Biomolecular machines

[rwenzori]

You're more likely to get others to read your posts if you post links with a brief summary in your own words. No one bothers to read your long posts as currently posted.

 

[Phronesis]

Not a single one of the 10, 000+ views actually read anything? Ruheaally. No ways rainman, you must be a freakin genius to know that... oh wait :erm:.

 

[rwenzori]

Not a single one of the 10, 000+ views actually read anything? Ruheaally. No ways rainman, you must be a freakin genius to know that... oh wait :erm:.

OK! All those who read all the detail of TelePhrone's quotemines say "aye", those who couldn't be bothered say "nay".

Neigh.

 

[Phronesis]

Go troll somewhere else. BTW, I am not TelePhrone (probably one of your or your lacky's sock puppets).

 

[rwenzori]

Go troll somewhere else. BTW, I am not TelePhrone (probably one of your or your lacky's sock puppets).

My sockpuppet old boy, mine.

 

[TelePhrone]

Neigh.

 

[BCO]

OK! All those who read all the detail of TelePhrone's quotemines say "aye", those who couldn't be bothered say "nay".

Neigh.

You see? It's easy! All you have to do is ignore anything that contradicts your theory, nitpick others' arguments, force them to explain themselves, accuse them of lying, accuse them of conspiring against the truth, exhaust them with dumps of links or citations, repeat yourself, and compare yourself to Galileo, because he had problems convincing the orthodoxy too.

From the handbook.

 

[Phronesis]

Awesome. The troll count from the usual pointless posse rises. Tell you pointless trollies what, why don't you create a separate thread where everyone can vote.

Just to remind the usual pointless trolls... again:
The purpose of the thread is to lump together all the interesting discoveries regarding the intracellular biomolecular machinery that are crucial for life to exist. Feel free to post interesting discoveries and perhaps describe the functionality of the intracellular biomolecular machines.

 

[Phronesis]

Biomolecular Machines.... Tha Lab version

More videos:
1) Ribosome
2) Accurate Scientific Visualizations of the T4 bacteriophage infection process and replication.

This site has among the best high quality biomedical animations.

 

[HapticSimian]

Walls of text =

And no, phrony, you don't need to be a genius to know that nobody reads through your glorious dissertations - the glaring lack of comments is enough of an indicator.

If you feel its your duty to edjumacate us, post a description with perhaps an excerpt or two, along with a link & we'll 'clicky' if we're interested. As your posts are currently constructed I can guaran-damn-tee you just about nobody gives them a second look...

 

[rwenzori]

Just to remind the usual pointless trolls... again:
The purpose of the thread is to lump together all the interesting discoveries regarding the intracellular biomolecular machinery that are crucial for life to exist. Feel free to post interesting discoveries and perhaps describe the functionality of the intracellular biomolecular machines.

Actually, I think the purpose of this thread is to proclaim "Wow! Jesus designed and made a-farking-mazing little bio-machines upon which we depend for life!".

 

[Phronesis]

Well, that explains your and the rest of your ilk's trolling. Anyway...more magnificantly complicated and optimal molecular machines...

New Images Capture Cell's Ribosomes At Work

ScienceDaily (Aug. 23, 2009) — Researchers at the University of California, Berkeley, have for the first time captured elusive nanoscale movements of ribosomes at work, shedding light on how these cellular factories take in genetic instructions and amino acids to churn out proteins.

Above is an entire ribosome with its changes in position color-coded — ranging from blue, indicating no movement, to red, indicating large movements. (Credit: Cate research group, UC Berkeley image)​

Ribosomes, which number in the millions in a single human cell, have long been considered the "black boxes" in molecular biology. "We know what goes in and what comes out of ribosomes, but we're only beginning to learn about what is going on in between," said the study's principal investigator, Jamie Cate, UC Berkeley associate professor in chemistry and molecular and cell biology, and a faculty scientist at Lawrence Berkeley National Laboratory.

The achievement, described in the Aug. 21 issue of the journal Science, could eventually lead to significant advances in the fight against human disease, the researchers said.

They point out that many infectious diseases involve ribosomal warfare between humans and our bacterial or viral invaders. Important antibiotic drugs, like spectinomycin, capreomycin and aminoglycosides, exploit the structural differences between human and bacterial ribosomes to selectively attack the bacteria. Some viruses, like polio and hepatitis C, hijack human ribosomes, forcing them to pump out proteins that are beneficial for the viruses.

