Term
| What does it mean to say that the genetic code is degenerate? |
|
Definition
| Degeneracy results because there are more codons than encodable amino acids. For example, if there were two bases per codon, then only 16 amino acids could be coded for (4²=16). Because at least 21 codes are required (20 amino acids plus stop), and the next largest number of bases is three, then 4³ gives 64 possible codons, meaning that some degeneracy must exist. |
|
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Term
|
Definition
| A sequence of three adjacent nucleotides constituting the genetic code that specifies the insertion of an amino acid in a specific structural position in a polypeptide chain during the synthesis of proteins. |
|
|
Term
| In which direction does translation of mRNA take place? |
|
Definition
| Translation takes place in the 5' to 3' direction. |
|
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Term
| What protein would be synthesized from the following DNA sequence: 5'-CCA CCA CCA-3'? |
|
Definition
|
|
Term
| What protein would be synthesized from the following DNA sequence: 5'-UCU CUC UCU-3'? |
|
Definition
|
|
Term
| What is the exception to the rule that the genetic code is universal? |
|
Definition
|
|
Term
|
Definition
|
|
Term
| How is the reading frame established? |
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Definition
| The initiation codon AUG indicates where protein synthesis will start. |
|
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Term
|
Definition
| A way of breaking a sequence of nucleotides in DNA or RNA into three letter codons which can be translated in amino acids. |
|
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Term
| How can insertions and deletions of a single base cause errors in the protein product? |
|
Definition
| Insertions and deletions shift the reading frame, which leads to changes in the amino acid sequence. |
|
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Term
|
Definition
| A type of mutation that causes the replacement of a single base nucleotide with another nucleotide of the genetic material. This can, but does not necessarily, lead to an amino acid change. |
|
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Term
| What is the frequent result of a shift in the reading frame? |
|
Definition
| Often, disruption of the reading frame leads to the fortuitous appearance of a STOP codon in the new reading frame, resulting in the production of a truncated protein product. |
|
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Term
|
Definition
| An adaptor molecule composed of RNA, typically 73 to 93 nucleotides in length, that is used in biology to bridge the three-letter genetic code in messenger RNA (mRNA) with the twenty-letter code of amino acids in proteins. The role of tRNA as an adaptor is best understood by considering its three-dimensional structure. One end of the tRNA carries the genetic code in a three-nucleotide sequence called the anticodon. The anticodon forms three base pairs with a codon in mRNA during protein biosynthesis. The mRNA encodes a protein as a series of contiguous codons, each of which is recognized by a particular tRNA. On the other end of its three-dimensional structure, each tRNA is covalently attached to the amino acid that corresponds to the anticodon sequence. This covalent attachment to the tRNA 3’ end is catalyzed by enzymes called aminoacyl-tRNA synthetases. Each type of tRNA molecule can be attached to only one type of amino acid, but, because the genetic code contains multiple codons that specify the same amino acid, tRNA molecules bearing different anticodons may also carry the same amino acid. |
|
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Term
|
Definition
| tRNA to which its associated amino acid is adhered. Its role is to deliver the amino acid to the ribosome where it will be incorporated into the polypeptide chain that is being produced. A specific amino acid is added to each tRNA, which is crucial since it means that only that particular amino acid will be incorporated when the anticodon of that tRNA fits (can form a transient base pair with) the next codon of the mRNA that is being translated into protein. |
|
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Term
| On which end of tRNA is the attached amino acid? |
|
Definition
|
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Term
| Aminoacyl tRNA synthetase |
|
Definition
| An enzyme that catalyzes the esterification of a specific amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA. This is sometimes called "charging" the tRNA with the amino acid. Once the tRNA is charged, a ribosome can transfer the amino acid from the tRNA onto a growing peptide, according to the genetic code. |
|
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Term
| What is the structure of tRNA (cartoon)? |
|
Definition
[image]
All tRNAs have certain basic structural features in common:
• A cloverleaf secondary structure, stabilized predominantly by Watson-Crick base pairing.
• Base-pairing between the 5' and 3' ends forms the acceptor or amino acid stem. This stem has the nucleotides -CCA-OH at it's 3' end, which is where the amino acid will be attached by a specific amino- acyl tRNA synthetase.
