Nucleic Acids: Structure and Function

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Questions and Answers

If a newly discovered virus contains uracil but not thymine as one of its nitrogenous bases, which type of nucleic acid is most likely to make up its genome?

  • Peptide nucleic acid
  • Single-stranded DNA
  • Double-stranded DNA
  • Ribonucleic acid (correct)

Which of the following is a critical function of nucleic acids in living organisms?

  • Catalyzing metabolic reactions as enzymes
  • Encoding and transmitting genetic information (correct)
  • Storing energy for cellular activities
  • Providing structural support within cells

A nucleotide is composed of which of the following?

  • A pentose sugar and a phosphate group
  • A nitrogenous base and a phosphate group
  • A nitrogenous base, a pentose sugar, and a phosphate group (correct)
  • A pentose sugar and a nitrogenous base

How does the pentose sugar in DNA differ from the pentose sugar in RNA?

<p>DNA contains deoxyribose, which has one less oxygen atom than ribose in RNA. (C)</p> Signup and view all the answers

An unknown molecule is found to contain a nitrogenous base, a pentose sugar, but no phosphate group. What is this molecule most likely to be?

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

A DNA sequence described as a palindrome contains inverted repeats with what kind of symmetry?

<p>Twofold symmetry over two strands of DNA. (D)</p> Signup and view all the answers

Which of the following nitrogenous bases is a purine?

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

Mirror repeats differ from palindromes in that mirror repeats:

<p>lack complementary sequences within the same strand. (D)</p> Signup and view all the answers

What is the function of messenger RNA (mRNA) as proposed by Jacob and Monod?

<p>To carry genetic information from DNA to ribosomes for protein synthesis. (D)</p> Signup and view all the answers

Which of the following statements accurately describes the role of functional nucleotides such as ATP?

<p>They act as the energy currency in metabolic transactions. (C)</p> Signup and view all the answers

Which of the following best describes the relationship between nucleic acids and proteins within a cell?

<p>Nucleic acids contain the informational code that determines the structure of proteins. (C)</p> Signup and view all the answers

The process of transcription can be best described as:

<p>the formation of mRNA on a DNA template. (B)</p> Signup and view all the answers

Which of the following best describe a monocistronic mRNA?

<p>It codes for only one polypeptide. (B)</p> Signup and view all the answers

How does a polycistronic mRNA differ from a monocistronic mRNA?

<p>Polycistronic mRNA codes for multiple polypeptide chains. (B)</p> Signup and view all the answers

Which cellular component or process is directly linked to an increase in cytoplasmic RNA?

<p>An increase in protein synthesis. (D)</p> Signup and view all the answers

What structural feature is associated with palindromic DNA sequences due to their self-complementary nature?

<p>Hairpin or cruciform structures (B)</p> Signup and view all the answers

Which statement accurately describes the arrangement of the two DNA strands in a double helix?

<p>The strands run antiparallel, with one strand oriented 5' to 3' and the other 3' to 5'. (D)</p> Signup and view all the answers

What type of bond connects complementary bases in a DNA double helix?

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

According to Chargaff's rules, if a DNA molecule contains 20% Adenine, what percentage of Guanine would be present?

<p>30% (C)</p> Signup and view all the answers

Which of the following contributes most significantly to the stability of the DNA double helix, aside from hydrogen bonding?

<p>Base-stacking interactions between adjacent base pairs. (C)</p> Signup and view all the answers

In the tertiary structure of DNA, where are the hydrophilic components located?

<p>Facing outward, interacting with the surrounding water. (A)</p> Signup and view all the answers

What is the primary difference between the 5' and 3' ends of a DNA strand?

<p>The 5' end has a phosphate group attached to the sugar, while the 3' end has a hydroxyl group. (B)</p> Signup and view all the answers

If a mutation resulted in a DNA strand where adenine (A) was replaced by guanine (G), which of the following consequences is most likely?

<p>The DNA strand would still bind to the original complementary strand, but with a different number of hydrogen bonds (B)</p> Signup and view all the answers

Which of the following is NOT a characteristic of the DNA double helix?

