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BMS2042 > Model Organisms and the Human Genome Project > Flashcards

Model Organisms and the Human Genome Project Flashcards

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1
Q

Definition

a method of DNA sequencing first commercialized by Applied Biosystems, based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication

A

Sanger sequencing

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2
Q

Definition

free-living (not parasitic), transparent nematode (roundworm), about 1 mm in length, that lives in temperate soil environments

A

Caenorhabditis elegans

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3
Q

What are the advantages of zebrafish as a model organism?

A
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4
Q

Difference between individuals occurs due to what?

A

SNP and Copy Number Variations

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5
Q

Define

Deuterostome

A

a subtaxon of the Bilateria branch of the subkingdom Eumetazoa, within Animalia, and are distinguished from protostomes by their deuterostomic embryonic development; in deuterostomes, the first opening (the blastopore) becomes the anus, while in protostomes, it becomes the mouth

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6
Q

What are the advantages of using nematodes as a model organism?

A
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7
Q

Definition

a class of DNA sequencing methods currently under active development

A

Third generation sequencing

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8
Q

Definition

Scientific name for the zebrafish

A

Danio rerio

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9
Q

Definition

a small mammal of the order Rodentia, characteristically having a pointed snout, small rounded ears, and a long naked or almost hairless tail. Scientific name for the mouse

A

Mus musculus

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10
Q

Define

Phylogenetic tree

A

a diagram that represents evolutionary relationships among organisms

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11
Q

Why was the Human Genome Project started?

A
  • Make a complete and accurate sequence of the human genome
  • Identify all genes
  • Understand the tole of genes in cell differentiation, development, ageing, metabolism etc.
  • Personalised medicine
  • Role in disease
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12
Q

Definition

an approach used to identify genes (or set of genes) responsible for a particular phenotype of an organism

A

Forward genetics

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13
Q

What are the disadvantages of mice as model organisms?

A
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14
Q

Define

Euchromatin

A

chromosome material which does not stain strongly except during cell division. It represents the major genes and is involved in transcription

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15
Q

Definition

the whole set of molecular interactions in a particular cell

A

Interactome

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16
Q

Definition

a subtaxon of the Bilateria branch of the subkingdom Eumetazoa, within Animalia, and are distinguished from protostomes by their deuterostomic embryonic development; in deuterostomes, the first opening (the blastopore) becomes the anus, while in protostomes, it becomes the mouth

A

Deuterostome

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17
Q

What are the disadvantages of using yeast as a model organism?

A
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18
Q

Define

SINEs

A

Short sequences of non-coding DNA present at high frequencies in various eukaryotic genomes

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19
Q

What collection of sequencing methods does Monash use?

A

Next generation sequencing

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20
Q

Definition

Short sequences of non-coding DNA present at high frequencies in various eukaryotic genomes

A

SINEs

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21
Q

Definition

a method of DNA sequencing (determining the order of nucleotides in DNA) based on the “sequencing by synthesis” principle. It differs from Sanger sequencing, in that it relies on the detection of pyrophosphate release on nucleotide incorporation, rather than chain termination with dideoxynucleotides

A

Pyrosequencing

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22
Q

Definition

an international research effort to determine the DNA sequence of the entire human genome

A

Human genome project

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23
Q

Definition

the study of transcriptomes and their functions

A

Transcriptomics

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24
Q

Definition

a species of fly (the taxonomic order Diptera) in the family Drosophilidae. The species is known generally as the common fruit fly (though inaccurately) or vinegar fly

