Here is the video clip about translation that we watched in class:

Stephen C. Meyer’s new book Signature in the Cell looks fascinating.  Faith Interface gives a synopsis and links to a new, related video, Journey Inside The Cell. Several links to debates Meyer has participated in can be found here.

In the 21st century, the information age has finally come to biology. We now know that biology at its root is comprised of information rich systems, such as the complex digital code encoded in DNA. Groundbreaking discoveries of the past decade are revealing the information bearing properties of biological systems.

Dr. Stephen C. Meyer, a Cambridge trained philosopher of science is examining and explaining the amazing depth of digital technology found in each and every living cell such as nested coding, digital processing, distributive retrieval and storage systems, and genomic operating systems.

Meyer is developing a more fundamental argument for intelligent design that is based not on a single feature like the bacterial flagellum, but rather on a pervasive feature of all living systems. Alongside matter and energy, Dr. Meyer shows that there is a third fundamental entity in the universe needed for life: information.

A new video, Journey Inside The Cell, launched today dramatically illustrates the evidence for intelligent design within DNA, as described in Stephen C. Meyer’s book, Signature in the Cell: DNA and the Evidence for Intelligent Design (HarperOne 2009).

The original animation by Light Productions reveals in intricate detail how the digital information in DNA directs protein synthesis inside the cell, revealing a world of molecular machines and nano-processors communicating digital information . . .

Of the three branched chain amino acids (BCAAs), most research suggests that leucine is the MVP. This has led some experts to suggest just supplementing with leucine alone. A new study done by Baylor University suggest differently. The study reported that subjects taking all three BCAAs before AND after weightlifting experienced a greater boost in markers of protein synthesis than those taking just leucine at the same times. Greater protein synthesis can lead to greater muscle growth, so consider supplementing with10-20 grams of BCAAs within 30 minutes before and after workouts.

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Research News
How to Build Muscle and Increase Strenght With FHL1 Amino Acids that Tell Muscle Cells to Build Protien Decrease Fat and Over Muscle with Growth Factor

Bethesda, MD – A visit to the meat counter at any supermarket is proof positive that a good number of Americans are avoiding carbohydrates and consuming high levels of protein and fat, in accordance with the Atkins diet. This carbohydrate-free, fat- and protein- rich diet is for those seeking immediate weight loss, which means most of us.But what do others, such as weight lifters and callisthenic enthusiasts, do about carbohydrates? Their goal is muscle preservation and strengthening, but for years, different theories have been offered about the effectiveness of carbohydrates in maintaining an appropriate muscle protein balance. A new study may lead to a truce in the debate at the nation’s gymnasiums, and those dedicated to resistance training may finally have an answer as to whether carbohydrates have a positive role in muscle development.

Background

Resistance exercise — also called strength training — increases muscle strength and mass, bone strength, and the body’s metabolism. The different methods for resistance training include free weights, weight machines, calisthenics and resistance tubing. When using free weights, dumbbells, and bars stacked with weight plates, you are responsible for both lifting the weight and determining and controlling your body position through the range of motion.

The body’s net muscle protein balance (i.e., the difference between muscle protein synthesis and protein breakdown) generally remains negative in the recovery period after resistance exercise in the absence of nutrient intake, i.e., the muscle’s protein is breaking down complex chemical compounds to simpler ones. However, it has been demonstrated that infusion or ingestion of amino acids after resistance exercise stimulates muscle protein synthesis. Furthermore, as little as six grams of essential amino acids (EAA) alone effectively stimulates net protein synthesis after a strenuous resistance exercise session.

The body’s response to the six grams of EAA does not appear to differ when 35 grams of carbohydrates are added. This reflects the uncertainty of the independent effects of carbohydrates on muscle protein metabolism after resistance exercise. Additionally, it is unclear how carbohydrate intake causes changes of net protein balance between synthesis and breakdown and how it relates to changes in plasma insulin concentration.

