Molecular genetics and Related Topics

Transformation (genetics)

Schematic of bacterial transformation – for which artificial competence must first be induced.

In molecular biology and genetics, transformation is the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane(s).

Diagrammatic representation of Watson and Crick's DNA structure

Molecular biology

Branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including molecular synthesis, modification, mechanisms, and interactions.

Diagrammatic representation of experiment

Schematic relationship between biochemistry, genetics and molecular biology

Two percent agarose gel in borate buffer cast in a gel tray.

Proteins stained on a PAGE gel using Coomassie blue dye.

Molecular genetics, the study of gene structure and function, has been among the most prominent sub-fields of molecular biology since the early 2000s.

Cell biology

Branch of biology that studies the structure, function, and behavior of cells.

The process of cell division in the animal cell cycle

Research in cell biology is interconnected to other fields such as genetics, molecular genetics, molecular biology, medical microbiology, immunology, and cytochemistry.

Max Delbrück

German–American biophysicist who participated in launching the molecular biology research program in the late 1930s.

Delbrück's workplace in Berlin: Kaiser Wilhelm Institute for Chemistry, now the Free University of Berlin.

Drawing of a plaque in Buttrick Hall, Vanderbilt University commemorating the work of Max Delbrück.

Meanwhile, he set up University of Cologne's institute for molecular genetics.

This image shows an example of the central dogma using a DNA strand being transcribed then translated and showing important enzymes used in the processes

Forward genetics

Forward genetics is a molecular genetics approach of determining the genetic basis responsible for a phenotype.

Fungus

Any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms.

Fungal cell cycle showing Dikaryons typical of Higher Fungi

Omphalotus nidiformis, a bioluminescent mushroom

In 1729, Pier Antonio Micheli first published descriptions of fungi.

Mold growth covering a decaying peach. The frames were taken approximately 12 hours apart over a period of six days.

The 8-spore asci of Morchella elata, viewed with phase contrast microscopy

The bird's nest fungus Cyathus stercoreus

Prototaxites milwaukeensis (Penhallow, 1908)—a Middle Devonian fungus from Wisconsin

Arbuscular mycorrhiza seen under microscope. Flax root cortical cells containing paired arbuscules.

Diagram of an apothecium (the typical cup-like reproductive structure of Ascomycetes) showing sterile tissues as well as developing and mature asci.

The dark filaments are hyphae of the endophytic fungus Epichloë coenophiala in the intercellular spaces of tall fescue leaf sheath tissue

The lichen Lobaria pulmonaria, a symbiosis of fungal, algal, and cyanobacterial species

The plant pathogen Puccinia magellanicum (calafate rust) causes the defect known as witch's broom, seen here on a barberry shrub in Chile.

Gram stain of Candida albicans from a vaginal swab from a woman with candidiasis, showing hyphae, and chlamydospores, which are 2–4 µm in diameter.

Ergotamine, a major mycotoxin produced by Claviceps species, which if ingested can cause gangrene, convulsions, and hallucinations

Saccharomyces cerevisiae cells shown with DIC microscopy

The mold Penicillium rubens was the source of penicillin G.

A selection of edible mushrooms eaten in Asia

Stilton cheese veined with Penicillium roqueforti

Amanita phalloides accounts for the majority of fatal mushroom poisonings worldwide. It sometimes lacks the greenish color seen here.

Grasshoppers killed by Beauveria bassiana

Advances in molecular genetics have opened the way for DNA analysis to be incorporated into taxonomy, which has sometimes challenged the historical groupings based on morphology and other traits.

Biodiversity of a coral reef. Corals adapt to and modify their environment by forming calcium carbonate skeletons. This provides growing conditions for future generations and forms a habitat for many other species.

Ecology

Study of the relationships between living organisms, including humans, and their physical environment.

Termite mounds with varied heights of chimneys regulate gas exchange, temperature and other environmental parameters that are needed to sustain the internal physiology of the entire colony.

Interspecific interactions such as predation are a key aspect of community ecology.

A riparian forest in the White Mountains, New Hampshire (USA) is an example of ecosystem ecology

Generalized food web of waterbirds from Chesapeake Bay

A trophic pyramid (a) and a food-web (b) illustrating ecological relationships among creatures that are typical of a northern boreal terrestrial ecosystem. The trophic pyramid roughly represents the biomass (usually measured as total dry-weight) at each level. Plants generally have the greatest biomass. Names of trophic categories are shown to the right of the pyramid. Some ecosystems, such as many wetlands, do not organize as a strict pyramid, because aquatic plants are not as productive as long-lived terrestrial plants such as trees. Ecological trophic pyramids are typically one of three kinds: 1) pyramid of numbers, 2) pyramid of biomass, or 3) pyramid of energy.

