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RNA World

Background vocabulary: monomer and polymer

Monomer Polymer Lego analogy

Life today

Living things have genetic information stored in a polymer of DNA.

That info gets copied into polymers of RNA.

That is translated, with the help of mRNA, into polymers of proteins.

And each of these steps needs special enzymes.

Interesting thought

Life in today’s cells, and even viruses, is wicked complicated.

Hard to imagine all it all evolved, all at once. But who says it had to do it all at once?

Maybe one simple kind of reaction developed, then later, other kinds of reactions, and then over a loooong period of time, even other types.

Life in the very beginning

Perhaps once upon a time, RNA was all that life had.

Pieces of RNA were both the genes and the catalyst.

  e.g. RNA could do base pairing with itself, bend, and graph other molecules.

RNA World GIF

RNA sequences could be copied by other RNAs.

Only later did DNA and proteins evolve.

This is the idea of the RNA world

A hypothetical stage in the history of life on Earth

Idea – RNA developed before DNA and proteins developed.

Alexander Rich first proposed the concept in 1962

Alexander Rich RNA

Growing amounts of evidence for this is strong enough that the hypothesis has gained wide acceptance.

How is RNA like DNA?

Both can store and replicate genetic information;

How is RNA like an enzyme?

Both can catalyze (start) chemical reactions.

Are any enzymes today made of RNA?

the ribosome is composed primarily of RNA.

Ribosomes are part of many important enzymes, such as Acetyl-CoA, NADH, etc.

So why does life depend on DNA replication nowadays?

DNA is more stable than RNA

 

What does RNA, and DNA, look like?

 

RNA_I_Figure2

How would RNA monomers assemble into polymers?

How could copies be made?

first genes may have been RNA nucleotides

So let us look at the possible in steps, in order.

At the far left is long ago… then an RNA based world of life developed… and later a DNA and protein based world of life developed.

RNA World Abiogenesis

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Oils

“Oil” is a general name for any kind of molecule which is

nonpolar

that just means that its electrons are evenly distributed

PHET Polar molecules app

liquid at room temperature

of course, it could become solid if cooled, or evaporate if heated

Molecule has one end which is hydrophobic and another end which is lipophilic

The hydrophobic end likes to stick to water molecules. But hates sticking to oils.

The lipophilic end likes to stick to oil molecules, but hates sticking to water,

hydrophobic hydrophilic

Made with many C and H atoms

Oils are usually flammable. Here we see oils in an orange skin interacting with a candle.

flammable orange oil

So Petroleum is?

Petroleum is a mix of naturally forming oils, which we drill from the Earth, and use in a variety of ways. See our article on petroleum and producing power.

Rotary catalytic mechanism of mitochondrial ATP synthase

Introduction

(Text in this section adapted from “ATP synthase.” Wikipedia, The Free Encyclopedia. 27 Mar. 2019.)

ATP synthase is an enzyme that creates the energy storage molecule adenosine triphosphate (ATP).

ATP is the most commonly used “energy currency” of cells for all organisms. It is formed from adenosine diphosphate (ADP) and inorganic phosphate (Pi).

The overall reaction catalyzed by ATP synthase is:

  • ADP + Pi + H+out ⇌ ATP + H2O + H+in

The formation of ATP from ADP and Pi is energetically unfavorable and would normally proceed in the reverse direction.

In order to drive this reaction forward, ATP synthase couples ATP synthesis during cellular respiration to an electrochemical gradient created by the difference in proton (H+) concentration across the mitochondrial membrane in eukaryotes or the plasma membrane in bacteria.

Molecular animation of ATP synthase

Here is a three dimensional animation of all the proteins working together in this complex. We see it situated in a lipid bilayer (organelle membrane.)

GIF mitochondrial ATP synthase

Here is another animation of a similar complex.

GIF mitochondrial ATP synthase 2

Video

Rotary catalytic mechanism of mitochondrial ATP synthase

Learning Standards

(TBA)

Biology, Chemistry, Simple machines

Epistasis

The following intro comes from – Biology 110H Basic Concepts, Stephen,  haeffer; Variation in Dominance, Multiple Alleles, Epistasis, Pleiotropy, and Polygenic Inheritance, Penn State.

Sometimes a gene at one location on a chromosome can affect the expression of a gene at a second location (epistasis). A good example of epistasis is the genetic interactions that produce coat color in horses and other mammals.

In horses, brown coat color (B) is dominant over tan (b).

Gene expression is dependent on a second gene that controls the deposition of pigment in hair.