Interpretation of the response of muscle protein to insulin is complicated by the fact that a systemic increase in insulin concentration causes a fall in plasma amino acid concentrations, and this reduced amino acid availability could potentially counteract a direct effect of insulin on synthesis. A past study found that the normal postexercise increase in muscle protein breakdown was slowed by insulin, thus improving net muscle protein balance. However, whereas local infusion of insulin may effectively isolate the effect of insulin per se, the response may differ from when insulin release is stimulated by ingestion of carbohydrates.

A New Study

Accordingly, a new study set out to investigate the independent effect of carbohydrate intake on muscle protein net balance during recovery from resistance exercise. The authors of “Effect Of Carbohydrate Intake on Net Muscle Protein Synthesis During Recovery from Resistance Exercise,” are Elisabet Børsheim, Melanie G. Cree, Kevin D. Tipton, Tabatha A. Elliott, Asle Aarsland, and Robert R. Wolfe, all from the Department of Surgery, Metabolism Unit, Shriners Hospitals for Children-Galveston, University of Texas Medical Branch, Galveston, TX. Their findings appeared in the February 2004 edition of the Journal of Applied Physiology. The journal is one of 14 peer-reviewed scientific journals published each month by the American Physiological Society (www.APS.org).

Methodology

Sixteen recreationally active and healthy subjects took part in the study. At least one week before an experiment, subjects were familiarized with the exercise protocol, and their one repetition maximum, a maximum weight possible with a leg extension, was determined. The subjects were assigned to one of two groups: carbohydrate group (CHO; n = or placebo group (n = 8). Subjects were instructed not to exercise for at least 48 hours before an experiment, not to use tobacco or alcohol during the 24 h before an experiment, and not to make any changes in their dietary habits.

The two groups of eight subjects performed a resistance exercise bout (10 sets of eight repetitions of leg presses at 80 percent of one repetition maximum) before they rested in bed for four hours. One group (CHO) received a drink consisting of 100 grams of carbohydrates one hour after exercise; the placebo group received a noncaloric placebo drink. Leg amino acid metabolism was determined by infusion of 2H5- or 13C6-labeled phenylalanine, sampling from femoral artery and vein, and muscle biopsies from vastus lateralis, the lateral head of quadriceps muscle of anterior (extensor) compartment of thigh.

Results

Key findings of the study included: 

• Plasma glucose concentration was significantly increased in the carbohydrate group until 210 min after intake of drink. 
• Plasma concentration of insulin reflected the changes in glucose concentration. The drink intake did not affect arterial insulin concentration in the placebo group, whereas arterial insulin increased by several times after the drink in the CHO group. 
• Arterial phenylalanine (a common amino acid in proteins) concentration did not change after intake of drink in the placebo group but decreased and stabilized in the CHO group. 
• Net muscle protein balance between synthesis and breakdown did not change in the placebo group but improved in the CHO group during the second and third hour after the drink. The improved net balance in the CHO group was due primarily to a progressive decrease in muscle protein breakdown.

Conclusions

This study is the first to compare net muscle protein balance (protein synthesis minus breakdown) after carbohydrate ingestion with control after exercise. The principal finding was that intake of 100 grams of carbohydrates after resistance exercise improved muscle net protein balance.

The findings from this research demonstrate that carbohydrates intake alone can improve net protein balance between synthesis and breakdown. In this work, the gradual improvement in net muscle protein balance after carbohydrate intake was due principally to a progressive reduction in breakdown. However, the improvement was small compared with previous findings after intake of amino acids or amino acids and carbohydrates.

The researchers conclude that intake of carbohydrates alone after resistance exercise will modestly improve the anabolic effect of exercise. However, amino acid intake is necessary for a maximal response, one desired by most participating in resistance exercise programs.

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Article adapted by Sports Performance Research from original press release.

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Contact: Donna Krupa

American Physiological Society 

Source: Journal of Applied Physiology. The journal is one of 14 peer-reviewed scientific journals published each month by the American Physiological Society (www.APS.org).

The American Physiological Society (APS) was founded in 1887 to foster basic and applied science, much of it relating to human health. The Bethesda, MD-based Society has more than 10,000 members and publishes 3,800 articles in its 14 peer-reviewed journals every year.

