#Protein Biomolecule

[kelemengabi]

Coherence octave entanglment

[unganseylike]

had my version of drunk history tonight when someone w no science background wanted a detailed description of my research whilst i was several drinks in

[science-education-technology]

What is Cryogenic Transmission Electron Microscopy or Cryo-TEM?. This is an introductory lecture about Cryogenic Transmission Electron Microscopy (Cryo-TEM) to the interdisciplinary audience. Topics including, conventional TEM imaging, negative staining, supercritical drying, and single particle reconstruction are covered in this lecture.

[scienceforthefuture]

The Four Vital Macromolecules of Biology: Structure, Differences, and Functions

Biology is an intricate tapestry of interactions and functions, with the fundamental building blocks being macromolecules. These large molecules play significant roles in almost all biological functions and processes. They are crucial for the structure, function, and regulation of the body’s tissues and organs. Let’s delve into the four primary macromolecules, exploring their differences and…

[hellsite-proteins]

Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity.

making a protein out of an explanation about proteins feels like a weird ouroboros moment, and i love it

letter sequence in this ask matching protein-coding amino acids:

PrteinsarelargeimleclesandmacrmleclesthatcmprisenermrelngchainsfaminacidresidesPrteinsperfrmavastarrayffnctinswithinrganismsincldingcatalysingmetalicreactinsDNAreplicatinrespndingtstimliprvidingstrctretcellsandrganismsandtransprtingmleclesfrmnelcatintantherPrteinsdifferfrmneantherprimarilyintheirseqencefaminacidswhichisdictatedythencletideseqenceftheirgenesandwhichsallyresltsinprteinfldingintaspecificstrctrethatdeterminesitsactivity

protein guy analysis:

this is a weird looking structure, with recognizable elements in the front half while the rest is a complete mess. we got a beta sheet, which is always neat to see! still, the whole thing is really spread out and looks ready to cause problems. i am not a religious person, but if i did believe in the concept of angering the gods, i would not still be running this blog. i don't hate this shape as much as some of the others, but that is an incredibly low bar and i still very much hate what i see

predicted protein structure:

[humancelltournament]

Propaganda!

The cell nucleus is a membrane-bound organelle found in eukaryotic cells. The cell nucleus contains nearly all of the cell's genome. Nuclear DNA is often organized into multiple chromosomes – long strands of DNA dotted with various proteins, such as histones, that protect and organize the DNA. The genes within these chromosomes are structured in such a way to promote cell function. The nucleus maintains the integrity of genes and controls the activities of the cell by regulating gene expression.

Nucleotides are organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver.

[mindblowingscience]

Hold up your hands in front of your face. For most people, they will be mirrored copies of each other: You can hold them palm-to-palm and they will match up, but you cannot superimpose them. Molecules also exhibit this handedness, or chirality. They come structured in two mirrored, non-superimposable forms. And it's a fascinating quirk of life that almost all biomolecules will only work in one of their two forms. Natural amino acids – the building blocks of proteins – are almost always left-handed, or sinistral. Natural sugars like those that make up RNA and DNA, on the other hand, are almost always right-handed, or dextral. If you replace any of these molecules with the other form, the whole system breaks down.

Continue Reading.

[mangocustard16]

Scholarly Sparks✨Part1 boo seungkwan  x reader

| synopsis: Seungkwan and Y/N have always been known for their intense rivalry in academia. They clashed in class discussions, exchanged heated arguments, and even took pleasure in getting under each other's skin. Little did they know that this passionate competition would eventually lead to something more profound.

| pairing: academic rival!seungkwan x gn!reader

| genre: fluff

| warnings: none

| w.c: 620

Seoul University's lecture hall was a battleground, and within it, Seungkwan and Y/N were the undisputed champions of academic sparring. They were two stars, equally brilliant and equally determined, shining fiercely in the intellectual firmament. The air was charged with tension whenever they crossed paths, their debates fueling late-night discussions among their peers.

