Chapter 15 - Gene Regulation Flashcards
Unit 6 part 2 (also some of ch 13 and 17, sorry)
Why aren’t all genes constantly being transcribed into protein all the time? Use E-Coli needs to answer
Sometimes you gotta wait and see what food I eat so you know what you’re breaking down to produce specific proteins to do that - you don’t need to have it all going at once or you’re wasting energy.
Is the regulation of tryptophan (trp) synthesis positive or negative inhibition?
Negative - more trp = less produced, so level goes closer to set point
How is gene regulation different from feedback regulation?
Fewer steps (no need for the sensor and integrating sensor and potentially effector?)
How is gene regulation similar to feedback inhibition?
Levels are brought closer to the set point
What is the advantage of grouping genes of related function into one transcription unit?
1 on and off switch can control a whole bunch of functionally related genes - you save energy and they’re coordinately controlled
What is an operon? (you can rewrite bc rn it’s KA)
a set of genes that are transcribed under control of a single promoter, resulting in one long mRNA that contains coding sequences for multiple genes + the regulatory DNA sequences that control their expression (including the promoter and binding sites for any repressor or activator proteins).
What is the operator in an operon?
the on/off switch segment where repressor protein binds
What is the promoter in an operon?
the RNA polymerase binding site (with the TATA box)
What are the operon genes?
Genes in the operon (( ͡° ͜ʖ ͡°)) that get transcribed into mRNA that is translated into protein
how does a repressor protein work and where is the gene for the repressor?
It’s a regulatory protein produced by a different gene - it binds to the operator (which is just in front of the genes that would be transcribed), blocking the path of RNA polymerase so the genes can’t be transcribed - no transcription = no protein
What are regulatory genes?
Genes that encode repressor proteins
What is a corepressor?
A molecule (which is prolly a type of ligand) that cooperates with a repressor protein (makes it active/on) to switch an operon off - Example: Tryptophan
What is an inducible operon?
An operon that can be turned on with the removal of a repressor - Default OFF + Catabolic
What is a repressible operon?
An operon that can be turned off with the addition of a repressor - Default ON + Anabolic
Is the Lac operon inducible or repressible?
Incudible
Is the Trp operon inducible or repressible?
Repressible
Summarize the trp operon
. TRP builds up enough to bind to the repressor protein’s allosteric site
. The repressor protein binds to the operator (because its shape has changed due to being activated)
. RNA polymerase is blocked by the repressor protein
. Transcription and therefore protein synthesis stops
What is an inducer?
A small molecule (prolly a type of ligand) that inactivates a repressor by binding to it and changing its shape and triggers the expression of a gene/operon
Example: Allolactose (what you find in a lac operon_)
Summarize the lac operon
. Lactose/Allolactose (rearranged versions of each other) builds up and binds to the active repressor
. This changes the shape so it no longer fits
. RNA pol can now attach and transcribe and genes are expressed
. This breaks down the lactose so it stops binding
. The repressor goes back
Virus vs Bacteria
Bacteria are alive, viruses are not
Viruses are much smaller
Bacteria divide by binary fission, viruses steal (a lot) to divide and survive
Neither have endomembrane systems
What is the lytic cycle?
A virus life cycle where the phage injects its DNA into the host, gets its own proteins synthesized inside the cell, uses that to make new phages, and lysing the cell to let all of that good stuff out (well not good but you get the point)
What is the lysogenic cycle?
A cell cycle where the viral DNA gets injected and merges with the bacteria DNA and divides and gets replicated as a part of the bacteria and only ever expresses itself by random chance when it gets excised from the mother loop and can express itself (but often times the cell WILL NOT POP)
What is Transformation?
Bacteria assimilates DNA as a plasmid from the environmentWh
What is Transduction?
Bacteria assimilates DNA from viruses
What is Conjugation?
Cell to cell transfer of DNA
What is differential gene expression?
The expression of different genes by cells with the same genome
What are the different locations for gene expression regulation?
- Chromatin modification/Dna unpacking
- Transcription
- RNA processing
- Transport to cytoplasm
- Degradation of mRNA
- Translation
- Protein processing
- Degradation of protein
- Transport to cellular function
What is histone acetylation?
Addition of an acetyl group to an amino acid in a histone tail - this promotes transcription by opening up the chromatin structure (too condensed is a bad thing)
What is DNA methylation?
