Genetics Chapter 13_ EX3

According to adaptor hypothesis, is each of the following statements true or false? 1. sequence of anticodons in tRNA directly synthesizes codon sequences in mRNA, with some room for wobble. 2. amino acid attached to trna directly recognizes codon sequences in mrna 3. amino acid attached to trna affects the binding of the trna to a codon sequence in mrna

. True B. False C. False

Place a single word in each sentence to make it correct. There are ____________ possible codons. Multiple codons can code for the same amino acid so, we say the genetic code is ____________ . The code is considered ____________ although there are some exceptions to the rules. Codons that specify the same amino acid are termed ____________ . The third base in a codon is called the ____________ base. Options- Overlapping, wobble, universal, 64, loose, degenerate, synonymous, 20

1. 64 2. degenerate 3. universal 4. synonomous 5. wobble

For each of the following, rank in order from best to worst as sequences that could be used to initiate translation according to Kozak's rules GACGCCAUGG GCCUCCAUGC GCCAUCAAGG GCCACCAUGG

1. GCCACCAUGG 2. GACGCCAUGG 3. GCCUCCAUGC 4. GCCAUCAAGG The last one does not have a start codon, so it would not work. The third one may be translated, but very poorly.

Indicate which category of protein function the listed protein likely falls into. (transport, cell shape and organization, movement, cell signaling, cell surface recognition, enzymes) Ubiquitin ligase, which attaches ubiquitin molecules to a protein, targeting it for destruction MreB, a bacterial protein important for helping maintain the rod-shape of certain bacteria The IP3 receptor, which functions as a calcium channel in the endoplasmic reticulum Actin assembles and diassembles, allowing cells to migrate

1. enzymes 2. cell shape and organization 3. transport 4. movement

he following statements describe translation. Determine if the statement applies to only prokaryotes, to only eukaryotes, or to both. 1. The first tRNA used is charged with a formyl methionine. 2. Translation occurs in the cytoplasm. 3. Requires a Shine-Dalgarno sequence to be present on the mRNA. 4. Translation occurs cotranscriptionally 5. Initiation requires a 7-methylguanosine cap on the mRNA. 6. Requires a release factor to terminate translation.

1. prokaryotes 2. both 3. prokaryotes 4. prokaryotes 5. eukaryotes 6. both

Choose true or false for each of the following statements. 1. All tRNAs have the sequence CCA at their 3' end. 2. The wrong amino acid is used to charge a tRNA about 1 out of every 1000 charging events. 3. The codon in the mRNA and the anticodon on the tRNA bind in an antiparallel fashion. 4. There are 64 different tRNAs in the cell. 5. There are 20 different aminoacyl-tRNA synthetases in the cell. 6. The 3' nucleotide of the anticodon on the tRNA is involved in wobble.

1. true 2. false 3. true 4. false 5. true 6. false

Choose true or false for each of the following statements. 1. Bacteria have only one kind of ribosome. 2. Ribosomes have large and small subunits. 3. Eukaryotic ribosomes are assembled in the cytosol. 4. Ribosomes are composed solely of rRNAs. 5. In eukaryotes, ribosomes found in mitochondria and chloroplasts have a different composition than that of cytosolic ribosomes.

1. true 2. true 3. false 4. false 5. true

If tRNA molecule carries glutamic acid, what are the two possible anticodon sequences that it could contain?

3-CUU-5 or 3-CUC-5

Select all the anticodons that could bind to the codon for serine. Choose all that apply. Check All That Apply 5'-AGA-3' 5'-GGA-3' 5'-AGG-3' 5'-IGA-3' 5'-AGI-3' 5'-AGU-3' 5'-UGA-3'

5'-AGG-3' 5'-AGI-3' 5'-AGU-3' 5'-UGA-3'

During the elongation stage of translation, new tRNAs enter at which site? Multiple Choice P site A site. E site

A site.

