Biochem 8.2 Untitled Quiz
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Questions and Answers

What is the primary structure that forms the backbone of nucleic acids?

  • Fatty acid chains
  • Sugars linked to phosphates (correct)
  • Steroid rings
  • Amino acid sequences

What role do histone proteins play in relation to DNA?

  • They negatively charge DNA strands
  • They neutralize and store negatively charged DNA (correct)
  • They help synthesize RNA
  • They facilitate nucleotide modifications

Which enzyme is responsible for synthesizing RNA?

  • RNA polymerase (correct)
  • DNA polymerase
  • Reverse transcriptase
  • RNA ligase

What is the first nucleotide in a growing nucleic acid strand incorporated into the chain?

<p>The nucleotide at the 5' end (C)</p> Signup and view all the answers

What mechanism is employed by some DNA polymerases to correct nucleotide errors?

<p>3'-5' exonuclease activity (A)</p> Signup and view all the answers

What is the consequence of deamination in nitrogenous bases?

<p>It removes the nitrogenous base from the sugar (B)</p> Signup and view all the answers

What type of bond do exonucleases hydrolyze to remove nucleotides?

<p>Phosphodiester bonds at the ends (A)</p> Signup and view all the answers

Which occurs when a nucleic acid grows?

<p>The 3' end attacks the 5' end of the next nucleotide (C)</p> Signup and view all the answers

What role do pi interactions play in the structure of DNA?

<p>They stabilize the specific DNA conformation. (B)</p> Signup and view all the answers

Which of the following is true about RNA's structure during transcription?

<p>RNA temporarily pairs with the DNA template strand. (A)</p> Signup and view all the answers

What characterizes the helical structure formed by RNA folding on itself?

<p>It involves hydrogen bonding between complementary bases. (A)</p> Signup and view all the answers

Which of the following accurately describes the representation of tRNA structures?

<p>2D structures depict complementary base pairing clearly. (B)</p> Signup and view all the answers

What do Chargaff’s rules specify regarding the composition of DNA?

<p>The number of guanine bases equals the number of cytosine bases. (A)</p> Signup and view all the answers

Which statement is true regarding RNA's biological functions?

<p>RNA can fold into complex three-dimensional shapes. (D)</p> Signup and view all the answers

How are the phosphodiester bonds represented in RNA structures?

<p>As solid lines between adjacent nucleotides. (B)</p> Signup and view all the answers

In which conformation do bases in a DNA double helix primarily reside?

<p>Stacked almost on top of each other. (D)</p> Signup and view all the answers

What is the pairing rule for purines and pyrimidines in DNA?

<p>Every purine is paired with a pyrimidine. (C)</p> Signup and view all the answers

Chargaff's rules apply to which type of nucleic acid structure?

<p>Double-stranded DNA only. (A)</p> Signup and view all the answers

If a double-stranded DNA molecule contains 200 base pairs and 97 guanine bases, how many thymine bases are present?

<p>103 (C)</p> Signup and view all the answers

Which statement is true regarding base pairing within RNA?

<p>Guanine pairs with uracil in RNA. (B)</p> Signup and view all the answers

What environmental condition can disrupt the stability of nucleic acid secondary structures?

<p>Extreme pH levels. (D)</p> Signup and view all the answers

In a DNA-RNA complex, how do the bases pair when adenine is present?

<p>Adenine pairs with uracil in RNA. (C)</p> Signup and view all the answers

What is the optimal pH for DNA annealing?

<p>Near 7.4. (C)</p> Signup and view all the answers

What occurs during wobble pairing in tRNA?

<p>Some bases pair differently than expected. (D)</p> Signup and view all the answers

What type of bond is formed during nucleotide polymerization?

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

Which group of the nucleotide reacts with the phosphate group of another nucleotide?

<p>3' hydroxyl group (A)</p> Signup and view all the answers

Which of the following correctly describes nucleoside triphosphate (NTP) in nucleotide polymerization?

<p>NTPs serve as the building blocks for nucleic acid synthesis. (C)</p> Signup and view all the answers

What is released during the condensation reaction in nucleotide polymerization?

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

What is the sequence of a nucleic acid traditionally written from?

