Microbiology Exam 3 (Chapter 10)

What is the largest genome?

-Some bacteria have more genes than eukaryotes due to lack of/presence of introns -largest prokaryotic genome to date at 14.8 Mbp

noncoding RNA and examples

-Some genes encode RNA that is not translated -lack start codons and may have multiple stop codons -transfer RNA (tRNA) -ribosomal RNA (rRNA) -noncoding regulatory RNA molecules (identified by transcriptomics)

Functional ORF

-actually encodes a protein, can be identified by computer -Bacterial and archaeal genomes are a series of open reading frames (ORFs)

Metagenome

total genetic component of all cells present in a particular environment

Epigenome

total possible epigenetic changes

chromosomal islands

Many genes encoding defense systems are clustered in chromosomal islands which also contain numerous open reading frames (ORFs) of unknown function

Genome annotation

converting raw sequence data into a list of genes and other functional sequences present in the genome

Microbiome

total component of microorganisms in a particular environment

Metagenomics

analyzes pooled D N A or R N A from environmental sample containing organisms which have not been isolated/identified

Which genetic material is most closely related to nuclear-encoded mitochondrial genes that are required for translation and energy generation?

bacterial genes

What are ddNTP's

chain terminators preventing further elongation of DNA chain -insert randomly, producing chains of varying length

Methylome

Total methylates sites on the DNA (wether epigenetic or not)

What has microbial genome sequencing led to

- Discovery of heat stable enzymes - Study gene expression, detect horizontal gene transfer, monitor disease outbreak, discover CRISPR, understand metabolism, determine growth requirements - Solving medical mysteries (ex: cause of black death) - Identifying new microbial phyla

What were the first genomes sequenced? When were the first bacterial genomes published?

-First genomes sequenced were small viruses -First bacterial genome published in 1995

In the sanger method of DNA sequencing, how are DNA chains randomly terminated in reactions using DNA polymerase?

By having a small amount of dideoxyribonucleoside triphosphate in the reaction *******

What can proteomics reveal

Can be used to detect post-translational modifications

The field of study that can reveal how genes function, reveal how organisms interact with the environment, and show evolutionary relationships is ________

Comparative genomics

A researcher planning to determine the genomes of all of the species present in a diverse wetland environment using metagenomics would encounter the problem that __________. A. it is difficult to work out genomes of organisms in aquatic environments B. metagenomics approaches cannot be used to determine complete genomes C. metagenomics approaches are only appropriate for terrestrial environments D. it is difficult to assemble complete genomes when many species are present

D. it is difficult to assemble complete genomes when many species are present Note: Metagenomics can be used in aquatic and terrestrial environments. However, determining the complete genomes of the organisms present is easiest in terrestrial or aquatic environments with low species diversity.

Which of the following is not a method of horizontal gene transfer? A. transduction B. conjugation C. transformation D. vertical inheritance

D. vertical inheritance

An organisms entire complement of genetic information, including noncoding DNA is known as the _____

Genome

What type of genes are typically most abundant in bacterial genomes

Metabolic genes typically most abundant in bacterial genomes

What plays a role in antibiotic resistance

Mobilome which can spread resistance to other genes and heterologous expression

What are the short DNA fragments called that are used to initiate DNA synthesis in the Sanger dideoxycytidine sequencing method?

Primers

Exome

The part of the RNA pool encoded by axons that remain after introns are removed

Genome

The total complement of genetic information of a cell or virus

Sequencing

determining the precise order of nucleotides in a DNA or RNA molecule

Genomics

discipline of mapping, sequencing, analyzing, and comparing genomes

Metaproteomics

environmental samples shows collective metabolic potential of a community

Proteomics and methods

genome-wide study of structure, function, and activity of an organism's proteins -Mass spectrometry allows unambiguous determination of molecular formula, and can be used to identify peptides -High-pressure liquid chromatography (HPLC) is used to separate proteins by differences in chemical properties -Matrix-assisted laser desorption ionization (MALDI): advanced mass spectrometry method where sample is fixed to matrix, ionized, vaporized, and molecular formula is determined

Mycobiome

the total complement of fungi in a natural environment

Codon bias (usage) and its relationship with ORFs

some codons used more frequently than others -if ORF codon bias differs greatly from organism's consensus, may be nonfunctional or may have been obtained via horizontal gene transfer

Bioinformatics

storing and analyzing sequences and structures of nucleic acids and proteins

Knockout mutations

systematically inactivating genes

Hypothetical proteins

uncharacterized ORFs; proteins that likely exist but whose function is currently unknown -have uninterrupted reading frames, start and stop codons, ribosome-binding site -lack sufficient amino acid sequence homology with known proteins for identification assign to family or general function

