What has to be bound to a cyclin depenent protein kinase for it to be active?
a cyclin molecule
What are 4 general mechanisms by which cdks are regulated?
1. presence of cyclin molecule (only active when present) 2. cellular growth factors regulate synthesis 3. phosphorylation 4. inhibitory regulating proteins
What is a cellular checkpoint?
checkpoints prevent cell cycle progression if an essential process is not complete
What are the 3 steps in DNA damage checkpoint activation (STEP)?
1. sensor proteins bind to DNA damage and recruit transducer kinases (ATM, ATR) 2. Transducer kinases amplify signal by phosphorylating effector kinases (ChK1 and Chk2) 3. Transducer and effector kinases phosphorylate protein effectors (p53, cdk) which modulate cell processes and stop the cell cycle
What is the mechanism by which cdks and checkpoint proteins regulate cell entry into S phase (cell division blocked by p53)?
G1 checkpoint 1. DNA damage activates p53 (TF) 2. p53 regulates p21 and upon p53 activation, p21 [c] increases in the cell 3. p21 then binds and inhibits cdk2/cyclinE so Rb stays attached to E2F (thereby inactive) cell won't enter S phase
What is APC?
Anaphase promoting complex- a ubiquitin ligase activated by M-cdk; APC activates anaphase and triggers degradation of M-cyclins
What is the role of p21 in checkpoint regulation of cell cycle into S phase?
inhibits cdk2/cyclinE when bound (so Rb isn't phyosphorylated)
What are the 3 chemical components of DNA and RNA?
- phosphate - Sugar (ribose (RNA) or 2' deoxyribose (DNA)) -Base: purines and pyrimidines
What is base-pairing?
bases of RNA and/or DNA pair together via hydrogen bonds`
What is Hoogsteen pairing?
An additional type of interaction between pairs of bases; T Hydrogen bonds with an AT pair or C+ bonds with a GC pair; allows for the formation of 3 and 4 stranded DNA structures
What are the properties of B-form DNA?
- double stranded DNA - right handed helix - 10.4 base pairs/ helical turn
Define the terms in L = T+W, how do they affect DNA structure?
L: linking number T: twist W: writhe Affect topolgy of DNA
What is the G0 phase of the eukaryotic cell cycle?
non-dividing cells; terminally differentiated cells aka most the cells in our body
Most the cells in our body are in which phase of the cell cycle?
What occurs during the 4 phases of the cell cycle, G1, S, G2 and M?
G1: RNA and protein synthesis (no DNA synthesis) S: DNA synthesis --> doubles amount of DNA in cell; RNA and protein synthesis occurs as well G2: No DNA synthesis; RNA and protein synthesis continure M: Mitosis- nuclear division, and cytokinesis- cell division, yield 2 daughter cells
Which phase of the cell cycle, G1 S G2 or M typically takes the longest?
What are cyclin specifically degraded by during the cell cycle?
the ubiquitin pathway
How does the presence of TF E2F affect the cell cycle?
E2F up regulates synthesis of proteins required for DNA synthesis and some cdks and cyclins
What does Rb stand for?
When TF E2F is bound to Rb it is active/inactive.
How is Rb-E2F binding reduced during normal cell division (passage into S phase)?
cdk2-cyclinE phosphorylates Rb, reducing its binding to E2F
Most cells have checkpoints at which 4 places in the cell cycle?
1. G1 checkpoint- before entering S phase 2. intra-S phase 3. G2 checkpoint- before M phase 4. M checkpoint- before end of M phase
At the G1 checkpoint, what causes the cell cycle to stop at the end of G1?
At the intra-S phase checkpoint, what causes the cell cycle to stop in S phase?
DNA damage or blocked replication forks
What is the role of p53 in checkpoint regulation of cell cycle into S phase?
catches damaged DNA and activates and regulates p21; mutations in p53 abolish the G1 checkpoint
More than 50% of human tumors have a mutation in which TF?
What do the transducer kinases ATM and ATR do?
regulate cell division and proliferation
How does caffeine affect checkpoint regulation of the cell cycle?
caffeine blocks checkpoint activation by inhibiting ATM and ATR
What is the chemical difference between RNA and DNA?
RNA has a 2' -OH group and DNA has a 2' -H instead
What composes a nucleoside?
base + sugar
What composes a nucleotide?
base + sugar + phosphate
What are the purine bases in DNA and RNA
adenine and guanine
What are the pyrimidines in DNA and RNA
DNA: cytosine and thymine RNA: uracil
Bases of DNA and RNA are generally charged/uncharged at physiological pH?
What are the base pairs in DNA and RNA?
DNA G-C A-T RNA G-C A-U
How many H bonds are between G-C and A-T in DNA base pairs?
G-C: 3 A-T: 2
There are ___ base pairs per turn and __Å per base pair in the B-form of DNA
10.4 bp per turn and 3.4Å
The B-form of DNA double helix is called what after its discoverers?
T/F- H bonds are low nrg bonds and can therefore be broken easily.
What are the 3 forms of DNA and which is the most common?
A, B and Z B is the most common
Which form of DNA forms a left handed helix?
When is Hoogsteen pairing (alternate DNA forms) most stable?
At low pH where C is protonated
What are 3 types of cell adhesion proteins?
-gap junctions -desmosomes -tight junctions
What are 2 examples of multipass transmembrane proteins?
-transporters -ion channels
What are 3 examples of hydrophobic molecules that can covalently interact with proteins to anchor them to the membrane?