{"id":2162,"date":"2011-05-03T18:51:06","date_gmt":"2011-05-03T18:51:06","guid":{"rendered":"http:\/\/thetravellerslastjourney.com\/shai\/?p=2162"},"modified":"2019-08-25T03:51:47","modified_gmt":"2019-08-25T03:51:47","slug":"the-inner-life-of-a-cell","status":"publish","type":"post","link":"https:\/\/thetravellerslastjourney.com\/shai\/2011\/05\/03\/the-inner-life-of-a-cell\/","title":{"rendered":"The Inner Life of a Cell"},"content":{"rendered":"

Editorial notes<\/strong>: This scientific analysis was found as a ‘draft’ entry in Everything2.<\/sub> It was last updated on 03\/05\/2011.<\/em><\/span><\/p>\n

In 2006 Harvard presented a short movie they’d contracted called\u00a0The Inner Life of a Cell<\/em>. This eight and a half minute production was a\u00a03D\u00a0animation of (ostensibly) what a cell could look like on an\u00a0atomic\u00a0level*<\/sup><\/a>.<\/p>\n

\n

This forms the final chapter of my three-part introduction to molecular biology. If you haven’t read the other three parts yet, perhaps you’d like to do so now. If you haven’t\u00a0and<\/em>\u00a0you’re not inclined yet, go ahead and watch the movie, maybe that\u00a0John Williamsesque score will inspire you.<\/p>\n

The following is an explanation of what goes on in the video. It’s not thorough. Its purpose is to help contextualise some of the things I’ve written in the previous parts. If you already have a molecular biology background you might want to skip down past the next bit to the bottom where I’ll have a short critique of the film.<\/p>\n

The previous chapters of this introduction had introduced\u00a0atoms and their relation to proteins and described\u00a0the relationship of DNA to RNA to proteins<\/a>.<\/p>\n

How to coordinate this? Some of you might want to watch the film in its entirety first. Try and get a high-quality version and watch it in full screen. Note that there are different versions out there, some with the original music, some 3minutes (preview), some the full 8.5minutes, and some with the original commentary (which is technical). Presumably,\u00a0your local video website\u00a0has them all. Afterwards, I’d recommend opening this page up and also the video in a small window on top of this page. It might be helpful to know that there are\u00a0websites\u00a0that download youtube films onto your computer, although you’ll need an\u00a0appropriate program\u00a0to read them. Most people enjoy the one with the music.\u00a0Please don’t ask me for a link \ud83d\ude09<\/a><\/small><\/p>\n

\n

Plot summary: An\u00a0immune cell<\/a>\u00a0is needed to attack some disease. It travels through the bloodstream until it gets a signal to stop. It now needs to crawl in between the blood vessel walls to get to the infected area. To do this the cell makes new proteins and sends them out to the outside of the cell where they can grab onto the blood vessel walls.<\/p>\n

The times listed below are approximate and vary with videos. My reference video was 8:12 minutes long (I used the one with the voiceover).<\/small><\/p>\n

0:00-0:54 \u2013 A white blood cell crawls along the blood vessel wall with grabbing proteins<\/h4>\n

The film starts off with blood rushing through a\u00a0blood vessel<\/strong>\u00a0(e.g. a vein or artery) and a\u00a0white blood cell\u00a0trudging along the vessel wall. The main force moving the white blood cell or\u00a0leukocyte<\/strong>\u00a0\u2013 which is an immune cell responsible for attacking\u00a0threats<\/a>\u00a0\u2013 is obviously the blood flow around it. But leukocytes are generally not in a rush, and when not on the job are just patrolling.<\/p>\n

We soon see\u00a0grabbing proteins<\/a>\u00a0sticking out of the leukocyte (purple) which reach onto proteins sticking out of the blood vessel wall (yellow). This is one way the cell is holding onto the wall as it rolls along.<\/p>\n

The cell has heaps of little\u00a0bumps<\/a>\u00a0where it concentrates these grabbing proteins, and the grabbing proteins are designed to let go and grab on as needed. Continuously. All the time. Countless of them.<\/p>\n

0:54-1:54 \u2013 The cell receives a signal that there\u2019s inflammation nearby<\/h4>\n