• An anticodon loop in the middle that interacts with the codon of mRNA
• A complex tertiary structure (comparable to complexity of proteins) maintained by hydrogen-bonding
• An anticodon loop in the middle that interacts with the codon of mRNA (mostly non-Watson/Crick type hydrogen bonding) and stacking of bases that results in an overall L-shape with the anticodon on one end and acceptor stem at the other end.
|
|
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Term
| T or F: There is a separate tRNA for every codon? |
|
Definition
| False! Some tRNAs work with several different codons. This is explained by the "Wobble hypothesis", which suggests that the first two bases of the codon:anticodon interaction are constrained by normal Watson-Crick base-pairing, but that the requirements for hydrogen bonding at the third base are less stringent. |
|
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Term
|
Definition
| suggests that the first two bases of the codon:anticodon interaction are constrained by normal Watson-Crick base-pairing, but that the requirements for hydrogen bonding at the third base are less stringent. Third position wobble permits G to pair with U and I to pair with U or A. The rules of wobble are consistent with the structure of the genetic code (i.e. different codons for a single amino acid often differ only at the third base) and the sequences of the available tRNA anticodons. |
|
|
Term
| What is the wobble position? |
|
Definition
| The bases paired at the 5' end of the anticodon and the 3' end of the codon. |
|
|
Term
| How are amino acids linked to their corresponding tRNAs? |
|
Definition
Through the action of the enzyme amino-acyl tRNA synthetase. The reaction has two steps:
1) Activation of amino acid by reaction with ATP to form the aminoacyl adenylate. (Charge up the amino acid.)
2. Reaction of activated amino acid with 3'-OH of tRNA to form the aminoacyl-tRNA. (Transfer charged amino acid to CCA-OH of tRNA.) |
|
|
Term
| Aminoacyl-tRNA synthease reaction (diagram). |
|
Definition
|
|
Term
|
Definition
An organelle whose function is to assemble the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule. They can be dissociated into one large and one small subunit. Subunits are designated by their characteristic
sedimentation coefficient (S) - a measure of how fast a particle (macromolecule) sediments during centrifugation - which can be thought of as a rough approximation of the size of a particle. |
|
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Term
| What are the subunits of the prokaryotic 70S ribosome? |
|
Definition
| A 50S large subunit and a 30S small subunit. |
|
|
Term
| What is the ratio of RNA:protein in both prokaryotic and eukaryotic ribosomes? |
|
Definition
| Prokaryotic ribosomes have an RNA:protein ratio of 2:1, and eukaryotic ribosomes have proportionally more. |
|
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Term
| What are the subunits of the eukaryotic 80S ribosome? |
|
Definition
| 60S large subunit and 40S small subunit. |
|
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Term
| In what ways are the structures of prokaryotic and eukaryotic ribosomes similar, and how are they different? |
|
Definition
There is substantial homology in the rRNA structure between eukaryotes and prokaryotes, however, there is little homology in the ribosomal proteins. The complex folding of the RNA portion is highly conserved but the proteins are not - this is due to the fact that it is actually the RNA that is the catalyst for peptide bond formation - hence,
ribosomes are giant ribozymes. |
|
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Term
|
Definition
| An RNA molecule with a well defined tertiary structure that enables it to catalyze a chemical reaction (e.g. ribosomes). Ribozyme means ribonucleic acid enzyme. |
|
|
Term
| What are the component parts of the eukaryotic 60S subunit? |
|
Definition
| 5S rRNA, 28S rRNA, 5.8S rRNA, and ~49 proteins. |
|
|
Term
| What are the component parts of the eukaryotic 40S subunit? |
|
Definition
| 18S rRNA and ~33 proteins. |
|
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Term
| T or F: Protein synthesis differs drastically between prokaryotes and eukaryotes. |
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Definition
| False, the process of protein synthesis is largely conserved from bacteria to man and the remaining differences are important targets for antibiotics. |
|
|
Term
| In what direction is mRNA "pulled through" the ribosome? |
|
Definition
| It is pulled from the 5' end. |
|
|
Term
| Where does most activity take place on the ribosome? |
|
Definition
| Most activity takes place at the interface between the large and small subunits. |
|
|
Term
| What are the three sites on the large subunit where tRNA can bind? |
|
Definition
The A, P, and E sites.
1) Aminoacyl or A site - site of attachment of the incoming amino-acyl tRNA.
