DNA, RNA, and Proteins - AP Biology
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Which of these is a key characteristic of all enzymes?
Which of these is a key characteristic of all enzymes?
These are all definitive traits of an enzyme. Enzymes are proteins which are extremely helpful in speeding up certain reactions without being depleted by the reactions themselves (as such, they are catalysts for these reactions). Enzymes reduce the amount of energy needed for a reaction to occur, generally because they facilitate reactions by recognizing reactants and bringing them into contact with each other. This occurs when the reactants bind to certain parts of the enzyme (active sites), which causes the enzyme to change shape and bring the reactants into contact with each other (and then the reactants can bind to form the product).
These are all definitive traits of an enzyme. Enzymes are proteins which are extremely helpful in speeding up certain reactions without being depleted by the reactions themselves (as such, they are catalysts for these reactions). Enzymes reduce the amount of energy needed for a reaction to occur, generally because they facilitate reactions by recognizing reactants and bringing them into contact with each other. This occurs when the reactants bind to certain parts of the enzyme (active sites), which causes the enzyme to change shape and bring the reactants into contact with each other (and then the reactants can bind to form the product).
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Which of the following enzymes is directly associated with polypeptide formation, and has the function of binding amino acids to each other at the ribosome?
Which of the following enzymes is directly associated with polypeptide formation, and has the function of binding amino acids to each other at the ribosome?
Peptidyl transferase is the enzyme that works in conjunction with tRNA molecules to extend a growing polypeptide chain at the ribosome during translation. Ligase is not used at all in translation, nor is topoisomerase or ATP synthase. tRNA synthetase is used to bind the correct amino acids to corresponding tRNA molecules, but it is not used to extend the polypeptide at the ribosome.
Peptidyl transferase is the enzyme that works in conjunction with tRNA molecules to extend a growing polypeptide chain at the ribosome during translation. Ligase is not used at all in translation, nor is topoisomerase or ATP synthase. tRNA synthetase is used to bind the correct amino acids to corresponding tRNA molecules, but it is not used to extend the polypeptide at the ribosome.
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Which of the following enzymes performs the critical function of removing RNA primers from DNA in DNA replication, and replacing the RNA with DNA?
Which of the following enzymes performs the critical function of removing RNA primers from DNA in DNA replication, and replacing the RNA with DNA?
While all the answer choices are important in DNA replication, only DNA Polymerase I performs this particular function. Ligase helps bind the newly replaced DNA nucleotides to the rest of the DNA strand. DNA polymerase III is the main synthesizing enzyme of DNA replication, and creates the majority of the DNA strand. DNA polymerase II is less well known than I and III, but it is believed to perform as a repair enzyme which removes incorrectly paired segments of DNA (which can then be filled back in by DNA polymerase I).
While all the answer choices are important in DNA replication, only DNA Polymerase I performs this particular function. Ligase helps bind the newly replaced DNA nucleotides to the rest of the DNA strand. DNA polymerase III is the main synthesizing enzyme of DNA replication, and creates the majority of the DNA strand. DNA polymerase II is less well known than I and III, but it is believed to perform as a repair enzyme which removes incorrectly paired segments of DNA (which can then be filled back in by DNA polymerase I).
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Which of the following statements about enzymes is true?
Which of the following statements about enzymes is true?
Enzymes have an "optimal temperature," or best temperature that they work at. If that temperature is below or above its optimal temperature, the enzyme will decrease in activity; if the temperature change is great enough, the enzyme could even denature (no longer work).
Enzymes have an "optimal temperature," or best temperature that they work at. If that temperature is below or above its optimal temperature, the enzyme will decrease in activity; if the temperature change is great enough, the enzyme could even denature (no longer work).
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Why are enzymes necessary for most cellular reactions?
Why are enzymes necessary for most cellular reactions?
An enzymes function is to speed up chemical reactions by lowering the activation energy. If our bodies did not have enzymes, the reactions would take place, but too slowly for our cells to adequately function.
An enzymes function is to speed up chemical reactions by lowering the activation energy. If our bodies did not have enzymes, the reactions would take place, but too slowly for our cells to adequately function.
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Cellular respiration involves a series of chemical reactions. Which of the following is a primary way that enzymes affect these reactions?
Cellular respiration involves a series of chemical reactions. Which of the following is a primary way that enzymes affect these reactions?
The questions is asking how enzymes affect reactions. The function of an enzyme is to speed up chemical reactions, which will increase the overall rate of the reaction, thus "increasing the rate of the reaction" is the correct answer.