A bit of background is needed for this scene beyond what I\u2019ve given previously, but only briefly: the actual wall of human cells is called a\u00a0membrane<\/strong>. The membrane is made up of\u00a0phospholipids<\/strong>\u00a0which are molecules that are sperm shaped with the head sticking outwards and the tail on the inside. The membrane is\u00a0double layered. They show a cross-section in the film which makes this obvious.<\/p>\n

One way the cell carries proteins around the membrane is on\u00a0rafts<\/strong>. These are part of the membrane, but their molecules are less flexible, and so can stick together and essentially float through the membrane sea of molecules, while carrying their loads. There\u2019s aren\u2019t important for the story… yet.<\/p>\n

Now, something important happens. This spot in the blood vessel is near a site of inflammation, and so needs the leukocyte to exit and do its job. It tells the leukocyte this message by presenting special inflammation molecules to it. In the video, we see this as the little\u00a0yellow molecule<\/a>\u00a0presented by the\u00a0orange protein<\/a>\u00a0to the receptor protein on the leukocyte surface. This sets off a whole host of other events on the inside of the cell \u2013 which is where we\u2019ll be going shortly \u2013 but keep in mind that this is happening all over the leukocyte\u2019s surface, not just in this one spot. In any event, it will result in the leukocyte making a \u201cdecision\u201d to go to the site of inflammation.<\/p>\n

1:54-2:13 \u2013 News of the inflammation is conveyed to the inside of the cell<\/h4>\n

As soon as we get inside the cell you can see the cell membrane from the inside \u2013 including a raft floating off, and also parts of the cell\u2019s skeleton \u2013 called\u00a0cytoskeleton<\/strong>\u00a0\u2013 which are the various long structural protein-links you see. Important now is to keep in mind that when the inflammatory signal was received on the outside, it causes the receiving protein to change on the inside. The receiving protein is\u00a0transmembrane, meaning that it spans the membrane width.<\/p>\n

Note that we don\u2019t actually get to see how that signal is conveyed, but most likely the inside of the receiving molecule modified some proteins it was associated with, and those went off to do other things, and so forth.<\/p>\n

2:13-4:12 \u2013Seeing the highways which will serve the cell\u2019s response<\/h4>\n

Now we get to focus on some of the cytoskeleton types. I won\u2019t go into them, but you see both those that sit on the surface and those that go deep into the cell.<\/p>\n

Cytoskeletons are built in a modular manner and are extended with lego-like protein units, and we get to see some of these built and taken apart.<\/p>\n

An important type of cytoskeleton \u2013 for this video \u2013 are\u00a0microtubules<\/strong>\u00a0which are seen as the green tube structures. They\u2019re far sturdier than the previous cytoskeletons we saw, and are used as highways for carrying things inside the cell.<\/p>\n

The cell has received word of the inflammation and will need to make and carry new proteins to the membrane as part of its response. One way it can carry proteins is by making\u00a0small balls of the membrane<\/a>\u00a0and putting the proteins of interest inside them. These cargo balls can be attached to a powerful\u00a0protein motor unit<\/a>, which slowly drags it along the microtubule.<\/p>\n

4:12-4:35 \u2013 Seeing some of the major players the cell will use to response<\/h4>\n

We also get to see some other areas of the cell which are affected by the cytoskeleton, including:<\/p>\n

Mitochondria<\/strong>\u00a0\u2013 the energy factory of the cell (seen as the slug-like structure) \u2013 the leukocyte might need to step up energy production in preparation for dealing with inflammation.<\/p>\n

Endoplasmic reticulum<\/strong>\u00a0and\u00a0Golgi<\/strong>\u00a0\u2013 factories for modifying protein (seen as a collection of blobs in the distant right around the same time we see the centrosome) \u2013 these will be involved in modifying the many new proteins that will be made to deal with the inflammation.<\/p>\n

Centrosome<\/strong>\u00a0\u2013 the place from which microtubules start out (seen as the sphere from which the microtubule emanate) \u2013 the cell may need to send out new microtubule as highways for transporting some of the new protein cargos.<\/p>\n

4:35-5:38 \u2013New proteins made to deal with an inflammatory response<\/h4>\n

The cell has received the signal and new instructions for protein manufacture have been copied from the DNA in the form of mRNA (messenger RNA). The mRNA is seen being sent out of the DNA\u2019s housing where it forms a loop and is read by a (green) group of proteins (ribosome<\/strong>) into a protein.<\/p>\n

