MMG 301 Exam 2 Questions with Correct Answers Graded A+
Describe the different information about an organism you can get from 16S rRNA gene sequences vs
whole genome sequences - Answers 16S rRNA- allow you to build the phylogenetic tree.
Genome-complete or partial genome.
Understand the basic method of Sanger dideoxy sequencing - Answers Involves DNA pol rxns on cloned
DNA fragments that included chain-terminating bases. Resulting fragments were separated by gel
electrophoresis.
Time consuming, but automation can improve speed.
State in general terms what is involved in the "shotgun sequencing" (without too much detail) strategy
of genome sequencing - Answers 1. Isolate genomic DNA from an organism
2. fragment a genome into small pieces using DNA-cutting enzymes
3. sequencing of random DNA fragments
4. sequence alignment
What technical improvements allowed pyrosequencing to increase sequence throughput; what is
detected in the pyrosequencing reactions - Answers AKA 2nd Gen Sequencing
Introduced massively parallel methods where thousands of simultaneous sequencing rxns were
performed. Miniaturization of rxns, robotics, and improvements in computing power aided development
of these methods.
Termed pyrosequencing because light producing rxn resulted from released pyrophosphate.
3rd & 4th gen - Answers Newer sequencing technologies allow detection of single-molecule rxns.
Be able to diagram or describe what sequence alignment is and how this is used to build long contiguous
sequences - Answers Data from ind seq rxns are fed into computer system that performs alignment.
1. Cleave DNA into fragments and sequence.
2. Computer analysis finds overlaps (different fragments having part of the same sequence).
3. Sequence is deduced.
Order the steps of a genome sequencing project from small fragment sequences to annotation -
Answers 1. Feed sequence data to software that aligns overlapping regions of the ind seqs into longer,
contiguous sequences (contigs).
2. Contigs are linked together into scaffolds.
,3. PCR amplify and seq any regions where there are gaps.
4. Analyze sequence for Open Reading Frames (ORFs) to obtain protein seqs (Gene prediction)
5. Compare protein seqs w/ regions or motifs of known proteins to assign function (annotation).
What are the features of a sequence that are used to detect an ORF - Answers ORF- regions of DNA that
encode proteins
ORFs are identified by a combination of detecting start codons, stop codons, ribosome binding sites, and
codon usage statistics.
The branch of biology dealing with computational approaches to storage, analysis, and comparison of
genomes. - Answers Bioinformatics
Genome Size - Answers The size of genomes can vary widely, depending on how a prokaryote is adapted
to its environment. Prokaryotes that are dependent on other organisms for survival have the smallest
genomes. This is because it is a parasite and gets it's nutrients from host cells and therefore needs fewer
genes.
Non parasitic organisms require more genes for nutrients and energy.
Describe what can a genome sequences reveal about uncultured organisms - Answers 95-99% of all
prokaryotes cannot be cultured in the lab; they live only in complex communities. Genome seqing can
reveal much about these microorganisms such as: metabolic pathways, energy production, nutrient
reqs., phylogenetic relationships.
Define metagenomics and provide examples of the application of metagenomic analysis to microbial
communities - Answers Complex microbial communities containing uncultured organisms can be
analyzed by genome and/or RNA sequencing.
Can analyze microbial communities that are found in interesting situations such as: what organisms are
there.
For ex: intestinal microbial community changes after antibiotic treatment.
DNA microarrays - Answers consist of a surface containing synthetic oligonucleotides that have specific
sequences to base-pair with mRNAs from each and every gene of a genome.
Understand the basics of what a DNA microarray is and what they are used for; how do the microarrays
quantitate mRNA levels - Answers Genome seq of an org can be used to create DNA microarrays for
measurement of mRNA and gene expression levels.
Oligonucleotides are chemically attached to the surface, and identical oligonucleotides are clustered into
spots. Microarray chips contain thousands of spots of oligonucleotides.
