Amino Acids

[foodchain]

Do the constitute everything chemically in regards to biological systems, such as any enzyme recorded or protein for instance? I never resolved this question for some reason.

[Comandante]

Not sure if I understand what you're asking but here's a brief explanation. Amino acids (20 of them) bind together to form peptides, simplest being that of 2 amino acids - a dipeptide. When you have very long chains of amino acids they are called polypeptides. Proteins are really chains of these very long polypeptides (from 100 to many thousands of amino acid residues make up a protein). Enzymes are really proteins, they are one type of protein. Other types of proteins include hormones, antibodies, toxins and others. I think these are referred to as roles of proteins rather than types of proteins but unsure, the main point is that they're all proteins. Proteins are found in all biological systems so therefore amino acids are found in all biological systems.

[foodchain]

Not sure if I understand what you're asking but here's a brief explanation. Amino acids (20 of them) bind together to form peptides, simplest being that of 2 amino acids - a dipeptide. When you have very long chains of amino acids they are called polypeptides. Proteins are really chains of these very long polypeptides (from 100 to many thousands of amino acid residues make up a protein). Enzymes are really proteins, they are one type of protein. Other types of proteins include hormones, antibodies, toxins and others. I think these are referred to as roles of proteins rather than types of proteins but unsure, the main point is that they're all proteins. Proteins are found in all biological systems so therefore amino acids are found in all biological systems.

 

I think there is more then 20 amino acids anymore, the question is basically is everything in a biological system, at a reduced level composed of amino acids, be its DNA, and enzyme or the composition of a human eye, in a reduced sense, is it all composed of amino acids?

[Comandante]

There are others yes but there is a 'main' or standard group of 20 of them that are found in proteins - hence biological systems. There are a few nonstandard ones also found in proteins but are generally rare.

 

Now I understand what you're asking. Well, if you go 'down' zooming in close enough you're eventually going to see only atoms, but if you're looking for amino acids I think you won't find them at all parts of a biological system. See a bone for example, there are calcium salts which aren't amino acids. Maybe there are other examples, I'm not sure.

[Comandante]

hmmm see if I've answered your question yet

[foodchain]

hmmm see if I've answered your question yet

 

As I worded it yes, but I guess what I was aiming at was the idea that the amino acids happen to be responsible for everything in biological systems, this is what I don’t know for sure really. If such were somewhat true, then you could study life in that format, such as just looking at the amino acids for instance in regards to biology.

[Comandante]

I think amino acids are responsible for most of the things happening in biological systems, but not all. Of that one though, I'm myself unsure

[FreeThinker]

Well, no. For example, DNA and RNA are nucleic acids composed of nucleotides which have a totally different chemical makeup compared to amino acids. Cell membranes are composed of phospholipids which are, once again, very different from amino acids. Also, other structures of the cells such as carbohydrates are also not made up of amino acids. In short, the answer is no.

[fredrik]

Like Freethinker says biomass is more than just proteins. As an example, the typical dry biomass composition of a yeast cell (not counting the water) is something like

 

proteins ~ 45%

carbohydrates ~ 40%

RNA/DNA material ~ 7%

Lipids ~ 3%

Ash/minerals ~ 5%

 

All of the different compounds are necessary for different tasks within a cell. Some relate to structure and compartmentization, some perform various catalytic functions, some are simply nutritional sources/pools, some are genetic code. The exact biomass composition is also different for different cells.

 

The study of each of the above compounds are interesting in different ways, and they all impact the function of the cell.

 

/Fredrik

[Genecks]

As I worded it yes, but I guess what I was aiming at was the idea that the amino acids happen to be responsible for everything in biological systems, this is what I don’t know for sure really. If such were somewhat true, then you could study life in that format, such as just looking at the amino acids for instance in regards to biology.

 

I see what you mean. I've often pondered this, but I never really analyzed it for more than a brief half-second. Amino acids make up proteins, and proteins tend to do most of the biological processes within humans.

 

However, tRNA tends to make the proteins by chaining and linking amino acids.