Seungkwan, with his sharp wit and unyielding arguments, was the embodiment of eloquence. Y/N, equally formidable, possessed an unwavering dedication to her beliefs. Their exchanges were a symphony of opposing ideas, and their rivalry was the stuff of legend. In whispered disagreements, they challenged each other's theories, dissected each other's perspectives, and pushed the boundaries of their intellects.

As they sat in the lecture hall, their hushed dispute echoed through the air, drawing the attention of those nearby.

"The structural complexity of proteins far outweighs the significance of nucleic acids in biomolecules.", hushed Seungkwan.

Y/N interjected, "That's exactly where you're wrong, Seungkwan. Without nucleic acids, the instructions for building those intricate proteins wouldn't even exist."

"But proteins carry out the majority of cellular functions. They're the workhorses of biology!"

"True, but without nucleic acids to store and transmit genetic information, life as we know it wouldn't be possible.", Y/N argued back.

Their argument delved deeper into the world of biomolecules, each counterpoint fueling their passion for the subject.

"Biomolecules are like puzzle pieces that fit together perfectly.", said Y/N leaning back into her seat.

"I don't agree with you."

"Nobody asked you to."

As the semester progressed, Seungkwan and Y/N's intellectual rivalry only grew more fervent. However, they found themselves drawn together by their shared discontent with Professor Lee's grading practices.

"Can you believe Professor Lee's grading? It's as if he has a personal vendetta against us.", said Seungkwan almost slamming his books on the table.

"I know, right? It's like he's not even afraid to show how biased he is", Y/N agreed.

Their frustration was palpable as they sipped their coffee in a dimly lit campus cafe. A knowing glint in Seungkwan's eye hinted at a deeper connection forming.

"Maybe we should team up and expose his grading bias.", Seungkwan suggested

"You're suggesting we work together?"

"Only if you can handle it."

"Challenge accepted."

Their alliance against Professor Lee marked a turning point in their relationship. Late nights were spent dissecting rubrics, comparing grades, and strategizing their next move. With each meeting, their competitiveness evolved into camaraderie, and their disagreements turned into friendly debates.

Seungkwan had discovered Y/N's favorite study spot, a quiet corner tucked away from prying eyes. It was a prime location for focused reading, and Y/N cherished it.

Driven by a mix of mischief and curiosity, decided to stake his claim. He took up residence at her cherished spot, just to see the irritation flash across her face. Something about it made his heart beat faster.

Y/N walked into the library, her eyes narrowing as she spotted Seungkwan comfortably settled in her corner. She approached him, a mixture of annoyance and bemusement on her face.

"You're here again, in my spot?", she said.

"Just to see you annoyed.", said Seungkwan in his teasing tone.

"You're unbelievable."

Their rivalry had transcended the classroom and was now spilling into every aspect of their academic lives, including the halls of the university library.

Days turned into weeks, and the library became their battleground. Seungkwan's presence in Y/N's favorite spot was a persistent thorn in her side. She tried sitting elsewhere, but it was never the same. The thrill of their library wars added a unique dimension to their interactions.

One evening, as Y/N approached her corner only to find Seungkwan once again occupying it, she couldn't help but smile.

"You're relentless.", she said almost grinning.

"And you're stubborn. But that's what makes this so interesting.", said Seungkwan shrugging his shoulders.

Their playful banter and the unspoken challenge in their eyes spoke volumes. Their library wars had become a peculiar courtship ritual, a way of acknowledging each other's presence and pushing the boundaries of their rivalry to new heights.

As they competed for space amidst the hushed whispers of knowledge, little did they realize that they were inching closer to a truth they were yet to admit to themselves—an undeniable attraction that went beyond rivalry, a connection that was growing stronger with each exchange of words and each shared smile in the library's quiet corners.

One sunday afternoon, the campus grounds provided an unexpected backdrop for Seungkwan and Y/N's rivalry.

Y/N had decided to enjoy the rare sunny day and was engrossed in a novel while sitting under a tree, the gentle breeze ruffling the pages of her novel. Seungkwan, with a mischievous glint in his eye, couldn't resist the opportunity to challenge her even in this idyllic setting.

