Translation. Flashcards
Define a codon?
A triplet of 3 nucleotides that codes for an amino acid.
What are monomers?
The individual building blocks in a polypeptide.
Define mutagens?
Chemical or physical agents that can cause DNA damage leading to mutations.
Define mutations?
Changes in the genetic material of a cell or virus.
Define point mutations?
Mutations in the genetic code that affect just 1 nucleotide.
E.g. A nucleotide that should be a T is changed to a C.
Define a polynucleotide?
A string of nucleotides that are been joined together.
How are nucleotides joined together in a polynucleotide?
By phosphodiester bonds at the 5 prime end and 3 prime end.
Define a polypeptide?
A string of amino acids that are joined together.
Do polypeptides have phosphodiester bonds?
No.
They molecules have peptide bonds which link an amino to a carboxyl end.
Define a polymer?
A substance that is composed of similar units e.g. a protein.
Define a polysome?
A collection of ribosomes that come together to synthesise a protein from 1 mRNA strand.
Define translation?
The process by which mRNA is translated to proteins.
When does translation occur?
After DNA has been transcribed to RNA.
Where does translation take place?
In the cytoplasm at the ribosomes.
What form of RNA will help the ribosomes translate mRNA to proteins?
tRNA will bring individual amino acids to the growing polypeptide chain.
How many known amino acids are there?
Over 300 amino acids.
How many amino acids can be made by the body?
20.
What will the body use individual amino acids to form?
As the individual building blocks for a protein.
What are the monomers that make up a protein?
Amino acids.
What are 5 examples of proteins that can be made from amino acids?
Enzymes.
Hormones.
Antibodies.
Spider webs.
Poisons.
What are the functional groups of an amino acid?
There is an amino end (NH3+).
A carboxylic acid end (COOH).
An R group.
What is the alpha carbon in an amino acid?
The carbon that is bound to the functional groups.
What is the alpha carbon on an amino acid bound to?
The carboxylic acid.
The amino group.
The R group.
A hydrogen.
What gives each amino acid their unique properties?
The R group.
What is used to classify each amino acid?
R groups.
E.g. if the R group is polar, then the amino acid is classified as a polar amino acid.
Is the alpha carbon found at carbon 1 in the amino acid?
No.
The carbon from the carboxylic acid is found at carbon 1 and the alpha carbon will be carbon 2.
What 8 amino acids make up the non-polar amino acids?
GAV The Lazy PIMP.
Glycine. (Gly.)
Alanine. (Ala.)
Valine. (Val.)
Tryptophan. (Trp.)
Leucine. (Leu.)
Phenylalanine. (Phe.)
Isoleucine. (Ile.)
Methionine. (Met.)
Proline. (Pro.)
What 3 amino acids make up the branched amino acids?
Leucine. (Leu.)
Isoleucine. (Ile.)
Valine. (Val.)
What 6 amino acids make up the polar uncharged amino acids?
CATS Grab Trout.
Cysteine. (Cys.)
Asparagine. (Asn.)
Threonine. (Thr.)
Serine. (Ser.)
Glutamine. (Gln.)
Tyrosine. (Tyr.)
What 3 amino acids make up the basic amino acids?
Basic HAL.
Histidine. (His.)
Arginine. (Arg.)
Lysine. (Lys.)
What 2 amino acids make up the acidic amino acids?
AGcidic.
Aspartic Acid. (Asp.)
Glutamic Acid. (Glu.)
What bonds join amino acids together?
Peptide bonds.
How is a peptide bond formed?
When a dehydration reaction allows the carboxylic end to bind to the amino end of another amino acid.
What functional groups are exposed in a polypeptide?
There will always be a terminal carboxyl and amino end.
The R groups will stick out to the side.
What is a dipeptide?
2 amino acids that are joined together.
What determines that nature of a polypeptide?
The R groups.
What is the beginning of a polypeptide marked by?
The amino group.
What is the end of a polypeptide marked by?
