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Genetics > Lecture--Chapter 21/22 > Flashcards

Lecture--Chapter 21/22 Flashcards

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1
Q

a chart that describes the relative locations of genes of other DNA segments on a chromosome

A

genetic map

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2
Q

cloning techniques are used to determine location of genes (number of base pairs between genes)

A

physical mapping

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3
Q

use labeled cDNA or RNA to localise a specific DNA or RNA sequence in tissue

A

In situ hybridisation

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4
Q

uses fluorescently labeled DNA DNA probes

A

fluorescence in situ hybridisation (FISH)

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5
Q

a segment of DNA found at a specific site that can be uniquely identified by PCR and gel electrophoresis

A

genetic markers

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6
Q

What are the common types of molecular markers?

A
  1. restriction fragment length polymorphism (RFLP)
  2. microsatellite
  3. sequence-tagged site (STS)
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7
Q

A site in a genome where the distance between two restriction sites varies among different individuals. These sites are identified by restriction enzyme digestion of chromosomal DNA and the use of Southern blotting.

A

restriction fragment length polymorphism (RFLP)

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8
Q

A site in the genome that contains many short sequences that are repeated many times in a row.

A

microsatellite

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9
Q

This is a general term to describe any molecular marker that is found at a unique site in the genome and is amplified by PCR.

A

sequence-tagged site (STS)

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10
Q

generated by restriction enzyme digests (EcoRI, once every 4096 bp)

A

RFLPs

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11
Q

have variation from small deletions, duplications, and mutations

A

RFLPs

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12
Q

also called short tandem repeats or short sequence repeats

A

microsatellites

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13
Q

ancestral individual in which a disease first appeared

A

founder

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14
Q

What are the aspects of physical mapping?

A
  1. higher resolution than RFLP and microsatellites
  2. used to actually isolate DNA that contains genes of interest
  3. very labour and time intensive
  4. clones that are generated can be used for sequencing genome
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15
Q

Physical mapping involves what?

A
  1. cloning a piece of DNA from a chromosome
  2. characterising the clone for its size, genes that it contains and their relative locations
  3. matching a piece of the cloned DNA to another cloned DNA and repeating the process until all the DNA of a given chromosome is identified and organised
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16
Q

What are the steps of mapping?

A
  1. a sample of chromosomal DNA is cut into smaller pieces with restriction enzymes
  2. the fragments are cloned into vectors to create a DNA library
  3. the pieces are organised according to their exact location on a chromosome
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17
Q

a collection of overlapping clones (vectors)

A

contig

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18
Q

What are the cloning vectors that can accept large pieces of DNA?

A
  1. yeast artificial chromosomes (YACs)
  2. bacterial artificial chromosomes (BACs)
  3. P1 artificial chromosomes (PACs)
  4. cosmids
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19
Q

inserts from several hundred thousand to 2 million bp

A

yeast artificial chromosomes (YACs)

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20
Q

inserts up to 300,000 bp long

A

bacterial artificial chromosomes (BACs) and P1 artificial chromosomes (PACs)

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21
Q

hybrid between a plasmid vector and a bacteriophage. These can accept DNA fragments in the range of tens of thousands of bp

A

cosmids

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22
Q

What was the first prokaryotic genome sequenced, and when was it?

A

H. influenzae, 1995

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23
Q

What was the first fungal genome sequenced, and when was it?

A

S. cerevisiae, 1996

24
Q

What was the first insect genome sequence, and when was it?

A

D. melanogaster, 2000

25
Q

What was the first plant genome sequenced, and when was it?

A

A. thaliana, 2001

26
Q

What was the first human genome sequenced, and when was it?

A

H. sapiens, 2003

27
Q

What are the genomes sequenced used for?

A
  1. initiatives in basic research
  2. efforts to understand infectious disease and human pathogens
  3. efforts to improve agriculture
  4. efforts to understand evolution from a gene level perspective
28
Q

What are the aspects of genome sequencing projects?

A
  1. the clones from a physical map can be used for sequencing
  2. all the clones that are sequenced can be used to generate the sequence of a chromosome as their relationship is known
  3. whole genomes have been sequenced using these techniques
29
Q

What are the aspects of shotgun sequencing?

