Gene and Related Topics

The structure of the DNA double helix. The atoms in the structure are colour-coded by element and the detailed structures of two base pairs are shown in the bottom right.

DNA

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Polymer composed of two polynucleotide 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 and many viruses.

Chemical structure of DNA; hydrogen bonds shown as dotted lines. Each end of the double helix has an exposed 5' phosphate on one strand and an exposed 3' hydroxyl group (—OH) on the other.

A section of DNA. The bases lie horizontally between the two spiraling strands ([[:File:DNA orbit animated.gif|animated version]]).

DNA major and minor grooves. The latter is a binding site for the Hoechst stain dye 33258.

From left to right, the structures of A, B and Z DNA

DNA quadruplex formed by telomere repeats. The looped conformation of the DNA backbone is very different from the typical DNA helix. The green spheres in the center represent potassium ions.

A covalent adduct between a metabolically activated form of benzo[a]pyrene, the major mutagen in tobacco smoke, and DNA

Location of eukaryote nuclear DNA within the chromosomes

T7 RNA polymerase (blue) producing an mRNA (green) from a DNA template (orange)

DNA replication: The double helix is unwound by a helicase and topoisomerase. Next, one DNA polymerase produces the leading strand copy. Another DNA polymerase binds to the lagging strand. This enzyme makes discontinuous segments (called Okazaki fragments) before DNA ligase joins them together.

Interaction of DNA (in orange) with histones (in blue). These proteins' basic amino acids bind to the acidic phosphate groups on DNA.

The lambda repressor helix-turn-helix transcription factor bound to its DNA target

The restriction enzyme EcoRV (green) in a complex with its substrate DNA

Recombination involves the breaking and rejoining of two chromosomes (M and F) to produce two rearranged chromosomes (C1 and C2).

The DNA structure at left (schematic shown) will self-assemble into the structure visualized by atomic force microscopy at right. DNA nanotechnology is the field that seeks to design nanoscale structures using the molecular recognition properties of DNA molecules.

Maclyn McCarty (left) shakes hands with Francis Crick and James Watson, co-originators of the double-helix model.

Pencil sketch of the DNA double helix by Francis Crick in 1953

A blue plaque outside The Eagle pub commemorating Crick and Watson

The information carried by DNA is held in the sequence of pieces of DNA called genes.

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

Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity.

Evolution

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Change in the heritable characteristics of biological populations over successive generations.

In 1842, Charles Darwin penned his first sketch of On the Origin of Species.

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

This diagram illustrates the twofold cost of sex. If each individual were to contribute to the same number of offspring (two), (a) the sexual population remains the same size each generation, where the (b) Asexual reproduction population doubles in size each generation.

Mutation followed by natural selection results in a population with darker colouration.

Simulation of genetic drift of 20 unlinked alleles in populations of 10 (top) and 100 (bottom). Drift to fixation is more rapid in the smaller population.

Homologous bones in the limbs of tetrapods. The bones of these animals have the same basic structure, but have been adapted for specific uses.

A baleen whale skeleton. Letters a and b label flipper bones, which were adapted from front leg bones, while c indicates vestigial leg bones, both suggesting an adaptation from land to sea.

Common garter snake (Thamnophis sirtalis sirtalis) has evolved resistance to the defensive substance tetrodotoxin in its amphibian prey.

Geographical isolation of finches on the Galápagos Islands produced over a dozen new species.

Tyrannosaurus rex. Non-avian dinosaurs died out in the Cretaceous–Paleogene extinction event at the end of the Cretaceous period.

The hominoids are descendants of a common ancestor.

As evolution became widely accepted in the 1870s, caricatures of Charles Darwin with an ape or monkey body symbolised evolution.

These characteristics are the expressions of genes that are passed on from parent to offspring during reproduction.

Mutation

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

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

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

Mutations in genes can have no effect, alter the product of a gene, or prevent the gene from functioning properly or completely.

