chapter 6

Linking an ORF with a specific function is an example of gene codon bias. expression. assembly. annotation.

annotation.

Most mobile DNA consists of plasmids. introns. transposable elements. linear chromosomes.

transposable elements.

Within Archaea and Bacteria, one megabasepairs of DNA encode about ________ open reading frames. 10 100 10,000 1,000

1,000

Typically ________ of ORFs in a genome cannot clearly be assigned a function. These ORFs are usually assigned and predicted to encode hypothetical proteins. < 1 % 30 % 5 % 90 %

30 %

Chloroplasts and mitochondria originated from ________ by a process known as ________. plants / gene deletion bacteria / chromosome reduction bacteria / endosymbiosis plants / endosymbiosis

bacteria / endosymbiosis

The science that applies powerful computational tools to DNA and protein sequences for the purpose of analyzing, storing, and accessing the sequences for comparative purposes is known as proteomics. metagenomics. genomics. bioinformatics.

bioinformatics.

Newer sequencing techniques require only one lane on an electrophoresis gel rather than four. How is this possible? The fragments of different lengths have different charges, meaning that they travel different distances in the electrophoresis gel. Computers are able to recognize the different bases by their structure. The different bases are recognized by their depth in the electrophoresis gel. Each base is identified with a different fluorescent color.

Each base is identified with a different fluorescent color.

The ion torrent sequencing method uses "the world's smallest pH meter" to detect the addition of bases. What change related to pH would be measured? Each time a new base is added, an H+ is added. A pH meter would record a decrease in H+ concentration in the environment as an increase in pH (greater alkalinity). Each time a new base is added, an H+ is removed. A pH meter would record an increase in H+ concentration in the environment as an increase in pH (greater alkalinity). Each time a new base is added, an H+ is added. A pH meter would record a decrease in H+ concentration in the environment as an increase in pH (reduced acidity). Each time a new base is added, an H+ is removed. A pH meter would record an increase in H+ concentration in the environment as a decrease in pH (greater acidity).

Each time a new base is added, an H+ is removed. A pH meter would record an increase in H+ concentration in the environment as a decrease in pH (greater acidity).

Determine why some prokaryotes have less DNA but more genes than eukaryotes. Eukaryotes have more introns in their chromosomes. Eukaryotes do not have introns in their chromosomes. Prokaryotes have more introns in their chromosomes. Eukaryotes have more exons in their chromosomes.

Eukaryotes have more introns in their chromosomes.

Horizontal gene transfer refers to the transfer of genes from one organism to another, as occurs during conjugation between bacteria. How does this differ from vertical gene transfer? In horizontal gene transfer, genes are transferred from one mature adult organism to another. In vertical gene transfer, genes are transferred from adults to offspring. In horizontal gene transfer, genes are transferred between two organisms of the same species. In vertical gene transfer, genes are transferred between two organisms of different species. Conjugation can involve horizontal or vertical gene transfer, depending on the physical orientation of the bacteria involved. In vertical gene transfer, genes are transferred by a vector such as a bacteriophage.

In horizontal gene transfer, genes are transferred from one mature adult organism to another. In vertical gene transfer, genes are transferred from adults to offspring.

In sequencing, it may be necessary to find a consensus nucleotide. What does this mean? It is an ambiguous nucleotide that is different in multiple fragments. It is a type of nucleotide used in shotgun sequencing. It is the nucleotide most commonly found at a particular location. In sequencing, it is a nucleotide found at the beginning of one fragment and the end of another.

It is the nucleotide most commonly found at a particular location.

Why is having few or no inteins related to having a very small genome? Inteins are responsible for nonessential enzymatic functions and organisms with small genomes produce minimal numbers of proteins. Organisms with very small genomes tend to have essential genes with minimal additional material. Inteins are the same as introns, so any organism with relatively few introns will have few inteins. Inteins are coded from introns and organisms with small genomes tend to lack introns

Organisms with very small genomes tend to have essential genes with minimal additional material.