Kinome

total set of protein kinases encoded by a genome

Heterologous expression

expressing a gene in a different host

Secretome

proteins that are secreted from the cell

Describe the chloroplast genome

-Chloroplast genomes mostly circular DNA -Typically two inverted repeats encoding copies of the three rRNA genes -Many genes encode proteins for photosynthesis and autotrophy -Encodes tRNAs, transcription and translation proteins -Introns common; primarily of self-splicing type

What is the different between genomics in the past and genomics now

-In the past only small viruses and bacteria were sequences -Now DNA sequences from bacteria, archaea, and viruses have been done (even eukaryotic genomes and human genomes)

How do you find and identify an ORF

-Locate start and stop codons and Shine-Dalgarno/ribosome-binding sites -Look for similarity to ORF s in other genomes or encodes functional domain -Search for similarities in databases such as GenBank using BLAST

Describe mitochondrial genomes and proteomes

-Primarily encode proteins for oxidative phosphorylation and proteins, rRNA, and tRNA for protein synthesis -Fewer proteins encoded than in chloroplasts -Diverse genome structures -contain small plasmids

What do smaller genomes encode for? what about larger ones?

-Smaller genomes encode more translational processes; larger genomes encode more transcriptional regulation and signal transduction

What is the smallest genome? What dies a small genome size mean?

-Smallest belong to parasitic or endosymbiotic prokaryotes -Small genome size means such symbionts are totally dependent on host for nutrients

Smallest eukaryotic genome belongs to_____

-Smallest eukaryotic genome belongs to nucleomorph endosymbiont -Smallest parasitic eukaryotic genome belongs to intracellular pathogen

RNA-Seq Analysis

-all RNA converted into cDNA and sequenced -shows which genes are transcribed and how many copies of each RNA are made -measures mRNA expression -identifies long untranslated regions -discovers noncoding RNAs -requires high throughput/second-generation sequencing -rRNA must be removed or mRNA enriched

What was the first widely used method of DNA sequencing

-dideoxy method invented by Nobel Prize winner Fred Sanger -copy original ssDNA -small amounts of dideoxyribonucleotides (ddNTPs) used with dNTPs -Entire chromosomes or large DNA molecules could not be sequenced in one reaction -still used to sequence plasmids and PCR products

What is a genome and what does it include

-entire complement of genetic information -includes genes encoding proteins, R N A, and regulatory sequences, and noncoding D N A

DISARM (defense island system associated with restriction-modification)

-gives resistance to eight tailed bacteriophages -encodes a methylase and may function similar to other restriction modification systems

What is genome assembly?

-putting fragments in the correct order and eliminating overlaps -identifies genes and other functional regions -computational -Map of complete genome is generated

Microarrays (gene chips)

-small solid supports to which genes or oligonucleotides are fixed and arrayed spatially in a known pattern -measure DNA or RNA that hybridizes (single strands forming double-stranded molecules by complementary or almost complementary base pairing) with known nucleic acid probes and fluorescence

Transcriptomics

-study of cell's global transcription, monitors total RNA (transcriptome) under a growth condition -two main approaches: microarrays and RNA-Seq

Describe the archaea genome

-typically devote a higher percentage of their genomes to energy and coenzyme production than Bacteria -fewer genes for carbohydrate metabolism and membrane functions than Bacteria -less studied

What is comparative genomics

-uses databases to prove genomes -correlation between genome size and ORF content -as genome size increases, number of genes proportionally increases (contrasts with eukaryotic genomes containing a large fraction of noncoding DNA (introns), especially in large genomes)

Which of these is true about genome size? A. Bacterial and archaeal, but not eukaryl, genome sizes generally correlate with ORF content. B. Only eukaryl genome sizes generally correlate with ORF content. C. Only bacterial genome sizes generally correlate with ORF content. D. Bacterial, archaeal, and eukaryl genome sizes generally correlate with ORF content.

A. Bacterial and archaeal, but not eukaryl, genome sizes generally correlate with ORF content.

Why was metagenomics so useful in identifying previously unknown Archaea? A. Metagenomics makes it easier to find and identify species that are difficult to culture. B. Metagenomics involves DNA sequencing, unlike prior techniques. C. Metagenomics requires genomes to be sequenced before they can be recognized in the environment. D. Metagenomics is used in a wider range of environments than other efforts to identify species.

A. Metagenomics makes it easier to find and identify species that are difficult to culture. Note: Other techniques also use DNA sequencing, and previous efforts to find species have sampled a wide range of environments. Metagenomics does not require full genomes to be known in order to detect new species.

