Chapter 12 Flashcards
What are the three basic concepts of gene regulation?
- Not all genes need to be transcribed (to produce RNA) or translated (to produce a protein) all the time.
- The way genes are regulated makes biochemical sense.
- Anything that is a protein (or even RNA) in a cell has a gene that codes for it (DNA polymerases, helicases, ribosomal proteins).
How can you regulate genes? (6 ways)
- Chromatin remodeling
- Transcriptional regulation
- mRNA processing
- mRNA stability
- Translational regulation
- Posttranslational modification
What are structural genes?
Encoding proteins like enzymes or other non-regulatory proteins.
What are regulatory elements?
DNA sequences that are not transcribed but play a role in regulating other nucleotide sequences.
What are regulatory genes?
Encode proteins that interact with other sequences and affect the transcription and translation of these sequences
What are constitutively expressed genes?
Usually expressed all the time. Sometimes referred to as “housekeeping genes”
What is positive and negative control?
Positive control: Genes that can be activated/turned on only when needed
Negative control: Genes that can be inhibited/turned off as needed
What is epigenetics? What can it influence?
The study of how your behavior and environment can cause changes that affect the way your genes work.
- Behavioral epigenetics: life experiences, especially
early in life, have long-lasting effects on behavior - Epigenetic changes induced by maternal behavior
- Epigenetic effects of early stress in humans
- Epigenetic effects of environmental chemicals
- Transgenerational epigenetic effects on metabolism
- Epigenetic effects in monozygotic twins
- Cancer development
What is an operon?
Promoter + additional sequences that control transcription (operator) + structural genes that are regulated by the operator.
Promoter + operator + structural genes
What are the four types of transcription control and what do they do?
- Negative Inducible: The regulatory protein on its own binds to the operator site to block transcription, turning it off. Produces a repressor protein and transcription is off.
- Negative Repressible: A repressor protein by itself doesn’t bind to the operator. Transcription is on. Because a repressor protein doesn’t bind to the operator by itself, it requires a co-repressor to bind to it, then it can bind to the operator. The co-repressor makes the repressor active, and transcription is turned off.
- Positive Inducible: Inactive activator doesn’t bind; transcription off. Activator protein doesn’t bind to the operator, but it does bind close to the promoter and helps recruit RNA polymerase to the promotor. In positive inducible gene regulation, an inducer binds to the activator, causing it to bind to the promotor. Transcription is on.
- Positive Repressible: Positive regulation occurs through the action of an activator protein. Transcription on. A co-repressor binds to the activator, causing it to not bind to the promoter. Transcription is off.
What is negative control brought about by? What about positive control?
Negative control (turning off) of an operon is brought about through repressor proteins- turn off transcription by binding to the operator sequence in the promotor- block RNA polymerase from getting to the promotor.
Positive control (turning on) of an operon is brought about through activator proteins- turn on or maybe accelerate transcription of a gene by helping to recruit RNA polymerase to a promotor.
Inducers vs. Corepressors
Some operons are usually “off,” but can be turned “on” by a small molecule, this molecule is called the inducer, and the operon is said to be inducible. Other operons are usually “on,” but can be turned “off” by a small molecule, the molecule is called a corepressor, and the operon is said to be repressible.
Repressible vs. Inducible
Some operons are inducible, meaning that they can be turned on by the presence of a particular small molecule. Others are repressible, meaning that they are on by default but can be turned off by a small molecule.
What is the lac operon (of E. coli) and what is the basic biochemical logic of it? What is done to regulate the expression of the structural genes?
Structural genes in the lac operon code for catabolic enzymes that allow E. coli to break down lactose.
If lactose is available, the enzymes to break it down should be made.
If no lactose is present, don’t waste energy making enzymes to break lactose down.
The lac operon is a negative inducible operon
Repressor protein = Lac repressor, the inducer = allolactose
What do each of these do?
Structural genes: lacZ, lacY, lacA
Regulatory elements: lacl, lacP, lacO
Structural genes:
lacZ: encoding an enzyme called beta galactosidases
lacY: encoding a transporter called permease
lacA: encoding transacetylase
Regulatory elements:
lacl: repressor encoding gene (regulatory gene)
lacP: operon promoter
lacO: operon operator
- When are lac genes strongly expressed?
2-3. When are lac genes not expressed? (with repressor protein and cAMP) - When are there very low (basal) levels of gene expression?
- Low glucose, lactose available
- High glucose, lactose unavailable
- Low glucose, lactose unavailable
- High glucose, lactose available
What is the trp operon of E. coli? What are the five structural genes? What is the basic biochemical logic of the trp operon?
The trp operon of E. coli is a negative repressible operon. Repressor protein= Trp repressor
Corepressor= tryptophan
trpE, trpD, trpC, trpB, trpA- five enzymes together convert chorismate to tryptophan. Anabolic enzymes that allow E. coli to make the amino acid tryptophan
If tryptophan is available, the cell doesn’t need to waste energy synthesizing the enzymes to make more of it. If there’s no tryptophan around, the enzyme should be synthesized to make it.
What happens when there is an addition of a methyl group to the histone protein tail? What about the addition of an acetyl group?
It usually strengthens the positive charge.
It usually weakens the positive charge.
What is DNA methylation?
The addition of methyl groups to nucleotide bases. Methylation of cytosine to produce 5-methylcytosine is the most common. Methylation near promoters results in inhibition of transcription. The methylation can be passed on to newly synthesized DNA.
