Molecular Biology of Cell Cycle and Signaling

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Questions and Answers

What is the primary function of the p53 protein in the cell cycle?

Inducing apoptosis in all cells

Promoting cell cycle progression

Regulating the G1-to-S checkpoint (correct)

Stimulating growth factor production

How does p53 contribute to DNA repair and cell cycle regulation?

By activating oncogenes that overlook DNA damage

By inhibiting the expression of repair genes

By inducing the expression of CDK inhibitor p21 (correct)

By promoting rapid entry into the S phase

What happens to Rb when p21 is expressed?

Rb remains unphosphorylated to inhibit E2F (correct)

Rb is phosphorylated to promote S phase

Rb is degraded to prevent any cell cycle arrest

Rb activates E2F leading to cell cycle progression

Which statement best describes the outcome of severe DNA damage in cells?

Cells may undergo apoptosis to avoid further mutations Signup and view all the answers

What is a feature of steroid signaling compared to extracellular protein signaling?

Steroid signaling involves direct entry into the nucleus Signup and view all the answers

What is the purpose of ATAC-seq in genomic studies?

To identify accessible chromatin regions, such as promoters and enhancers. Signup and view all the answers

Which factor primarily defines the activity state of a gene in relation to chromatin structure?

The sensitivity of the promoter to enzymatic digestion. Signup and view all the answers

How do histone modifications affect chromatin structure?

They lead to the addition or removal of specific chemical groups on histone tails. Signup and view all the answers

What is the role of Tn5 transposase in ATAC-seq?

To cut DNA at high frequency and insert sequencing primers. Signup and view all the answers

What does the remodeling of chromatin typically involve?

Repositioning or removal of nucleosomes by chromatin remodeling enzymes. Signup and view all the answers

What does a cotransduction frequency of 0.29 indicate for the genes arg1 and ser3?

The genes are closely linked. Signup and view all the answers

Which process allows for the uptake of DNA from the environment by recipient bacteria?

Transformation Signup and view all the answers

What conclusion can be drawn about the distance between arg1 and trp2 genes?

They are more than 2 minutes apart. Signup and view all the answers

Which of the following methods does NOT involve the transfer of genes between bacteria?

Replication Signup and view all the answers

What is the primary difference between vertical gene transfer and horizontal gene transfer?

Vertical gene transfer involves inheritance across generations. Signup and view all the answers

What are the factors that can contribute to the origin of cancer?

Intrinsic factors, extrinsic factors, and hereditary factors Signup and view all the answers

What is the role of cyclins in the cell cycle?

To activate cyclin-dependent kinases (CDKs) Signup and view all the answers

Which phase of the cell cycle is characterized by cells preparing for replication?

G1 phase Signup and view all the answers

What happens at the G1-to-S checkpoint?

Cells that receive improper signals will stop division Signup and view all the answers

Which environmental factor has been correlated with an increased risk for certain types of cancer?

Tobacco smoke Signup and view all the answers

Which of the following is true about molecular signatures of cancer-associated mutations?

They appear non-age related for most mutations Signup and view all the answers

What is a key requirement for cell proliferation?

Increase in cell size and activation of cell cycle genes Signup and view all the answers

What is the role of growth factors in the extracellular signals regulating the cell cycle?

They activate genes required for cell growth and progression Signup and view all the answers

What type of mutation can occur due to non-homologous end-joining (NHEJ)?

Indels (insertions or deletions) Signup and view all the answers

What are the components required for the CRISPR/Cas9 active complex?

Cas9, crRNA, and tracrRNA Signup and view all the answers

Which process allows for precise gene editing using the CRISPR/Cas system?

Homology directed repair (HDR) Signup and view all the answers

Which of the following statements about the CRISPR/Cas system is accurate?

It generates double strand breaks in eukaryotic genomes. Signup and view all the answers

What is the role of PAM (Protospacer Adjacent Motif) in the CRISPR/Cas9 system?

It facilitates the binding of Cas9 to target DNA. Signup and view all the answers

Who were recognized with the Nobel Prize in 2020 for their work on the CRISPR/Cas system?

Emmanuelle Charpentier and Jennifer Doudna Signup and view all the answers

What process occurs in bacteria as a defense mechanism against bacteriophage?

Spacer integration into CRISPR locus Signup and view all the answers

How is double strand break (DSB) induced in targeted sites using CRISPR/Cas9?

By targeting a specific PAM sequence Signup and view all the answers

What is the primary purpose of expressing enzymes in response to food sources?

