Download Class17 1-31 Win16 Cell Cycle Notes

A few of the innovative scientific contributions from
ancient Islam
A few of the innovative scientific contributions from
ancient Islam
Polling Question #7
6b. The relationship between glucose and cAMP is:
1. 
2. 
3. 
When glucose is high, cAMP is high
When glucose is high, cAMP is low
Glucose levels have no relationship to cAMP levels
Peer Instruction
ATP
Adenylyl
cyclase
cAMP
Two
phosphate
groups
Glucose allosterically
inhibits this enzyme
How does glucose influence levels of cAMP?
So, high [glucose] = _____ cAMP = ______ binding of RNA pol
at the lac operon
And low [glucose] = _____ cAMP = ______ binding of RNA pol
at the lac operon
Polling Question #8
What carbohydrates are present in the
scenario as shown?
FREQUENT TRANSCRIPTION
Glucose LOW
Lactose HIGH
1. 
2. 
3. 
4. 
CAP
site
Operator
High levels of glucose
High levels of lactose
Low levels of glucose
Low levels of lactose
lacZ
lacY
lacA
Peer Instruction
Describe the positive regulation of lac operon expression.
When glucose is high,
cAMP is absent:
CAP
lacZ
CAP site
lacY
RNA polymerase bound
loosely to promoter (blue DNA)
When glucose is low,
cAMP is present:
CAP
cAMP
lacZ
CAP site
RNA polymerase bound
tightly to promoter (blue DNA)
lacY
Polling Question #9
What will the output of lactose-usage
proteins be in the following scenario?
INFREQUENT TRANSCRIPTION
Glucose HIGH
Lactose HIGH
CAP
site
Operator
lacZ
lacY
lacA
Inducer-repressor complex
1.  Very high levels
2.  Low or medium levels
3.  It depends on unpredictable outside factors
Concept Questions
• 
The consensus promoter sequence of the Tau operon is ATTGCTGATC. Which of the
following promoters is more likely to give high expression levels: ATTGGTGATC or
AGTGCTTATT? (only one strand is shown for simplicity)
• 
What are the molecular interactions that determine the level of expression in either [high
glucose, high lactose] or [low glucose, low lactose]?
–  Why do these make logical sense for a functional cell?
• 
A regulation scheme in a new cell has genes A, B and C. The products of A and B repress
the expression of C, but the product of A increases the binding of the polymerase at the
promoter of B. The product of C increases the expression of A.
–  Is C a positive or negative regulator of B?
–  Is C a positive or negative regulator of its own expression?
–  Hint: Draw it out!
• 
Challenge: Imagine that a new strain of E. coli is found that regulates lac operon expression
based on levels of mercury in the environment. Design molecular interactions (or new
molecules) such that E. coli only produces high levels of lac operon products in low
mercury.
Tuesday January 31st, 2017
Class 17 Learning Goals
Understanding the Cell Cycle
•  What are the phases of the cell cycle, and how do cells decide when
to proceed through each phase?
•  Why are transitions between phases controlled by checkpoints?
•  What is the molecular basis of checkpoint control?
•  How does this relate to prokaryotic gene regulation?
Polling Question #1
In the cell cycle shown here,
where is Anaphase?
1.  In G2
2.  In G1
3.  In Interphase
4.  In M-phase
5.  In S-phase
6.  Anaphase does
not occur in the cell cycle
Mitosis
M
DIVISION
G2
G1
S
INTERPHASE
Peer Instruction
1) Label G1, G2, M, S, and
Interphase on this cell cycle.
2) When is DNA replication?
3) When do mitotic spindles need
to be correct and ready?
G1
S PHASE AND G2
MITOSIS
Chromosomes are shown partially
condensed to make them visible
Parent cell:
4 unreplicated
chromosomes
Parent cell:
4 replicated
chromosomes
Sister
chromatids
Replicated chromosomes
condense at the start of
mitosis.
1) Explain the reasons for these three checkpoints.
Peer
Instruction
Metaphase Checkpoint
checkpoint
M-phase
checkpoint
G2 GCheckpoint
2
Pass this checkpoint if:
• all chromosomes are
attached to spindle
Pass this checkpoint if:
• chromosome replication
is successfully completed
• no DNA damage
• activated enzymes present
M
G2
G1
2) What is G0?
Pass this checkpoint if:
• nutrients are sufficient
• growth factors are present
• cell size is adequate
• chromosome is undamaged
G0
S
G1 checkpoint
G1 Checkpoint
P Inactive Cdk
Cyclin
Peer Instruction
P
Cyclin
Cdk
Cdk
P
P
(Binding)
Growth
factors
Activated Cdk P
P
Cyclin
Rb
Cdk
S-phase
P
Rb
ATP
E2F
E2F
Expression of
the E2F gene
E2F
ADP
Tight
Binding
Retinoblastoma Protein
(constitutively produced)
The players involved are:
•  growth factors sent from nearby cells
•  CDK (an enzyme that is always present)
•  Cyclin (an enzyme that is sometimes present)
•  Rb (a protein with two binding sites)
•  E2F (a protein with one binding site)
Decipher the molecular control of the G1 checkpoint.
P Inactive Cdk
Cyclin
Polling Question #3
P
Cyclin
Cdk
Cdk
P
P
(Binding)
Growth
factors
Activated Cdk P
P
Cyclin
Rb
Cdk
S-phase
P
Rb
ATP
E2F
E2F
Expression of
the E2F gene
E2F
ADP
Tight
Binding
Retinoblastoma Protein
(constitutively produced)
Do the social growth factors shown here from
nearby cells tend to increase or decrease
passage through this checkpoint?