There will be instructions for all sorts of protein, varying from structural proteins, to signalling proteins, surface receivers, to attacking proteins for dealing with any possible threats.<\/p>\n

The leukocyte needs some of the proteins for activities inside the cell, but others it will need on the surface or even outside. For these, the ribosome gets hold of the mRNA and then attaches to the endoplasmic reticulum (which we saw above) and makes the protein straight into it.<\/p>\n

5:38-6:32 \u2013 Select proteins are designed to be sent to the surface<\/h4>\n

As just stated, some of the proteins will be needed to be placed into cargo balls and taken to the surface. The endoplasmic reticulum sorts these and packs them accordingly. We see them bud off here and then carried off.<\/p>\n

Before arriving at the surface, some of these cargo proteins will need to be adjusted, and so the cargo is taken to the Golgi (which is similar to the endoplasmic reticulum) where it undergoes various layers of sorting and modification. By \u201cmodification<\/a>” I mean that small molecules are removed or added.<\/p>\n

Once that\u2019s done, the cargo can continue to the surface.<\/p>\n

6:32-6:42 \u2013 The new proteins reach the surface membrane<\/h4>\n

When the cargo reaches the cell membrane, it literally\u00a0fuses<\/a>\u00a0with it. The proteins which were inside the cargo are released outside the cell, while those that were part of the cargo\u2019s membrane are now part of the cell\u2019s membrane.<\/p>\n

6:42-8:00 \u2013 the new protein is responsible for grabbing tight and stopping the cell\u2019s motion<\/h4>\n

Do you remember at the beginning when the cell received the inflammation molecule news? That caused the receptor molecule to change its\u00a0shape<\/a>\u00a0and cause other proteins and molecules inside the cell to signal. That resulted in all sorts of things, including the production of new proteins.<\/p>\n

It also resulted in processes which made new rafts on the membrane and caused specific proteins to cluster inside them.<\/p>\n

The new proteins that the cell just made are clustered into rafts where they\u2019re ready to do their job. They look similar to the grabbing proteins we saw at the movie\u2019s beginning, but they\u2019re slightly different. These proteins are much stronger and don\u2019t let go. They stop the leukocyte where it is so that it can squeeze itself in between the blood vessel walls.<\/p>\n

The entire pathway we saw was just one small part of what made the leukocyte stop. And countless other activities are involved in each of the countless steps which make it possible for\u00a0a leukocyte to get out of the bloodstream<\/a>, and eventually reach the site of inflammation and deal with what it finds there.<\/p>\n

Fin.<\/h4>\n

I could comment further on what we just saw, but I’d hope I don’t need to. I also hope that this write-up achieved some of\u00a0its intentions<\/a>. I would appreciate any feedback on what it may not have achieved, and would also be interested to hear whether there was some process you saw which was\u00a0too<\/em>\u00a0incredible which I might be inclined to write-up on… Thanks.<\/p>\n

\n

*<\/sup><\/a>\u00a0A very short critique, really just meant to highlight ONE MAJOR SIGNIFICANT limitation of the film which can be misleading. Everything in the movie floats in the right direction to be helpful. Chaos doesn’t seem to an issue. Essentially, this is what a cell would look like if it was designed by a\u00a0watchmaker<\/a>. If I may be\u00a0gnomic<\/a>\u00a0at last, then I would remind you that biology is\u00a0order<\/a> through\u00a0chaos<\/a>.<\/small><\/p>\n","protected":false},"excerpt":{"rendered":"

