The Molecular Basis of Inheritance

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The Molecular Basis of Inheritance & From Gene to Protein

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Biol 1002 - Spring 2013

The Molecular Basis of Inheritance &a...
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The Molecular Basis of Inheritance & From Gene to Protein Due: 9:00am on Wednesday, April 24, 2013 Note: You will receive no credit for late submissions. To learn more, read your instructor's Grading Policy
Activity: DNA and RNA Structure
Click here to complete this activity. Then answer the questions.
Part A
In the accompanying image, a nucleotide is indicated by the letter _____.
ANSWER: B D E C A
Correct
B is indicating a single nucleotide.
Part B
Which of these is a difference between a DNA and an RNA molecule? ANSWER:
session.masteringbiology.com/myct/assignmentPrintView?assignmentID=1937216
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DNA is a polymer composed of nucleotides, whereas RNA is a polymer composed of nucleic acids. DNA contains five-carbon sugars, whereas RNA contains six-carbon sugars. DNA contains uracil, whereas RNA contains thymine. DNA is double-stranded, whereas RNA is single-stranded. DNA contains nitrogenous bases, whereas RNA contains phosphate groups.
Correct
(With some exceptions) DNA is a double-stranded molecule and RNA is a single-stranded molecule.
Part C
This is an image of a(n) _____.
ANSWER: nucleic acid amino acid nucleotide none of the above thiol
Correct
Nucleotides are composed of a pentose sugar, a nitrogenous base, and a phosphate group.
Part D
The letter A indicates a _____.
ANSWER:
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phosphate group nitrogenous base sugar none of the above nucleotide
Correct
Phosphate groups contain phosphorus..
Part E
A nitrogenous base is indicated by the letter _____.
ANSWER: B E D C A
Correct
This is a nitrogenous base.
Part F
You can tell that this is an image of a DNA nucleotide and not an RNA nucleotide because you see a _____.
ANSWER:
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thymine nitrogenous base, not a uracil nitrogenous base phosphate group, not a uracil double-stranded molecule, not a single-stranded molecule sugar with two, and not three, oxygen atoms uracil nitrogenous base, not a thymine nitrogenous base
Correct
DNA nucleotides are composed of deoxyribose sugars, whereas RNA nucleotides are composed of ribose sugars.
Part G
Which of these nitrogenous bases is found in DNA but not in RNA? ANSWER: cytosine uracil adenine guanine thymine
Correct
DNA contains thymine; RNA does not.
Part H
Which of these is(are) pyrimidines?
ANSWER: B, C, and D A and B B and C C, D, and E A, B, and C
Correct
Pyrimidines are single-ring structures.
Part I
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In a nucleotide, the nitrogenous base is attached to the sugar's _____ carbon and the phosphate group is attached to the sugar's _____ carbon. ANSWER: 1' ... 2' 2' ... 1' 2' ... 3' 1' ... 5' 1' ... 3'
Correct
The nitrogenous base is attached to the sugar's 1' carbon and the phosphate group is attached to the sugar's 5' carbon.
Part J
Nucleic acids are assembled in the _____ direction. ANSWER: 5' to 3' 2' to 3' 1' to 5' 4' to 5' 5' to 1'
Correct
New nucleotides are added to the 3' end of a growing polynucleotide.
Part K
In a DNA double helix an adenine of one strand always pairs with a(n) _____ of the complementary strand, and a guanine of one strand always pairs with a(n) _____ of the complementary strand. ANSWER: guanine ... adenine thymine ... cytosine cytosine ... uracil cytosine ... thymine uracil ... cytosine
Correct
This is referred to as specific base pairing.
DNA Replication (1 of 2): DNA Structure and Replication Machinery (BioFlix tutorial)
DNA is composed of two strands that are bound together, resembling a rope ladder with rigid rungs. This DNA ladder is twisted, forming what is called the double helix. The structure of the DNA double helix depends on the complementary pairing of bases between the two strands. Replication of DNA requires that the two strands of the helix separate, as shown in the image below. New daughter molecules are constructed by the sequential addition of nucleotides and the formation of base pairs between the new strand and the parent (template) strand. The replication of the double helix results in two daughter molecules, each composed of one parent strand and one new strand. The enzymes that accomplish the replication of DNA are called DNA polymerases.
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Before beginning this tutorial, watch the DNA Replication animation. Pay particular attention to the structure of the DNA, how the double helix is unwound to form a replication bubble, and how nucleotides are added to the new strands in the replication bubble.
Part A - The chemical structure of DNA and its nucleotides

