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Why E.Coli get bigger if they replicate faster?

Why E.Coli get bigger if they replicate faster?



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When E. Coli divide faster, they tend to have larger volumes. If the same cells are grown in a poorer medium, they'll have longer replication cycles and shrink. What is the explanation of this phenomenon?

Refs.

http://book.bionumbers.org/how-many-ribosomes-are-in-a-cell/ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0023126


Rapidly dividing bacteria contain more than one bacterial chromosome, and often more than two. The chromosomes take large amount of space in the cytoplasm and also attach to the cytoplasmic membrane. More chromosomal DNA requires larger cytoplasmic surface area; larger surface, larger volume.


Here's one way to think about this. The key question is "how does the cell decide when to divide"?

You can imagine there are two major mechanisms:

  1. The cell needs to accomplish some task that takes more or less a constant amount of time (DNA replication may be a close example). After that's done it can divide

  2. The cell needs to accumulate a certain amount of biomass to grow to a certain size (protein synthesis is closer to this). When it gets there, it can divide.

(1) is often called the "timer" hypothesis and (2) the "sizer" hypothesis.

If (1) was true, then cells would grow at the same rate regardless of the medium. If (2) was true, then all cells would always have the same size regardless of the medium. Neither statement is true, so the truth is some combination of both effects.

However, under the timer hypothesis, larger cell size with faster growth rate comes out naturally, since the cell size will be determined by the amount of biomass that can accumulate during the constant time. So as long as there is some aspect of "waiting for something that takes a certain amount of time", you will get a positive correlation between size and growth rate.

Now this is an extremely naive explanation. In fact, not all bacteria show this correlation. There are also models other than "timer" and "sizer" -- e.g. here's an "adder" model that also explains the size effect.

Google "cell size control in bacteria" for a ton more papers.


Within its tiny cell, the bacterium E. coli contains all the genetic information it needs to metabolize, grow, and reproduce. It can synthesize every organic molecule it needs from glucose and a number of inorganic ions. Many of the genes in E. coli are expressed constitutively that is, they are always turned "on". Others, however, are active only when their products are needed by the cell, so their expression must be regulated.

  • If the amino acid tryptophan (Trp) is added to the culture, the bacteria soon stop producing the five enzymes previously needed to synthesize Trp from intermediates produced during the respiration of glucose. In this case, the presence of the products of enzyme action represses enzyme synthesis.
  • Conversely, adding a new substrate to the culture medium may induce the formation of new enzymes capable of metabolizing that substrate. If we take a culture of E. coli that is feeding on glucose and transfer some of the cells to a medium contain lactose instead, a revealing sequence of events takes place.
    • At first the cells are quiescent: they do not metabolize the lactose, their other metabolic activities decline, and cell division ceases.
    • Soon, however, the culture begins growing rapidly again with the lactose being rapidly consumed. What has happened? During the quiescent interval, the cells began to produce three enzymes.
    • a permease that transports lactose across the plasma membrane from the culture medium into the interior of the cell
    • beta-galactosidase which converts lactose into the intermediate allolactose and then hydrolyzes this into glucose and galactose. Once in the presence of lactose, the quantity of beta-galactosidase in the cells rises from a tiny amount to almost 2% of the weight of the cell.
    • a transacetylase whose function is still uncertain.

    Scientists Created Bacteria With a Synthetic Genome. Is This Artificial Life?

    In a milestone for synthetic biology, colonies of E. coli thrive with DNA constructed from scratch by humans, not nature.

    Scientists have created a living organism whose DNA is entirely hu man-made — perhaps a new form of life, experts said, and a milestone in the field of synthetic biology.

    Researchers at the Medical Research Council Laboratory of Molecular Biology in Britain reported on Wednesday that they had rewritten the DNA of the bacteria Escherichia coli, fashioning a synthetic genome four times larger and far more complex than any previously created.

    The bacteria are alive, though unusually shaped and reproducing slowly. But their cells operate according to a new set of biological rules, producing familiar proteins with a reconstructed genetic code.

    The achievement one day may lead to organisms that produce novel medicines or other valuable molecules, as living factories. These synthetic bacteria also may offer clues as to how the genetic code arose in the early history of life.

    “It’s a landmark,” said Tom Ellis, director of the Center for Synthetic Biology at Imperial College London, who was not involved in the new study. “No one’s done anything like it in terms of size or in terms of number of changes before.”

    Each gene in a living genome is detailed in an alphabet of four bases, molecules called adenine, thymine, guanine and cytosine (often described only by their first letters: A, T, G, C). A gene may be made of thousands of bases.

    Genes direct cells to choose among 20 amino acids, the building blocks of proteins, the workhorses of every cell. Proteins carry out a vast number of jobs in the body, from ferrying oxygen in the blood to generating force in our muscles.

    Nine years ago, researchers built a synthetic genome that was one million base pairs long. The new E. coli genome, reported in the journal Nature, is four million base pairs long and had to be constructed with entirely new methods.

    The new study was led by Jason Chin, a molecular biologist at the M.R.C. laboratory, who wanted to understand why all living things encode genetic information in the same baffling way.