"You really can't escape reading, can you?"

"Seungkwan? What are you doing here?", said Y/N surprised to meet him on a sunday.

"Just thought I'd take a break from the library and enjoy some fresh air.", said Seungkwan

"Fresh air? Or just another chance to challenge me?", teased Y/N

"Both, perhaps.", chuckled Seungkwan.

Their banter had become as much a part of their interactions as their shared passion for knowledge. They fell into a comfortable rhythm, their conversations a blend of rivalry and camaraderie.

"You know, Seungkwan, you're like a persistent rain cloud that follows me around."

"I prefer to think of myself as a source of intellectual stimulation.", Seungkwan defended

Their playful arguments continued, the campus grounds providing a serene contrast to their lively exchanges. The trees overhead offered shade, the soft hum of distant conversations filled the air, and the sun cast a warm glow on the pages of Y/N's book.

"You really love reading, don't you?", he whispered.

"And you, linguistics."

"It's fascinating, isn't it? How language shapes our understanding of the world.", said Seungkwan lying down on the grass his eyes searching yours.

Their rivalry had taken on a different flavor in this tranquil setting. Amidst the open space and the beauty of nature, they found themselves sharing more than just academic challenges.

"It's strange, Seungkwan. We argue so much, yet I look forward to our debates.", Y/N admits.

"That's because it's never dull with you, Y/N."

Their conversation deepened as they discussed their academic aspirations and their dreams for the future.

As they sat on the campus grounds, the playful rivalry between Seungkwan and Y/N was juxtaposed against the peaceful surroundings. It was a moment of unexpected connection, where their competitive sparks blended with the warmth of the sun and the serenity of the campus, leaving them both with a sense that perhaps there was more to their relationship than academic competition.

<Part 2>

[materialsscienceandengineering]

Integrating small-angle neutron scattering with machine learning enhances measurements of complex molecular structures

Small-angle scattering (SAS) is a powerful technique for studying nanoscale samples. So far, however, its use in research has been held back by its inability to operate without some prior knowledge of a sample's chemical composition. Through new research published in The European Physical Journal E, Eugen Anitas at the Bogoliubov Laboratory of Theoretical Physics in Dubna, Russia, presents a more advanced approach, which integrates SAS with machine learning algorithms. Named α-SAS, the technique can analyze molecular samples without any need for extensive preparation or computing resources, and could enable researchers to gain more detailed insights into the properties of complex biomolecules: such as proteins, lipids, and carbohydrates.

Read more.

[gallifreyinstituteforlearning]

Hello! I am a molecular biologist, and I was wondering if I could get your opinion on some of my theories on Gallifreyans.

I haven't read through everything on your blog yet, but I'm working my way through it (lol). So some of this may not be quite accurate with what you have set up thus far.

Basically, I want to briefly discuss alternative splicing! Anyway, in metazoans, alternative splicing outcomes can be regulated in a time and tissue specific manner by legitimately hundreds of biomolecules such as RNA binding proteins, chromatin remodelers, hormones, etc etc. It is subject to epigenetic regulation as alternative splicing and transcription are coupled (and splicing largely occurs cotranscriptionally), so details such as DNA methylation, nucleosome positioning, histone modifications, etc can change the balance of different mRNA isoforms. This is largely because these factors will either help recruit splicing factors (or inhibit their recruitment) or because it will slow RNA Polymerase II elongation.

Onto my theories. I have been thinking for a little while that the lindos hormone can perhaps modulate splicing, triggering the production of regeneration-specific isoforms. Perhaps their bodies work so fast that isoforms promoting totipotency trigger a temporary transition away from the cells' differentiated states.

I also think it could be possible that they have some novel ability to, say, "unsplice," which humans cannot do. This could potentially allow them to use already made transcripts and then completely change them to produce unique proteins without needing to transcribe another mRNA. This could feasibly allow them to rapidly change what proteins are in each cell (perhaps quick enough that it occurs within the regeneration itself). Although, there would be some instability while now unused proteins get degraded or the splicing/unsplicing ratio stabilizes (the molding period). This would require intense regulation as well as unsplicing and resplicing would now be posttranscriptional, but I digress.