Do the following events during bacterial translation occur primarily wihtin 30s subunit, within 50s, or at interface between these two ribosomal subunits 1. mRNA-tRNA recognition 2. Peptidyl transfer reaction 3. exit of polypeptide from ribosome 4. Binding of initiation factors IF1, 2, and 3

A. On the surface of the 30S subunit and at the interface between the two subunits B. Within the 50S subunit C. From the 50S subunit D. To the 30S subunit

In which of the ribosomal sites, A P, or E, could the following be found? 1. tRNA without an amino acid sequence 2. tRNA with a polypeptide attached 3. tRNA with a single amino acid attached

A. The E site and P sites. (Note: A tRNA without an amino acid attached is only briefly found in the P site, just before translocation occurs.) B. P site and A site (Note: A tRNA with a polypeptide attached is only briefly found in the A site, just before translocation occurs.) C. Usually the A site, except for the initiator tRNA, which can be found in the P site.

For each of the following initiation factors, how would eukaryotic initiation be affected if it were missing?1. eIF2 2. eIF4 3. eIF5

A. The initiator tRNA would not bind to the 40S ribosomal subunit. B. mRNA would not bind to the 40S ribosomal subunit, and/or the start codon would not be recognized because the secondary structure in the mRNA was not unwound. C. The 60S ribosomal subunit would not assemble after the start codon had been identified.

Describe structural features that all tRNA molecules have in common

All tRNA molecules have some basic features in common. They all have a cloverleaf structure with three stem-loop structures. The second stem-loop contains the anticodon sequence that recognizes the codon sequence in mRNA. At the 3 end of each tRNA, there is an acceptor stem, with the sequence CCA, that serves as an attachment site for an amino acid. Most tRNAs also have base modifications within their nucleotide sequences.

Describe anticodon of a single tRNA that could recognize the codons 5'AAC-3' and 5'AAU3'. What types of base modification to this tRNA would allow it to also recognize 5'aaa3'?

An anticodon that was 3-UUG-5 would recognize the two codons. To recognize 5-AAA-3, it would have to be modified to 3-UUI-5.

How and when does formylmethionine become attached to the initiator tRNA in bacteria?

An enzyme covalently attaches a formyl group to methionine after the methionine has been attached to the tRNA containing a UAC anticodon.

The covalent attachment amino acid to rRNA is an endergonic reaction. In other words, it requires an input of energy for the reaction to proceed. Where does the energy come from to attach amino acids to tRNA molecules?

As shown in Figure 13.11, the energy comes from ATP. It is this energy conversion that explains the term "charged tRNA."

Discuss significance of modified bases within tRNA molecules

Bases that have been chemically modified can occur at various locations throughout the tRNA molecule. The significance of all of these modifications is not entirely known. However, within the anticodon region, base modification may alter base pairing to allow the anticodon to recognize two or more different bases within the codon.

A tRNA has anticodon sequence 3'-CCI-5'. What codons can it recognize?

C10. It can recognize 5-GGU-3, 5-GGC-3, and 5-GGA-3. All of these specify glycine.

The term subunit can be used in a variety of way. What is the difference between protein subunit and ribosomal subunit?

C21. A protein subunit is a polypeptide. A ribosomal subunit is a much larger complex that is composed of RNA and many proteins. A ribosomal subunit is a much larger structure compared to a protein subunit.

Which steps during the translation of bacterial mRNA involve an interaction between complementary strands of RNA?

C30. The initiation phase involves the binding of the Shine-Dalgarno sequence to the rRNA in the 30S subunit. The elongation phase involves the binding of anticodons in tRNA to codons in mRNA.

What is function of nucleolus?

C31. The nucleolus is a region inside the eukaryotic nucleus where the assembly of ribosomal subunits occurs.

What is a polysome?

C33. A polysome is an mRNA molecule with many ribosomes attached to it.

ou are doing research in bacteria on the effects of mutating the Shine-Dalgarno sequence. You change some nucleotides in the Shine-Dalgarno sequence and find that translation is greatly reduced. What other element in the bacteria could you change that would have a good chance of restoring translation in the bacterial strain with the altered Shine-Dalgarno sequence? Multiple Choice Change the anti-codon on the initiator tRNA Change the start codon Change the sequence of the 16S rRNA Change IF1 or IF3

Change the sequence of the 16S rRNA

What is an activated amino acid?

In the context of translation, an activated amino acid has had AMP attached to it. This provides necessary energy so that the amino acid can be attached to the correct tRNA.