The carboxylic group.
Which 3 scientists cracked the genetic code and when?
Marshall Nirenberg.
Robert Holley.
Har Gbind Khorana
In 1968.
What 2 things did Nirenberg use to decipher the genetic code?
He used synthetic mRNA’s.
An in vitro translation system.
How did the synthetic mRNAs and the in vitro translation system work in Nirebergs experiment to decipher the genetic code?
He added mRNA sequences and then looked to see which amino acids were formed.
E.g. If he used mRNA this sequence UUUUUUUUUUUU he got PHE-PHE-PHE-PHE.
Or, if he used UCUCUCUCUCUC he got SER-LEU-SER-LEU.
What did the results of Nirenbergs experiment tell him about the genetic code?
Each mRNA codon is coded for by a triplet of three nucleotides.
E.g. AUG always codes for methionine and it is also the start codon.
How many triplets are there in the genetic code?
64 triplets.
How many of the 64 triplets code for amino acids?
61 code for amino acids and the other 3 are stop codons.
What are the 3 stop codons and what are their colours?
UAA (ochre).
UAG (amber).
UGA (opal).
How is the genetic code always produced?
As a line of single letters.
There is no punctuation or spaces in the code and it is non-overlapping.
How is the DNA code read?
It is read continuously at a rate of 3 nucleotides at a time and no nucleotides are ever skipped.
Why is the genetic code said to be degenerate?
As more than 1 codon can code for an amino acid e.g. UUG and CUC can code for leucine.
Which codons will not code for more than 1 amino acid?
AUG which codes for methionine and UGG which codes for tryptophan.
Why can the genetic code never be confused?
As one codon can only code for single amino acid.
What amino acid will always be the 1st to be produced in a polypeptide?
Because AUG is the start codon, it means that methionine will always be the start of a polypeptide sequence.
What tells us that a sequence of nucleotides in mRNA are read in sequences of 3?
The reading frame.
If the location of the start codon is unknown on a strand of mRNA, how many possible reading frames could there be?
There are 3 possible reading frames that can be used for any piece of mRNA if the location of the start codon is unknown.
What would be the 3 possible reading frames of the following mRNA?
-AGACUCAGCGUUACCAGA-.
-AGACUCAGCGUUACCAGA-.
The 1st sequence may be correct.
If it is incorrect, we can move the reading frame one letter to the right.
-GACUCAGCGUUACCAGAA-.
If it is still incorrect then we can move the reading frame one more nucleotide to the right.
-ACUCAGCGUUACCAGAAU-.
One of these 3 possibilities will be correct.
How many possible reading frames are found on a strand of DNA where the start codon is unknown?
DNA will have 6 possible reading frames as it has 2 strands.
What can a DNA mutation result in?
The formation of faulty proteins as the same mutation will be transcribed to the mRNA.
What is a point mutation?
A change to a single nucleotide in a DNA sequence.
Why can a point mutation affect how a protein is made?
As a new amino acid will be placed in the protein and this will change the structure of the protein.
What is a common disease that arises due to a point mutation?
Sickle cell disease.
What is the point mutation that occurs in sickle cell disease?
The normal gene for haemoglobin contains the sequence CTT in its DNA.
A person with sickle cell will have a codon reading CAT instead.
How does the CAT codon in people with sickle cell affect transcription?
The RNA transcript will contain the codon GUA instead of GAA.
How does the faulty RNA transcript affect transcription in people with sickle cell?
It will code for valine instead of glutamic acid which will make haemoglobin will faulty.
Can some DNA mutations occur spontaneously?
Yes.
What are physical or chemical agents that can cause mutations?
Mutagens.
What are the 2 categories of genetic mutations that can occur?
Substitution mutations.
Insertion and deletion mutations.
What are the 4 types of substitution mutations?
Nucleotide pair substitutions.
Silent mutations.
Missense mutations.
Nonsense mutations.
What are substitution mutations characterised by?
They are mutations where part of the genetic code is removed and replaced with different nucleotides.
Define nucleotide pair substitutions?
Where a complimentary pair of nucleotides in a DNA strand is substituted for another pair.
Define silent substitutions?
Mutations that have no effect on the amino acid that is produced.
This is due to redundancy of the genetic code.
Define missense mutations?
These mutations will code for an amino acid, but it is the wrong amino acid.
Define nonsense mutations?
They change a codon into a stop codon and they will almost always lead to a non-functional protein.
What are insertion and deletion mutations?
They occur when parts of the genome are removed and not replaced.
Or when new nucleotide pairs are added to increase the size of the genome.
Define a one or more nucleotide pair insertion or deletion mutation?
When more than 1 pair of nucleotides may be removed or added into the chain.
Why can one or more nucleotide pair insertion or deletion mutations be disastrous?
Yes.
As they can change the reading frame meaning that the wrong proteins are synthesised.
What are frameshift mutations?
Mutations that change the reading frame.
Can both the insertion and deletion of nucleotides cause a frameshift mutation
Yes.
Are substitution or insertion and deletion mutations often worse for the sufferer?
Insertion and deletion mutations tend to be much worse than substitution mutations.
How can frameshift mutations be reversed?
By a process called a nearby addition mutation.
How does a nearby addition mutation reverse a frameshift mutation?
They will add a pair of nucleotides to the DNA strand which will repair the mutation.
What are the 2 subunits that make up the ribosome?
The large and small subunit.
Which ribosomal subunit will read the mRNA?
Both subunits of the ribosome will read the mRNA.
In what direction will the ribosomes read mRNA?
In the 5 to 3 direction.
What happens as the ribosomes reads each codon of mRNA?
tRNA will bring the corresponding amino acids to form the polypeptide.
What are the 3 sites that make up a ribosome?
The A site.
The P site.
The E sight.
How are the amino acids separated into different forms?
Each form carries a specific amino acid on one end and an anticodon on the other end.
How is the anticodon shown on a tRNA?
The nucleosides that make up tRNA will fold in such a way that the anticodon is shown.
What does the anticodon on an amino acid consist of?
3 nucleotides that are used to base pair to a complimentary codon on mRNA.
What are the last 3 nucleotides of tRNA at the 3 prime end?
The last 3 nucleotides of tRNA are always CCA-3.
How is the unique amino acid on a tRNA attached to the tRNA?
The carboxyl group is attached to the ribose of the last ribonucleoside at the 3 prime end.
The last ribose is always adenine.
How many structures does tRNA have?
A primary, secondary and tertiary structure.
What is the primary structure of a tRNA?
A single strand that is around 80 nucleotides long.
It has the sequence CCA on the 3 prime end.
An anticodon that is complimentary to a codon on RNA.
What is the secondary structure of a tRNA?
It is formed the pairing of some of the nucleotides within the RNA molecule causing the molecule to fold.
What is the tertiary structure of a tRNA?
The twisting of the folded tRNA molecule to for a structure that looks like a cloverleaf.
The activation of tRNA consists of how many steps?
2.
What is the 1st step of the activation of a tRNA?
The attachment of an amino acid to the tRNA.
How is the amino acid attached to the tRNA in step 1 of tRNA activation?
An enzyme recognises the amino acid to be attached.
It will bind to this amino acid and an ATP molecule.
Which enzyme will attach the tRNA in step 1 of tRNA activation?
An aminoacyl-tRNA synthetase.
What is step 2 of the activation of a tRNA?
The attachment of the tRNA to an amino acid.
How does aminoacyl-tRNA synthetase recognise which tRNA to attach an amino acid to?
It contains an RNA codon which will scan a molecule of tRNA for its anticodon.
If the anticodon matches the RNA codon then the enzyme can attach the tRNA to the amino acid.
What is the tRNA and amino acid complex also known as?
Aminoacyl tRNA (charged tRNA).