<p>5' end to 3' end (A)</p> Signup and view all the answers

How is a dinucleotide formed?

<p>By linking two nucleotides via a phosphodiester bond (D)</p> Signup and view all the answers

What term is used to describe nucleic acids that contain a few nucleotides?

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

What is the significance of the carbon numbering system in nucleotides?

<p>It is essential for understanding the structure of nucleic acids. (D)</p> Signup and view all the answers

What is the function of DNA ligase in nucleotide repair?

<p>To provide the energy needed to repair the nick (C)</p> Signup and view all the answers

What is the primary structure of a nucleic acid composed of?

<p>The arrangement of nucleotides (A)</p> Signup and view all the answers

Which base pairing occurs in DNA?

<p>Adenine pairs with Thymine (A)</p> Signup and view all the answers

What structural feature contributes to the stability of the DNA double helix?

<p>Hydrogen bonding between complementary bases (C)</p> Signup and view all the answers

What is meant by the term 'antiparallel orientation' of DNA strands?

<p>One strand runs 5' to 3' while the other runs 3' to 5' (D)</p> Signup and view all the answers

What role does the hydrophobic effect play in the structure of DNA?

<p>It helps stabilize the double helix structure (C)</p> Signup and view all the answers

What occurs if there is a single mismatch in base pairing during DNA annealing?

<p>It can significantly reduce the favorability of annealing (B)</p> Signup and view all the answers

Which of the following accurately describes complementary bases in DNA?

<p>Each base pair consists of one purine and one pyrimidine (D)</p> Signup and view all the answers

How does a change in pH affect the functional groups in bases?

<p>It can lead to protonation or deprotonation of functional groups. (D)</p> Signup and view all the answers

What role do histones play in eukaryotic DNA structure?

<p>They interact with negatively charged phosphate groups to stabilize DNA. (D)</p> Signup and view all the answers

Which factor has the greatest impact on the melting temperature (Tm) of a double helix?

<p>The length of the helix and its GC content. (D)</p> Signup and view all the answers

What occurs to the strands of a double helix when subjected to higher temperatures?

<p>The strands denature and come apart. (B)</p> Signup and view all the answers

What is the significance of GC content in a double helix?

<p>Higher GC content results in a higher melting temperature due to more hydrogen bonds. (B)</p> Signup and view all the answers

What is the melting temperature (Tm) in the context of DNA?

<p>The temperature at which 50% of the double helices denature. (B)</p> Signup and view all the answers

How do salts influence DNA stability?

<p>They stabilize the phosphate groups through cation interaction. (A)</p> Signup and view all the answers

In the context of PCR, what is manipulated to optimize the melting temperature?

<p>The GC content and salt conditions. (C)</p> Signup and view all the answers

Flashcards

What are nucleic acids made of?

Nucleic acids, like DNA and RNA, are polymers formed by linking nucleotides together.

How are nucleotides linked in nucleic acids?

The 3' hydroxyl group of one nucleotide reacts with the 5' phosphate group of another nucleotide, forming a phosphodiester bond.

What are the ends of a nucleic acid called?

The end of a nucleic acid with a free 5' phosphate group is called the 5' end, while the end with a free 3' hydroxyl group is called the 3' end.

What is released during nucleic acid synthesis?

Nucleic acid synthesis is a condensation reaction where pyrophosphate (PPi) is released, not water.

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How is nucleic acid sequence written?

The sequence of a nucleic acid is typically written from the 5' end to the 3' end.

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What are short and long nucleic acids called?

Oligonucleotides are short nucleic acid chains, while longer chains are called polynucleotides.

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What are the components of a nucleotide?

Nucleotides are composed of a sugar, a phosphate, and a nitrogenous base.

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What is nucleic acid polymerization ?

The process of adding nucleotides to a growing nucleic acid chain.

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What is the primary structure of a nucleic acid?

The linear sequence of nucleotides in a DNA or RNA molecule.

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What is the secondary structure of a nucleic acid?

The three-dimensional arrangement of a nucleic acid, formed by interactions between the bases.

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What is the most well-known secondary structure in nucleic acids?