The dominant gene (C) codes for the presence of pigment in hair, whereas the recessive gene (c) codes for the absence of pigment.

If a horse is homozygous recessive for the second gene (cc), it will have a white coat regardless of the genetically programmed coat color (B gene) because pigment is not deposited in the hair.epistasis in horse punnett square

The figure above demonstrates this scenario. Several of the white horses have genotypes for brown or tan coat color in the first gene, but are completely white because they are homozygous recessive for the gene controlling pigment deposition.

_________________________

Great resource here – “The term epistasis describes a certain relationship between genes, where an allele of one gene (e.g., ‘spread’) hides or masks the visible output, or phenotype, of another gene (e.g., pattern). Epistasis is entirely different from dominant and recessive, which are terms that apply to different alleles of the same gene (e.g., ‘bar’ is dominant to ‘barless’ and recessive to ‘check’).”

Click Epistasis, Genetic Science Learning Center, Univ of Utah

Epistasis: Gene Interaction and Phenotype Effects
By: Ilona Miko, Nature Education 1(1):197

Epistasis: Gene Interaction and Phenotype Effects. Nature education.

Elements necessary for life

Major elements – CHONSP

Carbon – Used as the major building unit of all organic molecules.

Hydrogen – major component of water. Major component of all organic molecules.

Oxygen – major component of water. Must be transported by our red blood cells.

Nitrogen – needed in all amino acids and proteins. Needed in chlorophyll, which is necessary for photosynthesis.

Sulphur – Used in in fats, body fluids, skeletal minerals, and most proteins.

Phosphorus – Necessary to make DNA and RNA. Also a component of bones and teeth.

periodoc table elements for life biological

Microbial Genomics and the Periodic Table, Lawrence P. Wackett, Anthony G. Dodge and Lynda B. M. Ellis

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periodic table elements life biological

Microbial Genomics and the Periodic Table, Lawrence P. Wackett, Anthony G. Dodge and Lynda B. M. Ellis

 

There are many essential trace elements in humans

Arsenic – “Despite its poisonous reputation, may be a necessary ultratrace element for humans. It is a necessary ultratrace element for red algae, chickens, rats, goats, and pigs. A deficiency results in inhibited growth (*)

Boron – essential for cell membrane characteristics and transmembrane signaling

Calcium ions are essential for muscle contractions and the clotting of blood. Necessary for cell walls, and bones.

Chlorine – Digestive juices in the stomach contain hydrochloric acid.

Chromium – essential trace element that potentiates insulin action and thus influences carbohydrate, lipid and protein metabolism.

“Chromium is an essential trace element and has a role in glucose metabolism. It seems to have an effect in the action of insulin. In anything other than trace amounts, chromium compounds should be regarded as highly toxic.” (*)

“Cobalt salts in small amounts are essential to many life forms, including humans. It is at the core of a vitamin called vitamin-B12. “ (*)

“Copper is essential for all life, but only in small quantities. It is the key component of redox enzymes and of haemocyanin.” (*)

Fluorine forms a salt with calcium. This salt makes the teeth and bones stronger.

“Iodine is an essential component of the human diet and in fact appears to be the heaviest required element in the diet. Iodine compounds are useful in medicine.” (*)

Iron – used in the hemoglobin molecules, allows your blood to hold oxygen. Iron is only about 0.004 percent of your body mass,

Magneisum “Chlorophylls (responsible for the green colour of plants) are based upon magnesium. Magnesium is required for the proper working of some enzymes.” (*)

Manganese – essential for the action of some enzymes

“Molybdenum is a necessary element, apparently for all species. … plays a role in nitrogen fixation, enzymes, and nitrate reduction enzymes.” (*)

Nickel is an essential trace element for many species. Unknown if so in humans.

“Potassium salts are essential for both animals and plants. The potassium cation (K+) is the major cation in intracellular (inside cells) fluids (sodium is the main extracellular cation). It is essential for nerve and heart function.” (*)

Selenium – essential component of one of the antioxidant defense systems of the body
“essential to mammals and higher plants, but only in small amounts…. may help protest against free radical oxidants and against some heavy metals.” (*)

Silicium – probably essential for healthy connective tissue and bone

Sodium (Na+) and potassium (K+) ions – transmission of nerve impulses between your brain and all parts of the body.

Tin – expected to have a function in the tertiary structure of proteins

Tungsten is needed in very tiny amounts in some enzymes (oxidoreductases)

Vanadium – possible role as an enzyme cofactor and in hormone, glucose, lipid, bone and tooth metabolism.