Will cells carry a tRNA to match every RNA codon?
No.
If a cell does not carry a tRNA to match every RNA codon, how does it add the correct amino acid?
By a property known as wobble.
How does the wobble property allow a cell to receive the correct amino acids even if that cell doed not carry a tRNA to match an RNA codon?
A single tRNA molecule can bind to different codons.
How can a single tRNA molecule can bind to different codons?
By forming non-traditional base pairs.
What does the ability of tRNA to form non-traditional base pairs allow for?
For a single tRNA molecule to recognise multiple codons
How does wobble affect an amino acid that is coded for by multiple codons?
The amino acid only needs 1 tRNA that will code for all those codons.
When will the 2 subunits of a ribosome come together?
During protein synthesis.
What are the ribosomal subunits composed of?
They are made up of specific proteins and rRNA.
How does the mRNA fit into the ribosomal structure?
It will fit in between the 2 subunits.
What do the differences in structure of prokaryotic and eukaryotic ribosomes allow Drs to do?
They can use drugs to target and destroy prokaryotic ribosomes without harming eukaryotic ribosomes.
What is the structure of the prokaryotic ribosomal subunits?
Both subunits add up to 70S.
The small subunit is 30S.
The large subunit is 50S.
What is the structure of the eukaryotic ribosomal subunits?
Both ribosomal subunits add up to 80S.
The small subunit is 40S.
The large subunit is 60S.
How is the 30S subunit involved in the early stages of transcription in E.coli?
It is involved in the initial binding of the ribosome to mRNA.
How is the 50S subunit involved in the early stages of transcription in E.coli?
It is involved in peptidyl transferase activity.
Are the A, P and E sites of the ribosome found on any particular subunit?
Both subunits will contribute to the A, P and E sites.
What is P site of the ribosome responsible for?
For holding the tRNA that carries the growing polypeptide chain.
What is A site of the ribosome responsible for?
It holds the tRNA that is carrying the next amino acid to be added to the chain.
What is E site of the ribosome responsible for?
It is the exit site where tRNAs that have dropped off their amino acids can leave the ribosome.
What are the 2 different populations of ribosomes that are found in the cell?
Free and bound ribosomes.
Where can the bound ribosomes be found?
They are attached to the ER.
What proteins are made by bound ribosomes?
They make proteins that involved in the endomembrane system and proteins that are secreted from the cell.
What proteins are made by free ribosomes?
Proteins that are found in the cytosol.
Can a free ribosome become bound and vice versa?
Yes.
The types of ribosome are identical and interchangeable.
When will free ribosomes become bound?
When they need to synthesise a polypeptide that is destined for the ER or to go outside of the cell.
How do free ribosomes become bound?
When signal recognition particle binds to a signal peptide and will guide the ribosomal complex to the ER.
How is a polypeptide that is made by a bound ribosome secreted?
The polypeptide will be secreted into the ER.
What are polysomes?
Many ribosomes that come together and read the same mRNA so they can make proteins very quickly.
What are the 3 stages of polypeptide formation?
Initiation.
Elongation.
Termination.
Does translation require any additional helper proteins?
Yes.
All of the stages require helper proteins.
What molecule will provide energy for polypeptide formation?
GTP.
At what stage of translation will mRNA bind to a tRNA and the ribosomes?
The initiation stage.
What is the 1st step of initiation of translation?
The small subunit binds to mRNA and to an initiator tRNA.
What happens during the initiation of translation after the small subunit has bound to mRNA?
The small subunit will move along the RNA until it reaches the AUG start codon.
What happens during the initiation of translation after the small subunit has reached the start codon on mRNA?
The initiator tRNA will bring the 1st amino acid which is always methionine.
When will the large subunit bind to the small subunit during the initiation of translation?
They bind after the initiator tRNA has bought in methionine.
What is the translation initiation complex?
The large and small ribosomal subunit bound to the mRNA and the initiator tRNA.
