Bacterial Genomics (Exam 4) Flashcards
Regarding Bacterial Genomics:
1 gene = 1 _______.
kilobase (kb)
1 kilobase = 1000 _____ or ______.
base pairs or nucleotides
1 Megabase = ________ bases and _____ kilobase(s).
1 million bases
1000 kilobases
A genome consists genes. 1 gene encodes for 1 ______ or _____.
protein OR RNA
(T/F) You can sequence an entire bacterial chromosome at once.
False - need to break into chunks and reassemble
Which bacterial organism was one of the first genomes sequenced chosen due to it having the fewest number of genes?
Mycoplasma genitalum
Which bacterial organism is the best studied gram-negative organism regarding genomics?
E. coli
_______ software is used to “hunt” for genes, finding stop codons within possible reading frames.
Artemis
Artemis software is the first step in ________.
annotation
In Bacterial Genomics, when you have a protein-coding sequence but don’t know its function, this is called ______ ______.
hypothetical protein
The human genome is MUCH larger than bacterial genomes due to lots of _______.
filler
The human genome is ________ Mbp.
3,000
(T/F) Metabolic capability, flagella & pili genes, adhesin genes, toxin genes, most surface proteins, and antigenic variation can ALL be deduced from a typical genome sequence.
True
Repetitive sequences with a bacterial genome mediate _________.
antigenic/phase variation
(T/F) Repetitive sequences that mediate antigenic variation in a bacterial genome are good targets for subunit vaccines.
False
Sequencing a region multiple times within 1 genome sequence can indicate ______ ______ variation.
high frequency
Comparison of one or more closely related species or isolates is called:
comparative genomics
______ ______ presents all genes present within a species.
pan genome
_____ ______ represents all genes within every strain that is within a species.
core genome
Core genome gets (bigger/smaller) with more added isolates. Pan genome gets (bigger/smaller) with more isolates.
smaller
bigger
LEE Pathogenicity Island of E. coli making lab strains virulent stains for:
locus of enterocyte effacement
“Next gen” sequencing revealed mutation in ______ ______ which helps guide transcription of certain genes (example: capsule mutants with capsule genes but NO capsule present).
regulatory protein
Genetic sequencing of bacteria can be done to trace an outbreak and develop what assay?
RT-PCR (real-time)
(T/F) Bacterial Genomics can help determine cross-reactivity between species antigens.
True
Comparing different loci within a chromosome, there are at least 3 locations in the genome of Mycoplasma species have the same 3 genes with a distinct set of ______ ______ between them.
surface antigens
Comparing 5 different species/isolates of Mycoplasma, the genes (unique/similar) to each of the 5 strains is a target for _____.
unique
PCR
(T/F) Synthetic bacteria can be made in a lab.
True
Synthetic bacteria can be for ______ or ______.
fuel (for cells)
vaccines
Match the term:
- ALL genes
- ALL transcripts (mRNA)
- ALL proteins
- genome
- transcriptome
- proteome
Use of converting ______ to _____ with reverse transcriptase for transcriptional profiling by RNA-seq has replaced microarray analysis.
mRNA to cDNA
Clusters of co-regulated genes when genes are transcribed together are called:
operons
Complete genome sequence reveals every candidate for protein antigen. This is potentially useful for what 2 purposes?
- serology
- subunit vaccines
Using bacterial genomics to narrow down bacteria vaccine candidates is done using:
reverse vaccinology
What is the biggest limitation to Reverse Vaccinology?
must avoid phase variable genes
A proteome can be used to identify a _______ target.
antibiotic