The addition of methyl groups to histones to condense the chromatin and block transcription
What is the result of having a heavily methylated X Chromosome?
It’s inactive and genes aren’t expressed. The methylation gets passed down as cells divide (it can be inherited)
What is epigenetic inheritance?
Inheritance of traits that don’t come from the nucleotide sequence (like having something methylated) (this could explain why 1 twin has schitzophrenia and the other doesn’t)
What are control elements?
Segments of noncoding DNA having particular nucleotide sequences that serve as binding sites for transcription factors (which are proteins)
(this may be a repeat) What are transcription factors?
Regulatory proteins that bind to DNA and affect transcription of specific genes
What are enhancers and where are they in relation to the gene?
Groups of distal (far) control elements that are thousands of nucleotides away (up or down stream but if it makes me pick only one i’d go with up) from the gene (sometimes in an intron)
How do transcription factors enhance or decrease the tranctription of a gene? (activators interact with transcription factors to affect gene expression)
DNA binding domain binds to DNA
Activation domains bind other regulatory proteins or components of the transcription machinery -> protein-protein interactions –> more transcription
In prokaryotes, functionally related genes are usually clustered into 1 operon. What do eukaryotes do?
Co-expressed genes are typically scattered across different chromosomes, so every gene in a dispersed group has to have a specific combination of control elements
How can alternative RNA splicing result in different proteins derived from the same initial RNA transcript?
Introns are spliced out and sometimes different exons between the introns are also spliced out
how does mRNA degradation happen?
(this one’s super funky, sorry!)
When it gets degraded, proteins can’t be formed
Enzymes can break it down
newly discovered RNA molecules can degrade or block expression of mRNA
How can initiation of translation be regulated to control gene expression?
It can be blocked by regulatory proteins that bind to specific sequences or the UTR (untranslated region) so ribosomes can’t attach
How can proteins be activated, processed, and degraded?
Regulatory proteins can be acgtivated or inactivated by adding phosphate groups (reversible), some others acquire sugars or get moved to the right place
Attach ubiquitin to destroy the protein
General vs specific transcription factors
General/ basal - used for transcription of any gene
Specific - control expression of specific individual genes
What is a plasmid and where does it come from?
It’s a small circular loop of separately replicated DNA
It comes from the environment
What is a cloning vector?
Artificially synthesized/manipulated DNA that can be used to transfer DNA (this isn’t very concise, I don’t really get it)
What are the steps of cloning a gene?
- Insert gene into plasmid/cloning vector
- Put plasmid into bacterial cell
- The host cell is grown in a culture to form clone cells with the cloned gene
- Use it for various stuff
Why are restriction enzymes important for making recombinant bacteria?
They cut the DNA around the gene at palindrome sequences (on the OG Dna) that the gene of interest can bind to
What is cDNA?
Copied DNA
cDNA vs normal DNA
cDNA only has coding sequences, normal DNA has coding and noncoding sequences. This allows bacteria to use it without making a 15000000000 mile long chain since it doesn’t do mRNA processing
What does Cas9 normally do in bacteria?
Helps defend bacteria against bacteriophage infections (by doing a snip snip)
What do scientists use Cas9 for when editing genes?
It cuts any sequence it’s directed to by guide RNA
What is a gene drive?
Engineering a new allele so it’s much more favored for inheritance than the wild type (biased inheritance DRIVES the allele through the population)
What is CRISPR and what does it do? (not CRISPR-Cas9, just CRISPR)
It makes the guide RNA (I THINK it makes the palindromes so the Cas9 can cut there but I’m not sure)
What are the applications of the Crispr-Cas9 system?
It can be used to correct genetic defects and cure human diseases or drive up different allele frequency (like mosquitos that can’t transmit malaria)
Complementary base pairing during cloning/with restriction enzymes
Makes sticky ends sticky
Also allows the DNA to replicate with RNA pol
Complementary base pairing in PCR
Used for taq polymerase to add new nucleotides and make a bunch more copies
Complementary base pairing in DNA sequencing
Binding to tell what’s there (3rd generation? We don’t know her (note to self - check appendix A ch 13.4 questions))
Crispr-Cas9 uses complementary base pairing to…
allow the Cas complex to bind to the target gene
What 2 main structures can be found in all viruses?
nucleic acid enclosed in a protein coat
What are some of the types of genomes that viruses can have?
