Brainscape's Knowledge GenomeTM

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


See full index

Animal kingdom > Genomics > Flashcards

Genomics Flashcards

1
Q

What does the tree of life assume ?

A

A monophyletic view of life

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

What does the tree of life highlight ?

A

The first divergence events

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

What is a synapomorphy ?

A

A characteristic or trait present in an ancestral species that is only shared by its descendants in that distinguishes a clade from other organisms.

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

What changed the traditional classification of prokaryotes being a single kingdom

A

Studies on methanobacterium and methanosarcina

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

What allowed the classification of the new taxon archaebacteria

A

Methanogens that are equidistant from eukaryotes and bacteria

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

What are the differences between archaebacteria and eubacteria ?

A

Their membranes are composed of glycerol-ether phospholipids.
They have a L-glycerol
Phospholipids consist of isoprenoid side chains with multiple side branches

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is a paralogous gene ?

A

Homologous gene that occurred due to duplication event

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is a homolog ?

A

Homologs denote genes that derive from the same ancestral sequence

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

What is the difference between orthologs and paralogs ?

A

Orthologsare corresponding genes in different lineages and are a result of speciation, whereasparalogsresult from a gene duplication.

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

What does reticulate evolution refer to ?

A

An evolutionary processes that allows some lineages to merge and produce new lineages. The evolutionary process cannot be modelled by trees

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

Who first described prokaryotes ?

A

Robert hooke

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

What are the types of first generation sequencing ?

A

Maxam-Gilbert Method

Sanger Dideoxy Method

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

What are the types of second generation sequencing ?

A

Illumina sequencing

Ion Torrent

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

What are the types of third generation sequencing ?

A

Pacific biosciences

Nanopore

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What method can determine DNA molecules of up 500bp and relies on toxic chemicals ?

A

Maxam-Gilbert Method

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

What are the key steps in the maxim-gilbert method ?

A
  1. Attain single strand of DNA
  2. Label the DNA radioactively with 32 p to the 5’ end
  3. Separate DNA into 4 tubes and add chemicals that cleave specific nucleotides
  4. This gives different sized DNA strands
  5. Run gel electrophoresis on acrylamide gel
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is the key element of Sanger sequencing ?

A

2’,3’ dideoxynucleoside triphosphates, which lack the hydroxyl group at the 3’ position.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What do ddNTPs do ?

A

They terminate DNA synthesis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What are the key steps in the Sanger Dideoxy Method ?

A
  1. Denature DNA and add radioactive primer
  2. Seperate into 4 tubes and add ddNTP polymerase and dNTPs
  3. Run through denaturing gel
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What does a dNTP do ?

A

Extends DNA strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What are the 4 limitations of the initial Sanger dideoxy method ?

A

Cant run everything in one lane
Unable to read sequences at the top of gel
Cost
Low throughput

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

How are the limitations of Sanger dideoxy method over come ?

A

fluorescently labelled ddNTPs which can be read by a laser

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

How many bp does a single Sanger sequencing cover ?

A

Up to 1000

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Why do we need to assemble sequences into Contigs ?

A

Genomes are too big

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What is a contig ?

A

DNA sequence built up from a number of smaller overlapping sequences during a sequencing project.

26
Q

What is scaffolding ?

A

is a technique used to link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length.

27
Q

What is coverage

A

the number of reads that include a given nucleotide in the reconstructed sequence

28
Q

What is a read ?

A

each sequenced piece of a genome

29
Q

What are the two types of Sanger sequencing ?

A

Hierarchal shotgun sequencing

Whole genome shotgun sequencing

30
Q

What are the steps in whole genome sequencing ?

A 
DNA extraction
Library construction
Random sequencing phase
Gap closure phase
Annotation
31
Q

What do the 2nd generation sequencing methods have in common ?

A
  1. The DNA has to be fragmented

2. Clonal amplification (different PCR methods)

32
Q

What is the problem with Illumina sequencing ?

A

Slow and produces short sequence lengths

33
Q

What sequencing methods are synthesis based ?

A

Illumina

Ion torrent

34
Q

What sequencing methods use the ion semiconductor approach ?

A

Oxford Nanopore
Ion torrent
Illumina

35
Q

What does illumina sequencing rely on ?

A

Reversible terminators

36
Q

What is a benefit of illumina sequencing and what was a major advancement ?

A

Don’t have to move DNA around

Paired end sequencing

37
Q

What does illumina sequencing generate in the flow cell ?

A

millions of dense clusters of dsDNA

38
Q

What are the key steps in illumina sequencing ?