The questions is asking how enzymes affect reactions. The function of an enzyme is to speed up chemical reactions, which will increase the overall rate of the reaction, thus "increasing the rate of the reaction" is the correct answer.
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Which of the following most accurately describes the primary structure of a protein?
Which of the following most accurately describes the primary structure of a protein?
The primary structure of a protein is simply the linear amino acid sequence from which the protein is made. "Secondary structure" refers to the folding and coiling of this single strand as it interacts with itself, forming hydrogen bonds between amino acids of that strand. Alpha helices and beta-pleated sheets are two different types of secondary structures that can be formed by hydrogen-bonding between amino acids of a protein sequence that has folded over onto itself. "Tertiary structure" refers to the final three-dimensional structure of a single protein subunit. "Quaternary structure" refers to the non-covalent interactions between multiple protein subunits which come together to form a larger protein.
The primary structure of a protein is simply the linear amino acid sequence from which the protein is made. "Secondary structure" refers to the folding and coiling of this single strand as it interacts with itself, forming hydrogen bonds between amino acids of that strand. Alpha helices and beta-pleated sheets are two different types of secondary structures that can be formed by hydrogen-bonding between amino acids of a protein sequence that has folded over onto itself. "Tertiary structure" refers to the final three-dimensional structure of a single protein subunit. "Quaternary structure" refers to the non-covalent interactions between multiple protein subunits which come together to form a larger protein.
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In RNA, three nucleotide bases together determine the amino acid that is added to the growing polypeptide chain during translation. This three base grouping is known as a(n) .
In RNA, three nucleotide bases together determine the amino acid that is added to the growing polypeptide chain during translation. This three base grouping is known as a(n) .
The three base grouping in RNA that determines the amino acid created in translation is known as a codon. Gene refers to the region on DNA that codes for a given trait. Operators and promoters are also located on DNA, and act as regulatory elements.
The three base grouping in RNA that determines the amino acid created in translation is known as a codon. Gene refers to the region on DNA that codes for a given trait. Operators and promoters are also located on DNA, and act as regulatory elements.
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In terms of histone modification, what will result in a greater rate of gene expression?
In terms of histone modification, what will result in a greater rate of gene expression?
Histone acetylation is the process of adding acetyl groups to positively charged lysine groups of histones. This process loosens the histone which allows for an easier initiation of transcription, which will lead to greater gene expression. DNA methylation does the opposite by adding methyl groups to DNA and lowering the rate of transcription. Alternative RNA splicing deals with RNA having certain introns and exons spliced out in a manner that produces different strands of mRNA from the same template strand of RNA. Addition of 5’ Terminal Cap and the addition of 3’ Poly A Tail relate to gene expression in that they both have to do with creating mature mRNA that is ready for translation into protein.
Histone acetylation is the process of adding acetyl groups to positively charged lysine groups of histones. This process loosens the histone which allows for an easier initiation of transcription, which will lead to greater gene expression. DNA methylation does the opposite by adding methyl groups to DNA and lowering the rate of transcription. Alternative RNA splicing deals with RNA having certain introns and exons spliced out in a manner that produces different strands of mRNA from the same template strand of RNA. Addition of 5’ Terminal Cap and the addition of 3’ Poly A Tail relate to gene expression in that they both have to do with creating mature mRNA that is ready for translation into protein.
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You find a specialized type of RNA in the nucleus but nowhere else in the cell, including the cytoplasm. What type of RNA is it?
You find a specialized type of RNA in the nucleus but nowhere else in the cell, including the cytoplasm. What type of RNA is it?
mRNA will be found in both the nucleus and in the cytoplasm because it is transcribed from DNA in the nucleus and then exported to the cytoplasm to go through translation. tRNA will be found in the cytoplasm because it is an integral part of translation in that it delivers amino acids to the ribosome. rRNA will also be found in the cytoplasm because it couples with ribosomal proteins to make up the ribosomes found in the cytoplasm. scRNA is also known as small cytoplasmic RNA and has a function that is still not very well known, but they are mostly only found in the cytoplasm. snRNA, or small nuclear RNA, are only found in the nucleus and are an integral part of splicing introns of RNA so it can go onto becoming mRNA.
mRNA will be found in both the nucleus and in the cytoplasm because it is transcribed from DNA in the nucleus and then exported to the cytoplasm to go through translation. tRNA will be found in the cytoplasm because it is an integral part of translation in that it delivers amino acids to the ribosome. rRNA will also be found in the cytoplasm because it couples with ribosomal proteins to make up the ribosomes found in the cytoplasm. scRNA is also known as small cytoplasmic RNA and has a function that is still not very well known, but they are mostly only found in the cytoplasm. snRNA, or small nuclear RNA, are only found in the nucleus and are an integral part of splicing introns of RNA so it can go onto becoming mRNA.