1 or 2 strand Dna or Rna (in a linear circular molecule)
What is the capsid? What shapes does it come in?
The protein shell encasing the viral genome - rod shaped, polyhedral, or more complex
What are viral envelopes and what function do they have in animal viruses?
Envelopes derived from host cell membranes containing host phosphoplipids and membrane proteins and glycoproteins - cloaks capsid and helps viruses infect and also protects them
What do bacteriophages do?
Eat bacteria
What kind of genetic material does a bacteriophage have?
2 strand DNA
How does phage therapy work?
Engineer phages that eat sick bacteria but leave good ones alone to cure diseases
T or F Viruses only replicate in host cells
true
How does a virus replicate within a cell?
Binds to host cell, inserts viral genome
Host enzymes
- replicate viral genome
- transcribe it into viral mRNA that gets translated into proteins
Self assembly and then they exit (and lyse)
How do bacteria defend themselves against phages?
- Natural selection so phages don’t want to bind
- They use restriction enzymes to cut up foreign DNA
- Use crispr-cas system to alter genes and remember the phages so if they come back they’ll be sorry
What happens in the lytic cycle?
Virus attaches, inserts its DNA, synthesizes its genomes and proteins with host resources (enzymes), self assembles, and releases while LYsing the cell
What is a virulent phage?
A phage that only replicates with the lytic cycle
Describe the lysogenic cycle
Phage binds to the surface of the cell and inhjects its linear DNA, which combines with host DNA to form a prophage. Then, as the cell divides, the viral DNA is replicated along with the bacteria DNA until it randomly gets spliced out, circularizes, and goes into the lytic cycle.
What is a temperate phage?
A phage that can replicate with both the lytic and lysogenic cycle.
What is a retrovirus?
A virus with revers transcriptase that can transcribe RNA into DNA so it can go back into RNA (but the RNA already has the introns cut out)
What does the Viral Envelope do?
It surrounds the capsid
What does the capsid do?
Sheathes the DNA
How does a retrovirus replicate? (HIV) (Best card in this deck ;) )
- Binds to cell
- Fuses with membrane and releases its guts
- Reverse transcriptase catalyzes synthesis of DNA complementary to RNA and then more DNA to match the RNA
- DNA is incorporated into og cell’s DNA and it undergoes the lysogenic then lytic cycle (I think)
What is the central dogma?
Information flows from DNA to RNA to Protein
Why are retroviruses exceptions to the central dogma?
RNA –> DNA
What do siRNA and miRNA do?
They bind to complementary sequences (at least 7-8 nucleotides) in mRNA molecules. Then, they degrade the mRNA or block its translation. siRNAs do the same thing.
What is Cell Differentiation?
The process by which cells become specialized in structure and function
What is morphogenesis?
The development of the form of an organism and its structures (involving multiple cells)
How does distribution of cytoplasmic determinants affect embryo development? (this has a lot of big ol’ fancy words but srsly isn’t that complicated dw)
Organelles and other substances (like cytoplasmic determinants) are distributed unevenly throughout the cell. When dividing, the cytoplasmic determinants in different parts of the cell are in the new cells in different concentrations, and the ones that the nucleus is exposed to determine how it develops.
How do inductive signals affect embryo development?
Signals from the environment (especially from other nearby embryonic cells) can help determine what a cell differentiates into (this is called induction)
What is meant by determination?
The point at which a cell is irreversably committed to becoming a particular cell type.
In a precursor cell, signals from other cells lead to activation of myoD, a master regulatory gene, and the cell makes myoD protein, which is a transcription factor.
How does differentiation affect myoblasts?
it uses the mod protein it made to stimulate a gene that makes another transcription factors and that chain continues for a bit until proteins are made
It also turns on genes to stop cell division.
Nondividing myoblasts fuse to become muscle fibers.
What are homoeotic genes?
Master Regulator Genes that direct the development of particular body segments or structures
- Control developmental fates of groups of cells
- where stuff goes and how far apart
Describe the bicoid experiment
- Bicoid injected into the forming embryo’s head area
- grows two anterior structures
Induction…?
Why do mutations make a larger contribution to bacterial genetic variation as compared to humans?
No proofreading/ happens often and quickly