2) Peptidyl or P site - site of attachment of the peptidyl tRNA - After the peptide is transferred from the 3' end of the previous tRNA to the amino terminus of the incoming amino acid, the peptide is attached to the incoming tRNA and the tRNA advances from the A site to the P site, so that the A site can accept the next amino-acyl tRNA.
3) Exit or E site – harbors the spent tRNA prior to releasing it. |
|
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Term
|
Definition
| Aminoacyl site - site of attachment of the incoming amino-acyl tRNA. |
|
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Term
|
Definition
| Peptidyl site - site of attachment of the peptidyl tRNA - After the peptide is transferred from the 3' end of the previous tRNA to the amino terminus of the incoming amino acid, the peptide is attached to the incoming tRNA and the tRNA advances from the A site to the P site, so that the A site can accept the next amino-acyl tRNA. |
|
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Term
|
Definition
| Exit site - harbors the spent tRNA prior to releasing it. |
|
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Term
|
Definition
| An aminoacyltransferase as well as the primary enzymatic function of the ribosome, which forms peptide links between adjacent amino acids using tRNAs during the translation process of protein biosynthesis. (A ribozyme.) |
|
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Term
| T or F: The large and small ribosomal subunits are disassembled and reassembled for the synthesis of each polypeptide. |
|
Definition
|
|
Term
| What is one major difference in the translation of proteins between prokaryotes and eukaryotes? |
|
Definition
| One major difference is that transcription and translation are spatially separated in eukaryotes (transcription occurs in the nucleus and translation in the cytoplasm) but not in prokaryotes (translation of an mRNA often begins before transcription is complete). |
|
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Term
| Protein synthesis (diagram) |
|
Definition
|
|
Term
| What are the three steps of translation? |
|
Definition
1) Initiation — mRNA binds and is aligned in correct reading frame, initiator aminoacyl tRNA binds, ribosome assembles from small and large subunits.
2) Elongation — Aminoacyl tRNA binds and checks codon-anticodon match, new peptide bond is formed, growing chain is translocated from A-site to P-site, and mRNA is pulled along so that next codon is exposed to A-site.
3) Termination — Release factor(s) bound to GTP bind to stop codon in A-site, peptidyl tRNA in P-site is hydrolyzed to release peptide chain and leave tRNA in P-site. tRNA, release factors, and mRNA are released from ribosome after GTP hydrolysis and ribosome dissociates into large and small subunit. |
|
|
Term
|
Definition
mRNA binds and is aligned in correct reading frame, initiator aminoacyl tRNA binds, ribosome
assembles from small and large subunits. |
|
|
Term
|
Definition
| Aminoacyl tRNA binds and checks codon-anticodon match, new peptide bond is formed, growing chain is translocated from A-site to P-site, and mRNA is pulled along so that next codon is exposed to A-site. |
|
|
Term
|
Definition
| Release factor(s) bound to GTP bind to stop codon in A-site, peptidyl tRNA in P-site is hydrolyzed to release peptide chain and leave tRNA in P-site. tRNA, release factors, and mRNA are released from ribosome after GTP hydrolysis and ribosome dissociates into large and small subunit. |
|
|
Term
| How is the start (AUG) codon recognized in prokaryotes? |
|
Definition
In prokaryotic mRNAs, a 5-10 nucleotide sequence is found 4-7 bp upstream of the relevant AUG--called the Shine-Dalgarno sequence. This sequence is complementary to the 3' end of the 16S rRNA
and hydrogen bonds with it, aligning the mRNA. Since the ribosome binds interior to the message, bacteria often have polycistronic messages (multiple proteins can be translated from the same mRNA after alignment of the ribosome at different Shine-Dalgarno sequences within the mRNA). |
|
|
Term
|
Definition
| A ribosomal binding site in the mRNA, generally located 8 basepairs upstream of the start codon AUG. This sequence helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning it with the start codon. |
|
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Term
|
Definition
| Multiple proteins can be translated from the same mRNA after alignment of the ribosome at different Shine-Dalgarno sequences within the mRNA. |
|
|
Term
| Are eukaryotic mRNAs polycistronic? |
|
Definition
| No, eukaryotic mRNAs are monocistronic. |
|
|
Term
| How is the start (AUG) codon recognized in eukaryotes? |
|
Definition
