Molecular Biology Quiz on DNA and Vaccines

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Questions and Answers

What is the amount of purines lost per day in a mammalian cell?

  • 5,000 purines
  • 20,000 purines
  • 15,000 purines
  • 10,000 purines (correct)

Which of the following describes an effect of alkylating agents on DNA?

  • They increase the stability of DNA structures.
  • They enhance DNA replication.
  • They cause DNA damage. (correct)
  • They create cyclobutane uracil dimers.

Which of these processes is involved in DNA modification by exogenous damage?

  • Mutations (correct)
  • Translation
  • Transcription
  • Splicing

Which of the following is NOT a step in the natural process of DNA replication?

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

What is the purpose of protected phosphoramidites in DNA synthesis?

<p>To facilitate selective protection during synthesis (A)</p> Signup and view all the answers

Which sequencing method is mentioned as part of the learning module?

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

What type of dimer is formed due to radiation damage in DNA?

<p>Cyclobutane uracil dimer (B)</p> Signup and view all the answers

What is NOT a goal of chemically synthesizing DNA?

<p>Increasing mutation rates (D)</p> Signup and view all the answers

What is a key advantage of nucleic acid vaccines?

<p>They can be produced quickly (A)</p> Signup and view all the answers

Which component is necessary for mRNA vaccines to effectively enter cells?

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

What disadvantage is associated with nucleic acid vaccines?

<p>They need to be stored at cold temperatures (B)</p> Signup and view all the answers

Which mRNA product is an example of a personalized vaccine for cancer?

<p>Biontech BNT111 (C)</p> Signup and view all the answers

How has the design process for mRNA vaccines improved according to recent developments?

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

What does the optimisation of delivery vectors for nucleic acid vaccines focus on?

<p>Enhancing the delivery of mRNA into cells (B)</p> Signup and view all the answers

What is one example of a latent virus targeted by future nucleic acid vaccines?

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

What characteristic of mRNA makes it challenging to handle in vaccine formulations?

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

What happens to the hydrogen bonds during the denaturation of DNA?

<p>They are broken, leading to strand separation. (D)</p> Signup and view all the answers

Which factor does NOT increase the melting temperature (Tm) of nucleic acid?

<p>Higher concentration of UV light (C)</p> Signup and view all the answers

What occurs during the annealing process in DNA?

<p>Separated strands rejoin under appropriate conditions. (A)</p> Signup and view all the answers

What type of base pairing is associated with a DNA dimer?

<p>Watson-Crick base pairing (A)</p> Signup and view all the answers

Which type of structure is RNA more stable than DNA by approximately 20 °C?

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

What role does a template strand play in DNA replication?

<p>It serves as a guide for synthesizing the daughter strand. (A)</p> Signup and view all the answers

Which of the following does NOT represent a method by which DNA can be modified?

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

What is the consequence of melting temperature (Tm) increasing?

<p>DNA strands are less likely to separate. (C)</p> Signup and view all the answers

What is the first step in engineering a nucleic acid vaccine?

<p>Identify a target antigen and epitope (C)</p> Signup and view all the answers

Which of the following is an example of an mRNA-based vaccine?

<p>Pfizer–BioNTech COVID-19 vaccine (A)</p> Signup and view all the answers

How does mRNA enter the cells during the process of vaccination?

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

In recombinant technology, what is a significant challenge that may arise?

<p>All of the above (D)</p> Signup and view all the answers

What is the purpose of designing a DNA/mRNA sequence in vaccine development?

<p>To instruct cells to produce a target epitope (A)</p> Signup and view all the answers

Which of the following accurately describes the difference between a nucleobase, a nucleoside, and a nucleotide?

<p>A nucleobase is a nitrogenous base, a nucleoside is a nucleobase linked to a sugar, and a nucleotide is a nucleoside linked to one or more phosphate groups. (A)</p> Signup and view all the answers

What is the primary reason nucleobases absorb UV light at 250–270 nm?

<p>Due to π to π* electronic transitions. (B)</p> Signup and view all the answers

Which statement accurately describes tautomers in nucleobases?

<p>Tautos differ in the location of protons and can exist in solution. (B)</p> Signup and view all the answers

Which of the following correctly identifies the structure of ribofuranose?