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Suppose a mutation in an organism's genome produces a malformed version of tRNA synthetase. This malformed version of the enzyme is completely non-functional. What would be the direct effect on the cell producing non-functional tRNA synthetase?
Suppose a mutation in an organism's genome produces a malformed version of tRNA synthetase. This malformed version of the enzyme is completely non-functional. What would be the direct effect on the cell producing non-functional tRNA synthetase?
tRNA synthetase plays a vital role in translation, but not transcription. tRNA synthetase is the enzyme that binds specific amino acids to corresponding tRNA molecules, and then the tRNA molecules transport the amino acids to the ribosome to create a polypeptide. tRNA molecules are not consumed in this process, and tRNA reserves will not be depleted if tRNA synthetase were non-functional.
tRNA synthetase plays a vital role in translation, but not transcription. tRNA synthetase is the enzyme that binds specific amino acids to corresponding tRNA molecules, and then the tRNA molecules transport the amino acids to the ribosome to create a polypeptide. tRNA molecules are not consumed in this process, and tRNA reserves will not be depleted if tRNA synthetase were non-functional.
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Eukaryotic cells are able to modify the primary mRNA transcript in a number of different ways. Which of the following answer choices is an advantage of post-transcriptional modification?
Eukaryotic cells are able to modify the primary mRNA transcript in a number of different ways. Which of the following answer choices is an advantage of post-transcriptional modification?
Post-transcriptional modification is very beneficial to eukaryotic cells, especially because spliceosomes allow for one primary mRNA transcript to code for multiple different proteins. During this modification, introns are removed from the mRNA transcript, and the exons (remaining segments of mRNA) are shuffled around into the order that creates the protein the cell needs at the moment. While the poly-A tail and methyl cap are also very useful, the poly-A tail is on the 3' end, and the methyl cap is on the 5' end.
Post-transcriptional modification is very beneficial to eukaryotic cells, especially because spliceosomes allow for one primary mRNA transcript to code for multiple different proteins. During this modification, introns are removed from the mRNA transcript, and the exons (remaining segments of mRNA) are shuffled around into the order that creates the protein the cell needs at the moment. While the poly-A tail and methyl cap are also very useful, the poly-A tail is on the 3' end, and the methyl cap is on the 5' end.
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Which of the following mutations is a single nucleotide base pair change that results in a codon for a different amino acid?
Which of the following mutations is a single nucleotide base pair change that results in a codon for a different amino acid?
A missense mutation is a type of point mutation (single base pair change) that alters the codon to the creation of a different protein.
A silent mutation is also a point mutation with a change in one base pair, but with the resulting strand still coding for the same protein (hence the term "silent").
A nonsense mutation changes a codon from coding for an amino acid to coding for termination of the protein. The protein may or may not still be functional depending on how much of it is terminated when the mutation occurs.
An insertion is a mutation in which one or more base pairs is added to the coding sequence. Unless the insertion is in a multiple of three (preserving the frame because a codon is made up of three base pairs), it results in a "frame shift" that alters the reading frame of the codons to the right, causing it to code for a different set of proteins.
A deletion is another type of frame shift mutation, in which a base pair (or more) is deleted from the coding sequence, altering the reading frame to code for different proteins in many cases. As with insertions, if the deletion is in a multiple of 3, the frame is preserved as each codon consists of 3 base pairs.
A missense mutation is a type of point mutation (single base pair change) that alters the codon to the creation of a different protein.
A silent mutation is also a point mutation with a change in one base pair, but with the resulting strand still coding for the same protein (hence the term "silent").
A nonsense mutation changes a codon from coding for an amino acid to coding for termination of the protein. The protein may or may not still be functional depending on how much of it is terminated when the mutation occurs.
An insertion is a mutation in which one or more base pairs is added to the coding sequence. Unless the insertion is in a multiple of three (preserving the frame because a codon is made up of three base pairs), it results in a "frame shift" that alters the reading frame of the codons to the right, causing it to code for a different set of proteins.
A deletion is another type of frame shift mutation, in which a base pair (or more) is deleted from the coding sequence, altering the reading frame to code for different proteins in many cases. As with insertions, if the deletion is in a multiple of 3, the frame is preserved as each codon consists of 3 base pairs.
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Many enzymes have sites on them where the binding of specific molecules will increase or decrease the activity of the enzyme. What is the name of this type of site?
