Term
| What is the order of sequence from DNA to protein? |
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Definition
| DNA - > Transcription -> RNA -> Translation -> Protein |
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Term
| What is the bacterium model organism? |
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Definition
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Term
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Definition
1)Provides a framework for understanding more complex organisms
2)Provides an understanding of bacteria as pathogens
3)Easy to manipulate and take up recombinant DNA
4)See how antibiotics affect bacteria |
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Term
| How many strands does DNA have? |
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Definition
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Term
| How many strands does RNA have? |
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Definition
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Term
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Definition
| rATP, rCTP, rGTP and rUTP |
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Term
| What are the three regions of a gene? |
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Definition
| Promoter sequence, gene region and terminator sequence |
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Term
| Where are the two consensus sequences? |
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Definition
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Term
| How many base pairs are between the -35 and the -10 consensus sequences? |
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Definition
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Term
| How many base pairs are between the -10 and the start-site sequences? |
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Definition
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Term
| What is the normal sequence of bases that make up the -35 consensus sequence? |
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Definition
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Term
| What is the normal sequence of bases that make up the -10 consensus sequence? |
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Definition
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Term
| How consensus sequences determined? |
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Definition
| Looking at the most common base at each of the positions of a number of promoters |
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Term
| Which ion is required for RNA Polymerase to work? |
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Definition
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Term
| Which components make up the Core RNA Polymerase? |
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Definition
2 x alpha
1 x beta
1 x beta'
1 x omega |
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Term
| Which factor is also required for RNA Polymerase to work? |
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Definition
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Term
| What two components make up the Holoenzyme? |
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Definition
| The Core RNA Polymerase AND the sigma factor |
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Term
| How many domains are in the sigma factor? |
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Definition
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Term
| What does the 1.1 domain of the sigma factor do? |
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Definition
| Prevents binding to promoters in the absence of RNA polymerase |
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Term
| What do the 1.2, 2.2, 2.3 and 2.4 domain of the sigma factor do? |
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Definition
| Mediate binding to the -10 consensus sequence |
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Term
| What do the 4.1 and 4.4 domain of the sigma factor do? |
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Definition
| Mediate binding to the -35 consensus sequence |
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Term
| What number is the main sigma factor? |
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Definition
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Term
| What other number sigma factors also exist and are sometimes used? |
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Definition
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Term
| What to 32 and 54 sigma factors mediate? |
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Definition
| Binding to other promoter seqeunces |
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Term
| What happens during the initiation stage of transcription? |
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Definition
| The sigma factor binds the RNA polymerase and the strand of DNA is opened up |
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Term
| What happens during the elongation stage of transcription? |
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Definition
| The sigma factor leaves the RNA polymerase and the RNA polymerase transcribes the anti-sense strand using complimentary base pairing |
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Term
| In what direction does RNA polymerase read DNA? |
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Definition
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Term
| How many nucleotides can be transcribed per second in E.coli? |
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Definition
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Term
| Does RNA Polymerase have a proof reading function? |
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Definition
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Term
| What is the error rate of RNA Polymerase? |
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Definition
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Term
| What are the two types of termination? |
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Definition
| Factor Independent and Rho dependant |
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Term
| How does Factor Independent termination occur? |
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Definition
| The palindromic GC sequence causes a hairpin loop to form that reduces the RNA Polymerases' affinity for the strand and so is pulled off |
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Term
| What are the two common features of factor independent terminator strands? |
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Definition
1)Series of 4-10 consecutive A-T base pairs
2)A G and C rich region that is palindromic before the A/T region |
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Term
| What is a palindromic sequence? |
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Definition
| Opposite base pairing on the strand strand |
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Term
| What makes up the structure of the Rho factor? |
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Definition
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Term
| How the Rho factor powered? |
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Definition
| By nucleoside triphosphates |
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Term
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Definition
| A helicase enzyme that unwinds the DNA/RNA complexes |
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Term
| How does the Rho factor cause termination? |
