Chapter 25 Post-lecture (Proteins)
The following polynucleotide was synthesized and used as a template for peptide synthesis in a cell-free system from E. coli. 5′...GCGCGCGCGCGCGCG...3′ Part A Part complete What polypeptide would you expect to be produced?
-Ala-Arg-Ala-Arg-Ala-
According to wobble rules, what codons should be recognized by the anticodon 5′-ICC-3′? What amino acid residue do they correspond to? Match the words in the left column to the appropriate blanks in the sentences on the right.
Because I in the anticodon 5′ end can wobble to pair with A, U, or C in the codon 3′ end, 5′ ...ICC...3′ can pair with 3 ′ ...AGG ,3′ ... UGG , or 3′ ...CGG . They correspond to Gly.
During translation, nucleotide base triplets (codons) in mRNA are read in sequence in the 5' → 3' direction along the mRNA. Amino acids are specified by the string of codons. What amino acid sequence does the following mRNA nucleotide sequence specify? 5′−AUGGCAAGAAAA−3′ Express the sequence of amino acids using the three-letter abbreviations, separated by hyphens (e.g., Met-Ser-Thr-Lys-Gly).
Met-Ala-Arg-Lys
What amino acid sequence does the following DNA template sequence specify? 3′−TACAGAACGGTA−5′ Express the sequence of amino acids using the three-letter abbreviations, separated by hyphens (e.g., Met-Ser-His-Lys-Gly).
Met-Ser-Cys-His
Part C Why does such a mutation usually not have deleterious effects?
Most mRNAs code 2-3 different stop codons in a row that definitely stop translation.
Part B Part complete Predict polypeptides produced when (GUA)n is used with an E. coli system. Select all that apply.
Val-Val-Val... Ser-Ser-Ser...
RNA processing converts the RNA transcript into _____.
mRNA
Part A Part complete Complete the following vocabulary exercise related to the process of translation of mRNA to protein by the ribosome. Match the words in the left-hand column with the appropriate blank in the sentences in the right-hand column.
1. Termination of translation happens when the ribosome hits a stop codon on the mRNA. 2. The RNA that has an amino acid attached to it, and that binds to the codon on the mRNA, is called atRNA. 3. The process, performed by the ribosome, of reading mRNA and synthesizing a protein is called translation. 4. Amino acids are attached to tRNA by enzymes called aminoacyl-tRNA synthetase. 5. Initiation of translation always happens at the start codon of the mRNA.
Part D On which chromosome is the BCR gene normally located?
22
Part C - Codon size and the genetic codePart complete Life as we know it depends on the genetic code: a set of codons, each made up of three bases in a DNA sequence and corresponding mRNA sequence, that specifies which of the 20 amino acids will be added to the protein during translation. Imagine that a prokaryote-like organism has been discovered in the polar ice on Mars. Interestingly, these Martian organisms use the same DNA → RNA → protein system as life on Earth, except that there are only 2 bases (A and T) in the Martian DNA, and there are only 17 amino acids found in Martian proteins. Based on this information, what is the minimum size of a codon for these hypothetical Martian life-forms?
5 bases
An important validation of the genetic code occurred when George Streisinger determined the amino acid sequence of bacteriophage T4 lysozyme and of mutants induced by proflavin, a dye with a planar structure that can intercalate (fit) between successive base pairs in DNA and induce frameshift mutations−that is, mutations involving additions or deletions of a single base. Streisinger and colleagues found that a particular single-base insertion mutation could be suppressed, with wild-type function restored, by a mutation that evidently involved a single-base deletion at a nearby site. Shown below are portions of the amino acid sequence of wild-type T4 lysozyme and the putative double mutant. The remaining parts of the sequence were unchanged. Identify mRNA sequences that could encode each of these amino acid sequences. Wild-type ...Lys-Ser-Pro-Ser-Leu-Asn-Ala... Double mutant ...Lys-Val-His-His-Leu-Met-Ala... Identify the sequence of the wild-type mRNA. Match the codons in the left column to the appropriate blanks in the mRNA sequence on the right.