    The production of each amino acid in the cell is directed by three bases arranged in the DNA strand. Each of these trios is known as a codon. The codon TCT, for example, ensures that an amino acid called serine is attached to the end of a new protein.

    Since there are only 20 amino acids, you’d think the genome only needs 20 codons to make them. But the genetic code is full of redundancies, for reasons that no one understands.

    Amino acids are encoded by 61 codons, not 20. Production of serine, for example, is governed by six different codons. (Another three codons are called stop codons they tell DNA where to stop construction of an amino acid.)

    Like many scientists, Dr. Chin was intrigued by all this duplication. Were all these chunks of DNA essential to life?

    “Because life universally uses 64 codons, we really didn’t have an answer,” Dr. Chin said. So he set out to create an organism that could shed some light on the question.

    Image

    After some preliminary experiments, he and his colleagues designed a modified version of the E. coli genome on a computer that only required 61 codons to produce all of the amino acids the organism needs.

    Instead of requiring six codons to make serine, this genome used just four. It had two stop codons, not three. In effect, the researchers treated E. coli DNA as if it were a gigantic text file, performing a search-and-replace function at over 18,000 spots.

    Now the researchers had a blueprint for a new genome four million base pairs long. They could synthesize the DNA in a lab, but introducing it into the bacteria — essentially substituting synthetic genes for those made by evolution — was a daunting challenge.

    The genome was too long and too complicated to force into a cell in one attempt. Instead, the researchers built small segments and swapped them piece by piece into E. coli genomes. By the time they were done, no natural segments remained.

    Much to their relief, the altered E. coli did not die. The bacteria grow more slowly than regular E. coli and develop longer, rod-shaped cells. But they are very much alive.

    Dr. Chin hopes to build on this experiment by removing more codons and compressing the genetic code even further. He wants to see just how streamlined the genetic code can be while still supporting life.

    The Cambridge team is just one of many racing in recent years to build synthetic genomes. The list of potential uses is a long one. One attractive possibility: Viruses may not be able to invade recoded cells.

    Many companies today use genetically engineered microbes to make medicines like insulin or useful chemicals like detergent enzymes. If a viral outbreak hits the fermentation tanks, the results can be catastrophic. A microbe with synthetic DNA might be made immune to such attacks.

    Recoding DNA could also allow scientists to program engineered cells so that their genes won’t work if they escape into other species. “It creates a genetic firewall,” said Finn Stirling, a synthetic biologist at Harvard Medical School who was not involved in the new study.

    Researchers are also interested in recoding life because it opens up the opportunity to make molecules with entirely new kinds of chemistry.

    Beyond the 20 amino acids used by all living things, there are hundreds of other kinds. A compressed genetic code will free up codons that scientists can use to encode these new building blocks, making new proteins that carry out new tasks in the body.

    James Kuo, a postdoctoral researcher at Harvard Medical School, offered a note of caution. Tacking bases together to make genomes remains enormously costly.

    “It’s just way too expensive for academic groups to keep pursuing,” Dr. Kuo said.

    But E. coli is a workhorse of laboratory research, and now it’s clear that its genome can be synthesized. It’s not hard to imagine that prices will fall as demands for custom, synthetic DNA rise. Researchers could apply Dr. Chin’s methods to yeast or other species.


    Move over CRISPR, the retrons are coming

    3D-model of DNA. Credit: Michael Ströck/Wikimedia/ GNU Free Documentation License

    While the CRISPR-Cas9 gene editing system has become the poster child for innovation in synthetic biology, it has some major limitations. CRISPR-Cas9 can be programmed to find and cut specific pieces of DNA, but editing the DNA to create desired mutations requires tricking the cell into using a new piece of DNA to repair the break. This bait-and-switch can be complicated to orchestrate, and can even be toxic to cells because Cas9 often cuts unintended, off-target sites as well.

    Alternative gene editing techniques called recombineering instead perform this bait-and-switch by introducing an alternate piece of DNA while a cell is replicating its genome, efficiently creating genetic mutations without breaking DNA. These methods are simple enough that they can be used in many cells at once to create complex pools of mutations for researchers to study. Figuring out what the effects of those mutations are, however, requires that each mutant be isolated, sequenced, and characterized: a time-consuming and impractical task.

    Researchers at the Wyss Institute for Biologically Inspired Engineering at Harvard University and Harvard Medical School (HMS) have created a new gene editing tool called Retron Library Recombineering (RLR) that makes this task easier. RLR generates up to millions of mutations simultaneously, and "barcodes" mutant cells so that the entire pool can be screened at once, enabling massive amounts of data to be easily generated and analyzed. The achievement, which has been accomplished in bacterial cells, is described in a recent paper in PNAS.

    "RLR enabled us to do something that's impossible to do with CRISPR: we randomly chopped up a bacterial genome, turned those genetic fragments into single-stranded DNA in situ, and used them to screen millions of sequences simultaneously," said co-first author Max Schubert, Ph.D., a postdoc in the lab of Wyss Core Faculty member George Church, Ph.D. "RLR is a simpler, more flexible gene editing tool that can be used for highly multiplexed experiments, which eliminates the toxicity often observed with CRISPR and improves researchers' ability to explore mutations at the genome level."