Sorry to bother you with the long post, I just had too many nerdy ideas going through my head. Thanks!

-gallifreyanhotfive

Molecular Biology: 'Unsplicing'

Oh, you thrill me with your biology talk! Molecular biology is not a speciality so apologies in advance for any limited response.

🔬 Lindos and Its Variations

Something to be covered in the new Anatomy and Physiology guide is a wider look at the role of Lindos in Time Lords, so we're hitting the nail on the head here.

Under stress, injury, or during the process of regeneration, the lindal gland significantly increases its production of the hormone Lindoneogen like a caffeine-fueled scientist, resulting in a corresponding surge in lindos cell production. There are several forms of lindos cells, including:

Lindopoetic Progenitor Cells (LPCs): Dormant cells that spring into action upon Lindoneogen stimulation.

Lindopoietic Stem Cells (LSCs): Residing in the yellow bone marrow, ready to differentiate under the guidance of Lindoneogen and the catalytic influence of artron, into ...

Lindoblasts and Phagolindotropes: Specialised cells responsible for regenerating tissue and recycling cellular components from the previous incarnation.

Haemolindocytes: Circulating cells that endow Gallifreyan blood with its regenerative properties.

💡Splicing and Lindoneogen

Lindoneogen could play a key role in alternative splicing, creating specific mRNA isoforms vital for regeneration. This implies that Lindoneogen is not just a cellular signal but also a molecular tool for crafting the necessary protein portfolio for regeneration. So Lindoneogen may trigger the production of specific mRNA isoforms that are vital for the regeneration process, which could lead to the expression of proteins that facilitate the transition of cells into a more pluripotent state.

🖇️Unsplicing

Love this idea. 'Unsplicing' as your concept presents would be particularly relevant during regeneration. It could allow cells to quickly alter their protein expression profiles without the lag of new mRNA transcription. This rapid adaptation would be pretty handy for the efficient transition of cells to suit the requirements of the new incarnation.

🔗Integrating with Lindos Cells

This concept of 'unsplicing' could be particularly prominent in the function of phagolindotropes. As these cells are responsible for consuming the previous incarnation’s cells and replacing them with new ones, their ability to 'unsplice' and rapidly change protein expression would be pretty useful. This mechanism might also support the functions of lindoblasts and haemolindocytes in tissue regeneration and blood adaptability.

🏫 So ...

The addition of splicing and unsplicing mechanisms to the lindos theory suggests a more complex and dynamic process than simple cellular proliferation and differentiation, with dynamic genetic adaptations at the molecular level highlighting the advanced biological capabilities of Gallifreyans. Good work, Batman!

More content ... →📫Got a question? | 📚Complete list of Q+A →😆Jokes |🩻Biology |🗨️Language |🕰️Throwbacks |🤓Facts →🫀Gallifreyan Anatomy and Physiology Guide (pending) →⚕️Gallifreyan Emergency Medicine Guides →📝Source list (WIP) →📜Masterpost If you're finding your happy place in this part of the internet, feel free to buy a coffee to help keep our exhausted human conscious. She works full-time in medicine and is so very tired 😴

[unganseylike]

and now, for something completely random:

i think that in every field of study or work, there are things people in that field consider to be fundamental knowledge and are shocked to find out most don't know. as an aspiring biologist, sometimes i feel more affronted by this than i should, because i assume the study of life is relevant to humans as living things ourselves. for example, i was really surprised that a lot of people i asked had never heard of archaea. it's a whole domain of life! and there's only three domains! but i can accept that bacteria are discussed all the time in medicine and the news, while archaea are non-pathogenic so even though they are super cool (and also found in your guts) they're not that relevant to most people. a year ago, i was also surprised to find that my mom didn't know what RNA is. I was like, mom the life-altering pandemic we have all experienced is caused by an RNA based virus, so you must've heard it mentioned on the news. but also, RNA is like. how we work. this briefly awakened me to the fact that many people are not familiar with the central dogma (DNA-> mRNA -> protein) that basically governs all life.