“Zinc is the key component of many enzymes. The protein hormone insulin contains zinc.” (*)

(*) WebElements: THE periodic table on the WWW
https://www.webelements.com/arsenic/biology.html

Australopithecus skeleton

Australopithecus skeleton

A team of Northeast Ohio researchers announced a rare and important find – the partial skeleton of a 3.6 million-year-old early human ancestor belonging to the same species as, but much older than, the iconic 3.2 million-year-old Lucy fossil discovered in 1974.

Less than 10 such largely intact skeletons 1.5 million years or older have been found. Greater Cleveland researchers have played leading roles in three of those discoveries, reinforcing the region’s prominence in the search for humanity’s origins.

The new specimen is called Kadanuumuu (pronounced Kah-dah-NEW-moo). The nickname means “big man” in the language of the Afar tribesmen who helped unearth his weathered bones from a hardscrabble Ethiopian plain beginning in 2005.

“Big” is an apt description of both Kadanuumuu’s stature and his significance. The scientists who analyzed the long-legged fossil say it erases any doubts about stubby Lucy and her kind’s ability to walk well on two legs, and reveals new information about when and how bipedality developed.

“It’s all about human-like bipedality evolving earlier than some people think,” said Cleveland Museum of Natural History anthropologist Yohannes Haile-Selassie,

– http://www.cleveland.com/science/index.ssf/2010/06/partial_skeleton_from_lucys_sp.html

– —
“Many dozens of A. afarensis fossils have been uncovered since Lucy was discovered in 1974, but none as complete as this one. Kadanuumuu’s forearm was first extracted from a hunk of mudstone in February 2005, and subsequent expeditions uncovered an entire knee, part of a pelvis, and well preserved sections of the thorax.
“We have the clavicle, a first rib, a scapula, and the humerus,” says physical anthropologist Bruce Latimer of Case Western Reserve University in Cleveland, Ohio, one of the co-leaders on the dig. “That enables us to say something about how [Kadanuumuu] was using its arm, and it was clearly not using it the way an ape uses it. It finally takes knuckle-walking off the table.” At five and a half feet tall, Kadanuumuu would also have towered two feet over Lucy, lending support to the view that there was a high degree of sexual dimorphism in the species.”

– Archaeology, “Kadanuumuu” – Woranso-Mille, Ethiopia Volume 64 Number 1, January/February 2011 by Brendan Borrell

http://www.cleveland.com/science/index.ssf/2010/06/partial_skeleton_from_lucys_sp.html

Alzheimer’s disease

Alzheimer’s disease

alzheimers disease
Possible causes of Alzheimer’s diseases

We currently don’t know the cause of Alzheimer’s disease. There may be more than one cause.

Prions

Two proteins central to the pathology of Alzheimer’s disease act as prions—misshapen proteins that spread through tissue like an infection by forcing normal proteins to adopt the same misfolded shape—according to new UC San Francisco research.

Using novel laboratory tests, the researchers were able to detect and measure specific, self-propagating prion forms of the proteins amyloid beta (A-β) and tau in postmortem brain tissue of 75 Alzheimer’s patients. In a striking finding, higher levels of these prions in human brain samples were strongly associated with early-onset forms of the disease and younger age at death.

by University of California, San Francisco

Alzheimer’s disease is a ‘double-prion disorder,’ study shows

Herpes virus

Alzheimer’s disease: mounting evidence that herpes virus is a cause, The Conversation US, Oct 19, 2018

Ruth Itzhaki, Professor Emeritus of Molecular Neurobiology, University of Manchester

More than 30m people worldwide suffer from Alzheimer’s disease – the most common form of dementia. Unfortunately, there is no cure, only drugs to ease the symptoms. However, my latest review, suggests a way to treat the disease. I found the strongest evidence yet that the herpes virus is a cause of Alzheimer’s, suggesting that effective and safe antiviral drugs might be able to treat the disease. We might even be able to vaccinate our children against it.

The virus implicated in Alzheimer’s disease, herpes simplex virus type 1 (HSV1), is better known for causing cold sores. It infects most people in infancy and then remains dormant in the peripheral nervous system (the part of the nervous system that isn’t the brain and the spinal cord). Occasionally, if a person is stressed, the virus becomes activated and, in some people, it causes cold sores.

We discovered in 1991 that in many elderly people HSV1 is also present in the brain. And in 1997 we showed that it confers a strong risk of Alzheimer’s disease when present in the brain of people who have a specific gene known as APOE4.

The virus can become active in the brain, perhaps repeatedly, and this probably causes cumulative damage. The likelihood of developing Alzheimer’s disease is 12 times greater for APOE4 carriers who have HSV1 in the brain than for those with neither factor.

