Molecular - White

Question 1

What makes cells different?

Answer 1

Differences in gene expression

Question 2

What is the make up of a transcription factor?

Answer 2

N–DNA binding module — dimerization module — activation module —- regulatory module –C

Dimerization and regulatory are optional, DNA binding and activation are a must

Question 3

Helix-turn-helix motif

Answer 3

Simplest; two alpha helices connect by a short chain of aas that make the “turn” at a fixed angle; longer helix portion = DNA binding module; helix-turn-helix proteins bind DNA as dimers

Question 4

Zinc Finger domain

Answer 4

Includes Zn atom in the DNA binding motif; binds to major groove of DNA

Question 5

Leucine supper motif

Answer 5

Two alpha helical DNA binding domains; dimerization through leucine zipper region; interactions b/w hydrophobic aa side chains (leucines) at every 7 aa down 1 side of alpha-helix –> forms zipper structure, grabs DNA like clothes pin

Question 6

Helix loop helix domain

Answer 6

Consists of a short alpha chain connected by a loop to a second longer alpha chain. Can occur as homodimers or heterodimers. 3 domains: DNA binding domain, dimerization domain and activation domain.

Question 7

What are the 2 ways in which RNA is de stabilzed?

Answer 7

1. Decapping: exposed mRNA degraded from 5’ end (serves to protect RNA from RNA degrading enzymes)
2. mRNA degraded from 3’ end through poly-A tail and into coding region

Question 8

Post-translational processing and modifications

Answer 8

Required by proteins to be functional; proteins must fold into their 3D conformations helped by chaperones; bind cofactors

Ex: non-covalent interactions like folding and cofactor binding; covalent modification by glycosylation, phosphorylation, acetylation; binding to other subunits

Question 9

Protea some

Answer 9

Apparatus that deliberately destroys aberrant protein

Question 10

What are 2 examples of controls of gene expression?

Answer 10

1. Methylation and genomic imprinting: what genes get expressed (or not) from mom and dad
2. X-chromosome inactivation: even things out XX vs. XY - 2X chromosomes vs. 1 X chromosome

Question 11

What are the 3 transition checkpoints in the cell cycle control system?

Answer 11

1: Start: G1 to S; cell commits to cell cycle entry and chromosome duplication
2. G2/M: move into chromosome alignment on spindle in metaphase
3. Metaphase to anaphase transition; trigger sister chromatid separation and cytokinesis

Question 12

Cdks

Answer 12

Heart of cell-cycle control system; ACTIVITES of them rise and fall during cell cycle (not numbers); dependent on cyclins (must be bound to have protein kinase activity)

Question 13

What are the proteins that regulate Cdks?

Answer 13

Cyclins

Question 14

What is the property of Cdk when cyclin is not bound (inactive)?

Answer 14

The active site of Cdk is blocked by the T loop; binding cyclin causes the T loop to move out of the active site (Cdk partly active); phosphorylation of Cdk at T loop fully activates it (cave site)

Question 15

What protein causes the phosphorylation of Cdk in the cave site to make it fully active?

Answer 15

CAK (Cdk activating kinase)

Question 16

Condensin

Answer 16

At the end of S phase, chromosomes dramatically compact and sister chromatids become deistic separate units b/c of Condensin

Question 17

What activates APC/C to complete mitosis?

Answer 17

M-Cdk

Question 18

Force One in chromosome movement

Answer 18

Depolymerization: major force pulls the kinetochore and chromosome toward the spindle pole; depolymerization of the plus end of the microtubules drives the pulling of the kinetochore poleward

Question 19

Force 2 of chromosome movement:

Answer 19

Microtubules flux: microtubules are moved toward spindle poles while being dismantled at minus ends; tubulin added at plus end while being removed at minus end

Question 20

Force 3 of chromosome movement

Answer 20

Polar Ejection Force: kinesin 4, 10 motors on chromosomes interact w/ microtubules and transport chromosomes from poles; push pull phenomenon

Question 21

Procaspases

Answer 21

Inactive caspase precursor

Question 22

Executioner caspases:

Answer 22

Destroys actual target - executes apoptosis (caspase-3)

Question 23

What forms the apoptosome?

Answer 23

When cytochrome c is released from mitochondria, it binds to a protein called Apaf1 to form it.

Question 24

BH123 in apoptosis

Answer 24

BH123 proteins become activated, form aggregation in mitochondrial outer membrane and induce the release of cytochrome c - the apoptosome is formed

Question 25

Bcl2 proteins

Answer 25

Blocks BH123 from aggregated and allowing release of cytochrome c

Question 26

BH3-only protein

Answer 26

Inactivates Bcl2 to allow BH123 to aggregate

Question 27

IAPs

Answer 27

Block caspases

Question 28

Anti-IAPs

Answer 28

Neutralize the IAPs and liberate caspases

Question 29

Oncogenes

Answer 29

Over activity mutation: GOF; involves single mutation event and activation of gene causing proliferation (dominant); “gas pedal”

Question 30

Tumor suppressor genes

Answer 30

Under activity mutations; LOF; involve genes that inhibit growth. Mutation event: one gene - no effect; second mutation causes problems (recessive); “brakes”

Question 31

What are the different ways proto-oncogenes can be activated in to oncogenes?

Answer 31

1. Deletion or point mutation in coding sequence
2. Regulatory mutation
3. Gene amplification
4. Chromosome rearrangement

Question 32

What are the 2 major categories of tumor suppressor genes?

Answer 32

1. Proteins that normally restrict cell growth and proliferation
2. Proteins that maintain the integrity of the genome

Question 33

Hereditary Rb

Answer 33

LOF or deletion of 1 copy of Rb in every cell b/c defect is inherited so predisposed to be cancerous; but have 1 good copy of Rb; somatic event occurs which elimates the good copy and get a loss of heterozygosity

Question 34

Sporadic form of Rb

Answer 34

Cancerous cells have both copies of Rb mutated; 2 hit hypothesis; Rb is a regulator of the cell cycle

Question 35

What mutation is important in colorectal cancer?

Answer 35

Loss in APC mutation - LOF; APC is a tumor suppressor gene