<p>A five-membered ring structure containing ribose sugar. (B)</p> Signup and view all the answers

What does the acid dissociation constant (Ka) indicate in nucleic acids?

<p>The degree of ionization of an acid in solution. (B)</p> Signup and view all the answers

Which feature of pyrimidine bases enhances their hydrogen bonding capabilities?

<p>They act as strong H-bond donors and acceptors. (C)</p> Signup and view all the answers

Which of the following statements about the N-glycosidic bond in nucleotides is correct?

<p>It is formed between the nitrogenous base and a pentose sugar. (C)</p> Signup and view all the answers

What role does effective photoprotection play concerning nucleobases?

<p>It helps maintain the integrity of genetic information by decaying excited states quickly. (C)</p> Signup and view all the answers

What is a common characteristic of purine bases at pH 7?

<p>They are neutral molecules with good H-bond properties. (B)</p> Signup and view all the answers

What is the process that makes purification easier after each step in oligonucleotide synthesis?

<p>Solid phase synthesis (B)</p> Signup and view all the answers

In the context of oligonucleotide synthesis, what is the typical efficiency required for high-yield synthesis?

<p>0.995 (B)</p> Signup and view all the answers

What is the probability of successful synthesis after 30 coupling steps at an efficiency of 0.995?

<p>86% (A)</p> Signup and view all the answers

What is a primary component used in the DNA sequencing process known as the Sanger technique?

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

What is the role of dideoxynucleotides in the Sanger sequencing method?

<p>Terminating DNA chain synthesis (A)</p> Signup and view all the answers

What does the term 'massive parallel sequencing' refer to?

<p>Next-generation sequencing (NGS) (D)</p> Signup and view all the answers

What is the primary feature of capillary electrophoresis in the Sanger technique?

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

What problem does dimethoxytrityl specifically protect against during synthesis?

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

Flashcards

Nucleic Acid

A polymer of nucleotides. Includes DNA and RNA.

Nucleotide

A subunit of nucleic acid, consisting of a nucleobase, a pentose sugar, and a phosphate group.

Nucleobase

A nitrogen-containing heterocyclic molecule that is one component of a nucleotide.

Nucleoside

A nucleobase linked to a pentose sugar. Examples include adenosine (A) and guanosine (G).

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Ribofuranose

A five-carbon sugar found in RNA. Ribose has a hydroxyl group at the 2' position.

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Deoxyribose

A five-carbon sugar found in DNA. Deoxyribose lacks a hydroxyl group at the 2' position.

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Phosphate Group

A molecule composed of a phosphate group. An important component of nucleotides.

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N-glycosidic Bond

The linkage between a nucleobase and a sugar in a nucleoside.

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Tautomerism

The phenomenon where a molecule can exist in different forms, with the same molecular formula but different structures.

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Acid Dissociation Constant (Ka)

A measure of the strength of an acid. It measures the tendency of an acid to donate a proton (H+).

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DNA Denaturation

The process of breaking hydrogen bonds between DNA strands, causing the double helix to separate into two single strands.

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DNA Annealing

The process of re-forming hydrogen bonds between complementary DNA strands, causing them to come back together as a double helix.

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Melting Temperature (Tm)

The temperature at which half of the DNA molecules in a solution have denatured.

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GC content and Tm

A DNA molecule with a higher GC content will have a higher melting temperature (Tm) because G-C base pairs have three hydrogen bonds, making them more stable than A-T base pairs, which have two hydrogen bonds.

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DNA Replication

The process by which DNA makes a copy of itself.

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Stages of DNA Replication

The process of DNA replication is divided into three stages: initiation, elongation, and termination.

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Polymerase Chain Reaction (PCR)

A technique used to amplify a specific DNA sequence in vitro.

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Epigenetics

Changes to DNA that do not alter the nucleotide sequence but still affect gene expression.

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Dimethoxytrityl (DMT)

A chemical group used to protect a molecule from unwanted reactions during synthesis. It's like a shield that prevents other molecules from attaching to a sensitive spot.

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Oligonucleotide synthesis

The process of building a new strand of DNA or RNA from individual nucleotides. It's like adding bricks to build a wall.

