Gene to Protein, part 2

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Gene to Protein, part 2

Due: 3:00pm on Monday, September 29, 2014
You will receive no credit for items you complete after the assignment is due. Grading Policy

The Genetic Code

DNA is transcribed to messenger RNA (mRNA), and the mRNA is translated to proteins on the ribosomes. A sequence of three nucleotides on an mRNA
molecule is called a codon. As you can see in the table, most codons specify a particular amino acid to be added to the growing protein chain. In addition, one
codon (shown in blue) codes for the amino acid methionine and functions as a start signal. Three codons (shown in red) do not code for amino acids, but
instead function as stop signals.

Part A - 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.

Hint 1. How to interpret the table of codons

The table of codons shows the start codon in blue and the three stop codons in red. All other codons (shown in black) appear in the middle of the
amino acid sequences that make up proteins.
To read the table, locate the first letter in the codon on the left side of the table, then locate the second letter along the top, and the third letter down
the right side of the table. Follow those letters across and down to identify the amino acid associated with that three-letter codon.

Hint 2. What is the start codon?

Identify the start codon.
ANSWER:
AUG

Hint 3. What are the stop codons?

Enter the three stop codons, separated by commas.
ANSWER:
UAG, UGA, UAA

ANSWER:

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Correct
Nearly every mRNA gene that codes for a protein begins with the start codon, AUG, and thus begins with a methionine. Nearly every protein-coding
sequence ends with one of the three stop codons (UAA, UAG, and UGA), which do not code for amino acids but signal the end of translation.

Part B - Translation of mRNA

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).

Hint 1. How to approach the problem

First, subdivide the sequence into the individual three-letter codons. Then, refer to the table of codons to find the three-letter abbreviation for the
amino acid that corresponds to each codon.

Hint 2. An example problem

This chart shows how to decode an example mRNA sequence. Labels indicating directionality (for example, 5 3) are not needed when writing
amino acid sequences.
Example mRNA sequence

5 AUGUCGACUAAGGGA 3

Codon sequence

AUG UCG ACU AAG GGA

Amino acid sequence

(three-letter abbreviation)

Met

Ser

Thr

Lys

Gly

Hint 3. Can you identify the individual codons in the mRNA sequence?
To identify the amino acids specified by the mRNA sequence, you first need to subdivide the sequence into codons of three nucleotides each. This
can be done by placing a space between each codon. Which of the following is the correct division of the codons for the sequence given? Look for
the correct placement of spaces.
ANSWER:

5
5
5
5
5

A UGG CAA GAA AA 3

AU GGC AAG AAA A 3
AUG GCA AGA AAA 3
AUGG CAA GAA AA 3
AU GGCA AGAA AA 3

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Hint 4. Can you decode GCA?

Which amino acid does the codon GCA code for?
Express your answer using the three-letter abbreviation of the amino acid.
ANSWER:
Ala

ANSWER:
Met-Ala-Arg-Lys

Correct
An amino acid sequence is determined by strings of three-letter codons on the mRNA, each of which codes for a specific amino acid or a stop signal.
The mRNA is translated in a 5 3 direction.

Part C - The role of DNA in determining amino acid sequences

Before a molecule of mRNA can be translated into a protein on the ribosome, the mRNA must first be transcribed from a sequence of DNA.

What amino acid sequence does the following DNA nucleotide 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).

Hint 1. How to approach the problem

Follow these steps to convert a DNA sequence into an amino acid sequence.
1. First, transcribe the DNA sequence to determine the mRNA sequence. Be sure to remember the following:
The mRNA strand is complementary to the DNA strand.
Uracil (U) takes the place of thymine (T) in RNA to pair with A on the DNA.
The RNA is assembled in an antiparallel direction to the template strand of DNA. A 3 5 direction in DNA is transcribed
in a 5 3 direction in RNA.
2. Next, subdivide the mRNA sequence into the individual three-letter codons in the 5 to 3 direction.
3. Then, refer to the table of codons to identify the three-letter abbreviation for the amino acid that corresponds to each codon.

Hint 2. An example problem

This chart shows how to decode an example DNA sequence. Remember to first determine the mRNA sequence that is complementary to the DNA
template strands sequence. Be sure to write the mRNA sequence in a 5 to 3 direction, and to use U to pair with A.
Example DNA sequence (template strand)

3 TACGAATCAGCTGTA 5

Complementary DNA sequence

5 ATGCTTAGTCGACAT 3

mRNA sequence

5 AUGCUUAGUCGACAU 3

Codon sequence

AUG CUU AGU CGA CAU

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Amino acid sequence (three-letter abbreviation)

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Met

Leu

Ser

Arg

His

Hint 3. What mRNA sequence is transcribed from the DNA sequence?

What mRNA nucleotide sequence would be transcribed from the DNA sequence in this problem?

3 TACAGAACGGTA 5

ANSWER:

5
3
3
5

ATGTCTTGCCAT 3
AUGUCUUGCCAU 5
TACAGAACGGTA 5
AUGUCUUGCCAU 3

ANSWER:
Met-Ser-Cys-His

Correct
Before mRNA can be translated into an amino acid sequence, the mRNA must first be synthesized from DNA through transcription. Base pairing in
mRNA synthesis follows slightly different rules than in DNA synthesis: uracil (U) replaces thymine (T) in pairing with adenine (A). The codons specified
by the mRNA are then translated into a string of amino acids.

Activity: The Triplet Nature of the Genetic Code

Click here to view this animation.

Then answer the questions.

Part A
True or false? A codon is a group of three bases that can specify more than one amino acid.

Hint 1.
What is a codon?
ANSWER:
True
False

Correct
A codon is a group of three bases that can specify only one amino acid.

Part B

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Which of the following statements about mutations is false?

Hint 1.
What types of mutation can occur in a gene sequence?
ANSWER:
Addition and deletion mutations disrupt the primary structure of proteins.
A deletion mutation results in the loss of a base in the DNA sequence.
A knock-out mutation results in a total absence of the mutated protein.
An addition mutation results in an added base in the DNA sequence.

Correct
A knock-out mutation refers to the loss of a protein's function but not necessarily to its complete absence.

Part C
If a DNA sequence is altered from TAGCTGA to TAGTGA, what kind of mutation has occurred?

Hint 1.
Determine how the two sequences differ.
ANSWER:
Deletion.
Both addition and deletion.
Addition.
None.

Correct
The original sequence has lost the base C.

Part D
Which mutation(s) would not change the remainder of the reading frame of a gene sequence that follows the mutation(s)?

Hint 1.
Think about how the genetic code is organized into "words."
ANSWER:
One addition and two deletion mutations.
One addition and one deletion mutation.
One addition mutation.
One deletion mutation.

Correct
This combination results in no net change in the number of bases, so the reading frame would eventually be restored.

Part E
If the sequence ATGCATGTCAATTGA were mutated such that a base were inserted after the first G and the third T were deleted, how many amino acids
would be changed in the mutant protein?

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Hint 1.
Determine the reading frame of the codons in the mutated sequence.
ANSWER:
One.
Three.
Two.
None.

Correct
The second and third codons in the new sequence are different from the original codons.

Part F
If a mutated DNA sequence produces a protein that differs in one central amino acid from the normal protein, which of the following kinds of mutations could
have occurred?

Hint 1.
Think about the effects of different mutations on a codon sequence.
ANSWER:
An addition mutation
A deletion mutation.
An addition mutation and a deletion mutation.
None.

Correct
If the mutations occur within the same codon, only that codon (amino acid) will be altered.

Point Mutations
DNA polymerase is very accurate and rarely makes a mistake in DNA replication. Occasionally, however, an error in replication, known as a point mutation, is
introduced. There are two general categories of point mutationsframeshift mutations (also called base-pair insertions or base-pair deletions) and base
substitution mutations (shown in the diagram).

Part A - Base substitution mutations and frameshift mutations

If a segment of DNA were replicated without any errors, the replicated strand would have the following sequence of nucleotides:
5' - ACTACGTGA - 3'
Sort the following replicated DNA sequences by the type of point mutation each contains (frameshift, base substitution, or neither), as compared to the
correct sequence shown above.
Sort the items into the appropriate bins.