Many enzymes have sites on them where the binding of specific molecules will increase or decrease the activity of the enzyme. What is the name of this type of site?
The correct answer is "allosteric site." A molecule that binds to an enzyme's allosteric site induces a conformational change in the enzyme, decreasing or increasing the affinity of the enzyme’s binding sites to the substrate. The binding site binds and orients the substrate. The catalytic site lowers the activation energy of the reaction. The binding site and the catalytic site together make up the active site. Cofactors are parts of certain enzymes and are required for those enzymes to function.
The correct answer is "allosteric site." A molecule that binds to an enzyme's allosteric site induces a conformational change in the enzyme, decreasing or increasing the affinity of the enzyme’s binding sites to the substrate. The binding site binds and orients the substrate. The catalytic site lowers the activation energy of the reaction. The binding site and the catalytic site together make up the active site. Cofactors are parts of certain enzymes and are required for those enzymes to function.
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Given the partial sequence of a single DNA strand shown below, what will be the sequence of the complementary strand that is produced during DNA replication?
3' - ATCGAAGTGC - 5'
Given the partial sequence of a single DNA strand shown below, what will be the sequence of the complementary strand that is produced during DNA replication?
3' - ATCGAAGTGC - 5'
The question specifies that this is DNA replication. U (uracil) is found only in RNA and T (thymine) is found only in DNA. In DNA, A (adenine) pairs with T (thymine) and G (guanine) pairs with C (cytosine) so the complementary strand will have "A" where the original has "T," "G" where the original has "C," "C" where the original has "G" and "T" where the original has "A."
DNA strands run antiparallel, so the 3' end on the new strand will go opposite the 5' end on the original and vice versa. In this case, that means the complementary strand will run from 5' to 3' to read 5' - TAGCTTCACG - 3'. This sequence is shown in bold below:
5' - TAGCTTCACG - 3'
3' - ATCGAAGTGC - 5'
The question specifies that this is DNA replication. U (uracil) is found only in RNA and T (thymine) is found only in DNA. In DNA, A (adenine) pairs with T (thymine) and G (guanine) pairs with C (cytosine) so the complementary strand will have "A" where the original has "T," "G" where the original has "C," "C" where the original has "G" and "T" where the original has "A."
DNA strands run antiparallel, so the 3' end on the new strand will go opposite the 5' end on the original and vice versa. In this case, that means the complementary strand will run from 5' to 3' to read 5' - TAGCTTCACG - 3'. This sequence is shown in bold below:
5' - TAGCTTCACG - 3'
3' - ATCGAAGTGC - 5'
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If a structural gene in an organism's genome is comprised of 33% adenine nucleotides, what percentage of the gene is comprised of cytosine nucleotides?
If a structural gene in an organism's genome is comprised of 33% adenine nucleotides, what percentage of the gene is comprised of cytosine nucleotides?
According to Chargaff's rule, DNA nucleotides pair in a 1:1 ratio. Therefore, if we know how much of the particular gene is made up of one nucleotide, we can extrapolate that known variable to find the other three unknown variables.
To do so, you must remember that adenine pairs with thymine, and cytosine pairs with guanine (A-T, C-G), and that since the ratio between each pair is 1:1 then a gene with 33% adenine must also have 33% thymine. Combine these numbers and subtract from 100: the number leftover is the % of total cytosine and guanine in the gene.
100% - 66% = 34%
Finally, since we know that 34% of the DNA is both C and G, and that the ratio between C-G is 1:1, C and G must both be 17%.
According to Chargaff's rule, DNA nucleotides pair in a 1:1 ratio. Therefore, if we know how much of the particular gene is made up of one nucleotide, we can extrapolate that known variable to find the other three unknown variables.
To do so, you must remember that adenine pairs with thymine, and cytosine pairs with guanine (A-T, C-G), and that since the ratio between each pair is 1:1 then a gene with 33% adenine must also have 33% thymine. Combine these numbers and subtract from 100: the number leftover is the % of total cytosine and guanine in the gene.
100% - 66% = 34%
Finally, since we know that 34% of the DNA is both C and G, and that the ratio between C-G is 1:1, C and G must both be 17%.
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If a structural gene in an organism's genome is comprised of 29% guanine nucleotides, what percentage of the gene is comprised of cytosine nucleotides?
If a structural gene in an organism's genome is comprised of 29% guanine nucleotides, what percentage of the gene is comprised of cytosine nucleotides?
This question is designed to catch a) students who are not reading the question carefully, and b) students unsure of which nucleotides pair with which.
The correct answer is 29%, because cytosine pairs with guanine in a 1:1 ratio. If you answered 21%, then you likely thought the question was more complex than it was.