A

Drosophila melanogaster

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25
# Define *Mus musculus*
a small mammal of the order Rodentia, characteristically having a pointed snout, small rounded ears, and a long naked or almost hairless tail. Scientific name for the mouse
26
# Define Copy number variation (CNV)
a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals in the human population
27
# Define Genomics
the branch of molecular biology concerned with the structure, function, evolution, and mapping of genomes
28
Why are human not feasible to conduct research on?
Low progeny numbers Can not genetically manipulate High cost Not true breeding Long generation time ETHICS
29
# Definition chromosome material which does not stain strongly except during cell division. It represents the major genes and is involved in transcription
Euchromatin
30
# Definition A cloning method based on the generation of random large fragments of DNA which are inserted (cloned) into vectors to form a genome library—a large number of different recombinant DNA molecules
Shot gun cloning
31
What was the original method used to sequence the genome?
Sanger sequencing
32
# Define *Saccharomyces cerevisiae*
a species of yeast. It has been instrumental to winemaking, baking, and brewing since ancient times
33
# Define Forward genetics
an approach used to identify genes (or set of genes) responsible for a particular phenotype of an organism
34
# Definition the branch of molecular biology concerned with the structure, function, evolution, and mapping of genomes
Genomics
35
# Definition a diagram that represents evolutionary relationships among organisms
Phylogenetic tree
36
# Define Third generation sequencing
a class of DNA sequencing methods currently under active development
37
# Define *Danio rerio*
Scientific name for the zebrafish
38
# Definition the study of proteomes and their functions
Proteomics
39
What are the advantages of mice as model organisms?
40
Roughly what percentage of the human genome encode proteins?
~2%
41
What are the disadvantages of using nematodes as a model organism?
42
# Definition a method that is used to help understand the function of a gene by analyzing the phenotypic effects of specific engineered gene sequences
Reverse genetics
43
# Define Interactome
the whole set of molecular interactions in a particular cell
44
# Define *Drosophila melanogaster*
a species of fly (the taxonomic order Diptera) in the family Drosophilidae. The species is known generally as the common fruit fly (though inaccurately) or vinegar fly
45
# Define Shot gun cloning
A cloning method based on the generation of random large fragments of DNA which are inserted (cloned) into vectors to form a genome library—a large number of different recombinant DNA molecules
46
# Define Sanger sequencing
a method of DNA sequencing first commercialized by Applied Biosystems, based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication
47
# Define Human genome project
an international research effort to determine the DNA sequence of the entire human genome
48
How does Sanger Sequencing work?
49
What are the disadvantages of using Drosophila as a model organism?
50
What are the advantages of using yeast as a model organism?
51
What is clone-by-clone sequencing?
In clone-by-clone sequencing, the genome is broken up into large chunks, 150 kilobases long (150,000 base pairs). The location of these chunks on the chromosomes is recorded (mapped) to help with assembling them in order after sequencing. The chunks are then inserted into Bacterial Artificial Chromosomes (BACs) and put inside bacterial cells to grow. The chunks of DNA are copied each time the bacteria divide to produce lots of identical copies. The DNA in the individual bacterial clones is then broken down into even smaller, overlapping fragments. Each fragment is 500 base pairs long so that they are a more manageable size for sequencing. These fragments are put into a vector that has a known DNA sequence. The DNA fragments are then sequenced, starting with the known sequence of the vector and extending out into the unknown sequence of the DNA. Following sequencing, the small fragments of DNA are pieced together by identifying areas of overlap to reform the large chunks that were originally inserted into the BACs. This ‘assembly’ is carried out by computers which spot areas of overlap and piece the DNA sequence together. Then, by following the map constructed at the beginning, the large chunks can be assembled back into the chromosomes as part of the complete genome sequence.
52
# Define Pyrosequencing
a method of DNA sequencing (determining the order of nucleotides in DNA) based on the "sequencing by synthesis" principle. It differs from Sanger sequencing, in that it relies on the detection of pyrophosphate release on nucleotide incorporation, rather than chain termination with dideoxynucleotides
53
# Definition an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait
Genome-wide association study (GWAS)
54
# Definition chromosome material of different density from normal (usually greater), in which the activity of the genes is modified or suppressed
Heterochromatin
55
# Define LINES
a group of non-long terminal repeat retrotransposons which are widespread in the genome of many eukaryotes
56
What are the two types of first generation sequencing methods?
Sanger sequencing Capillary electrophoresis sequencing
57
# Define Transcriptomics
the study of transcriptomes and their functions
58
# Definition a group of non-long terminal repeat retrotransposons which are widespread in the genome of many eukaryotes
LINES
59
# Definition a field of molecular biology that attempts to make use of the vast wealth of data given by genomic and transcriptomic projects (such as genome sequencing projects and RNA sequencing) to describe gene (and protein) functions and interactions
Functional genomics
60
# Definition a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals in the human population
Copy number variation (CNV)
61
# Define Capillary electrophoresis sequencing
a family of electrokinetic separation methods performed in submillimeter diameter capillaries and in micro- and nanofluidic channels
62
# Define Genome-wide association study (GWAS)
an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait
63
# Define Proteomics
the study of proteomes and their functions
64
# Definition a species of yeast. It has been instrumental to winemaking, baking, and brewing since ancient times
*Saccharomyces cerevisiae*
65
What things do you need to consider when studying model organisms?
1. What question can be asked in the animal? 2. Is it feasible? 3. Is it ethical? 4. What are the genetics, has the genome been sequenced? 5. Can it be genetically manipulated? 6. What are the drawbacks?
66
# Define Heterochromatin
chromosome material of different density from normal (usually greater), in which the activity of the genes is modified or suppressed
67
# Definition a family of electrokinetic separation methods performed in submillimeter diameter capillaries and in micro- and nanofluidic channels
Capillary electrophoresis sequencing
68
# Define Functional genomics
a field of molecular biology that attempts to make use of the vast wealth of data given by genomic and transcriptomic projects (such as genome sequencing projects and RNA sequencing) to describe gene (and protein) functions and interactions
69
# Definition the haploid set of chromosomes in a gamete or microorganism, or in each cell of a multicellular organism
Genome
70
# Define Genome
the haploid set of chromosomes in a gamete or microorganism, or in each cell of a multicellular organism
71
What are the Next Generation Sequencing methods?
Pyrosequencing Sequencing by synthesis
72
# Define *Caenorhabditis elegans*
free-living (not parasitic), transparent nematode (roundworm), about 1 mm in length, that lives in temperate soil environments
73
True or False: Transcriptomics and proteomics are not genome sequencing techniques
True
74
What are the disadvantages of the zebrafish as a model organism?
75
# Define Reverse genetics
a method that is used to help understand the function of a gene by analyzing the phenotypic effects of specific engineered gene sequences
76
What are the advantages of using Drosophila as a model organism?

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