Gene expression

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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.

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.

Gene expression is the 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.

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

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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.

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.

Genetics is a branch of biology concerned with the study of genes, genetic variation, and heredity in organisms.

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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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.

Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes.

Diagram of a fly from Robert Hooke's innovative Micrographia, 1665

Biology

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Scientific study of life.

In the Bohr model of an atom, electrons (blue dot) orbit around an atomic nucleus (red-filled circle) in specific atomic orbitals (grey empty circles).

Model of hydrogen bonds (1) between molecules of water

Organic compounds such as glucose are vital to organisms.

A phospholipid bilayer consists of two adjacent sheets of phospholipids, with the hydrophilic tails facing inwards and the hydrophobic heads facing outwards.

The (a) primary, (b) secondary, (c) tertiary, and (d) quaternary structures of a hemoglobin protein

Structure of an animal cell depicting various organelles

Example of an enzyme-catalysed exothermic reaction

Photosynthesis changes sunlight into chemical energy, splits water to liberate O2, and fixes CO2 into sugar.

In meiosis, the chromosomes duplicate and the homologous chromosomes exchange genetic information during meiosis I. The daughter cells divide again in meiosis II to form haploid gametes.

Punnett square depicting a cross between two pea plants heterozygous for purple (B) and white (b) blossoms

Bases lie between two spiraling DNA strands.

The extended central dogma of molecular biology includes all the processes involved in the flow of genetic information.

Regulation of various stages of gene expression

Construction of recombinant DNA, in which a foreign DNA fragment is inserted into a plasmid vector

Model of concentration gradient building up; fine yellow-orange outlines are cell boundaries.

Comparison of allopatric, peripatric, parapatric and sympatric speciation

Bacteria – Gemmatimonas aurantiaca (-=1 Micrometer)

Diversity of fungi. Clockwise from top left: Amanita muscaria, a basidiomycete; Sarcoscypha coccinea, an ascomycete; bread covered in mold; chytrid; Aspergillus conidiophore.

Bacteriophages attached to a bacterial cell wall

The xylem (blue) transports water and minerals from the roots upwards whereas the phloem (orange) transports carbohydrates between organs.

Reproduction and development in sporophytes

Negative feedback is necessary for maintaining homeostasis such as keeping body temperature constant.

Diffusion of water and ions in and out of a freshwater fish

Different digestive systems in marine fishes

Circulatory systems in arthropods, fish, reptiles, and birds/mammals

Asynchronous muscles power flight in most insects. a: Wings b: Wing joint c: Dorsoventral muscles power upstrokes d: Dorsolongitudinal muscles power downstrokes.

Mouse pyramidal neurons (green) and GABAergic neurons (red)

Processes in the primary immune response

Brood parasites, such as the cuckoo, provide a supernormal stimulus to the parenting species.

Terrestrial biomes are shaped by temperature and precipitation.

Reaching carrying capacity through a logistic growth curve

A (a) trophic pyramid and a (b) simplified food web. The trophic pyramid represents the biomass at each level.

Fast carbon cycle showing the movement of carbon between land, atmosphere, and oceans in billions of tons per year. Yellow numbers are natural fluxes, red are human contributions, white are stored carbon. Effects of the slow carbon cycle, such as volcanic and tectonic activity, are not included.

Efforts are made to preserve the natural characteristics of Hopetoun Falls, Australia, without affecting visitors' access.

For instance, all organisms are made up of cells that process hereditary information encoded in genes, which can be transmitted to future generations.

Genome

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All genetic information of an organism.

An image of the 46 chromosomes making up the diploid genome of a human male. (The mitochondrial chromosome is not shown.)

Part of DNA sequence - prototypification of complete genome of virus

Log-log plot of the total number of annotated proteins in genomes submitted to GenBank as a function of genome size.

The Oxford Dictionary suggests the name is a blend of the words gene and chromosome.

Heredity

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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.