Microarrays measure gene expression by quantitating the levels of each mRNA in a cell.
, Made of many dots, each containing different oligonucleotides that will specifically base pair with each
possible mRNA from a seqd genome.
Steps of DNA microarrays - Answers 1. Use one microbe grown under 2 different conditions.
2. Isolate mRNA and convert into DNA
3. Tag w/ fluorescent tag
4. Hybridize on chip and analyze.
RNA-seq - Answers isolation and sequencing of all RNA in a cell.
Differentiate between vertical and horizontal gene transfer - Answers Vertical-mother cell to daughter
cell
Horizontal- genes-> environment, cells, viruses-> recipient cell
Three types of horizontal gene transfer? - Answers transformation, transduction, and conjugation.
Researchers can find clusters of additional genes that are only found in the pathogen. These clusters are
known as ________. - Answers Pathogenicity Islands
Describe the overall goal of controlling gene transcription (turning off transcription of genes that are not
needed) - Answers All of these mechanisms assure precise regulation of metabolism of the thousands of
simultaneous biochemical rxns w/in the cell.
Gene Expression - Answers the conversion of DNA genetic information into a functional protein.
Going from gene to translation product, state the control steps where regulation can occur.**********
- Answers Transcription is the first step in gene expression, so the cell can save the most resources by
stopping transcription of genes that are not required.
Differentiate an operon from a regulon - Answers Operon-DNA segment with control of transcription
genes
Regulon-genes/operons spread throughout genome but regulated together.
Diagram the basic structure of a repressor protein, and a DNA inverted repeat - Answers
Explain regulation of transcription by negative control with a repressor protein using the arg operon
(repression by arginine), and lac operon (induction by lactose) as examples - Answers Negative control
of transcription involves DNA-binding proteins that prevent transcription of genes under specific
conditions.
Arg- add arginine to medium of growing cells, genes for arginine synthesis shut down.
Arg binds to free repressor protein. Arginine-repressor protein complex can then bind to operator.
Describe the different information about an organism you can get from 16S rRNA gene sequences vs
whole genome sequences - Answers 16S rRNA- allow you to build the phylogenetic tree.
Genome-complete or partial genome.
Understand the basic method of Sanger dideoxy sequencing - Answers Involves DNA pol rxns on cloned
DNA fragments that included chain-terminating bases. Resulting fragments were separated by gel
electrophoresis.
Time consuming, but automation can improve speed.
State in general terms what is involved in the "shotgun sequencing" (without too much detail) strategy
of genome sequencing - Answers 1. Isolate genomic DNA from an organism
2. fragment a genome into small pieces using DNA-cutting enzymes
3. sequencing of random DNA fragments
4. sequence alignment
What technical improvements allowed pyrosequencing to increase sequence throughput; what is
detected in the pyrosequencing reactions - Answers AKA 2nd Gen Sequencing
Introduced massively parallel methods where thousands of simultaneous sequencing rxns were
performed. Miniaturization of rxns, robotics, and improvements in computing power aided development
of these methods.
Termed pyrosequencing because light producing rxn resulted from released pyrophosphate.
3rd & 4th gen - Answers Newer sequencing technologies allow detection of single-molecule rxns.
Be able to diagram or describe what sequence alignment is and how this is used to build long contiguous
sequences - Answers Data from ind seq rxns are fed into computer system that performs alignment.
1. Cleave DNA into fragments and sequence.
2. Computer analysis finds overlaps (different fragments having part of the same sequence).
3. Sequence is deduced.
Order the steps of a genome sequencing project from small fragment sequences to annotation -
Answers 1. Feed sequence data to software that aligns overlapping regions of the ind seqs into longer,
contiguous sequences (contigs).
2. Contigs are linked together into scaffolds.
,3. PCR amplify and seq any regions where there are gaps.