The DNA double helix is composed of two strands of DNA; each strand is a polymer of DNA nucleotides. Each nucleotide consists of a sugar, a phosphate group, and one of four nitrogenous bases. The structure and orientation of the two strands are important to understanding DNA replication. Drag the labels to their appropriate locations on the diagram below. Use only the pink labels for the pink targets, and the blue labels for the blue targets. Labels can be used once, more than once, or not at all.
Hint 1. Distinguishing the 3' and 5' ends of a DNA strand

A strand of DNA consists of a linear polymer of DNA nucleotides. The "backbone" of the DNA strand consists of a repeating pattern of sugar and phosphate groups in which the phosphate of one nucleotide is covalently attached to the sugar of the next nucleotide. This sugarphosphate-sugar arrangement is called a phosphodiester linkage. The two ends of a DNA strand are distinct from each other. The 5' end has a phosphate group, which is attached to the 5' carbon of a deoxyribose sugar. At the 3' end, there is a hydroxyl (-OH) group attached to the 3' carbon of a deoxyribose sugar.
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Hint 2. What are the components of a DNA strand?

A strand of DNA consists of a sequence of covalently linked DNA nucleotides. Drag the terms on the left to the appropriate blanks on the right to complete the sentences. ANSWER:
ANSWER:
Correct
The DNA double helix is constructed from two strands of DNA, each with a sugar-phosphate backbone and nitrogenous bases that form hydrogen bonds, holding the two strands together. Each DNA strand has two unique ends. The 3' end has a hydroxyl (-OH) group on the deoxyribose sugar, whereas the 5' end has a phosphate group. In the double helix, the two strands are antiparallel, that is, they run in opposite directions such that the 3' end of one strand is adjacent to the 5' end of the other strand.
Part B - The role of DNA polymerase III

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In DNA replication in bacteria, the enzyme DNA polymerase III (abbreviated DNA pol III) adds nucleotides to a template strand of DNA. But DNA pol III cannot start a new strand from scratch. Instead, a primer must pair with the template strand, and DNA pol III then adds nucleotides to the primer, complementary to the template strand. Each of the four images below shows a strand of template DNA (dark blue) with an RNA primer (red) to which DNA pol III will add nucleotides. In which image will adenine (A) be the next nucleotide to be added to the primer?
Hint 1. Watch DNA polymerase III add nucleotides to a new DNA strand
In bacteria, a new strand of DNA is synthesized by the enzyme DNA pol III, using one of the two parental DNA strands as a template. Watch how DNA pol III adds new nucleotides to one end of the growing strand.
Hint 2. Which bases form pairs in DNA?

In a DNA double helix, the two complementary strands of DNA are held together by hydrogen bonds between pairs of nitrogenous bases on each strand. This pairing of bases between the two strands is the basis of many of DNAs unique properties. Drag the terms on the left to the appropriate blanks on the right to complete the sentences. ANSWER:
Hint 3. To which end of a primer does DNA polymerase add new nucleotides?
In bacteria, DNA polymerase III is the enzyme that adds new nucleotides to a primer or growing strand of DNA. Which of the following statements correctly describes the formation of the bond between a new nucleotide and the primer? ANSWER:
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The newly added nucleotide forms a bond with the hydroxyl (-OH) group on the 3' end of the primer. The newly added nucleotide forms a bond with the phosphate group on the 3' end of the primer. The newly added nucleotide forms a bond with the hydroxyl (-OH) group on the 5' end of the primer. The newly added nucleotide forms a bond with the phosphate group on the 5' end of the primer.
ANSWER:
Correct
In the example above, DNA pol III would add an adenine nucleotide to the 3' end of the primer, where the template strand has thymine as the next available base. You can tell which end is the 3' end by the presence of a hydroxyl (-OH) group. The structure of DNA polymerase III is such that it can only add new nucleotides to the 3' end of a primer or growing DNA strand (as shown here). This is because the phosphate group at the 5' end of the new strand and the 3' -OH group on the nucleoside triphosphate will not both fit in the active site of the polymerase.
Part C - The replication bubble and antiparallel elongation

