Genophores & Chromosomes
Cell central holds the principal genetic material, but not all of a cell’s genome. For a prokaryote, cell central is the nucleoid, with the primary genetic package in a genophore. For a eukaryote, cell central is the nucleus, containing chromosomes.
Genophores
A prokaryote’s nucleoid holds a cell’s genome in a single genophore: a large double-stranded DNA molecule, generally circular in shape. A nucleoid is not enclosed in a membrane. Having only a single copy of each gene makes a prokaryote haploid.
A typical prokaryote has 2,000 to 4,000 genes; a housefly, mouse, or human: ~20,000. An ocean bacterium, Pelagibacter ubique, has the most efficient genome known: 1,354 genes; no clutter, no noncoding sequences, no duplicate entries, no viral genes, nor any introns.
220 human genes come courtesy of horizontal gene transfer from a prokaryotic pal: bacteria. This was a direct transfer, not a product of ancestral lineage.
A fundamental concept in biology is that heritable material, DNA, is passed from parent to offspring, a process called vertical gene transfer. An alternative mechanism of gene acquisition is through horizontal gene transfer (HGT), which involves movement of genetic material between different species. HGT is well known in single-celled organisms such as bacteria. HGT has contributed to the evolution of many, perhaps all, animals and that the process is ongoing. ~ English biochemist Alastair Crisp et al
Genetic Exchange
Hereditary genetic transmission – from one cell generation to the next – is vertical gene transfer. In contrast, gene sharing among cells or organisms is horizontal gene transfer.
Prokaryotes, particularly bacteria, pick up genetic material in 3 main ways. 1st, they may scavenge gene-bearing snippets from dead cells in the vicinity. 2nd, viruses inject genes into infected cells. 3rd, bacteria often voluntarily release genes for others, in packets called plasmids.
A plasmid is a tightly-folded ball of DNA which can replicate independently of the cellular DNA. A plasmid is considerably smaller than a nucleoid.
Prokaryotes are prolific plasmid exchangers. Horizontal gene transfer is rampant among microbes. As a social service, to preserve a community under attack, bacteria practice HGT to provide antibiotic resistance to others.
The ecology of animals creates a network of constant gene exchange for the microbiome within. The microbiome is a major determinant of an animal’s health. Genetic exchange is a critical component of that.
HGT is also employed by eukaryotes. HGT is not as common among animals as it is plants, which frequently exchange genes, even entire genomes.
Plants that grow in close vicinity may incorporate a neighbor’s genome via chloroplast capture: obtaining the genome of another plant by uptake of an organelle. Parasitic plants steal the genes of their host to better understand and adapt to their roost.
Viruses have the simplest genophores. Their RNA or DNA lack structural protein templates. Viruses get away with this sketchy setup by hijacking other cells for their replication.
Viruses are fervent traders, acquirers, and manipulators of genic matter. They know what they need, and how to get and use genes to attain their objectives.
Chromosomes
Every complete set of chromosomes contains the full code. The chromosome structures are instrumental in bringing about the development they foreshadow. They are architect’s plan and builder’s craft in one. ~ Erwin Schrödinger
In contrast to prokaryotes, a eukaryotic cell has a membrane-enclosed nucleus, with proteins – histones – that fold and pack DNA into highly organized chromosomes.
A chromosome is an elaborately coiled and knotted package of genetic material in a eukaryotic cell, comprising DNA genes, regulatory elements such as histones, and other nucleotide sequences.
Chromosomes are not simply compacted gene chains, evenly spaced. A chromosome is a complex structure, with distinct spatial features that play important roles in replication, transcription, and regulation of gene expression.
“Chromosome folding follows a pattern, which is important for ensuring their proper function.” ~ American geneticist Elphege Nora
Within a chromosome are regions densely packed with working DNA, while other areas are genetic deserts. The genome is organized in a fractal fashion: a self-similar Matryoshka of nested genetic information, efficiently organized by usage.
Nuclear chromosomes are packaged by proteins into organic origami. This compact packaging lets long DNA molecules fit into a cell nucleus.
While the sizes of chromosomes vary considerably by species, all are elongated cylinders. This self-organized superstructure is ubiquitous because it is the most efficient shape to access the layered information within.
Each chromosome has 2 arms: one short and one long. Chromosomes are tucked into cell nuclei; hence the origin of the term nucleic acid.
A DNA molecule may be linear or circular, extending from 100,000 to 10 billion nucleotides in a long chain. Stretched out, a single DNA molecule may be several centimeters long, but it would take a stack 50,000 deep to be as thick as a human hair.
A nucleosome is the basic nuclear DNA package in eukaryotes: a DNA segment wound around a core of 8 histones, like a thread wrapped around a spool.
Nucleosomes are folded in a successive hierarchical series of structures, eventuating in a chromosome. This both highly compacts DNA, and, by virtue of histones, creates a layer of regulatory control, which ensures proper gene expression, at least in healthy cells.
Histones do not merely act as a central hub and spooler for DNA. They also act as an antibacterial agent. Histones hang out on lipid droplets: ubiquitous cellular fat-storage organelles. If a bacterium is detected, a histone troop heads out to kill it.
As a higher level of organization, chromosomes are spun into yarns. A chromosomal yarn is a related group of genes and the regulatory elements necessary for gene activity.
The DNA of individual genes is wrapped around nucleosomes to form a ‘beads-on-a-string’ structure. These beads-on-a-string subsequently fold up to form ‘yarns-on-a-string,’ where each yarn is a group of genes. This domainal organization of chromosomes is a fundamental organizing principle of genomes. ~ American geneticist Job Dekker
Via yarns, chromosomes are spatially folded so that genes are functionally organized into isolated domains. The folding pattern brings together genes and their regulatory elements into a spatial cluster, so that the activity of the genes in a yarn is easily coordinated, without interference from other genes.
“The three-dimensional organization of chromosomes allows distal genomic elements to be brought together and to functionally interact with each other. At certain points during development it is thus possible to precisely orchestrate the activity of genes that are far away from each other on the linear chromosome thread, but that are actually in contact physically, within a chromosome yarn. The downside of this type of organization is that a single mutation altering the organization of such a ‘chromosome yarn’ can affect a whole group of genes.” ~ Elphege Nora
Life Cycle
The contents of chromatin and its chromosomes undergo structural changes during the cell cycle.
Interphase is the 90% of a cell’s life cycle when it lives its everyday life: eating, producing bioproducts, doing cellular business, and growing. Interphase also includes preparation for cell division.
During interphase, nucleosomes with active genes are more loosely packaged than inactive genes. In preparing to divide, during prophase, chromatin packages tighten up. The nucleolus disappears. DNA has already been replicated prior to prophase.
Chromatin compaction is a dynamic process, full of decisions which can foreclose access to the genetic codes within, thus thwarting transcription. This suppression happens via epigenetic regulation.
Metaphase is the stage of cell division where chromosomes migrate to opposite poles of a cell. During anaphase, 2 identical daughter chromosomes form.
Next comes telophase, which starts with 2 daughter nuclei forming. Cytokinesis follows, with the cytoplasm bifurcated. The outcome of telophase is 2 daughter cells, each with a selfsame set of chromosomes.
Ploidy
Ploidy is the number of chromosome copies a eukaryote has. Ploidy varies. With 2 sets of chromosomes, humans are diploid, as are nearly all mammals.
Plants switch between haploid and diploid states during their life cycle, as do algae, fungi, and slime molds. This is termed alternation of generations.
While female eusocial insects, such as bees, wasps, and ants, are diploid, males are haploid because they develop from unfertilized, haploid egg cells. Hence these eusocial insects are referred to as haplodiploid.
Telomeres
“Telomeres ensure genome stability.” ~ American microbiologist Janelle Vultaggio
A telomere is a region of repetitive nucleotide sequences at each end of a chromatid (a freshly copied chromosome).