A
  1. does not require a detailed physical map
  2. sheared DNA is size-selected, cloned into appropriate vectors, and sequenced
  3. pairwise end sequencing and sequence assembly are used by using computers
30
Q

What are the steps of hierarchical genome shotgun sequencing?

A
  1. clone large fragments into BACs and create contigs.
  2. shear each BAC into smaller pieces and subclone
  3. do shotgun sequencing
  4. based on overlapping regions, create one contiguous sequence
31
Q

What are the steps of whole genome shotgun sequencing?

A
  1. shear DNA into small and large pieces
  2. clone pieces into vectors
  3. do shotgun sequencing with multiple reads (coverage)
  4. based on overlapping regions, create one contiguous sequence
32
Q

What is an example of a second-generation DNA sequence?

A
  1. Roche 454/FLX Pyrosequencer
33
Q

What is done for DNA preparation using the Roche 454/FLX Pyrosequencer?

A

DNA fragments are bound to small beads, which are dropped into tiny wells in a fibre-optic chip.

34
Q

process hundreds of thousands of reads in parallel and do not require cloning chromosomal fragments

A

new sequencing platforms

35
Q

What are the steps of pyrosequencing?

A
  1. cleave genomic DNA into fragments
  2. attach oligonucleotide adaptors
  3. denature DNA, attach primer-coated beads to one strand
  4. emulsify beads to one per droplet
  5. put beads into a picoliter plate
  6. add sequencing reagents, enzymes, and substrates
  7. measure release of PPi by formation of light
36
Q

The goal of functional genomes is:

A

to elucidate the roles of genetic sequences in a given species

37
Q

create a sequence-indexed library of mutations in the genome

A

insertional mutagenesis

38
Q

In fuctional genomics, ____ and/or ____ mutant collections are established.

A

knock-out; knock-down

39
Q

Steps of insertional mutagenesis in an Arabidopsis:

A
  1. random insertion of T-DNA
  2. sequence flanking plant DNA
  3. do gene annotation
  4. develop a web accessible search interface
  5. deposit mutant lines in a public stock facility
40
Q

study of the genome, its genes, and other nucleic acid sequences

A

genomics

41
Q

study of all of the proteins produced and how they interact with each other

A

proteomics

42
Q

gene chips are also known as

A

DNA microarrays

43
Q

What are the functions of DNA microarrays?

A
  1. monitor the mRNA expression of thousands of genes simultaneously
  2. glass or silicon slides with known fragments of bound ssDNA
  3. probed with labeled cDNA made from isolated mRNA
44
Q

What are the different types of applications of DNA microarrays?

A
  1. cell-specific gene expression
  2. gene regulation
  3. tumour profiling
  4. genetic variation
45
Q

A comparison of microarray data using cDNAs derived from RNA of different cell types can identify genes that are expressed in a certain manner.

A

cell-specific gene expression

46
Q

Environmental conditions play an important role in this. A comparison of microarray data may reveal genes that are induced under one set of conditions and repressed under another.

A

gene regulation

47
Q

Different types of cells exhibit striking differences in their profiles of gene expression.

A

tumour profiling

48
Q

Microarrays are used to identify disease-causing alleles in humans and mutations that contribute to quantitative traits in plants and other species.

A

genetic variation

49
Q

Proteomic research is:

A

technically challenging

50
Q

Proteome is often several times ___ than the genome (alternative splicing and post-translational modifications)

A

more complex

51
Q

Proteins are not as _____ as DNA.

A

stable

52
Q

What are the different applications of protein microarrays?

A
  1. protein expression

2. protein function

53
Q

An antibody microarray can measure protein expression because each antibody in a given spot recognises a specific amino acid sequence.

A

protein expression

54
Q

The substance specificity and enzymatic activities of groups of proteins can be analysed by exposing a functional protein microarray to a variety of substrates. Protein-protein interactions

A

protein function

55
Q

the whole set of molecular interactions in a particular cell

A

interactome

56
Q

Likely better correlates with organismal complexity than any other measure

A

interactome

Genetics (18 decks)

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