To utilize the food when it is present Signup and view all the answers

Which of the following statements best describes how gene expression is regulated in eukaryotes?

Pre-mRNA undergoes RNA processing before becoming mRNA Signup and view all the answers

How does the expression of repressible genes typically change?

They are turned off in response to specific factors Signup and view all the answers

What role do transcription factors play in gene expression?

They enhance or inhibit the ability of RNA polymerase to transcribe genes Signup and view all the answers

Why is it inaccurate to assume that a gene being transcribed means a functional protein is present in a cell?

mRNA processing can prevent protein formation Signup and view all the answers

What characterizes constitutive gene expression?

Expression is continuously high regardless of environmental conditions Signup and view all the answers

What is the function of an activation domain (AD) in transcription factors?

It enhances the transcription process by RNA polymerase Signup and view all the answers

How does the expression of genes differ in response to pathogens compared to nutrients?

Pathogen-resistance proteins are required only when challenged Signup and view all the answers

In what way can gene expression levels be modulated?

They can be increased or decreased, even if constitutive Signup and view all the answers

What is one outcome of deregulated gene expression in multicellular organisms?

Uncontrolled cell proliferation, potentially leading to cancer Signup and view all the answers

What is the role of the lacY gene in lactose utilization?

It encodes Lac Permease for lactose transport. Signup and view all the answers

What is the effect of adding lactose in the presence of low glucose on lacZ and lacY expression levels?

There is a 1000-fold increase in their expression. Signup and view all the answers

Which of the following describes the function of lacI and lacO mutants?

They lead to high levels of lacY and lacZ expression regardless of lactose presence. Signup and view all the answers

What is the primary function of the lacP promoter within the lac operon?

It acts as a binding site for the sigma factor. Signup and view all the answers

How can one test whether lacI or lacO encodes a protein or a DNA binding site?

By knocking out the gene and analyzing the downstream effects. Signup and view all the answers

What happens to Rb when p21 is activated by p53?

Rb remains unphosphorylated and inhibits E2F. Signup and view all the answers

How does p53 contribute to the cellular response to DNA damage?

It activates genes that control apoptosis and DNA repair. Signup and view all the answers

What is a potential consequence of mutations in TP53?

Premature entry of cells into the cell cycle. Signup and view all the answers

Which statement accurately reflects the role of signaling pathways in cell proliferation?

Extracellular signaling pathways are typically more complex than steroid signaling pathways. Signup and view all the answers

What is a key role of the Wnt signaling pathway in cell growth?

It is involved in the transduction of extracellular signals for growth. Signup and view all the answers

What is the consequence of both copies of a tumor suppressor gene being mutated?

Loss of function mutations lead to cancer. Signup and view all the answers

Which statement about tumor suppressor mutations is true?

Both gene copies must be mutated to have an effect. Signup and view all the answers

Which type of mutation requires only one copy of a gene to be mutated?

Dominant oncogenic mutation Signup and view all the answers

How do mutations in somatic cells affect germ cells?

Somatic mutations do not affect germ cells. Signup and view all the answers

Which mechanism can lead to cancer via mutations?

Both intrinsic and extrinsic mechanisms. Signup and view all the answers

What is the purpose of using gene-specific primers in the process described?

To ensure that specific transcripts are amplified Signup and view all the answers

What is a primary advantage of using real-time PCR compared to traditional gel PCR?

Real-time PCR does not require gel electrophoresis Signup and view all the answers

Which step is essential for the detection of a specific RNA transcript using in situ hybridization?

Synthesis of a complementary probe labeled with a detectable marker Signup and view all the answers

What role does alkaline phosphatase play in the in situ hybridization process?

It converts a colorless substrate into a visible product Signup and view all the answers

What is the main advantage of using RNA-seq for transcript analysis?

It provides direct analysis of transcripts without requiring cloning Signup and view all the answers

In the context of RNA extraction, what is the significance of using a fixed embryo for in situ hybridization?

It allows for the preservation of spatial RNA distribution Signup and view all the answers

During RNA-seq, what happens after cDNA generation from an RNA sample?

The cDNA is sequenced directly using next-generation sequencing Signup and view all the answers

Which of the following is a crucial requirement for successfully hybridizing a probe to target mRNA?

The probe must be single-stranded and labeled with a reporter Signup and view all the answers

What is the primary function of the eyeless gene in transgenic research?

It is responsible for generating ectopic eyes. Signup and view all the answers

What is the primary role of microRNAs in gene expression?

They prevent the translation or cause degradation of specific mRNAs. Signup and view all the answers

Which component is NOT required for the expression of human growth hormone in E. coli?

