Biotech Final-Lecture 1

Question 1

What is a PUF?

Answer 1

A protein of unknown function.

Question 2

What is bioinformatics?

Answer 2

A powerful and commonly used tool to assist in characterizing the function of a protein of interest.

Question 3

What are two different common computer bioinformatics tools?

Answer 3

1) Prediction of protein function

2) Database mining

Question 4

What is prediction of protein function? (The bioinformatics tool)

Answer 4

Taking a primary protein sequence and, based on a conserved domain search (CD search), predict the likely function of a PUF.

Question 5

The prediction of protein function compares multiple proteins and determines the putative function of a protein based on _______ domains among functionally _______ proteins.

Answer 5

i) conserved

ii) homologous

Question 6

When using the prediction of protein function, we are often looking at protein ______.

Answer 6

Orthologs

Question 7

What are orthologs?

Answer 7

Genes in different species that evolved from a common ancestral gene by speciation. Normally, orthologs retain critical domains throughout evolution.

Question 8

What is database mining?

Answer 8

Database program where one can gather a wealth of organized information of any protein of interest rapidly.

Question 9

What does database mining use?

Answer 9

Uses a computer software and generally different mass spec. data to quickly determine the identity of a PUF or function based on similar domains determined by a computer algorithm.

Question 10

PTEN affects what in the Tor pathway?

Answer 10

PI3 (makes it PI2)

Question 11

What is the significance of recombinant protein production? What is the use of this?

Answer 11

1) Required for in-vitro studies of the pathway of a given protein
2) Required for determining the 3D structure
3) Determining functional architecture
4) Provide functional clues on the protein
5) Elucidate molecular details of catalysis

Question 12

What is the significance of Mass Spectrometry to PTEN biology?

Answer 12

1) Elucidation of regulatory mechanisms controlling protein function
2) Identification of interacting proteins
3) Mapping of PTMs

Question 13

What is the significance of mammalian cell culture system?

Answer 13

1) Visualize PTEN localization in human cells
2) Characterization of PTEN on cellular processes
3) Test mutations for effect on PTEN function
4) Capture novel interacting proteins prior to MS using CoIP
5) Critical for discovering novel functions of proteins