But this realization was lost to my subconscious until recently. i was at a party and chatting with my friend's boyfriend, a computer programmer. i was trying to explain my work but we of course came to a common misunderstanding that all molecular biologists are familiar with: colloquial use of the word protein is so different than its use in molbio. people think of protein and they think of it as a nutrient, i think of a gene product that serves some specific purpose. so i'm explaining the idea that we can study specific proteins, and the context of my model organism and he goes "i didn't think a bacteria could have something as complicated as a protein." at the time i was like huh thats a weird misconception and told him about the four biomolecules (i was also drunk enough that i hesitated naming all four, which i think says something lol).

but now his offhand comment is haunting me because what does he think DNA is for? DNA encodes proteins! This brought me to the realization that while most people know we have DNA and likely know that all living things have DNA, they probably don't know what purpose it physically serves. sure, they know it gets inherited and determines your eye color or whatever, and they know there are genes with a specific sequence that can be mutated and that mutations change something. It even seems like most people have heard of CRISPR. but i don't know that it's as widespread knowledge that genes encode proteins (before it is said, yes i know the central dogma is not 100% true and 1 gene= 1 protein isnt necessarily correct, but let's not get into it). Like people absolutely know DNA is inheritable information, but do they understand what this "information" actually means? Cells don't care that DNA dictates eye color, they are making enzymes and structures and transporters. Idk why this is haunting me, but maybe it's because it has clicked this common miscommunication we have around proteins is probably because people don't know the physiological purpose of DNA. And also because of course bacteria have proteins. i literally don't mean this in a superiority complex way, it's just fascinating to me that there's a broad familiarity with some aspects of molecular biology but not widespread knowledge of how they actually work...and how all living things work!

Anyway. What are things in your field that you are surprised to find most people don't know?

[science-lover33]

Exploring the Marvels of Biological Macromolecules: The Molecular Machinery of Life (Part 1)

In the captivating realm of biochemistry, biological macromolecules stand as the cornerstone of life itself. These intricately structured molecules, each with its unique role, orchestrate the complex symphony of biological processes. Let's dive deep into the world of macromolecules and unravel their astounding intricacies.

Carbohydrates, a group of organic compounds, are fundamental biomolecules in biochemistry. These compounds, composed of carbon (C), hydrogen (H), and oxygen (O) atoms, play multifaceted roles in various biological processes, acting as both an essential energy source and critical structural elements.

Monosaccharides: The Building Blocks

At the most basic level, carbohydrates are composed of monosaccharides, which are simple sugars. Glucose, fructose, and galactose are examples of monosaccharides. They serve as the fundamental building blocks from which more complex carbohydrates are constructed.

Polysaccharides: Storage and Structure

Carbohydrates manifest as polysaccharides, intricate macromolecules created by linking numerous monosaccharide units. Glycogen, found in animals, and starch, prevalent in plants, are storage forms of glucose. In contrast, cellulose, another glucose-based polysaccharide, forms the structural component of plant cell walls.

Energy Production: Glucose Metabolism

Carbohydrates' primary function within biological systems is to provide energy. Glucose, a hexose sugar, undergoes catabolic processes such as glycolysis and cellular respiration to generate adenosine triphosphate (ATP), the cellular energy currency. The controlled release of energy from carbohydrates fuels vital cellular functions.

Regulation of Blood Glucose: Hormonal Control

Maintaining blood glucose levels within a narrow range is crucial for homeostasis. Hormones like insulin and glucagon intricately regulate glucose levels, ensuring cells have a steady supply of this essential fuel source.

Structural Carbohydrates: Cellulose and Chitin

Carbohydrates also contribute to the structural integrity of cells and organisms. Cellulose, a linear polymer of glucose, forms the rigid cell walls of plants. Similarly, chitin, composed of N-acetylglucosamine units, provides structural support in the exoskeletons of arthropods and the cell walls of fungi.