November 2007

This has got nothing particularly to do with Zoology, but it really is worth watching. You think chalk-and-talk lectures are boring? Here’s an example of how they did things in the 1970s. A group of hip lecturers in California (where else?) decided to teach protein synthesis by getting their students to dance it… The first 2-3 minutes have a straightforward account of the process by a chap in a tie and a NASA haircut (turns out he’s Paul Berg, 1980 Nobel Prize Winner in Chemistry). Then it gets interesting, with loads of students who could be your grandparents romping about to some rather cool music. Looks like everyone had a whale of a time. Do you think we should try something similar?

And if that reminds you of this Fatboy Slim video, I suspect it’s probably not a coincidence.

Har Gobind Khorana was born on 1922 in Raipur, Punjab. Dr. Khorana received his B.Sc. and M.Sc. degrees from the Punjab University in Lahore (in present day Pakistan) and his Ph.D. from the University of Liverpool(England), where he went in 1945 on a Government of India Fellowship. Dr. Khorana spent a year in Zurich in 1948-49 as a post-doctoral fellow and returned to India for a brief period in 1949. He returned to England in 1950 and spent two years at Cambridge. While at Cambridge, he worked with professors Kenner and Todd. His interest in proteins and nucleic acids took root at that time. In 1970 he became the Alfred Sloan Professor of Biology and Chemistry at the Massachusetts Institute of Technology where he continues his work.

He was awarded the Nobel Prize in Physiology or Medicine in 1968 for his work on the interpretation of the genetic code and its function in protein synthesis. And also awarded the Louisa Gross Horwitz Prize from Columbia University in the same year.

Nothing to do with Catholicism or Religion, but my friend showed me this 70s era video about protein translation. If you are a science person, you should be able to appreciate this video. Even as a regular human being you should be able to appreciate it for its entertainment value.

I would normally post something like this only on Facebook, but since I gave that up for Lent, I wanted to show it to you guys here. I hope you enjoyed it and realize that this is what is happening continuously in your cells!!!

-NDB

I moved my site to its own domain. Please use following link for the information you are looking for:

http://www.ilearnttoday.com/index.php/the-blood-brain-barrier

This is a re-post for the class of 2009 to revise and the 2010 group to catch on the first time… As always, click on the shadowed images for a link to an animation, or visit the links posted below.

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Core (for everyone):

Click4Biology page

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Additional Higher Level:

Click4Biology page: Transcription – Translation

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Further resources:

There are many decent Flash animations and the like on the internet, but the majority cannot be embedded. Below this YouTube video, there are some direct links to resources, some of which can be easily saved.

Learn.Genetics @ Utah

Transcribe and Translate (good, basic, interactive)

How do fireflies glow? (puts it in context)

University of Nebraska:

Protein Synthesis overview (Good enough for SL)

Transcription Details (fits DP Bio HL very well)

Translation Details (fits DP Bio HL very well)

John Kyrk: (visit the parent site at www.johnkyrk.com – excellent)

Transcription (fits DP Bio HL very well)

Translation (fits DP Bio HL very well)

St. Olaf College

Transcription (clear and simple)

Translation (clear and simple)

EDIT:  Two more animations (from mrhardy’s wikispace, original source unknown)

Transcription

Translation

WH Freeman

RNA Splicing tutorial (HL only)

Bio3400

Translation with a genetic code dictionary (shows position in the ribosome)

Some more in-depth animations (newly added):

Translation from Wiley Interscience

Translation from LSU Medschool

Translation from The Chinese University in Hong Kong

Protein targeting from Rockefeller University

Protein Synthesis is the creation of protein.

But first – what exactly is protein?

Well, according to this poll, approximately 10% of the people surveyed were absolutely sure that they know what protein was! Ten percent!

Here’s the poll:

Now, about protein. Protein is, according to the Merriam Webster dictionary, “the total nitrogenous material in plant or animal substances”. Let’s break that definition down a bit. Nitrogenous is, well, nitrogen-ous. The adjective version of nitrogen. So that must mean – containing Nitrogen! So, basically, Protein is “the nitrogen-filled stuff in plants or animals.”