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Solid phase synthesis

A method of oligonucleotide synthesis where the growing chain is attached to a solid support. It's like building a model on a sturdy base.

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Four steps per cycle

In oligonucleotide synthesis, each cycle involves four steps: deprotection, coupling, capping, and oxidation. It's like a recipe with four ingredients to build a biomolecule.

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Coupling efficiency

The ability to create new bonds to form a larger molecule. It's like connecting train carriages to make a longer train.

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Assembly PCR

A method of linking together short DNA fragments to create a longer sequence. It uses PCR to amplify the desired sequence.

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Sanger sequencing

A method of DNA sequencing that uses a chain termination reaction. Short fragments with different fluorescent labels reveal the order of nucleotides.

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Dideoxynucleotides

Short DNA or RNA fragments with a specific nucleotide added at the end. They are used to identify the final nucleotide in Sanger sequencing.

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Nucleic Acid Vaccine

A type of vaccine that uses genetic material (DNA or mRNA) to trigger an immune response against a specific pathogen. This material encodes for a pathogen antigen, which the immune system will recognize and produce antibodies against.

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mRNA Vaccine

A type of nucleic acid vaccine that delivers mRNA coding for a specific viral protein. The mRNA is encased in a lipid nanoparticle to protect it from degradation and help it enter cells.

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Recombinant Technology

A method to modify genetic material in the lab, enabling the production of tailored proteins. It involves inserting a gene of interest into a host cell, which then expresses the desired protein.

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IPTG (Isopropyl Beta-D-1-Thiogalactopyranoside)

A substance that can trigger the production of a specific protein in a host cell. It is often used in recombinant technology to stimulate the expression of a desired protein.

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Host Cell

A living organism (such as bacteria, yeast, or mammalian cells) used to produce large quantities of a desired protein within a controlled laboratory setting.

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Primer

A short single-stranded DNA sequence used as a starting point for DNA replication by DNA polymerase. Primers are essential for initiating DNA synthesis and are typically about 10-20 nucleotides long.

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DNA Polymerase

DNA polymerase is an enzyme responsible for replicating DNA. It reads the original DNA strand and uses it as a template to create a complementary new strand.

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Cyclobutane Uracil Dimer

A type of DNA damage caused by exposure to radiation, particularly ultraviolet (UV) sunlight. This damage involves the formation of a cyclobutane ring between two adjacent thymine bases in a DNA strand, distorting the DNA structure.

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6,4-Dithymine Photoproduct

A type of DNA damage caused by radiation, particularly ultraviolet (UV) sunlight. This damage forms a covalent bond between two thymine bases in a DNA strand, altering the normal DNA structure.

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Chemical DNA Synthesis

The process of synthesizing DNA molecules in a laboratory setting. It utilizes protected nucleotides and an automated synthesis cycle to create specific DNA sequences.

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Protected Nucleotides

Chemically modified nucleotides used in DNA synthesis to prevent unwanted reactions during the synthesis process. Protecting groups allow the synthesis to occur in a controlled manner, preventing side reactions and ensuring the desired sequence is created.

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What are nucleic acid vaccines?

Nucleic acid vaccines are a new type of vaccine that uses genetic material to induce an immune response.

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How do viral-vector vaccines work?

Viral-vector vaccines use a modified virus to deliver the genetic material that encodes the antigen of interest.

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How do mRNA vaccines work?

mRNA vaccines use a messenger RNA molecule to instruct cells to produce the antigen.

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What are the challenges of delivering mRNA?

mRNA is chemically unstable and highly negatively charged, requiring special delivery mechanisms like lipid nanoparticles to get it into cells.

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What are the advantages of nucleic acid vaccines?

Nucleic acid vaccines can be designed and produced very quickly, making them ideal for responding to emerging infectious diseases.

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What are some disadvantages of nucleic acid vaccines?

Current nucleic acid vaccines often need to be stored at cold temperatures, limiting their accessibility in some settings.

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What are some future applications of nucleic acid vaccines?

Researchers are exploring potential applications for nucleic acid vaccines against latent viruses, cancer, and even personalized therapies.

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What is the significance of nucleic acid vaccines?