DNA replication always begins at an origin of replication. In bacteria, there is a single origin of replication on the circular chromosome, as shown in the
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image here. Beginning at the origin of replication, the two parental strands (dark blue) separate, forming a replication bubble. At each end of the replication bubble is a replication fork where the parental strands are unwound and new daughter strands (light blue) are synthesized. Movement of the replication forks away from the origin expands the replication bubble until two identical chromosomes are ultimately produced.
In this activity, you will demonstrate your understanding of antiparallel elongation at the replication forks. Keep in mind that the two strands in a double helix are oriented in opposite directions, that is, they are antiparallel. Drag the arrows onto the diagram below to indicate the direction that DNA polymerase III moves along the parental (template) DNA strands at each of the two replication forks. Arrows can be used once, more than once, or not at all.
Hint 1. Watch the two DNA polymerases at a replication fork
This short clip shows two DNA polymerases synthesizing two new DNA strands at a replication fork. Note the direction that DNA pol III moves on each parental strand. In the animation, the lower strand is shown forming a loop after the replication fork. It may help you to visualize that loop extended straight out from the replication fork, like the upper strand. Does the polymerase on the lower strand move in the same direction or in the opposite direction as the polymerase on the upper strand?
Hint 2. What will be the directionality of the two new DNA strands?
This image shows a replication bubble in a bacterial chromosome. The region enclosed by the box includes the two parental DNA strands (dark blue) and the two newly synthesized strands (light blue). Each of the images below shows the same four segments of DNA. Which of the following correctly represents the directionality of the two new DNA strands (light blue) compared to the two parental strands?
ANSWER:
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ANSWER:
Correct
DNA polymerase III can only add nucleotides to the 3' end of a new DNA strand. Because the two parental DNA strands of a double helix are antiparallel (go from 3' to 5' in opposite directions), the direction that DNA pol III moves on each strand emerging from a single replication fork must also be opposite. For example, in the replication fork on the left, the new strand on top is being synthesized from 5' to 3', and therefore DNA pol III moves away from the replication fork. Similarly, the new strand on the bottom of that same replication fork is being synthesized from 5' to 3'. But because the bottom parental strand is running in the opposite direction of the top parental strand, DNA pol III moves toward the replication fork. In summary, at a single replication fork, one strand is synthesized away from the replication fork, and one strand is synthesized toward the replication fork. When you look at both replication forks, note that a single new strand is built in the same direction on both sides of the replication bubble.
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Part D - Unwinding the DNA

As DNA replication continues and the replication bubble expands, the parental double helix is unwound and separated into its two component strands. This unwinding and separating of the DNA requires three different types of proteins: helicase, topoisomerase, and single-strand binding proteins. Sort the phrases into the appropriate bins depending on which protein they describe.
Hint 1. Watch helicase unwind DNA
As the replication bubble expands, the two strands of parental DNA must be separated from each other, a process often referred to as unwinding the DNA. This is accomplished by an enzyme called helicase. Watch helicase (the green protein) unwind the DNA at the replication fork.
Hint 2. How does topoisomerase work?

Topoisomerase is an enzyme that relieves the strain (tighter twisting) caused by the unwinding of parental DNA by the helicase at the replication fork. Which of the following statements correctly describes how topoisomerase functions? ANSWER:
Topoisomerase breaks a covalent bond between a deoxyribose sugar and a nitrogenous base in one parental strand. Topoisomerase breaks a covalent bond in the backbone of one parental strand. Topoisomerase breaks covalent bonds in the backbones of both parental strands. Topoisomerase breaks hydrogen bonds between the two parental strands.
Hint 3. What is the function of single-strand binding proteins?

Which of the following statements correctly describes the role of single-strand binding proteins in DNA replication? ANSWER:
Single-strand binding proteins bind to the newly synthesized strand of DNA immediately after the DNA polymerase. Single-strand binding proteins bind to double-stranded DNA, causing the two strands to separate into single strands. Single-strand binding proteins bind to double-stranded DNA ahead of the replication fork, relieving the strain caused by helicase. Single-strand binding proteins bind to parental DNA immediately after the helicase, preventing the two single strands from joining and re-forming a double helix.
Hint 4. The role of hydrogen bonds in DNA structure

