Exam 3 Flashcards
Define Translation
- process where an mRNA molecule is read by the ribosome to make a protein
The mRNA is read in pairs of three nucleotides called______
Codons
Each codon encodes one of (how many) amino acids
20
Ribosomes reads the codons and links the amino acids together in the correct order by forming _________
Peptide Bonds
Define tRNA
- RNA molecules that read the mRNA in groups of three and bring in the correct amino acid
What two things the tRNA molecule contains?
- Amino acid attachment site
- amino acid covalently attached (via an ester bond)
- amino acid covalently attaches to either the 2’ or 3’ -oh of the ribose
- amino acid covalently attached (via an ester bond)
- Anticodon region
- a group of three nucleotides that will base pair with the codon it is reading
- there is at least one tRNA for each amino acid
- a group of three nucleotides that will base pair with the codon it is reading
When an amino acid is attached to a tRNA it is called an _____________
aminoacyl-tRNA
Define Genetic Code
- relationship between the sequence of bases in DNA and the sequence of amino acids in proteins
What are some features of the genetic code?
- 3 nucleotides represent an amino acid
- each of the 20 amino acids are represented by a codon
- the code is nonoverlapping
- the nucleotides are always read in pairs of three without overlap
- ex) the ABCDEF is read ABC DEF NOT ABC BCD CDE etc.
- the nucleotides are always read in pairs of three without overlap
- the code is read continuously
- no nucleotides are every skipped
- the code is degenerate
- mose amino acids are encoded by more than one codon
- exceptions are amino acids Methionine and Trytophan b/c they only have one codon each
- mose amino acids are encoded by more than one codon
There are (how many) total codons?
- 64
- 61 codons for amino acids
- 3 are stop (termination) codons
- 61 codons for amino acids
Define Synonyms
- codons that encode for the same amino acid
- most differ at the 3rd position of the codon (wobble position)
What are some advantages of having a degenerate genetic code with multiple synonyms for amino acids?
- if not defenerate, then we would have 20 codons that encode amino acids and 44 stop codons
- 64 possible triplets from the nucleotide bases
- probability of mutating to a termination codon would be higher leading to a nonfunctional truncated protein
- silent mutation may occur resulting in the same amino acid being produced
Silent Mutation
- a mutation that results in the same amino acid being produced
- lowers the change of deleterious mutations
- ex) mutation of CCC (encodes proline) to CCA still results in a proline amino acid
- lowers the change of deleterious mutations
Translation Powerpoint
Slide 13
Question
True of False
The genetic code is universal
False
The genetic code is Nearly universal but there are differences
What is a E. coli Ribosome?
- a large complex containing protein and ribosomal RNA (rRNA) that is approx. 2.5 Mdaltons in size
- estimated that the approx. 20,000 ribosomes in an E. coli cell makes up approx. 1/4 of the total cell mass
- ribosome can be broken down into a large subunit (50S) and a small subunit (30S)
- 50S
- 34 proteins and 2 rRNA molecules
- 30S
- 21 proteins and 1 rRNA molecule
- 50S
What type of RNA structure is located in the 30S?
16S
True or False
RNA makes up approx. 2/3 of the total ribosoma mass
True
True or False
mRNA passes through the cleft formed by the two subunits
True
Translation PP
Slide 17
What is the basic steps/overview of translation?
- ribosome reads the codons in an mRNA transcript in the 5’ to 3’ direction
- amino acids arrive at the ribosome covalently linked to a tRNA
- the tRNA anticodon region base pairs with the correct codon in the mRNA
How does the ribosme know where to start in translation?
- mRNA contains a purine rich region that pairs with the 16S rRNA of the ribosome
- Shine-Dalgarno sequence
- this region is upstream of the sequence that pairs with the initiator tRNA that starts protein synthesis
- Shine-Dalgarno sequence
True or False
The Shine-Dalgarno sequence binds with the 16S rRNA region down steam of the sequence that pairs with the initiator tRNA that starts protein synthesis.
False
The region is upstream
not down
Translation Initiation has several steps.
Explain in detail the steps.
- the 30S subunit binds IF-1 and IF-3 then the mRNA
- the 1st tRNA binds at P site via codon anti-codon binding
- the 16S rRNA binds Shine-Dalgarno to ensure proper alighnment
- the IF-1 and IF-3 binds at A site and E site respectively
- purpose is to not allow the 50S subunit bind yet
- the 1st tRNA binds at P site via codon anti-codon binding
- IF-2 hydrolyzes GTP thus dissociating IF-1, 2, and 3 leaving the initiation complex
- once everything is properly aligned, IF-2 triggers the release of all the IF proteins thus allowing the 50S subunit it bind to the 30s subunit
- ribosome is now ready to start translation
What are the three active sites in a ribosome during translation?
- A (aminoacyl)
- P (peptidyl)
- E (exit)
How does creating a peptide bond work in a ribosome?
- the first tRNA (initiator tRNA) binds to the P-site
- tRNA arrives and base pairs with mRNA in the A-site
- peptide bond is formed between the two amino acids on the tRNAs by the 23S rRNA in the 50S subunit (peptidyl transferase center)
- once a peptide bond is formed, hydrolysis of GTP provides energy that translocates the mRNA and tRNAs
- the two tRNAs now occupy the P and E sites
- tRNA in the E site will dissociate from the ribosome
- next amino acid can added through same mechanism
- continues until a stop codon is read
What is RF1 and what is it used for?
- release factor
- when a stop codon binds the A site, this protein will bind and trigger the peptide to release
- a water molecule attachks the ester bond between the tRNA and the last amino acid in the P-site, causing peptide release
- hydrolysis
- a water molecule attachks the ester bond between the tRNA and the last amino acid in the P-site, causing peptide release
- when a stop codon binds the A site, this protein will bind and trigger the peptide to release
True or False
A ribosome reads the mRNA in the 3’-5’ direction to make a polypeptide
False
ribsome reads the mRNA in the 5’-3’ direction
True or False
Proteins are synthesized from N-terminal to C-terminal
True
True or False
Proteins are the most versatile of the macromolecules and perform functions in essentially all biological processes
True
True or False
Every protein has a unique 3D shape that dictates its function
True
Proteins can be classified based on their ________
function
Proteins are ________ _________ made up of ________called _____ ______
organic polymers; monomoers; amino acids