| At the 5' end of each mRNA is attached a 7-methyl guanosine residue (known as the 5' cap). The cap structure on mRNA allows recognition of the 5' end of the mRNA by ribosomes and the mRNA is then scanned by the ribosome with Met-tRNAiMet bound until it sees the first AUG. A small consensus sequence upstream of the first AUG may also aid in positioning the ribosome (Kozak sequence). |
|
|
Term
|
Definition
| A sequence which occurs on eukaryotic mRNA and has the consensus (gcc)gccRccAUGG, where R is a purine (adenine or guanine) three bases upstream of the start codon (AUG), which is followed by another 'G'. The Kozak consensus sequence plays a major role in the initiation of the translation process. This sequence on an mRNA molecule is recognized by the ribosome as the translational start site, from which a protein is coded by that mRNA molecule. The ribosome requires this sequence, or a possible variation (see below) to initiate translation. |
|
|
Term
| T or F: Both prokaryotic and eukaryotic mRNA have a 5' cap. |
|
Definition
| False. Only eukaryotic mRNA have a 5' cap. This is used in the recognition of the start AUG codon. |
|
|
Term
|
Definition
| A special tRNA for initiation, is allowed to go straight to the P site without requiring the act of peptide bond formation to signal the advance of the tRNA. |
|
|
Term
|
Definition
| Ancillary protein factors that associate transiently with components of the translation machinery to help in the assembly and disassembly of complexes. |
|
|
Term
| What are the initiation factors in prokaryotes? |
|
Definition
|
|
Term
|
Definition
| In prokaryotes, (Assisted by IF-1) - Binds to the small ribosomal subunit and promotes the dissociation of small and large ribosomal subunits so that a new round of protein synthesis can be initiated. It then helps the 30S subunit to recognize the Shine-Dalgarno sequence of the mRNA. |
|
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Term
|
Definition
| In prokaryotes, binds to initiator tRNA and GTP, allowing it to bind to the small ribosomal subunit. |
|
|
Term
| In prokaryotes, what binds to the small ribosomal subunit and promotes the dissociation of small and large ribosomal subunits so that a new round of protein synthesis can be initiated? |
|
Definition
|
|
Term
| In prokaryotes, what binds initiator tRNA and GTP, thus allowing it to bind to the small ribosomal subunit? |
|
Definition
|
|
Term
| How many initiation factors are in eukaryotes? |
|
Definition
| Eukaryotes have more than 10 eIFs. |
|
|
Term
|
Definition
(Eukaryotic initiation factor 2) - The eukaryotic equivalent of IF2 in prokaryotes. This binds to tRNA and GTP, allowing it to bind to the small ribosomal subunit. This initiation factor is very important
for the regulation of protein synthesis. |
|
|
Term
| What is the role of GTP in translation? |
|
Definition
| GTP causes conformational changes in components of the ribosome that accelerate reactions, and it's hydrolysis to GDP + Pi forces reactions to be irreversible. Translation can occur in the absence of GTP, but very slowly. |
|
|
Term
| T or F: Initiation factors are part of the ribosome. |
|
Definition
| False. Initiation factors are ancillary factors that help assemble and disassemble transient complexes. They join the ribosome, do their job, and leave. |
|
|
Term
| Describe the initiation of an initiation complex in the prokaryote. |
|
Definition
1. IF-1 and IF-3 promote the dissociation of the ribosomal subunits. They remain bound to the small (30S) subunit to help in recognition of the Shine-Dalgarno sequence of the mRNA.
2. A complex of IF-2+GTP+fMet-tRNAfMet along
with the mRNA bind to the small subunit.
3. In a step that expends energy in the form of a high-energy phosphoanhydride bond in GTP, the large ribosomal subunit binds as the initiation factors are expelled.
4. The initiator tRNA, hydrogen bonded to the AUG start codon, is immediately moved to the P site of the large ribosomal subunit and the initiation phase is complete.
5. The first peptide bond is formed, shunting the initiator tRNA to the E site. |
|
|
Term
| Describe the initiation of an initiation complex in the eukaryote. |
|
Definition
1) eIF3 (An initiation factor within the small (40S) subunit (the target of poliovirus)) binds to the CAP structure of the mRNA molecule.
2. A complex of eIF-2 + GTP + Met-tRNAiMet along
with the mRNA bind to the small subunit.
3. In a step that expends energy in the form of a high-energy phosphoanhydride bond in GTP, the large ribosomal subunit binds as the initiation factors are expelled.
4. The initiator tRNA, hydrogen bonded to the AUG start codon, is immediately moved to the P site of the large ribosomal subunit and the initiation phase is complete.