Sea otters, an example of a keystone species

Social display and colour variation in differently adapted species of chameleons (Bradypodion spp.). Chameleons change their skin colour to match their background as a behavioural defence mechanism and also use colour to communicate with other members of their species, such as dominant (left) versus submissive (right) patterns shown in the three species (A-C) above.

Mutualism: Leafhoppers (Eurymela fenestrata) are protected by ants (Iridomyrmex purpureus) in a mutualistic relationship. The ants protect the leafhoppers from predators and stimulate feeding in the leafhoppers, and in return, the leafhoppers feeding on plants exude honeydew from their anus that provides energy and nutrients to tending ants.

Bumblebees and the flowers they pollinate have coevolved so that both have become dependent on each other for survival.

Parasitism: A harvestman arachnid being parasitized by mites. The harvestman is being consumed, while the mites benefit from traveling on and feeding off of their host.

The leaf is the primary site of photosynthesis in most plants.

The architecture of the inflorescence in grasses is subject to the physical pressures of wind and shaped by the forces of natural selection facilitating wind-pollination (anemophily).

The layout of the first ecological experiment, carried out in a grass garden at Woburn Abbey in 1816, was noted by Charles Darwin in The Origin of Species. The experiment studied the performance of different mixtures of species planted in different kinds of soils.

Microbiomes were discovered largely through advances in molecular genetics, which have revealed a hidden richness of microbial diversity on the planet.

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.

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.

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.

Colonies of E. coli produced by cellular cloning. A similar methodology is often used in molecular cloning.

Trait inheritance and molecular inheritance mechanisms of genes are still primary principles of genetics in the 21st century, but modern genetics has expanded beyond inheritance to studying the function and behavior of genes.

Heredity

Passing on of traits from parents to their offspring; either through asexual reproduction or sexual reproduction, the offspring cells or organisms acquire the genetic information of their parents.

DNA structure. Bases are in the centre, surrounded by phosphate–sugar chains in a double helix.

Aristotle's model of inheritance. The heat/cold part is largely symmetrical, though influenced on the father's side by other factors; but the form part is not.

Table showing how the genes exchange according to segregation or independent assortment during meiosis and how this translates into Mendel's laws

An example pedigree chart of an autosomal dominant disorder.

An example pedigree chart of an autosomal recessive disorder.

An example pedigree chart of a sex-linked disorder (the gene is on the X chromosome)

Hereditary defects in enzymes are generally inherited in an autosomal fashion because there are more non-X chromosomes than X-chromosomes, and a recessive fashion because the enzymes from the unaffected genes are generally sufficient to prevent symptoms in carriers.

On the other hand, hereditary defects in structural proteins (such as osteogenesis imperfecta, Marfan's syndrome and many Ehlers–Danlos syndromes) are generally autosomal dominant, because it is enough that some components are defective to make the whole structure dysfunctional. This is a dominant-negative process, wherein a mutated gene product adversely affects the non-mutated gene product within the same cell.

In case the involved loci are known, methods of molecular genetics can also be employed.

Bacteriophage Lambda Structural Model at Atomic Resolution

Lambda phage

Bacterial virus, or bacteriophage, that infects the bacterial species Escherichia coli (E. coli).

Bacteriophage lambda virion (schematic). Protein names and their copy numbers in the virion particle are shown. The presence of the L and M proteins in the virion is still unclear.

Linear layout of lambda phage genome with major operons, promoter regions and capsid coding genes.

Lambda phage J protein interaction with the LamB porin

Lambda phage DNA injection into the cell membrane using Mannose PTS permease (a sugar transporting system) as a mechanism of entry into the cytoplasm

Early activation events involving N protein

Lysis plaques of lambda phage on E. coli bacteria

Diagram showing the retro-regulation process that yields a higher concentration of xis compared to int. The mRNA transcript is digested by bacterial RNase starting from the cleaved hairpin loop at sib.

A simplified representation of the integration/excision paradigm and the major genes involved.

Lysogen repressors and polymerase bound to OR1 and recruits OR2, which will activate PRM and shutdown PR.

Transcriptional state of the PRM and PR promoter regions during a lysogenic state vs induced, early lytic state.

The function of LexA in the SOS response. LexA expression leads to inhibition of various genes including LexA.

Protein interactions that lead to either Lytic or Lysogenic cycles for Lambda phage

Visual representation of repressor tetramer/octamer binding to phage lambda L and R operator sites (stable lysogenic state)

Diagram of temperate phage life cycle, showing both lytic and lysogenic cycles.

Some base pairs with serve a dual function with promoter and operator for either cl and cro proteins.

Protein cl turned ON, with repressor bound to OR2 polymerase binding is increased and turn OFF OR1.

Lysogen repression all 3 sites bound is a low occurrence due to OR3 weak binding affinity. OR1 repression increases binding affinity to OR2 due to repressor-repressor interaction. Increased concentrations of repressor increase binding.

Lambda phage has been used heavily as a model organism, and has been a rich source for useful tools in microbial genetics, and later in molecular genetics.