Louis
Posts: 6436
Joined: Jan. 2006
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| Quote (RFJE @ Feb. 10 2009,03:41) | Thanks, you made me feel so welcome, guys and girls. Should I put the official research first or my thoughts first.
How about the official research. This is so fun. And I thought I was really stupid for a minute. Love y'all.
To form protein, the amino acids are linked by dehydration synthesis to form peptide bonds.
Dehydration Synthesis
Definition
noun, plural: dehydration syntheses
A chemical reaction that builds up molecules by losing water molecules.
It is a type of condensation reaction in which monomers join together into polymers while losing water molecules. This process is carried out by losing (-OH) from one of the monomers and (H) from another monomer. The two unstable monomers join together, and the (-OH) and (H) combine forming water (H2O).
Condensation
a chemical reaction between two molecules which links them together and expels a molecule of water. For example: the joining of two amino acids by a peptide bond during the formation of a polypeptide.
----"AWAY FROM THE WATERY ENVIRONMENT"
As a polypeptide chain forms, it naturally twists and bends into its native conformation. One of the things that helps determine the native conformation of a protein is the side chains of all the amino acids involved. Remember some amino acid side chains are hydrophobic while others are hydrophilic. In this case, the “likes” attract: all the hydrophobic side chains (here represented by yellow beads) try to “get together” in the center of the molecule, away from the watery environment, while the hydrophilic side chains are attracted to the outside of the molecule, near the watery environment.References:
* Berkow, Robert, ed. 1999. The Merck Manual. 17th ed. Merck, Sharp & Dohme, Rahway, NJ.
* Borror, Donald J. 1960. Dictionary of Root Words and Combining Forms. Mayfield Publ. Co.
* Campbell, Neil A., Lawrence G. Mitchell, Jane B. Reece. 1999. Biology, 5th Ed. Benjamin/Cummings Publ. Co., Inc. Menlo Park, CA. (plus earlier editions)
* Campbell, Neil A., Lawrence G. Mitchell, Jane B. Reece. 1999. Biology: Concepts and Connections, 3rd Ed. Benjamin/Cummings Publ. Co., Inc. Menlo Park, CA. (plus earlier editions)
* Marchuk, William N. 1992. A Life Science Lexicon. Wm. C. Brown Publishers, Dubuque, IA.
-----LEFT HANDED AMINO ACIDS EXCLUSIVELY PRODUCED IN ORGANISMS
Only L amino acids are constituents of proteins. For almost all amino acids , the L isomer has S (rather than R) absolute configuration (Figure 3.5). Although considerable effort has gone into understanding why amino acids in proteins have this absolute configuration, no satisfactory explanation has been arrived at. It seems plausible that the selection of L over d was arbitrary but, once made, was fixed early in evolutionary history.
* W.H. Freeman and Co.
Figure 3.5. Only L Amino Acids Are Found in Proteins. Almost all L amino acids have an S absolute configuration (from the Latin sinister meaning “left”). The counterclockwise direction of the arrow from highest- to lowest-priority substituents indicates that the chiral center is of the S configuration.
I believe that this will confirm two of the points I made. In this research I quote, "...all the hydrophobic side chains...try to 'get together' in the center of the molecule, away from the watery environment...."
This is in a cell that has DNA, not in a primordial soup. Just one dissolving peptide bond ruins the protein, or severely hinders it from functioning correctly. And how many proteins do we need for life? Nobody can tell, but its going to take more than a few, and of course in the right sequence. How did this happen randomly with no DNA to guide it? And where did DNA get the information?
The other point is left handed amino acids--only produced in organisms. Miller's random (with intelligent help) experiment produced left handed and mirror imaged AA which can not produce organic protein.[I]
Do I get an A for effort guys? |
RFJE,
Oh dear. I spy quote mines and goalpost shifts. That'll be strike one.
1) Even though formation of the amide/peptide bond is a condensation reaction, as shown above, it doesn't necessarily have to operate in the absence of water (see comment re equilibrium processes). Repeating your original claim when it's been shown to be wrong doesn't reinforce it, especially when all you do is repeat it with copy and pastes you obviously don't understand.
Let's look at a basic chemical mechanism for formation of an amide/peptide bond under the Schotten-Baumann conditions I mention above:
Look at step 2 where the chloride ion is eliminated to reform the carbon oxygen double bond. The side product formed at this stage is NaCl which is insoluble in ether. The reaction requires water at this stage to solvate the side product. Not only that but the base, NaOH, is also insoluble in ether, for the reaction to work some water has to be present. Solvolysis of the NaOH requires water (in this instance). So no RFJE, your claims that a) amino acids break down in water and b) that the peptide/amide bind cannot form in the presence of water are false.
