11 - From RNA to Protein Part I

Translation

Converting the mRNA sequence into the language of amino acids

What is an exception of using the code

Mitochondria

What is the adaptor molecule for translation

tRNA

What is tRNA

Small set of RNA molecules

Characteristics of tRNA

80 nucleotides in length

Contains some double helical segments

Two critical regions of unpaired nucleotides

What are the two critical regions of unpaired nucleotides

Anticodon

Aa attachment site

Anticodon

Complementary to mRNA codon

Where is the amino acid attachment site

3’ end

What is a wobble

First two positions of the codon must be matched correctly with the anticodon, but there can be mismatch in the third

How is tRNA synthesized and where

By RNA polymerase III in the nucleus

How is tRNA synthesized

First as a precursor molecule with introns that must be removed

How is the splicing of tRNA different

No lariat formation, only a “cut-and-paste” action using an endonuclease and a ligase

What form must tRNA be in otherwise it is useless

Cloverleaf form PRIOR to modifications

Why is there ~50 different tRNAs

Because of chemical modifications of some bases

Aminoácido-tRNA synthetase

Required by tRNA for recognition and attachment of the correct amino acid to 3’ end

How many AA-tRNA syntheases

20, each specific for one amino acid

What is the reaction of tRNA coupled to

Hydrolysis of ATP

What must synthetase recognize

Matching tRNA anticodon

What are the nucleotide biding pockets

Complementary in shape and charge to a nucleotide in the anticodon

Synthetase active site has what

High affinity for the appropriate amino acid

What mechanism is there to ensure appropriate amino acid fit

Second proofreading mechanism (for AAs similar in structure) moves bound amino acid into an editing site; if it fits, its rejected by editing site

What kind of bonds are formed between amino acids

Peptide bonds

Where are the peptide bonds formed on the chain

Between caro yo group at end of growing peptide chain and free amino group on incoming amino cid

What direction is protein syntehsized

N to C

What energy is used to attach next aa

Caro yo end is still covalently attached to tRNA, the breaking of this bond is used

How many different ribosomal proteins make u the ribosome

50

How many subunits fit together

2, one large one small

What is the small subunit responsible for

Matching tRNA to codon on mRNA

What is the large subunit responsible for

Catalyzes the formation of peptide bonds between amino acids

How many binding sites on a ribosome for RNA

4

What do the A and P site do

Hold tRNAs tightly if the anticodon forms base pairs with a complementary codon on the mRNA

What does the E site do

Exit site of tRNA

What does the site that isn’t EPA do

For mRNA

What are the four major steps to chain elongation

1. tRNA binding

2. Peptide bond formation

3. Large subunit translocation

4. Small subunit translocation

Peptide synthesis steps

1. Aminoacyl-tRMA molecule binds to a vacant A tie as long as the codon and anticodon match’ p site is bound by another tRNA

2. Carboxyl end of polypeptide chain is released from the tRNA at the P-site and new peptide bond is formed

3. Large subunit translocatees relative to the small subunit; sites are now hybrid: E and P on large subunit, P and A on small

4. Smal subunit translocates, moving into the mRNA 3 nucleotides into the A-site

   1. This resets the ribosome

Where does a new aminoacyl-tRNA bind

MRNA codon in A-site

How is the mRNA strand translated

5’ to 3’ direction starting with amine terminus

What factors speed up translation process

Elongation factors, EF1 and EF2

What is another purpose of EF1 and EF2 besides speeding up process

Check tRNA/aino acid pairing for accuracy, by calling GTP forth or not

How is codon-anticodon match checked

• small rRNA subunit forms h bonds between codon and anticodon; if match if correct, GTP hydrolysis occurs which moves the translation process along

• If match is incorrect, tRNA leaves ribosome

Accuracy of aa matching

99.99%

Ribosomes

Proteins + rRNA

What s rRNA responsible for

Catalytic activity in forming covalent peptide bonds, not proteins

What are ribozymes

RNA molecules that have catalytic activity

What are tRNA also responsible for

Catalytic activity by donating and OH to the active site