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Prokaryotic Gene Regulation
Eukaryotic Gene Regulation
DNA Sequencing & Genomics
Cell Signaling
Cell Cycle
100
What are the ideal conditions for transcription of the Lac operon?
High lactose and low glucose
100
Explain how histone modification affects chromatin compactness. 
Addition of acetyl groups to histones by HAT pushes the DNA open, while removal of acetyl groups by HDAC allows for charge interactions between the histone and DNA that promote tight packing. 
100
How are ddNTPs different from dNTPs?
They lack a 3' OH, so DNA polymerase cannot extend them
100
Where are the receptors for lipid soluble signals? For lipid insoluble signals?
In the cytoplasm; in the plasma membrane
100
In what phase are cells that don't divide?
G0
200
What is an example of negative regulation and positive regulation in the Lac operon?
Negative: the LacI repressor prevents transcription

Positive: the cAMP-CRP complex promotes transcription

200
What is the function of miRNA? 
to promote degradation of mRNA or block translation of mRNA
200
What kind of sequencing would we use to sequence an entire genome?
High throughput / Illumina
200
How is Ras activated? How is it inactivated?
Activated by dropping GDP and picking up a new GTP

Inactivated by hydrolyzing its GTP into GDP

200
How is CDK activity regulated?
It is regulated post-translationally by presence of cyclins, which bind and cause a confromational change that activates the kinase
300
What is the ideal number of LacI proteins to have in the cell and why?

(1, 2, 10, 40)

40

LacI bounces around the cell until it happens to come across the operator sequence it binds to. If we just had a couple copies of the protein, most of their time would be spent away from the operator and transcription of the operon would not be repressed in the absence of lactose. Having 40 copies ensures that the operator is almost always bound when there is no lactose present. 

300
What are reported genes used for a what is a common characteristic of their expression?
Used for finding enhancers

When expressed, they often have a easily recognizable effect, such as glowing or changing color

300
What is an open reading frame? Can we find noncoding RNAs like miRNAs by looking for ORFs?
A sequence of coding DNA without a stop codon

No. these RNA will not be translated and thus it doesn't matter if there are stop codons in the middle of it

300
MAPKK has a mutation that causes it to be continuously active. Describe an inhibitor that would prevent excessive cell proliferation. 

An inhibitor of MAPKK

An inhibitor of MAPK

An inhibitor of transcription

(just need one)

300
What causes accumulation of cyclins?

Cyclins will be expressed if checkpoint criteria are met

400
What is IPTG and how is it used?
It is an analog to lactose that can be processed by beta-galactosidase

It is used to assess bgal activity because the enzyme changes IPTG from colorless to blue

400
Name two ways that methylation blocks gene transcription. 

Methyl groups change the shape and chemistry of the major groove, so transcription factors cannot recognize their binding site.

Methylation also recruits HDAC to compact the surrounding DNA .

400
Explain three uses of cDNAs.
1. to find where in the genome a gene is located

2. to find where introns and exons are in a gene

3. to find out if alternative splicing is occurring

4. to find out which genes are typically transcribed in a cell and at what relative levels

5. can compare sequence to other known protein coding sequences in order to hypothesize about the gene's function

400
Define an effector protein and determine what the effector in the MAPK pathway is. 

Define: the last protein in the chain, the one that carries out the direct action that the signal was intended to produce

Example: the regulatory transcription factor phosphorylated by MAPK

400
Name the three checkpoints and what criteria are needed to pass each. 

G1 (aka G1/S): Cell must be big enough to divide, have enough nutrients, have undamaged DNA, and receive signals to divide

G2: Make sure chromosomes are done replicating and DNA is undamaged 

M: make sure chromosomes are attached to spindle


500

The bacterium S. lc uses the molecule pizza as a primary food source and cupcake as a secondary food source if pizza is not present. Explain how to conduct a genetic screen using replica plating to find bacteria that have a mutation in their pizza metabolism genes. 

1. Mutagenize bacteria / introduce random mutations to bacterial genome

2. plate/grow bacteria on cupcake only media

3. use replica plating to transfer some bacteria to pizza only media

4. observe which colonies grow and which do not

5. colonies that grow on cupcake but not pizza must have a mutation in their pizza metabolism genes. 

500
Name two factors that affect RNA stability in the cytoplasm. 
Length of polyA tail

RNA-binding proteins bound to the UTR may promote or prevent degradation of the mRNA

500
What is the function of an siRNA and what two ways does it do its job?
Functions to silence retrotransposons

Can target mRNA from retrotransposon in cytoplasm and degrade it

Can find location of retrotransposon in genome and cause sequence to be methylated

500
What is signal branching? Make up an example using the MAPK pathway.

When cell responds to a single signal in multiple ways

For example, maybe MAPKK could phosphorylate MAPK and promote changes in gene expression that cause cell proliferation (as usual) AND ALSO phosphorylate/activate a protein that promotes [insert other reasonable effect]

500
Name four targets of MPF (a specific cyclin-CDK complex)

Phosphorylates proteins associated with 

1. chromatin to cause condensation

2. nuclear lamins to cause nuclear envelope breakdown

3. microtubule proteins to activate the spindle

4. Ubiquitin ligase, leading to degradation of cyclin, so it can effectively turn itself off