In DNA replication in vivo, RNA primers are used. However, researchers use DNA primers instead in the lab because DNA primers are more stable. Why might this be the case? RNA has a relatively short half life compared with DNA and does not need to be as stable to perform its functions in the cell. RNA is usually single-stranded and the double-stranded nature of DNA makes it more stable. DNA has a more stable structure because the deoxyribose in DNA is a larger molecule than the ribose in RNA. RNA molecules are shorter than DNA molecules, making them more stable.

RNA has a relatively short half life compared with DNA and does not need to be as stable to perform its functions in the cell.

Codon usage and even the genetic code itself varies from one organism to the next. True False

True

A computer program recognizes an ORF by looking for ribosomal binding sites, start codons, and stop codons with an appropriate number of nucleotides between each element. What is a drawback of this approach? Unusual, but legitimate genes and non-coding RNA may be missed. Too many ORFS are identified, most of which are stretches on non-coding junk DNA. We lack the computing power to complete the analyses in a timely manner, thus many genomes are only partially annotated. Codon bias causes incorrect annotations.

Unusual, but legitimate genes and non-coding RNA may be missed

An open reading frame (ORF) encodes for mRNA. a polypeptide. a carbohydrate. a carbohydrate or a polypeptide.

a polypeptide.

To determine if you have identified a functional open reading frame (ORF), you should have found within the sequence __________. < 300 nucleotides a start codon a start codon and a ribosomal binding site (RBS) a RBS

a start codon and a ribosomal binding site (RBS)

Which of these organisms is likely to have the largest genome? an autotrophic bacterium a yeast cell a chloroplast an extremophile Archaean due to the demands of surviving in harsh environments

a yeast cell

Chromosomal islands are similar to plasmids __________. because both elements contain inverted repeats because both elements replicate independently of the chromosome because both elements are found separate from the chromosome because both elements contain nonessential genes

because both elements contain nonessential genes

The field of study that can reveal how genes function, reveal how organisms interact with the environment, and show evolutionary relationships is __________. proteomics comparative genomics transcriptomics genomics

comparative genomics

Microarrays can be used to analyze global gene expression. detect pathogens, analyze global gene expression, and detect unwanted food additives or substitutes. detect unwanted food additives or substitutes. detect pathogens.

detect pathogens, analyze global gene expression, and detect unwanted food additives or substitutes.

Gene duplication is essential to organisms because __________. duplicate genes are free to evolve into new genes duplicate genes prevent the evolution of new genes duplicate genes slow down the possibility of evolution duplicate genes will ensure the organism will always have a backup copy in case of mutation

duplicate genes are free to evolve into new genes

In general, prokaryotic genome size is correlated to lifestyle. Which type of prokaryote typically has the smallest genome? parasite free-living heterotroph endosymbiont autotroph

endosymbiont

When compared with Bacteria, species of Archaea seem to devote a higher percentage of their genomes to genes encoding proteins involved in transcription. energy and coenzyme production. carbohydrate metabolism. cell membrane functions.

energy and coenzyme production.

Based on the evolutionary tree shown below, RubisCO Form II and RLP beta are orthologs. RLP alpha | RLP beta Ancestral gene | | RLP ancestor | | | | | Duplicate gene | RubisCO Form II | | RubisCO ancestor RubisCO Form I | | RubisCO Duplicate | RubisCO Form III True False

false

Heterotrophs need only a few more genes than autotrophs. True False

false

It is generally accepted that independent mutation rather than gene duplication is the mechanism for evolution of most new genes. True False

false

Comparing the different generations of DNA sequencing, which would be most appropriate for a 10 Mbp piece of DNA that could not be fragmented? second generation third generation first generation fourth generation

fourth generation

Arrange the following genetic components in the correct order. genome, proteome, transcriptome, metabolome genome, transcriptome, proteome, metabolome genome, transcriptome, metabolome, proteome genome, metabolome, transcriptome, proteome

genome, transcriptome, proteome, metabolome

Genes from different sources that are related in sequence due to shared evolutionary ancestry are called ________ genes, and groups of such genes are known as ________. homologous / gene families homologous / functional genes orthologous / gene families paralogous / functional genes

homologous / gene families

Transcriptome analysis is useful in relation to genome analysis because it results in amino acid sequence and is, thus, easier to analyze. it is NOT dependent on nucleic acid sequencing technology. it reveals interactions between molecules and, thus, provides more information than genome analysis. it analyzes RNA, thus it reveals which genes are expressed under different conditions.

it analyzes RNA, thus it reveals which genes are expressed under different conditions.

