Bacterial Genomics (Exam 4)

Question 1

Regarding Bacterial Genomics:
1 gene = 1 _______.

Answer 1

kilobase (kb)

Question 2

1 kilobase = 1000 _____ or ______.

Answer 2

base pairs or nucleotides

Question 3

1 Megabase = ________ bases and _____ kilobase(s).

Answer 3

1 million bases
1000 kilobases

Question 4

A genome consists genes. 1 gene encodes for 1 ______ or _____.

Answer 4

protein OR RNA

Question 5

(T/F) You can sequence an entire bacterial chromosome at once.

Answer 5

False - need to break into chunks and reassemble

Question 6

Which bacterial organism was one of the first genomes sequenced chosen due to it having the fewest number of genes?

Answer 6

Mycoplasma genitalum

Question 7

Which bacterial organism is the best studied gram-negative organism regarding genomics?

Answer 7

E. coli

Question 8

_______ software is used to “hunt” for genes, finding stop codons within possible reading frames.

Answer 8

Artemis

Question 9

Artemis software is the first step in ________.

Answer 9

annotation

Question 10

In Bacterial Genomics, when you have a protein-coding sequence but don’t know its function, this is called ______ ______.

Answer 10

hypothetical protein

Question 11

The human genome is MUCH larger than bacterial genomes due to lots of _______.

Answer 11

filler

Question 12

The human genome is ________ Mbp.

Answer 12

3,000

Question 13

(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.

Answer 13

True

Question 14

Repetitive sequences with a bacterial genome mediate _________.

Answer 14

antigenic/phase variation

Question 15

(T/F) Repetitive sequences that mediate antigenic variation in a bacterial genome are good targets for subunit vaccines.

Answer 15

False

Question 16

Sequencing a region multiple times within 1 genome sequence can indicate ______ ______ variation.

Answer 16

high frequency

Question 17

Comparison of one or more closely related species or isolates is called:

Answer 17

comparative genomics

Question 18

______ ______ presents all genes present within a species.

Answer 18

pan genome

Question 19

_____ ______ represents all genes within every strain that is within a species.

Answer 19

core genome

Question 20

Core genome gets (bigger/smaller) with more added isolates. Pan genome gets (bigger/smaller) with more isolates.

Answer 20

smaller
bigger

Question 21

LEE Pathogenicity Island of E. coli making lab strains virulent stains for:

Answer 21

locus of enterocyte effacement

Question 22

“Next gen” sequencing revealed mutation in ______ ______ which helps guide transcription of certain genes (example: capsule mutants with capsule genes but NO capsule present).

Answer 22

regulatory protein

Question 23

Genetic sequencing of bacteria can be done to trace an outbreak and develop what assay?

Answer 23

RT-PCR (real-time)

Question 24

(T/F) Bacterial Genomics can help determine cross-reactivity between species antigens.

Answer 24

True

Question 25

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.

Answer 25

surface antigens

Question 26

Comparing 5 different species/isolates of Mycoplasma, the genes (unique/similar) to each of the 5 strains is a target for _____.

Answer 26

unique
PCR

Question 27

(T/F) Synthetic bacteria can be made in a lab.

Answer 27

True

Question 28

Synthetic bacteria can be for ______ or ______.

Answer 28

fuel (for cells)
vaccines

Question 29

Match the term:

1. ALL genes
2. ALL transcripts (mRNA)
3. ALL proteins

Answer 29

1. genome
2. transcriptome
3. proteome

Question 30

Use of converting ______ to _____ with reverse transcriptase for transcriptional profiling by RNA-seq has replaced microarray analysis.

Answer 30

mRNA to cDNA

Question 31

Clusters of co-regulated genes when genes are transcribed together are called:

Answer 31

operons

Question 32

Complete genome sequence reveals every candidate for protein antigen. This is potentially useful for what 2 purposes?

Answer 32

1. serology
2. subunit vaccines

Question 33

Using bacterial genomics to narrow down bacteria vaccine candidates is done using:

Answer 33

reverse vaccinology

Question 34

What is the biggest limitation to Reverse Vaccinology?

Answer 34

must avoid phase variable genes

Question 35

A proteome can be used to identify a _______ target.

Answer 35

antibiotic