    Retrons: from enigma to engineering tool

    Retrons are segments of bacterial DNA that undergo reverse transcription to produce fragments of single-stranded DNA (ssDNA). Retrons' existence has been known for decades, but the function of the ssDNA they produce flummoxed scientists from the 1980s until June 2020, when a team finally figured out that retron ssDNA detects whether a virus has infected the cell, forming part of the bacterial immune system.

    While retrons were originally seen as simply a mysterious quirk of bacteria, researchers have become more interested in them over the last few years because they, like CRISPR, could be used for precise and flexible gene editing in bacteria, yeast, and even human cells.

    "For a long time, CRISPR was just considered a weird thing that bacteria did, and figuring out how to harness it for genome engineering changed the world. Retrons are another bacterial innovation that might also provide some important advances," said Schubert. His interest in retrons was piqued several years ago because of their ability to produce ssDNA in bacteria—an attractive feature for use in a gene editing process called oligonucleotide recombineering.

    Recombination-based gene editing techniques require integrating ssDNA containing a desired mutation into an organism's DNA, which can be done in one of two ways. Double-stranded DNA can be physically cut (with CRISPR-Cas9, for example) to induce the cell to incorporate the mutant sequence into its genome during the repair process, or the mutant DNA strand and a single-stranded annealing protein (SSAP) can be introduced into a cell that is replicating so that the SSAP incorporates the mutant strand into the daughter cells' DNA.

    "We figured that retrons should give us the ability to produce ssDNA within the cells we want to edit rather than trying to force them into the cell from the outside, and without damaging the native DNA, which were both very compelling qualities," said co-first author Daniel Goodman, Ph.D., a former Graduate Research Fellow at the Wyss Institute who is now a Jane Coffin Childs Postdoctoral Fellow at UCSF.

    Another attraction of retrons is that their sequences themselves can serve as "barcodes" that identify which individuals within a pool of bacteria have received each retron sequence, enabling dramatically faster, pooled screens of precisely-created mutant strains.

    To see if they could actually use retrons to achieve efficient recombineering with retrons, Schubert and his colleagues first created circular plasmids of bacterial DNA that contained antibiotic resistance genes placed within retron sequences, as well as an SSAP gene to enable integration of the retron sequence into the bacterial genome. They inserted these retron plasmids into E. coli bacteria to see if the genes were successfully integrated into their genomes after 20 generations of cell replication. Initially, less than 0.1% of E. coli bearing the retron recombineering system incorporated the desired mutation.

    To improve this disappointing initial performance, the team made several genetic tweaks to the bacteria. First, they inactivated the cells' natural mismatch repair machinery, which corrects DNA replication errors and could therefore be "fixing" the desired mutations before they were able to be passed on to the next generation. They also inactivated two bacterial genes that code for exonucleases—enzymes that destroy free-floating ssDNA. These changes dramatically increased the proportion of bacteria that incorporated the retron sequence, to more than 90% of the population.

    Name tags for mutants

    Now that they were confident that their retron ssDNA was incorporated into their bacteria's genomes, the team tested whether they could use the retrons as a genetic sequencing "shortcut," enabling many experiments to be performed in a mixture. Because each plasmid had its own unique retron sequence that can function as a "name tag", they reasoned that they should be able to sequence the much shorter retron rather than the whole bacterial genome to determine which mutation the cells had received.

    First, the team tested whether RLR could detect known antibiotic resistance mutations in E coli. They found that it could—retron sequences containing these mutations were present in much greater proportions in their sequencing data compared with other mutations. The team also determined that RLR was sensitive and precise enough to measure small differences in resistance that result from very similar mutations. Crucially, gathering these data by sequencing barcodes from the entire pool of bacteria rather than isolating and sequencing individual mutants, dramatically speeds up the process.

    Then, the researchers took RLR one step further to see if it could be used on randomly-fragmented DNA, and find out how many retrons they could use at once. They chopped up the genome of a strain of E. coli highly resistant to another antibiotic, and used those fragments to build a library of tens of millions of genetic sequences contained within retron sequences in plasmids. "The simplicity of RLR really shone in this experiment, because it allowed us to build a much bigger library than what we can currently use with CRISPR, in which we have to synthesize both a guide and a donor DNA sequence to induce each mutation," said Schubert.

    This library was then introduced into the RLR-optimized E coli strain for analysis. Once again, the researchers found that retrons conferring antibiotic resistance could be easily identified by the fact that they were enriched relative to others when the pool of bacteria was sequenced.

    "Being able to analyze pooled, barcoded mutant libraries with RLR enables millions of experiments to be performed simultaneously, allowing us to observe the effects of mutations across the genome, as well as how those mutations might interact with each other," said senior author George Church, who leads the Wyss Institute's Synthetic Biology Focus Area and is also a Professor of Genetics at HMS. "This work helps establish a road map toward using RLR in other genetic systems, which opens up many exciting possibilities for future genetic research."