Later, we and others found that HSV1 infection of cell cultures causes beta-amyloid and abnormal tau proteins to accumulate. An accumulation of these proteins in the brain is characteristic of Alzheimer’s disease.

We believe that HSV1 is a major contributory factor for Alzheimer’s disease and that it enters the brains of elderly people as their immune system declines with age. It then establishes a latent (dormant) infection, from which it is reactivated by events such as stress, a reduced immune system and brain inflammation induced by infection by other microbes.

Reactivation leads to direct viral damage in infected cells and to viral-induced inflammation. We suggest that repeated activation causes cumulative damage, leading eventually to Alzheimer’s disease in people with the APOE4 gene.

Presumably, in APOE4 carriers, Alzheimer’s disease develops in the brain because of greater HSV1-induced formation of toxic products, or less repair of damage.

New treatments? The data suggest that antiviral agents might be used for treating Alzheimer’s disease. The main antiviral agents, which are safe, prevent new viruses from forming, thereby limiting viral damage.

In an earlier study, we found that the anti-herpes antiviral drug, acyclovir, blocks HSV1 DNA replication, and reduces levels of beta-amyloid and tau caused by HSV1 infection of cell cultures.

It’s important to note that all studies, including our own, only show an association between the herpes virus and Alzheimer’s – they don’t prove that the virus is an actual cause. Probably the only way to prove that a microbe is a cause of a disease is to show that an occurrence of the disease is greatly reduced either by targeting the microbe with a specific anti-microbial agent or by specific vaccination against the microbe.

Excitingly, successful prevention of Alzheimer’s disease by use of specific anti-herpes agents has now been demonstrated in a large-scale population study in Taiwan. Hopefully, information in other countries, if available, will yield similar results.

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Corroboration of a Major Role for Herpes Simplex Virus Type 1 in Alzheimer’s Disease

Ruth F. Itzhaki, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom

Front. Aging Neurosci., 19 October 2018, https://doi.org/10.3389/fnagi.2018.00324

Strong evidence has emerged recently for the concept that herpes simplex virus type 1 (HSV1) is a major risk for Alzheimer’s disease (AD). This concept proposes that latent HSV1 in brain of carriers of the type 4 allele of the apolipoprotein E gene (APOE-ε4) is reactivated intermittently by events such as immunosuppression, peripheral infection, and inflammation, the consequent damage accumulating, and culminating eventually in the development of AD….

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How an outsider in Alzheimer’s research bucked the prevailing theory — and clawed for validation

Sharon Begley, Stat News, 10/29/2018

Robert Moir was damned if he did and damned if he didn’t. The Massachusetts General Hospital neurobiologist had applied for government funding for his Alzheimer’s disease research and received wildly disparate comments from the scientists tapped to assess his proposal’s merits.

It was an “unorthodox hypothesis” that might “fill flagrant knowledge gaps,” wrote one reviewer, but another said the planned work might add little “to what is currently known.” A third complained that although Moir wanted to study whether microbes might be involved in causing Alzheimer’s, no one had proved that was the case.

As if scientists are supposed to study only what’s already known, an exasperated Moir thought when he read the reviews two years ago.

He’d just had a paper published in a leading journal, providing strong data for his idea that beta-amyloid, a hallmark of Alzheimer’s disease, might be a response to microbes in the brain. If true, the finding would open up vastly different possibilities for therapy than the types of compounds virtually everyone else was pursuing.

But the inconsistent evaluations doomed Moir’s chances of winning the $250,000 a year for five years that he was requesting from the National Institutes of Health. While two reviewers rated his application highly, the third gave him scores in the cellar. Funding rejected.

Complaints about being denied NIH funding are as common among biomedical researchers as spilled test tubes after a Saturday night lab kegger. The budgets of NIH institutes that fund Alzheimer’s research at universities and medical centers cover only the top 18 percent or so of applications. There are more worthy studies than money.

Moir’s experience is notable, however, because it shows that, even as one potential Alzheimer’s drug after another has failed for the last 15 years (the last such drug, Namenda, was approved in 2003), researchers with fresh approaches — and sound data to back them up — have struggled to get funded and to get studies published in top journals. Many scientists in the NIH “study sections” that evaluate grant applications, and those who vet submitted papers for journals, have so bought into the prevailing view of what causes Alzheimer’s that they resist alternative explanations, critics say.