4. Analyze sequence for Open Reading Frames (ORFs) to obtain protein seqs (Gene prediction)
5. Compare protein seqs w/ regions or motifs of known proteins to assign function (annotation).
What are the features of a sequence that are used to detect an ORF - Answers ORF- regions of DNA that
encode proteins
ORFs are identified by a combination of detecting start codons, stop codons, ribosome binding sites, and
codon usage statistics.
The branch of biology dealing with computational approaches to storage, analysis, and comparison of
genomes. - Answers Bioinformatics
Genome Size - Answers The size of genomes can vary widely, depending on how a prokaryote is adapted
to its environment. Prokaryotes that are dependent on other organisms for survival have the smallest
genomes. This is because it is a parasite and gets it's nutrients from host cells and therefore needs fewer
genes.
Non parasitic organisms require more genes for nutrients and energy.
Describe what can a genome sequences reveal about uncultured organisms - Answers 95-99% of all
prokaryotes cannot be cultured in the lab; they live only in complex communities. Genome seqing can
reveal much about these microorganisms such as: metabolic pathways, energy production, nutrient
reqs., phylogenetic relationships.
Define metagenomics and provide examples of the application of metagenomic analysis to microbial
communities - Answers Complex microbial communities containing uncultured organisms can be
analyzed by genome and/or RNA sequencing.
Can analyze microbial communities that are found in interesting situations such as: what organisms are
there.
For ex: intestinal microbial community changes after antibiotic treatment.
DNA microarrays - Answers consist of a surface containing synthetic oligonucleotides that have specific
sequences to base-pair with mRNAs from each and every gene of a genome.
Understand the basics of what a DNA microarray is and what they are used for; how do the microarrays
quantitate mRNA levels - Answers Genome seq of an org can be used to create DNA microarrays for
measurement of mRNA and gene expression levels.
Oligonucleotides are chemically attached to the surface, and identical oligonucleotides are clustered into
spots. Microarray chips contain thousands of spots of oligonucleotides.
Microarrays measure gene expression by quantitating the levels of each mRNA in a cell.
, Made of many dots, each containing different oligonucleotides that will specifically base pair with each
possible mRNA from a seqd genome.
Steps of DNA microarrays - Answers 1. Use one microbe grown under 2 different conditions.
2. Isolate mRNA and convert into DNA
3. Tag w/ fluorescent tag
4. Hybridize on chip and analyze.
RNA-seq - Answers isolation and sequencing of all RNA in a cell.
Differentiate between vertical and horizontal gene transfer - Answers Vertical-mother cell to daughter
cell
Horizontal- genes-> environment, cells, viruses-> recipient cell
Three types of horizontal gene transfer? - Answers transformation, transduction, and conjugation.
Researchers can find clusters of additional genes that are only found in the pathogen. These clusters are
known as ________. - Answers Pathogenicity Islands
Describe the overall goal of controlling gene transcription (turning off transcription of genes that are not
needed) - Answers All of these mechanisms assure precise regulation of metabolism of the thousands of
simultaneous biochemical rxns w/in the cell.
Gene Expression - Answers the conversion of DNA genetic information into a functional protein.
Going from gene to translation product, state the control steps where regulation can occur.**********
- Answers Transcription is the first step in gene expression, so the cell can save the most resources by
stopping transcription of genes that are not required.
Differentiate an operon from a regulon - Answers Operon-DNA segment with control of transcription
genes
Regulon-genes/operons spread throughout genome but regulated together.
Diagram the basic structure of a repressor protein, and a DNA inverted repeat - Answers
Explain regulation of transcription by negative control with a repressor protein using the arg operon
(repression by arginine), and lac operon (induction by lactose) as examples - Answers Negative control
of transcription involves DNA-binding proteins that prevent transcription of genes under specific
conditions.
Arg- add arginine to medium of growing cells, genes for arginine synthesis shut down.
Arg binds to free repressor protein. Arginine-repressor protein complex can then bind to operator.