 

I'm thinking you're question is the following:

 

Are amino acids the basis for all biological actions and reactions within biological species?

 

Amino acids are also chemicals formed together, which make proteins. So, chemicals are held responsible for making the amino acids. The amino acids are used to make proteins, but they can't be made unless made by tRNA.

 

Primarily, I'm thinking yes. If you don't have the amino acids/protein(s), then you can't do action X from part B. However, if you don't have part B, then the amino acids/protein(s) can't do action X.

 

Protein (composed of amino acids) are responsible for actions and reactions. However, they need something to combine with to do those things. So, they are a major part. However, they don't do "everything."

 

DNA is not entirely composed of amino acids. I know that for sure.

 

DNA -> mRNA -> tRNA -amino acids-converted to-> proteins -> proteins + part B = biological actions and reactions

 

Then again, there might be some proteins that simply decompose, but I don't have an encyclopedic knowledge on amino acid combinations and protein possibilities.

[CharonY]

Ouch. Freethinker and fredrik already mentioned this but:

DNA is not entirely composed of amino acids. I know that for sure.

DNA is composed of something entirely different (desoxyribose+sugar) than amino acids. Period. Stating anything else is severely misleading.

 

What might be a bit confusing is that most of the effectors in a cell are proteins which in turn consist of peptide bound amino acids, but this has already been mentioned. Of course there are few other structural components necessary for enzymatic reactions, most notably rRNAs (which again are nucleic acids and not amino acids).

 

Just as a clarification:

However, tRNA tends to make the proteins by chaining and linking amino acids.

This is not correct. The tRNA only transports the amino acids to the ribosome (in which the "linking" occurs) and is responsible (via its anti codon) for the correct coupling of the genetic code.

[Genecks]

1) Yeah, I should have edited that bit about DNA. I was too lazy to do so.

2) Right, I forgot about the ribosomes.

[Aftabnadim]

As I worded it yes, but I guess what I was aiming at was the idea that the amino acids happen to be responsible for everything in biological systems, this is what I don’t know for sure really. If such were somewhat true, then you could study life in that format, such as just looking at the amino acids for instance in regards to biology.

 

Amino acids link together to form a polpeptide that we are called proteins there is no specific figure for amino acids in a protein that is an insulin contains just 51 amino acids in its polypeptide chain and we call it protein

It is the sequence of 20 kinds of amino acids that are responsible for all biological functions and the mutation in one of amino acid code results in diseases like anemia i-e the replacement of glutamic acid with valine results in sickle cell anemia which is uncurable disease

[ecoli]

ribosomes are composed on mostly RNA, and also some proteins. Also, RNA can act as enzymes. So, not all enzymes are proteins (though the vast majority are).

[foodchain]

Amino acids link together to form a polpeptide that we are called proteins there is no specific figure for amino acids in a protein that is an insulin contains just 51 amino acids in its polypeptide chain and we call it protein

It is the sequence of 20 kinds of amino acids that are responsible for all biological functions and the mutation in one of amino acid code results in diseases like anemia i-e the replacement of glutamic acid with valine results in sickle cell anemia which is uncurable disease

 

Yes and many other issues exist currently in regards to mutations. Such as so many "generations" ago our ability to produce ascorbic acid internally was basically turned off, though like many other structures such still exists in vestigial. Its so difficult to comprehend billions of years you know.

 

I know its rather shortsighted, but many people are in the business of attempting to find a short cut to the explanation of biological phenomena, so I thought I should jump on the bandwagon. I think what’s funny is natural selection can be applied to a majority of physical processes really, such as what environments allow a hurricane to persist or come about, but such is purely speculation. I still do wonder about naturally occurring amino acids in a colloid as a basis to attempt to understand the beginnings of life, but many in the past point to clay of all things, or bubbles really. I mean really that so much ground could probably be covered in biology if we could know what came first, so sort of “code” or the cell.