Based on what we just learned about protein, Protein Synthesis would be the making of nitrogen-filled stuff found in plants or animals. But how does that happen, exactly? I mean, we know that Protein Synthesis is the making of protein, but how is the protein made? I couldn’t sit down and make protein, of course, but how does protein synthesis somehow make it?

Well, let’s find out!

There are two main steps to protein synthesis: Transcription & Translation. I’ll go through them one by one.

1. Transcription: When the information from the DNA is transferred to the RNA. During the Transcription, the DNA is used as a “template”- kind of like the template of this blog- to make a new strand of RNA; also, only part of the DNA is transcribed. Only one strand! But that means that only one strand of the RNA is produced. It works out well, though. When the transcription is done, the RNA “disconnects” from the DNA – so now people can make many copies of that RNA from the very same gene in a very small amount of time. Not only does the RNA “disconnect”- kind of like when a laptop is done charging and you unplug it- but the DNA closes.
2. Translation: When the mysterious language of “nucleotide bases” is translated into the native language (for the cells) of “amino acids.” Think of Nucleotide Bases as a secret code, and you’re trying to decode it into the cell’s version of English, a language all the cells can understand – Amino Acids.  Translation takes place in the cytoplasm, and it involves three different kinds of RNA: Ribosomes, tiny organelles attached to the outside of the ER, Transfer RNA (tRNA) molecules, molecules that transport the amino acids to the ribosomes, and Messenger RNA (mRNA) molecules, molecules that, once synthesized in the nucleus, gets its genetic code translated into the amino acid sequence to run protein synthesis.

I also found this moving picture about how protein is made.

Note: You have to click on the picture first in order to make it move.

So there we have it! Everything you need to know about Protein Synthesis, wrapped up into one little post. All about how it works, what it is, and even a cute little moving picture about it!

Remember, when it comes to science – move it!

-m

“Ingestion of only a small amount of amino acids, combined with carbohydrates, can increase muscle protein anabolism”

Kevin Tipton & Robert Wolfe in Exercise, Protein Metabolism, and Muscle Growth.

In other words: amino acids can help help build muscle. Athletes have known this for a long time. What is key though is the timing.

Citing a landmark study, Tipton and Wolfe discuss

“a recent study [where] subjects ingested a solution consisting of 6g essential amino acids plus 35g of carbohydrate either immediately prior to resistance exercise or immediately following exercise. The reponse of net muscle protein balance when the drink was consumed immediately prior to exercise was considerably greater than when the drink was consumed after exercise.”

This is a significant point. People have all ways considered the ‘window of opportunity’ that exists post-exercise, but this study showed that ingesting before exercise is better.

It has to do with the need for the amino acids to be present in the right cells at the right time. The right time is during and after exercise, and so people have assumed this is the best time to deliver the amino acids. But by consuming the amino acids before exercise the amino acids are delivered to the cells during exercise. This ensures there is never a deficit of amino acids in the muscle – they are present when most needed.

“Blood flow to the muscles following exercise is not as great, so amino acids delivery to the muscle is comparatively less when the amino acids are consumed after exercise. “

The article quoted is:

K. D. Tipton and R. R. Wolfe, ‘Exercise, protein metabolism, and muscle growth‘, International Journal of Sports Nutrition and Exercise Metabolism 11: 109-132 (2001).

Found this useful source on North Harris College’s linklist. 

Wiley.com have produced this online resource for Biochemistry and the Chemistry of Life, and it contains a whole load of interactives and animations.

It is an ideal resource for: photosynthesis, respiration, DNA replication, transcription, translation, cell structure, enzymes and protein synthesis.

I believe in the philosophical usefulness of analogies.  They elucidate, they persuade, they allow us to discover otherwise overlooked similarities.  Recently I came up with an analogy between Philosophy (as the “Science of Belief”) and the internal cellular process of Protein Synthesis.