Where does the small ribosomal subunit bind to mRNA in eukaryotes?
To the 5 cap on the mRNA.
It then migrates along the RNA to find the start codon and methionine can be bought in.
How does the 30S subunit of prokaryotic ribosomes bind to mRNA?
It has a complimentary sequence to the Shine Delgarno sequence, allowing it to pair to the SDS.
What kind of methionine is bought in as the first amino acid in prokaryotes?
F-methionine (formulated methionine) is always used as the 1st amino acid in prokaryotes.
What is the 30S initiation complex?
F-methionine.
GTP.
The 30S subunit.
What helps the prokaryotic 50S subunit to bind to the 30S initiation complex?
Initiation factors (proteins).
What is formed when the 50S subunit binds to the 30S initiation complex in prokaryotes?
The 70S initiation complex
What is the elongation stage of translation characterised by?
The addition of individual amino acids to the growing polypeptide.
Where do individual amino acids enter the ribosome?
At the A site.
How are the amino acids bought in to the ribosomal complex?
By tRNA molecules that use their anticodons to recognise complimentary codons on mRNA.
What happens in the elongation stage of translation after the tRNA molecules have recognised their complimentary codons?
The tRNA molecules will bind to the mRNA.
What happens in the elongation stage of translation after the tRNA molecules have bound to the mRNA?
The amino acids on the tRNAs are joined together by peptide bonds.
Where on the ribosome are incoming amino acids added to the polypeptide?
The incoming amino acids are added at the A site.
Where on the ribosome is the final amino acid of the chain where an incoming amino acid can be added to?
The amino acid that an incoming amino acid can be added to will be at the P site.
What enzymatic activity forms peptide bonds between the amino acids during the elongation stage of translation?
Peptidyl transferase activity which occurs on the large subunit.
What are the elongation factors that are used in translation?
Proteins that help the elongation process.
What are the 3 ways that elongation factors help translation?
Codon recognition.
Peptide bond formation.
Translocation.
How do elongation factors help with codon recognition?
The elongation factor EF-TU and a GTP molecule guide a tRNA to the A site of the ribosome.
How do elongation factors help with peptide bond formation?
Peptidyl transferase forms the peptide bonds between amino acids.
How do elongation factors help with translocation?
Peptide bond formation causes a tRNA in the P site to release its AA and leave the ribosome via the exit site.
The ribosome can move to the next codon where the process will repeat itself.
When will termination of translation occur?
When a stop codon in the mRNA reaches the A site of the ribosome.
Can tRNA’s recognise the stop codon?
No tRNA is able to recognise the stop codon.
What happens when the ribosome reaches a stop codon?
It tells the A site to accept a protein called a release factor.
What are the effects of the release factor during the termination of translation?
It adds water to the polypeptide and this causes the release of the polypeptide from the ribosome.
What happens when the polypeptide is released from the ribosome?
The ribosomal complex will come apart.
What is the release factor that is used in the termination of translation in eukaryotes?
eRF-1.
What are the release factors that are used in the termination of translation in prokaryotes?
RF1 which will recognise UAA and UAG.
RF2 which recognises UAA and UGA.
RF3 which will stimulate termination.
Where does the synthesis of polypeptides always begin and finish?
In the cytoplasm unless the polypeptide is destined to go outside of the cell.
What often happens to the polypeptide after it has been released form the ribosomes?
It must be modified as translation is often not able to make a functional protein.
When will the polypeptide formed in translation form its 3D structure?
During and after synthesis.
What proteins will sometimes help the polypeptide form its secondary and tertiary structure?
Chaperone proteins.
What kind of protein will not be functional?
A badly folded protein.
What are some post translational modifications for proteins?
Phosphorylation.
Glycosylisation.
Lipid anchoring.
What post translational modifications do trypsinogen and insulin need?
They need to be cleaved by enzymes so that they can be activated.
What feature on some proteins allows them to perform self cleavage?
Intein.
