Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

GENE221 > Module Five > Flashcards

Module Five Flashcards

1
Q

what is a genome?

A

the total complement of genetic information of a cell or a virus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

what are the features of the bacterial genome?

A
  • Double stranded DNA
  • Usually cirular
  • Usually one chromosome
  • Size ranges from 0.112 Mb to 14.7 Mb
  • Can contain plasmids
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

what is genomics?

A

the discipline involving the mapping sequence and analysis of genomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

what are the steps in bacterial genomics and comparative genomics?

A
  1. Determine genome sequence of bacterium
  2. Identify genes/features in bacterial genome
  3. Biological interpretation of genome content
  4. Comparison of genome content of two or more bacteria
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

what are the methods for genome sequencing?

A

Sanger sequencing

Next-generation sequencing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What are the features of next-generation sequencing?

A
  • no cloning step required (no problem with toxic genes)
  • Massively parallel sequence data
  • Short read technology (and long read technology)
  • More sequence reads for time/cost
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

what are the stages of next-generation sequencing?

A
  • gDNA
  • Parallel Sequencing
  • Alignment
  • Sequence
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

how is genomic DNA prepared in Illumina sequencing?

A

random fragments of genomic DNA and ligate adapters to both ends of the fragmentsq

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

how does the DNA attach to the surface in Illumina sequencing?

A

Binds single-stranded fragments randomly to the inside surface of the flow cell channels

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

what is bridge amplification in Illumina sequencing?

A

Add unlabeled nucleotides and enzyme to initiate solid-phase bridge amplification

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

what is the first chemistry cycle in Illumina sequencing?

A

Determine first base
-to initiate the first sequencing cycle, add all four labeled reversible terminators, primers, and DNA polymerase enzyme to the flow cell.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

what is the image of the first chemistry cycle in Illumina sequencing?

A

after laser excitation, capture the image of emitted fluorescence from each cluster on the flow cell. Record the identity of the first base for each cluster

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

what happens before initiating the next chemistry cycle in Illumina sequencing?

A

The blocked 3’ terminus and the fluorophore and each incorporated base are removed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

what are the steps of Illumina sequencing?

A
  1. Prepare genomic DNA sample
  2. Attach DNA to surface
  3. Bridge amplification
  4. Denature the double stranded molecules
  5. First chemistry cycle: determine the first base
  6. Image of first chemistry cycle
  7. Before initiating the next chemistry cycle
  8. sequence read over multiple chemistry cycles
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

what is genome annotation?

A

Just a selection of automated annotation tools

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

what are some examples of automated annotation tools?

A 
RAST
Prokka
PGAP
BEACON
BASyS
....
17
Q

What is NCBI?

A

Prokaryotic Genome Annotation Process

18
Q

What is PGAP?

A

Automated annotation

19
Q

what is automated annotation?

A

Automated genome annotation is fast/consistent

human (manual) annotation can add value

20
Q

what can the genes present in the genome do?

A

can determine the biology of that organism

21
Q

what can determine the genome content?

A

The biology or niche inhabited by a bacterium can determine genome content

22
Q

what is metabolic modeling?

A

sets of metabolic genes can be analyzed and used to determine what metabolism a bacterium has

23
Q

what is part of the accessory (pan) genome?

A 
Transposons
Insertion sequences (IS)
Genomic islands 
Prophages 
Plasmids
24
Q

what are the features of the accessory genome?

A
  • These can be active/inactive

- Highly ‘flexible’ part of the bacterial genome that drives rapid evolution

25
Q

what is comparative genomics?

A

Comparative genomics is the comparison of genome structure and function across different biological species or strains

26
Q

what is the purpose of the comparison of genomes?

A
  • comparison can aid in identifying differences
  • The regions of difference can help identify genes involved in particular process
  • close comparisons
  • distant comparisons

GENE221 (6 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions