Tonon: Lecture I

Question 1

Central Dogma

Answer 1

DNA to RNA to proteins

Question 2

What drives gene expression?

Answer 2

RNA polymerase II

Question 3

What is a gene?

Answer 3

group of introns and exons, but some genes only have 1 exon

genes also have promoters and enhancers

Question 4

What is epigenetics? What is an example?

Answer 4

External factors that influence the way genes work

DNA methylation, which reduces transcription or histone function

Question 5

Compare and contrast the following in regards to bacteria and mammals:

DNA Replication
Cell Cycle
Transcription Speed
Translation
Half-Life

Answer 5

faster in bacteria
bacteria
same, but mammals have more to transcribe
same
faster (shorter) in bacteria

Question 6

Why do mammalians take longer to get new RNAs and proteins?

Answer 6

post-translational modifications

Question 7

Are RNA and proteins bigger in bacteria or mammalian cells?

Answer 7

they are the same in both

Question 8

monoclonal antibody vs polyclonal antibody

Answer 8

monoclonal are recognized by a single epitope

polyclonal are recognized by many epitopes

Question 9

What is a heatmap?

Answer 9

It is a representation of the amount of specific genes expressed in different tissues

Question 10

What are house-keeping proteins?

Answer 10

they are proteins that are found in all cells

the main one used in WB is actin as a positive-control because it is always expressed at the same levels in all cells

Question 11

What is an example of a protein that can be used as a loading control in WB?

Answer 11

actin

Question 12

What percentage of total protein mass is represented by housekeeping proteins?

Answer 12

75%

Question 13

What are the 2 groups of housekeeping proteins?

Answer 13

proteins that are truly expressed in every cell type

proteins derived from cells present in every tissue

Question 14

Why are DNA and RNA easier to analyze?

Answer 14

they are hybridized

the complementary sequence is always there

Question 15

What is Tonon’s favorite method to analyze mRNA?

Answer 15

SAGE

Question 16

What are the 3 principles SAGE is based on?

Answer 16

short sequence tag of DNA/RNA can identify a sequence in the genome

sequence tags can be linked to form longer molecules that can be cloned and sequenced

expression level is known due to the number of times a particular tag is observed

Question 17

How does SAGE work?

Answer 17

https://www.youtube.com/watch?v=kot_IKoqMYU

Question 18

What are some disadvantages to SAGE?

Answer 18

complicated preparation
large amount of sequencing
labor intensive
not sensitive
introduced the same year as microarrays

Question 19

What is a microarray?

Answer 19

https://www.youtube.com/watch?v=NgRfc6atXQ8

Question 20

What are the 3 possible results from a microarray?

Answer 20

red: CY5 - the gene is under-expressed in the cancer cell
yellow: CY3 & CY5 - the gene is expressed the same
green: CY3 - the gene is over-expressed in the cancer cell