Nucleotides and Nucleic Acids Quiz
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Questions and Answers

Which nucleotide bond is formed to position N1 in pyrimidines?

  • Ionic bond
  • Hydrophobic bond
  • N-glycosidic bond (correct)
  • Phosphodiester bond

What is the angle associated with anti conformation around the N-glycosidic bond?

  • 270°
  • 90°
  • 180° (correct)

Which of the following codes represents a deoxyribonucleotide?

  • dA (correct)
  • A
  • AMP
  • dAMP (correct)

What is a common minor nucleoside in eukaryotic DNA?

<p>5-Methylcytosine (B)</p> Signup and view all the answers

What happens to adenosine to create inosine in tRNA?

<p>De-aminating (A)</p> Signup and view all the answers

Which function is not associated with nucleotides?

<p>Storage of genetic information (C)</p> Signup and view all the answers

Which statement about the DNA backbone is true?

<p>It is negatively charged. (B)</p> Signup and view all the answers

N6-Methyladenosine is primarily found in which type of organism?

<p>Bacteria (D)</p> Signup and view all the answers

What is the primary function of pseudouridine in RNA?

<p>Stabilizing the structure of tRNA (D)</p> Signup and view all the answers

Which nucleobase is exclusive to RNA?

<p>Uracil (B)</p> Signup and view all the answers

What feature distinguishes nucleotides from nucleosides?

<p>Presence of a phosphate group (C)</p> Signup and view all the answers

At neutral pH, which of the following nucleobases is considered a neutral molecule?

<p>Cytosine (A), Uracil (B), Adenine (C), Thymine (D)</p> Signup and view all the answers

Which type of bond connects the pentose sugar to the nucleobase in a nucleotide?

<p>N-glycosidic bond (C)</p> Signup and view all the answers

What kind of structural isomerism is exhibited by nucleobases?

<p>Tautomerism (C)</p> Signup and view all the answers

Which component of nucleotides is responsible for energy storage?

<p>Phosphate group (C)</p> Signup and view all the answers

Which of the following statements about DNA structure is incorrect?

<p>It contains ribose sugar. (D)</p> Signup and view all the answers

What is primarily responsible for the degradation of mRNA in cells?

<p>RNase enzymes (B)</p> Signup and view all the answers

What is the significance of the 5’ and 3’ ends in RNA?

<p>They determine the direction of reading the sequence (B)</p> Signup and view all the answers

Which enzyme is known to cleave double-stranded RNA into oligonucleotides?

<p>Dicer (B)</p> Signup and view all the answers

What role does S-RNase play in plants?

<p>It prevents inbreeding (D)</p> Signup and view all the answers

Which pairs correctly represent the Watson-Crick base pairs in DNA?

<p>A with T and C with G (B)</p> Signup and view all the answers

What is one of the novel features of DNA structure discovered by Watson and Crick?

<p>Hydrogen bond interactions between bases (A)</p> Signup and view all the answers

Why are RNase enzymes abundant in nature?

<p>To degrade unwanted RNA (D)</p> Signup and view all the answers

What characteristic of RNA makes it less stable than DNA?

<p>The ribose sugar in its backbone (C)</p> Signup and view all the answers

What did Franklin and Wilkins provide that was critical to Watson and Crick's discovery?

<p>Data on helical parameters (C)</p> Signup and view all the answers

How does RNA hydrolysis predominantly occur in nature?

<p>Through base-catalyzed reactions (D)</p> Signup and view all the answers

What is the outcome of DNA denaturation concerning covalent and hydrogen bonds?

<p>Covalent bonds remain intact, hydrogen bonds are broken. (D)</p> Signup and view all the answers

Which enzyme is primarily responsible for catalyzing the synthesis of new DNA strands during replication?

<p>DNA polymerase (A)</p> Signup and view all the answers

Which statement about the melting temperature (Tm) of DNA is accurate?

<p>GC-rich regions melt at higher temperatures than AT-rich regions. (C)</p> Signup and view all the answers

What is the primary function of tRNA in the context of protein synthesis?

<p>To match amino acids with the mRNA code. (A)</p> Signup and view all the answers

During the process of DNA replication, what is the first step that occurs?

<p>Strand separation. (B)</p> Signup and view all the answers

Which of the following statements is true about messenger RNA (mRNA)?

<p>One mRNA molecule may code for multiple proteins. (B)</p> Signup and view all the answers

What defines a palindromic sequence in DNA?

<p>A sequence identical when read in opposite directions. (A)</p> Signup and view all the answers

What is a significant consequence of high-temperature DNA denaturation?

<p>The strands dissociate completely. (B)</p> Signup and view all the answers

Which form of detection can be used to identify specific DNA molecules in a complex mixture?

<p>Radioactive detection (B)</p> Signup and view all the answers

What impact does ionic strength have on DNA denaturation?

<p>Higher ionic strength increases the Tm of DNA. (B)</p> Signup and view all the answers

Flashcards

Nucleotide

A molecule composed of a nitrogenous base, a pentose sugar, and a phosphate group. They are the building blocks of nucleic acids like DNA and RNA.

Nucleoside

A molecule composed of a nitrogenous base and a pentose sugar. They are the building blocks of nucleotides, but they lack the phosphate group.

Nitrogenous Base

Organic molecule containing nitrogen. It's a key component of nucleotides, which in turn form DNA and RNA. There are two main types: purines and pyrimidines.

Nucleic Acid

A nucleic acid is a polymer made up of chains of nucleotides linked together by phosphodiester bonds. DNA and RNA are important examples.

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Primary Bases of DNA and RNA

Adenine, guanine, cytosine, thymine (DNA only), and uracil (RNA only) are the five primary nitrogenous bases that make up DNA and RNA.