5. The first peptide bond is formed, shunting the initiator tRNA to the E site. |
|
|
Term
| T or F: Elongation factors are part of the ribosome. |
|
Definition
| False. As with the IFs, the EFs are not part of the ribosome, they only attach for their specific job. |
|
|
Term
|
Definition
| Aminoacyl tRNA binds and checks codon-anticodon match, new peptide bond is formed, growing chain is translocated from A-site to P- site, and mRNA is pulled along so that next codon is exposed to A-site. |
|
|
Term
| How many elongation factors do prokaryotes have? |
|
Definition
3:
1) EF-Tu
2) EF-Ts
3) EF-G |
|
|
Term
| How many elongation factors do eukaryotes have? |
|
Definition
|
|
Term
|
Definition
| Prokaryotic elongation factor that binds to GTP and to the aminoacyl-tRNA and brings them to the A site on the ribosome, which requires hydrolysis of GTP and leaved an inactive EF-Tu-GDP complex. |
|
|
Term
|
Definition
| Prokaryotic elongation factor that regenerates EF-Tu after its job is done. |
|
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Term
|
Definition
| Prokaryotic elongation factor that moves mRNA by 3 bp (from the A site to the P site of the ribosome) in a process that ! requires hydrolysis of GTP. |
|
|
Term
|
Definition
Eukaryotic elongation factor that has two subunits that together perform the functions of the prokaryotic EF-Tu and EF-Ts, which is to:
1) binds to GTP and to the aminoacyl-tRNA and brings them to the A site on the ribosome, which requires hydrolysis of GTP and leaved an inactive EF-Tu-GDP complex, and
2) Regenerates EF-Tu after it's job is done |
|
|
Term
|
Definition
| Eukaryotic elongation factor that moves mRNA by 3 bp (from the A site to the P site of the ribosome) in a process that ! requires hydrolysis of GTP. |
|
|
Term
| Describe the elongation cycle in prokaryotes. |
|
Definition
1. EF-Tu forms a complex in the cytosol with GTP and aminoacyl-tRNA.
2. This complex binds to the ribosome, kicking out the tRNA in the E site. GTP is hydrolyzed to GDP and the aminoacyl-tRNA is left bound to A-site of ribosome as EF-Tu, now complexed with GDP, dissociates from the ribosome.
3. Formation of peptide bond: The new aminoacyl tRNA at the A-site attacks the aminoacyl linkage at the tRNA in the P-site, resulting in transfer of the peptide chain being synthesized onto the tRNA in the A site. This reaction is catalyzed by a peptidyl transferase enzymatic activity which resides on the ribosome.
4. Translocation: The uncharged tRNA left in the P-site moves to the E site. The tRNA with attached
peptide (peptidyl tRNA) is translocated from the A-site to the P-site and the mRNA is pulled along with tRNA during translocation because of codon-anticodon interaction. Translocation, which requires hydrolysis of another GTP, is catalyzed by EF-G in prokaryotes and eEF-2 in eukaryotes.
5. End result: A growing polypeptide chain attached to tRNA in P-site, mRNA moved by 3 nucleotides so that a new codon is exposed, A site is empty, E site contains the spent tRNA. The cycle continues until a STOP codon is reached. |
|
|
Term
| Describe the elongation cycle in eukaryotes. |
|
Definition
1. eEF-1 forms a complex with GTP and aminoacyl-tRNA.
2. This complex binds to the ribosome, kicking out the tRNA in the E site. GTP is hydrolyzed to GDP and the aminoacyl-tRNA is left bound to A-site of ribosome as eEF-1, now complexed with GDP, dissociates from the ribosome.
3. Formation of peptide bond: The new aminoacyl tRNA at the A-site attacks the aminoacyl linkage at the tRNA in the P-site, resulting in transfer of the peptide chain being synthesized onto the tRNA in the A site. This reaction is catalyzed by a peptidyl transferase enzymatic activity which resides on the ribosome.
4. Translocation: The uncharged tRNA left in the P-site moves to the E site. The tRNA with attached
peptide (peptidyl tRNA) is translocated from the A-site to the P-site and the mRNA is pulled along with tRNA during translocation because of codon-anticodon interaction. Translocation, which requires hydrolysis of another GTP, is catalyzed by EF-G in prokaryotes and eEF-2 in eukaryotes.