<p>The two strands run parallel to each other. (B)</p> Signup and view all the answers

What primarily dictates the minimum length of an mRNA molecule?

<p>The length of the polypeptide chain it encodes. (C)</p> Signup and view all the answers

If a scientist discovers a mutation that significantly reduces the stability of DNA, which aspect of its role would be most compromised?

<p>Its capacity to serve as a repository of genetic information. (B)</p> Signup and view all the answers

In the context of DNA's tertiary structure, what is the significance of the major and minor grooves?

<p>They provide locations for proteins to bind and interact with the DNA. (D)</p> Signup and view all the answers

How does the arrangement of deoxyribose and phosphate groups in the DNA double helix contribute to its stability in an aqueous environment?

<p>The hydrophilic backbones of deoxyribose and phosphate groups are outside the double helix, facing the surrounding water. (C)</p> Signup and view all the answers

What is the primary role of chromatin in eukaryotic cells?

<p>To package DNA into a smaller volume and control gene expression. (A)</p> Signup and view all the answers

At which level of chromatin organization does the nucleosome represent?

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

If a drug prevented the formation of proper chromatin structure, which cellular process would be most directly affected?

<p>DNA replication and gene expression (A)</p> Signup and view all the answers

During DNA replication, an error occurs where guanine is inserted instead of adenine on one strand. What will be the corresponding base on the complementary strand after replication?

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

Why is thymine, rather than uracil, typically found in DNA?

<p>The repair systems in cells can easily recognize and remove uracil resulting from cytosine deamination. (A)</p> Signup and view all the answers

What would be the long-term consequence if cytosine deamination was not effectively repaired in DNA?

<p>A decrease in G≡C base pairs and an increase in A=U base pairs. (C)</p> Signup and view all the answers

What is the primary consequence of an AP site (apurinic/apyrimidinic site) in DNA?

<p>A block in DNA replication and transcription because of the missing base. (A)</p> Signup and view all the answers

Why is depurination of ribonucleotides in RNA generally considered physiologically insignificant compared to depurination in DNA?

<p>Damaged RNA molecules are easily replaced by newly synthesized RNA, minimizing the impact of depurination. (A)</p> Signup and view all the answers

What type of DNA damage is most likely to result from exposure to UV light?

<p>Formation of cyclobutane pyrimidine dimers. (B)</p> Signup and view all the answers

How does ionizing radiation (e.g., X-rays and gamma rays) primarily damage DNA?

<p>By causing ring opening and fragmentation of bases and breaks in the DNA backbone. (C)</p> Signup and view all the answers

Incubating DNA at pH 3 causes selective removal of the purine bases, resulting in a derivative called apurinic acid. Why does acidic pH cause this?

<p>Acidic pH protonates the purine bases, making them more susceptible to hydrolysis. (C)</p> Signup and view all the answers

Suppose a cell has a mutation that impairs its ability to repair cyclobutane pyrimidine dimers. What is the most likely consequence of this mutation if the cell is exposed to UV radiation?

<p>Increased frequency of mutations in the cell's DNA. (B)</p> Signup and view all the answers

Why is RNA susceptible to hydrolysis in an alkaline environment, while DNA is resistant?

<p>The absence of a 2'-OH group in DNA prevents the formation of a cyclic 2',3'-phosphate intermediate. (D)</p> Signup and view all the answers

What is the primary outcome of mild acid hydrolysis (pH about 3) on a polynucleotide?

<p>Selective cleavage of the β-glycosidic bond of purine nucleotides, resulting in an apurinic polynucleotide. (B)</p> Signup and view all the answers

What impact does the use of hydrazine have on nucleic acids?

<p>It results in a pyrimidine polynucleotide. (A)</p> Signup and view all the answers

During the determination of a base ratio in a polynucleotide, why is it important to carefully consider cytosine deamination?