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DNA Denaturation

The process by which the two strands of a DNA molecule separate due to factors like heat, pH changes or certain chemicals.

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DNA Annealing

The process where two complementary single strands of DNA associate to form a stable double helix structure.

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Mutation

A change in the nucleotide sequence of DNA. These can be spontaneous or induced by mutagens.

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N-Glycosidic Bond

The bond is formed to the anomeric carbon of the sugar in the (\beta) configuration. The bond is formed to position N1 in pyrimidines and N9 in purines. This bond is stable towards hydrolysis, particularly in pyrimidines, and is cleaved by acid.

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N-Glycosidic bond conformation

The torsion angle about the N-glycosidic bond (N-C1') is denoted by the symbol (\chi). The atoms involved in defining this angle are O4'-C1'-N9-C4 for purines, and O4'-C1'-N1-C2 for pyrimidines.

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Syn Conformation

A conformation around the N-Glycosidic bond where the angle is close to 0 degrees. In this conformation the base is near the sugar.

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Anti Conformation

A conformation around the N-Glycosidic bond where the angle is close to 180 degrees. In this conformation the base is far from the sugar.

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Anti conformation in DNA

The anti conformation is the most common conformation found in B-DNA.

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Deoxyribonucleotides

The nucleotides in DNA are made of a deoxyribose sugar, a phosphate group, and one of the four nitrogenous bases: adenine (A), guanine (G), cytosine (C), or thymine (T).

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Ribonucleotides

The nucleotides in RNA made of a ribose sugar, a phosphate group, and one of the four nitrogenous bases: adenine (A), guanine (G), cytosine (C), or uracil (U).

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Phosphodiester Linkages

Covalent bonds formed between nucleotides in a polynucleotide chain. These bonds are formed between the 5' phosphate group of one nucleotide and the 3' hydroxyl group of the next nucleotide. The result is a negatively charged backbone.

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RNA Structure

RNA is a linear polymer of nucleotides with a ribose sugar. It is unstable and can be broken down by enzymes called RNases.

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RNase Function

RNase enzymes catalyze the hydrolysis of RNA by breaking its phosphodiester bonds. They play vital roles in cellular processes and defense against viral infections.

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S-RNase in Plants

S-RNase is a type of RNase found in plants that prevents self-fertilization by degrading pollen RNA.

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RNase P: Ribozyme

RNase P is a ribozyme, an enzyme made of RNA, involved in the processing of tRNA precursors. It removes unnecessary sequences to create mature tRNA.

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Dicer and RNA Interference

The enzyme Dicer cleaves double-stranded RNA into smaller oligonucleotides, which are then used in RNA interference and antiviral defense.

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Base-Catalyzed RNA Hydrolysis

RNA hydrolysis is accelerated by base catalysis, a chemical reaction that uses hydroxide ions to break the phosphodiester bonds in the RNA backbone.

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Hydrogen Bonding and Base Pairs

Two bases can bind together through hydrogen bonds, forming a base pair. This base pairing is critical for the structure of DNA and RNA.

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Watson-Crick Base Pairs

In double-stranded DNA, the bases adenine (A) always pairs with thymine (T), while guanine (G) pairs with cytosine (C).

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Discovery of DNA Structure

The discovery of DNA's double helix structure revolutionized biology, revealing the molecular basis of inheritance and paving the way for modern biotechnology.

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Friedrich Miescher and Nuclein

Friedrich Miescher, in 1868, was the first to isolate “nuclein,” a substance later identified as DNA, from cell nuclei. This marked the beginning of understanding the chemical composition of DNA.

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What does it mean that DNA strands are antiparallel?

The two strands of DNA run in opposite directions, with one strand oriented 5' to 3' and the other 3' to 5'.

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Describe the process of DNA replication.

Each DNA strand acts as a template for the synthesis of a new complementary strand. This results in two DNA molecules, each with one original strand (parent strand) and one newly synthesized strand (daughter strand).

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What is the role of DNA polymerases in DNA replication?

DNA polymerases are enzymes responsible for catalyzing the synthesis of new DNA strands during replication. They read the template strand and add complementary nucleotides to the growing new strand.

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Explain what palindromic sequences are in DNA.

Palindromic sequences are DNA segments that read the same forward and backward on both strands. These sequences can form hairpins and cruciforms due to complementary base pairing within the same strand.

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What is Messenger RNA (mRNA) and what is its role?

Messenger RNA (mRNA) is a type of RNA molecule that carries genetic information from DNA to ribosomes, where proteins are synthesized. It plays a crucial role in protein synthesis.

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What is Transfer RNA (tRNA) and what is its role?

Transfer RNA (tRNA) molecules are responsible for bringing the correct amino acid to the ribosome based on the mRNA code during protein synthesis. They have complex structures and act as adaptors in the translation process.

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What is DNA denaturation, and how can it occur?

DNA denaturation is the process where the double helix structure of DNA is disrupted, causing the two strands to separate. This can be caused by factors like heat, pH changes, or certain chemicals.

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What is the melting temperature (Tm) of DNA, and what factors affect it?

The melting temperature (Tm) of DNA is the temperature at which half of the DNA molecules are denatured. It is influenced by factors like base composition (high CG content increases Tm), DNA length (longer DNA has higher Tm), and environmental conditions (high salt increases Tm).

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Is DNA denaturation reversible? Explain.

DNA denaturation is reversible, and the separated strands can re-associate (anneal) to form a double helix again when conditions are favorable. This is a crucial process in techniques like PCR.

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What is DNA hybridization?

Hybridization of DNA involves the pairing of two near-complementary DNA strands, even if they are not perfectly matched. This technique is used in various applications, including DNA detection, amplification, and evolutionary studies.

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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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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.

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