RNAS

Dendrogramma is a monotypic genus of siphonophore

… identified in 2014 from a collection of specimens gathered in 1986. Although specimens were at first identified as two species, D. enigmatica and D. discoides, these were later shown to represent varieties of a single species.

When Dendrogramma was first discovered, it was speculated that the genus could not be classified into any existing phylum. However, examination of RNA material identified it as a siphonophore in 2016. The specimens are presumed to represent parts (bracts) of a larger organism whose entire morphology is unknown.

This diagram, depicting the holotype, was included in the article which first described Dendrogramma.

Photograph: Jean Just, Reinhardt Møbjerg Kristensen, and Jørgen Olesen

(via: Wikipedia)

ART OF THE CELL: RNA Polymerase GIF

In Autumn, the proteins in our cells, change colors and put on a fantastic display before they flutter softly to the ground… no wait, that’s leaves. Nonetheless, this RNA polymerase sports the latest fall colors, inspired by the view from my windows. RNA Polymerases create strands of RNA from a DNA template in the nucleus. The RNA can go on to be used in the process of protein translation outside the nucleus. Sadly, cellular proteins are too small to actually have any color at all; the wavelengths of visible light are much larger, but at least we don’t have to rake them.

Nucleic Acids

Nucleic acids are the “genetic software” of the cell, allowing organisms to pass on their complex components to the next generation. You might know them better as DNA (deoxyribonucleic acid) or RNA (ribonucleic acid): the macromolecules responsible for storing and transmitting hereditary information. They’re the reason you have blonde hair, or long fingers, or a gigantic nose. Without them, no organism could produce offspring, so they’re essential for all life.

Nucleic acids are made up of a chain of monomers called nucleotides, which are in turn made up of five-carbon sugars, a nitrogenous base, and one or more phosphate groups. That might seem like an extra level of complication, but we need to know this to understand their structure.

Consider, for example, a DNA molecule:

The two strands running down on either side are called the molecule’s “sugar phosphate backbone”, which are connected in the middle by nitrogenous bases that pair up to the adjacent strand.There are four kinds of bases: Adenine and Guanine, which are purines, and Cytosine and Thymine, which are pyrimidines. In RNA, Thymine is replaced with Uracil (a pyrimidine). Purines have two rings and pyrimidines have one ring, so the groupings just refer to structure.

(Source)

The bases are almost always shortened to A, G, C, T & U. Their order determines how life is built—they encode a sequence of amino acids, which instruct how proteins are built. We’ll learn more about later.

Nitrogenous bases are hydrophobic, meaning they hate water. This is crucial to the structure of the DNA, because the strands are oriented so the bases face each other rather than the outside world, protecting them from water. The bases pair together using hydrogen bonds—purines always pair with pyrimidines, so A pairs with T (U in RNA), and C with G.  In any given DNA molecule, the amount of A equals the amount of T, and the amount of C equals the amount of G. This is important because it maintains a uniform diameter for the helix of DNA.

The person who realised this equality was Austrian biochemist Erwin Chargaff, and he was a contemporary of American biologist James Watson and English physicist Francis Crick, who you might have heard of. In 1953, they were the first to publish the spiralling, double-helix structure of DNA. (See my article on Rosalind Franklin for the reason I’m not a fan of Watson and Crick.)

DNA strands have a polarity, meaning they have a direction—strands are always synthesised from the 5’ (said “five prime”) end to the 3’ end. I’ll talk a whole lot more about how this happens later on. The important thing to know now is that when two strands are connected in a DNA molecule, they run antiparallel–in opposite directions.

So, what about an RNA molecule?

For starters, DNA is located in a different place to RNA:

RNA only has a single strand, and it’s made from a different sugar: ribose instead of deoxyribose. Basically, this means it has one more OH group. RNA also has a completely different function. While DNA is the blueprint for life, RNA is the guy who actually gets things done. Different types of RNA are specialised for different functons: mRNA (messenger RNA) carries the blueprints between DNA and ribosomes in order to make proteins; rRNA (ribosomal RNA) essentially makes up the ribosomes; and tRNA (transfer RNA) carries amino acids into the ribosome for synthesis into proteins.

In summary: nucleic acids are made up sugars, phosphate groups, and nitrogenous bases, and their function is to encode, transmit, and express hereditary information. Next article, we’ll take a look at how scientists learned that nucleic acids are the genetic material of life.

Body images sourced from Wikimedia Commons

Further resources: Structure of Nucleic Acids at Educationportal

Structural differences between DNA and RNA.

DNA, or deoxyribonucleic acid, is like a blueprint of biological guidelines that a living organism must follow to exist and remain functional. RNA, or ribonucleic acid, helps carry out this blueprint’s guidelines. Of the two, RNA is more versatile than DNA, capable of performing numerous, diverse tasks in an organism, but DNA is more stable and holds more complex information for longer periods of time.

