Block 3 CFP2

Question 1

A visual representation of all the chromosomes in a cell’s nucleus when stained by Giemsa. Define by dark bands and light bands giving each chromosome a unique appearance

Answer 1

Cytogenetic Mapping

Genomics

Question 2

Also known as gene mapping, this technique allows DNA fragments to be assigned a place on a chromosome after overlapping fragments have been created

Answer 2

Physical Clone Map

Genomics

Question 3

A microarray that allows entire genomes to be analyzed and compared with a single hybridization

Answer 3

CGH

Genomics

Question 4

using restriction digest to detect mutations and identify them using agarose gel, nitrocellulose/ nylon membrane and radioactive probes

Answer 4

RFLP and southern blotting

Genomics

Question 5

a microarray that can detect many single nucleotide polymorphisms simulataneously

Answer 5

SNP chips

Genomics

Question 6

a method of testing for SNP using oligonucleotide probes

Answer 6

ASO technique

Genomics

Question 7

Use of fluorescent probes on an interphase or metaphase chromosome to detect abnormalities in a DNA sample

Answer 7

FISH

Genomics

Question 8

a layout of the number and appearance of each chromosome to detect abnormalities in a DNA sample

Answer 8

Karyotype

Genomics

Question 9

Shotgun Sequencing

Answer 9

1. Genomic DNA is extracted
2. DNA digested by restriction enzymes
3. Fragments are separated by electrophoresis
4. Fragments (contigs) are sequenced
5. overall sequence is based on fragment overlap

Genomics

Question 10

Dideoxynucleotides?

Answer 10

Sanger sequencing, terminate DNA synthesis

Genomics

Question 11

After electrophoresis and blotting unto nylon membranes, radioactive probes specific to a transcript (mRNA) are used to identify a particular mRNA from a sample

Answer 11

Northern Blotting

Transcriptomics

Question 12

Allows visualization of a specific gene that is being expressed by attaching a reporter gene to its promoter

Answer 12

Reporter genes

Transciptomics

Question 13

mRNA is converted to cDNA and small pieces of each cDNA are extracted. These sequences are called tags and are joined together to form a strip (concatemer). The concatemer is then sequenced and processed by a computer to determine patterns of mRNA expression. No sequence knowledge required

Answer 13

SAGE

Transcriptomics

Question 14

mRNA is converted to cDNA, tagged and fluorescently labelled. The cDNA is amplified using PCR, then attached to beads. Each bead can hold about 100,000 copies of single cDNA. Each cDNA is sequenced and identified. Small amounts of transcripts can be accurately identified. No sequence knowledge required

Answer 14

Massively Parallel Signature Sequencing

Transcriptomics

Question 15

used to compare 2 different samples. Each sample is labelled with a different fluorescent dye and hybridized to the same chip, competing for binding to the same spot.

Answer 15

Two channel microarray

Transcriptomics

Question 16

a single sample is labelled with a fluorescent dye and hybridized to a microarray chip containing probes

Answer 16

One channel microarray

Transcriptomics

Question 17

in the expression array, probes are made from DNA sequences across the length of a chromosome, across particular regions of a genome, or the entire genome of an organism. cDNA is allow to hybridize to the probes and in this way it is possible to scan the genome for areas not previously known to contain genes and id chromosomal regions that are transcriptionally active

Answer 17

Tiling Array

Transcriptomics

Question 18

Separating and retrieving proteins using liquid capillary action, cation exchange or reverse-phase

Answer 18

chromatography

proteomics

Question 19

the process of peptide ionization followed by separation of ions based on mass and charge

Answer 19

Mass spectrometry

proteomics

Question 20

Proteins chemically fragmented; fragments sequenced by removing amino acids from the N-terminal; proteins identified using existing databases

Answer 20

Edman Sequencing

proteomics

Question 21

Labeling of proteins from 2 different sources with different isotopes of an atom. The samples are mixed and then Mass Spec is done to ID the proteins are present in the 2 samples and the quality of these proteins

Answer 21

ICAT

proteomics

Question 22

Use of transcription factor domains to look for interactions between proteins to influence gene expression

Answer 22

Yeast 2-hybrid system

proteomics

Question 23

breakdown of proteins using different kinds of enzymes

Answer 23

proteolysis

proteomics

Question 24

the digestion of proteins using trypsin

Answer 24

Trypsinization

proteomics

Question 25

insertion of known proteins into phage coats in order to ID interactions with unknown proteins

Answer 25

Phage display approach

proteomics

Question 26

a measure of the quality of the alignment between the query sequence and the search results

Answer 26

Score Value

Question 27

Attaching biological information, such as regulation, biochemical function and expression to genomic elements

Answer 27

Functional Annotation

Question 28

The number of different alignments with scores that are equivalent to or better than alignment scores that are expected to occur by chance

Answer 28

E-value

Question 29

Identifying genomic elements such as genes and other important sequences like coding regions and regulatory motifs

Answer 29

Structural Annotation

Question 30

Obtaining biological information from unprocessed sequence data to create a labeled genome

Answer 30

genome annotation

Question 31

a presentation of 2 compared sequences showing the regions of greatest statistical similarity

Answer 31

Alignment

Question 32

A sequence to be used in a BLAST search that is made up of amino acids or nucleotides that can be either in FASTA format, Bare sequence or an identifier such as Accession number

Answer 32

Query Sequence