MIDTERMS AAAAAAAAAAAAAAAA Flashcards
What takes up most of a cells mass except for water
protein
What percent of genes are shared between human cells
30-60
Do you need a primer for transcription
no you idiot
What is the abortive transcription
When 10 nucleotides are formed, sigma factor is released. This can happen in eukaryotes but with general transcription factors instead of sigma factor
What is a hairpin structure
A looping of mRNA that happens in transcription which causes the RNA polymerase to leave the DNA strand
What are gene regulatory proteins or transcription factors? What do they bind to, specifically?
They regulate gene expression by binding to regulatory sequences of DNA called cis factors.
What are two types of gene regulatory proteins/transcription factors
Activators and repressors
What is an operon
multiple genes transcribed into one RNA molecule
What is the Trp operon, how does the trp repressor work
5 genes encode enzymes for tryptophan synthesis, transcription regulated by a single operator. the Trp repressor binds to the operator sequence to prevent RNA polymerase from binding. the trp repressor binds 2 molecules of tryptophan to bind to the helix-turn helix binding motif in the major groove of DNA
What is the most common DNA binding motif
the binding of a gene regulatory protein in the major groove of DNA (such as with trp operon)
Explain the lac operon in E coli. What does Ecoli prefer
Ecoli uses lactose when there is no glucose. The operon is turned on when using lactose. However, E coli prefers glucose
What activates the lac operon, under what condition
Catablite Activator Protein (CAP) which increases when glucose decreases. This increases cAMP which changes CAP conformation, and allows it to bind to DNA. It binds to promoters to help yoink RNA polymerase and get RNA poly. to bind.
What represses the lac operon and under what conditions
Lac repressor protein shuts off the operon when there is no lactose. This is because allolactose increases as lactose increases, releasing lac repressor from the operator (conformational change).
What does DNA sequencing, DNA microarrays, 2D gel electrophoresis show you
Respectively, info about DNA, RNA, and proteome
What is negative and positive regulation in prokaryotic transcriptional regulation
Repressor preventing activity, and activator promoting activity
What are the two ways ligands can control gene-regulating proteins
Ligands can yoink regulatory protein from the DNA or yeet the regulatory protien onto it
Where can regulatory elements be found
Upstream or downstream of the promoter. Downstream and within genes is common for eukaryotes.
What is kissing :3
I’m a visual learner btw (jk its when distant regulatory elements like NRTC loops back allowing NRTC to interact with RNA polymerase at a distance. can happen in both eukaryotes and prokaryotes)
Explain how the lambda repressor and cro protein work
The lambda repressor binds to the cro side of the operator, which activates its own synthesis, and most bacteriophage DNA is not transcribed. The cro protein binds to the other side and activates its own synthesis as well. It’s also a repressor. They both essentially prevent transcription from one side
Explain the prophage state of lambda DNA after it enters the host
Lambda DNA is put into hist genome after lambda repressor binds to the operator. The cell divides and this leads to lambda DNA dividing with host DNA (it gets a free ride)
Explain how a bacteria may switch from prophage to lytic pathway
When the host reacts to DNA damage
Explain the lytic pathway after lambda DNA enters host
Cro blocks lambda repressor, and bacterial DNA is extensively transcribed, so theres a shit ton of viral proteins needed for formation of new viruses. Then lambda DNA gets replicated and gets put into viruses. Cell lysis, and the viruses leaves >:) muahahahahah
What promotes prophage state in bacteriaphage infected bacteria
If conditions are good for growth and cell division, then lambda repressor turns off cro, maintaining prophage state.
What is a transcriptional circuit (simply?)
When A protein is coded for by a certain piece of DNA, and this A protein then goes back and either activates or represses the operator.
Explain the flip flop device
One DNA codes for A which stops B synthesis. The B DNA stops A synthesis. Its also known as indirect positive feedback loop
Explain feedforward loop
Protein A activates B and Z synthesis. Protein B activates Z synthesis. Z is super duper ultra mega activated >:)
Explain cell memory in the context feed forward loops
A cell has a gene, and initial transitent signal turns the gene on. Now you make the protein. The protein facilitates its own creation (positive feedback) so its sons and daughters and children all have the protein and have the gene activated
How can feedforward loops be used to measure duration of a signal
Both A and B are needed to activate Z, so the sensitivity of Z is decreased. output of Z is only achieved with prolonged input.
What is synthetic biology
Constructing artificial regulatory circuits and examining behavior in cells
What is a repressilator, what happens with the protein synthesized IRL
A is expressed, B repressed, C expressed. C then represses A which expresses B, repressing C. It’s like a bunch of people who really want to fuck with everyone else. IRL the protein amount oscillates up and down but overall goes up due to there being more overall bacteria
What is transcription attenuation
Present in both eukaryotes and prokaryotes. RNA gets a structure that fucks with RNA polymerase and Regulatory proteins can bind to RNA and interfere with attenuation. Prokaryotes, plants, and some fungi use riboswitches to regulate gene expression.
What is a riboswitch
(Someone who isn’t a ribotop or a ribobottom /j) short RNA sequences that change conformation when bound by a small molecule. some do transcription attenuation, some do stuff other than transcription attenuation. an example is when high purine, purine binds to the riboswitch, changing it conformationally, and then RNA polymerase is pried off.
