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Introduction
Intro Cont.
Transcription regulation
Operons
Operons cont./RANDOM
100
Why are cells different from each other?
Gene expression differs in all cells.
100
Where do proteins typically bind: The minor or the major groove?
Major groove.
100
Why do transcription factors often bind as dimers?
A single monomer only binds 6-8 bp sequences, which can occur once ever ~4100 sequences, which is not specific enough. A dimer increases the amount of the bp that have to bind, which increases the specificity of the sequence as well as the strength of the bond (affinity)
100
What is an operon?
A functioning unit of nucleotide sequences that contains multiple structural genes under the control of a single promoter.
100
Draw the central dogma.
Draw it.
200
What is genomic equivalency?
Every cell contains a complete copy of the genome.
200
What are some ethical problems surrounding cloning?
Too many to count. (Discuss examples briefly)
200
Distinguish the difference between activator/repressor interaction with RNAP in eukaryotes/prokaryotes
In prokaryotes, activators and repressors interact directly with RNAP; in eukaryotes, all interaction is through a mediator.
200
How is the production of tryptophan regulated? What is the co-repressor?
Then there is no tryptophan, the operon will be on, and the RNAP will transcribe mRNA. When there is tryptophan, the operon will have a repressor bind the operon, and the co-repressor will help it stay on the strand. The co-repressor is tryptophan.
200
How does DNA looping facilitate long-distance interactions?
NtrC uses ATP to loop around and make the RNAP go to the open complex and GO.
300
Explain how genomic equivalency was proved through a carrot.
The carrot was separated into separate cells, one cell was taken and cloned, they formed an embryo, which formed a plant, which turned into a carrot.
300
What part of the amino acid interacts with the DNA?
The amino acid side chains.
300
What is basal transcription?
It is the level of transcription that is found in the absence of any regulators.
300
Are there operons in Eukaryotes?
No; they are monocistronic.
300
Describe the allosteric regulation of CAP.
CAP can only bind to DNA when it has cAMP. CAP-cAMP, when bound to the DNA, will "turn off" the genes that utilize glucose. cAMP is negatively regulated by glucose. Think about it: If there is glucose, there will be no cAMP to make the CAP-cAMP, and the genes to utilize glucose will go on using glucose.
400
Explain the cow experiment that gave evidence for genomic equivalency.
There were two cows, a black cow and a spotted cow. The unfertilized egg was taken from the brown cow, and the meiotic spindle and the chromosomes were removed. The donor cell w/ nucleus was fused to the egg cell, which caused it to become a zygote. An embryo formed, and it was then placed inside a foster mother. The resulting calf was a spotted cow, which was proof that it worked.
400
What is a helix-turn-helix motif? What does the recognition helix do? /What does the other helix do?
It is two helices separated by a loop. The recognition helix interacts with the DNA sequences. The other helix or helices interact with the backbone and stabilizes the interaction of the HTH and the DNA.
400
What is an operator?
DNA sequence that will bind repressors. (Silencers also bind repressors)
400
Fill out positive/negative regulation chart of lac operon
See board.
400
Describe the allosteric regulation of the Lac repressor
In absence of lactose, the lac repressor binds the DNA. When lactose enters the cell, it will then change into allolactose. Allolactose is an inducer, which means its presences causes transcription, and so it binds to the lac repressor and alters the shape, so the repressor can no longer bind to the DNA and repress transcription. Think about it: if there is lactose, the lac repressor will fall off.
500
How did the cow experiment prove genomic equivalency? What would we know occurred if the cow had come out black like its womb-mother?
The epithelial cells from the oviduct of the spotted female cow were enough to give rise to a whole new individual, which proves that the whole genome is encoded in every cell. If the cow had come out black like the womb-mother, it would have shown that not all of the chromosomes/spindle was removed from the egg.
500
Why might a cell want to turn a gene on/off at different times?
Example: prokaryotes. They like glucose, but they have genes to metabolize lactose. If there is no glucose around, but there is lactose, they might want to turn the lactose genes on so they can have a food source.
500
What is allostery?
Regulation of a protein's function by altering its shape.
500
Fill out allosteric regulation of the lac operon
See board
500
If a tree falls in the forest but no one is around to hear it, what color are the cat's eyes?
Blue. Duh.