Beta-lactoglobulin enhancer Signup and view all the answers

How does RNA interference (RNAi) mainly facilitate gene regulation?

By introducing in vitro synthesized double-stranded RNAs into cells. Signup and view all the answers

What role does glyphosate play in genetically modified crops?

It inhibits the EPSPS enzyme in plants. Signup and view all the answers

What is the significance of the hairpin structure formed in microRNAs?

It allows the formation of a ribonucleoprotein complex for gene silencing. Signup and view all the answers

What is a significant advantage of using transgenic sheep for human protein production?

They are capable of post-translational modifications. Signup and view all the answers

Which statement about genetically modified organisms (GMOs) is true?

GMOs can contribute to disease resistance in crops. Signup and view all the answers

Which of the following describes a potential outcome when an mRNA has high complementarity with a microRNA?

The mRNA will be completely degraded. Signup and view all the answers

What limits the effectiveness of RNAi as a gene regulation tool?

Variable knockdown effects and possible off-target effects. Signup and view all the answers

Which of the following describes a major obstacle in producing certain human proteins in E. coli?

Inability to perform post-translational modifications Signup and view all the answers

What process is used to produce antithrombin III in transgenic sheep?

Injection of modified DNA into sheep ova Signup and view all the answers

What characteristic distinguishes microRNAs from other types of RNAs?

They are small and regulate gene expression through rRNA mechanisms. Signup and view all the answers

Why might not all genes be regulated by microRNAs in eukaryotes?

Specific genes may lack complementary target sites in their 3’ UTR. Signup and view all the answers

What is the primary benefit of transgenic crops designed to carry bacterial EPSPS?

Resistance to herbicides, allowing for easier weed control. Signup and view all the answers

Which feature of microRNAs allows them to regulate multiple genes simultaneously?

They have partial complementarity with multiple mRNAs. Signup and view all the answers

Study Notes

Bacterial and Organellar Genetics

Tree of Life includes Bacteria, Archaea, and Eukaryotes. Archaea domain is missing from the diagram provided.
Eukaryotes have multiple, paired, linear chromosomes (in diploids).
Bacteria have single, circular chromosomes.
Eukaryotes have two copies of each gene (in diploids); Bacteria have one copy per gene.
Recombination in eukaryotes includes sex, meiosis, segregation, independent assortment, and crossing over. Bacterial recombination includes conjugation, transformation, and transduction.
Bacteria are highly variable in size, structure, habitat, and metabolism.
Bacterial chromosomes differ from eukaryotic chromosomes in several aspects, including DNA location, lack of membrane-bound organelles, and DNA tertiary structure.
Recombination, concept of “species” is more vague for bacteria, individuals may show high variability in genes.
Bacteria, as a common ancestor with eukaryotes, share some characteristics for DNA technology, but detail differences exist.
Escherichia coli is used as a standard bacterium in lab studies, found normally in mammals and birds; also, usually harmless but some pathogenic strains exist.
Bacteria can be grown in liquid culture or on agar plates.
Biofilms are groups of microorganisms that adhere to a surface and reside in a secreted matrix.

Conjugation

Bacteria transfer genetic material through cell-to-cell contact.
F+ strains act as donors, and F– strains act as recipients, they contain the F-factor plasmid (a minichromosome) that replicates independently of the main chromosome.
Plasmids may contain genes for resistance to antibiotics.
F+ can only transfer the F plasmid to a recipient F- cell.
Hfr strains have the F factor integrated into the main bacterial chromosome, allowing for the transfer of host chromosomal genes to the recipient.

Transduction

Accidental transfer of genetic material occurs when a bacteriophage incorporates bacterial DNA into its phage capsid.
Genes are located closer together that are more likely to be co-transduced.
Cotransduction frequency = (# of transducing phage containing both genes) / (# of transducing phage containing one gene)
d = distance between two genes; L = size of the chromosome piece in minutes.

Transformation

Bacteria pick up free DNA from the environment (not via physical contact).
Recombinant bacterial colonies can be selected on media.
The presence of a marker gene can help identify cells that have been transformed.

Auxotrophs

Auxotrophs: cannot grow in the absence of a specific chemical substance required for their growth. Specifically refers to carbon source mutants.
Often involve sugars.

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Description

Explore the intricate roles of proteins like p53 and Rb in the regulation of the cell cycle and DNA repair mechanisms. Understand key concepts such as chromatin structure, histone modifications, and the impact of steroid signaling. This quiz covers essential molecular biology topics crucial for advanced studies in genetics and cell biology.