Chapter 9: Proteins and translation

What are proteins?

Polymeric structures made out of 20 different amino acids that share almost the same structure with the exception of their side-chain

WHat are the 2 most important functional groups in amino acids?

The carboxyl group and amino group as they are essential in the production of amino acids

What are the 4 different classes of amino acids?

• Nonpolar

• Polar and uncharged

• Positively charged

• Negatively charged

What is the primary protein structure?

The structure that contains a sequence of amino acids bonded by peptide bonds

What is the secondary protein structure?

The local folding of the peptide chain of amino acids

What are the two types of secondary structures?

Alpha helical and beta sheet, with the alpha helical structure being the most common

What is the tertiary protein structure?

An overall 3D structure that is made out of secondary protein structure and sometimes involves the binding of small cofactors

What is the relationship between a DNA sequence and a protein sequence?

A DNA sequence is lined up in a specific order that determines the proteins sequence

what does a codon consist of?

A combination of 3 nucleotides that determines a single amino acid and can provide 64 different possibilites

What does genetic code not overlapping mean?

It means that codons are read 3 at a time and dont overlap one another

How is genetic code continuous?

It is read without interruption starting at a fixed point to the end without any gaps

What proves genetic code is continuous?

When 3 bases are inserted or deleted in RNA, the phenotype does not become mutated

Why is genetic code degenerate?

There are several ways to make the same amino acids

What occurs if one or two bases are inserted or deleted in RNA?

Mutation occurs

How are some codons able to change into stop codons?

Through the change of a single nucleotide

Why is the starting codon, AUG, special?

Its coupled with other sequences to signal where translation begins

what are ribosomes RNA (rRNA)?

They are RNAs that provide support to the structure of ribosomes and are able to catalyze protein synthesis

How do tRNA fold?

They fix into a cloverleaf shape with the bottom of the loop containing anticodons that form base pairing with the mRNA transcript

How are tRNA transcribed?

They are transcribed with nucleotides that are important for reading genetic codons and are altered by enzymes into other nucleotides

What is wobble base pairing?

A type of RNA base pairing that allows for flexibility at the 3rd position of the anticodon and 1st position of the mRNA transcript

How does wobble base pairing help when tRNA is not present for translation?

Another tRNA will help continue the process even if the 3rd position isnt a perfect anticodon match

What occurs to tRNA after being transcribed?

It gets catalyzed by an enzyme called aminoacyl-tRNA syntheses

What is aminoacyl-tRNA syntheses?

A process that allows for a specific amino acid to bind to its corresponding tRNA molecule, forming a charged tRNA

What occurs in the aminoacyl-tRNA syntheses process?

In the first step: the enzyme binds both the amino acid and the tRNA molecule to its active site in order to check whether the tRNA is able to be charged with the amino acid and if the amino acid can couple with the tRNA

In the second step: A condensation reaction occurs that allows for the tRNAs 3’ hydroxyl group to bind to the carboxyl group of the amino acid. Resulting in a charged tRNA

What occurs as ribosomes reads an mRNA transcript?

The mRNA transcript is read in triplet codons, ensuring the tRNA can deliver the correct amino acid in order for ribosomes to synthesize it

What is the A site of the ribosome?

The site where a charged tRNA enters the ribosome and delivers its amino acid to the mRNA codon match in the ribosome

What is the P site of the ribosome?

The site where the amino acids are bonded together by peptide bonds and form polypeptide chains

What is the E site of the ribosome?

The site where uncharged tRNA exits from the ribosome after the amino acid has been delivered

What occurs in the initiation phase of translation in bacteria?

The shine-dalgarno sequence in the mRNA transcript binds to the 16S rRNA and recruits the small ribosome subunit

Then initiation factors recruit initiator tRNA to the small subunit to bind to the start codon on the mRNA, with some hydrolyzing GTP to proceed. causing the large subunit to associate with the small subunit to begin translation

What occurs in the initiation phase of translation in eukaryotes?

the 5’ and 3’ ends are recognized by initiation factors and binds to them, forming 2 different complexes. Then the tRNA binds to the start codon on the mRNA and once all factors are present, the large subunit is recruited and begins translation

What occurs in the elongation phase of translation?

A second tRNA arrives to the A-site to deliver a second A.A then moves to the P-site to form into a polypeptide chain with the amino acid present from the initiation tRNA

Ribosome will then move one codon down towards the 3’ direction, moving each tRNA to the next site over, with the uncharged tRNA from the P-site exiting from the E-site and a new tRNA from the A-site moving to the P-site

What if the A.A isnt a good match during elongation?

It will be rejected and wont allow for translation to continue until a good match is present

What occurs during the termination phase of translation?

Release factors bind to the stop codon and cause the polypeptide chains formed in the p-site to be released and causing the ribosome subunits to dissociate from one another and fall off the mRNA

What occurs if there is a mutant tRNA that changes the original amino acid in a cell?

A suppressor mutation rescues the cell by recognizing the mutant tRNA and brings in the correct amino acid that removes the mutant one, ensuring the cell is able to survive survive

What occurs after translation is completed?

mRNA is exported out of the cytosol and the protein goes through a secreted pathway to reach its final destinaiton

How is translation regulated in eukaryotes?

They are regulated by developmental signals that affects the function of initiation/elongation factors