Intro to Gene Regulation
What is the 'master blueprint' for our cells?
Aka, what serves as the instructions to carry out tasks?
The genome
Define genomic equivalence
Every cell in an organism has the same, complete genome. This gives the potential to recreate the entire organism.
How do insulators affect transcription?
Insulators prevent/block the effects of enhancers or silencers
In the origami cell analogy, what does each fold of the paper represent?
A wave a gene expression that commits the cell to being more differentiated
What is an operon?
Genes with related function meant to work together in same pathway that are a part of the same stretch of DNA
Define catabolism and anabolism
Catabolism: Formation of raw materials from larger molecules (breaking down)
Anabolism: Formation of larger molecules from raw materials (synthesis)
What type of stem cells do adult bodies have? Which cell is totipotent?
1. All adult stem cells are multipotent
2. The fertilized egg is the only totipotent cell
Why can't the core promoter solely control gene expression at the transcriptional level?
All cells contain a core promoter, and its role is to only bind RNA Pol II. Thus, its on a on/off basis without nuance.
How are introns removed from pre-mRNA?
TRUE
What does β-galactosidase do?
Breaks down lactose into simple sugars
When chromatin is transcriptionally active (being used), what is their shape like?
Transcriptionally active chromatin exists as euchromatin; they're unraveled and loose.
What is the difference between the core promoter and regulatory sequences?
Core promoter: Promoter region before the gene that recruits RNA Pol II via TFs
Regulatory sequences: Additional DNA sequences that affects rate of transcription via TFs
What is the Iron-response element (IRE)?
mRNA sequence that binds the IRE-binding protein, which influences translation of ferritin and the transferrin receptor
What is the purpose of DNAase I?
Tool for detecting whether genes in a specific cell is being used
Can tell us what regions of DNA are exposed and tightened (methylated)
What are Hox genes?
Genes that regulate early development of an animal's body plan
What is X-inactivation?
In female mammals, only one X chromosome is expressed in every cell. The other is condensed into a Barr body by proteins made from Xist RNA
Why can regulatory sequences be distal and/or downstream of the gene?
DNA loops and bends, so even distal or downstream regulatory sequences can affect the core promoter
What is the significance of the C-Terminal Domain of RNA Pol II?
Phosphorylation patterns at serines in a 7 residue repeat attracts proteins for 5' capping, Poly(A) tail addition, and alternative splicing
mRNA processing begins co-transcriptionally. What does this mean?
It means RNA processing (addition of 5' cap, poly(A) tail, and splicing) occurs at the SAME TIME as transcription
Why is there a large difference in number between our number of genes and total DNA size?
Why can we make so many protein products despite this large gap?
1. Most of our DNA sequence regulates genes, and aren't actually genes themselves.
2. Alternative splicing allows for many different protein products to be made from a single gene.
What is the structure of CpGs?
Why are CpGs found primarily in promoter regions?
1. CpGs are on the same strand, a cytosine and guanine linked by a phosphodiester bond.
2. CpGs are found in promoter regions to permanently inhibit gene expression in certain genes.
In a given sequence of a DNA binding motif for a transcription factor, what do the varying heights of the letters mean?
How common the nucleotide is seen at that position within the site
Which protein products are made and which are blocked in the presence of high iron concentration? In low iron concentration?
High iron: Ferritin is made, transferrin receptor is not made
Low iron: Ferritin is not made, transferrin receptor is made
All cell types contain same genome, so it is up to those cells to control which genes get used or not as they become differentiated. How do they do this?
When looking at the same gene, it can be transcribed in high/normal/low levels. This is due to the fact that certain cells have certain proteins (activator/repressor) that recognize regulatory elements (DNA binding sequences aka motifs - enhancers, insulators, silencers) and bind to these "staging areas" to attract other TFs to enhance, decrease, or have moderate levels of transcription.