What do general transcription factors do, name the 5 needed by RNA polymerase 2
help position eukaryotic RNA polymerases at eykaryotic promoters. The 5 are TFIID, TFIIB, TFIIF, TFIIE, TFIIH.
What does RNA polymerase II code for
protein coding genes
What does the mediator do
correctly positions TFIIH, influences general transcription proteins
What do elongation factors do
Prevent DNA polymerase from dissociating
What are coactivators and corepressors
Shit that assemble on gene regulatory proteins but don’t directly bind to DNA
What are the two parts of a eukaryotic activator protein, how are they positioned on the DNA
DNA binding domain (DBD) recognizes specific DNA sequence. Activation domain (AD) actually accelerates transcription. DBD is the foot part and AD is the doorknob part
How do activator proteins facilitate transcription
Attracting, positioning, modifying general transcription factors, mediators, RNA polymerase II. They either directly act on components like prokaryotic activators (e.g. bind somewhere on DNA and succc the thing it wants close) or by indirectly modifying chromatin structure
How many base pairs around neocleosomes, how many times around octamer core, how long is linker DNA (just like get the general range)
Nucleosomes are 147 bp, wound 1 2/3 around octamer, linker DNA 10-80 bp
What are the 4 major ways activator proteins activate chromatin
Remodelling nucleosomes use chromatin remodelling complex, using ATP to pull DNA along nucleosome. Histone removal, histone replacement (need histone chaperones), specific patterns of histone modification
What is the histone code
Acetylation, methylation, phosphorylation on histone tails. Modifications are dynamic and determined by DNA. code readers provide meaning
What termini are histone tails
Histone tails are usually N-termini, C termini can stick out too but its rare
How does eukaryotic repression happen
Competitie DNA binding, masking activation (the thing where the doorknobs are fighting), direct interaction with general transcription factors, recruitment of chromatin remodelling complexes, deacetylation by recruitinng deacetylases, methyl transferase recruiting.
How do reader writer proteins stabilize chromatin
A reader protein recruits writer which starts domino effect of reader-writers complex. DNA methylase enzyme is attracted by the reader which methylates nearby cytosines, stabilizing chromatin.
Methylation of chromatin and blocking of gene expression as a result is an example of what
epigenetic inheritance
How does the human interferon gene have regulation
Activator attracts histone acetyltransferase, acetylates H4K8, H4K9, activator protein attracts histone kinase that phosphorylates H4S10, and serine modification signals the acetyltransferase to acetylate H3K14. Remember that there are 2 tails for H3 because there are 2 H3s
What is RNA capping
Addition of modified guanine to the 5’ end of pre-mRNA, distinguishing it from other types of RNA. Done by cap binding complex that prevents 5’exonuclease from cutting phosphodiester bonds (it cannot cut the weird guanine)
What is splicing done by
The spliceosome
What marks proper splicing
EJCs
How is the sex lethal gene regulated
The splice site is blocked, which makes a shit ton more spliced. Like the stuff between two introns are spliced out too
How is the transformer gene regulated
Sex lethal makes Sxl protein which blocks the splice site and makes an intron longer
How is the doublesex gene regulated
The transformer gene creates a protein that activates a splice site, which prevents the exon from being spliced (best to double check with slides for the drosophila related genes because the diagrams help a lot)
What makes a male drosophila
Nonfunctional Sxl, nonfunctional Tra, inactive 3’ splice for doublesex
How is eukaryotic transcription terminated
CstF (cleavage stimulating factor) and CPSF (cleavage and polyadenylation specificity factor) are on RNA polymerase tail and transfer onto 3’ processing sequence. RNA get cleaved, poly A polymerase adds a ton of not genome encoded As.
What binds RNA processing proteins before they go to RNA
C-terminal domain of RNA polymerase
What causes the RNA processing proteins to be yeeted on
Phosphorylation of RNA polymerase
What are markers of mature RNA you need to move it out of the nucleus
Cap binding complexes, exon-junction complexes, poly A binding proteins.
What can you not have on proteins for export
snRNPs must be lost for export
What happens to messed up RNAs that aren’t fit for export? how much RNA leaves the nucleus
1/20 leaves the nucleus. messed up RNA will be degraded in the nucleus by the exosome.
How do eukaryotes make sure the mRNA is good quality once it is exported out of the nucleus?
5’ cap bound by elF4E, poly A binding protein bound by elF4G. These 2 recruit small ribosomal complexes to start translation. This makes sure both ends of the RNA are intact
What is nonsense mediated mRNA decay? What should happen if the splicing is normal?
Normal conditions will have EJCs displaced by moving ribosome. Stop codon is on the last exon. Abnormal splicing will cause a premature stop codon which leads to EJCs still on RNA. UPF degrades fucky wucky mRNA
Where is nonsense mediated mRNA decay important
In the immune system where a lot of DNA rearrangement happens to make antibodies.
How do prokaryotes control for mRNA quality
Ribosomes get stuck on broken and incomplete RNAs, and a special tmRNA (好礼貌的rna草) gets yoinked to the A side, and puts alanine onto the chain. The tmRNA acts as the template for the next tRNAs, making an 11 amino acid tag, and proteases will be attracted to shit with the tag and eat it.