Telomeres protect the end of the chromatid from deterioration, or from fusion with neighboring chromosomes. Telomeres have been likened to the plastic caps at the end of shoelaces, as they keep the ends from fraying or becoming entangled. (The end of a telomere tidily loops back into the main body of the telomere.)
Each time a human cell divides, its telomeres shorten a bit. A telomere is refurbished by its telomerase enzyme, but cell division takes a toll.
A cell reaches decrepitude and no longer divides when its telomeres become too short. Such cellular senescence is the natural aging process.
“As telomeres shorten during normal aging, they activate a DNA damage response to arrest cell growth, which protects DNA from harm. The pathway controlling growth arrest, however, is commonly altered in cancer cells, allowing malignant cells to divide despite shortened telomeres.” ~ Austrian cytologist Jan Karlseder
“Telomere dysfunction triggers autophagy. Activation of autophagy is critical for cell death. Loss of autophagy function is required for the initiation of cancer.” ~ Jan Karlseder et al
G-Quadruplexes
Guanine-rich DNA sequences of a particular form have the ability to fold into 4-stranded structures called G-quadruplexes. ~ English chemist Julian Huppert & Indian chemist Shankar Balasubramanian
DNA is typically a double-stranded helix, coiling into densely packed chromosomes. But a strand may double up, particularly at telomeres, which are rich in guanine.
Via hydrogen bonds, G-rich strands naturally self-associate into G-quadruplexes. These squarish 4-strand DNA structures act in various cellular pathways, including gene expression, DNA replication, and telomere maintenance. As an aberration, G-quadruplexes are instrumental in cancer.
Comparative Chromosomes
The number of chromosomes varies widely between species. Humans have 46.
Most organisms carry 10 to 50 chromosomes. A salamander has 20 times more DNA than a human. A mosquito has 6 chromosomes, but a silkworm has 56. A mouse has 40, a duck 60, a goldfish 94, and a toucan 106. One species of fern has 630 chromosome pairs per cell.
Humans are most closely related to chimpanzees and bonobos, which have 48 chromosomes: 2 more than people. But 1 human chromosome has the information stored in 2 chimp chromosomes.
Genetic drift of humans from chimps and bonobos began 5 mya. Yet the DNA sequences differ by less than 1%. Chimp blood can substitute for human in transfusions.
Chimps and bonobos diverged after humans left the lineage. Chimp-bonobo genetic drift started 2 MYA.
Humans lack 510 DNA sequences that chimps, macaques, and mice share. Most of those sequences are thought to be genetically unimportant, if not entirely vacant of genes.
Though genetic differences between humans and chimpanzees may be statistically slight, they are phenotypically significant. One lost sequence allows expansion of certain brain regions in humans during development. Another controls production of sensory facial whiskers and penile spines, which humans lack.
Penile spines help males ejaculate quickly during intercourse. Quick impregnation increases the immediate prospect for reproduction. Lacking penile spines results in longer copulation times, affording emotional bonding between mating partners; something quite instrumental in human evolutionary success.
Genic Content
Of the 6 billion base pairs in every human cell, only 120 million code for proteins. Over 98% of the human genome is noncoding DNA: genes that do not encode protein sequences. Humans are not alone in this. Most codons in higher eukaryotes are deemed noncoding.
The “extra” genes in eukaryotes exist as introns or repetitive sequences. The enzymes that duplicate DNA sometime slip extra copies of a gene into a chromosome. These genetic replicas, which often have a slight variation, comprise ~5% of the human genome.
Selfsame regions are repeated hundreds or even thousands of times. This is a genetic legacy of evolution, beginning with the combination of genomes from single-celled prokaryotes that joined together in a eukaryotic endeavor.
The massive expansion of genetic code in later-evolved organisms likely came from invasive elements. Although this proliferation may represent something of a burden for coordinated gene expression programs, it also affords genomic plasticity and a data-oriented path for evolution, as well as some degree of stochastic gene regulation.
Noncoding DNA often plays some role in biochemical functions, such as during transcription, in promoting and regulating conversion of DNA into RNA. Near-duplicate genes in the human genome may have been responsible for brain enlargement in early hominids.