5'... AAA AGU CCA UCA CUU AAU GCA ...3'
Part B Part complete Identify the sequence of the double mutant mRNA. Match the codons in the left column to the appropriate blanks in the mRNA sequence on the right.
5'... AAA GUC CAU CAC UUA AUG GCA... 3'
Part F Which segment of the normal ABL protein aligns with the query sequence? Provide your answer in this format: number of first amino acid, number of last amino acid. (For example, if the first amino acid is 23 and the last amino acid is 413, enter 23, 413.)
80,246
Once elongation is underway, tRNAs involved in the process occupy a series of sites on the complexed ribosome. The occupation of sites occurs in the following order.
A Site, P Site, E Site
Part B How might this affect translation globally within a cell? Match the words in the left column to the appropriate blanks in the sentences on the right.
A change in the structure of a tRNA anticodon would be expected to interfere with normal termination an add additional amino acids at the C-terminus.
Using the information in the table, explain how a point mutation could change a codon for Glu to a codon for Val. Match the items in the left column to the appropriate blanks in the sentences on the right.
A change of the A in the GAG codon for glutamate to the U would change the codon to GUG , which codes for valine.
Part D Part complete What is the proper sequence of events in the formation of a peptide bond?
A-site tRNA bears the incoming amino acid. The P-site tRNA carries the growing peptide chain. Peptide bond formation attaches the P-site tRNA peptide to the amino acid of the A-site tRNA.
Part A - Locations of the processes involved in protein synthesisPart complete In eukaryotic cells, the processes of protein synthesis occur in different cellular locations. Drag the labels to the appropriate targets to identify where in the cell each process associated with protein synthesis takes place.
A: formation of ribosomal subunits B: attachment of an amino acid to tRNA C: translation of cytoplasmic proteins D: transcription an RNA processing E: translation of secreted proteins
Part E Part complete tRNA synthetases play a key role in protein biosynthesis by catalyzing the specific aminoacylation of tRNA at their 3' ends, a two step reaction termed "charging" of tRNA. The tutorial depicts the binding of glutaminyl-tRNA synthetase and tRNAGln. A uracil (U35) provides a key element for the recognition of tRNAGln by the synthetase enzyme. U35 of the tRNA is anchored in place by specific amino acids in the synthetase protein interacting ionically with the nearby backbone phosphates. Given what you know about ionic bonds and the phosphate backbone of RNA, what type of amino acids are involved in this interaction?
Amino acids with positively charged side chains
Part B Part complete According to wobble rules, what codons should be recognized by the anticodon 5′-GCU-3′? What amino acid residue do they correspond to? Match the words in the left column to the appropriate blanks in the sentences on the right.
Because G in the anticodon 5′ end can pair with U or C in the codon 3′ end, 5′ ...GCU...3′ can pair with 3 ′ ... UGA or 3′ ...CGA. They correspond to Ser.
At which stage in the translation does the polypeptide chain begin folding?
Folding begins during translation once the N-terminal end emerges from the ribosome
When polynucleotides are synthesized with repeating triplets of nucleotide residues, one, two, or three different polypeptide chains will be produced in cell-free synthesis. Part A Part complete Choose the correct explanation why these different results are possible. Match the words in the left column to the appropriate blanks in the sentences on the right.
In a cell-free system, a polynucleotide sequence can be read in up to three different reading frames, which can resultin up to three different amino acid sequences synthesized, providing that one of the three different reading frames is not a stop codon.
Sort two features into each stage of translation they describe. Drag the appropriate items to their respective bins.
Initiation The mRNA binds to the small subunit of a ribosome. A methionine-carrying tRNA has an anticodon UAC that occupies the AUG site of mRNA at the 5' end. Elongation The ribosome shifts exactly one codon to the right. The ribozyme present in the large ribosomal subunit catalyzes peptide bond formation. Termination The stop codon present on mRNA does not code for any amino acid. The ribosomal subunits, mRNA, and polypeptide chain separate.
Which of the following statements concerning peptide bond formation is correct?
It is catalyzed by peptidyl transferase.
Using BLAST: What Can a Protein Sequence Reveal about Cancer? Part A Based on the information given in the three different sections, which of the following statement(s) correctly describe(s) the hit that is most similar to the query sequence? Select all that apply.