Glycoproteins and Glycolipids: Molecular Signaling

Carbohydrates are often attached to proteins (glycoproteins) and lipids (glycolipids) on cell surfaces. These complex molecules participate in cell recognition and molecular signaling, which is crucial for various cellular processes, including immune responses and cell adhesion.

[demi-shoggoth]

2023 Reading Log pt 12

56. Life Between the Tides by Adam Nicholson. This book really, really wants to be High Literary Art. The author writes about tide pools and coastal organisms, but is much more interested in dissecting what these have represented in art, culture and a Jungian sense of shared humanity more than he is in the actual animals, algae and other things he encounters. Throughout the book, he builds three artificial tide pools, each time devising ways to carve rock and set up filters to catch water but exclude some organisms, and I couldn’t help but think, why? Why not find natural tide pools and observe them? Why must you put your stamp on a coastline? His whole thesis seems to be something about the beauty of how the shore is a liminal place, between land and water, where ecosystems and humans alike exist in an unstable equilibrium, and yet he feels the need to attempt to control it, and does not reflect much on the contradiction. I did not care for this book, as either a work of natural history or philosophy.

57. Spirit Beings in European Folklore 1 by Benjamin Adamah. A birthday gift from my girlfriend, @abominationimperatrix. This is one of a four part encyclopedia of European monsters—this volume focuses on Scandinavia and the British Islands. The decision to edit it into multiple volumes was made relatively late in the book’s development, and it shows—there are cross references to entries that do not appear in this book, but are in other volumes. The author is an occultist, and so plays somewhat coy with whether or not he believes in the literal existence of supernatural entities; near as I can tell from this volume, he’s a believer in the idea that they have material reality as thoughtforms created by human imagination. Putting aside that quirk (which is fairly easy to do), this is a pretty good compendium of monsters, especially but not limited to the sorts of things that would be called “fey” and “undead” in RPG terms. I do have the whole set, and am looking forward to reading the rest of them.

58. If It Sounds Like a Quack… by Matthew Hongolz-Hetling. This book is a look into “alternative medicine” grifts and cranks, following the stories of six quacks from their origins to the modern day. This modern day is the COVID era, where even the most reasonable-sounding of them goes off the deep end into conspiracy theories and anti-immigrant hysteria. The author does an excellent job of using alternative medicine as a lens to look at how consensus reality has been damaged in the United States, and there are a surprising amount of connections, both direct and indirect, between these frauds and perhaps the most successful con artist of the modern era, Donald Trump (who the book refers to exclusively as “the game show host”). The book has a light touch and is very funny throughout, which makes the ending, where he discusses how people are committing real murders in the belief that COVID vaccines are turning people into zombies, hit all the harder.

59. Remnants of Ancient Life by Dale E. Greenwalt. This is a book about biomolecules found in fossils, from the famous (like pigments found in dinosaur feathers) to the rather more obscure (using trace elements to pinpoint the affinities of conodonts and Tullimonstrum). The author is an entomologist by trade, and so is a little bit unclear about the appropriate taxonomy for other groups—an editing pass over the chapters about dinosaurs would have been useful. Perhaps the most interesting chapter is on the supposed discovery of dinosaur proteins, such as collagen and even intact blood vessels, which have been almost entirely done by the lab of Mary Schwietzer, and thus are the subject of a lot of debate and skepticism.

60. Strange Bedfellows by Ina Park. This is a book about sexually transmitted infections. It can be divided roughly in half—the first half is chapter long looks at particular topics, like the stigmatization of herpes and the possible health risks of vigorous pubic hair removal. The second half is a historical survey of the history of government investigation of sexual health, including both unethical human experiments such as at Tuskegee and Guatemala, as well as the history of contract tracing in public health offices. The author’s voice comes through strongly—she’s funny and opinionated and not at all ashamed at working in a sex related field. Mary Roach wrote one of the blurbs on the back of the book, and that seems like a pretty apt comparison.