A
  1. Fragment DNA and attach to surface of flow cell using adaptors which contains a primer
  2. Initiate bridge PCR with unlabelled NTPs
  3. When PCR complete, millions of clusters are formed, add 4 labelled reversible terminators, primers and DNA pol to begin sequencing.
  4. Excite clusters with a laser allowing fluorescents to be captured
  5. Remove reversible terminators and repeat cycle by adding more ddNTPs
  6. data aligned and compared to reference sequences
39
Q

What is a key aspect of ion torrent sequencing ?

A

Exploits the fact that addition of a dNTP

to a DNA polymer releases an H+ion

40
Q

What are the steps in ion torrent sequencing ?

A
  1. The input DNA is fragmented, Adaptors are added and one molecule is placed onto a bead.
  2. molecules are amplified on the bead by emulsion PCR
  3. Each bead is placed into a single well of a slide. The slide is flooded with a single species of dNTP, along with buffers and polymerase, one NTP at a time.
  4. The pH is detected in each of the wells, as each H+ion released will decrease the pH.
41
Q

How is third generation sequencing characterised ?

A

The lack of DNA or RNA amplification in template library preparation.

42
Q

What are the benefits of third generation sequencing ?

A
  1. Avoid polymerase chain reaction-introduced error and amplification bias.
  2. Real time measurements
  3. Much higher throughput than first and second generation techniques.
  4. Lower price per Mbp generated sequence
  5. Longer reads
43
Q

What is a ZMW ?

A

zero-mode waveguide wells- creates an illuminated observation volume that is small enough to observe only a single nucleotidebeing incorporated by the DNA polymerase

44
Q

What are the steps within Pacific bioscience sequencing ?

A
  1. The platform uses a DNA polymerase anchored to the bottom surface of a ZMW.
  2. Differentially labelled nucleotides enter the ZMW via diffusion and occupy the ‘detection volume’ .
  3. During an incorporation event, the labelled nucleotide is ‘held’ within the detection volume by the polymerase for tens of milliseconds.
  4. As each nucleotide is incorporated, the label located on the terminal phosphate is cleaved off and diffuses out of the ZMW
45
Q

What are the benefits of Pacific bioscience sequencing ?

A

Very efficient: fewer expensive chemicals have to be used
Very sensitive
Long reads (10-15 Kbp)

46
Q

What are the positive and negatives of nanopore sequencing ?

A

Strengths: cheap, fast, simple, large reads, scalable, …

Problem: rather high error rate

47
Q

What is a Q score ?

A

measures the probability that a base is incorporated incorrectly (Higher Score indicates a smaller probability of error).

48
Q

What is Phredd 33 ?

A

A method of quality encoding during genome assembly.

49
Q

What are the 2 methods of assembling contigs ?

A

De novo= No scaffold sequence to guide alignment.

Read mapping=Reads are aligned to a reference sequence.

50
Q

What are the 2 assembly algorithms ?

A

Greedy method- Incremental build. Builds using highest scoring overlap.
Graph based: Pre-processes the data to produce a graph structure of pairwise overlap info.

51
Q

What type of graph deals with repetitive DNA regions and how does it work ?

A

de Bruijn- Split short reads into shorter uniform reads.

52
Q

What is the K value ?

A

The length of the string

53
Q

What does velvet do and what is it ?

A

A genome assembler that use de Bruijn graph based algorithm. Takes short reads and removes errors to produce high quality contigs.

54
Q

What is the N50 statistic ?

A

The N50 value informs researcher that 50% of the genome is assembled in contigs larger than the N50 value.

55
Q

What is genome annotating ?

A

Attaching biological meaningful info to genome sequences.

56
Q

What is an ORF ?

A

Open reading frame- Part of the reading frame that contains no stop codons. UAA UGA UAG

57
Q

What are the 3 methods for gene prediction ?

A

AB initio method- Uses info from genomic sequence such as GC content and ORFs
Database similarity - Uses public databases to identify sequences that are similar
Combiners: Use both techniques

58
Q

What does hierarchical shotgun sequencing require ?

A

A genome map as preliminary data

59
Q

What are the 9 steps in hierarchical shotgun sequencing?

A
  1. Fragmentation of genome
  2. Inserted into plasmid
  3. Plasmid Cloned in e.coli
  4. Investigate order of clones in genome using hybridisation, to give full genome map.
  5. Take each clones and fragment DNA
  6. Apply sequencing method
  7. Form contigs
  8. Merge contigs
60
Q

What are the steps in bridge PCR ?

A
  1. initiated by the addition of unlabelled NTPs.
  2. DNA amplification occurs and then DNA folds and form a bridge due to hybridisation of adapters.
  3. Add polymerase and primers to make a complementary strand.
  4. Increase the temp to break bridge connection leaving two ssDNA, the forward and reverse strand.
  5. This form millions of clusters for illumina sequencing

Animal kingdom (13 decks)

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