In a DNA double helix, the two strands of DNA are held together by hydrogen bonds between complementary base pairs. When two single complementary strands of DNA are near each other, hydrogen bonding between the bases usually causes the two strands to join and form a double helix.
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ANSWER:
Correct
At each replication fork, helicase moves along the parental DNA, separating the two strands by breaking the hydrogen bonds between the base pairs. (This makes the two parental DNA strands available to the DNA polymerases for replication.) As soon as the base pairs separate at the replication fork, single-strand binding proteins attach to the separated strands and prevent the parental strands from rejoining. As helicase separates the two parental strands, the parental DNA ahead of the replication fork becomes more tightly coiled. To relieve strain ahead of the replication fork, topoisomerase breaks a covalent bond in the sugar-phosphate backbone of one of the two parental strands. Breaking this bond allows the DNA to swivel around the corresponding bond in the other strand and relieves the strain caused by the unwinding of the DNA at the helicase.
DNA Replication (2 of 2): Synthesis of the Leading and Lagging Strands (BioFlix tutorial)
In the DNA double helix, the two DNA strands are antiparallel, with their sugar-phosphate backbones oriented in opposite directions. Copying of each parental strand proceeds in both directions from the origin of replication, producing leading and lagging strands that are ultimately joined to create a daughter strand. Because DNA polymerase III can only add new nucleotides to the 3' end of the sugar-phosphate backbone, synthesis of the leading and lagging strands is necessarily different. Before beginning this tutorial, watch these three segments of the DNA Replication animation. Pay particular attention to the differences in how the leading and lagging strands are synthesized.
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Part A - Comparing the leading and lagging strands

As the two parental (template) DNA strands separate at a replication fork, each of the strands is separately copied by a DNA polymerase III (orange), producing two new daughter strands (light blue), each complementary to its respective parental strand. Because the two parental strands are antiparallel, the two new strands (the leading and lagging strands) cannot be synthesized in the same way.
Drag each phrase to the appropriate bin depending on whether it describes the synthesis of the leading strand, the synthesis of the lagging strand, or the synthesis of both strands.
Hint 1. Watch the synthesis of the leading and lagging strands
Synthesis of the leading and lagging strands at a replication fork differs because the two parental DNA strands are oriented in opposite directions, that is, they are antiparallel. Watch this clip from the DNA Replication animation to see the differences in how the leading and lagging strands are made. Look at the parental DNA (dark blue) as it moves through the polymerase on the leading strand. Are nucleotides being added to (elongating) the new daughter strand on the end closer to the replication fork or the end farther away from the replication fork? Now look at the lagging strand. Which end of this daughter strand is elongating -- the one closer to the replication fork or the one farther away from the replication fork? In the animation, the lagging strand is shown forming a loop after the replication fork. It may help you to visually disconnect the polymerase on the lagging strand from the complex at the replication fork so that the lagging strand also extends out to the right of the screen.
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Hint 2. In which direction do the leading and lagging strands elongate?

At a replication fork, the two parental DNA strands separate, and each strand is copied by a DNA polymerase III, synthesizing a new, complementary strand. The diagram below shows a replication fork with the two parental DNA strands labeled at their 3' and 5' ends. The newly synthesized DNA strands are not shown, but the polymerase on each parental strand is shown (labeled 1 and 2).
Remembering that the new (daughter) DNA strands will run antiparallel to the parental strands, which of the following statements correctly describes the direction in which the two strands will elongate? ANSWER: Both strands elongate toward the replication fork. Polymerase 1 elongates its strand away from the replication fork, but polymerase 2 elongates its strand toward the replication fork. Both strands elongate away from the replication fork. Polymerase 1 elongates its strand toward the replication fork, but polymerase 2 elongates its strand away from the replication fork.
Hint 3. The role of RNA primers in DNA replication

DNA polymerase III cannot initiate the synthesis of a new daughter strand; it can only add nucleotides to the 3' end of an existing strand that is paired with a parental (template, dark blue) strand. The enzyme primase creates a short RNA primer (red) that is complementary to the parental strand. This primer serves as a starting point for DNA pol III, which adds nucleotides to the 3' end of the primer. Think about the number of primers needed for a strand that is synthesized continuously versus a strand that is made in many smaller fragments.
ANSWER:
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Correct
Because DNA polymerase III can only add nucleotides to the 3' end of a new DNA strand and because the two parental DNA strands are antiparallel, synthesis of the leading strand differs from synthesis of the lagging strand. The leading strand is made continuously from a single RNA primer located at the origin of replication. DNA pol III adds nucleotides to the 3' end of the leading strand so that it elongates toward the replication fork. In contrast, the lagging strand is made in segments, each with its own RNA primer. DNA pol III adds nucleotides to the 3' end of the lagging strand so that it elongates away from the replication fork. In the image below, you can see that on one side of the origin of replication, a new strand is synthesized as the leading strand, and on the other side of the origin of replication, that same new strand is synthesized as the lagging strand. The leading and lagging strands built on the same template strand will eventually be joined, forming a continuous daughter strand.
Part B - RNA primers on the leading and lagging strands

The diagram below shows a replication bubble with synthesis of the leading and lagging strands on both sides of the bubble. The parental DNA is shown in dark blue, the newly synthesized DNA is light blue, and the RNA primers associated with each strand are red. The origin of replication is indicated by the black dots on the parental strands.
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Rank the primers in the order they were produced. If two primers were produced at the same time, overlap them.
Hint 1. The role of RNA primers in DNA replication

DNA polymerase III cannot initiate the synthesis of a new daughter strand; it can only add nucleotides to an existing strand that is paired with a parental (template, dark blue) strand. The enzyme primase creates a short RNA primer (red) that is complementary to the parental strand. This primer serves as a starting point for DNA pol III, which adds nucleotides to the 3' end of the primer.
Hint 2. Synthesis of the first primer on the lagging strand

As a replication bubble forms at an origin of replication, the primers for the leading strands are produced first. In the image below, you can see that the first parts of the leading strands have already been synthesized by the time the first lagging strand primers are produced. The reason for this lag is that about 1500 nucleotides (the average length of a bacterial lagging strand segment) of parental DNA must be exposed at the replication fork before lagging strand synthesis can begin. This makes room for the first lagging strand segment between the first primer and the origin of replication. DNA polymerase III produces the first lagging strand segments (not shown) by adding nucleotides to the 3' ends of the lagging strand primers.
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Hint 3. Which primer on the lagging strand was produced last?

As the replication bubble expands, a new primer must be added to initiate each successive segment of the lagging strand. On either side of the replication bubble, the most recently added RNA primer on the lagging strand will be located ANSWER: closest to the origin of replication. closest to the replication fork.
ANSWER:
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Correct
As soon as the replication bubble opens and the replication machinery is assembled at the two replication forks, the two primers for the leading strands (primers a and h) are produced. The production of the first primers on the lagging strands (those closest to the origin of replication, b and g) is delayed slightly because the replication forks must open up further to expose the template DNA for the lagging strands. After completion of the first segments of the lagging strands, additional template DNA must be exposed before the second primers (c and f) can be produced. And after completion of the second segments, additional template DNA must be exposed before the third primers (d and e) can be produced. In summary, because of the way the replication bubble expands, the lagging strand primers near the origin of replication were produced before the primers near the replication forks.
Part C - Synthesis of the lagging strand

In contrast to the leading strand, the lagging strand is synthesized as a series of segments called Okazaki fragments. The diagram below illustrates a lagging strand with the replication fork off-screen to the right. Fragment A is the most recently synthesized Okazaki fragment. Fragment B will be synthesized next in the space between primers A and B.
Drag the labels to their appropriate locations in the flowchart below, indicating the sequence of events in the production of fragment B. (Note that pol I stands for DNA polymerase I, and pol III stands for DNA polymerase III.)
Hint 1. Watch synthesis of the lagging strand
The fact that the lagging strand is produced as a sequence of fragments, each with its own RNA primer, means that a lot of processing must be done in order to produce a continuous new DNA strand. Watch for the unique roles of DNA polymerase I in replacing the RNA primers and DNA ligase in joining the DNA fragments.
Hint 2. How does DNA polymerase I function in lagging strand synthesis?

In bacteria, the three primary enzymes involved in lagging strand synthesis are DNA polymerase III, DNA polymerase I, and DNA ligase. Select the two phrases that correctly describe the functions of DNA polymerase I. ANSWER:
binds to the 3' end of an RNA primer replaces the RNA nucleotides of primers with DNA nucleotides leaves a gap in the sugar-phosphate backbone after replacing the last RNA nucleotide of a primer joins the sugar-phosphate backbone between a new DNA fragment and the previous fragment
ANSWER:
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Correct
Synthesis of the lagging strand is accomplished through the repetition of the following steps. Step 1: A new fragment begins with DNA polymerase III binding to the 3' end of the most recently produced RNA primer, primer B in this case, which is closest to the replication fork. DNA pol III then adds DNA nucleotides in the 5' to 3' direction until it encounters the previous RNA primer, primer A. Step 2: DNA pol III falls off and is replaced by DNA pol I. Starting at the 5' end of primer A, DNA pol I removes each RNA nucleotide and replaces it with the corresponding DNA nucleotide. (DNA pol I adds the nucleotides to the 3' end of fragment B.) When it encounters the 5' end of fragment A, DNA pol I falls off, leaving a gap in the sugar-phosphate backbone between fragments A and B. Step 3: DNA ligase closes the gap between fragments A and B. These steps will be repeated as the replication fork opens up. Try to visualize primer C being produced to the right (closest to the replication fork). Fragment C would be synthesized and joined to fragment B following the steps described here.
The Genetic Code

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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 proteincoding 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?
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 Codon sequence 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:
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Hint 4. Can you decode GCA?

Which amino acid does the codon 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?
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.
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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) Complementary DNA sequence mRNA sequence Codon sequence Amino acid sequence (three-letter abbreviation) 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?
ANSWER:
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: Overview of Protein Synthesis
Part A
Click on the diagram to start the animation. 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?
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ANSWER: RNA processing gene expression polypeptide formation transcription translation
Correct
Transcription is the process by which a DNA template is used for the manufacture of several different types of RNA.
Part B
Click on the diagram to start the animation. What name is given to the process in which the information encoded in a strand of mRNA is used to construct a protein?
ANSWER: RNA processing gene expression polypeptide formation transcription translation
Correct
Translation is the process by which information encoded in RNA is used to manufacture a polypeptide.
Part C
Click on the diagram to start the animation. What name is given to the process in which pre-mRNA is edited into mRNA?
ANSWER:
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RNA processing gene expression polypeptide formation transcription translation
Correct
RNA processing edits the RNA transcript that has been assembled along a DNA template.
Part D
Polypeptides are assembled from _____. ANSWER: hexoses glycerol nucleotides proteins amino acids
Correct
Proteins are composed of amino acid monomers.
Part E
RNA processing converts the RNA transcript into _____. ANSWER: a protein DNA a eukaryotic cell mRNA a polypeptide
Correct
The editing of the RNA transcript produces mRNA.
Activity: RNA Synthesis
Click here to view this animation.
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Then answer the questions.
Part A
What is the process called that converts the genetic information stored in DNA to an RNA copy?
Hint 1.
Most of these terms describe part of the gene expression process. One describes the process of making two identical copies of DNA from one parental DNA molecule. ANSWER: Transcription Replication Translation Translocation
Correct
DNA is transcribed to give an RNA copy.
Part B
DNA does not store the information to synthesize which of the following?
Hint 1.
DNA contains the code to make specific types of products, including copies of itself. ANSWER: Organelles DNA Proteins Messenger RNA
Correct
Synthesis of organelles is not directly coded in the DNA.
Part C
Transcription begins at a promoter. What is a promoter?
Hint 1.
A promoter is an essential part of a gene. ANSWER: A site found on the RNA polymerase A site in DNA that recruits the RNA Polymerase A site where many different proteins will bind A nontranscribed sequence on the DNA Part of the RNA molecule itself
Correct
This is the site where the RNA polymerase must bind to initiate transcription.
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Part D
Which of the following statements best describes the promoter of a protein-coding gene?
Hint 1.
Transcription of a gene is initiated by its promoter. ANSWER: The promoter is a nontranscribed region of a gene. The promoter is a site found on RNA polymerase. The promoter is part of the RNA molecule itself. The promoter is a site at which only RNA polymerase will bind.
Correct
The promoter is the regulatory region of a protein-coding gene at which RNA polymerase must bind to initiate transcriptionit is not transcribed into the RNA.
Part E
What determines which base is to be added to an RNA strand during transcription?
Hint 1.
Consider the purpose of the template. ANSWER: The order of the chemical groups in the backbone of the RNA molecule The previous base Base pairing between the DNA template strand and the RNA nucleotides Base pairing between the two DNA strands
Correct
Transcription involves the formation of an RNA strand that is complementary to the DNA template strand.
Part F
Which of the following terms best describes the relationship between the newly synthesized RNA molecule and the DNA template strand?
Hint 1.
The relationship between the RNA strand and the DNA template strand is similar to that of the two strands of a DNA double helix. ANSWER: Complementary Identical Permanently base-paired Covalently bound
Correct
Because the template strand determines the nucleotides to be added to the RNA strand, using the same complementarity rules of the DNA, they will be complementary to each other.
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Part G
What happens to RNA polymerase II after it has completed transcription of a gene?
Hint 1.
In eukaryotes, RNA polymerase II can transcribe any protein-coding gene, depending on the presence of regulatory proteins. ANSWER: It joins with another RNA polymerase to carry out transcription. It is free to bind to another promoter and begin transcription. It begins transcribing the next gene on the chromosome. It is degraded.
Correct
The enzyme is free to transcribe other genes in the cell.
Activity: Transcription
Part A
In the diagram below, the gray unit represents _____.
ANSWER: RNA DNA transcription factors RNA polymerase the promoter
Correct
RNA polymerase untwists a portion of the DNA double helix.
Part B
In the diagram below, the green unit represents _____.
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ANSWER: RNA DNA transcription factors RNA polymerase the promoter
Correct
The promoter is the region of DNA at which the process of transcription begins.
Part C
In the diagram below, the two blue strands represent _____.
Hint 1.
RNA is not a double helix. ANSWER: RNA DNA transcription factors RNA polymerase the promoter
Correct
DNA is a double helix.
Part D
Which of these correctly illustrates the pairing of DNA and RNA nucleotides? ANSWER:
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GTTACG CAATCG GTTACG CAAUGC GTTACG GTTACG GTTACG ACCGTA GTTACG UAACAU
Correct
In RNA, uracil takes the place of thymine.
Part E
The direction of synthesis of an RNA transcript is _____. ANSWER: 1' > 5' 5' > 3' 1' > 3' 3' > 5' 2' > 4'
Correct
Nucleotides are added to the 3' end of RNA.
Chapter 17 Question 8
Part A
Which of the following provides some evidence that RNA probably evolved before DNA? ANSWER: RNA polymerase makes a single-stranded molecule. RNA polymerase uses DNA as a template. RNA polymerase does not require localized unwinding of the DNA. DNA polymerase has proofreading function. DNA polymerase uses primer, usually made of RNA.
Correct
Activity: RNA Processing
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Part A
During RNA processing a(n) _____ is added to the 5' end of the RNA. ANSWER: 3' untranslated region a long string of adenine nucleotides 5' untranslated region coding segment modified guanine nucleotide
Correct
The 5' cap consists of a modified guanine nucleotide.
Part B
During RNA processing a(n) _____ is added to the 3' end of the RNA. ANSWER: 3' untranslated region a long string of adenine nucleotides 5' untranslated region coding segment modified guanine nucleotide
Correct
A poly-A tail is added to the 3' end of the RNA.
Part C
Spliceosomes are composed of _____. ANSWER: snRNPs and other proteins polymerases and ligases introns and exons the RNA transcript and protein snRNPs and snurps
Correct
These are the component of spliceosomes.
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Part D
The RNA segments joined to one another by spliceosomes are _____. ANSWER: caps exons snRNPs tails introns
Correct
Exons are expressed regions.
Part E
Translation occurs in the _____. ANSWER: cytoplasm lysosome nucleus mitochondrion nucleoplasm
Correct
Ribosomes, the sites of translation, are found in the cytoplasm.
Part A
Which of the following is the first event to take place in translation in eukaryotes? ANSWER: binding of the larger ribosomal subunit to smaller ribosomal subunits covalent bonding between the first two amino acids base pairing of activated methionine-tRNA to AUG of the messenger RNA the small subunit of the ribosome recognizes and attaches to the 5' cap of mRNA elongation of the polypeptide
Correct
Part A
The genetic code is essentially the same for all organisms. From this, one can logically assume which of the following? ANSWER:
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All organisms have experienced convergent evolution. A gene from an organism can theoretically be expressed by any other organism. DNA was the first genetic material. The same codons in different organisms translate into the different amino acids. Different organisms have different numbers of different types of amino acids.
Correct
Part A
The "universal" genetic code is now known to have exceptions. Evidence for this can be found if which of the following is true? ANSWER: If a single mRNA molecule is found to translate to more than one polypeptide when there are two or more AUG sites. If several codons are found to translate to the same amino acid, such as serine. If one stop codon, such as UGA, is found to have a different effect on translation than another stop codon, such as UAA. If UGA, usually a stop codon, is found to code for an amino acid such as tryptophan (usually coded for by UGG only). If prokaryotic organisms are able to translate a eukaryotic mRNA and produce the same polypeptide.
Correct
Part A
The following question refers to this table of codons.
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A peptide has the sequence NH2-phe-pro-lys-gly-phe-pro-COOH. Which of the following sequences in the coding strand of the DNA could code for this peptide? ANSWER: 5' ACT-TAC-CAT-AAA-CAT-TAC-UGA 5' GGG-AAA-TTT-AAA-CCC-ACT-GGG 3' AUG-AAA-GGG-TTT-CCC-AAA-GGG 5' TTT-CCC-AAA-GGG-TTT-CCC 3' UUU-CCC-AAA-GGG-UUU-CCC
Correct
Chapter 17 Pre-Test Question 4