[queenlucythevaliant]

So @keendaanmaa expressed an interest in amino acid fun facts a couple of days ago, and I’ve been thinking that it might be fun to do little informal reflections on journal articles here on my blog: basically giving a really rough summary and then connecting it to my faith. We’ll see how it goes in general. For now though, here’s a really neat article on the evolutionary origin of amino acid homochirality that I read this week!

Real quick definitions for anyone who never had to sit through an organic chem class: 

Chirality is basically whether an asymmetric molecule is right or left handed. 

Biological molecules have L (left-handed) and D (right-handed) enantiomers. An enantiomer (or you’ll sometimes hear the more general word stereoisomer) is simply a specific asymmetric molecule that can’t be turned to produce its mirror image. 

Amino acids can exist as both L and D enantiomers, but in biological systems you’ll only ever find the L enantiomers. This is called homochirality, and it can seem kinda arbitrary. 

Incidentally, the sugars that compose carbohydrates and, importantly, nucleotides, are always D enantiomers in nature. Actually, all the major biomolecules have some sort of homochirality associated with them. 

Phosphorylation is the process by which ATP, GTP, a kinase, or whatever other energy molecule/intermediary sticks another molecule with a phosphate group and energy is released. This will be important later.

Because homochirality in living organisms is ubiquitous (as far as we know) and also like I said kinda arbitrary, trying to discern why it exists is an important area of origin-of-life research. Clearly, the last universal common ancestor already exhibited this trait. So where did it come from?

This article posits that L-amino acids are favored because of the way that the relationship between amino acids and nucleotides (ie the genetic code) came about. Basically, it’s energetically favorable to use opposite enantiomers for amino acids and nucleotides because it reduces steric hinderance (atoms/groups of atoms getting in each others’ way) during the translation process from messenger RNA to amino acid sequence. Thus, there would be selective pressure in favor of homochirality. So, in essence, we were either going to end up with all L-sugars in nucleotides and all D-amino acids, or all D-nucleotides and L-amino acids as a result of stereoselection (a form of natural selection that is specific to sterioisomers.) 

This is pretty intuitive; the interesting thing is how we ended up with the latter scenario specifically. 

So the advent of phosphorylation is the evolutionary event that probably gave rise to modern nucleotides. You can also phosphorylate amino acids pretty easily, generating phosphoryl N-amino acids (aaNs). There’s a long history of experiments demonstrating that this process can occur spontaneously under reasonable prebiotic conditions. Once these nucleotides and amino acids exist, they can interact more easily to form amino acid 5′-nucleotides, autocatalytic molecules that can eventually condense to form simple proteins and RNAs. 

(Quick note to the Ken Ham crowd: I don’t think you understand the degree to which biochemical reactions occur spontaneously just because it’s energetically favorable. Our bodies have rigged the system with enzymes, but that only works because they’re creating the right energetic conditions. The exception proves the rule.)

However! It’s important to note that these reactions would be occurring on surfaces rather than in bulk solution. This changes how the molecular pieces fit together. On flat surfaces, aaNs line up under particular constraints that place polar regions in maximum contact with the surface. When nucleotides adopted the phospho-ribose backbone that characterizes them today, all these constraints would make it so that for a few amino acids, only the L-enantiomers could reasonably interact with the RNA. Thus, we get specific selection for L-amino acids and D-sugars rather than just random purifying selection in either direction. 

I picked a pretty technical article to start with, so I’m not going to go into the specific biochemistry and mathematical modeling that the researchers did to back this up, but it’s there in the article above if you want to check it out. 

And I!! Just think this is so cool!! Because like. Look. Random purifying selection is actually pretty powerful but there’s a deeper explanation here! I love molecular biology because it’s just so, so elegant. When I looked at the inner workings of a cell for the first time in seventh grade, it always seemed as though there had to be some consciousness sitting at a control panel somewhere telling all the molecules what to do and where to go. It didn’t seem possible that it could all just run off of chemistry. But it does!

God created all these crazy intricate rules for chemistry and he follows them all. He made sterics and free energy and he did it with such patience and such precision. It’s hard for humans to be both patient and precise; not so for God.

I just. Can you see why I find these processes sublime and glorious?