 

To attempt to look at life from a purely chemical perspective I find very important, but I know that you cant reverse engineer every chemical reaction. Molecular biology for the most part looks at life not only from the chemical but from the physical perspective, one and the same I think but for the sake of modern perception they differ, blame it on ancient philosopher types me thinks.

 

Amway’s, thanks for the post. I thought in major that I was really talking about genetics in some abstracted fashion, but I learned from posters that I was not, so it pays to come to this site.

[marjan]

Sorry if my question sounds dumb:-( (I'm a chemist not biologist) and Just like to know when working with proteins what precaution should be considered? I know the general precaustion such as: keeping them in 4 degree and keeping things strile... just need to know more.

Any reply welcome.

Many thanks

Marjan

[CharonY]

There are a number of precautions. It is a little bit of a difference if you work with a single purified protein or with a crude extract and whether you need to retain stability.

 

In general:

- work somewhat quick. Even at 4° C they are not stable forever

-avoid repeated freezing and thawing, but do not store for longer time at 4° C either. Do your experiments quickly or aliquot your sample accordingly and store them at -80°

- use the right buffer conditions (obviously)

- avoid contamination. For one you do not want your skin proteins in your extract (actually hands are not the main contamination source but the face and dandruff) and you do not want to introduce proteinases incidently here it is more important to work cleanly than sterile, if you get my drift

- if possible/necessary use proteinase inhibitors unless the buffer is inhibitory itself or if you have highly purified a single protein species

-avoid strong radiation (e.g. too much direct sunlight, depends on the protein)

That's just what I can think of at the moment. The precise precautions might vary from experiment to experiment (e.g. if you want to label something).

[lucaspa]

I think there is more then 20 amino acids anymore, the question is basically is everything in a biological system, at a reduced level composed of amino acids, be its DNA, and enzyme or the composition of a human eye, in a reduced sense, is it all composed of amino acids?

 

1. There are many more than 20 amino acids. It's just that there are 20 that are coded by DNA to be in proteins. There are some other amino acids that show up as intermediates in metabolism.

 

2. No, amino acids are not "everything in a biological system". Amino acids are the constituents of proteins.

 

DNA/RNA are composed of nucleic acids. Nucleic acids are, in turn, compounds of nitrogenous ringed bases (such as adenine), ribose (a sugar), and phosphate. DNA is deoxyribose, which is ribose without an OH group.

 

Glycogen is a chain of glucose -- a sugar.

 

Glycosaminoglycans are chains of sugars. There are different glycosaminoglycans composed of different sugars.

 

Lipids are long chain hydrocarbons and form about 50% of cell membranes. They are also the basis of the molecules that make up the mylenated sheath around nerves.

 

Does this help?

[lucaspa]

Sorry if my question sounds dumb:-( (I'm a chemist not biologist) and Just like to know when working with proteins what precaution should be considered? I know the general precaustion such as: keeping them in 4 degree and keeping things strile... just need to know more.

Any reply welcome.

Many thanks

Marjan

 

In addition to CharonY, avoid heat above 50° C. That will denature the protein.

 

Avoid strong acids and bases, keep them about pH 7.0

 

Avoid denaturing solutions such as 4 M GdnHCl or 6 M urea. Also avoid ammonium chloride solutions as they will precipitate proteins.

 

Summary: try as much as possible to keep proteins in physiological solutions at ~ pH 7.0 and less than or equal to 37° C.

 

If you are going to store them for a long time, lyophilize them (freeze-dry) and store at -80°C. You can also store them in solution at -20° or -80° for shorter periods of time (about a year or 2) as long as the freezer is not frost-free (self-defrosting). The defrost cycle heats things up and can thaw the protein. As CharonY said, avoid repeated freeze-thaw cycles as this will denature the protein.

[lucaspa]

Amino acids link together to form a polpeptide that we are called proteins there is no specific figure for amino acids in a protein that is an insulin contains just 51 amino acids in its polypeptide chain and we call it protein

 

We call smaller polypeptides proteins. The distinction between "polypeptide" and "protein" is artificial. Proteins are polypeptides and polypeptides are proteins. The terms are interchangeable.