Part A
What is the function of RNA polymerase?
Hint 1.
Compare RNA polymerase to DNA polymerase. ANSWER: It relies on other enzymes to unwind the double helix. It proceeds slowly along the DNA strand, requiring about a minute to add two nucleotides to the growing mRNA molecule. It unwinds the double helix and adds nucleotides to a growing strand of RNA. It adds nucleotides to the 5' end of the growing mRNA molecule. All of the above.
Correct
RNA polymerase has several functions in transcription, including unwinding the DNA double helix and adding RNA nucleotides.
Part A
Which of the following is a function of a poly-A signal sequence? ANSWER: It is a sequence that codes for the hydrolysis of the RNA polymerase. It codes for a sequence in eukaryotic transcripts that signals enzymatic cleavage ~1035 nucleotides away. It adds the poly-A tail to the 3' end of the mRNA. It allows the 3' end of the mRNA to attach to the ribosome. It adds a 7-methylguanosine cap to the 3' end of the mRNA.
Correct
Score Summary: Your score on this assignment is 85.5%. You received 12.83 out of a possible total of 15 points.
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The Molecular Basis of Inheritance

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4/24/13

The Molecular Basis of Inheritance & From Gene to Protein

Biol 1002 - Spring 2013

Activity: DNA and RNA Structure

Click here to complete this activity. Then answer the questions.

The Molecular Basis of Inheritance & From Gene to Protein

The Molecular Basis of Inheritance & From Gene to Protein

The Molecular Basis of Inheritance & From Gene to Protein

ANSWER: B, C, and D A and B B and C C, D, and E A, B, and C

The Molecular Basis of Inheritance & From Gene to Protein

The Molecular Basis of Inheritance & From Gene to Protein

Part A - The chemical structure of DNA and its nucleotides

Hint 1. Distinguishing the 3' and 5' ends of a DNA strand

The Molecular Basis of Inheritance & From Gene to Protein

Hint 2. What are the components of a DNA strand?

Part B - The role of DNA polymerase III

The Molecular Basis of Inheritance & From Gene to Protein

Hint 2. Which bases form pairs in DNA?

The Molecular Basis of Inheritance & From Gene to Protein

Part C - The replication bubble and antiparallel elongation

The Molecular Basis of Inheritance & From Gene to Protein

Hint 1. Watch the two DNA polymerases at a replication fork

The Molecular Basis of Inheritance & From Gene to Protein

The Molecular Basis of Inheritance & From Gene to Protein

Part D - Unwinding the DNA

Hint 1. Watch helicase unwind DNA

Hint 2. How does topoisomerase work?

Hint 3. What is the function of single-strand binding proteins?

Hint 4. The role of hydrogen bonds in DNA structure

The Molecular Basis of Inheritance & From Gene to Protein

The Molecular Basis of Inheritance & From Gene to Protein

Part A - Comparing the leading and lagging strands

Hint 1. Watch the synthesis of the leading and lagging strands

The Molecular Basis of Inheritance & From Gene to Protein

Hint 2. In which direction do the leading and lagging strands elongate?

Hint 3. The role of RNA primers in DNA replication

The Molecular Basis of Inheritance & From Gene to Protein

Part B - RNA primers on the leading and lagging strands

The Molecular Basis of Inheritance & From Gene to Protein

Hint 1. The role of RNA primers in DNA replication

Hint 2. Synthesis of the first primer on the lagging strand

The Molecular Basis of Inheritance & From Gene to Protein

Hint 3. Which primer on the lagging strand was produced last?

The Molecular Basis of Inheritance & From Gene to Protein

Part C - Synthesis of the lagging strand

Hint 1. Watch synthesis of the lagging strand

Hint 2. How does DNA polymerase I function in lagging strand synthesis?

The Molecular Basis of Inheritance & From Gene to Protein

The Genetic Code

The Molecular Basis of Inheritance & From Gene to Protein

Part A - Understanding the genetic code

Hint 1. How to interpret the table of codons

Hint 2. What is the start codon?

Hint 3. What are the stop codons?

The Molecular Basis of Inheritance & From Gene to Protein

Part B - Translation of mRNA

Hint 1. How to approach the problem

Hint 2. An example problem

The Molecular Basis of Inheritance & From Gene to Protein

Hint 4. Can you decode GCA?

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

Hint 1. How to approach the problem

The Molecular Basis of Inheritance & From Gene to Protein

Hint 2. An example problem