"Inside the ribosome, antibiotics and viruses are using chemistry to either fight or promote disease," said Cate, who conducted the work with research specialist Wen Zhang and graduate student Jack Dunkle, both co-lead authors of the study, in his lab at UC Berkeley. "But what sort of chemistry? The short answer is that we have a lot still to learn. Once we find out, that knowledge could lead to more effective antibiotics, or new treatments against devastating diseases like hepatitis C."

In the protein manufacturing process, the genetic code - or instruction manual - for making proteins lies inside a cell's double-stranded DNA. When the cell needs to produce more proteins, the DNA unzips into two separate strands, exposing the protein code so it can be duplicated by single-stranded messenger RNA (mRNA). The mRNA dutifully delivers that code to the ribosome, which somehow reads the instructions, or "data tape," as each amino acid is added to a growing protein chain.

At the same time, other RNA molecules, called transfer RNA (tRNA), bring to the ribosome amino acids, the raw building blocks needed for protein construction.

To help elucidate the ribosome's movements as it interacts with mRNA and tRNA, the researchers used X-ray crystallography to obtain a highly detailed picture of the ribosome - a mere 21 nanometers wide - from an Escherichia coli bacterium. In addition to revealing atomic level detail, the technique allowed the researchers to capture the ribosome mid-action, a challenge because it acts fast, adding 20 new amino acids to a protein chain every second.

"Scientists used to think that the ribosome made a simple two-stage ratcheting motion by rotating back and forth as it interacts with mRNA and tRNA," said Cate, who is also a member of the California Institute for Quantitative Biomedical Research (QB3) at UC Berkeley. "What we captured were images of the ribosome in intermediate stages between the rotations, showing that there are at least four steps in this ratcheting mechanism."

"We suspect that the ribosome changes its conformation in so many steps to allow it to interact with relatively big tRNAs while keeping the two segments of the ribosome from flying apart," said Cate. "It's much more complicated than the simple ratcheting mechanism in a socket wrench."

Cate said that while this study marked a major accomplishment in cracking open the "black box" of ribosomal function, there are far more details yet to be revealed. Advances in imaging techniques over the next decade should allow researchers to go beyond the snapshots taken in this study to high-resolution movies of a ribosome's movements, he said.

"I'm looking forward to producing a movie of a ribosome with enough resolution and enough frames per millisecond that we can see what is happening at a molecular level," said Cate. "It would be great to watch and really understand how the ribosome makes a protein, how antibiotics interfere with a bacterial ribosome, or why a strand of genetic code in a hepatitis C virus is so effective at hijacking a human ribosome. We still have a long way to go, but we're working hard."

This research was supported by the National Institutes of Health and the U.S. Department of Energy.

Here is a movie, but the above information suggests the movie might be a bit outdated.. due to "It's much more complicated than the simple ratcheting mechanism in a socket wrench."

Ribosome movie

 

[Phronesis]

More marvelous machines...

New Research Supports Model For Nuclear Pore Complex

ScienceDaily (Aug. 29, 2009) — To protect their DNA, cells in higher organisms are very choosy about what they allow in and out of their nuclei, where the genes reside. Guarding access is the job of transport machines called nuclear pore complexes, which stud the nuclear membrane. Despite these gatekeepers’ conspicuously large size (they are made of 30 different proteins), they have proved largely inscrutable to researchers over the years. But bit by bit, scientists are learning how these machines work.

Paring the pore. A new model of how the nuclear pore complex might work suggests that an interaction between two proteins -- key elements of the yellow ring pictured above -- link together, forming a flexible fence around the pore's opening. (Credit: Joseph Alexander, Erik Debler and Andre Hoelz)​

 

[Phronesis]

An exquisitely tuned mechanosensory system...

Dividing Cells 'Feel' Their Way Out Of Warp

ScienceDaily (Sep. 10, 2009) — Every moment, millions of a body's cells flawlessly divvy up their genes and pinch perfectly in half to form two identical progeny for the replenishment of tissues and organs — even as they collide, get stuck, and squeeze through infinitesimally small spaces that distort their shapes.

Cytokinesis Feedback: Screen shot of a video showing how dividing cells "feel" their way out of warp. (Credit: Johns Hopkins Medicine)​

Now Johns Hopkins scientists, working with the simplest of organisms, have discovered the molecular sensor that lets cells not only "feel" changes to their neat shapes, but also to remodel themselves back into ready-to-split symmetry. In a study published September 15 in Current Biology, the researchers show that two force-sensitive proteins accumulate at the sites of cell-shape disturbances and cooperate first to sense the changes and then to resculpt the cells. The proteins — myosin II and cortexillin I — monitor and correct shape changes in order to ensure smooth division.