I am, sometimes, of the opinion that a useful way to answer the question “What is Philosophy?” is “The Science of Belief”, by which I mean, a relatively rigorous rational conscious cognitive process of belief formation by means of inference to the best explanation.  Doing the best we can to create and maintain a set of beliefs which happens to be (in some sense) accurate to the actual state of affairs.  As both an argument for, and an elucidation of this position: I introduce you to Philosophy as: Rational Noetic Activity (RNA)…An analogy…

(Please accept the simplifications, this is only meant to be accurate to the extent which is useful for this analogy rather than for biological precision)  Human bodies are made (partially but essentially) of proteins.  Proteins are curled up “chains” of amino acids.  Amino acids are organic molecules.  There happen to be 20 amino acids from which the proteins in the human body are assembled.  The assembly instructions for proteins are embodied in DNA.  DNA is two long and interconnected polymers of the four nucleotides adenine, cytosine, guanine and thymine held together by sugars and phosphates.  The order of these four nucleotides provides the instructions for protein assembly.  RNA is (usually) a single strand of nucleotides.  The process of RNA transcription is the process by which enzymes synthesize RNA based on the structure of the DNA molecule.  Then amino acids are brought together and assembled into chains by matching them up with the order of nucleotides on the RNA molecule.  After assembly, the amino acids curl up (how and why they form the shapes they do is one of the great current mysteries of biology) and form proteins, which then go on to take part in pretty much every cellular process (including the process just described!). 

Now, let us examine in what way Philosophy can be applied to this model analogously…Let us equate DNA with the external world, the “actual state of affairs”.  It is a relatively stable storehouse of information relatively (but not totally) independent of observational influence, and embodies the “stuff” from which philosophical agents assemble their beliefs; the recipe for conscious opinion concoction.  The Proteins will be viewed as analogous to the belief states and/or propositional opinions which will in turn make up the totality of their cognitive “soma”; the “body” of beliefs of the individual agent.  This leaves the process of RNA transcription and Protein Synthesis to be analogous to: Philosophy.  This is why, as you may have suspected, I have so cleverly christened philosophy Rational Noetic Activity.

The process of doing philosophy can be viewed as analogous to interpreting the external world (enzymatic synthesis of RNA molecules based on the information contained in/on DNA), and then assembling belief states/propositional opinions in language (assembling amino acids into protein chains).  This leads us to extend our analogy one step further.  Perhaps we would do well to consider amino acids as analogous to words, and protein chains to sentences of natural language.  By doing this we would on the one hand fall into some technical philosophical problems of belief vs opinion, propositional attitudes, etc. but we would gain another level of accuracy and usefulness from our analogy.  If we accept that in some general sense there is a useful concept called “belief” which can in some useful sense be viewed to consist of (or be translatable into) linguistic entities (sentences, propositions), this analogy should hold.

Then, to extend the analogy even further!  The totality of proteins which make up an individual body then goes out into an actual environment in which it is subject to the mechanisms of natural selection and evolution over time.  A body which is made of “optimal” (for survival) proteins will have selective benefits over those which do not.  This is why it is important to have a high-fidelity system of protein synthesis from the DNA information.  To turn this back on the philosophy analogy: an agent would be more likely to thrive if its belief states were accurate to the external world.  So, the more progress we can make towards perfecting the process of philosophy as Rational Noetic Activity, the more likely our beliefs/opinions, which are being expressed as linguistic strings (amino acid chains) are to be in accordance with the information contained in the external world (the DNA), and the more likely we, as agents with a “body of beliefs” are to survive and succeed.

Surely there are more useful tidbits to be mined from this analogy, but I will (for now) leave those up to you.  But even this sketch, I feel, serves as a good example of how analogies serve to convey understanding and argument for a position simultaneously and (hopefully) effectively!

DNA Replication

DNA Replication Fork

How Translation Works

mRNA Synthesis (Transcription)

Protein Synthesis

How Tumor Suppressor Genes Blocks Cell Division

Control of Gene Expression in Eukaryotes

How Nucleotides are Added in DNA Replication

Hershey and Chase Experiment

Meselson and Stahl Experiment

Mutation by Base Substitution

Addition and Deletion Mutations

Thymine Dimers Formation and Repair

cDNA

Processing of Gene Information – Prokaryotes versus Eukaryotes

How Spliceosomes Process RNA

Restriction Endonucleases

Early Genetic Engineering Experiment

Restriction Fragment Length Polymorphisms

Constructing Vaccines

The Ti Plasmid

Cloning a Gene

Steps in Cloning a Gene

Construction of a Plasmid Vector

DNA Probe (DNA hybridization)