Hint 1. How to approach the problem

In order to determine the type of point mutation contained in a DNA sequence, it is helpful to write the mutated sequences below the correct
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sequence so you can see the differences. The table below displays examples.
Correct Sequence

ATGCAT

Substitution 1

ATCCAT

Substitution 2

ATGCTT

Frameshift 1

ATGGCAT

Frameshift 2

ATCAT

Frameshift mutations will change the number of nucleotides in a sequence; base substitution mutations will change the composition of the sequence
but not the number of nucleotides.

Hint 2. How many bases are in each mutated segment?

The correct DNA sequence contains nine bases. Which of the mutated sequences also contain(s) nine bases?
Select all that apply.
ANSWER:
5' - ACTTACGTGA - 3'
5' - ACTCGTGA - 3'
5' - ACTAAGTGA - 3'
5' - ACTACGTGT - 3'

ANSWER:

All attempts used; correct answer displayed

A base substitution mutation can occur if the DNA polymerase inserts the wrong nucleotide base as it synthesizes a new strand of DNA. A frameshift
mutation can occur if the DNA polymerase leaves out a nucleotide or adds an extra nucleotide to the sequence. Certain forms of cancer occur because
of mutations in DNA sequences that are located in so-called mutational hotspots. These hotspots are locations in the DNA sequence where mutations
occur more often than in other places.

Part B - Types of base substitution mutations

When a base substitution mutation occurs, one nucleotide in a replicating DNA sequence is substituted for another, which results in the production of a
mutant strand of DNA. The result of the mutation depends on how the substituted nucleotide base alters the string of amino acids coded by the mutant
DNA.
The three types of base substitution mutations are nonsense mutations, missense mutations, and silent mutations. Each type is defined by how it affects
protein synthesis.

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Label the four mutated DNA segments shown below according to the type of point mutation each represents. Use the codon table above to determine how
each mutation would affect the amino acid coding for each segment.
Drag the labels to their appropriate locations to identify the type of point mutation shown.

Hint 1. How to approach the problem

All base substitution mutations alter one base within the DNA sequence, causing a new base pair to form as the DNA replicates. This change in turn
alters the mRNA sequence when the DNA is transcribed. The effect of this nucleotide substitution on the translation of the mRNA to a protein will
depend on what amino acid is now coded for by the altered base sequence. There are three possible outcomes that can result:
nonsense mutation: the new base changes an amino acid codon to a stop codon, ending protein synthesis and resulting in a shorter
and usually nonfunctional protein.
missense mutation: the new base leads to the insertion of a different amino acid than had been coded for, possibly altering the
resulting proteins structure.
silent mutation: the new base does not change the amino acid sequence coded for by the original DNA strand.
You will have to refer to the table of amino acid codons to predict which of the three possible outcomes will occur for each mutant DNA segment.

Hint 2. How do the three types of base substitution mutations differ?

Drag the terms on the left to the appropriate blanks on the right to complete the sentences.
ANSWER:

ANSWER:

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Correct
Point mutations in DNA sequences can profoundly affect protein synthesis, or they can have no effect at all. Point mutations can be beneficial to an
organism but are more commonly neutral or harmful.

Part C - Severity of point mutations

Generally speaking, which of the following mutations would most severely affect the protein coded for by a gene?

Hint 1. How to approach the problem

You know that each type of genetic mutation will affect the sequence of the gene, which will in turn affect the protein it codes for to varying extents.
You need to consider how base substitution mutations typically affect proteins compared to how frameshift mutations typically affect proteins.

Hint 2. Which mutation will affect an amino acid sequence the least?
Of the mutations listed below, which one will likely change the amino acid sequence of the protein coded by the gene the least?
ANSWER:
a base substitution at the beginning of the gene
a base substitution at the end of the gene
a frameshift deletion at the beginning of the gene
a frameshift deletion at the end of the gene

ANSWER:
a base substitution at the beginning of the gene
a base substitution at the end of the gene
a frameshift deletion at the beginning of the gene
a frameshift deletion at the end of the gene

Correct
A frameshift mutation at the beginning of a gene would affect every codon after the point where the mutation occurred. During protein synthesis,
incorrect amino acids would be inserted from the point where the frameshift mutation occurred on; the resulting protein would most probably be
nonfunctional. For this reason, a frameshift mutation at the beginning of a gene is generally the most severe type of mutation.

Score Summary:

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Your score on this assignment is 0.0%.

You received 0 out of a possible total of 3 points.

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