5. End result: A growing polypeptide chain attached to tRNA in P-site, mRNA moved by 3 nucleotides so that a new codon is exposed, A site is empty, E site contains the spent tRNA. The cycle continues until a STOP codon is reached. |
|
|
Term
|
Definition
An enzyme residing on the ribosome that catalyzes the reaction for the new aminoacyl tRNA at the A-site attacks the aminoacyl linkage at the tRNA in the P-site, resulting in transfer of the peptide chain being synthesized onto the tRNA in the A
site. |
|
|
Term
| Which elongation factors catalyze translocation in the prokaryotes and eukaryotes? |
|
Definition
| EF-G in prokaryotes and eEF-2 in eukaryotes. |
|
|
Term
| How many release factors do prokaryotes have? |
|
Definition
Prokaryotes have 3 RFs:
1) RF-1
2) RF-2
3) RF-3 |
|
|
Term
| How many release factors do eukaryotes have? |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| Binds GTP and stimulates RF-1 and RF-2 binding. |
|
|
Term
| Describe the termination process. |
|
Definition
1. Stop codons have no corresponding tRNAs, but instead are recognized by release factors which carry with them a bound GTP.
2. Binding of the RF alters the activity of peptidyl transferase, causing it to add H20 instead of an amino acid to the peptidyl-tRNA. This removes the peptide from the tRNA. The uncharged tRNA is moved to the E site.
3. GTP is then hydrolyzed to GDP and Pi, changing the conformation of the ribosome so that the mRNA, tRNA, RFs and GDP + Pi are released. |
|
|
Term
| What is the average error rate in translation? |
|
Definition
| 1/10^4 amino acids or 1 in every 25 protein molecules on average has a mistake. These errors can be either attaching the wrong amino acid to the tRNA or incorrect base pairing of tRNA to the codon. |
|
|
Term
| When can proofreading take place during translation? |
|
Definition
1) When the amino acyl synthetase binds the amino acid to the tRNA. Amino acyl synthetases have two active sites:
- One recognizes the correct tRNA and attaches the amino acid.
- The other can recognize and remove an incorrectly attached amino acid (thus wasting the !
two high-energy phosphoanhydride bonds that were expended to attach the incorrect amino acid).
2) When the aminoacyl-tRNA first binds to the A site of the ribosome, GTP is hydrolyzed but the EF- Tu:GDP complex remains associated, preventing peptide bond formation. If base pairing is correct, then the EF-Tu:GDP complex is released and peptide bond formation proceeds. If base pairing is not correct, then the aminoacyl-tRNA dissociates, along with EF-Tu:GDP (thus wasting the high-energy phosphoanydride bond that was invested prior to this step of proofreading). |
|
|
Term
| Proofreading during amino acyl synthetase activity. |
|
Definition
[image]
Amino acyl synthetases have two active sites
-
- one recognizes the correct tRNA and attaches the amino acid
-
- the other can recognize and remove an incorrectly attached amino acid (thus wasting the !
two high-energy phosphoanhydride bonds that were expended to attach the incorrect amino acid).
|
|
|
Term
| Proofreading during elongation. |
|
Definition
[image]
When the aminoacyl-tRNA first binds to the A-site of the ribosome, GTP is hydrolyzed but the EF- Tu:GDP complex remains associated, preventing peptide bond formation. If base pairing is correct, then the EF-Tu:GDP complex is released and peptide bond formation proceeds. If base pairing is not correct, then the aminoacyl-tRNA dissociates, along with EF-Tu:GDP (thus wasting the high-energy phosphoanydride bond that was invested prior to this step of proofreading). |
|
|
Term
|
Definition
| A reaction involving the transfer of one or more amino acids from one peptide chain to another. |
|
|
Term
| What is the energy consumption at each step of protein synthesis? |
|
Definition
1) During synthesis of aminoacyl tRNA: 2 bonds from ATP
2) During initiation: 1 GTP
3) During elongation: 2 GTP (one for each amino acid incorporated)
4) When the polypeptide is released: 1 GTP
5) During proofreading: unknown. |
|
|
Term
| What is the energy consumption during synthesis of aminoacyl tRNA? |
|
Definition
|
|
Term
| What is the energy consumption during initiation? |
|
Definition
|
|
Term
| What is the energy consumption during elongation? |
|
Definition
| 2 GTP (one for each amino acid incorporated) |
|
|
Term
| What is the energy consumption when the polypeptide is released? |
|
Definition
|
|
Term
| What is the energy consumption during proofreading? |
|
Definition
|
|
Term
| Because protein synthesis is so expensive, when and how is it controlled? |
|
Definition
| It's generally controlled at the initiation step, usually by regulating the availability of eIF-2. |
|
|
Term
| Explain how protein synthesis is controlled through regulating eIF-2 activity. |
|
Definition
| The rate of protein synthesis is controlled in a large part by the activity of eIF-2 (carries GTP and initiator tRNA to the ribosome), which can be phosphorylated by specific protein kinases to decrease the rate of protein synthesis (a kinase is an enzyme that attaches a phosphate to a protein and in many cases changes it's conformation and therefore it's activity). As the 60S ribosomal subunit binds to the 40S initiation complex, an inactive GDP-eIF-2 complex is released (in prokaryotes IF-2 immediately releases GDP). eIF-2 must be regenerated by the action of another IF (eIF-2B), which binds to eIF-2 and replaces the GDP with GTP to regenerate an active eIF-2. When eIF-2 is phosphorylated by any one of various protein kinases that serve to regulate the rate of protein synthesis, it binds tightly to both GDP and eIF-2B, preventing the exchange for GTP and blocking initiation of translation. |