2) The formation of long chain polypeptides and protein folding are a very different case from forming simple amino acids (see Strecker synthesis for example) or simple di/polypeptides i.e. the amide/peptide bond. Any polymer forming in any solution adopts a conformation of some description. As the comment you quote (without attribution I note) mentions the conformation of the polypeptide forming depends on the hydrophilicity/hydrophobicity of the polymer forming. This has absolutely NOTHING to do with whether or not polypeptides can form in aqueous environments (they can and do) but what conformation they adopt in what environment, i.e. their tertiary (and perhaps quaternary) structure.
This was your original claim:
| Quote | | Presence of water is a problem: Some amino acids break down in water by the process called hydrolysis. It actually breaks the bonds of the amino acids preventing them from forming the chains that build proteins. |
Since amino acids demonstrably do not break down (at an appreciable rate at RTP, modest pH etc) in water (in fact they form zwitterions which are horribly stable and a pain in the arse for the synthetic chemist on occasion, you have to pH buffer aqueous solutions of amino acids to get them to behave), and since the presence of water is demonstrably not a problem for the formation of the amide bonds, in fact in many amide forming conditions it's essential, the first part of your claim is false. Not only that, as the article you misquote above notes, water does not inhibit the formation of large polypeptides, the solvation/environment of the forming polypeptide influences the conformation of the polypeptide. So again, your second, goalpost shifted claim based on a quote mine, and your original misunderstood claim are false, based as they are on your lack of understanding of chemistry.
3) No one is proposing that complex proteins got together, in the absence of DNA, right at the start of the origin of life. There are a variety of proposed scenarios, all of which require that you understand chemistry sufficiently to appreciate how an amide bond forms! Again, it would behove you to inform yourself BEFORE you spout off about topics you obviously don't understand. For example, in one scenario, self-replication is all that is required. All of this is covered in the book I recommended.
4) AGAIN, there are a variety of possible, perfectly natural mechanisms for the origins of homochirality. Personally (for a variety of technical reasons I'm not going to go into) I would advocate that on earth autocatalytic processes not unlike the Soai reaction in their kinetics would be the most likely candidate. If only because the process amplifies very slight deviations from racemic mixtures to produce almost perfectly enantiopure material. If you're interested check out the work of Prof Donna Blackmond at Imperial College, London, on the subject. The Wikipedia article I provided for you gives a few basic ideas about the origins of homochirality, please read it. So, again, the fact that there are perfectly natural mechanisms for the origin homochirality demonstrate that your claim that "homochirality is a problem for evolutionists" is false. The fact that the Miller-Urey experiment did not magically poof life into existence in a test tube is not a problem, it wasn't meant to. It's also not the only experiment that is relevant to abiogenesis, which of course you'd know if you bothered to minimally educate yourself on a subject before bloviating about it. So no, nothing you quoted confirms your claim which was:
| Quote | 2. THE BIGGEST PROBLEM--All amino acids come in left and right handed forms called "enantiomers." Living things have only the left handed amino acids. When Stanley Miller attempted life in a test tube, he produced only a racemic mixture of right and left handed amino acids that is detrimental to life.
So intelligent life tried to set up a random mixture of supposed ingredients and could not do it. It proved that some random amino acids could be produced. |
Your misunderstanding of the Miller-Urey experiment, and the field of study in general, is not evidence. Sorry.
5) The Miller-Urey experiment was, again, meant to demonstrate that one could produce amino acids from conditions like those proposed for the early earth. Regardless of the specific stereochemistry of the amino acids produced, it was a resounding success in that it accomplished what it set out to do. See above.
6) Where did DNA get its information? The sequence of bases in the primary structure of DNA constitutes information (in the technical sense). You're trying to put the cart before the horse.
7) Ahhh trying to have it both ways I see. Because Miller and Urey were intelligent and set up their experiments, they imparted some magical property "intelligence" to the experiment, therefore intelligence is required to make these things. You are assuming what you are trying to prove, literally begging the question, a logical fallacy. For starters, even though it is controversial, the simplest amino acid (glycine) has been (tentatively) observed in space, i.e. it has formed in the absence of "intelligent input". Even if that were not the case, your claim is still logically fallacious. Not only that but it demonstrates a serious misunderstanding of the nature of the experiment (or indeed any experiment). Would you say the same thing if the Miller-Urey experiment had failed to produce any amino acids at all? No, you wouldn't, which neatly demonstrates the intellectually dishonest and bad faith mode of argumentation you employ.
8) "One dissolving peptide bond ruins the protein", since no one is suggesting that complex, modern proteins are required for the vastly simpler origins of life and since the peptide bond is actually highly stable, this complaint isn't even relevant.
9) People CAN tell how many proteins (or indeed how many "anything") are needed for "life", minimal "living" systems are currently the objects of extensive research. Your complaint relies on a) ignorance of current research and b) and equivocation on what constitutes "life".
10) A for effort? No. You get an F for failing to minimally educate yourself about a topic before bloviating erroneously about it. My sympathy for you is running out.
Louis
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Bye.
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) relevant replies in the right order. Let me know if I've messed up.