An important clue(s) that a sequence is a functional ORF is (are) that __________. MARK ALL THAT APPLY. A. it has a ribosome binding site B. it has start and stop codons C. it contains a bound dideoxynucleotide D. it has a similar sequence to a sequence known to encode a functional protein domain in another species

A. it has a ribosome binding site B. it has start and stop codons D. it has a similar sequence to a sequence known to encode a functional protein domain in another species

If a researcher finds a sequence of DNA that has an unusual codon bias compared with the rest of the DNA for the organism, this probably means that __________. MARK ALL THAT APPLY. A. the DNA contains a functional gene(s) that was (were) obtained through horizontal gene transfer B. the DNA is expressed far more than would be expected by chance C. the DNA contains a high density of ribosome binding sequences D. the DNA does not contain functional genes

A. the DNA contains a functional gene(s) that was (were) obtained through horizontal gene transfer D. the DNA does not contain functional genes

If you compare a bacterium and a eukaryote of the same genome size, A. the bacterium likely has more genes. B. the bacterium likely has more insertion elements. C. the eukaryote likely has more metabolic pathways. D. all of the above are true.

A. the bacterium likely has more genes.

What can you predict if you find an organism that has an exceptionally tiny genome? A. It is probably a eukaryote. B. It is probably a symbiont that is dependent on its host. C. It is probably a free-living organism that can also be parasitic. D. It is probably an archaeal cell.

B. It is probably a symbiont that is dependent on its host. Note: An organism that has an exceptionally tiny genome is probably a symbiont that is dependent on its host. This means that it does not need to produce as many proteins itself as it can use those produced by its host. Eukaryotes generally have relatively large genomes with large amounts of noncoding DNA.

The proteome and the translatome __________. A. are the same unless an organism has a mutation B. differ because the translatome includes only proteins produced under specfiic conditions and the term "proteome" can be broader C.differ because the translatome includes all products of translation and the proteome is narrower D. are generally identical in most cells

B. differ because the translatome includes only proteins produced under specfiic conditions and the term "proteome" can be broader Note: The term "proteome" can be used narrowly to mean the same thing as translatome or can be used more broadly to mean all proteins produced by a cell regardless of conditions. Whether an organism has a mutation does not affect whether its proteome and translatome are the same.

Which of the following is not included in the genome? A. noncoding regions of DNA B. proteins C. coding regions of DNA D. genes that encode RNAs

B. proteins

Which question could best be answered using comparative genomics? A. How quickly does antibiotic resistance evolve? B. What is the best way to identify an ORF? C. Do all organelle genes need to be located within an organelle? D. What is the minimum number of genes necessary for life?

D. What is the minimum number of genes necessary for life? Note: By looking at organisms with very small genomes, it is possible to identify which genes are critical for life. Comparative genomics may be useful in addressing other questions in a less direct way. However, it is not the best approach in all cases.

An example of heterologous expression would be __________. A. sequencing the genome of a newly discovered bacterium to try to identify genes similar to those of known species B. allowing a bacterium to transfer an F plasmid to another bacterium through conjugation C. examining the exome of a eukaryotic cell D. inserting an unknown gene from one bacterium into another unrelated bacterium to see what was produced

D. inserting an unknown gene from one bacterium into another unrelated bacterium to see what was produced Note: Heterologous expression means that a gene is being expressed by a different bacterium from the one in which it is normally found. Therefore, sequencing a gene or examining an exome would not be examples of heterologous expression. When an F plasmid is transferred, recombination can occur between different versions of a gene that is normally found in a particular species. This is not the same as transferring an entirely new gene into a bacterium that normally doesn't have it.

If you did a metagenomic analysis of a natural pond environment, you would probably find that __________. A. it was relatively easy to assemble complete genomes compared with examining an extreme environment B. there were no archaeans present C. there was a low diversity of microbial species present D. virus genes were the most abundant genes present

D. virus genes were the most abundant genes present Note: This type of environment tends to have a high diversity of microbial species present, making it more difficult to assemble complete genomes than in a more extreme, less diverse environment. In a diverse assemblage of microbes, archaeans would probably be present.

Sequencing an organisms genome often leads to identification of hypothetical proteins. Which are characterized as ___________

Proteins that likely exist though their function is unknown

What is the genome-wide study of the structure, function, and regulation of an organism proteins called?

Proteomics

What is the next generation sequencing

Pyrosequencing (second-generation) uses luciferase to detect incorporation of dNTPs

Transcriptome

Total RNA produced in an organism under a specific set of conditions

Virome

Total complement of viruses in an environment

Resistome

Total set of antibiotic resistance genes in a cell

Mobilome

Total set of mobile genetic elements in a cell

What do scientist call the entire complement of RNA produced under a given set of conditions?

Transcriptome

Where were eukaryotic cell organelles derived from? how do we know?

eukaryotic cell organelles derived from endosymbiotic bacteria -share many fundamental bacterial traits

Metabolome

the total complement of small molecules and metabolic intermediates

Glycome

the total complement of sugars and other carbohydrates

Interactome

the total set of interactions between proteins (or other macromolecules)

Proteome

the total set of proteins encoded by a genome; sometimes also used in place of translatome

Translatome

the total set of proteins present under specified conditions