|
|
Term
|
Definition
| An enzyme that attaches a phosphate to a protein and in many cases changes its conformation and therefore its activity. |
|
|
Term
|
Definition
| An enzyme that attaches a phosphate to a protein and in many cases changes its conformation and therefore its activity. |
|
|
Term
| What happens when eIF-2 is phosphorylated? |
|
Definition
| It binds tightly to both GDP and eIF-2B, preventing the exchange for GTP and blocking initiation of translation. |
|
|
Term
| Phosphorylation of eIF-2 (diagram) |
|
Definition
[image]
1. eIF-2-GTP brings the initiator tRNA to the 40S subunit and is inactivated as GTP is hydrolyzed and the Initiation Complex is formed.
2. Normally, eIF-2-GDP is recycled to eIF-2 GTP via interaction with eIF-2B.
3. However, phosphorylation of eIF-2-GDP by a protein kinase locks the eIF-2/eIF-2B complex in the inactive, GDP bound form.
|
|
|
Term
| Regulation of synthesis of globin in response to heme availability (diagram) |
|
Definition
[image]
Often, it is advantageous for a cell to synthesize a protein only when it is needed. A well studied example is the synthesis of globin in reticulocytes (immature RBCs), which occurs only when it's iron-containing prosthetic group, heme, is available for assembly into hemoglobin. This occurs by the inhibition of translation when heme is not available. In the absence of heme, cells activate a protein called HCI (heme-controlled inhibitor) which phosphorylates eIF-2. When heme becomes available again, HCI is inactivated, the phosphate removed, and eIF-2 can be recycled. |
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Term
| Regulatory elements within the structure of the eukaryotic mRNA (diagram) |
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Definition
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- 5'-cap structure: protects 5' end of RNA from ribonucleases and allows eukaryotic cells to distinguish between mRNA and other types of RNA. CAP is recognized by one of the eIFs in the small ribosomal subunit and is required for translation of most mRNAs. - 5' untranslated region (5'-UTR): Often contains sequences important for translational efficiency - Coding region: Region that actually encodes protein. - 3' untranslated region (3'-UTR): Can contain signal sequences that target the mRNA to be translated at specific places in the cell (e.g. ribosomes in the endoplasmic reticulum for secreted proteins), or to be transported to particular locations within the cell to cause a concentrated amount of protein to be synthesized in a particular area. Can also contain sequences important for mRNA stability (see example of ferritin mRNA). - poly A tail: Varying numbers of adenosines added post-transcriptionally. Stabilizes the 3' end of the mRNA. Shortens in the cytosol but is always greater than 30 nucleotides. May also catalyze the assembly of large ribosomal subunit. |
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Term
| How does the 5'-cap structure participate in regulation of transcription? |
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Definition
| Protects 5' end of RNA from ribonucleases and allows eukaryotic cells to distinguish between mRNA and other types of RNA. CAP is recognized by one of the eIFs in the small ribosomal subunit and is required for translation of most mRNAs. |
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Term
| How does the 5' untranslated region (5'-UTR) participate in regulation of transcription? |
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Definition
| Often contains sequences important for translational efficiency. |
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Term
| How does the 3' untranslated region (3'-UTR) participate in regulation of transcription? |
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Definition
| Can contain signal sequences that target the mRNA to be translated at specific places in the cell (e.g. ribosomes in the endoplasmic reticulum for secreted proteins), or to be transported to particular locations within the cell to cause a concentrated amount of protein to be synthesized in a particular area. Can also contain sequences important for mRNA stability (see example of ferritin mRNA below). |
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Term
| How does the poly A tail participate in regulation of transcription? |
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Definition
| Contains varying numbers of adenosines added post-transcriptionally. Stabilizes the 3' end of the mRNA. Shortens in the cytosol but is always greater than 30 nucleotides. May also catalyze the assembly of the large ribosomal subunit. |
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Term
| Regulation of ferritin/transferrin receptor translation in response to iron availability (diagram) |
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Definition
Translation of the mRNA encoding ferritin, an intracellular iron storage protein, is increased rapidly if the concentration of iron within the cell increases. At the same time, translation of the mRNA encoding the transferrin receptor, which imports iron, is decreased. Both of these effects are mediated by aconitase (or iron response factor, IRF), which, in the absence of iron, binds to a specific stem-loop structure (referred to as the iron response element, IRE) present in both of these mRNA's.