The double helix structure of DNA, where two complementary DNA strands wind around each other.

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What is annealing of DNA strands?

The process of forming a double-stranded DNA molecule from two single strands by base pairing.

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What is the orientation of DNA strands in a double helix?

The orientation of the two DNA strands in a double helix, where the 3' end of one strand aligns with the 5' end of the other strand.

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What are complementary base pairs?

The interaction between two bases in DNA, where guanine pairs with cytosine and adenine pairs with thymine.

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How does the hydrophobic effect contribute to DNA structure?

The hydrophobic effect helps stabilize the double helix structure of DNA by minimizing the contact between the bases and water.

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How does base pairing affect DNA stability?

The stability of DNA is dependent on the complementary base pairing between the two strands. Mismatches, even a single one, disrupt the stability of the double helix.

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What is a nucleic acid?

A nucleic acid is a large molecule made up of a chain of nucleotides.

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Describe the structure of a nucleic acid backbone.

The backbone of a nucleic acid consists of alternating sugar and phosphate groups. This backbone is negatively charged due to the phosphate groups.

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Which enzymes are involved in nucleic acid synthesis?

Nucleic acids are synthesized by enzymes called DNA polymerase (for DNA) and RNA polymerase (for RNA).

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How are the 5' and 3' ends of a nucleic acid defined?

The nucleotide at the 5' end is the first to be incorporated into the chain. The nucleotide at the 3' end is the last to be added.

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Describe the mechanism of nucleic acid elongation.

The 3' end of the growing nucleic acid attacks the 5' end of the next nucleotide to be added.

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How are errors in DNA synthesis corrected?

DNA polymerase can sometimes insert the wrong nucleotide. To correct errors, it has 3'-5' exonuclease activity that removes nucleotides from the 3' end.

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Describe the process of repairing a deaminated base in DNA.

Deamination is a chemical change that can occur in nitrogenous bases. Glycosylase removes the affected base, and endonuclease removes the sugar. DNA polymerase then inserts a new nucleotide.

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Chargaff's Rules in DNA-RNA Complex

The total number of adenine bases in a DNA-RNA complex is equal to the sum of the thymine and uracil bases in the complex.

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pH and DNA Annealing

The optimal pH for DNA annealing is near 7.4 because the hydrogen bonding participants in each base are neutral and can form the expected hydrogen bonds with their complementary bases.

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Hydrogen Bonding in DNA Stability

The hydrogen bonding between A-T and G-C base pairs in DNA contributes significantly to its stability. The more hydrogen bonds present, the more stable the DNA.

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Environmental Factors and DNA Stability

The stability of the double helix is affected by environmental conditions like pH, salt concentration, and temperature.

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Chargaff's Rules: Purines and Pyrimidines

The sum of purines (adenine and guanine) equals the sum of pyrimidines (thymine and cytosine) in double-stranded DNA because each purine base pairs with a pyrimidine base.

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Chargaff's Rules: Double-Stranded DNA

Chargaff's rules only apply to double-stranded nucleic acids, specifically DNA. Each individual strand can have any number of bases, but only when paired with its complement do the rules hold.

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Chargaff's Rules in RNA

Chargaff's rules do not apply to RNA universally, while the number of adenine bases equals the number of uracil bases instead of thymine, there are exceptions due to 'wobble pairing'.

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Chargaff's Rules in DNA-RNA Pairing

When a DNA strand pairs with an RNA strand, the RNA strand contains uracil, which pairs with adenine in the DNA strand. Therefore, the total number of adenine bases in the complex is equal to the sum of thymine and uracil bases.

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Why does DNA form a double helix?

The nitrogenous bases in DNA (Adenine, Guanine, Cytosine, Thymine) are hydrophobic and prefer to interact with each other instead of water. The sugar-phosphate backbone of DNA is hydrophilic and interacts favorably with water, resulting in the double-helix structure where the bases are tucked inside and the backbone is exposed.

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What is pi stacking and why is it important for DNA?

This type of interaction helps stabilize the specific conformation of DNA. The aromatic nature of the bases creates a favorable interaction.

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How can RNA form different structures?