Biological Mechanism Passes On Long Term Epigenetic ‘Memories’

According to epigenetics — the study of inheritable changes in gene expression not directly coded in our DNA — our life experiences may be passed on to our children and our children’s children. Studies on survivors of traumatic events have suggested that exposure to stress may indeed have lasting effects on subsequent generations. But how exactly are these genetic “memories” passed on?

A new Tel Aviv University study pinpoints the precise mechanism that turns the inheritance of environmental influences “on” and “off.” The research, published last week in Cell and led by Dr. Oded Rechavi and his group from TAU’s Faculty of Life Sciences and Sagol School of Neuroscience, reveals the rules that dictate which epigenetic responses will be inherited, and for how long.

“Until now, it has been assumed that a passive dilution or decay governs the inheritance of epigenetic responses,” Dr. Rechavi said. “But we showed that there is an active process that regulates epigenetic inheritance down through generations.”

“A Tunable Mechanism Determines the Duration of the Transgenerational Small RNA Inheritance in C. elegans” by Leah Houri-Ze’evi, Yael Korem, Hila Sheftel, Lior Faigenbloom, Itai Antoine Toker, Yael Dagan, Lama Awad, Luba Degani, Uri Alon, and Oded Rechavi in Cell. Published online February 24 2016 doi:10.1016/j.cell.2016.02.057

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Post-Transcriptional Processing

•Only in the Nucleus for Eukaryotes •Primary transcript processed in 3 ways: –1. ADDition of nucleotides –2. DELETion of nucleotides –3. Modification of Nitrogenous Bases •5’ cap and 3’ Poly A tail •snRNP and the Spliceosome of Doom! –INtrons = IN nucleus –EXtrons = EXit the nucleus

DNA TECHNOLOGY

Clone Library = plasmid and replication

Polymerase chain reaction (PCR) : ‘fast’ cloning

•Heat to denature •Mix with primers, let cool = primers hybridize •Add polymerase to amplify complementary strands

Southern Blot

•1. Chop up DNA •2. Efield to spread out pieces by SIZE •3. Blot it! •4. Add Radioactive DNA or RNA Probe •5. Visualize on radiographic film  GENETIC CODE •Degenerative – more than one series of nucleotides may code for ANY A.A. •Unambigous = one series of nucleotides = one A.A. •Universal code! •START! AUG •STOP! UAA, UAG, UGA •4^3 = 64 –Ex. protein of 100 A.A. = there are 20^100 possible amino acids sequences for the protein 

Three members of crew at work on the starboard engine gantry of a Royal Navy Air Service North Sea (N.S.) type non-rigid airship during an anti-submarine patrol off the British coast circa 1918. None appear to be wearing a safety line. On the upper level the mechanic is standing next to his compartment from which he controlled the 240HP Fiat engines. On the lower level a gunner mans his gun.

Squid recode their genetic make-up on-the-fly to adjust to their surroundings

The principle of adaptation—the gradual modification of a species’ structures and features—is one of the pillars of evolution. While there exists ample evidence to support the slow, ongoing process that alters the genetic makeup of a species, scientists could only suspect that there were also organisms capable of transforming themselves ad hoc to adjust to changing conditions.    

Now a new study published in eLife by Dr. Eli Eisenberg of Tel Aviv University’s Department of Physics and Sagol School of Neuroscience, in collaboration with Dr. Joshua J. Rosenthal of the University of Puerto Rico, showcases the first example of an animal editing its own genetic makeup on-the-fly to modify most of its proteins, enabling adjustments to its immediate surroundings. The research, conducted in part by TAU graduate student Shahar Alon, explored RNA editing in the Doryteuthis pealieii squid.

“We have demonstrated that RNA editing is a major player in genetic information processing rather than an exception to the rule,” said Dr. Eisenberg. “By showing that the squid’s RNA-editing dramatically reshaped its entire proteome—the entire set of proteins expressed by a genome, cell, tissue, or organism at a certain time—we proved that an organism’s self-editing of mRNA is a critical evolutionary and adaptive force.” This demonstration, he said, may have implications for human diseases as well.

Scientists discover a new role for RNA in safeguarding human chromosome number

Molecular biologists at UT Southwestern Medical Center have identified a gene called NORAD that helps maintain the proper number of chromosomes in cells, and that when inactivated, causes the number of chromosomes in a cell to become unstable, a key feature of cancer cells.                                

Previously, genes that encode the recipe for making proteins have been implicated in maintaining the proper number of chromosomes in a cell. The NORAD gene, however, does not encode a protein. Instead, NORAD produces a long noncoding RNA, a type of molecule that was not previously known to be important in chromosome maintenance, the researchers report in the journal Cell.

“In the absence of the NORAD RNA, the number of chromosomes in cells becomes highly abnormal,” explained Dr. Joshua Mendell, Professor of Molecular Biology at UT Southwestern and a Howard Hughes Medical Institute Investigator. “This is an entirely new function for a noncoding RNA and may have implications in cancer biology since genomic instability is a hallmark of tumor cells.”

Researchers began studying this particular molecule because the RNA kicks into action after DNA is damaged; they therefore termed it Noncoding RNA Activated by DNA Damage, or NORAD.

Journal reference: Cell