[cavenewstimes]

Scientists Shed New Light on the “Dark Matter” of Cellular Biology

Scientists have actually developed an unique fluorogenic probe to light up the interactions in between sugars and proteins, vital for comprehending different biological procedures and illness. Scientists at the University of Montreal’s Chemistry Department have actually produced an ingenious fluorogenic probe for examining interactions in between sugars and proteins, 2 households of biomolecules…

[jcmarchi]

Shedding new light on sugars, the “dark matter” of cellular biology - Technology Org

New Post has been published on https://thedigitalinsider.com/shedding-new-light-on-sugars-the-dark-matter-of-cellular-biology-technology-org/

Shedding new light on sugars, the “dark matter” of cellular biology - Technology Org

Scientists at Université de Montréal’s Department of Chemistry have developed a new fluorogenic probe that can be used to detect and study interactions between two families of biomolecules essential to life: sugars and proteins.

Our idea was to label sugar molecules with a chromophore, a chemical that gives a molecule its colour,” explained Cecioni. “The chromophore is actually fluorogenic, which means that it can become fluorescent if the binding of sugar with the lectin is efficiently captured. Image credit: Cecioni Lab

The findings by professor Samy Cecioni and his students, which open the door to a wide range of applications, were published in mid-October in the prestigious European journal Angewandte Chemie.

Found in all living cells

Sugar is omnipresent in our lives, present in almost all the foods we eat. But the importance of these simple carbohydrates extends far beyond tasty desserts. Sugars are vital to virtually all biological processes in living organisms and there is a vast diversity of naturally occurring sugar molecules.

“All of the cells that make up living organisms are covered in a layer of sugar-based molecules known as glycans,” said Cecioni. “Sugars are therefore on the front line of almost all physiological processes and play a fundamental role in maintaining health and preventing disease.”

“For a long time,” he added, “scientists believed that the complex sugars found on the surface of cells were simply decorative. But we now know that these sugars interact with many other types of molecules, particularly lectins, a large family of proteins.”

Driving disease, from flu to cancer

Like sugars, lectins are found in all living organisms. These proteins have the unique ability to recognize and temporarily attach themselves to sugars. Such interactions occur in many biological processes, such as during the immune response triggered by an infection.

Lectins are attracting a lot of attention these days. This is because scientists have discovered that the phenomenon of lectins “sticking” to sugars plays a key role in the appearance of numerous diseases.

“The more we study the interactions between sugars and lectins, the more we realize how important they are in disease processes,” said Cecioni. “Studies have shown how such interactions are involved in bacteria colonizing our lungs, viruses invading our cells, even cancer cells tricking our immune system into thinking they’re healthy cells.”

Difficult to detect…until now

There are still many missing pieces in the puzzle of how interactions between sugars and lectins unfold because they are so difficult to study. This is because these interactions are transient and weak, making detection a real challenge.

Two of Cecioni’s students, master’s candidate Cécile Bousch and Ph.D. candidate Brandon Vreulz, had the idea of using light to detect these interactions. The three researchers set to work to create a sort of chemical probe capable of “freezing” the meeting between sugar and lectin and making it visible through fluorescence.

The interaction between sugar and lectin can be described using a “lock and key” relationship, where the “key” is the sugar and the “lock” is the lectin. Chemists have already created molecules capable of blocking this lock-and-key interaction, and can now to identify exactly what sugars are binding to lectins of high interest to human health.

“Our idea was to label sugar molecules with a chromophore, a chemical that gives a molecule its colour,” explained Cecioni. “The chromophore is actually fluorogenic, which means that it can become fluorescent if the binding of sugar with the lectin is efficiently captured. Scientists can then study the mechanisms underlying these interactions and the disturbances that can arise.”

Cecioni and his students are confident their technique can be used with other types of molecules. It may even be possible to control the colour of new fluorescently labelled probes that are created.

By making it possible to visualize interactions between molecules, this discovery is giving researchers a valuable new tool for studying biological interactions, many of which are critical to human health.

Source: University of Montreal

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