Lectures 19-20

Question 1

What is a genome?

Answer 1

the total genetic information (or _DNA sequence__) carried by a cell or
an organism

Question 2

What is genomics?

Answer 2

biological studies utilizing the entire __DNA sequence__
information of an organism(s)

Question 3

What does the recombinant DNA technique construct?

Answer 3

genomic & cDNA libraries

Question 4

cDNAs are the complimentary DNAs of what?

Answer 4

mRNAs synthesized by reverse transcriptase enzyme from virus

Question 5

What is the transcriptome?

Answer 5

the entire complement of __RNAs__ produced by a cell

Question 6

What is the proteome?

Answer 6

The entire complement of proteins produced by a cell

Question 7

What is proteomics?

Answer 7

the systematic study of the amounts, modifications,
interactions, localization, and functions of all or subsets of proteins at the whole-
organisms, tissue, cellular and subcellular levels.

Question 8

What can replicate single-stranded cDNA into double-stranded cDNA (ds cDNA)?

Answer 8

DNA polymerase

Question 9

Who developed DNA sequencing?

Answer 9

Frederick Sanger

Question 10

What is the mechanism of DNA sequencing?

Answer 10

1. Same concept as DNA replication
2. Use _di-deoxynucleotides __ to stop the replication
3. Only one strand is used as the template
4. Use _1__primer instead of two as in PCR
5. Set up 4 reactions with regular nucleotides and a single dideoxynucleotide.
6. Generate DNA fragments of different lengths
7. Run the products on gel and read the sequence from bottom to top of gel

Question 11

What is automated DNA sequencing?

Answer 11

1. Use __fluorescence__ labeled dideoxynucleotides
2. Reaction is done in __1_ tube.
3. Data are read and assembled by computer
4. Sequencers provide accurate sequences up to __1000__ bp long.

Question 12

What are the procedures of the genome sequencing project?

Answer 12

1. Generate recombinant plasmids containing DNA fragments (clones)
2. use automatic sequencer to obtain nucleotide sequences
3. assembly of DNA clones by actual __sequences___
   2
4. _annotation__ – to identify genes and their locations

Question 13

How much bp does the human genome contain?

Answer 13

3.2 billion

Question 14

How many base pairs encode proteins?

Answer 14

1%

Question 15

How many genes are in the human body?

Answer 15

30,000, which are unequally distributed

Question 16

How many proteins are compared to genes?

Answer 16

300,000 to 30,000 by alternative splicing

Question 17

What does the genomic experiment FISH used for? (uses labeled DNA probe)

Answer 17

1. to locate a DNA fragment or gene
2. to examine chromosome structures

Question 18

What does the genomic experiment microarray used for? (uses flourescence-labeled RNA or cDNA probes)

Answer 18

1. to examine the expression profiles, i.e. __transcriptome____.
2. to compare transcriptional regulation or differences between tissues or
   conditions.

Question 19

What is the G1 phase of the cell cycle?

Answer 19

primary growth

Question 20

What is the S phase of the cell cycle?

Answer 20

DNA synthesis

Question 21

What is the G2 phase of the cell cycle?

Answer 21

second growth

Question 22

What is the M phase of the cell cycle?

Answer 22

mitosis (nuclear division) & cytokinesis (cytoplasmic division)

Question 23

What is the G0 phase of the cell cycle?

Answer 23

resting state (or quiescence) – neurons and skeletal muscle cellls

Question 24

What are the major cdks and cyclins at S-Cdk complex?

Answer 24

cyclin A pairs with Cdk2

Question 25

What are the major cdks and cyclins at M-Cdk complex?

Answer 25

cyclin B pairs with Cdk1

Question 26

What are the major cdks and cyclins at G1-Cdk complex?

Answer 26

cyclin D pairs with Cdk4

Question 27

What are the characteristics of cyclin?

Answer 27

1. expressed in a __cyclic__ fashion (Fig. 18-6)
2. no enzyme activity
3. bind and __activate__ Cdks

Question 28

What makes up Cdk?

Answer 28

1. bound by cyclin
2. activated by phosphorylation then dephosphorylation (more below)

Question 29

activation cycle example

Answer 29

M-Cdk
a. Cyclin B binds and activates Cdk1 inhibitory phosphorylation of M-Cdk 
b. Cdc25 activates M-Cdk by dephosphorylation positive feedback phosphorylates
more Cdc25  activate _APC__  complete M phase

Question 30

deactivation cycle example

Answer 30

APC  __ubiquitylation__ of cyclin B  degradation of cyclin B
 de-activation of M-Cdk

Question 31

What does DNA damage inhibit?

Answer 31

G1/S Cdk and S-Cdk

Question 32

DNA damage inhibition cycle

Answer 32

DNA damage  kinases  phosphorylate __p53__ transcription of p21
_p21__ protein binds and inhibits G1/S-Cdk and S-Cdk

Question 33

What are the two types of cell death?

Answer 33

necrosis___ & __apoptosis__ (programmed cell death)

Question 34

What is apoptosis carried out by?

Answer 34

family of proteases called caspases

Question 35

What are procaspases activated through?

Answer 35

cleavage and assembly

Question 36

What are the main proteins that regulate the activation of procaspases?

Answer 36

members of the Bcl2 family

Question 37

What are the two members of the Bcl2 family used in apoptosis?

Answer 37

Bax and Bak

Question 38

Bax and Bak form channels on the mitochondria releasing what?

Answer 38

cytochrome C___ which binds to adaptor protein and then activates the
first caspase, __procaspase 9____.