1How do we protect mRNA from enzyme degradation?
Your 5' methyl cap, and your 3' poly A tail
2How do we degrade mRNA?
Use enzymes to remove poly A tail or methyl head, (deadynlase, decapping enzymes, exosome)
3What is alternative splicing?
when different exons or introns are taken out of the "same" mRNA to create variable proteins
4What helps promote degration of mRNA?
RBP adenosine rich element which helps recruit enzymes
5How is alternative splicing regulated
splicing enhancers / silencers
SR proteins (bind to enhancers and recruit spliceosome, hnRNPS bind to silencers and do the opposite)
6What do RBP's do?
prevent SR proteins or hnRNPS from binding to mRNA
7Why does mRNA stability matter?
How fast an mRNA is degraded determines how long it is around to create its protein product
8What is nonsense mediated decay?
When mRNA is broken down because premature stop codons were sensed
9Why break down mutated mRNA?
The resultant protein could be harmful AND its a waste of energy
10What other RNA's are there?
tRNA, rRNA and snRNA
11What does tRNA do?
Carry amino acids to ribosomes to add to peptide chain
12siRNA
A silencer RNA, it detects a specific sequence on mRNA, binds to it and causes the mRNA to be broken down via recruiting RNA induced silencing complex
13What is RISC? what does it do?
RNA induced silencing complex, it breaks down mRNA to regulate it
14What does miRNA do?
Forms hairpin structure, reocgnizes sequence of mRNA and either completely break it down or simply inhibit translation
15What happens if siRNA or miRNA is damaged / inhibited?
Disease! it has many complex functions
16What do long noncoding RNA's do?
They act as a sponge for miRNA's to "block" it from mRNA
17Can only RNA's or enzymes regulate translation?
NO! proteins can get in the way of closed loop structures and slow translation
18Why have a closed loop structure?
You may need to make a lot of that protein, want to save energy by using the same mRNA, save space in the cell, and lowers chance of error by introducing new mRNA's
19Why mess with a closed loop instead of breaking down mRNA
Its more energetically favorable and allows for tight regulation
20What is mRNA localization
mRNA is localized to a specific area of the cell and only allowed to be translated at that region
21What tends to turn proteins on or off?
Phosphorylation
22What is the function of adding ubiquitin?
Whenever this is added to a protein it marks a protein to be broken down by proteosomes
23What is epigenetics?
Heritbale genomic alternations that are not encoded in the DNA sequence
24Specific pattern of epigenetic modifications present in a cell at a given period of time
Epigenome
25What are the three major epigenetic mechanisms?
Methylation (reversible), Chromatin remodeling, noncoding of expression via noncoding RNAs
26Where does methylation occur
on the DNA almost exlucisely on cytosine next to guanine
27How does methylation impact dna transcription
It decreases the rate
28How accesible is hetereochromatin?
it is non accessible
29How accessible is euchromatin?
Very accessible
30How can methyl groups be removed?
By failing to copy over the packing pattern in dna replication, or by removing methyl groups from the methylated cytosine
31How do we get cell differentiation?
By methylating genes you dont want expressed
32Which base gets methylated
Cytosine
33In mammals, when does DNA methylation take place?
After DNA replication and during cell differentiation
34Patterns of CpG hypomethylation are asscoiated w/ genes involved in tissue specific functions T or F
True
35Is making chromatin an active or passive process?
Active, it requires ATP
36What is a correct description of a nucleosome?
A unit of chromatin composed of DNA wrapped around a core of histone proteins, aiding in DNA compaction and regulation
37How do we unwind or wind histones?
By modifying the chemicals on the tails of histones (on their N terminal)
38What is a "writer"
Adds chemical groups to histones
39What is a "reader"
intereperets the chemical groups on histones
40What is an "eraser"
Proteins that remove chemical groups
41How does acetyl impact transcription?
It increases transcription
42How simple is histone modification?
it can be very complex! over 20+ modifications that interact
43If a CpG island in a promotor is unmethylated the gene is silenced T or F
False
44What are the types of noncoding rnas
miRNAs, siRNA, piRNAs
45What noncoding rna silences gene expression
miRNA and siRNA
46what noncoding rna silences genes in GERM cells
piRNA
47Why do we want noncoding RNAs close to key parts? promotors and introns?
It helps to regulate
48What is one way that long noncoding RNAs turn on or off genes
they can form rna protein complexes w/ chromatin regulators
49Decoy long noncoding RNA
bind transcription factors to trap them and prevent their job
50Adaptor long noncoding RNA
bring two or more porteins together to allow them to do their job (GTFs forming transcription complex)
51Guide long noncoding RNA
targtes gene silencing in an allele specific fashion
52Are methylation patterns passed on from parent to offspring?
Somewhat! youll get methylation marks of maternal and/or paternal chromsomes in areas
53What is monoallelic gene expression?
when one allele is active and one is transcriptionally silent
54Is an imprinted gene active or not?
It is not active
55What is a barr body?
Incredibly tightly packed X chromsome
56What gene is expressed on the active X chromsome in X blocking?
TSIX
57What are the four possible states for autosomal inactivation
M on P off, M off P on, M on P on, M off P off
58What is a stochastic event?
A random event, usually referring to autosomal inactivation
59What is highly correlated with activation of transcription?
Histone acetylation
60What is a reciprocal cross?
When you switch the gender that had the trait (determines if something is sex linked)
61What is autosomal inheritence?
Inheritence on non sex chromosomes
62What can influence gene expression?
Physical location, temperature (enviornment), nutrition (enviornment),