Lecture 25 Flashcards
rRNA cell type
prokaryotic
eukarytoic
rRNA is…
ribosomal RNA
rRNA function
structural and functional componenets of the ribosome
mRNA is…
messenger RNA
mRNA cell type
prokaryotic
eukaryotic
mRNA function
carries genetic code for proteins
tRNA is..
transfer RNA
tRNA cell type
prokaryotic
eukaryotic
tRNA function
helps incorporate amino acids into polypetide chain
snRNA is…
small nuclear RNA
snRNA cell type
eukaryotic
snRNA function
processing of pre-mRNA
snoRNA is…
small nucleolar RNA
snoRNA cell type
eukaryotic
snoRNA function
processing and assembly of rRNA
miRNA is…
micro RNA
miRNA cell type
eukaryotic
miRNA function
inhibits translation of mRNA
siRNA is…
small interfering RNA
siRNA cell type
eukaryotic
siRNA function
triggers degradation of other RNA moelcules
piRNA is
piwi-interacting RNA
piRNA cell type
eukaryotic
piRNA function
suppresses the transcription of transposable elements in reproductive cells
crRNA is…
CRISPR RNA
crRNA cell type
prokaryotic
crRNA function
assists destruction of foreign DNA
lncRNA is…
long noncoding RNA
lncRNA cell type
eukaryotic
lncRNA function
variety
ribosome
- complex of rRNAs and protein
- 2 subunits
- does not fully assemble until translation
describe prokaryotic ribosome
70S
large 50S
small 30S
describe eukaryotic ribosome
80S
large 60S
small 40S
unit for ribosome size
Svedberg units
based on migration using velocity centrifugation
Why do the subunits size not add to get the full ribosome size?
the unit is based on migration which depends on size, density, and conformation not just molecular weight
large prokaryotic ribosome subunit
23 S rRNA
5 S rRNA
31 proteins
small prokaryotic ribosome subunit
15 S rRNA
21 proteins
snoRNA is important…
in isolating the individual rRNAs form the initial transcript
this is a type of RNA processing
precursor rRNA
contains all rRNA except 5s rRNA in eukaryotes
Describe processing for rRNA with snoRNA
- Methylation occurs to precursor rRNA and identifies separate rRNA-to-be molecules - spacer sequences are not methylated
- Pre-rRNA is cleaved to produce distinct molecules
occurs in the nucleolus
this process occurs in both pro and eukaryotes but there is no nucleolus or snoRNAs in prokaryotes
Where do snoRNA come from
- sometimes transcribed from own genes by RNA pol II or pol III
- sometimes come from intron areas of pre-mRNA molecules
how does tRNA get its secondary structure?
base pairing
describe tRNA processing
- initial transcript contains several tRNA molecules
- tRNAs are separated
- 5’ and 3’ ends are trimmed
- intron is removed in eukaryotes - it can now take its cloverleaf secondary structure
- 3’ end is modified by a CCA addition in eukaryotes
- some bases are modified to get the tRNA in its final L-shaped structure
anticodon is…
located next to the intron which will be removed during tRNA processing
5’-CCA-3’
sequence added to the 3’ end of tRNA during processing
inosine
- unusual base found in tRNA
- derivative of guanine - so is purine
- found at 5’ end of anticodon when present
- pairs with adenine, uracil, and cytosine
- impacts translation
pseudouridine
- similar to uracil turned sideways
- attaches to ribose at the 5 position of pseudouridine ring rather than 1 position
dihydrouridine
- similar to uracil
- normal double bond between 5 and 6 is saturated so there is a single bond and extra hydrogen molecules
What are the unusual bases in tRNA
- inosine
- pseudouridine
- dihydrouridine
tRNA is responsible for…
binding to an amino acid and bringing the amino acid to the ribosome for incorporation into a protein
acceptor stem
3’ end of tRNA
amino acid binds to the 3’ end of tRNA
variable loop
between the anticodon loop and T loop on tRNA
varies in size between different tRNA molecules
the components of tRNA
cloverleaf structure with intrastrand complementary pairing on 4 stems
results in… D loop T loop anticodon loop variable loop
how is the final structure of tRNA formed
areas of D and T loop of the cloverleaf secondary structure pair up causing a twisted helical, L-shaped structure
3 types of processing to convert pre-mRNA into mature mRNA
- addition of 5’ cap
- 3’ cleavage and addition of polyA tail
- RNA splicing
capping the RNA - processing mRNA
occurs as soon as 5’ end of pre-mRNA is free of RNA polymerase
gives stability
aids in splicing efficiency
aids in translation efficiency since cap binding proteins bind to the cap and the ribosome binds to cap-binding proteins
describe capping the RNA in processing of mRNA
- 1 phosphate is removed from 5’end of RNA
- guanine nucleoside tri-P is added in 5’-5’ linkage
- methyl groups are added to position 7 on guanine ring and to 2’ position of sugar of the next 2 nucleotide
Why is mRNA capped and not tRNA?
cap is important in allowing mRNA to bind to ribosome for translation
Importance of polya tail
- protects the mRNA
- helps initiate translation
- involved in termination of translation
how does the poly-A tail protect mRNA
- tail length determines stability
- when too short, the mRNA is recycled
- tail shortens as mRNA ages
how does the poly-A tail aid in translation?
