Chapter 9 Quiz

Two techniques have been utilized to understand the proteome. The one that has the drawback of not detecting low abundance proteins is___________ while the technique that is more thorough but much more difficult to set up is ____________.

2-dimensional electrophoresis with mass spectrometry; protein array

Which of the following is NOT an example of comparative genomics?

A comparison of the gene expression profile of Arabidopsis plants grown at 25 degrees centigrade with the profile of plants grown at 35 degrees centigrade.

Which of the following can be determined from a metagenomic analysis of human gut microflora. A- Organisms responsible for the production of unique previously unknown chemicals can be characterized by examining the ORF sequences present in the human gut metagenome. B- Evolutionary relationships of the organisms found in the metagenome can be determined by comparing the 16S ribosomal RNA sequences found. C- The genotype of the human at all of the critical disease causing haplotypes can be determined from the DNA sample obtained from fecal samples obtained from a human's gut. D- The species and abundance of all of the bacteria, archea, and other organism present can be determined by comparing the assembled genomic sequences obtained from pyrosequencing the entire DNA sample obtained from a sample.

A, B, C, and D are all applications of human gut metagenomic analysis

Polymerase chain reaction (PCR) is a technique for making essentially unlimited amounts of a specific double stranded DNA sequence in a test tube using DNA polymerase. Place the steps of a PCR reaction shown below in the proper sequence. A- Use thermostable DNA polymerase to extend the DNA strand from the primer. B- Separate the strands of the template DNA by heating the reaction to a relatively high temperature. C- Reduce the temperature and allow the forward and reverse primers that are complementary to the two strands to anneal at the complementary sequence.

B>C>A

Which of the following is(are) NOT applications of bioinformatics. A- finding genes within a genomic sequence aligning sequences in databases to determine how similar they are (or their degree of similarity) B- predicting the structure and function of gene products C- describing the interactions between genes and gene products at a global level within the cell. D- using polymerase chain reaction to determine the function of a set of genes in the genome. E- postulating phylogenetic relationships for sequences from different species.

D only

A valuable tool for assessing the transcriptome (i.e., the genes actively expressed in cells or tissues in response to specific signals or environmental changes) is

DNA mircoarrays or DNA chips

Why is the eukaryotic proteome so much larger than the number of genes found in an organism?

Differential intron splicing can produce more than one protein product from a gene, and proteins are further posttranslationally modified.

As a result of the human genome sequencing project we now know that there are regions on the chromosomes which have higher than average densities of genes. Which of the following is NOT a characteristic of these high density regions of the genome?

High gene density regions tend to organize around the outside of the nucleus nearer the nuclear membrane

Collection of information about the alleles present at a broad range of SNPs within the genome of 4 human populations that have been native to specific regions of the world in relative isolation, i.e. Asians, Africans, Northern Europeans, and South Americans have revealed certain blocks of genetically linked SNPs called haplotype blocks that are much larger than other haplotype blocks, and that are specific to either some or to all of the populations above. One such haplotype block contains a gene for Lactase, the enzyme for degrading milk sugar. In the Northern European population, a haplotype block containing lactase contains a mutant lactase form that is differently regulated, such that lactase is persistent into adulthood, and those individuals in the population that do not inherit this mutation are lactose intolerant as adults. What is the interpretation of these results?

Large haplotype blocks indicate events that have occurred relatively recently in evolutionary time, and define chromosomal regions containing a gene that is being actively selected for. Large haplotype blocks are evidence for linkage disequilibrium in these human populations. A lactase gene that persists into adulthood provides a selective advantage to humans who consume dairy products into adulthood, and this selective advantage can be demonstrated at the population genetics level using haplotype analysis.

The analysis of the genomes of the community of all microorganisms found in a given environment is referred to as __________. What does this technology allow us to do?

Metagenomics; Investigate the types and abundance of all microorganisms in the sample regardless of whether they can be grown in culture or not.

Viral diseases are among the most difficult diagnoses to obtain with certainty. Which genomic technique(s) has (have) greatest potential to efficiently identify known and novel viruses that can cause disease?

Oligonucleotide array for known virus specific genes

Utilizing transcriptome analysis to determine how a patient will respond to a given drug is one of the applications of

Pharmacogenomics

_________ is a comparative genomic technique that allows the determination of DNA sequences that change in copy number in the genome during the development of the disease state or in other situations.

Representational Oligonucleotide Microarray Analysis (ROMA)

For many types of cancerous tumors, different genes are expressed or not expressed in individual tumors, even though the gross tumor morphology and histology remains unchanged from one patient to the next. How can this individual molecular tumor phenotype be characterized and used in the treatment of cancer?

The gene expression profile for a specific tumor can be correlated with a database of information on what drugs have been shown to be effective in treating tumors expressing specific genes. This would provide better and more information to assist patients in determining the therapy that would be most successful.

Proteomics is the cataloging and analysis of all of the proteins made by a cell. Which of the following is not a goal of proteomics?

To determine the sequences of each protein found in a cell, to identify every protein in the proteome, and to enter the data into databases. To analyze globally protein levels in different cell types and at different stages in development. To understand the biochemical functions of all of the proteins in the proteome.

RNAi is a mechanism used to prevent specific gene expression in eukaryotic cells. Which of the following steps is(are) NOT a part of the RNAi process?

binding of a small regulatory RNA to mRNAs to prevent the ribosome from translating the double-stranded region of the mRNA

Beedle and Tatum made mutations in the Neurospora selected mutants with a particular genotype, and then identified and mapped the genes which have now been sequenced. This is an example of __________. When the genome of Neurospora was sequenced, the sequence of certain genes of unknown function was revealed. These specific gene sequences were removed from the genome, and the phenotype generated by such removal was determined. This is an example of ___________.

forward genetics; reverse genetics

Studies of gene function often use the approach of systematically inactivating or silencing genes. These "knockouts" are termed _______ mutations.

loss-of-function

As a result of the human genome sequencing project we now know that there are regions on the chromosomes which have lower than average densities of genes. Which of the following is NOT a characteristic of these high density regions of the genome?

low gene density regions tend to have shorter intron sequences

It is possible to examine the expression of all 6000 plus genes in the yeast genome (global expression analysis) during sporulation versus during normal growth. From such an experiment we can learn that there are specific genes expressed only during specific stages of sporulation. There are other specific genes expressed only during sporulation, and there are still other genes that are never expressed during sporulation. This is an example of data collected using a(n) __________.

microarray

The complete set of proteins in a cell is its

proteome

The execution a microarray or gene chip experiment for transcriptome analysis requires all of the following steps EXCEPT

sequence of genome of the organisms to be utilized

The sequence of the genome of the alga Chlamydomonas reinhardii was recently sequenced. Initially, the open reading frames (ORFs) in the genome were determined, and then the potential function of each ORF identified by using the BLAST search utility at NCBI to determine which genes from other organisms had sequences most closely related to those of the genes from Chlamydomonas. This is an example of using a _____________ to determine gene function.

sequence similarity search

The number of mRNA transcripts in a cell fluctuate over time as the pattern of gene expression changes. These transcripts are collective referred to as

the transcriptome

Homologous recombination is the critical process used to construct a gene knockout in which organism(s)?

yeast & mouse