BIOMG 3320 LEC 20

What does breakage of high energy bonds do?

It releases energy

What type of bonds are in hydrolysis reactions

High energy bonds

Which high energy bond in ATP is broken and releases energy

The high energy phosphoanhydride bond between gamma and beta phosphate in ATP is broken and releases energy

Does the breakdown of pyrophosphate release energy

Yes, it also releases energy

What does this energy from breaking bonds in ATP and pyrophosphate provide?

It provides the driving force of chemical reactions

What type of energy bonds are ester bonds

They are intermediate energy bonds

What does breakage of ester bonds do? And how does this compare with hydrolysis?

Breakage of ester bonds also releases energy but much lower than hydrolysis

What type of energy bonds are amides and peptides bonds?and what is an example?

They are the lowest energy bond. || Ex: Glycylglycine + H2O → 2 glycine

What type of bonds/reactions have the highest energy?

Hydrolysis reactions. I.. phosphoanhydride bond between gamma and beta phosphate in ATP and the breakdown of pyrophosphate

What type of bonds have the lowest energy?

Amides and peptide bonds

Organize the types of bonds from highest to lowest

Phosphoanhydride bonds (hydrolysis reaction is highest) || Ester bonds (intermediate) || Amides and Peptide bonds (lowest)

What is the purpose of the first reaction of charging tRNAs

To form aminoacyl adenylate

Describe the mechanism of the first reaction (forming aminoacyl adenylate)

1. The alpha carboxyl group of an amino acid attacks alpha-beta phosphoanhydride to form 5' aminoacyl adenylate. || In doing so, pyrophosphate is released and a mixed anhydride bond is formed. Thus, the amino acid is now activated

What gives the energy to form a 5' aminoacyl adenylate?

Breakage of high energy phosphoanhydride bond

Is the mixed anhydride bond also an energy containing bond

Yes, the mixed anhydride bond that was formed in the first reaction of charging tRNAs is also an energy containing bond

How does the amino acid become activated (charged tRNA pathway)

The alpha carboxyl group of an amino acid attacks the alpha beta phosphoanhydride bond of ATP to form 5' aminoacyl adenylate, which releases pyrophosphate and forms a mixed anhydride bond.

What is the purpose of the second reaction of charging tRNAs?

To attach amino acid to the tRNA

Describe the mechanism of the second reaction of charging tRNAs (attaching amino acid to tRNA)

1. The aminoacyl group is transferred directly to the 3' OH of the 3' terminal A residue off tRNA, generating the amino acyl tRNA product || 2. The aminoacyl tRNA is formed and an esterbond is formed

How is the aminoacyl tRNA product generated?

The aminoacyl group is transferred directly to the 3'OH of the 3' terminal A residue of tRNA

Where is the amino acyl group directly transferred?

To the 3'OH of the 3'terminal A residue of tRNA

What is the overall flow from charging?

You flow from high to low energy state as you go from high energy phosphoanhydride bond to intermediate ester to low energy peptide bond between amino acids as you build a protein

What is the overall reaction of charging tRNAs?

Amino Acid + tRNA + ATP - Mg2+--> aminoacyl-tRNA + AMP + 2Pi

What is the change in Gibbs's free energy / Delta G

-29 kJ/mol || Goes to a more favorable state!

What is the charging of amino acid to tRNA catalyzed by?

Aminoacyl tRNA synthetase

What allows aminoacyl tRNA synthetase to recognize amino acids/tRNA specifically?

Aminoacyl tRNA synthetase has specific anticodon and 3' end to recognize amino acids/tRNA specifically

What is the Second Genetic Code?

It refers to the specific recognition between aminoacyl-tRNA synthetase and tRNAs

How many synthetases are there per amino acid?

There is one synthetase for each amino acid due to specific catalytic domains

How many tRNAs can each synthetase recognize?

Each synthetase can recognize multiple tRNAs if each of those tRNAs code for the same amino acid

Finish these... 1 amino acid,.... And more than 1 tRNA,....

1 amino acid, 1 synthetase || More than 1 tRNA, 1 synthetase

What enzyme reads the structure of a tRNA?

Aminoacyl-tRNA synthetase reads the structure of a tRNA

What if tRNA is loaded with the wrong amino acid?

Proofreading ability from ile-tRNA synthetase?

What two sites does tRNA's have

An editing site and an activation site

Describe how proofreading occurs in tRNA?

For isoleucine-tRNA, a valine could bind the activation site, but it is also smaller than isoleucine, so it will fit into the editing site as well. When it binds to the editing site, it will be hydrolyzed to valine and AMP. Now a correct isoleucine can bind the tRNA

Does Gln-tRNA synthetase need an editing site to distinguish Gln form Glu (pollev)**

No

What is protein synthesis catalyzed by?

By the ribosome, a supramolucular molecule

• What are the 3 ways that the Amino-acyl tRNA synthetase ensures that proteins are made correctly (proofreading)!?

1.) the initial binding of the amino acid to the enzyme. : Both steps happen on the same active site of the synthetase but the initial binding of the the amino acid to the enzyme, in order to get activated to aminoacyl AMP, is very specific to the shape of the amino acid

2.)When you make the incorrect amino acyl AMP product, it can bind to a second active site (hydrolytic active site) on the enzyme which will hydrolyze that aminoacyl AMP

3. Most of the synthetases can work in reverse, they can hydrolyze the ester linkages between tRNA and amino acids, this hydrolysis is much faster for incorrectly charged tRNAs

Where does the binding of codon and anticodon occur?

Via the ribosome

How many different macromolecules cooperate to synthesize polypeptides?

Almost 300 different macromolecules cooperate to synthesize polypeptides

How much chemical energy used by a cell for all biosynthetic reactions does protein synthesis account for?

Protein synthesis can account for up to 90% of the chemical energy used by a cell for all biosynthetic reactions

How many ribosomes does each E. coli cell contain and what percent of dry weight of the cell is it?

Each E. coli cell contains 15,000 or more ribosomes, making up almost 25% of the dry weight of the cell

What is the number for the bacterial ribosome?

70S

What is the 70S bacterial ribosome broken into?

It is broken into large 50S and small 30S subunits

What is the number for the Eukaryotic Ribosome?

80S

What is the 80S Eukaryotic Ribosome broken into?

It is broken into large 60S and small 40S subunits

How much RNA and protein are in ribosomes

⅔ RNA and ⅓ Protein

What did Nomura demonstrate in 1960?

That both ribosomal subunits can be broken down into their protein and RNA components, and then reconstituted in vitro.