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Definition
| It moves quicker than the RNA polymerase along the strand behind it. Eventually it catches up and pushes of the RNA polymerase terminating the strand |
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Term
| How do cells use transcription to react to changes in the environment? |
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Definition
| Altering the sets and levels the genes are expressed |
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Term
| What are the two strategies for regulating transcription initiation? |
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Definition
| Repression and Activation |
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Term
| How does repression work as a strategy for regulating transcription initiation? |
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Definition
| Repressor protein blocks the RNA polymerase and will not activate RNA polymerase until it is removed |
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Term
| How does activation work as a strategy for regulating transcription initiation? |
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Definition
| RNA polymerase is bound to promoter but will not begin transcription unless another protein allows it to begin transcribing |
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Term
| What are the gene regions along the lac operon? |
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Definition
| PlacI, lacI, Plac, O1, lacZ, lacY, lacA |
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Term
| What does PlacI do in the lac operon? |
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Definition
| Acts as the promoter sequence for the lacI gene |
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Term
| What does lacI do in the lac operon? |
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Definition
| Contains the gene for the lac repressor |
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Term
| What does Plac do in the lac operon? |
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Definition
| Acts as a promoter for the whole lac operon |
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Term
| What does O1 do in the lac operon? |
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Definition
| Acts as a binding site for the lac repressor that will prevent transcription |
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Term
| What does lacZ do in the lac operon? |
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Definition
| Contains the gene for B-galactosidase |
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Term
| What does lacY do in the lac operon? |
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Definition
| Contains the gene for lactose permease |
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Term
| What does lacA do in the lac operon? |
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Definition
| Contains the gene for acetylase |
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Term
| Transcription of the lac operon only occurs under which conditions? |
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Definition
| Abscense of glucose AND presence of lactose |
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Term
| How many amino acids are present in the lac repressor? |
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Definition
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Term
| What type of molecule does the lac repressor form? |
|
Definition
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|
Term
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Definition
| A molecule made up of four identical sub-units but not covelantly bonded |
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Term
| Why is the lac repressor a homotetramer? |
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Definition
| Because secondary operator sites (O2 and O3) are also present and these must also be blocked |
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Term
| What is the main inducer for the lac operon? |
|
Definition
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Term
| What is the alternative inducer for the lac operon? |
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Definition
| Other B-glactosidases like IPTG |
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Term
| How does allolactose induce the lac operon? |
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Definition
| Allolactose binds to the repressor protein which reduces the proteins affinity for the DNA so the repressor protein leaves |
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Term
| Outline how glucose induces transcription of the lac operon? |
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Definition
1)No glucose results in the conversion of ATP into cAMP
2)cAMP then binds to the CAP protein which starts transcription |
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Term
| How does the CAP protein initiate transcription? |
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Definition
| It binds to the RNA polymerase activating it |
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Term
| In conditions of glucose and no lactose what occurs in terms of the lac operon? |
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Definition
| Repressor protein present, CAP not present so no transcription |
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Term
| In conditions of no glucose and no lactose what occurs in terms of the lac operon? |
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Definition
| CAP present but RNA polymerase still blocked by repressor protein so no transcription |
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Term
| In conditions of glucose and lactose what occurs in terms of the lac operon? |
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Definition
| CAP not present but no repressor protein so a little transcription occurs |
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Term
| In conditions of no glucose and lactose what occurs in terms of the lac operon? |
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Definition
| CAP present and no repressor protein so transcription occurs |
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Term
| Which organism requires a CAP protein in order to regulate transcription for toxins? |
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Definition
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Term
| What is the genetic code? |
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Definition
| Sequence of four bases that codes for 20 amino acids |
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Term
| What are the features of the genetic code? |
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Definition
| Triplet code, degenerate and non-overlapping |
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Term
| Is the genetic code universal? |
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Definition
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Term
| How many nucleotides make up a tRNA? |
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Definition
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Term
| How many areas are invariant in a tRNA molecule? |
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Definition
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Term
| How many areas are semi-variant in a tRNA molecule? |
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Definition
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Term
| How many phosphate groups do each nucleotide or tRNA have? |