Nucleic acid vaccines offer a new and promising approach to vaccine development, with the potential to revolutionize how we protect ourselves from infectious diseases.

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Study Notes

Lecture 1 - Building Blocks of Nucleic Acids

  • Nucleic acids are made up of nucleobases, nucleosides, and nucleotides.
  • Nucleobases are nitrogen-containing heteroaromatic molecules (derivatives of pyrimidine or purine).
  • Nucleosides are composed of a nucleobase linked to a pentose sugar (ribose or deoxyribose).
  • Nucleotides are composed of a nucleobase, a pentose sugar, and one or more phosphate groups.
  • Nucleobases are planar or almost planar structures.
  • Nucleobases absorb UV light around 250-270 nm.
  • Excited states of common nucleobases decay rapidly due to radiationless transitions, which effectively protects genetic material.
  • Hydrogen bonds are important for base pairing.
  • Acid dissociation constant (Ka) is a measure of the strength of an acid.
  • pKa = -log Ka
  • Strong acids have high Ka and low pKa values.
  • Weak acids have low Ka and high pKa values.
  • Purine bases include adenine and guanine, they are good H-bond donors and acceptors.
  • Pyrimidine bases include cytosine, thymine, and uracil, they are good H-bond donors and acceptors.
  • Tautomerism is discussed (keto-enol and lactam-lactim).
  • Ribofuranose (ribose) and deoxyribose are discussed.
  • β-N-Glycosidic bond is important for linking nucleobases to the sugar.
  • The bond is formed to position N1 in pyrimidines and to position N9 in purines.
  • This bond is stable toward hydrolysis, especially in pyrimidines.

Lecture 2 - Structure of Nucleic Acids

  • Nucleic acid strands interact in different ways to form stable structures e.g., DNA/RNA dimers, trimers, and G-quadruplex.
  • Watson-Crick base pairs are the predominant interactions in double-stranded DNA (A with T, G with C).
  • Hoogsteen base pairs are formed by hydrogen bonds with more than two bases.
  • Hairpins, cruciforms, and other interactions form more complex structures.
  • DNA denaturation involves breaking hydrogen bonds; UV absorbance increases.
  • RNA often forms more complex structures than DNA.
  • RNA duplex is more stable than DNA at higher temperatures, and more robust to degradation.
  • DNA strand separation, elongation, and termination are discussed at length.
  • Polymerase Chain Reaction (PCR) is a method used to replicate DNA in a lab setting.
  • Steps involved in PCR are discussed.

Lecture 3 - DNA replication

  • DNA replication is the process of copying DNA.
  • The process of DNA replication in nature involves initiation, elongation, and termination.
  • The method of replicating DNA in vitro (PCR) is described.
  • DNA modification by biochemical processes (epigenetics) is described.
  • DNA modification by exogenous damage (mutations) is described.

Lecture 4 - DNA (chemical) synthesis and sequencing

  • Chemical synthesis of DNA uses protected nucleotides and special coupling cycles.
  • Sanger sequencing, Illumina sequencing, and nanopore sequencing are described.

Lecture 5 - DNA Transcription

  • DNA is converted into RNA through transcription.
  • The central dogma of molecular biology is explained.
  • Transcription initiation, elongation, and termination are described.
  • Post-transcriptional processing: sequence capping and splicing are described.
  • Reverse transcription is mentioned.

Lecture 6 - Bioinformatics

  • Bioinformatics is the study of biological data.
  • Various "omics" approaches (genomics, transcriptomics, proteomics) are used.
  • Common bioinformatics tasks such as sequence alignment and database searching are described.
  • Online databases such as GenBank and UniProt are introduced.

Lecture 7 - RNA Translation

  • RNA translation is the process of converting RNA into proteins.
  • Codons, codon tables, codon usage are explained.
  • tRNA construction and the wobble hypothesis are described.
  • Ribosome structures, translation process, and polysomes are covered.

Lecture 8 - Recombinant Technology

  • Recombinant technology involves creating modified DNA that doesn't naturally occur.
  • Steps in recombinant protein expression and induction using IPTG are listed.

Lecture 9 - Newest research

  • Nucleic-acid based vaccines are further explored.
  • De novo protein design, and research from the Rhys Lab (Ben Orton) are mentioned.

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