Fourth-generation sequencing methods no longer use ________ to detect nucleotide incorporation. charge mass pH light

light

The advantage(s) of second-generation DNA sequencing compared to the Sanger method are the result of miniaturization of reaction size. increased computing power. increased length of DNA sequences obtained. miniaturization of reaction size and increased computer power.

miniaturization of reaction size and increased computer power.

The pan genome of a species is the genomic content that is present in one or more strains of the same species. hypothetical or uncharacterized genome content of a species. common to all strains of the same species. shared with all other prokaryotes.

present in one or more strains of the same species.

The evolutionary origin of mitochondria is demonstrated by which of the following key genomic characteristics? linear and circular genome structure in different organisms rRNA genes most closely related to Bacteria variable numbers of protein-encoding genes large stretches of AT-rich DNA

rRNA genes most closely related to Bacteria

Mobile DNA elements are more common in the genomes of rapidly evolving species. Archaea. pathogens. hyperthermophiles.

rapidly evolving species.

The most abundant genes in prokaryotic genomes are those involved in DNA replication. those involved in transport. those involved in metabolism. those involved in translation.

those involved in metabolism.

RNA-Seq analysis is a method aimed at defining a(n) metagenome. interactome. transcriptome. metabolome.

transcriptome.

The first genome sequenced was that of a eukaryote. archaeon. virus. bacterium.

virus.

Functional analysis of the genome of a prokaryote shows that 20% of the genome is for metabolism, 1 % biosynthesis of amino acids, 8% peptide ABC transporters, and 2% replication. What can you determine about the environment this organism lives in? The organism lives in an environment rich in lipids. The organism lives in an environment rich in sugars. The organism lives in an environment rich in hydrocarbons. The organism lives in an environment rich in organic material, particularly amino acids and proteins.

The organism lives in an environment rich in organic material, particularly amino acids and proteins.

Horizontal gene flow can be accomplished in prokaryotes by __________. replication and conjugation conjugation, transduction, and transformation replication, conjugation, and transduction conjugation, transformation, and replication

conjugation, transduction, and transformation

Microorganisms that grow in extreme environments typically contain larger genomes when compared to microbes that grow in non-extreme environments. True False

false

The largest cellular genomes belong to prokaryotes that are parasitic or pathogenic. True False

false

Genomes of species in both Bacteria and Archaea show a strong correlation between genome size and noncoding RNA. number of ORFs. codon bias. number of introns.

number of ORFs.

Genome assembly relies on systems biology. accurate gene annotation. overlap of a large numbers of short sequences. codon bias.

overlap of a large numbers of short sequences.

In Sanger sequencing and in many newer sequencing techniques, labeled precursors are used. What are these precursors? DNA polymerase RNA primers or nucleotides that will be incorporated into the newly synthesized DNA fluorescent dyes

primers or nucleotides that will be incorporated into the newly synthesized DNA

very first DNA sequencing technology called the Sanger method relies on the incorporation of dideoxynucleotides that terminate chain extension during DNA synthesis. the release of protons whenever a new nucleotide is added to a growing strand of DNA. nanopore technology that separates DNA molecules based on charge differences. nuclear magnetic resonance (NMR) analysis.

the incorporation of dideoxynucleotides that terminate chain extension during DNA synthesis.

The entire complement of RNA produced under a given set of conditions is called a(n) proteome. array. transcriptome. genome.

transcriptome.

Genes for DNA replication and transcription make up only a small fraction of the typical prokaryotic genome. True False

true

Genomic analysis led to the discovery that pathogenic organisms often lack genes for amino acid biosynthesis. True False

true

The key characteristic of third-generation sequencing is the ability to sequence single molecules of DNA. True False

true

The relative percentage of genes devoted to protein synthesis in small-genome organisms is high compared with that of large-genome organisms. True False

true