Its accession number is CAM33009.1. It is a chimeric protein. It is identical to the query sequence in length and amino acid sequence.
Part C Part complete Predict polypeptides produced when (UUA)n is used with an E. coli system. Select all that apply.
Leu-Leu-Leu... Tyr-Tyr-Tyr... Ile-Ile-Ile...
What name is given to the process in which pre-mRNA is edited into mRNA?
RNA processing
Part B - The role of RNA in the flow of genetic informationPart complete Indicate at which step of the replication-transcription-translation process each type of RNA first plays a role. During which step of the replication-transcription-translation process does each type of RNA first play a role? Drag each item to the appropriate bin.
Replication: empty Transcription/ RNA processing: mRNA Translation: rRNA and tRNA
Understanding the genetic code Use the table to sort the following ten codons into one of the three bins, according to whether they code for a start codon, an in-sequence amino acid, or a stop codon. Drag each item to the appropriate bin.
Start/methionine: AUG Stop codon: UAA, UGA, and UAG amino acid: AAA, UGC, GCA, ACU, AUC, CAC
Part B Part complete What information would this give you about the code? Select all that apply.
The code is unpunctuated. The code is non-overlapping.
Do you expect the pI for the sickle-cell β-globin to be higher or lower than the pI for wild-type β-globin? Explain.
The pI of the sickle-cell globin will be higher than the wild-type globin because the mutation replaces a negatively charged side chain with one that carries no charge.
Although there are 61 codons in the universal genetic code that specify amino acids, most organisms possess fewer than 45 different tRNAs. Some tRNAs can be used to read different codons due to flexibility in the base pairing of the mRNA codon and the anticodon. These "wobble" base pairs allow for non Watson Crick hydrogen bonding, and therefore allow a single tRNA to read multiple codons. Which of the following best describes the structural basis of the wobble hypothesis?
The pairing of the third (3') base of the mRNA codon and the first (5') base of the tRNA anticodon are less constrained by base stacking.
Which of the following best describes the first step in the formation of the translation initiation complex?
The small ribosomal subunit binds to an mRNA sequence near the 5' end of the transcript
A nonsense codon can be suppressed. Suppression is a mutation at an unlinked site that restores wild-type function at the mutant site without changing the original mutation. Suppression of nonsense mutations was found to alter the structures of particular tRNAs. Part A Part complete Consider a nonsense mutation resulting from alteration of a trp codon and identify a specific mutation in a tRNA-encoding gene that could result in translation of the nonsense codon. Match the words in the left column to the appropriate blanks in the sentences on the right.
The tRNA anticodon sequence for 5'-UGG-3' is 3' - ACC-5'. consider a nonsense mutation reesulting from a GC→AT transition that changes the second nucleotide in the trp codon from 5'- UGG-3' to 5'-UAG-3'. This nonsense mutation could be suppressed by a GC→AT transition in the gene for a glutamate tRNA that changes the anticodon from 5'-CUC-3' to 5'-CUA-3'. This corresponds to a 5' GAG-3' codon, which would result in the original tryptophan codon being translated as gluatamate. A 5'-CUA-3' anticondon will bind to a 5'-UAG-3' codon and will result in the nonsense condon being translated as glutamate.
Part B - Roles of RNA in protein synthesis in eukaryotesPart complete RNA plays important roles in many cellular processes, particularly those associated with protein synthesis: transcription, RNA processing, and translation. Drag the labels to the appropriate bins to identify the step in protein synthesis where each type of RNA first plays a role. If an RNA does not play a role in protein synthesis, drag it to the "not used in protein synthesis" bin.
