Analyzing Cells, Molecules, and Systems

In the process of cell fractionation by centrifugation, what is the expected order of pellet formation when the centrifugation speed is progressively increased?

What is the primary principle behind separating proteins using gel-filtration chromatography?

In SDS polyacrylamide-gel electrophoresis (SDS-PAGE), what is the function of the detergent sodium dodecyl sulfate (SDS)?

What is the typical number of times normal human fibroblasts can divide in culture before they stop, a process known as replicative cell senescence?

Which technique is most suitable for separating DNA molecules that are less than 500 nucleotides long and differ in length by as little as a single nucleotide?

What is a key difference between a genomic DNA library and a cDNA library?

The polymerase chain reaction (PCR) is an iterative process. If a single double-stranded DNA molecule is the starting template, how many double-stranded DNA molecules that are the exact length defined by the primers are first generated?

In mass spectrometry for protein identification, what is the role of the MALDI ion source?

What is the primary advantage of using tandem mass spectrometry (MS/MS) over standard mass spectrometry (MS)?

What is the defining characteristic of a 'dominant-negative' mutation?

A complementation test is performed by mating two individuals that are homozygous for different recessive mutations that produce the same phenotype. What does it mean if the offspring show a normal (wild-type) phenotype?

What type of cloning vector is based on the F plasmid of E. coli and is preferred for stably maintaining very long DNA sequences up to 1 million nucleotide pairs?

What is the primary function of a reporter gene like GFP (green fluorescent protein) when its coding sequence is placed under the control of a gene's cis-regulatory sequences?

The CRISPR/Cas9 system has been adapted for genome engineering. What is the direct result of the Cas9 protein making a double-strand break in a target gene in the absence of an engineered repair template?

In the technique of epistasis analysis for a biosynthetic pathway, if a double mutant carrying null mutations in gene A and gene B shows the same phenotype as a single mutant with a null mutation in gene A, what can be concluded about the order of gene function?

According to the text, what is the approximate resolution of a modern electron microscope for biological objects, and how does this compare to a conventional light microscope?

What is the primary purpose of using heavy-metal salts like osmium, lead, and uranium in preparing thin sections for transmission electron microscopy (TEM)?

What are single-nucleotide polymorphisms (SNPs)?

The analysis of the ArgR transcription regulator in E. coli is used as a problem in the chapter. If ArgR is a transcription repressor that is modulated by arginine, what is the expected effect of abundant arginine on ArgR's binding to its regulatory sequences?

What is the primary reason that a collection of mutant strains, where each gene is systematically deleted, is considered an invaluable resource for investigating gene function?

In the technique of affinity chromatography, how is the purified protein typically eluted from the column after it has bound to the matrix?

What is the typical difference in nucleotide sequence between the genomes of any two humans?

The text describes an experiment where a 480-nucleotide-pair section of the Eve gene's regulatory region was placed in front of a lacZ reporter gene. What was the observed outcome in Drosophila embryos?

What is the phenomenon called where a cell culture, after a finite number of divisions, stops proliferating due to excessive stimulation under culture conditions?

In a BLAST search result for comparing two protein sequences, what does a very low Expectation (E) value, such as e-111, indicate?

What is the purpose of using RNA interference (RNAi) in experimental biology?

What is a major limitation of two-dimensional gel electrophoresis for separating proteins?

The text describes an ultracentrifuge that can rotate at speeds of up to 80,000 rpm. What is the approximate maximum force this can generate relative to gravity?

What technique uses DNA hybridization with labeled probes to determine the specific locations of genes on isolated chromosomes?

In the mathematical analysis of a simple transcriptional activator (protein A) binding to a promoter (pX), what is the relationship between the equilibrium constant (K), the association rate constant (kon), and the dissociation rate constant (koff)?

What is the primary role of β-mercaptoethanol in the sample buffer for SDS-PAGE?

How can the CRISPR/Cas9 system be modified to activate or repress a gene without cutting the DNA?

In two-dimensional gel electrophoresis, what property of proteins is used for separation in the first dimension?

What is the term for a cell that is capable of proliferating indefinitely in culture and can be derived from normal cells by providing them with the gene for the catalytic subunit of telomerase?

When performing quantitative RT-PCR to measure mRNA levels, what is the initial enzymatic step?

What is a 'haplotype block' in the context of human genetics?

What is the defining feature of 'insertional mutagenesis'?

When analyzing a gene regulatory network, what is the typical function of a rapid negative feedback loop?

What distinguishes the method of equilibrium sedimentation from velocity sedimentation in an ultracentrifuge?

What is the primary purpose of tandem affinity purification (TAP) tagging?

What is the key insight about protein lifetime (τ) and the response time of a gene regulatory system that is revealed by mathematical analysis?

According to the description of Illumina sequencing, how is the entire genome sequence reconstructed after billions of short DNA fragments are sequenced in parallel?

What is the primary function of the enzyme reverse transcriptase in the context of creating a cDNA library?

What is the typical resolution of structured illumination microscopy (SIM), a superresolution fluorescence technique?

The text discusses how a delayed negative feedback loop can generate oscillations. This is demonstrated by comparing a three-stage loop to a five-stage loop. What is the key finding?

What is the purpose of using a protease like trypsin or collagenase when isolating cells from animal tissues?

In the context of the mathematical analysis of gene regulation, what is an 'incoherent feed-forward motif'?

What is the primary advantage of single-molecule real-time (SMRT) sequencing compared to Illumina sequencing?

What is a 'knockout mouse'?

How does Western blotting (immunoblotting) allow for the detection of a specific protein in a complex mixture?