This question is designed to catch a) students who are not reading the question carefully, and b) students unsure of which nucleotides pair with which.
The correct answer is 29%, because cytosine pairs with guanine in a 1:1 ratio. If you answered 21%, then you likely thought the question was more complex than it was.
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There is a certain type of chemical bonding between the paired nucleotides on each strand of DNA which helps maintain the double-helix structure of DNA by attracting each strand to the other. What type of bonding is responsible for this?
There is a certain type of chemical bonding between the paired nucleotides on each strand of DNA which helps maintain the double-helix structure of DNA by attracting each strand to the other. What type of bonding is responsible for this?
The correct answer is hydrogen bonding, and each nucleotide attracts its pairing mate because they have corresponding number of hydrogen bonds. Adenine is attracted to thymine to create two hydrogen bonds, and cytosine is attracted to guanine to form three hydrogen bonds. While phosphodiester bonds are very important in creating the strand of DNA, they are not the bond that keeps the two strands in the double helix structure.
The correct answer is hydrogen bonding, and each nucleotide attracts its pairing mate because they have corresponding number of hydrogen bonds. Adenine is attracted to thymine to create two hydrogen bonds, and cytosine is attracted to guanine to form three hydrogen bonds. While phosphodiester bonds are very important in creating the strand of DNA, they are not the bond that keeps the two strands in the double helix structure.
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With respect to DNA, the terms 3' and 5' (pronounced 3-prime and 5-prime, respectively) are used in order to refer to one strand or the other. What do these two terms signify?
With respect to DNA, the terms 3' and 5' (pronounced 3-prime and 5-prime, respectively) are used in order to refer to one strand or the other. What do these two terms signify?
When nucleotides bond together and form DNA strands, the first and last nucleotides in the strand have slightly different structures than the rest of the nucleotides between them. On one end of the strand, the nucleotide has an exposed hydroxyl group bound to the third carbon in the carbon ring: this end of the strand is thus called 3'. On the opposite end of the strand, the nucleotide has a phosphate group attached to the 5' carbon in the carbon ring, and is thus called the 5' end. These two groups are exposed because they are used in the bonding of nucleotides to one another to form the strand, but each strand ends with one nucleotide that only is bound on one side: thus, leaving either the hydroxyl or phosphate group exposed (depending on which end you are observing).
These terms are useful because they allow us to discuss the directionality of DNA-related events- if we didn't have terms for directionality the concept would be much more confusing. Example: "DNA polymerase synthesizes the new DNA strand in the 5'-3' direction." Without 3'/5' how would we determine which way the reaction occurs?
When nucleotides bond together and form DNA strands, the first and last nucleotides in the strand have slightly different structures than the rest of the nucleotides between them. On one end of the strand, the nucleotide has an exposed hydroxyl group bound to the third carbon in the carbon ring: this end of the strand is thus called 3'. On the opposite end of the strand, the nucleotide has a phosphate group attached to the 5' carbon in the carbon ring, and is thus called the 5' end. These two groups are exposed because they are used in the bonding of nucleotides to one another to form the strand, but each strand ends with one nucleotide that only is bound on one side: thus, leaving either the hydroxyl or phosphate group exposed (depending on which end you are observing).
These terms are useful because they allow us to discuss the directionality of DNA-related events- if we didn't have terms for directionality the concept would be much more confusing. Example: "DNA polymerase synthesizes the new DNA strand in the 5'-3' direction." Without 3'/5' how would we determine which way the reaction occurs?
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Which type of bond makes up the backbone of DNA strands by linking together adjacent nucleotides?
Which type of bond makes up the backbone of DNA strands by linking together adjacent nucleotides?
DNA and RNA nucleotides are linked together through phosphodiester bonds. A strong covalent bond (ester bond) forms between the 3' carbon atom of the sugar pentose of one nucleotide and a phosphate group, and a second ester bond forms between the phosphate group and the 5' carbon atom of the sugar pentose of another nucleotide. This alternation of sugar and phosphate groups forms a strong backbone and is also the reason why DNA is antiparallel and forms in the 5' to 3' direction.
DNA and RNA nucleotides are linked together through phosphodiester bonds. A strong covalent bond (ester bond) forms between the 3' carbon atom of the sugar pentose of one nucleotide and a phosphate group, and a second ester bond forms between the phosphate group and the 5' carbon atom of the sugar pentose of another nucleotide. This alternation of sugar and phosphate groups forms a strong backbone and is also the reason why DNA is antiparallel and forms in the 5' to 3' direction.
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