Editorial notes: This scientific analysis was found as a ‘draft’ entry in Everything2. It was last updated on 03\/05\/2011. In 2006 Harvard presented a short movie they’d contracted called\u00a0The Inner Life of a Cell. This eight and a half minute production was a\u00a03D\u00a0animation of (ostensibly) what a cell could look like on an\u00a0atomic\u00a0level*. This forms […]<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[159,206,204,197,16],"tags":[],"metadata":[101],"class_list":["post-2162","post","type-post","status-publish","format-standard","hentry","category-all-posts","category-biology","category-everything2","category-film-review","category-science","metadata-editor_notes"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack-related-posts":[{"id":1779,"url":"https:\/\/thetravellerslastjourney.com\/shai\/2011\/05\/03\/defining-molecular-biology-2\/","url_meta":{"origin":2162,"position":0},"title":"Defining molecular biology","author":"Pala","date":"May 3, 2011","format":false,"excerpt":"Editorial notes: This Essay was found as a 'draft' entry in Everything2. It was last updated on 03\/05\/2011. To\u00a0me,\u00a0molecular biology is that part of\u00a0biology\u00a0that is concerned with the\u00a0molecules\u00a0that make up biological systems. It is concerned with those molecules' lives, and the way they interact with each other. It manipulates molecules\u2026","rel":"","context":"In "All Posts"","block_context":{"text":"All Posts","link":"https:\/\/thetravellerslastjourney.com\/shai\/all-posts\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":979,"url":"https:\/\/thetravellerslastjourney.com\/shai\/2016\/12\/19\/developmental-biology-on-one-leg-or-a-collaboration-of-memories-and-allegorical-hand-waving\/","url_meta":{"origin":2162,"position":1},"title":"Developmental biology on one leg; or, a collaboration of memories and allegorical hand-waving","author":"Pala","date":"December 19, 2016","format":false,"excerpt":"There should be no doubt in the mind of the reflective sapiens that their biological basis is the least likely and most astounding object within all that they have known or imagined. But why? I force the reader to expand this sense of astonishment by (before leaping into a strict\u2026","rel":"","context":"In "All Posts"","block_context":{"text":"All Posts","link":"https:\/\/thetravellerslastjourney.com\/shai\/all-posts\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1757,"url":"https:\/\/thetravellerslastjourney.com\/shai\/2010\/12\/12\/thinking-about-atoms-in-biology-2\/","url_meta":{"origin":2162,"position":2},"title":"Thinking about atoms in biology","author":"Pala","date":"December 12, 2010","format":false,"excerpt":"This is not an introduction to chemistry or even to atomic theories. It's an introduction to what atoms are with the aim of providing enough background to be useful for understanding\u00a0molecular biology. Introduction \"Nothing exists except atoms and empty space; everything else is opinion.\"\u00a0(Democritus\u00a0c. 400\u00a0BCE) Atoms are the building blocks\u2026","rel":"","context":"In "All Posts"","block_context":{"text":"All Posts","link":"https:\/\/thetravellerslastjourney.com\/shai\/all-posts\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1773,"url":"https:\/\/thetravellerslastjourney.com\/shai\/2011\/03\/14\/dna-as-the-mastercode-2\/","url_meta":{"origin":2162,"position":3},"title":"DNA is the mastercode","author":"Pala","date":"March 14, 2011","format":false,"excerpt":"The central\u00a0dogma\u00a0of biology says that\u00a0DNA\u00a0encodes\u00a0RNA\u00a0which encodes\u00a0proteins In the beginning,\u00a0you were a\u00a0single cell\u00a0made up from a fused\u00a0sperm\u00a0and\u00a0egg. This cell had 23 pairs of chromosomes which together made up all your DNA -\u00a0chromosomes\u00a0are what DNA looks like when it's tightly wrapped. DNA is a long code made up of four\u00a0nucleotides\u00a0that form a\u2026","rel":"","context":"In "All Posts"","block_context":{"text":"All Posts","link":"https:\/\/thetravellerslastjourney.com\/shai\/all-posts\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1675,"url":"https:\/\/thetravellerslastjourney.com\/shai\/2011\/05\/03\/5-ht2a-receptor-2\/","url_meta":{"origin":2162,"position":4},"title":"5-HT2A receptor","author":"Pala","date":"May 3, 2011","format":false,"excerpt":"Many drugs, and most drugs that are directed at cognitive processes (e.g. anti-depressants, hallucinogenics) target\u00a0receptors. Receptors are\u00a0proteins involved in the way\u00a0cells\u00a0in the body signal to each other. The following is a review of one particular type of receptor called the 5-HT2A\u00a0receptor, and it's role in mediating the effects of\u00a0LSD. 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Just hovering over them will give you some insight into Shai's unique way\u2026","rel":"","context":"In "All Posts"","block_context":{"text":"All Posts","link":"https:\/\/thetravellerslastjourney.com\/shai\/all-posts\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]}],"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/padotI-yS","_links":{"self":[{"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/posts\/2162","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/comments?post=2162"}],"version-history":[{"count":0,"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/posts\/2162\/revisions"}],"wp:attachment":[{"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/media?parent=2162"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/categories?post=2162"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/tags?post=2162"},{"taxonomy":"metadata","embeddable":true,"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/metadata?post=2162"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}