    Another feature that distinguishes RLR from CRISPR is that the proportion of bacteria that successfully integrate a desired mutation into their genome increases over time as the bacteria replicate, whereas CRISPR's "one shot" method tends to either succeed or fail on the first try. RLR could potentially be combined with CRISPR to improve its editing performance, or could be used as an alternative in the many systems in which CRISPR is toxic.

    More work remains to be done on RLR to improve and standardize editing rate, but excitement is growing about this new tool. RLR's simple, streamlined nature could enable the study of how multiple mutations interact with each other, and the generation of a large number of data points that could enable the use of machine learning to predict further mutational effects.


    How E. coli Cells Work in the Human Gut

    Molecular and cell biologist Ken Campellone has discovered a key factor in how harmful E. coli affect people’s intestines.

    A scanning electron microscope image of the pedestal formed by harmful E. coli in the human large intestine. (Ken Campellone/UConn Photo)

    Ken Campellone, assistant professor of molecular and cell biology in the College of Liberal Arts and Sciences, in his laboratory in Beach Hall. (Christine Buckley/UConn Photo)

    The bacterium Escherichia coli, commonly known as E. coli, has a duplicitous reputation. Scientists tell us that most strains of the microbe live peacefully in our guts or the guts of other mammals, munching on bits of food, causing no harm or even creating benefits for their hosts.

    But the grotesque imagery of E. coli infections tells a different story: After eating food contaminated with pathogenic strains, people can experience vomiting, diarrhea, and dysentery. And in rare cases, the bacteria can lead to kidney failure and even death.

    Ken Campellone, assistant professor of molecular and cell biology in the College of Liberal Arts and Sciences, wants to understand how these bacteria can play such different roles. By focusing on the interactions between one of the deadliest E. coli strains and the cells of the human gut, he’s learning not only how the bacteria works, but how our own cells work, too.

    Recently, Campellone discovered a particular protein in the cells of the human large intestine that is taken over by E. coli cells and helps to bind the bacterium to the intestinal wall.

    “Pathogens have found really clever ways of taking over the normal processes of our cells,” he says. “Often they know more about our own cells than we do, and it’s really intriguing.”

    The strain of E. coli that Campellone studies belongs to a group of the bacteria called enterohemorrhagic E. coli, or EHEC, that often makes international news when people eat contaminated meat or vegetables. In 2011, an outbreak of a hemorrhagic strain in Germany infected more than 3,700 people, killing 45. The Centers for Disease Control and Prevention estimate that about 75,000 infections occur each year in the United States.

    The reason for this high level of virulence, says Campellone, is a series of genetic acquisitions by the harmful bacteria. Scientists have sequenced several types of E. coli, and they’ve found more than 1,000 genes in the harmful group that are not present in the harmless, or commensal, group.

    But, he adds, of the roughly 1,000 genes that have been identified as pathogenic, relatively few have been characterized.

    “We know very little about the genes in EHEC that are different from the commensal version,” he says. “My goal is to better understand how a group of genes that encode proteins called effectors take over their human cell targets.”

    In particular, the most dangerous types have acquired the genes to produce a poisonous substance called Shiga toxin, which Campellone says can produce an illness ranging from unpleasant to life-threatening.

    “If the toxin is just released into your intestines, you would get diarrhea and dysentery,” he says. “But if it enters your bloodstream, it can cause serious kidney damage and become fatal.” Plus, he adds, there are currently no known medicines for the blood poisoning syndrome, and antibiotics only make the symptoms worse. Patients just have to wait and hope.

    Campellone’s research focuses on how the trafficking and organization of proteins control the shape of cells. When E. coli affix themselves to the intestinal wall, they disrupt its normal organization. They do this by delivering bacterial proteins into the cell, which in turn recruit specific intestinal cell proteins that normally shape the cell.

    A scanning electron microscope image of the 'pedestal' formed by harmful E. coli in the human large intestine. (Ken Campellone/UConn Photo)

    In 2004, Campellone was the first to identify a protein that the E. coli injects into the intestinal cells, causing the production of a fleshy bulge that lifts the attached bacteria away from the wall. Scientists call this lump a “pedestal” – because it really does look like one – but they still aren’t sure what its purpose is.

    Campellone also recently discovered a protein in human intestinal cells that interacts with the bacterial protein to help create the pedestal. He published these results in the June 2012 issue of The Journal of Biological Chemistry.

    The discovery is significant because if a drug was developed that could block the pedestal from being produced, then the E. coli might not be able to stick to the intestinal wall, he explains. In that case, the bacteria might simply wash through a person’s system, causing little harm.

    In the classroom and in his laboratory, Campellone says these examples from his research give his students real-life examples of the information they learn about cell structure.

    “When we teach cell biology, we show students that a lot of what we know about how human cells normally function is from studying infections,” he says, pointing out that many cellular proteins have only been discovered in the context of pathogens trying to exploit them.

    “Being able to ask scientific questions experimentally in the laboratory and then get an answer that could benefit people – that’s the most exciting part for the students, and for me,” he says. “You can be the first person in the world to know something.”


