What is the role of Edeine
Binds to small ribosomal unit to block P site
How does in vitro transcription and translation work
all necessary RNA polymerase, ribosomes, tRNAs, translation factors are isolated in a tube, just add DNA and protein is produced
in bacterial mrnas, degradation is initiated by what?
an endonuclease, usually RNase E
What inhibits RNase E activity
a 5’ triphosphate
What do stem-loop structures do
inhibit exonucleases
what helps degradation as bacterial mrnas are deconstructued
3’ poly(A) tract
can endonuclease activity initiate degredation in eukaryotes?
yes
what is the first step in RNA degredation in eukaryotes
poly(a) tail shortening by a deadenylase
do 3’ poly(A) tails hinder or aid degredation in eukaryotes
hinder
what do decapping enzymes do
remove the 5’cap
What is viral ‘highjacking’ of translation
viral mrnas develop ways to compete for translation
how do mrnas hijack translation
shut down translation of host mRNAs to hoard resources
what is an example of viral hijacking
piconaviruses that cleave translation factors, flu viruses remove the 5’ xcap
what is the role of picornavirsues
inhibit cap-dependent tranlsation, so themselves use cap-independant tranlsation by isng EREs within the 5’ UTR to directly recruit ribosomes
what to rotaviruses lack
a 3’ poly(A) tail
What do Viral mRNAs do to elimate the need to use hostprotein factors
make a closed loop complex via RNA-RNA interactions
what are the three main principles of regulatory RNAs
- to yield the molecule
- employ complementary base pairing wtih DNA/RNA targets
- interact with other components (like proteins) to carry out their functions
how do regulatory RNAs identify their targets
through base pairing
what are the three ways regulatory RNAs can be encoded
- on the dna strand antisense to the target
- in a separate DNA region (trans)
- as part of the target (cis)
how long are sRNAs usually
100-300 nt
how are most sRNAs encoded
most encoded in trans
where to sRNAs usually bind
close to the Shine-Delgarno motif
how do some sRNAs affect degredation
by recruiting ribonucleases to the target
What happens to RyhB when iron levels are low
ribosomes are prevented from binding, RyhB recruits Rnase E and the mRNA is degraded
T or F: sRNAs can interact with multiple targets
T
What kind of protein is Hfq
chaperone protein
What is the role of the chaperone protein Hfq
a hexameric protein that helps sRNAs find their targets
Wha thappens when Hfq levels in a cell are low
sRNAs compete for Hfq and it becomes part of the regulatory system
High chitosugar levels induce what
transcription of a ‘decoy mRNA’
T or F: regulatory RNAs are the same in eukaryotes vs bacteria
true
are eukaryotic sRNAs longer or shorter than bacterial sRNAs
shorter
what are the three classes of eukaryotic sRNAs
microRNAs (miRNAs)
Small interfering RNAs (siRNAs)
Repeat-associated small interfering RNAs (rasiRNAs)
What is argonaute
binds to sRNAs and facilitates their interactions with complementary molecules
T or F; All eukaryotic sRNAs carry out their functions in association with Arg
T
What are the four Argnaute domains
N, PAZ, Mid and PIWI
What does PAZ do
binds the 3’ end of bound RNA
what does Mid do
interacts with the 5’ end of RNA
What does PIWI do
related to RNase H and interacts wtih the whole RNA
Where are sRNAs dervied from
from different types of long percursor molecules
Where are miRNAs derived from
primary transcripts of genes
where are si RNAs derived from
double stranded RNAs
where are rasiRNAs derived from
repetitive regions of the genome
what do processing cuts do
cut precursor RNAs to correct sRNA size
What is drosha
relies on accessory protein for positioning and determination of fragment length
what is dicer
determines the length of cleaved fragments by securing the 3’of the RNA with the PAZ domain and cutting it
what are dicer and drosha
cutting enzymes
T or F: several miRNAs can be produced from the same pri-miRNA
True
what happens in the microprocessor complex
produces a 60-70 nt hairpin with 3’ OH and 5’ monophosphate, hairpin exported from the nucleus
where are siRNAs derived from
double stranded RNAs from various endo or exogenous sources
T are F: siRNAS are involved in clelular defense against exogenous RNAS
true
how are MiR:miR* and siR:siR* similar
both have 3’OH and 5’ monophosphates
both undergo post-transcriptional modifications such as methylation
what is the RISC complex
the guide RNA-Argonaute complex,
what does miRISC do
usually pairs initially via 2-8 nucleotide seed sequence, 3’ end remains tightly bound by the PAZ domain
what doe sthe siRISC do
an bind along its full length, releases PAZ domain and induces conformational change that activates PIWI domain
