Genomic Equivalency
Vocab
Operons
Transcriptional Regulation
Random
100
What makes different cells different? What is genomic equivalency?
Different expression of genes in different cells. Every cell contains a complete copy of the genome.
100
What is an activator? What does it do/what does it bind to?
It is a gene regulatory protein that binds to an enhancer that up-regulates transcription
100
Are operons in prokaryotes, eukaryotes, or both? Why?
They are in prokaryotes, because they are monocistronic, and that means that multiple genes are under the control of one promoter.
100
What are the two components you need for transcription regulation? What are the two ways that these elements can affect transcription?
Gene-regulatory proteins (repressors, activators) and a specific DNA sequence (enhancer, operator). Up-regulate it, down-regulate it.
100
What level of protein structure is a dimer?
Quaternary
200
What's an example of a protein expressed in all cells? Why?
Beta actin. It's in the mitotic spindle.
200
What is a cis-regulatory sequence? Where are they typically in regards to the genes that they control?
cis-=same. They are DNA sequences that are on the same chromosome as the gene that they control; typically, they are upstream from the gene that they control.
200
Why is it beneficial to have DNA organized as operons?
Can turn on/off related genes all at once; very efficient.
200
Why do most proteins bind to the major groove?
They bind to the major groove because they have more sequences there, and they can easily tell the difference, whereas in the minor groove, C-G and G-C or A-T and T-A can look similar to each other and it can easily bind in the wrong place.
200
If you have a lot of glucose surrounding a bacterial cell, how will that affect the formation of CAP-cAMP?
CAP-cAMP will not form.
300
Explain the cow experiment and how that proved genomic equivalency. What would have happened if it had gone wrong/not worked? What would we know must have happened?
Cow experiment-A cow egg was taken, meiotic spindle and nucleus removed, fused with another cow's nucleus from a skin cell, became a zygote, implanted in the egg-mother, came out black like the donor of the nucleus. This proved that the skin cell had the directions to make a whole new organism in it. If it hadn't worked, it would come out just like the cow who it was implanted in. The spindle and the chromosome would not have been completely removed.
300
What is an HTH motif? What does the recognition helix bind to? What does the other helix do?
An HTH is a motif of two proteins linked together; used for DNA binding. The recognition helix binds to the DNA. The other helix or helices bind to the backbone.
300
What does lactose turn into once it enters the cell? How does this help regulate the operon?
Lactose becomes allolactose, which binds to repressor, makes it change shape, and has it fall off. Think about it; if there's lactose, you're not gonna repress the lac operon.
300
What are different types of bonds can the amino acid side-chain have to the DNA?
Hydrophobic, hydrophilic, ionic bonds.
300
Is an HTH motif in prokaryotes, eukaryotes, or both?
Both
400
How much money do you have to pay a Korean to clone your cat/dog?
$50,000 and up seems to be the going price.
400
What is a ligand?
Molecule that binds to a protein
400
Fill out the lac operon on the board if the gene is on/off
See board
400
What level of protein structure is the Amino Acid side chain involved in?
Tertiary
400
How do you pack a cell into heterochromatin?
Reader-writer complex. https://stedwards.instructure.com/courses/4555/pages/lecture-notes-module-1?module_item_id=10468
500
What are the different ways that a cell could express parts of its DNA while not expressing other parts? (Think back to section 1)
Heterochromatin remodeling.
500
What is an operator? What does it bind to? What is a silencer? What does it bind to?
A section of DNA that binds repressors. A section of DNA that binds repressors. https://www.quora.com/What-is-the-difference-between-an-operator-and-silencing-region-on-a-genome
500
What are two ways a ligand would increase transcription? What are two ways it would decrease transcription? Label each case where the ligand is a co-repressor, inhibitor, or an inducer.
Ligand binds and helps activator bind (inducer), ligand binds and makes repressor fall off (inducer). Ligand binds and helps repressor bind (co-repressor), ligand binds and makes activator fall off (inhibitor).
500
Why do HTH often bind as homodimers?
They bind as dimers because it increases specificity, as there is a longer DNA base sequence that needs to be recognized in order for the protein to bind; creates a higher affinity for the strand.
500
In one particular lac operon, it will either transcribe at basal levels or lower, even with the absence of glucose and the presence of lactose. Where is the mutation?
The mutation is in the activator/enhancer.
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