    Bacteria and E. Coli in Water

    Water, like everything else on Earth, including you, is full of bacteria. Some bacteria are beneficial and some are not. Escherichia coli (E. coli) bacteria, found in the digestive tract of animals, can get into the environment, and if contacted by people, can cause health problems and sickness. Find out the details here.

    Bacteria and E. Coli in Water

    Escherichia coli or E. coli is a type fecal coliform bacteria that is commonly found in the intestines of animals and humans. E. coli in water is a strong indicator of sewage or animal waste contamination. Sewage and animal waste can contain many types of disease causing organisms. Consumption may result in severe illness children under five years of age, those with compromised immune systems, and the elderly are particularly susceptible.

    Bacteria are common single-celled organisms and are a natural component of lakes, rivers, and streams. Most of these bacteria are harmless to humans however, certain bacteria, some of which normally inhabit the intestinal tract of warm-blooded animals, have the potential to cause sickness and disease in humans. High numbers of these harmless bacteria often indicate high numbers of harmful bacteria as well as other disease-causing organisms such as viruses and protozoans.

    One method of determining bacteria counts is to count the number of bacteria colonies that grow on a prepared medium.

    Escherichia coli (abbreviated as E. coli) are bacteria found in the environment, foods, and intestines of people and animals. E. coli are a large and diverse group of bacteria. Although most strains of E. coli are harmless, others can make you sick. Some kinds of E. coli can cause diarrhea, while others cause urinary tract infections, respiratory illness and pneumonia, and other illnesses.

    Total coliform

    Total coliforms are gram-negative, aerobic or faculative anaerobic, nonspore forming rods. These bacteria were originally believed to indicate the presence of fecal contamination, however total coliforms have been found to be widely distributed in nature and not always associated with the gastrointestinal tract of warm blooded animals. The number of total coliform bacteria in the environment is still widely used as an indicator for potable water in the U.S.

    Fecal coliform

    Fecal coliform bacteria are a subgroup of coliform bacteria that were used to establish the first microbial water quality criteria. The ability to grow at an elevated temperature (44.5 degrees Celsius) separate this bacteria from the total coliforms and make it a more accurate indicator of fecal contamination by warm-blooded animals. Fecal- coliform bacteria are detected by counting the dark-blue to blue-grey colonies that grow on a 0.65 micron filters placed on mFC agar incubated in a 44.5º C oven for 22-24 hours. The presence of fecal coliforms in water indicates that fecal contamination of the water by a warm-blooded animal has occurred, however, recent studies have found no statistical relationship between fecal coliform concentrations and swimmer-associated sickness.

    Escherichia coli (E. coli) is a rod-shaped bacteria commonly found in the gastrointestinal tract and feces of warm-blooded animals. It is a member of the fecal coliform group of bacteria and is distinguished by its inability to break down urease. E. coli numbers in freshwater are determined by counting the number of yellow and yellow brown colonies growing on a 0.45 micron filter placed on m-TEC media and incubated at 35.0º C for 22-24 hours. The addition of urea substrate confirms that colonies are E. coli. This bacteria is a preferred indicator for freshwater recreation and its presence provides direct evidence of fecal contamination from warm-blooded animals. Although usually harmless, E. coli can cause illnesses such as meningitis, septicemia, urinary tract, and intestinal infections. A recently discovered strain of E. coli (E. coli 0157:H7) can cause severe disease and may be fatal in small children and the elderly.

    The relation between bacteria counts and sickness

    Consumption of or contact with water contaminated with feces of warm-blooded animals can cause a variety of illnesses. Minor gastrointestinal discomfort is probably the most common symptom however, pathogens that may cause only minor sickness in some people may cause serious conditions or death in others, especially in the very young, old, or those with weakened immunological systems.


    E. coli

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    E. coli, (Escherichia coli), species of bacterium that normally inhabits the stomach and intestines. When E. coli is consumed in contaminated water, milk, or food or is transmitted through the bite of a fly or other insect, it can cause gastrointestinal illness. Mutations can lead to strains that cause diarrhea by giving off toxins, invading the intestinal lining, or sticking to the intestinal wall. Therapy for gastrointestinal illness consists largely of fluid replacement, though specific drugs are effective in some cases. The illness is usually self-limiting, with no evidence of long-lasting effects. However, dangerous strains, such as E. coli O157:H7 and E. coli O104:H4, can cause bloody diarrhea, kidney failure, and death in extreme cases. Proper cooking of meat and washing of produce can prevent infection from contaminated food sources. E. coli also can cause urinary tract infections in women.


    60+ HSC Biology Terms and Definitions:

    Heredity

    Term Definition Example and related concepts
    Sexual reproductionGenetic information comes from two sexes, and gametes must meet and fuseFor humans, the egg and sperm will meet. For flowers, the ovule and the pollen will meet.
    Asexual reproductionDoesn’t require an egg and sperm (gametes) to meet, and usually comes from one organism Bacteria can split from a single cell in a process called binary fission
    GameteGametes are cells which can give rise to a new organism when they meet with a gamete of the opposite gender.Gametes usually have a haploid chromosomes (half the number of chromosomes in an adult).
    External fertilisationEgg and sperm meet outside the female bodyFish and frogs can release their eggs and sperm outside their body. Water assists in keeping them moist.
    Internal fertilisationEgg and sperm meet inside the female bodySeen in humans, dogs and cats
    Binary fissionType of asexual reproduction where bacteria ‘split’ in half, each half becomes a new daughter cellWhen comparing the life cycle between prokaryotes and eukaryotes, there are similarities that can be drawn. Both replicate their DNA, and both increase the size of the cell to create two daughter cells except this occurs in the organism level for bacteria, and the cell level for humans.
    BuddingType of yeast asexual reproduction where cells grow bigger until a little ‘bud’ forms on the mother cell. This bud grows bigger until it is big enough to break off. Great demonstration of budding is the immortal hydra
    MitosisCell division where daughter cells have the same number of chromosomes Human somatic cells replicate by mitosis. The new daughter cells are identical to the mother cell.
    MeiosisThe process by which cells are replicated but it is different from mitosis because 1 parent cell gives rise to 4 daughter cells, which are different because of crossing overHaploid gametes are produced from meiosis. It is important that the daughter cells aren’t identical to the mother cells.
    DNA replicationMaking new copies of DNA so new cells can have a copy DNA replication is a semi-conservative process which means that the two new DNA molecules that are made contains one strand of the original DNA
    TranscriptionThe process of copying information encoded in DNA into a ‘photocopy’ or RNA so the ribosome can read itDNA is hard to read because it is so long and the structure is different. mRNA is a direct copy of the sequences in DNA, making it easier to use the information encoded in the genome
    TranslationRibosome ‘reading’ the mRNA which tells it to recruit certain amino acids. Results in a polypeptide chaintRNAs carry amino acids to the growing polypeptide chain
    PolypeptidesPolypeptides are short proteins made up of chains of amino acidsPolypeptides are usually smaller than proteins but larger than peptides and amino acids
    ChromosomeA chromosome is a package of DNA, which is a long DNA molecule that is coiled tightly for easy storage and movementHumans have 46 chromosomes (26 pairs)
    GeneA gene codes for a particular characteristic. A gene is a section of our DNA moleculeThe gene for eye colour
    AlleleAllele is a form of a gene. For each gene, we have two alleles - one from mum and one from dadA blue eye allele and a brown eye allele
    PhenotypeThis is the physical characteristic of a genotypeBrown eyes are coded for by genotype ‘Aa’
    GenotypeA genotype is the genetic code for a characteristicAa
    Homozygous genotypesGenotypes where the two alleles are the sameAA or aa
    Heterozygous genotypesGenotypes where the two alleles are differentAa or Bb
    Simple dominanceWhere one allele is completely dominant over the other (the recessive allele)Where greenness is dominant over yellowness (of Mendel’s peas)
    Monohybrid crossA Medelian cross where the two individuals have the same genotypeCross of AA and AA or Aa and Aa
    Co-dominanceWhere two or more alleles have equal dominance (which gives rise to a third outcome)Snapdragons experiment, where a red one and a white one will cross to form a pink one. Red and white are co-dominant.
    Sex-linked genesA common genetic variation that occurs in >1% of the population >1% of people have a C T nucleotide mutation in a specific part of their DNA
    Single nucleotide polymorphism (SNP)A common genetic variation that occurs in >1% of the population >1% of people have a C T nucleotide mutation in a specific part of their DNA
    DNA sequencingFinding out what the sequence of DNA isIllumina technology is commonly used at and can find the sequence (CTTAGACCGA…) of almost all of the 3 billion base pairs that you have

    Genetic Change

    Term
    DefinitionExample and related concepts
    MutagenAnything causing mutationsCigarette smoke
    MutationA change in DNA sequencePoint mutations are one nucleotide differences in a gene (CTAGTA CTTGTA)
    Genetic flow/gene mutationIntroducing genes of one population into another by breeding between two populationsA bee carrying the pollen from one population of flowers to another can be considered genetic flow
    Genetic diversityVariation in a genetic pool for a particular characteristicGenetic diversity is the reason why some people have black hair, others have brown hair, and others still can have blonde or red hair.
    BiotechnologyUsing biology for industryWe can use massive cultures of bacteria to make drugs at the industrial scale
    Artificial inseminationTaking semen from a male animal and inserting it into a female uterus Farmers pick which cows mate to ensure that the cow with the best characteristics mate and to prevent inbreeding
    Artificial pollinationTaking pollen or stamen from one plant into the pistil of anotherThe characteristics of flowers can be mixed
    CloningCreating a genetically identical copy of an organism Whole organism cloning of dolly the sheep
    Transgenic organismsSpecies which are the result of genetic modification'Anti-freeze strawberries’

