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Questions and Answers
Which nucleotide bond is formed to position N1 in pyrimidines?
Which nucleotide bond is formed to position N1 in pyrimidines?
What is the angle associated with anti conformation around the N-glycosidic bond?
What is the angle associated with anti conformation around the N-glycosidic bond?
Which of the following codes represents a deoxyribonucleotide?
Which of the following codes represents a deoxyribonucleotide?
What is a common minor nucleoside in eukaryotic DNA?
What is a common minor nucleoside in eukaryotic DNA?
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What happens to adenosine to create inosine in tRNA?
What happens to adenosine to create inosine in tRNA?
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Which function is not associated with nucleotides?
Which function is not associated with nucleotides?
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Which statement about the DNA backbone is true?
Which statement about the DNA backbone is true?
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N6-Methyladenosine is primarily found in which type of organism?
N6-Methyladenosine is primarily found in which type of organism?
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What is the primary function of pseudouridine in RNA?
What is the primary function of pseudouridine in RNA?
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Which nucleobase is exclusive to RNA?
Which nucleobase is exclusive to RNA?
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What feature distinguishes nucleotides from nucleosides?
What feature distinguishes nucleotides from nucleosides?
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At neutral pH, which of the following nucleobases is considered a neutral molecule?
At neutral pH, which of the following nucleobases is considered a neutral molecule?
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Which type of bond connects the pentose sugar to the nucleobase in a nucleotide?
Which type of bond connects the pentose sugar to the nucleobase in a nucleotide?
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What kind of structural isomerism is exhibited by nucleobases?
What kind of structural isomerism is exhibited by nucleobases?
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Which component of nucleotides is responsible for energy storage?
Which component of nucleotides is responsible for energy storage?
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Which of the following statements about DNA structure is incorrect?
Which of the following statements about DNA structure is incorrect?
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What is primarily responsible for the degradation of mRNA in cells?
What is primarily responsible for the degradation of mRNA in cells?
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What is the significance of the 5’ and 3’ ends in RNA?
What is the significance of the 5’ and 3’ ends in RNA?
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Which enzyme is known to cleave double-stranded RNA into oligonucleotides?
Which enzyme is known to cleave double-stranded RNA into oligonucleotides?
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What role does S-RNase play in plants?
What role does S-RNase play in plants?
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Which pairs correctly represent the Watson-Crick base pairs in DNA?
Which pairs correctly represent the Watson-Crick base pairs in DNA?
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What is one of the novel features of DNA structure discovered by Watson and Crick?
What is one of the novel features of DNA structure discovered by Watson and Crick?
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Why are RNase enzymes abundant in nature?
Why are RNase enzymes abundant in nature?
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What characteristic of RNA makes it less stable than DNA?
What characteristic of RNA makes it less stable than DNA?
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What did Franklin and Wilkins provide that was critical to Watson and Crick's discovery?
What did Franklin and Wilkins provide that was critical to Watson and Crick's discovery?
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How does RNA hydrolysis predominantly occur in nature?
How does RNA hydrolysis predominantly occur in nature?
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What is the outcome of DNA denaturation concerning covalent and hydrogen bonds?
What is the outcome of DNA denaturation concerning covalent and hydrogen bonds?
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Which enzyme is primarily responsible for catalyzing the synthesis of new DNA strands during replication?
Which enzyme is primarily responsible for catalyzing the synthesis of new DNA strands during replication?
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Which statement about the melting temperature (Tm) of DNA is accurate?
Which statement about the melting temperature (Tm) of DNA is accurate?
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What is the primary function of tRNA in the context of protein synthesis?
What is the primary function of tRNA in the context of protein synthesis?
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During the process of DNA replication, what is the first step that occurs?
During the process of DNA replication, what is the first step that occurs?
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Which of the following statements is true about messenger RNA (mRNA)?
Which of the following statements is true about messenger RNA (mRNA)?
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What defines a palindromic sequence in DNA?
What defines a palindromic sequence in DNA?
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What is a significant consequence of high-temperature DNA denaturation?
What is a significant consequence of high-temperature DNA denaturation?
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Which form of detection can be used to identify specific DNA molecules in a complex mixture?
Which form of detection can be used to identify specific DNA molecules in a complex mixture?
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What impact does ionic strength have on DNA denaturation?
What impact does ionic strength have on DNA denaturation?
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Study Notes
Nucleotides and Nucleic Acids
- Nucleotides have many biological functions, including energy for metabolism (ATP), enzyme cofactors (NAD+), and signal transduction (cAMP).