"What we found is an exquisitely tuned mechanosensory system that keeps the cells shipshape so they can divide properly," says Douglas N. Robinson, Ph.D., an associate professor of Cell Biology, Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine.

More quality control systems.... biasing future evolutionary trajectories.

Evolution Coup: Study Reveals How Plants Protect Their Genes

ScienceDaily (Sep. 10, 2009) — Unlike animals and humans, plants can't run and hide when exposed to stressful environmental conditions. So how do plants survive? A new Université de Montréal study, published in the journal Proceedings of the National Academy of Sciences, has found a key mechanism that enables plants to keep dangerous gene alterations in check to ensure their continued existence.

"We've discovered a new pathway that plants use to protect their genes against dangerous alterations that could also allow some useful mutations to occur," says Normand Brisson, a Université de Montréal biochemistry professor who made his discovery with graduate students Alexandre Maréchal and Jean-Sébastien Parent.

"Such mutations played an important role in the evolution of plants with high nutritional value, resistance to disease and harsh climate that are so important to modern agriculture," adds Dr. Brisson. "Our results open new research avenues for the study of similar mechanisms of gene repair in humans that might be important for human evolution, our responses to stress and the prevention of devastating diseases."

How do plant genes mutate?

All living things are constantly exposed to stressors that can provoke gene mutations, yet if uncorrected such mutations can have disastrous consequences such as the development of cancers in humans or cell resistance to cancer-fighting drugs.

Cells have evolved a battery of mechanisms to correct mutations, including recently discovered strategies that can also modify the number of copies of individual genes. These corrective mechanisms have attracted a lot of scientific interest since they could play a key role in species evolution. For example, while chimps and humans have almost identical genes, differences present in the number of copies of individual genes could account for distinctions between these species.

Dr Brisson suspected that a protein family he has studied for years, called the "Whirlies" (because of their peculiar structure similar to a whirligig) might be important to protect against mutations in plant cells – specifically in the chloroplast – the engine of photosynthesis that allows plants to transform carbon dioxide into sugar and expel the oxygen we breathe.

Working with his students and Biochemistry Professor Franz Lang, they showed that Whirlies are key to preventing major rearrangements of genes that could result in the creation of multiple gene copies. The discovery is important, since the number of copies of a gene must be kept scrupulously in balance with other genes so they can function correctly together.

Even though gene multiplication can be thought of as detrimental, such multiplication can be an important adaptation to stressors and so keeping such mutations in check must be balanced against creating mutations that may actually help living things survive in changing conditions.

"As the effects of climate change and industrial pollution cause increasing concern for human health, we might overlook how increases in temperature and pollutants affect the plants we depend on for our survival,'' stresses Dr. Brisson. "These rapid changes in environmental conditions all cause great stress on crops, trees and wild plants and could have further unforeseen effects on their genes."

 

[rwenzori]

Creationist claim CI131 is of relevance to this whole thread:

In every case where a machine's origin can be determined, it is the result of intelligent agency. (A machine is a device for transmitting or modifying force or energy.) Out of billions of observations, there are no exceptions. It should be considered a law of nature that machines, including those in living organisms, have an intelligent cause.

 

[Phronesis]

Back in the "non-tinfoil hat" real world, people just want to know and figure out how biomolecular machines in cells work. You seem to be as irrelevant as ever. Shame. But if it makes you sleep better at night to make up and burn straw men.... so be it.

 

[Phronesis]

Threading machines:
Motor Mechanism for Protein Threading through Hsp104

The protein-remodeling machine Hsp104 dissolves amorphous aggregates as well as ordered amyloid assemblies such as yeast prions. Force generation originates from a tandem AAA+ (ATPases associated with various cellular activities) cassette, but the mechanism and allostery of this action remain to be established. Our cryoelectron microscopy maps of Hsp104 hexamers reveal substantial domain movements upon ATP binding and hydrolysis in the first nucleotide-binding domain (NBD1). Fitting atomic models of Hsp104 domains to the EM density maps plus supporting biochemical measurements show how the domain movements displace sites bearing the substrate-binding tyrosine loops. This provides the structural basis for N- to C-terminal substrate threading through the central cavity, enabling a clockwise handover of substrate in the NBD1 ring and coordinated substrate binding between NBD1 and NBD2. Asymmetric reconstructions of Hsp104 in the presence of ATPS or ATP support sequential rather than concerted ATP hydrolysis in the NBD1 ring.

