double helix is un'zipped' and unwound, then each separated strand (turquoise) acts as a template for replicating a new partner strand (green). Nucleotides (bases) are matched to synthesize the new partner strands into two new double helices.
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
Steps in DNA synthesis
Role of initiators for initiation of DNA replication.
Formation of pre-replication complex.
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.
The cell cycle of eukaryotic cells.
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

The primase used in this process differs significantly between bacteria and archaea/eukaryotes.

Blending inheritance leads to the averaging out of every characteristic, which as the engineer Fleeming Jenkin pointed out, makes evolution by natural selection impossible.

Genetics

Branch of biology concerned with the study of genes, genetic variation, and heredity in organisms.

Branch of biology concerned with the study of genes, genetic variation, and heredity in organisms.

Blending inheritance leads to the averaging out of every characteristic, which as the engineer Fleeming Jenkin pointed out, makes evolution by natural selection impossible.
Morgan's observation of sex-linked inheritance of a mutation causing white eyes in Drosophila led him to the hypothesis that genes are located upon chromosomes.
DNA, the molecular basis for biological inheritance. Each strand of DNA is a chain of nucleotides, matching each other in the center to form what look like rungs on a twisted ladder.
A Punnett square depicting a cross between two pea plants heterozygous for purple (B) and white (b) blossoms.
Genetic pedigree charts help track the inheritance patterns of traits.
Human height is a trait with complex genetic causes. Francis Galton's data from 1889 shows the relationship between offspring height as a function of mean parent height.
The molecular structure of DNA. Bases pair through the arrangement of hydrogen bonding between the strands.
DNA sequence
Walther Flemming's 1882 diagram of eukaryotic cell division. Chromosomes are copied, condensed, and organized. Then, as the cell divides, chromosome copies separate into the daughter cells.
Thomas Hunt Morgan's 1916 illustration of a double crossover between chromosomes.
The genetic code: Using a triplet code, DNA, through a messenger RNA intermediary, specifies a protein.
Siamese cats have a temperature-sensitive pigment-production mutation.
Transcription factors bind to DNA, influencing the transcription of associated genes.
Gene duplication allows diversification by providing redundancy: one gene can mutate and lose its original function without harming the organism.
This is a diagram showing mutations in an RNA sequence. Figure (1) is a normal RNA sequence, consisting of 4 codons. Figure (2) shows a missense, single point, non silent mutation. Figures (3 and 4) both show frameshift mutations, which is why they are grouped together. Figure 3 shows a deletion of the second base pair in the second codon. Figure 4 shows an insertion in the third base pair of the second codon. Figure (5) shows a repeat expansion, where an entire codon is duplicated.
An evolutionary tree of eukaryotic organisms, constructed by the comparison of several orthologous gene sequences.
The common fruit fly (Drosophila melanogaster) is a popular model organism in genetics research.
Schematic relationship between biochemistry, genetics and molecular biology.
Colonies of E. coli produced by cellular cloning. A similar methodology is often used in molecular cloning.

Organisms studied within the broad field span the domains of life (archaea, bacteria, and eukarya).