helps attachment of ribosome to mRNA
The poly-A tail allows…
mRNA to exist for a longer time in the cytoplasm before it is degraded
describe the poly-A tail
50-250 adenine nucleotides are added to the 3’ end by enzyme Poly(A) polymerase
spliceosome
snRNPs and pre-mRNA complex
structure at which introns are removed and exons are joined together
splicing
removing the introns and joining the exons together
occurs in spliceosome
snRNP
small nuclear ribonucleoproteins
formed by small nuclear RNAs with proteins - complex of ~300 proteins + 5 snRNA
uridine rich
snRNAs have regions complementary to…
small nuclear RNA the ends of exons, site within introns, or other snRNAs
What are the 3 basic signals for the spliceosome?
critical sequences at…
- 5’ slice site
- 3’ splice site
- branch point within the intron
Base pairing between ___ is important to proper splicing
pre-mRNA and snRNA
Describe formation of poly A tail
- pre-mRNA is cleave 11-30 nts downstream from consensus sequence
- adenine nucleotides are added to the 3’ end by Poly(A) polymerase
In the process of cleavage and polyadenylation, pre-mRNA is cleaved after…
AAUAAA sequence and before GU-rich sequence in transcribed RNA
Splicing requires ___ and depends on ____.
requires precise excision of introns and joining of exons
depends on key sequences at critical points
branch point
contains an adenine
In mRNA, the sequence containing the ends of the introns and include the adenine will read…
exon - GT…A…G - exon
Splicing process
- U1 and U2 bind to the primary transcript
- a complex of U4, U5, and U6 joins
- cleavage occurs at 5’ splice site allowing a lariat to form and release a complex of U1 and U4
- a transesterification reaction occurs between the guanine at the 5’ end of the intron and the adenine at the branch point
- cleavage occurs at the 3’ splice site and the exons are spliced together
U1 and U2
small ribonucleoproteins
where does U1 bind
5’ splice site
where does U2 bind
branch site
what holds the splicesome together
the interaction between mRNA and snRNAs
snRNPs are critical in…
proper positioning for splicing
base-pairing is important to the their binding to the RNA
Where are most conserved regions for splicing located?
in the intron
alternative splicing
a single pre-mRNA can undergo alternative splicing methods resulting in different functional mRNAs
can differ tissue to tissue or individual to individual
describe alternative splicing
- allows one primary transcript to produce different proteins
- the final mRNA may include all exons or only some of them
3’ cleavage sites
- a primary transcript may have different cleavage sites at the 3’ end
- depending on which one is use, a different length product may form
Both ___ and ___ produce different mRNAs from a single pre-mRNA
alternate splicing
multiple 3’ cleavage sites
RNA editing
- occurs in some, but not all, mRNA sequences
- type of posttranscriptional modification
- not one of the 3 types of processing as it doesn’t always occur
- specific sequence changes that are made to RNA after transcription
RNA editing occurs in…
some nuclear RNA
more common in organelle RNA
How was RNA editing detected
- 1986
- when the mRNA coding sequences of some genes were found to differ from the coding regions of the DNA they came form
most common types of RNA editing
- changes from cytosine to uracil
- changes from adenine to inosine
- inserting or deleting uracil residues
guide RNAs
aid in insertion and deletion types of RNA editing
describe guide RNA activity
- gRNA pairs with mRNA in an imperfect pairing
- the gRNA acts as template for addition or deletion of bases
- the mature mRNA is released
- the mature mRNA will now have sequence different from the sequence coded by the DNA it came from
RNAi is…
RNA interference
shuts off gene expression using dsRNA
Who received the Nobel prize for RNAi?
Fire and Mello
RNAi was discovered in…
C. elegans
How was RNAi discovered?
- injected dsRNA into C.elegans
- noticed genes with the same sequence as the injected RNA decreased expression - translation of the targeted genes was inhibited
How may RNAi be helpful?
may aid the cell by limiting the invasion of foreign genes
may censor the expression of the cell’s own genes
describe how RNAi works
- dsRNA is cleaved by the enzyme dicer to form miRNA or siRNA that is ~21 nts long
- these bind with proteins to form RNA induced silencing complex
- this base pairs with mRNA and either inhibits translation or degrades mRNA
miRNA
transcribed from a distinct gene and targets other genes for regulation
in RNAi activity it inhibits translation of the target gene
siRNA
comes from mRNA, transposons, or viral RNA and targets the genes it comes from
in RNAi activity it degrades mRNA
RISC
RNA induced silencing complex
base pairs with mRNA in RNAi activity to inhibit translation or degrade mRNA
formed by either miRNA or siRNA binding with proteins
the small RNA involved in RNAi
siRNA
miRNA
potential issue with treating medically with RNAi
may target the expression of a similar gene sequence rather than only that of interest
RNAi has been tested in treatment of
- macular degeneration - study halted
- cancer tumors
- nerve disorders
CRISPR
clustered regularly interspaced palindromic repeats
CRISPR are in…
prokaryotes
CRISP is…
a prokaryotic mechanism to protein bacteria from foreingn DNA by cleaving invading DNA (phage, etc)
How may CRIPR be used
manipulation of the system may allow for editing of targeted areas of DNA