“They were the most prominent people in the field, and really good at selling their ideas,” said George Perry of the University of Texas at San Antonio and editor-in-chief of the Journal of Alzheimer’s Disease. “Salesmanship carried the day.”

Dating to the 1980s, the amyloid hypothesis holds that the disease is caused by sticky agglomerations, or plaques, of the peptide beta-amyloid, which destroy synapses and trigger the formation of neuron-killing “tau tangles.” Eliminating plaques was supposed to reverse the disease, or at least keep it from getting inexorably worse. It hasn’t. The reason, more and more scientists suspect, is that “a lot of the old paradigms, from the most cited papers in the field going back decades, are wrong,” said MGH’s Rudolph Tanzi, a leading expert on the genetics of Alzheimer’s.

Even with the failure of amyloid orthodoxy to produce effective drugs, scientists who had other ideas saw their funding requests repeatedly denied and their papers frequently rejected. Moir is one of them.

For years in the 1990s, Moir, too, researched beta-amyloid, especially its penchant for gunking up into plaques and “a whole bunch of things all viewed as abnormal and causing disease,” he said. “The traditional view is that amyloid-beta is a freak, that it has a propensity to form fibrils that are toxic to the brain — that it’s irredeemably bad. In the 1980s, that was a reasonable assumption.”

But something had long bothered him about the “evil amyloid” dogma. The peptide is made by all vertebrates, including frogs and lizards and snakes and fish. In most species, it’s identical to humans’, suggesting that beta-amyloid evolved at least 400 million years ago. “Anything so extensively conserved over that immense span of time must play an important physiological role,” Moir said.

What, he wondered, could that be?

In 1994, Moir changed hemispheres to work as a postdoctoral fellow with Tanzi. They’d hit it off over beers at a science meeting in Amsterdam. Moir liked that Tanzi’s lab was filled with energetic young scientists — and that in cosmopolitan Boston, he could play the hyper-kinetic (and bone-crunching) sport of Australian rules football. Tanzi liked that Moir was the only person in the world who could purify large quantities of the molecule from which the brain makes amyloid.

Moir initially focused on genes that affect the risk of Alzheimer’s — Tanzi’s specialty. But Moir’s intellectual proclivities were clear even then. His mind is constantly noodling scientific puzzles, colleagues say, even during down time. Moir took a vacation in the White Mountains a decade ago with his then-6-year-old son and a family friend, an antimicrobial expert; in between hikes, Moir explained a scientific roadblock he’d hit, and the friend explained a workaround.

Moir’s inclination toward unconventional thinking took flight in 2007. He was (and still is) in the habit of spending a couple of hours Friday afternoons on what he calls “PubMed walkabouts,” casually perusing that database of biomedical papers. One summer day, a Corona in hand, he came across a paper on something called LL37. It was described as an “antimicrobial peptide” that kills viruses, fungi, and bacteria, including — maybe especially — in the brain.

What caught his eye was that LL37’s size and structure and other characteristics were so similar to beta-amyloid, the two might be twins.

Moir hightailed it to Tanzi’s office next door. Serendipitously, Tanzi (also Corona-fueled) had just received new data from his study of genes that increase the risk of Alzheimer’s disease. Many of the genes, he saw, are involved in innate immunity, the body’s first line of defense against germs. If immune genetics affect Alzheimer’s, and if the chief suspect in Alzheimer’s (beta-amyloid) is a virtual twin of an antimicrobial peptide, maybe beta-amyloid is also an antimicrobial, Moir told Tanzi.

If so, then the plaques it forms might be the brain’s last-ditch effort to protect itself from microbes, a sort of Spider-Man silk that binds up pathogens to keep them from damaging the brain. Maybe they save the brain from pathogens in the short term only to themselves prove toxic over the long term.

Tanzi encouraged Moir to pursue that idea. “Rob was trained [by Marshall] to think out of the box,” Tanzi said. “He thinks so far out of the box he hasn’t found the box yet.”

Moir spent the next three years testing whether beta-amyloid can kill pathogens. He started simple, in test tubes and glass dishes. Those are relatively cheap, and Tanzi had enough funding to cover what Moir was doing: growing little microbial gardens in lab dishes and then trying to kill them.

Day after day, Moir and his junior colleagues played horticulturalists. They added staph and strep, the yeast candida, and the bacteria pseudomonas, enterococcus, and listeria to lab dishes filled with the nutrient medium agar. Once the microbes formed a thin layer on top, they squirted beta-amyloid onto it and hoped for an Alexander Fleming discovery-of-penicillin moment.

How an outsider in Alzheimer’s research bucked the prevailing theory — and clawed for validation. Stat News