Ch 20 - Genomics and Proteomics

Thanks to metagenomic studies, we now know that for every one human cell you have in your body, there are _____ bacterial cells.

10 These bacteria, along with those that inhabit the skin and other parts of the human body, are termed the human microbiome.

All these are benefits of having the sequenced human genome, EXCEPT: association studies of genetic markers and disease. studies on the evolution of humans. examining genetic variation in Homo sapiens. 100 percent accuracy in predicting disease risk.

100 percent accuracy in predicting disease risk. Genome sequencing can only indicate if a person is at risk for developing a disease, but not a guaranteed diagnosis.

What is the effect of crossing over within a haplotype?

Crossing over breaks up the association of variants within an existing haplotype. Crossing over breaks up the association of variants within an existing haplotype.

What has largely replaced the use of restriction enzyme mapping?

DNA sequencing DNA sequencing is able to provide molecular markers that can be used to construct and refine genetic maps.

What is the definition of a paralog?

Homologous genes that occur in the same species (arising by duplication of a single gene in the evolutionary past). Paralogs are homologous genes found within the same species.

What is the definition of a heat map?

It is a visual representation of a continuous variable like the expression of a gene. A heat map is a visual representation of a continuous variable with the shade of the color indicating the value of the variable.

What is the definition of the proteome?

It is the identification of all the proteins encoded by the genome. The proteome is the entire complement of proteins that is or can be expressed by a cell, tissue, or organism.

Knowledge of a protein's structure is important because of all of these EXCEPT: It provides the amino acid sequence of the protein. The structure provides information about other molecules that interact with the protein. Knowledge of a protein's structure often suggests targets for potential drugs that might interact with the protein. Structure often provides important information about how a protein functions.

It provides the amino acid sequence of the protein. The amino acid sequence of a protein is an indication of its structure, while determining the sequence from structure is not straightforward.

How is mass spectrometry a useful tool for researchers studying the Human Proteome Project?

It would identify each protein and tell you how much of it was in your sample. A computer program searches through a database of proteins to find a match between the profile generated and the profile of a known protein, allowing the protein in the sample to be identified.

______________ is an analytical technique that measures the mass-to-charge ratio of ions.

Mass spectrometry

If you identify certain SNPs that are associated with a particular disease, have you found the causative agent of the disease?

Maybe. Although the presence of the SNP could be an indicator of the disease, it is likely that other genes and environmental factors also play a role which may not be illuminated by the presence of that particular SNP. The location of the disease-causing gene can be determined from the locations of associated SNPs, although it may not be the cause of the disease.

What is the difference between orthologs and paralogs?

Orthologs are in different species; paralogs are in the same species. Homologous genes (both orthologs and paralogs) often have the same or related functions, so after a function has been assigned to a particular gene, it can provide a clue to the function of a homologous gene.

Why do the positions and distances of genes in a genetic map sometimes differ from the positions and distances of the same genes on a physical map?

Rates of crossing over vary somewhat from one part of the chromosome to another. Genetic maps are based on recombination rates which vary somewhat from one part of the chromosome to another.

What is the relation between genome size and gene number in eukaryotes?

There is little association between genome size and the number of genes. There is no close relation between genome size and complexity among the multicellular eukaryotes.

In which technique do scientists use diffraction patterns of X-rays to determine protein structure?

X-ray crystallography With X-ray crystallography, crystals of the protein are bombarded with X-rays and the diffraction patterns of the X-rays are used to determine the structure.

What procedure can be used to solve the structures of complex proteins?

X-ray crystallography With X-ray crystallography, crystals of the protein are bombarded with X-rays and the diffraction patterns of the X-rays are used to determine the structure.

In _____________, an antibody to a specific protein is used to capture one protein from a complex mixture of proteins.

affinity capture

Proteomics is the study of:

all the proteins found in a cell

Linking a DNA sequence to information about its function and its relation to other genes is known as _____ the gene.

annotating After a gene has been identified, it must be annotated, which means linking its sequence information to other information about its function and expression, the protein it encodes, and similar genes in other species.

What are the goals of functional genomics?

determining the transcriptome and the proteome The goals of functional genomics include the identification of all of the RNA molecules transcribed from a genome, and all of the proteins encoded by the genome.