where are miRNA binding sites usually found
in the 3’ UTR of the target sequence
where does rasiRISCs do
can cleave target RNA, also have epigenetic effects
how are foreign nucleic acids removed in eukaryotes
by RNA interference (RNAi)
how is viral defence mediated in bacteria
CRISPR
how does CRISPR work
contains 20-50 nucleotieds, cleaved foreign DNA cleaved, transcribed by Cas proteins to give short crRNAs
What does dicer do
cleaves long dsRNA into short siRNA
what does RISC do
RNA-induced silencing complex (includes argonaute)
What is the purpose of CRISPR/Cas9
modification of HBB gene, rsponsible for Beta-thalassemia in embryos
t or f: sRNAS are larger and more complex than regulatory RNAs
Fals
What can riboswitches control
transcription, translation and RNA splicing
T or F: riboswitches adopt complex 3D configuration
T
Protein binding RNAs can act as _____ to bring proteins into close proximity with one another
tethers
What are the three things that regulatory RNAs can bind to in order to exert effects
Other RNAs, Metabolites (Riboswitches), and Proteins (Chaperones, Endonucleases)
What is PKU?
phenylketonuria, cannot metabolize phenylalanine and if consumed, mental retardation and ill helath results, genetic disorder, normally Phe converted to Tyr
what are SNPs and what do they do
single nucleotide polymorphisms, used as markers for genomic analysis of human diseases
what are microsattelites
can be used as genetic markers
what is classic mapping
identifies marker all over a genome correlates marker with trait of interest
T or F: SNPs and microsattelites are usually the cause of the rare disease under investigation
F
What are SNP chips
used to detect SNPs at specific genomic loci
recombination tends to take place in “___ ____”
“hot spots”
What are the two ways of finding the cause of disease
linkage analysis and association studies
What is linkage anaysis
Traces specific disease alleles within families
what are association studies
identify disease genes by studying large groups of unrelated individuals,
what is the common disease-common variant hypothesis
if a disease is common in a population, there will be a small number of allele for the gene that causes the disease
T or F; whole genome sequencing is initally focused on the exome
true
What is Pharmacogenomics
uses information from individual genomes to identify treatments that are more likely to be effective on certain individuals
what is the difference between gain of function and loss of function genetic causes
Loss of function is a lack of gene expression, while gain of function causes an expression of a gene that causes a disease phenotype
What are some of the pros and cons of chain termination dedeoxynucleotide sequencing
Pros: -Highly accurate -Widely avaliable -Short time -Cost manageable Cons: -expensive for fluorescent ddNTPS -requires a primer
What is Illumina dye sequencing
technique used to determine the series of base pairs in DNA , slide flooded with florescently labeled nucleotides
what are some of the pros and cosn of Illumina sequencing
Pros: -Highly accurate -lower cost Cons: -short sequences obtained that must be analyzed computationally
whats the difference ebtween a transition and transversion mutatoion
transition occurs if a purine is replaced by other purine or vice versa, whereas a transversion is a purine to a pyrimidine
what is dna damage often caused by
cell metabolites
T or F; DNA damage can occur from intra and extracellular agents
true
UV light promotes what?
pyrimidine dimers
what is an example of single point damage
depurination/depyrimidation
What is a mismatch repair
fixes mistakes made during replication, using the other strand as a template
what are the steps in a mismatch repairq
- mismatch recognized by MutH
- MutSLH complex assembles
- MutH nicks the new strand
- Nicked strand is digested by exonuclease
- DNA resynthesized
what can repetitive regions of DNA form
hairpins, and can be skipped during replication
what protein orchestrates apoptosis (cell death)
protein p53
how does protein p53 control cell death
by binding at promoters of target genes to increase proteins that inhibit the cell cycle or stimulate apoptosis
T or F: p53 is highly regulated
T
how does p53 function when no DNA damage is present
Whne no DNA damage is present, MDM2 ubiquitinates lysines in p53 C-terminal domain, targeting it for degredation
how does p53 function when DNA damage is present
kinase activity stimulated and results in phosphoyrilation of p53 and MDM2 so they no longer interact, p53 tetramerizes and interacts with transcription proteins, which acetylates histones and p53