Suppose it was possible to change the anticodon on a tRNA from 3'-CCG-5' to 3'-UGG-5' after the amino acid was already loaded. Predict the result in a translated polypeptide. What if you changed the sequence prior to the amino acid being loaded onto the tRNA? rev: 10_06_2015_QC_CS-28590 Multiple Choice In the first case there would be no change since the amino acid was already loaded. In the second case threonine would be found in the polypeptide where glycine was supposed to be. In the first case glycine would be found in the polypeptide where threonine was supposed to be. In the second case the changed tRNA would behave like a tRNA for threonine. In the first case tryptophan would be found in the polypeptide where proline was supposed to be. In the second case the changed tRNA would behave like a tRNA for tryptophan. In the first case threonine would be found in the polypeptide where glycine was supposed to be. In the second case the changed tRNA would behave like a tRNA for glycine.

In the first case glycine would be found in the polypeptide where threonine was supposed to be. In the second case the changed tRNA would behave like a tRNA for threonine.

Select the stages of translation (check all that apply). Check All That Apply Initiation Elongation Termination Assembly Transcription

Initiation Elongation Termination Assembly Transcription

What are 3 stages of translation? Discuss main events

Initiation: The mRNA, initiator tRNA, and initiation factors associate with the small ribosomal subunit; then the large subunit associates. Elongation: The ribosome moves one codon at a time down the mRNA, adding one amino acid at a time to the growing polypeptide. Three sites on the ribosome, the A, P, and E sites, are important in this process. The A site is where the tRNA (except for the initiator tRNA) binds to the ribosome and recognizes the codon in the mRNA. The growing polypeptide is then transferred to the amino acid attached to this tRNA. The ribosome then translocates so that this tRNA is now moved to the P site. The empty tRNA that was in the P site is moved into the E site. This empty tRNA in the E site is then expelled and the next charged tRNA can bind to the A site. Termination: A stop codon is reached and a termination factor binds to the A site. The hydrolysis of GTP initiates a series of events that leads to the disassembly of the ribosomal subunits and the release of the completed polypeptide.

An mRNA has the following sequence: 5'-CCCAUAUGCUGGGAUAUCGGUGAC-3'. What is the first codon translated? What is the last codon translated? How many amino acids are in the polypeptide? Multiple Choice Proline; Aspartic Acid; 8 Methionine; Arginine; 5 Proline; Arginine; 7 Methoinine; Serine; 6

Methionine; Arginine; 5

Describe sequence in bacterial mRNA that promotes recognition by the 30s subunit

Most bacterial mRNAs contain a Shine-Dalgarno sequence, which is necessary for the binding of the mRNA to the small ribosomal subunit. This sequence, UUAGGAGGU, is complementary to a sequence in the 16S rRNA. Due to this complementarity, these sequences will hydrogen bond to each other during the initiation stage of translation.

Is it neccessary for a cell to make 61 different tRNA molecules. corresponding to the 61 codons for amino acids? Explain

No, it is not. Due to the wobble rules, the 5 base in the anticodon of a tRNA can recognize two or more bases in the third (3) position of the mRNA. Therefore, any given cell type synthesizes far fewer than 61 types of tRNAs.

The initiator tRNA is special because it is the only tRNA that can initially bind at this site in the ribosome. Multiple Choice P site E site A site.

P site

If Nirenberg and Matthaei performed their cell-free translation experiment using an mRNA composed of 60% C and 40% A what radiolabeled amino acids would be incorporated into the precipitated polypeptides? Check All That Apply Phenylalanine Leucine Isoleucine Methionine Valine Serine Proline Threonine Alanine Tyrosine Histidine Glutamine Asparagine Lysine Aspartic acid glutamic acid Cysteine Tryptophan Arginine Glycine

Phenylalanine Leucine Isoleucine Methionine Valine Serine Alanine Tyrosine Aspartic acid glutamic acid Cysteine Tryptophan Arginine Glycine

Phenylketonuria occurs when the gene for the enzyme phenylalanine hydroxylase is mutated, leading to an undesirable build-up of the compound usually acted upon by phenylalanine hydroxylase. Based on what you know about the metabolic pathway involving this enzyme, what dietary changes do you presume phenylketonurics must make? Multiple Choice No dietary changes are required. Phenylketonurics should eat additional phenylalanine and reduced amounts of tyrosine. Phenylketonurics should eat reduced amounts of phenylalanine and increased amounts of tyrosine. Phenylketonurics must reduce their intake of phenylalanine, no change to tyrosine intake is required. Phenylketoneurics must increase their intake of phenylalanine, no change to tyrosine intake is required.