Transcription/RNA processing: ssNRA, pre-mRNA, and mRNA Translation: tRNA and rRNA not used in protein synthesis: RNA primers
Part A prokaryotes, the methionine that initiates the formation of a polypeptide chain differs from subsequently added methionines in that _______.
a formyl group is attached to the initiating methionine
Part C Part complete Which of the following images properly labels the components of the ribosome and tRNA?
https://session.masteringchemistry.com/problemAsset/1943362/2/tRNA_002a.jpg
When a peptide bond is formed between two amino acids, one is attached to the tRNA occupying the P site and the other _______.
is attached to the tRNA occupying the A site
Part B Scroll back to the Graphic Summary. The thick red bar directly underneath the color key for alignment scores represents the query sequence. The numbers below this line represent the positions of amino acids in the query sequence beginning at the N-terminal end (1) and ending at the C-terminal end (in this case, 235). The colored bars below the red query sequence bar show the hit sequences with their regions of similarity to the query sequence. In this search, only a few of the hits show similarity to the query sequence over its entire length. Most are similar to only parts of the query sequence. Identify the three main categories of hits in terms of similarity to the query sequence. (For help approaching this question, see Hint 1.)
sequences that are similar to the last 170 amino acids of the query sequence sequences that are similar to the entire length of the query sequence sequences that are similar to the first 75 amino acids of the query sequence
https://session.masteringchemistry.com/problemAsset/1943362/2/tRNA_005.jpg The image shows the four different surfaces of an glutaminyl-tRNA synthetase. Electrostatic interactions play a role in the interaction between this protein and tRNAGln. In these depictions, negatively charged surfaces of the protein are red and positively charged surfaces are blue. Given this information, which surface does tRNA bind to?
surface B
Part A - Properties of RNAPart complete Sort each description by the type of RNA it describes. Drag each item to the appropriate bin.
tRNA: has amino acids covalently attached contains an anticodon mRNA: contains exonas Specifies the amino acid sequence for a protein. rRNA: is the most abundant form of RNA is a component of ribosomes
Suppression of a nonsense mutation involves a change in nucleotide sequence of a tRNA molecule. Part A What part of the tRNA molecule is changed?
the tRNA anticodon
What name is given to the process in which a strand of DNA is used as a template for the manufacture of a strand of pre-mRNA?
transcription
What name is given to the process in which the information encoded in a strand of mRNA is used to construct a protein?
translation
Part E Only mutations that involve chromosomal rearrangements can result in the fusion of two different genes, which could code for a chimeric protein such as the BCR-ABL protein. Simple point mutations--insertion, deletion, or replacement of a single nucleotide--do not result in the fusion of two different genes. Which type of chromosomal rearrangement accounts for the creation of the gene that encodes the BCR-ABL chimeric protein? (For a review of the four different types of chromosomal rearrangements, see Hint 1.)
translocation
Part C Recall that each hit sequence has an accession number and short description associated with it. The text that describes each accession is submitted by the investigator who determines the gene or protein sequence and is usually a permanent part of the accession record; it is not updated as new information about the gene or protein is discovered. As a result, there is often a great deal of variability associated with descriptions of the same gene or protein. It is not uncommon to see descriptions that include "unnamed" or "unknown protein." For example, scroll to the Graphic Summary and mouse over the hits that are similar only to the C-terminal end (amino acids 70-235) of the query sequence. Notice the range of descriptions in the text box above the Summary figure. These include (among several others) tyrosine-protein kinase ABL1 isoform a unnamed protein product v-abl Abelson murine leukemia viral oncogene homolog 1 Chain A, Organization Of The Sh3-sh2 Unit In Active And Inactive Forms Of The C-abl Tyrosine Kinase Surprisingly, these all describe a small group of proteins with nearly identical sequences and functions. The common name for these proteins is Abelson murine leukemia protein, or ABL. They are all tyrosine-protein kinases, enzymes that regulate the activity of other proteins and are common in signal transduction pathways. Examine the descriptions for the group of hits that align with the N-terminal end of the query sequence. Which of the following terms are found among these descriptions? Select all that apply.
unnamed protein product breakpoint cluster region protein BCR variant protein
https://session.masteringchemistry.com/problemAsset/1943362/2/tRNA_001a.jpg This is a diagram of the secondary structure of a tRNA molecule. To which portion of the molecule is the amino acid attached? Which part binds to mRNA?
amino acid (1) / mRNA (6)
Polypeptides are assembled from _____.
amino acids
Translation is directly dependent on all of the following associations except _______.
complementary base pairing between mRNA and DNA