Sanger Sequencing

Microarrays

ELISA Enzyme-Linked Immunosorbent Assay

Complement Fixation Test

Southern Blot

Polymerase Chain Reaction

10.2.01
Rajdhani Express
Traveling even in the AC two tier of Shatabdi/ Madras Mail (or is it called Chennai mail now?) gives one this feeling – cut off from reality, far from the dirt, dust, larceny and prostitution of earth, this is an Avalon created by wily and successful men. I felt rather uncomfortable chaining my attaché to the seat – as if being on my first Rajdhani trip couldn’t let me off from my typical middle class extra alertness. Mrs. Vasin of D.S.P. Township, having boarded from Durgapur (She also manages a boutique), made a request to call her husband, showing that she knew of this particular facility of Rajdhani…id est, she has had many previous experiences of traveling in Rajdhani. Even though, of the three Rajdhanis that pass over Durgapur-Asansol, only the Sealdah-Delhi Rajdhani stops at Durgapur and this train had started for just over two years, only since Mamata became the Railway minister. Why, did Mrs. Vasin go through the trouble of chaining her luggage? Of course she did not.
Around fifteen to ten in the morning, an elderly gentleman entered the coach along with the railways attendant and requested for permission to check under the seats. His suitcase was missing from the A-1 coach. Mrs. Vasin was very hurt – “O my god, even in the Rajdhani these things happen, really India is –”. She kept her sentence incomplete. I filled the blanks in, in my mind – “Disgusting”.

Maybe it did not appear on my face, but yes, at that moment, a smile did sparkle within my head.

My name is Benu. See that hut at the corner of the road? That is a tea shop, and I work there. But don’t think I am an illiterate just because I work at a tea shop. I am the only one who knows how to read and write, in my family. When my father’s factory was open, I did study at the corporation school. I loved to go to school. My teachers said I had an aptitude for mathematics. But when I reached class three, one day, suddenly, my father’s factory closed. Then slowly everything in my life started changing – my parents, my house – everything. Even though our school was free, one day my father made me go to this tea shop to work. I was very hurt that day. I cried and cried, and at last my father said that he would send me back to school when the factory opened again. Since that day, for four years, I’ve been working at this tea shop from dawn to dusk, everyday.
My Master gives me five rupees for each day I work. I don’t get this money on the days I am sick, and can’t come. At the end of the week, when I hand over the week’s wages to my mother, the smile on her face makes me forget all my troubles. My Master is a good man – he doesn’t beat me. He gives me a cup of tea and a biscuit everyday, once at morning, and again at the evening. He even gives me the bread which he could not sell over the week. Other boys like me – working in the tea shops in the neighborhood get beaten by their masters for any slight mistake. But my Master has hit me only once in my four years. That day a cup slipped from my hands and broke. That was the day the doctors told me and my father that my mother won’t be able to walk again.
My Master is not a bad man, but the other, old man who works for my Master is. My Master cannot stand the sight of him because he is absent from work so frequently. And watch the fun – because my Master scolds him, he has to release his anger at me. He always scolds me, without any reason. Even his attires are shabby. I feel so angry at him. He is the reason some mornings I wake up and cannot bring myself to go to the shop. Then my mother has to persuade me, like when I was a little child, to go to work.
In the afternoons, my Master goes for his lunch after bringing down the shutters of the shop. I lie down on the bench and try to read the newspaper, spelling the words letter by letter.
Yesterday a wonderful thing happened. I saw that I was wearing my school uniform and walking towards the school gate, schoolbag slung over my shoulders. I meet my best friend Amit – he’s so surprised and happy to see me again. I tell him that my father’s factory has opened again. I will be coming to school like I did before. Suddenly the dirty old man who worked at the shop broke into my dreams with his harsh shouts and rough pushes. I hadn’t even realized when I had dozed off on the bench, reading the newspaper. Oh, only if the old man interrupted my dreams a little later. I could have seen my school compound in my dream.
Sometimes, just sometimes, I really wish that I could see my school compound once more.