What Are Proteins?

[hazelm]

The following quote is giving me a chance to ask about something I have wanted to clear up for some time.  It is merely serving as an example of what is puzzling me.  At https://www.sciencedaily.com/releases/2018/03/180326161000.htm  scientists ate talking about removing "plaques of brain protein.  Quote:

 

".....plaques of a brain protein called amyloid beta, a characteristic sign of Alzheimer's (and within these plaques) small amounts of another Alzheimer's protein:  APOE....."  (underscoring mine)

 

This is a bit hard to explain but I'll try.  Some time back on another forum someone was talking about what goes on in brain cells and called something a "protein".  At that time, the only "protein" I knew came from food and his comment didn't make sense to me.  When I questioned, the only reply I got was "this is  a different protein". 

 

My conclusion then was that the word "protein" is being used with two different definitions in science.  Now I am reading Dr. Rene Fester Kratz's "Biology for Dummies", Now I am back to this question of whether the proteins working inside cells to produce energy may be different from the proteins working in brain cells (and maybe elsewhere). 

 

So my clumsy question is are there two different structures in our bodies called proteins but which are totally different from each other.  The above use of the phrase "brain protein" is an example.  I gather from what I was told when I first raised the question that brain protein is not the protein we know of in food.

 

Can someone clarify, please?  Thank you.

Edited March 27, 2018 by hazelm

[exchemist]

The following quote is giving me a chance to ask about something I have wanted to clear up for some time.  It is merely serving as an example of what is puzzling me.  At https://www.sciencedaily.com/releases/2018/03/180326161000.htm  scientists ate talking about removing "plaques of brain protein.  Quote:

 

".....plaques of a brain protein called amyloid beta, a characteristic sign of Alzheimer's (and within these plaques) small amounts of another Alzheimer's protein:  APOE....."  (underscoring mine)

 

This is a bit hard to explain but I'll try.  Some time back on another forum someone was talking about what goes on in brain cells and called something a "protein".  At that time, the only "protein" I knew came from food and his comment didn't make sense to me.  When I questioned, the only reply I got was "this is  a different protein". 

 

My conclusion then was that the word "protein" is being used with two different definitions in science.  Now I am reading Dr. Rene Fester Kratz's "Biology for Dummies", Now I am back to this question of whether the proteins working inside cells to produce energy may be different from the proteins working in brain cells (and maybe elsewhere). 

 

So my clumsy question is are there two different structures in our bodies called proteins but which are totally different from each other.  The above use of the phrase "brain protein" is an example.  I gather from what I was told when I first raised the question that brain protein is not the protein we know of in food.

 

Can someone clarify, please?  Thank you.

Hello Hazel, a protein is a biologically produced polymer, made up of amino acid monomer units. Just as polythene (more correctly polyethylene) is made of chains of ethylene molecules linked together by chemical bonds, so a protein is a chain of amino acids linked by chemical bonds.

 

An amino acid is a molecule with an amine group (-NH2) at one end and a carboxylic acid group (-COOH) at the other.  The chains form by means of an "amide" link, in which -COOH combines with -NH2 to form -CONH - (a chemical group called an amide), with elimination of H2O, i.e. a molecule of water.

 

There are I think 21 amino acids found in biochemistry and they can all take part in forming polymers in various arrangements, so a huge number of combinations is possible.

 

In short, the term protein is a name for a large class of chemical compounds, rather than a single substance. So the term is not being used in two different senses, but you are right that there are different proteins. 

[hazelm]

Hello Hazel, a protein is a biologically produced polymer, made up of amino acid monomer units. Just as polythene (more correctly polyethylene) is made of chains of ethylene molecules linked together by chemical bonds, so a protein is a chain of amino acids linked by chemical bonds.

 

An amino acid is a molecule with an amine group (-NH2) at one end and a carboxylic acid group (-COOH) at the other.  The chains form by means of an "amide" link, in which -COOH combines with -NH2 to form -CONH - (a chemical group called an amide), with elimination of H2O, i.e. a molecule of water.

 

There are I think 21 amino acids found in biochemistry and they can all take part in forming polymers in various arrangements, so a huge number of combinations is possible.

 

In short, the term protein is a name for a large class of chemical compounds, rather than a single substance. So the term is not being used in two different senses, but you are right that there are different proteins. 

 

All right.  I stared at your last sentence and I think I finally got it.  A large class of chemical compounds.  If we want to know which particular "protein" a writer is referring, we need more than just the word "protein"  We need the writer to provide the chemical make-up or a special way of identifying which compound.  'ATP is a protein.  Dr. Kratz does just that when she includes a brief explanation of what ATP does.   This Science Daily article that I quoted gets us to comprehension by naming it as an amyloid beta and telling what it does/is.  

 

"a protein is a biologically produced polymer, made up of amino acid monomer units"   Now I see what I am missing.  Food polymers I recognize; just not with the term "polymer".  And, of course the body is also creating the unwanted proteins.  The question is "why"? 

 

The index of Dr Kratz's book shows polymerase chain reactions.   I'll skip over to that tonight.  Also, there's Wiki.

 

Thank you.  I think I have it now.  Yes? 

[exchemist]

All right.  I stared at your last sentence and I think I finally got it.  A large class of chemical compounds.  If we want to know which particular "protein" a writer is referring, we need more than just the word "protein"  We need the writer to provide the chemical make-up or a special way of identifying which compound.  'ATP is a protein.  Dr. Kratz does just that when she includes a brief explanation of what ATP does.   This Science Daily article that I quoted gets us to comprehension by naming it as an amyloid beta and telling what it does/is.  

 

"a protein is a biologically produced polymer, made up of amino acid monomer units"   Now I see what I am missing.  Food polymers I recognize; just not with the term "polymer".  And, of course the body is also creating the unwanted proteins.  The question is "why"? 

 

The index of Dr Kratz's book shows polymerase chain reactions.   I'll skip over to that tonight.  Also, there's Wiki.

 

Thank you.  I think I have it now.  Yes? 

More or less, I think so. 

 

A polymer is simply a long molecule made by joining a set of short molecules (known in this context as monomers) together. There are lots of man-made ones of course, but lots in nature too. Apart from proteins, there is also cellulose for instance, which gives plants their structural  strength. Cellulose is a polymer of a certain type of sugar molecules: what is called a polysaccharide. 

 

But ATP is not a protein. It is short for adenosine triphosphate. It is not made of linked amino acids,  and is not a polymer.   

[hazelm]

More or less, I think so. 

 

A polymer is simply a long molecule made by joining a set of short molecules (known in this context as monomers) together. There are lots of man-made ones of course, but lots in nature too. Apart from proteins, there is also cellulose for instance, which gives plants their structural  strength. Cellulose is a polymer of a certain type of sugar molecules: what is called a polysaccharide. 

 

But ATP is not a protein. It is short for adenosine triphosphate. It is not made of linked amino acids,  and is not a polymer.   

Oh!  Oh!  Back to chapter V.  The hardest part of learning a new topic is memorizing all the definitions.  :-)