    Infectious Disease

    TermDefinitionExample and related concepts
    PathogenA foreign body that can cause diseaseChickenpox
    AntigenMolecules made of protein which are on the surface of cells that trigger the immune response when they detect infectious pathogensThe Rhesus antigen causes our blood type to be + or -
    AntibodyMade by plasma cells which specifically target a pathogen by binding to it Starts getting released after the innate immune system can’t defeat the infection
    EpidemicAn infectious disease spreading across a wide rangeAIDS epidemic
    Innate immune systemMade up of neutrophils, macrophages and other cells to attack any non-specific response Any bacteria or virus entering gets attacked by the same molecules. E.g. regardless if it is S. aureus or E. coli, they get attacked by cytokines and other molecules
    Adaptive immune systemMade up of T cells and B cells and attack a specific pathogen T cells and B cells prepare chemicals and molecules to specifically attack either S. aureus or E. coli
    Cytokines Proteins that immune cells use to communicate with each other Cells can release growth factors (GFs), interferons (IFs) and interleukins (ILs)
    Cell differentiationHow cells become specialised for their different functions. They all start off exactly the sameWhite blood cells specialise from stem cells
    QuarantineIsolation after coming from another country to make sure they don’t spread potential diseasesWaiting to see if plants/animals have introduced infectious diseases prevents introducing the disease to an unimmune public
    Passive immunityInjection of someone else’s antibodies If you wait for your body to respond to neutralise snake bites, it’ll be too late. We use another animals’ antibodies and inject it into the affected person. These antibodies will act to neutralise the bite without needing an immune reaction
    Active immunityMaking your own antibodies After a vaccine, your body responds by making antibodies against the infectious agent

    Non-Infectious Disease and Disorders

    TermDefinitionExample and related concepts
    HomeostasisA process involving feedback networks (positive and negative) that means that organisms (like humans) can adapt to changes in their environmentWhen it is warm, mammals have mechanisms like sweating which allow us to adapt to the environment. If we did not have these mechanisms, our enzymes would denature!
    EnzymesA protein that is responsible for lowering the activation energy of a reaction, making it occur fasterBromalain is an enzyme found in pineapple and kiwi fruit.
    Lock and key model of substrate specificity for enzymes.
    Enzymes will become denatured if the temperature or pH changes outside of its optimal range.
    SubstratesMolecules part of a chemical reaction which react together to form the productsSubstrates are the molecules which go into enzymes
    OptimalBest for efficiency of a reactionOptimal temperature of most human chemical reactions and their enzymes is around 37 degrees Celsius (this is our human body temperature is around this range)
    Endotherm organismsOrganisms which control their own body temperature, independently of the outside environment‘Warm blooded’ animals, such as humans and other mammals
    EctothermOrganisms which do not control their own body temperature, and rely on the outside environment‘Cold blooded’ animals, such as lizards and other reptiles
    Adaptive advantage An advantage of a particular characteristic which helps the organism to adapt to the environment, according to the theory of evolution by natural selection An adaptive advantage for a frog living in a green forest is that it has green skin which allows it to camouflage, and thus survive and pass on its genetic characteristics to its offspring
    HormonesChemicals which are used to control organs in the bodyAnti-diuretic hormone (ADH) can tell the kidney to reabsorb more water, and so the need to urinate is decreased
    DiseaseDisturbance in normal structure and function caused by something outside the bodyCan be caused by improper diet or radiation exposure
    DisorderDisturbance in normal body structure and function caused by something inside the body Can be caused by genes, birth defects
    CancerUncontrolled growth of cellsStomach cancer is when stomach cells keep dividing and don’t stop
    IncidenceHow many new cases of this disease in x time?Estimated 14,320 new melanoma cases diagnosed in 2018
    PrevalenceHow many people have had this disease in x time? At the end of 2013, 53,215 people were living with melanoma
    MortalityNumber of deaths in a given time or location Skin cancer mortality in Australia is estimated to be 3.9% of all deaths in 2018
    Epidemiology The study of how a disease occurs and spreads and where it is most prevalentEpidemiology allows us to understand why a disease starts and spreads and how to tackle it
    Genetic engineeringChanging the characteristics of an organism by changing its genesMice that glow due to the insertion of a gene that makes fireflies glow

    Bacterial Variable Number Tandem Repeats

    Bacterial Genomes

    Bacterial genomes can represent highly dynamic entities where mutation and structural change can occur at high rates and generate high-frequency variants within populations. However, this is not uniform across genomes, as genomes are mosaics of gene-coding regions, intergenic spaces, and repeated elements that evolve at dramatically different rates. In some bacteria, the gene order and nucleotide sequences of the genomes are highly conserved and little variation is observed among different isolates, while in others there is great variation. This can be due, in part, to the evolutionary history of a particular bacterium (old, young, recently emerged pathogen, etc.), but the diversity is also a function of particular subgenomic components evolving at accelerated rates. The diversity of some gene-coding regions may be much lower and much less dynamic than in other non-gene-coding regions or hypermutable loci. Transposable elements and insertion sequence (IS) elements can be very active and mediate some of these genomic changes. Large or small chromosomal inversions frequently occur between inverted repeat sequences IS elements can generate inverted repeats and make excellent targets for homologous recombination. The focus of this article is a particular category of hypermutable loci called ‘variable number tandem repeats’ (VNTRs).