Maps of genes based on recombination frequencies are termed _____ maps.

genetic Genetic maps (also called linkage maps) provide a rough approximation of the locations of genes relative to the locations of other known genes.

Which of these is NOT used in the process of a mutagenesis screen?

heat map Heat maps are generated from microarrays as opposed to a mutagenesis screen.

cDNA from cancer cells is labeled with red fluorescent nucleotides, and cDNA from normal cells is labeled with green fluorescent nucleotides. The cDNAs are hybridized to a microarray that contains probes from a number of different genes. What does a red spot on the microarray indicate?

higher expression of the gene in cancer cells Red indicates higher expression of the gene in cancer cells.

SNPs are _____, and they _____ produce phenotypic differences.

inherited; usually do not Arising through mutation, SNPs are inherited as allelic variants in the same way as alleles that produce phenotypic differences, although SNPs often do not produce phenotypic differences.

Which of these is considered the first step in RNA sequencing? fragmentation and preparation of the cDNAs for sequencing conversion of the RNA to complementary DNA sequences converting the readouts from the sequencing machine into full-length RNA transcripts isolation of the RNA molecules of interest from cells

isolation of the RNA molecules of interest from cells First, the cells are lysed and the RNA chemically extracted which yields the total RNA of the cell.

The comparative approach to finding genes uses which method?

looking for sequence similarity between a new sequence and known genes The comparative approach looks for similarity between a new sequence and the sequences of all known genes.

Which method can tell you the precise molecular mass of a molecule?

mass spectrometry Mass spectrometry is a method for precisely determining the molecular mass of a molecule.

Most prokaryotic genomes consist of _____.

one circular chromosome Most prokaryotic genomes consist of a single circular chromosome; however, there are exceptions.

Maps of genes based on physical distances such as number of base pairs are termed _____ maps.

physical Physical maps are based on the direct analysis of DNA, and they place genes in relation to distances measured in number of base pairs, kilobases, or megabases.

Most organisms produce many more types of proteins than there are genes in their genome. How can there be more proteins than genes when all proteins must be encoded by DNA sequences?

posttranslational modifications The same gene sequence can encode several different proteins, due to the way they are modified after translation has taken place.

What is the goal of the Earth BioGenome Project.

sequencing all eukaryotic species found on Earth

Which of these is considered the fourth step in RNA sequencing?

sequencing of the cDNA In the penultimate step of RNA sequencing, overlapping fragments of a suitable size, usually about 200 bp in length, are sequenced.

What was the goal of the Human Genome Project.

sequencing the entire human genome

All of these are methods to study patterns of gene expression EXCEPT: shotgun sequencing. RNA sequencing. microarrays. reporter sequence.

shotgun sequencing. In whole-genome shotgun sequencing, small-insert clones are prepared directly from genomic DNA and sequenced, which determines structure but not expression.

Which of these is required for mapping restriction sites (restriction mapping)?

simultaneously cutting the DNA with two restriction enzymes (a double digest) Restriction mapping is carried out by first cutting the DNA with single restriction enzymes and then simultaneously cutting the same DNA with multiple restriction enzymes (a double digest).

A site in the genome where individuals differ in a single base pair is called a _____.

single-nucleotide polymorphism A single-nucleotide polymorphism is a substitution of a single nucleotide that occurs at a specific position in the genome, where each variation is present to some appreciable degree within a population.

The Human Proteome Project aims to catalog all of these EXCEPT: what proteins interact with each other in a cell. the identification of all of the RNA molecules transcribed. what proteins are present in different cell types. where each protein is located in cells.

the identification of all of the RNA molecules transcribed. This is the goal of the transcriptome as opposed to the proteome.

What is a challenge when sequencing an entire genome?

the large size of most genomes The main obstacle to sequencing a whole genome is the immense size of most genomes.

Which method separates proteins using charge and mass?

two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) One method for separating proteins is two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), in which the proteins are separated in one dimension by charge, separated in a second dimension by mass, and then stained.

Which of these is an example of a protein domain?

zinc finger DNA-binding proteins have a domain called a zinc finger, consisting of a loop of amino acids containing a zinc ion.