Phenylketonurics should eat reduced amounts of phenylalanine and increased amounts of tyrosine.

Beadle and Tatum used Neurospora to identify mutants affecting various biosynthetic pathways. Their research led them to develop the one gene, one enzyme hypothesis. We now know this hypothesis is too narrow in its description of genes. In what way(s) was their hypothesis is too narrow? (Check all that apply) Check All That Apply Some genes make RNAs that are not translated. Many proteins in the cell are not enzymes. They were unable to isolate all of the enzymes involved in methionine biosynthesis. Many proteins are composed of two or more different polypeptides; so more than one gene is involved in making the functional protein.

Some genes make RNAs that are not translated. They were unable to isolate all of the enzymes involved in methionine biosynthesis.

Explain functional roles of A P and E sites during translation

The A (aminoacyl) site is the location where a tRNA carrying a single amino acid initially binds. The only exception is the initiator tRNA, which binds to the P (peptidyl) site. The growing polypeptide is removed from the tRNA in the P site and transferred to the amino acid attached to the tRNA in the A site. The ribosome translocates in the direction, with the result that the two tRNAs in the P and A sites are moved to the E (exit) and P sites, and the uncharged tRNA in the E site is released.

an mRNA sequence 5'- AUG UAC UAU GGG GCG UAA -3' Describe amino acid sequence of the polypeptide that would be encoded.

The amino acid sequence is methionine-tyrosine-tyrosine-glycine-alanine. Methionine is at the amino terminal end, alanine at the carboxyl terminal end. The peptide bonds should be drawn as shown in Figure 13.4b.

Wobble rule If we assume tRNAs do not contain modified bases, what is minimum number of tRNAs needed to recognize the codons for: Leucine, Methionine, Serine

The answer is three. There are six leucine codons: UUA, UUG, CUU, CUC, CUA, and CUG. The anticodon AAU would recognize UUA and UUG. You would need two other tRNAs to efficiently recognize the other four leucine codons. These could be GAG and GAU or GAA and GAU. B. The answer is one. There is only one codon, AUG, so you need only one tRNA with the anticodon UAC. C. The answer is three. There are six serine codons: AGU, AGC, UCU, UCC, UCA, and UCG. You would need only one tRNA to recognize AGU and AGC. This tRNA could have the anticodon UCG or UCA. You would need two tRNAs to efficiently recognize the other four tRNAs. These could be AGG and AGU or AGA and AGU.

List components of eukaryotic ribosomal subunits and the location where the assembly of the subunits occurs within living cells

The assembly process for the ribosomal subunits is very complex at the molecular level. In eukaryotes, 33 proteins and one rRNA assemble to form a 40S subunit, and 49 proteins and three rRNAs assemble to form a 60S subunit. This assembly occurs within the nucleolus.

A tRNA has an anticodon 3'-GGU-5'. What amino acid?

The codon is 5-CCA-3, which specifies proline.

In bacteria, researches have isolated strains that carry tRNA mutation genes tht can change sequence of anticodon.When ACC is changed to CCC, tRNA still carries trytophan at 3' acceptor stem, even after alteration. 1. How would this mutation affect synthesis of polypeptides within bacterium? 2. What does mutation tell you about recognition between tryptophanyl tRNA synthetase and tRNA Trp? Does the enzyme primarily recognize the anticodon or not?

The mutant tRNA would recognize glycine codons in the mRNA but would put in the amino acid tryptophan where glycine was supposed to be in the polypeptide. B. This mutation tells us that the aminoacyl-tRNA synthetase is primarily recognizing regions of the tRNA molecule other than the anticodon region. In other words, tryptophanyl-tRNA synthetase (the aminoacyl-tRNA synthetase that attaches tryptophan) primarily recognizes other regions of the tRNATrp sequence (that is, other than the anticodon region). If aminoacyl-tRNA synthetases recognized only the anticodon region, we would expect glycyl-tRNA synthetase to recognize this mutant tRNA and attach glycine. That is not what happens.