    Gram Staining

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    In this technique, bacteria are stained with crystal violet, and then exposed to a decolorizer followed by counterstaining using safranin dye. After this exposure, the bacteria that appear purple are the ones that have retained crystal violet in their cells in spite of exposure to a decolorizer. These are Gram-positive bacteria. On the other hand, the bacteria that appear pink are the ones that get decolorized and take up safranin dye. These are Gram-negative bacteria.


    DNA Replication in Prokaryotes Vs. Eukaryotes

    Location

    Prokaryotes do not have nucleus and other membrane-bound organelles, like mitochondria, endoplasmic reticulum, and golgi bodies. The prokaryotic DNA is present as a DNA-protein complex called nucleoid. The replication occurs in the cytoplasm of the cell.

    In case of eukaryotes, the organisms that contain a membrane-bound nucleus, the DNA is sequestered inside the nucleus. Hence, the nucleus is the site for DNA replication in eukaryotes.

    Stage of Cell Division

    In prokaryotes, DNA replication is the first step of cell division, which is primarily through binary fission or budding.

    In eukaryotes, cell division is a comparatively complex process, and DNA replication occurs during the synthesis (S) phase of the cell cycle.

    Initiation

    DNA replication is initiated at a specific or unique sequence called the origin of replication, and ends at unique termination sites. The region of DNA between these two sites is termed as a replication unit or replicon.

    Prokaryotic DNA is organized into circular chromosomes, and some have additional circular DNA molecules called plasmids. The prokaryotic DNA molecules contain a single origin of replication and a single replicon. Moreover, these origin sites are generally longer than eukaryotic origin sites.

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    Eukaryotic DNA is comparatively very large, and is organized into linear chromosomes. Due to the high amount of material to be copied, it contains multiple origins of replication on each chromosome. DNA replication can independently initiate at each origin and terminate at the corresponding termination sites. Thus, each chromosome has several replicons, which enable faster DNA replication. The human genome that comprises about 3.2 billion base pairs gets replicated within an hour. If DNA replication was dependent on a single replicon, it would take a month’s time to finish replicating one chromosome.

    Direction of Replication

    Once initiated, DNA replication assembly proceeds along the DNA molecule, and the precise point at which replication is occurring is termed as the replication fork. Generally, in both prokaryotes and eukaryotes, the process of DNA replication proceeds in two opposite directions, from the origin of replication.

    However, in certain plasmids present in bacterial cells, unidirectional DNA replication has been observed. These plasmids replicate through the rolling circle model, wherein multiple linear copies of the circular DNA are synthesized and then circularized.

    Enzymes

    Although a similar set of enzymes are involved in prokaryotic and eukaryotic DNA replication, the latter one is more complex and varied. The initiator proteins, single-stranded DNA-binding protein (SSB), primase, DNA helicase, and DNA ligase are present in both prokaryotes and eukaryotes.

    Enzymes specific to prokaryotes:

    Enzyme Activity
    DNA Polymerase I 5′ to 3′ polymerase, 3′ to 5′ exonuclease, 5′ to 3′ exonuclease
    DNA Polymerase III 5′ to 3′ polymerase, 3′ to 5′ exonuclease

    Enzymes specific to eukaryotes:

    Enzyme Activity
    DNA polymerase α 5′ to 3′ polymerase
    DNA polymerase δ 5′ to 3′ polymerase, 3′ to 5′ exonuclease
    DNA polymerase ε 5′ to 3′ polymerase

    In addition, eukaryotes contain DNA polymerase γ, which is involved in mitochondrial DNA replication. Also, the topoisomerases, enzymes that regulate the winding and unwinding of DNA during the movement of replication fork, differ in their activity. Prokaryotes, generally use type II topoisomerase called DNA gyrase, that introduces a nick in both the DNA strands. On the contrary, most eukaryotes utilize type I topoisomerases, that cut a single strand of DNA, during the movement of the replication fork.

    Okazaki fragments

    During DNA replication, the synthesis of one strand occurs in a continuous manner, whereas that of the other strand occurs in a discontinuous manner through the formation of fragments. The former strand is termed as the leading strand, the latter as the lagging strand, and the intermediate fragments are termed as the Okazaki fragments. The reason for such a difference is the antiparallel nature of DNA strands, as against the unidirectional activity of the DNA polymerase.

    Prokaryotic Okazaki fragments are longer, with the typical length observed in Escherichia coli (E. coli) being about 1000 to 2000 nucleotides.

    The length of eukaryotic Okazaki fragments ranges between 100 and 200 nucleotides. Although comparatively shorter, they are produced at a rate slower than that observed in prokaryotes.

    Termination

    The termination of DNA replication occurs at specific termination sites in both prokaryotes and eukaryotes.

    In prokaryotes, a single termination site is present midway between the circular chromosome. The two replication forks meet at this site, thus, halting the replication process.

    In eukaryotes, the linear DNA molecules have several termination sites along the chromosome, corresponding to each origin of replication. However, the eukaryotic DNA replication is characterized by a unique end-replication problem, wherein a part of DNA present at the ends of the chromosome does not get replicated. So, the lagging strand is shorter than the leading strand. This problem is addressed in eukaryotes by the presence of non-coding, repetitive DNA sequence called telomeres, at the ends of chromosomes.

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