RNA can also form secondary structures, like hairpins, due to complementarity between bases within the same strand. This allows the RNA to fold and form specific 3D structures.

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What are Chargaff's rules?

According to Chargaff's rules, in a double-stranded DNA molecule, the number of adenine (A) bases always equals the number of thymine (T) bases, and the number of guanine (G) bases always equals the number of cytosine (C) bases.

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Optimal pH for DNA stability

The pH value where the functional groups of bases are neither protonated nor deprotonated, ensuring proper base pairing and DNA stability.

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What is the basis of Chargaff's rules?

The base pairing in DNA is due to the specific hydrogen bonding between adenine and thymine, and guanine and cytosine. This precise pairing is crucial for maintaining the double helix structure.

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How phosphate groups affect DNA stability

The repulsion between negatively charged phosphate groups in the DNA backbone can destabilize helix formation.

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Role of histones in DNA stability

Positively charged histones bind to negatively charged DNA, helping to stabilize and package DNA in eukaryotic cells.

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What is the primary structure of DNA?

The sequence of nucleotides in a DNA strand, determined by the order of bases. This sequence carries genetic information.

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What is the secondary structure of DNA?

The 3D arrangement of DNA, typically a double helix due to base pairing and stacking interactions, which contributes to its stability and function.

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How salts influence DNA stability

Cations from salts, such as Mg2+, interact with phosphate groups, counteracting their negative charge and stabilizing DNA.

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What is the tertiary structure of RNA?

The unique 3D conformation of a given RNA molecule, determined by its sequence and interactions between bases. This shape is crucial for RNA's function.

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Effect of temperature on DNA stability

Higher temperatures increase the movement of molecules, leading to the breaking of hydrogen bonds between DNA strands and denaturation.

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Melting temperature (Tm)

The temperature at which 50% of DNA molecules in a solution denature, indicating the stability of the DNA under specific conditions.

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How GC content affects Tm

Higher GC content leads to a higher melting temperature because G-C base pairs form three hydrogen bonds, making them more stable.

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Importance of Tm in PCR

The melting temperature of DNA is crucial for polymerase chain reaction (PCR), where specific temperatures are required for primer annealing and denaturation.

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Study Notes

Nucleic Acid Formation

  • Nucleic acids are polymers formed from nucleotides
  • DNA and RNA are two types of nucleic acids
  • Nucleotides are composed of a sugar, a phosphate group, and a nitrogenous base
  • The carbons in the sugar component are numbered using a prime symbol (')
  • Nucleic acids form when the 3' hydroxyl group of one nucleotide reacts with the 5' phosphate group of another
  • This forms a phosphodiester bond, linking the nucleotides
  • The reaction is a condensation reaction, where pyrophosphate (PP) is released instead of water
  • The 5' end of a nucleic acid has a free phosphate group
  • The 3' end has a free hydroxyl group
  • Nucleic acid sequences are written in the 5' to 3' direction

Base Pairing and Secondary Structure

  • The sequence of nucleotides is the primary structure of a nucleic acid
  • Nucleic acids can form secondary structures, such as the double helix in DNA
  • In DNA, two strands twist around each other forming a double helix structure
  • The strands are anti-parallel, meaning the 3' end of one strand aligns with the 5' end of the other
  • Hydrogen bonds between complementary bases (A-T and G-C) hold the two strands together
  • This gives complementary bases
  • Base pairing in nucleic acids follows Chargaff's rules:
    • The number of adenine bases equals the number of thymine bases
    • The number of guanine bases equals the number of cytosine bases
    • The sum of purines equals the sum of pyrimidines
  • These rules only apply to double-stranded nucleic acids

Double Helix Stability

  • Nucleic acid secondary structure can be disrupted by environmental factors (pH, salt, temperature)
  • Optimal pH for DNA annealing is near 7.4
  • Higher temperatures cause the hydrogen bonds holding the helix together to break, causing denaturation
  • Melting temperature (Tm) is the temperature at which 50% of the double helices in a solution denature
  • Higher GC content results in a higher melting temperature (Tm)
  • The melting curve's sigmoidal shape indicates cooperative denaturation, where separation of portions of the helix becomes easier as more portions separate

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