How does a eukaryotic ribosome select its start codon? Describe the sequences in eukaryotic mRNA that provide an optimal context for a start codon

The ribosome binds at the 5 end of the mRNA and then scans in the 3 direction in search of an AUG start codon. If it finds one that reasonably obeys Kozak's rules, it will begin translation at that site. Aside from an AUG start codon, two other important features are a guanosine at the +4 position and a purine at the -3 position.

What is role of aminoacyl-tRNA synthetase? The ability of aminoacyl-TRNA syntheases to recognize tRNAs has sometimes been called the 2nd genetic code. WHy has the function of this enzyme been described this way?

The role of aminoacyl-tRNA synthetase is to specifically recognize tRNA molecules and attach the correct amino acid to them. This ability is sometimes referred to as the "second genetic code" because the specificity of the attachment is a critical step in deciphering the genetic code. For example, if a tRNA has a 3-GGG-5 anticodon, it will recognize a 5-CCC-3 codon, which should specify proline. It is essential that the aminoacyl-tRNA synthetase known as prolyl-tRNA-synthetase recognizes this tRNA and attaches proline to the 3 end. The other aminoacyl-tRNA synthetases should not recognize this tRNA.

An mRNA sequence: 5'- GGCGAUGGGCAAUAAACCGGGCCAGUAAGC-3'. Identify start codon, determine amino acid sequence.

The start codon begins at the fifth nucleotide. The amino acid sequence would be Met Gly Asn Lys Pro Gly Gln STOP.

How many different sequences of mRNA could encode a peptide with a sequence proline-glycine-methione-serine

There are four proline codons, four glycine codons, one methionine codon, and six serine codons. We apply the product rule to solve this problem. 4416 = 96

In tertiary structure of tRNA, where is anticodon region relative to the attachment site for the amino acid? Are these adjacent to each other?

They are very far apart, at opposite ends of the molecule.

The genetic code is a triplet code, meaning that three nucleotides are necessary to code for one amino acid. If one or two nucleotides are inserted into a protein coding region it can cause a frame shift which would change the amino acid sequence. Assume instead, that the genetic code is made up of codons consisting of six nucleotides. The statements below describe nucleotide insertions into a protein coding region. Which would not cause a frame shift? Multiple Choice Three nucleotides are inserted. Nine nucleotides are inserted. Twelve nucleotides are inserted. Fifteen nucleotides are inserted.

Twelve nucleotides are inserted.

What does genetic code degenerate mea? Discuss universality of genetic code.

When we say the genetic code is degenerate, it means that more than one codon can specify the same amino acid. For example, GGG, GGC, GGA, and GGU all specify glycine. In general, the genetic code is nearly universal, because it is used in the same way by viruses, prokaryotes, fungi, plants, and animals. As shown in Table 13.2, there are a few exceptions, which occur primarily in protists and yeast and mammalian mitochondria.

You are studying a protein that contains the amino acid selenocysteine. To understand the protein better, you place the gene for this protein into a plasmid, so that you can control the expression of the gene in cells. When you look at the protein expressed from the plasmid, however, you are surprised to find that the protein encoded from the plasmid is shorter than the protein encoded from the genome. Why? Multiple Choice You forgot to include the SECIS, and therefore UGA functioned as a stop codon rather than a codon for selenocysteine. Selenocysteine can only be included in proteins encoded by the genome, therefore the UGA functioned as a stop codon, rather than a codon for selenocysteine. You likely placed the incorrect gene into the plasmid. You included the SECIS, and therefore the UGA functioned as a stop codon rather than a codon for selenocysteine.

You forgot to include the SECIS, and therefore UGA functioned as a stop codon rather than a codon for selenocysteine.

Genes are used to make RNA and some RNA is used to make proteins. Not all RNAs in the cell are destined to be translated. What RNAs will be translated? Multiple Choice tRNAs mRNAs tRNAs and mRNAs rRNAs and mRNAs tRNAs, mRNAs and rRNAs

mRNAs