Translation Flashcards
What is the function of tRNA?
A cell translates an mRNA message into protein with the help of transfer RNA
- tRNA transfer amino acids to the growing polypeptide in a ribosome
- Translation is a complex process in terms of its biochemistry and mechanics
How much amino acids are coded for by DNA?
More than 300 amino acids known, but only 20 coded for by DNA
-20 common amino acids with specific codons in the genetic code
What are the general structure off amino acids?
A central a-carbon atom
A Carboxylic acid group
An amino group
An H atom
A variable R group (side chain):
-any molecule can replace the ‘R’. For instance glycine has an -H and alanine has -CH3 .
- the variable R group defines different amino acid species
The a-carbon is carbon 2, the carboxyl carbon is 1.
Different amino acids are chosen in protein synthesis
Describe making a polypeptide
- Amino acids of a polypeptide chain are joined by a peptide bond formed between the carboxyl group of one amino acid and the amino group of an adjacent amino acid.
- The N-terminal end defines the beginning of the polypeptide chain and the C-terminal defines the end of the polypeptide chain
Who cracked the genetic code? How?
- In 1968, Marshall Nirenberg received the Nobel Prize for deciphering the genetic code. He. Shared the award with Robert W. Holley and Har Gobind Khorana
- Nirenberg used synthetic mRNAs and in vitro translation systems to decipher the genetic code. For example:
- a synthetic mRNA with the sequence UUUUUUUUUUUU translated to the polypeptide: Phe Phe Phe Phe
Or - a synthetic mRNA with the sequence UCUCUCUC translated to the polypeptide: Ser-Leu-Ser-Leu
Describe the mRNA code
This is a triplet code that consist of three nucleotides.
***Of the 64 triplets, 61 code for amino acids; 3 triplets are “stop” signals to end translation
How is the mRNA code read?
The code is comma free
The mRNA is read continuously, three nucleotides at a time, without skipping any nucleotides of the message
The code is never overlapping, the mRNA is read in successive groups of three nucleotides.
Explain the genetic code being universal
Almost all organisms found on earth use the same genetic language
Exceptions- mitochondria of some organisms and the genomes of the protozoan Tetrahymena have minor changes to the code
Explain the genetic code being degenerate
With two exceptions, (only AUG codes for methionine and only UGG codes for tryptophan), more than one codon occurs for each amino acid
What are the start and stop codons ?
AUG (which codes for methionine) is almost always the start codon for protein synthesis.
Three other codons do not specify an amino acid, but are stop codons indicating the termination of the translation process. These codons are UAG (amber), UAA( ochre) and UGA (opal)
What is the reading frame ?
A sequence of nucleotides in mRNA is read in sequential sets of three nucleotides which are translated into amino acids.
There are three possible reading frames in protein synthesis
- The same mRNA sequence can specify three completely different amino-acid sequences, depending on the ‘reading frame’.
What are mutations?
Changes in the genetic material of a cell or virus
What are point mutations?
Chemical changes in just one base pair of a gene
The properties of the genetic code make it such that a change in…
A single nucleotide in a DNA template strand can lead to the production of an abnormal protein
Mutations within a gene can be divided into two general categories:
- Nucleotide-pair substitutions
- One or more nucleotide-pair insertions or deletions
What is a nucleotide-pair solutions?
When one nucleotide is replaced and its partner with another pair of nucleotides
What are silent mutations?
These have no effect on the amino acid produced by a codon because of redundancy in the genetic code
What are missense mutations?
These still code for an amino acid, but not the correct amino acid
What are nonsense mutations?
When a change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein
What are insertions and deletions?
Insertions and deletions are additions or losses of nucleotide pairs in a gene
These mutations have a disastrous effect on the resulting protein more often than substitutions do
What 8s a frameshift mutation?
Insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation
When can spontaneous mutations occur?
Spontaneous mutations can occur during DNA replication, recombination, or repair
Mutagens are physical or chemical agents that can cause mutations
Are tRNA molecules identical?
Molecules of tRNA aren’t identical
Each carries a specific amino acid on one end
-Each has an anticodon on the other end; the anticodon base-pairs with a complementary codon on mRNA
What is an anticodon?
This is the sequence of three nucleotides that base-pairs with a codon in mRNA
Where is the amino acid attached to the tRNA?
The amino acid matching the codon/anticodon pair is attached to the 3’ end of the tRNA
What is the structure of tRNA?
- a tRNA molecule consists of a single RNA strand that is only about 80 nucleotides long- primary structure
- flattened into one plane to reveal its base pairing- secondary structure
- a tRNA molecule looks like a cloverleaf- tertiary structure
Because of hydrogen bonds, tRNA actually twists and folds into a three dimensional molecule
tRNA is roughly L-shaped
What two steps are required for translation?
- A correct match between a tRNA and an amino acid, done by the enzyme aminoacyl-tRNA synthetase
- A correct match between the tRNA anticodon and an mRNA codon
Sometimes cells do not carry tRNAs for all codons? How is this problem solved?
Wobble is a property that allows an identical tRNA to bind to different codons at the third base. This allows some tRNAs to bind to more than one codon
What is the function of ribosomes?