1.  Increase
2.  Decrease
3.  It is not possible to predict
P Inactive Cdk
Cyclin
Polling Question #3
P
Cyclin
Cdk
Cdk
P
P
(Binding)
Growth
factors
Activated Cdk P
P
Cyclin
Rb
Cdk
S-phase
P
Rb
ATP
E2F
E2F
Expression of
the E2F gene
E2F
ADP
Tight
Binding
Retinoblastoma Protein
(constitutively produced)
What happens when Cyclin and CDK bind?
1.  CDK loses a phosphate group
2.  CDK gains a phosphate group
3.  CDK probably changes shape
4.  Rb is can be phosphorylated by Cyclin/CDK
5.  Rb is can be dephosphorylated by Cyclin/CDK
P Inactive Cdk
Cyclin
Polling Question #4
P
Cyclin
Cdk
Cdk
P
P
(Binding)
Growth
factors
Activated Cdk P
P
Cyclin
Rb
Cdk
S-phase
P
Rb
ATP
E2F
E2F
Expression of
the E2F gene
E2F
ADP
Tight
Binding
Retinoblastoma Protein
(constitutively produced)
E2F is able to start S-phase:
1. 
2. 
3. 
4. 
When bound to RB.
When unbound by RB.
Always.
Whenever any cyclin is present.
P Inactive Cdk
Cyclin
Polling Question #5
P
Cyclin
Cdk
Cdk
P
P
(Binding)
Growth
factors
Activated Cdk P
P
Cyclin
Rb
Cdk
S-phase
P
Rb
ATP
E2F
E2F
Expression of
the E2F gene
E2F
ADP
Tight
Binding
Retinoblastoma Protein
(constitutively produced)
Would you classify Rb as a positive or negative
controller of passage through the G1 checkpoint?
1.  Neither positive nor negative
2.  Positive
3.  Negative
P Inactive Cdk
Cyclin
Peer Instruction
P
Cyclin
Cdk
Cdk
P
P
(Binding)
Growth
factors
Activated Cdk P
P
Cyclin
Rb
Cdk
S-phase
P
Rb
ATP
E2F
E2F
Expression of
the E2F gene
E2F
ADP
Tight
Binding
Retinoblastoma Protein
(constitutively produced)
How do you think E2F initiates S-phase?
Polling Question #6
P Inactive Cdk
Cyclin
P
Cyclin
Cdk
Cdk
P
P
(Binding)
Growth
factors
Activated Cdk P
P
Cyclin
Rb
Cdk
S-phase
P
Rb
ATP
E2F
E2F
Expression of
the E2F gene
E2F
ADP
Tight
Binding
Retinoblastoma Protein
(constitutively produced)
How do you think E2F initiates S-phase?
1. 
2. 
3. 
4. 
Directly catalyzing needed reactions
Increasing expression of S-phase-related genes
Destroying G2-phase-related proteins
Binding the promoter region of S-phase-related
genes and helping to recruit RNA polymerase
P Inactive Cdk
Cyclin
Peer Instruction
P
Cyclin
Cdk
Cdk
P
P
(Binding)
Growth
factors
Activated Cdk P
P
Cyclin
Rb
Cdk
S-phase
P
Rb
ATP
E2F
E2F
Expression of
the E2F gene
E2F
ADP
Tight
Binding
Retinoblastoma Protein
(constitutively produced)
Draw E2F, and include binding sites for other molecules.
-Where are they in relation to each other?
Does E2F binds to Rb or promoters more tightly?
Why is E2F called a ‘transcription factor’?
Peer
Instruction
1) Explain the reasons for these three checkpoints.
Metaphase Checkpoint
checkpoint
M-phase
checkpoint
G2 GCheckpoint
2
P
P
M
Cycli
n
Cdk P
Cdk
P
P
(Binding)
G2
E2F
Expression of
the E2F gene
E
2
F
E
2
F
F
G1 checkpoint
G1 Checkpoint
R
E
2b
S
G0
Cycli
n
Rb
E2
F
P
Cdk
Rb
Sphase
P
ATP
AD
P
E2
F
Concept Questions
• 
• 
• 
• 
• 
• 
The consensus promoter sequence of the Tau operon is ATTGCTGATC. Which of the
following promoters is more likely to give high expression levels: ATTGGTGATC or
AGTGCTTATT? (only one strand is shown)
What are the molecular interactions that determine the level of expression in either [high
glucose, high lactose] or [low glucose, low lactose]?
–  Why do these make logical sense for a functional cell?
A regulation scheme in a new cell has genes A, B and C. The products of A and B repress
the expression of C, but the product of A increases the binding of the polymerase at the
promoter of B. The product of C increases the expression of A. Hint: Draw it out!
–  Is C a positive or negative regulator of B?
–  Is C a positive or negative regulator of its own expression?
Challenge: Imagine that a new strain of E. coli is found that regulates lac operon expression
based on levels of mercury in the environment. Design molecular interactions (or new
molecules) such that E. coli only produces high levels of lac operon products in low
mercury.
Why does it make sense that a checkpoint would stop the cell cycle when it senses DNA
damage? What about low nutrients?
What is the effect on G1 checkpoint passage of:
–  A loss of E2F proteins? A loss of Rb proteins?
–  An increase of the binding strength between Rb and E2F proteins?