Leys: Genomics, Proteomics and Metabolomics

Question 1

of bases in the human genome

Answer 1

3 billion

Question 2

protein coding genes

Answer 2

20,000 - 25,000

Question 3

Alternative splicing/ gene promoters result in what?

Answer 3

4-6 different mRNAs from a single gene

Question 4

of protein coding mRNAs (transcriptome) may be as large as what?

Answer 4

100,000

Question 5

The original human genome project used what kind of approaches for sequencing?

Answer 5

Clone by clone and shotgun.

Question 6

How many gaps are remaining in the Human genome?

Answer 6

250 gaps (compared to 150,000 in draft)

Question 7

Since the completion of the human genome, sequencing capacity has _____ dramatically while costs have _____.

Answer 7

Increased, declined.

Question 8

OMIM

Answer 8

Online Mendelian Inheritance in Man (OMIM) database has >10,000 entries that associate human genes with inherited diseases.

Question 9

SNPs

Answer 9

Singe nucleotide polymorphisms are mapped base positions in the genome where nucleotie varies among people

Question 10

23 and me is an example of what?

Answer 10

Companies that are offering full genome scans to individuals for less than 100$. This analysis is based on SNP (single nucleotide polyorphism analysis)

Question 11

Chromosomal Microarray Analysis (CMA)

Answer 11

Labeled DNA hybridized to array of several million oligonucleotide on chips. This can be used for prenatal screening for early detection of chromosomal defects.

Question 12

Transcriptome

Answer 12

Complement of mRNAs, contaiing protein coding sequences but there are also other RNAs produced that play structural or regulatory functions (miRNA, siRNA, etc.)

Question 13

The transcriptiome can be studied using what?

Answer 13

Microarrays, a collection of complementary (cDNA) made from mRNA or synthetic oligonucleotides arranged on a solid phase slide in a defined order.

Question 14

How many oligonucleotide probes per genea are used?

Answer 14

Several

Question 15

Two samples of mRNA can be compared how?

Answer 15

by labeling each with a different fluorescent dye and hybridizing them to the same array. (eg two color arrays can compare normal and cancer cells(,

Question 16

What is replacing microarray aproaches as advances are made in sequencing technology?

Answer 16

RNAseq or sequencing the entire complement of RNA in a sample.

Question 17

Data Analysis is ________ intensive and requires what?

Answer 17

bioinformatics, requiring stringent statistical analyss.

Question 18

Proteomics is the study of what?

Answer 18

the protein complement of a cell.

Question 19

Comparative proteomics is?… to identify what?

Answer 19

the analysis of protein profiles from two or more samples (eg diseased vs healthy cells) to identify quantitative differences that could be responsible for observed phenotypes.

Question 20

Proteomics can identify ________________ that cannot be detected by transcriptome analysis.

Answer 20

posttranslational modifications

Question 21

How can you separate proteins?

Answer 21

2D polyacrylamide gel electrophoresis (PAGE) and Liquid chromatography (FPLC, HPLC) do what?

Question 22

Proteins can be identified using what?

Answer 22

Mass spectrometry.

Question 23

Metabolomics is what?

Answer 23

Identification and quantification of steady-state levels of intracellular metabolites (sugars, amimo acids, lipids, nucleotides, etc.) Because the technology to identify every metabolite in a biological sample is not available, targeted metabolomics is often carried out, where a few specific metabolites are measured.