Ribosomes facilitate specific coupling of tRNA anti codons with mRNA codons in protein synthesis
What are the subunits of the ribosome ?
The ribosome is made up of two subunits (large and small) which contain proteins and ribosomal RNA (rRNA)
Different ribosomes in eukaryotes and prokaryotes
Bacterial and eukaryotic ribosomes are somewhat similar but have significant differences:some antibiotic drugs specifically target bacterial ribosomes without harming eukaryotic ribosomes
Go in detail with differentiating eukaryotic and prokaryotic ribosomes
- The ribosome has two subunits each composed of rRNA and numerous proteins
- In E. Coli the small 30S subunit is involved in the initial binding to the mRNA
- The larger 50S subunit contributes the peptidyl transferase activity
- Both the 30S and 50S contribute to the E, P, and A sites
Give the anatomy and functioning of a ribosome
- A ribosome has three binding sites for tRNA
- The P site holds the tRNA that carries the growing polypeptide chain
- The A site chain holds the tRNA that carries the next amino acid to be added to the chain
- The E site is the exit site, where discharged tRNAs leave the ribosome
What are the stages of translation?
Initiation
Elongation
Termination
All three stages require protein “factors” that aid in the translation process
Explain the initiation of translation
The initiation stage of translation brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits
First, a small ribosomal subunit binds with mRNA and a special initiator tRNA
Then, the small Subunit moves along the mRNA until it reaches the start codon (AUG).
Proteins called initiation factors bring in the large subunit that completes the translation initiation complex
Explain the initiation of protein synthesis of prokaryotes
-A 30S ribosomal subunit, complexed with initiation factors and GTP binds to mRNA and fMet initiator tRNA to form a 30S initiation complex
The fMet initiator tRNA binds to the start codon AUG
-The 30S ribosome binds to a specific mRNA sequence called the Shine-Dalgarno sequence (typically 5’ -AGGAGG- 3’)
Differentiate the initiation of prokaryotic and eukaryotic protein synthesis
- The 50S ribosomal subunit binds, forming a 70S initiation complex during which time the initiation factors are released and GTP is hydrolyzed
- In eukaryotes, the small ribosomal subunit first binds to methylated cap at the 5’ end of the mRNA. It then migrated to the initiation site-usually the first AUG
Describe the elongation of the polypeptide chain
- During the elongation stage, amino acids are added one by one to the preceding amino acid at the C-terminus of the growing chain
- Each addition involves proteins called elongation factors and occurs in three steps: codon recognition, peptide bond formation, and translocation
Translation proceeds along the mRNA in a 5’ to 3’ direction
What are the steps of elongation?
- A group of proteins called elongation factors (EF-Tu) and GTP usher the appropriate tRNA into the A site of the ribosome
- Peptide bond formation between the two adjacent amino acids by peptidyltransferase
- The formation of the first peptide bond causes the initiating tRNA in the P site to release its amino acid and dissociates from the mRNA
- The ribosome moves along to the next codon (requires elongation factors and GTP)
What is the function of peptidyl transferase ?
The formation of a peptide bond between the first two amino acids (fMet and Ser) of a polypeptide chain is catalyzed on the ribosome by peptide transferase
Explain the termination of translation
- termination occurs when a stop codon (UAG, UAA and UGA) in the mRNA reaches the A site of the ribosome
- The A site accepts a protein called a release factor
- The release factor causes the addition of a water molecule instead of an amino acid
- This reaction releases the polypeptide, and the translation assembly then comes apart
- Eukaryotes possess a single releasing factor- eRF
- Prokaryotes possess three releasing factors: RF1 (recognizing UAA and UAG ), RF2 (recognizes UAA and UGA) and RF3 which stimulates termination
What is a polysome?
A number of ribosomes can translate a single mRNA simultaneously, forming a polyribosome. (Or polysome)
Polyribosomes enable a cell to make many copies of a polypeptide very quickly
Is translation sufficient to make a protein?
It usually isn’t
Polypeptide chains are modified after translation or targeted to specific sites in the cell
During and after synthesis, a polypeptide chain spontaneously coils and folds into its three dimensional shape
Some polypeptides come together to form the subunits of a protein
What are some post-transnational modifications?
Proteins may require other post-translational modifications before doing their job:
- Phosphorylation
- glycosylation
- lipid anchoring
Some polypeptides are activated by cleavage
-Zymogen activation of digestive enzymes
-Proteolytic cleavage of insulin
Some proteins are capable of splicing themselves using intern (auto-cleavage and peptide bond forming domains within a polypeptide)
Contrast the populations of ribosomes
Two populations of ribosomes are evident in cells: free ribosomes(in the cytosol) and bound ribosomes (attached to the ER)
Free ribosomes mostly synthesize proteins that function in the cytosol
Bound ribosomes make proteins of the endomembrane system and proteins that are secreted from the cell.
Ribosomes are identical and can switch from free to bound
Explain the functioning of SRP
- polypeptide synthesis always begin in the cytosol
- Synthesis finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ER
- Polypeptides destined for the ER or for secretion are marked by a single peptide
The signal mechanism for targeting proteins to the ER
- A signal-recognition particle (SRP) binds to the signal peptide
- The SRP brings the signal peptide and its ribosome to the ER