First a little background detail about this machine:
1) Amyloid aggregates are protein and carbohydrate aggregates that form as a result of protein misfolding or incorrect protein degradation.
2) This machine threads these aggregates and mechanically perform its specialized disaggregation function by converting chemical energy (ATP) into mechanical movement.

(From Wendler et al., 2009)
Figure 1. Cryo-EM Reconstructions of Hsp104N728A in the Presence of ATPgS, ATP, and ADP
(A) (Upper row) Class averages generated from the final data set obtained by multivariate statistical analysis in IMAGIC, containing an average of 15 images per
class. (Lower row) Corresponding reprojections of the 3D structures.
(B) Three-dimensional reconstructions of Hsp104N728A in the presence of ATPgS (blue), ATP (green), and ADP (yellow) as side view (upper row) and cut-open side view (lower row). Surface views show the density rendered at a threshold accounting for a molecular mass of 612 kDa. Red areas of the cut surfaces indicate highdensity core regions. Measurements are given in A ° .

(From Wendler et al., 2009)
Figure 2. Analysis of Nucleotide-Dependent Domain Movements​

From the article:

Conclusions
The rotations of the Hsp104 AAA+ domains qualitatively resemble those of the RecA-like gene4 helicase (Singleton et al., 2000), suggesting a conserved mechanism of ATP hydrolysis that is directed by the coiled-coil insertion in Hsp104NBD1to perform its specialized disaggregation function. The large domain movements upon ATP binding and hydrolysis in NBD1 strongly suggest a peristaltic mechanism of substrate threading from the N- to C-terminal side of the complex. Furthermore, we postulate that interdependent actions of NBD1 and NBD2 coordinate substrate translocation, ensuring continuous substrate handover during disaggregation. Our asymmetric reconstructions exclude a concerted hydrolysis in the AAA+ rings, suggesting instead that the observed intersubunit cooperativity generates a sequential firing order. These structural and biochemical results extend and validate the model of Hsp104 structure and function and provide mechanistic information about Hsp104’s disaggregative AAA+ motor activity.

 

[rwenzori]

“There are structures in the cell that don’t just resemble humanly built machines-they actually are machines in every sense of the word.” — William Dembski, Five Questions a Darwinist Would Rather Dodge, 2004

“Every sense of the word?” We don’t see a lot of equivocation or restraint in any of the above statements. But does Dembski really believe that certain cellular structures are machines in “every sense of the word?” Of course not. He wants his reader to take from this comment the sense that for him is most important, that these things had to have been transcendentally designed. Does Wells believe that calling a centriole a turbine (rather than simply noting that the centriole acts like a turbine) is an act of rigorous scientific observation? How could he? A “turbine” is a specific man-made device. Regardless of the degree to which centrioles act like turbines they cannot be said to “actually be turbines” unless one is proposing either that centrioles are designed and built by humans, or that the word “turbine” has no specific meaning. It is semantic sophistry. It is partisan rhetoric, not science. Wells clearly hopes that this suggestive terminology will communicate the need for his “designer.”

From this link - Very Like a… Machine? - Robert Camp -November 15, 2005.

 

[Phronesis]

A machine is a machine is a machine:

A machine performs a function and for it to be assembled, the following criteria need to be met.
Availability:
The parts needed for a machine to function need to be available.

Synchronization:
The availabaility of these parts need to be synchronized so that they are all present at the time the machine needs to function.

Localization:
The parts must be made available at the same site of the construction of the machine. Not at the same time necessarily, but at least at the same site at the time they are needed.

Interface compatibility:
The parts must be mutually compatible and capable of mutually interacting in a proper way.

Coordination:
The above four criteria are useless if the parts are not coordinated in the right way.


Biomolecular machines fit these criteria. Live with it.

 

[rwenzori]

A machine is a machine is a machine:

<snip twaddle>


Biomolecular machines fit these criteria. Live with it.

Nope. The word "machine" in your context is a convenient metaphor. The article I quoted in turn quotes this rather well-put paragraph:

“...let us not play into the hands of ID propagandists. For instance, be careful about using teleological words to describe biological entities in our teaching and writing. Calling cells “machines that do X” or describing biological structures as “well designed to do Y” will be duly cited in ID propaganda as one more biologist-supporting design.” — Raff, Stand up for evolution, Evolution and Development, 2005

Rather a good Ogden Nash couplet starts the article too LOL! You do know Ogden Nash, don't you, Phroners - or is he a bit too "cultural" for you?