Ch.23: Genomics II: Functional genomics, proteomics, and bioinformatics

Question 1

What is bioinformatics? What is the goal?

Answer 1

-the application of computational technology to manage and analyze large sets of data, such as those generated by the fields of genomics and proteomics

-to analyze biological information using a mathematical/computational approach

Question 2

What are DNA microarrays?

Answer 2

use to measure the differential expression of mRNA in two types of cells or a single cell grown under different condition

Question 3

What can RNA-Seq provide?

Answer 3

the sequences of RNAs and can be used instead of DNA microarrays to
compare differences in gene expression

Question 4

What is a important note for proteomics?

Answer 4

expressed genes do not always relate to protein abundance

Question 5

What s a important note for Posttranslational covalent modification?

Answer 5

Changes may be necessary to produce a functional
protein

Question 6

What is two-dimensional gel electrophoresis? What does it involve?

Answer 6

• a separation technique that can distinguish hundreds or even
  thousands of different proteins in a cell extract

-involves 2 different gels:
- The first gel separates the proteins by pH/charge
interactions using isoelectric focusing (IEF) electrophoresis via a polyacrylamide tube gel.
- The second gel separates the proteins by size using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) using a polyacrylamide slab gel

Question 7

What is an issue with developing protein miccroarrays?

Answer 7

is more challenging and require more work than the development of DNA microarrays:
1. Proteins are much more easily damaged by the manipulations
that occur during microarray formation.
2. Synthesis and purification of proteins is much more time-consuming compared to DNA.

Question 8

What is an important note when determining the coding sequence of a gene within a DNA sequence?

Answer 8

Potential ORFs that contain a start codon followed by a long stretch of sense codons without a stop codon can be identified and are good indicators of a coding DNA sequence

Question 9

What is B.L.A.S.T?

Answer 9

basic local alignment search tool
which is used to identify identical regions in either DNA or protein sequences

Question 10

Describe the 2 formations of homologous genes

Answer 10

-When two homologous genes are found in different species these genes are termed orthologs.
-When two homologous gens are found in a single organism these genes are termed paralog

Question 11

What is a conserved site?

Answer 11

a site that is identical or similar in multiple DNA or protein sequences