Eukaryotic microorganisms have fewer introns. 70% of the genes in the yeast Sacchromyces cerevisiae encode protein.
The coding genes of many prokaryotes exceed 90%. Sequences may be repeated in prokaryotes, but usually only a few copies.
There is a 300-fold difference between the genome sizes of yeast and mammals, but only a modest 4- to 5-fold increase in gene number.
The ratio of coding to noncoding and repetitive sequences is somewhat indicative of the complexity of the genome. Unicellular fungi have sparse noncoding DNA compared to any multicellular organism.
Bladderwort
Some evolved species have no truck with noncoding DNA. The carnivorous bladderwort plant is one.
An unusual and highly specialized plant, the bladderwort lives in fresh water and wet soil, and is endemic to every continent except Antarctica.
The bladderwort’s vegetative organs are not clearly distinguished into roots, stems, and leaves, as in most other angiosperms (flowering plants). But its bladder trap is one of the most sophisticated structures in the plant kingdom.
While many later-evolved species are biased toward archiving noncoding DNA, the bladderwort keeps its genome trim. The bladderwort has 28,500 coding genes: comparable to its relatives, the grape and the tomato. Whereas a grape has 590 million DNA base pairs, and a tomato has 780 million, one bladderwort species (Utricularia gibba) carries only 80 million. This is especially surprising considering that the bladderwort underwent 3 complete genome doublings since it split from the tomato lineage.
Replication Accuracy
In multicellular organisms, somatic cell replication is essential to replacing worn-out cells with fresh copies. While plants can grow themselves past genetic defects to a limited extent, animals must have good working replacements for proper functioning.
Nevertheless, from one cell generation to the next genomes are transmitted with many mistakes: somatically acquired deletions, duplications, and other mutations. This is even true of nerve cells in the human brain, which continue to function properly despite large numbers of genetic errors.
Error-prone replication is selective. Cells replicate the transcriptionally active portions of their genomes with care, then rush through the silent sections. Cells are often careless about replicating the unused parts of their genomes.
The brain may be particularly well-suited to coping with scattered genomic errors at the cellular level. During development, an overabundance of neurons are connectively networked. Then, during maturation, those cells that don’t sufficiently contribute are eliminated – a process analogous to plants pruning leaves which don’t photosynthetically pony up.
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It may even be that genomic eccentricities have a benefit yet unknown. Knowledge of genetics is in its infancy.
Sex Chromosomes
The test for whether or not you can hold a job should not be the arrangement of your chromosomes. ~ American politician Bella Abzug
One animal chromosome is of especial significance: X. In his investigation of chromosomes in 1890–1891, baffled German cytologist Hermann Henking came upon a stand-out. This outlier he named X. No one knows what he meant by it; perhaps merely a failure of imagination. Anyway, the designation stuck.
In many animal species, including mammals, X is one of 2 chromosomes determining sex. The other is Y, named as the next letter in the alphabet.
A female mammal has 2 X chromosomes; a male carries XY. If an egg gets Xs from both parents, a female is in the offing. A Y from dad means a male will be had.
The difference between X and Y is enormous. X is the largest, most gene-rich chromosome: more than 153 million base pairs, with around 10% (2,000) of the 20,000–25,000 human genes. By contrast Y is puny: 1/3rd the size of X, with but 78 genes, and many repetitive sequences.
At one point in evolutionary history, X and Y were equal in size and gene count. 300 million years wrought a mismatch in evolution of sexual specialization, with Y slacking off and X picking up the slack.
XY does more than determine sex. The combination is a risk in of itself.
Many genes vital to brain development reside in X. The X chromosome is also instrumental in human sperm production. This is an evolutionary advance in the past 80 million years, when mice and men diverged from a common ancestor.
Y lacks the complement of many X genes. Because of that, any recessive mutation on the maternally derived X becomes dominant in males, making males genetically the weaker sex. And a flaw in a male’s single X spells trouble.
Having 2 copies of a gene is handy. If one is defective, the other becomes the production template.
In females, one of the X chromosomes is largely deactivated, in a process termed X inactivation.