<p>Deamination of cytosine leads to the formation of uracil, which can be misread as thymine. (A)</p> Signup and view all the answers

How do 3'- and 5'-exonucleases differ in their mechanism of action?

<p>3'-exonucleases cleave mononucleotides from the 3' end of the polynucleotide, whereas 5'-exonucleases cleave from the 5' end. (D)</p> Signup and view all the answers

What distinguishes endonucleases from exonucleases in their cleavage activity on nucleic acids?

<p>Endonucleases cleave bonds at specific sites <em>within</em> the polynucleotide chain, whereas exonucleases remove nucleotides from the <em>ends</em> of the chain. (C)</p> Signup and view all the answers

How does the cleavage specificity of pancreatic RNase differ from that of RNase T1?

<p>Pancreatic RNase cleaves β-bonds when a pyrimidine nucleotide is attached to the α-bond, while RNase T1 cleaves β-bonds when a purine nucleotide is attached to the α-bond. (C)</p> Signup and view all the answers

What is the distinguishing feature of restriction endonucleases regarding their activity on DNA?

<p>They cleave the DNA double helix at a site of central symmetry in the nucleotide sequence. (A)</p> Signup and view all the answers

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Flashcards

Nucleic Acids

Macromolecules essential for all life forms that encode and express genetic information.

DNA

Deoxyribonucleic acid, a type of nucleic acid that carries genetic information in cells.

RNA

Ribonucleic acid, a nucleic acid involved in protein synthesis and carrying genetic information.

Nucleotide

Building blocks of nucleic acids, consisting of a nitrogenous base, sugar, and phosphate group.

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Nitrogenous Bases

Components of nucleotides categorized as purines or pyrimidines.

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Purines

A category of nitrogenous bases with a two-ring structure, including Adenine and Guanine.

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Pyrimidines

A category of nitrogenous bases with a one-ring structure, including Thymine, Cytosine, and Uracil.

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Nucleoside

A molecule consisting of a sugar and a nitrogenous base, without a phosphate group.

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Palindrome

A DNA sequence that reads the same forward and backward, with twofold symmetry.

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Inverted Repeats

Sequences in DNA that appear as reverse complements within the same strand.

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Hairpin Structure

A loop in a single-stranded nucleic acid created by base pairing within the strand.

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Cruciform Structure

A cross-shaped structure formed by inverted repeat sequences in double-stranded DNA.

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Mirror Repeat

A DNA sequence that has identical sequences on the same strand but not complementary.

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Messenger RNA (mRNA)

RNA that carries genetic information from DNA to ribosomes for protein synthesis.

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Transcription

The process of synthesizing mRNA from a DNA template.

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Monocistronic vs Polycistronic

Monocistronic mRNA codes for one protein; polycistronic mRNA codes for multiple proteins.

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Phosphodiester linkage

The bond between phosphate and ribose or deoxyribose in DNA/RNA strands.

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5'-phosphate and 3'-OH ends

The two ends of DNA/RNA strands, crucial for directionality.

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Base pairing

A: T and G: C bonds in DNA through hydrogen bonding.

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Antiparallel strands

The opposite orientation of the two strands in DNA.

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Chargaff's rule

A rule stating that A pairs with T and G pairs with C, maintaining equal numbers.

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Double helix structure

The coiled shape of DNA formed by two polynucleotide strands.

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Hydrogen bonding

Weak bonds between complementary bases, stabilizing the DNA structure.

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Base-stacking interactions

Non-specific interactions that stabilize the DNA double helix.

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mRNA length

The minimum length of an mRNA codes for a polypeptide chain based on nucleotide triplets.

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Noncoding RNA

Sequences in mRNA that do not code for proteins but regulate protein synthesis.

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Tertiary structure of DNA

Spatial arrangement of DNA atoms considering geometrical and thermodynamic constraints.

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Antiparallel DNA strands

Two strands of DNA running in opposite directions, maintaining complementary base pairing.

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Hydrophilic backbone

The outer part of the DNA double helix consisting of deoxyribose and phosphate groups that face water.

