High-energy bonds in protein synthesis

[GnothiSeauton]

Hey there, newbie writing
I have a question concerning biochemistry. I have to solve a problem:
What is the molar mass of mRNA which carries information for protein synthesis which has molar mass of 45100 and how many high-energy bonds do you have to spend for this protein synthesis? How many bases has gene that codes for this protein if we know that there is 45% of exons in that gene. Mr(amino acid)=110 Mr(nucleotide)=340

I calculated like this:
N(amino acid in this protein) = Mr(protein)/Mr(amino acid) = 45100/110 = 410
Conclusion: This protein consists of 410 amino acids

GENE:
N(nucleotide total (introns+exons)) = (410*3)/0,45 = 2733,33 => approx. 2734
Conclusion: This gene has totally 2734 nucleotides, so this gene has 2734 bases.

N(mRNA) = N(exons) = 410*3 = 1230

M(mRNA) = 1230 * 340 = 418 200

N(high-energy bonds) = N(nucleotides) - 1 = 1229 ???? I am really not sure about whether this is 1229 or 1230 or something else.

Is this all correct? I don't have solutions so please help

[MonDie]

What is the molar mass of mRNA which carries information for protein synthesis which has molar mass of 45100 and how many high-energy bonds do you have to spend for this protein synthesis?

 

I calculated like this:

N(amino acid in this protein) = Mr(protein)/Mr(amino acid) = 45100/110 = 410

Conclusion: This protein consists of 410 amino acids

 

How did you get 110?

You might estimate the average molar mass of an amino acid using the genetic code, accounting for degeneracy, but what to do about the acidic amino acids which can dissociate?

[GnothiSeauton]

Mr(amino acid) = 110 and Mr(nucleotide)=340 are given in a problem as an information, I did not calculate them.

Also, after I studied problem more carefully I came to conclusion is number of high energy bonds is 410, i.e. it is equal to the number of amino acids in a protein. Is that correct?

[MonDie]

I apologize.

[BabcockHall]

Do you need to know the number of high energy bonds for the synthesis of mRNA or for the protein?

[BabcockHall]

Mr(amino acid) = 110 and Mr(nucleotide)=340 are given in a problem as an information, I did not calculate them.

Also, after I studied problem more carefully I came to conclusion is number of high energy bonds is 410, i.e. it is equal to the number of amino acids in a protein. Is that correct?

Each peptide bond costs four high-energy phosphate bonds, assuming that the correct codon-anticodon interaction is selected every time.

[GnothiSeauton]

I need to calculate how many high energy bonds I need for assembling a protein. Since I have 410 amino acids I concluded that I need 410 high energy bonds.

[BabcockHall]

Can you explain your reasoning? I suggest you consider tRNA synthetases when totaling up the number of high-energy bonds that must be spent. I am also not sold on your calculation of number of high energy bonds for mRNA, but perhaps we can worry about proteins first, then RNA.

Edited August 15, 2015 by BabcockHall

[GnothiSeauton]

OK:

 

Well, bond between tRNA and amino acid which tRNA carries is highly-energized, thus unstable. When tRNA' anticodon clicks with mRNA's codon that unstable bond breaks and energy is released. That energy will be used to create a new peptide bond between two amino acids. So, if high energy bond breaks each time new amino acid comes, total number of high energy bonds should be equal to total number of amino acids.

[BabcockHall]

How many high energy bonds are spent to produce a charge tRNA (an aminoacyl tRNA)? During the three steps of protein synthesis, are any additional high-energy bonds spent in the form of GTP?

[GnothiSeauton]

Well, since each amino acid is bonded on tRNA when they come to mRNA, I guess it is 410 high energy bonds.

No GTP is mentioned.

[BabcockHall]

That guess is incorrect. The reaction between an amino acid and its cognate tRNA requires ATP as a substrate, and the reaction produces AMP and the charged tRNA. The third product is pyrophosphate, and its fate is to be hydrolyzed to two molecules of inorganic phosphate. What textbook are you using? If you think that GTP is not involved in protein synthesis (later in the process than the tRNA syntheses), then you need a better source of information on protein synthesis than whatever you are using now.

Edited August 18, 2015 by BabcockHall

[GnothiSeauton]

I use Karlson. It's a little bit confusing book.

I will try to find information about protein synthesis somewhere else and try to solve problem again. I think that number of amino acids I calculated correctly so I'll focus on high energy bonds

[BabcockHall]

Try looking in the index for the three steps of protein synthesis. Or try looking up recognition of the anticodon and translocation of the ribosome.

Edited August 18, 2015 by BabcockHall

[GnothiSeauton]

Ok I think I got it, this will be long:

1.transcription

-during transcription in order to make mRNA I have to gather nucleoside three phosphates.

-I need to gather only the exon part of DNA

-every time nucleoside three phosphate clicks with DNA, bond breaks

 

So,

 

Wrecked bonds in transcription=number of exons that are in DNA=number of nucleotides in mRNA

 

2.activation

a)AA+ATP->complex AMP-AA +PPi (1 bond is destroyed)

b)complex AMP-AA + tRNA->AA-tRNA +AMP (1 bond is destroyed)

 

total wrecked bonds in activation=2* number of amino acids

 

3.translation

total wrecked bonds=number of GTP=number of amino acids

 

Formula

wrecked bonds total=number of exons+2*number of amino acids+number of amino acids

wrecked bonds total=3*number of amino acids+number of exons

 

So, I guess: 1230+3*410=2460

Edited August 18, 2015 by GnothiSeauton

[BabcockHall]

Ef-Tu is the protein involved in codon/anticodon recognition, and this spends one GTP per peptide bond. Ef-G is responsible for translocation of the ribosome, and it also hydrolyzes GTP.

 

With respect to mRNA synthesis, look at the reaction catalyzed by RNA polymerase, and see if that helps.

[GnothiSeauton]

Think I did it!

 

In translation I use 4 energy bonds: one for initiation, one for aa binding, one for synthesis of peptide bond and one for translocation.

 

Total number on bonds: n(nucleotides-from transcription)+2n(aa due to activation)+4n(aa due to translation)

[BabcockHall]

I have been ignoring initiation and concentrating on adding one amino acid residue to a growing polypeptide. My bookkeeping is a bit different. There is no energy input in the step (sometimes called transpeptidation) in which the new peptide bond is actually formed. I agree that there is one high-energy bond spent for recognition and one for translocation. How many high-energy bonds are spent to make a charged tRNA?

[GnothiSeauton]

To make charged tRNA I need two bonds:

1st step AA +ATP->AA-AMP CPMLX + PPi (1 bond wrecked)

2nd step AA-AMP CMPLX +tRNA-> AA-tRNA +AMP (1 bond wrecked)

[BabcockHall]

You obtained the correct number of high-energy bonds, but you used nonstandard accounting. The bond between the alpha and beta phosphorus atoms in ATP is a high energy bond, so counting that one is fine. The hydrolysis of pyrophosphate to 2 molecules of inorganic phosphate is the other bond that is spent. Putting it another way, the sum of the reactions of an aminoacyl-tRNA synthetase and inorganic pyrophosphatase creates a charged tRNA but it also turns ATP into AMP and two molecules of inorganic phosphate. To resynthesize ATP requires that two phosphoanhydride bonds are re-formed.

Edited September 8, 2015 by BabcockHall

[GnothiSeauton]

Thank you so much!