 

It is the sequence of 20 kinds of amino acids that are responsible for all biological functions and the mutation in one of amino acid code results in diseases like anemia i-e the replacement of glutamic acid with valine results in sickle cell anemia which is uncurable disease

 

No, proteins are NOT responsible for ALL biological functions. In addition to E. coli's excellent example of ribosomes (which can make proteins using only RNA without proteins), lipids form a bilayer and a membrane without any protein involvement. Hyaluronic acid is a glycosaminoglycan and is mostly responsible for the slipperiness of joint fluid (like in the knee).

 

Most mutations do NOT result in any disease or change in the protein. A mutation of one amino acid CAN result in change of function of the protein. BUT, in most cases it does NOT and in the cases it does, very few of those lead to diseases.

 

BTW, in areas where malaria is endemic, sickle cell trait is a benefit. Being heterozygous for sickle cell is a benefit. Being homozygous for normal hemoglobin results in getting malaria and dying. Being homozygous for sickle cell hemoglobin results in sickle cell anemia and dying. Sickle cell trait is a classic example in natural selection of selection for the heterozygote.

 

BTW, in case anyone does not understand the terms used, such as heterozygote, glycosaminoglycan, etc, be sure to ask.

[CharonY]

We call smaller polypeptides proteins. The distinction between "polypeptide" and "protein" is artificial. Proteins are polypeptides and polypeptides are proteins. The terms are interchangeable.

 

While this is off topic, I have to add a comment. The definitions of polypeptide is indeed a bit blurry. However, proteins are usually larger polypeptides which have a biological function. Polypeptides are usually used to refer to chains of amino acids of medium length (whether they have a function or are synthetic with no functions, truncated proteins, whatever). Even smaller chains are referred to as oligoproteins. As mentioned, there are no clear cut distinctions between them. However proteins are essentially polypeptides, yet not all polypeptides are proteins.

 

On second thought I might have to add that this distinction is mainly valid in the realm of molecular biologists. I can imagine that (bio)chemists might prefer others.

[lucaspa]

While this is off topic, I have to add a comment. The definitions of polypeptide is indeed a bit blurry. However, proteins are usually larger polypeptides which have a biological function. Polypeptides are usually used to refer to chains of amino acids of medium length (whether they have a function or are synthetic with no functions, truncated proteins, whatever). Even smaller chains are referred to as oligoproteins. As mentioned, there are no clear cut distinctions between them. However proteins are essentially polypeptides, yet not all polypeptides are proteins.

 

On second thought I might have to add that this distinction is mainly valid in the realm of molecular biologists. I can imagine that (bio)chemists might prefer others.

 

Good second thought. Molecular biologists tend to view DNA coded polypeptides -- of whatever length -- as proteins. Polypeptides not coded by DNA tend to get the polypeptide designation. I haven't ever heard of "oligoprotein". That makes no sense. It should be "oligopeptide", analogous to "oligonucleotide".

 

Biochemists don't make that distinction. Glutathione, a tripeptide synthesized in the cytoplasm and a major antioxidant, is referred to as a "protein" all the time.

 

When Fox and others made polypeptides by thermal polymerization of amino acids, they called them "thermal proteins" as a concession to the many people who viewed "proteins" as referring only to polypeptides coded by DNA.

[CharonY]

It should be "oligopeptide", analogous to "oligonucleotide

Of course it should- I should reread my posts (or stop posting after staying awake for longer than 18h).

 

 

So: Oligopeptides is used to refer to short amino acid chains, usually around or below 50.

 

 

My apologies.

[lucaspa]

Of course it should- I should reread my posts (or stop posting after staying awake for longer than 18h).

 

 

So: Oligopeptides is used to refer to short amino acid chains, usually around or below 50.

 

 

My apologies.

 

No problem. One of the failings of forums is that we can't see you or hear your voice. If I had been able to do either, I probably would have guessed that you weren't all there. As it is, a reader has to take you as serious and meaning exactly what you say. Then respond as tho you were.