- Binding of aconitase to an IRE in the 5' UTR of the ferritin mRNA blocks initiation of translation on this message.
- Binding of aconitase to an IRE in the 3' UTR of the transferrin receptor RNA stabilizes the mRNA against degradation.
The presence of excess iron releases aconitase from the IRE, causing an increase in translation of ferritin and a decrease in translation of the transferrin receptor. |
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Term
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Definition
| (Also endogenous miRNA) Small interfering RNA, a class of double-stranded RNA molecules, 20-25 nucleotides in length, that is involved in the RNAi (RNA interference) pathway, where it interferes with the expression of a specific gene. RNAi works through the introduction of gene- specific dsRNA into a cell, and thus causing the homologous mRNA to be degraded, and is one of the many post-translational gene silencing mechanisms. |
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Term
| How does dsRNA regulate protein synthesis? |
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Definition
| By becoming processed to siRNA and down regulating translation by inducing mRNA degradation. |
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Term
| Antibiotics and their role in inhibiting protein synthesis |
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Definition
| In nature, antibiotics are substances produced by bacteria or fungi to kill other bacteria or fungi. They can act on many processes, (e.g. penicillin inhibits bacterial cell wall synthesis) but the majority act to inhibit different phases of protein synthesis. In general, inhibitors that are specific to prokaryotes are more useful than those that also inhibit eukaryotic protein synthesis. |
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Definition
| Viruses absolutely require the host protein synthesis apparatus to synthesize viral proteins. In some cases viruses contrive different means of making the translation of viral mRNAs more efficient than translation of cellular mRNAs. |
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Term
| What effect does poliovirus cause in the cell? |
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Definition
| Infection of cells with poliovirus causes the host mRNA translation to be strongly inhibited and poliovirus mRNAs to be translated rapidly. This is accomplished by a protease, encoded by the virus, that cleaves and inactivates the mRNA CAP binding protein (one of the eIFs in the 40S ribosomal subunit). As a result, host mRNAs are no longer recognized efficiently by the ribosome and host mRNA translation is inhibited. Poliovirus mRNA's can bind to the ribosome without having a CAP. |
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Term
| How do interferons (IFNs) inhibit translation and degrade mRNA? |
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Definition
Many viruses produce double-stranded RNAs (dsRNA) at some point in their life cycle. dsRNA is not normally present in cells and so becomes a signal to the cell that there is a viral infection, inducing the secretion of interferons (IFNs). IFNs then bind to the surface of other cells and induce the expression of two new enzymes that, when activated by the presence of dsRNA, inhibit protein synthesis (i.e. interferon treated, virally infected cells commit suicide in order to stop the attacking virus):
a) A ribosome-associated protein kinase. This protein kinase phosphorylates eIF-2 and prevents initiation of translation (just like HCI).
b) 2,5A synthetase. Produces unusual polymers of ATP that activate an endoribonuclease that cuts in the middle of both mRNAs (cellular and viral) and rRNAs. As a result, protein synthesis is slowed down by both the loss of mRNAs to be translated and the loss of rRNA to make ribosomes. |
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