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Definition
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Term
| What are the four modified bases in tRNA? |
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Definition
| Ribothymine, pseudouridine, hydrouridine and inosine |
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Term
| What are the five features of a molecule of tRNA? |
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Definition
| D-Loop, T-Loop, variable arm, anti-codon loop, amino acid acceptor site |
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Term
| Which part of a tRNA contains dihydrouridine? |
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Definition
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|
Term
| Which part of a tRNA contains pseudouridine? |
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Definition
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Term
| A tRNA joined to an amino acid is known as a? |
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Definition
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Term
| Which enzyme catalyses the reaction that joins a tRNA molecule to an amino acid? |
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Definition
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Term
| Outline the mechanism that creates an aminoacyl tRNA |
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Definition
1)AMP is added to the carboxyl group on the amino acid to form an intermediate compound called aminoacyl adenylate
2)The aminoacyl adenylate then reacts with the tRNA to form an aminoacyl tRNA |
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Term
| Which bond (aminoacyl or peptide) has the higher energy? |
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Definition
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Term
| How many different types of aminoacyl tRNA are they? |
|
Definition
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Term
| What are the different types of aminoacyl tRNA? |
|
Definition
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Term
| How does the aminoacyl tRNA synthetase know which aminoacyl tRNA to use? |
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Definition
| It looks at the identity elements |
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Term
| What two sites do aminoacyl tRNA synthetases have that read the identity elements? |
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Definition
| The activation site and the editing site |
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Term
| What does the activation site do? |
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Definition
| Reject aminoacyl tRNA's that have amino acids bigger than the correct one |
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Term
| What does the editing site do? |
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Definition
| Cleaves amino acids that are smaller than the correct one? |
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Term
| Using the activation and editing sites on the aminoacyl tRNA synthetases means that a mistake is made once in every? |
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Definition
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|
Term
| How does tRNA act as an adaptor between the protein and the mRNA? |
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Definition
| The anticodon reads each codon on the mRNA which then releases the amino acid to form a peptide bond with the rest of the protein |
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Term
| What is the Wobble hypothesis? |
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Definition
| The first two base pairs of the anticodon match up with Watson-Crick base pairings but the third does not have to follow that rule |
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Term
| If the base A is in the third position of the anti-codon it can/must be paired with? |
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Definition
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Term
| If the base C is in the third position of the anti-codon it can/must be paired with? |
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Definition
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Term
| If the base U is in the third position of the anti-codon it can/must be paired with? |
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Definition
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Term
| If the base G is in the third position of the anti-codon it can/must be paired with? |
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Definition
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Term
| If the base I is in the third position of the anti-codon it can/must be paired with? |
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Definition
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|
Term
| The standard ribosome size is known as? |
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Definition
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Term
| What is the size of the large sub-unit? |
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Definition
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Term
| What is the size of the smaller sub-unit? |
|
Definition
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Term
| What are the requirements for a ribosome to initiate initiation? |
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Definition
Initiation factors (IF1, IF2, IF3 and GTP)
A tRNAfMet |
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Term
| What are the requirements for a ribosome to initiate elongation? |
|
Definition
| Elongation factors (Ef-Tu, Ef-Ts, Ef-G and GTP) |
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Term
| What are the requirements for a ribosome to initiate termination? |
|
Definition
| STOP codon and release factors (RF1 and RF2) |
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Term
| Outline the mechanism of translation initiation? |
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Definition
1)30s sub-unit binds to binding site after recognising the Shine-Dalgarno sequence
2)The initiator tRNA binds to start codon AUG
3)50s subunit binds to 30s sub-unit to produce the 70s ribosome complex |
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Term
| What is the Shine Dalgarno sequence? |
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Definition
| The sequence recognised by the 30s sub-unit to begin transcription |
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Term
| Outline the role of the initiation factors in assembling a ribosome? |
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Definition
1)GTP binds to IF2 and thsi attaches the 30s sub-unit to the binding site
2)IF3 is released as initiator tRNA is bound
3)IF2 and IF1 are released when the 50s sub-unit binds |
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Term
| Which elongation factors create a peptide bond? |
|
Definition
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|
Term
| Which elongation factors release the tRNA body? |
|
Definition
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|
Term
| The peptide bond formation is catalysed by which enzyme? |
|
Definition
|
|
Term
|
Definition
| Recognises UAG and UAA STOP codons |
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Term
|
Definition
| Recognises UAA and UGA STOP codons |
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Term
|
Definition
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Term
|
Definition
| Releases the ribosome from the peptide |
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