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Chromatin

A complex of DNA, protein, and RNA in eukaryotic cells; packages DNA for cell functions.

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Chemical stability of DNA

DNA’s ability to resist degradation over time, which depends on its chemical structure.

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Cytosine Deamination

The process where cytosine loses an amine group, turning into uracil.

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Thymine's Role

Thymine replaces uracil in DNA to prevent misreading and mutations.

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AP Site

An abasic site in DNA resulting from the loss of purines.

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Depurination Rate

The frequency at which purines are lost from DNA, about 1 in 10^5 purines daily.

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Cyclobutane Dimers

DNA lesions formed by UV light linking adjacent pyrimidine bases.

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6-4 Photoproducts

A type of pyrimidine dimer created by UV irradiation, apart from cyclobutane dimers.

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Repair System For Uracil

Cellular mechanisms that recognize and remove uracil from DNA to prevent errors.

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Radiation Effects on DNA

Ionizing radiation can cause damage by breaking bases and the DNA backbone.

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Cyclic 2',3'-phosphate

A temporary structure formed during the hydrolysis of RNA, leading to 2' and 3'-phosphates.

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Acid hydrolysis

A process where the β-glycosidic bond in purine nucleotides is cleaved at low pH, leading to purine polynucleotides.

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Exonucleases

Nucleases that remove nucleotides from the ends of polynucleotides, either 3' or 5' ends.

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Endonucleases

Enzymes that cleave the bonds within a polynucleotide chain, creating shorter oligonucleotides.

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RNases

Ribonucleases that selectively degrade RNA by cleaving phosphodiester bonds.

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DNases

Deoxyribonucleases that degrade DNA by cleaving phosphodiester bonds.

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Restriction endonucleases

Enzymes that cut DNA at specific sequences, often at sites of central symmetry in the nucleotide sequence.

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Study Notes

Nucleic Acids

  • Nucleic acids are macromolecules essential for all life forms, encoding, transmitting, and expressing genetic information.
  • They are polymers of nucleotide monomers, each composed of a nitrogenous base, a 5-carbon sugar, and a phosphate group.
  • Divided into DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

Structure of Nucleotides

  • Nucleotides are the building blocks of nucleic acids.
  • They have three components: a nitrogenous base, a pentose (5-carbon sugar), and a phosphate group.
  • A nucleoside lacks the phosphate group.
  • Nitrogenous bases are divided into Purines (adenine (A) and guanine (G), two-ring structure) and Pyrimidines (thymine (T), cytosine (C), and uracil (U), one-ring structure). DNA contains A, G, T, and C; RNA contains A, G, U, and C.

Roles of Functional Nucleotides

  • Components of DNA and RNA.
  • Energy currency (mostly ATP).
  • Chemical links in cellular responses to hormones (e.g., cAMP).
  • Structural components of enzyme cofactors and metabolic intermediates (e.g., NAD+, FAD, FMN).
  • Derivatives of nucleotides:
    • NAD+/NADH, NADP+/NADPH, FAD/FADH2, FMN/FMNH2, cAMP, cGMP.

DNA Primary Structure

  • Phosphodiester bonds link successive nucleotides.
  • The 5'-phosphate group of one nucleotide is linked to the 3'-hydroxyl group of the next.
  • The DNA or RNA strands have 5' and 3' ends (phosphate end and hydroxyl end).

DNA Secondary Structure

  • Double helix structure with two strands.
  • Hydrogen bonds between complementary base pairs (A-T and G-C): A-T have two hydrogen bonds and G-C have three hydrogen bonds.
  • Antiparallel strands, running in opposite directions.
  • Base stacking interactions contribute to stability.

DNA Tertiary Structure

  • Various three-dimensional shapes.
  • Major and minor grooves.
  • Forms like B-DNA, A-DNA, and Z-DNA.

DNA Denaturation

  • DNA denaturation (melting) is the separation of DNA strands.
  • Factors influencing denaturation include high temperatures, extreme pH, and certain chemicals.
  • Higher G-C content results in higher melting temperatures.

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