Molecular Biology Quiz

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Questions and Answers

What is the reason for the spontaneous depurination of purines in a cell each day?

The N-glycosyl linkage between deoxyribose and purines hydrolyzes. (correct)

The enzyme deaminase continually acts on purines.

Purines are inherently unstable within the cell.

It is a result of the high reactivity of purines.

Which feature of RNA contributes to its lower stability compared to DNA?

Higher molecular weight of RNA.

Absence of a hydroxyl group at the 2' position.

Presence of two phosphate groups.

Presence of a hydroxyl group at the 2' position. (correct)

What is one of the types of DNA damage that Nucleotide Excision Repair (NER) is capable of repairing?

Inter-strand crosslinks

Pyrimidine dimers (correct)

Base mismatches

Single-strand breaks

What is the consequence of 15 minutes of sun exposure on keratinocytes?

Up to 10^5 lesions may arise. Signup and view all the answers

Which of the following agents is known to cause crosslinking in DNA?

Cisplatin Signup and view all the answers

What is the primary purpose of the demultiplexer in the sequence processing workflow?

To sort data by index into different samples. Signup and view all the answers

Which method of library preparation is characterized by the use of transposomes?

Tagmentation Signup and view all the answers

What is a downside of the amplification method for library preparation?

It is only effective if flanking regions are known. Signup and view all the answers

What is the role of the adapter sequences in library preparation?

To facilitate the binding of transposases. Signup and view all the answers

Which of the following statements about sequencing by synthesis is TRUE?

It includes both library preparation and sequencing steps. Signup and view all the answers

What is one of the major concerns with using CRISPR/Cas9 in gene editing related to its specificity?

Sequence-dependent off-targeting Signup and view all the answers

What effect can a Cas9 mutant with lowered off-target activity have on gene editing?

Decrease the risk of unintended edits Signup and view all the answers

What is one possible consequence of introducing a plasmid encoding Cas9 into the genome?

Integration into the genome Signup and view all the answers

How can lowering the expression level of Cas9 affect its functionality?

It reduces off-target cleavage risks. Signup and view all the answers

What should be considered when designing gRNA to minimize off-target effects?

The location of mismatches relative to the PAM sequence Signup and view all the answers

What is a major challenge in metagenomics when characterizing microorganism communities?

Representing the true composition of the community Signup and view all the answers

Which method allows for the analysis of specific regions in microbial communities?

16S amplicon sequencing Signup and view all the answers

In cancer genome sequencing, what does SNP stand for?

Single nucleotide polymorphism Signup and view all the answers

What is a primary benefit of using RNA sequencing (RNA-seq)?

It provides insights into gene expression Signup and view all the answers

Which of the following best describes amplicon sequencing?

A technique that targets specific DNA regions Signup and view all the answers

What is a significant outcome of analyzing 16S amplicon sequencing data in agriculture?

Revealing shifts in microbial populations under environmental stress Signup and view all the answers

What role does the PAM sequence play in the function of cas9?

It is recognized by cas9 to initiate DNA binding and cutting. Signup and view all the answers

Why is bulk experimentation used in genomic studies?

To observe mixed outcomes from thousands or millions of cells Signup and view all the answers

Which statement accurately reflects the cutting capability of cas9?

Cas9 cuts DNA in a precise manner three nucleotides upstream of PAM. Signup and view all the answers

What type of regions does PacBio sequencing aim to cover for maximum resolution?

Variable and conserved regions Signup and view all the answers

What comes as a consequence of genome rearrangements in cancer genomes?

Extreme genome aberrations and drug adaptation Signup and view all the answers

What is the significance of combining crRNA and tracrRNA into a single guide RNA (gRNA)?

It simplifies the genome editing process. Signup and view all the answers

Which cas9 ortholog is predominantly discussed in the context of genome editing?

Streptococcus pyogenes cas9 Signup and view all the answers

In what areas is metagenomics applied?

Research fields like ecology and biotechnology Signup and view all the answers

What was a key outcome of the research conducted by Jinek and Charpentier in July 2012?

They proposed a genome editing tool utilizing cas9, crRNA, and tracrRNA. Signup and view all the answers

What is the primary function of RNF8 in DNA damage signaling?

Ubiquitination of histones Signup and view all the answers

During which phases of the cell cycle is homologous recombination (HR) possible?

S phase and G2 Signup and view all the answers

Which of the following proteins are recruited to double-strand breaks (DSBs) during non-homologous end joining (NHEJ)?

DNA-PK and Ku70/Ku80 Signup and view all the answers

What happens to the levels of gammaH2AX and BRCA1 after silencing RNF8?

GammaH2AX levels remain the same while BRCA1 levels decrease Signup and view all the answers

Which proteins play a role in the short-range resection of DSBs during homologous recombination?

PARP1 and MRN Signup and view all the answers

What is the role of RAD51 during homologous recombination?

To displace RPA from ssDNA Signup and view all the answers

What are the consequences of Ku70/Ku80 binding to DSB ends?

Activation of Artemis for end processing Signup and view all the answers

During which step of homologous recombination do polymerases extend the invading strand?

Double Holliday junction formation Signup and view all the answers

Study Notes

DNA damage

DNA damage occurs constantly from both exogenous and endogenous factors.
Exogenous factors include exposure to mutagens like benzo-a-pyrene from smoke and UV light, which cause damage.
Radiation, like Chernobyl radiation, and chemotherapeutic agents also cause DNA damage.
Endogenous factors include hydrolysis (damaging through water), reactive oxygen species (ROS) and radicals, and replication/recombination errors.
The cell experiences approximately 30,000 endogenous DNA lesions per cell daily, mainly from hydrolysis.

DNA repair mechanisms

Base damage is repaired through base excision repair (BER).
Nucleotide damage from bulky adducts or bipyrimidine photoproducts is repaired through nucleotide excision repair (NER).
Interstrand crosslinks are repaired through NER or interstrand crosslink repair (ICLR).
Single strand breaks are repaired through single strand break repair (SSBR).
Double strand breaks are repaired through homologous recombination (HR) or non-homologous end joining (NHEJ).
Mismatch repair (MR) fixes mismatches during replication.

DNA repair defects

Mutations in DNA repair pathways can lead to a variety of disorders and increased susceptibility to cancer.
Xeroderma pigmentosum (XP) due to problems in NER, makes people vulnerable to ultraviolet (UV) light.

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Description

Test your knowledge on key molecular biology concepts such as DNA damage, RNA stability, and library preparation techniques. This quiz covers various important topics including spontaneous depurination, Nucleotide Excision Repair, and sequencing methods.