- Nucleic acids store genetic information (DNA), transmit genetic information (mRNA), process genetic information (ribozymes), and perform protein synthesis (tRNA and rRNA).
- Nucleotides are composed of a nitrogenous base, a pentose sugar, and a phosphate group.
- Nucleosides are composed of a nitrogenous base and a pentose sugar.
- Nucleobases are nitrogen-containing heteroaromatic molecules, mostly planar, and absorb UV light around 250-270 nm.
Pentose Sugars
- RNA contains a β-D-ribofuranose.
- DNA contains a β-2'-deoxy-D-ribofuranose.
- Different puckered conformations of the sugar ring are possible.
Nucleobases: Pyrimidines
- Cytosine is found in both DNA and RNA.
- Thymine is found only in DNA.
- Uracil is found only in RNA.
- All are good H-bond donors and acceptors.
- Cytosine pKa at N3 is 4.5.
- Thymine pKa at N3 is 9.5.
- Neutral molecules at pH 7.
Nucleobases: Purines
- Adenine and guanine are found in both RNA and DNA.
- They are also good H-bond donors and acceptors.
- Adenine pKa at N1 is 3.8.
- Guanine pKa at N7 is 2.4.
- Neutral molecules at pH 7.
Tautomerism
- Prototropic tautomers are structural isomers that differ in the location of protons.
- Keto-enol tautomerism is common in ketones.
- Lactam-lactim tautomerism occurs in some heterocycles.
- Both tautomers exist in solution, but the lactam forms are predominant at neutral pH.
UV Absorption
- Absorption of UV light at 250-270 nm is due to π → π* electronic transitions.
- Excited states of common nucleobases decay rapidly via radiationless transitions, providing effective photoprotection of genetic material.
- No fluorescence from nucleic acids.
Phosphate Groups
- Negatively charged at neutral pH.
- Typically attached to the 5' position.
- Nucleic acids are built using 5'-triphosphates.
- Nucleic acids contain one phosphate moiety per nucleotide.
N-Glycosidic Bond
- The pentose ring is attached to the nucleobase via an N-glycosidic bond.
- The bond is formed to position N1 in pyrimidines and to position N9 in purines.
- This bond is quite stable toward hydrolysis, especially in pyrimidines.
- Bond cleavage is catalyzed by acid.
Deamination
- Deamination is a very slow but significant modification to nucleotide residues in DNA.
- The net effect is 100 cytosine to uracil events/day in a typical mammalian cell.
- Methylated cytosine (5-methylcytosine, common in eukaryotes) is more susceptible to deamination
Depurination
- N-glycosidic bond hydrolysis is significant.
- This leads to the loss of ~10,000 purines per day in a typical mammalian cell.
DNA Denaturation (Melting)
- Covalent bonds remain intact during denaturation.
- Hydrogen bonds break, and the two strands separate.
- Base stacking is lost, and UV absorbance increases.
- Denaturation is often induced by high temperature or changes in pH.
Factors Affecting DNA Denaturation
- Midpoint of melting (Tm) depends on base composition (high CG content increases Tm).
- Tm depends on DNA length (longer DNA has a higher Tm).
- Tm depends on pH and ionic strength (high salt increases Tm).
Other Forms of DNA
- DNA exists in different forms, including A form, B form, and Z form. These differ in their helical sense, diameter, base pairs per helical turn, helix rise, and sugar pucker.
Messenger RNA (mRNA)
- Synthesized using a DNA template.
- Contains ribose instead of deoxyribose.
- Contains uracil instead of thymine.
- One mRNA may code for more than one protein.
Transfer RNA (tRNA)
- tRNA molecules have complex structures, actively studied to understand their function in matching amino acids to the mRNA code.
Nomenclature
- Deoxyribonucleotides and Ribonucleotides have specific, often abbreviated (one or three letter) names, associated with their structures, and should be learned.
Palindromic Sequences
- Palindromic sequences can form hairpins and cruciforms in DNA due to their complementary nature when reversed.
Molecular Mechanisms of Mutagenesis
- Various factors, both oxidative and chemical, can induce damage and mutations, which cells can sometimes repair but not always.
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Description
Test your knowledge on nucleotides, nucleic acids, and their biological functions. This quiz covers the structures of nucleotides, the role of nucleic acids in genetic information, and the differences between DNA and RNA. Discover how pentose sugars and nucleobases are involved in these essential biomolecules.
