Mutations and DNA Repair
What is a missense, silent, nonsense, frameshift, and non-frameshift mutation.
Say the answer
What is the main thing in Prokaryotic Gene Regulation? Lac what?
Operons
What is the idea of chromosome territory?
The idea that in interphase, chromosomes in the nucleus has its discrete domain and stays separate from other chromosomes.
Bonus: what are intrachromosomal domains?
What is alternative splicing?
Bonus: What were the 6 types of alternative splicing we learned and what do they do?
Changing areas to splice a pre-mRNA to create different forms of mRNA from identical pre-mRNA.
What are the three major types of epigenetic changes?
Bonus: What are CPG Islands?
Methylation: Takes place after replication and during differentiation of adult cells. Methyl groups block transcription factors from binding.
Histone modification and chromatin remodeling: Acetylation, methylation, and phosphorylation. Open and closes DNA
Noncoding RNA: miRNA and and lncRNA
What are transposable genetic elements? What can they do?
They are DNA elements that move within or between genomes and insert themselves into various locations within genome. They are found in all organisms but their precise function is unknown. They can act as naturally occurring mutagens causing inversions, double-stranded breaks, and translocations. Causing chromosomal damage.
If there is a high level of glucose and a high level of lactose, what will be the rate of transcription.
Basal
What are the three types of epigenetic modification?
What are the five critical features of epigenetic modification?
Nucleosome modification, Histone Modification (Acetylation/Methylation), and DNA methylation/Demethylation.
Epigenetic modification alters chromatin structure, transmissible during cell division, reversible, does not alter DNA sequence, and directly associated with gene transcription by altering accessibility to (transcription regulatory proteins, transcription activators, RNA polymerase 2).
Talk about epigenetic inheritance
What is Deadenylation-Dependent mRNA Decay?
Bonus: What are Adenosine-uridine rich elements?
Bonus: What is NMD
Exoribonuclease enzymes shorten length of poly-A tail called Deadenylation-dependent decay. Two pathways can include decapping or Exoribonucleolytic decay by exosome. Show image.
Cis-acting sequence element that regulates mRNA stability. Most common determinants for RNA stability in mammals.
NMD is nonsense-mediated decay. Basically mRNA with premature stop codon die.
What are the two methods that miRNA can impact gene expression? What are the four models and classes of lncRNAs.
Bonus: How are lncRNAs similar to mRNAs
miRNA can either lead to increased levels of mRNA degradation or lower levels of translation.
The 4 classes of lncRNAs are Antisense, Intronic, Bidirectional, and intergenic.
The four models are decoy, adapter, guide, enhancer.
lncRNAs have caps, tails, and introns.
What is the AMES test?
Used to test Chemicals for Potential Mutagenic Properties. Tests chemicals to revert mutant back into a WildType. If it reverts, its a mutagen and vice versa.
What does polycistronic mean? In what type of gene regulation is it present in?
In genetics, polycistronic means containing the genetic information for multiple cistrons, or genes, in a single messenger RNA (mRNA) molecule
What are Cis-acting and trans-acting elements? What is the main difference between the two? Name some examples of both.
Cis-acting sequences are located on the same chromosome as the gene that it regulates. Trans-acting element means that their coding sequence is located on a different chromosome than the gene it regulates.
Cis-acting: Promoters, Enhancers, Silencers, Insulators
Trans-acting: Transcription factors.
What are siRNAs and microRNAs?
Bonus: What are ceRNAs?
Both short double-stranded ribonucleotides.
siRNAs: Arise in cell due to virus infection—produce double-stranded RNA, which is recognized and cleaved by Dicer
microRNAs: Noncoding R N As that negatively regulate gene expression.
Show image
Competing endogenous RNAs. Acts kinda of like a decoy for microRNA. Made from lncRNAs
What is Monoallelic expression? What are the three main classes?
Only one allele is transcribed while the other is silent. The three classes include: Parent-of-Origin Monoallelic Expression: Imprinting, Random Monoallelic Expression: Inactivation of the X Chromosome, Random Monoallelic Expression of Autosomal Genes
What was the Luria-Delbruck experiment? What did it find?
The experiment demonstrated that genetic mutations in bacteria occur randomly and are not induced by environmental factors, such as exposure to a virus.
In the lac operon, when are cAMP levels high? What does the lac repressor bind to and what macromolecules causes it to fall off?
cAMP levels are higher when there is a low level of glucose. The lac repressor binds to the operator and a high concentration of lactose causes it to fall off.
Bonus: What type of operon is the lac operon?
What is the main macromolecule of transcription factors? What is the two domains of these factors?
Proteins. The two sites are the DNA-binding domain and the trans-activating domain. In the DNA-binding domain, it binds to a specific DNA sequence in the cis-acting regulatory site. The trans-activating domain activates or represses transcription by binding to other transcription factors or RNA polymerase.
What is Cytoplasmic Polyadenylation?
What is a zip code binding protein 1?
A method to "store" mRNA for future use. One example is a cis-regulatory element in the 3' UTR and is called the cytoplasmic polyadenylation element (CPE). Brings CPEB which then recruits PARN and Maskin.
ZBP1 is a cis-regulatory element in the mRNA 3' UTR sequence. It blocks translation until mRNA is localized to site of cell where it is needed.
How is Epigenetics and Cancer related?
Hypomethylation of gene that promote cell replication can create cancer. More specifically, cancer cell suppressors can also be hypermethylated to cause cancer.
Examples include hypermethylation of DNA repair gene of MLH1, BRCA1, and CDKN2A.
Bonus: What is the Rubinstein-Taybi syndrome?
What are the two types of mutations? What are specific examples of those mutations? James will try to explain the last two.
Spontaneous and Inducible
What are the four genes on the lac operon and the purpose of each?
lacI: This gene codes for the repressor protein that controls the expression of the other three genes. lacZ: Codes for the enzyme beta-galactosidase, which breaks down lactose. lacY: Codes for lactose permease, which transports lactose into the cell. lacA: Codes for beta-galactoside transacetylase, whose exact function in lactose metabolism is not fully understood
What are coactivators and enhanceosomes?
Coactivators interact with proteins and enable activators to contact promoter-bound factors and form complex “enhanceosome”
Enhanceosome Interacts with transcription complex and Repressor proteins at silencer elements decrease rate.
What is Ubiquitin-Meditated Protein Degradation?
Bonus: What protein causes an upregulation of a gene that increases ubiquitin?
Bonus: What is the most common type of posttranslational modification?
Targets a protein for degradation by modifying it with ubiquitin. This ubiquitin is then recognized by the proteasome.
P53 levels increase if cell suffers DNA damage or metabolic stress.
Phosphorylation usually induces conformational changes and therefore functional changes in proteins.
What is environmental induction of epigenetic change?
This term refers to the process by which environmental agents such as nutrition and temperature cause heritable changes in gene expression without altering the DNA sequence, exemplified by offspring effects from the 1944-1945 Dutch famine and protein-deficient diets in animal models