Chap 3 Flashcards
8 major types of RNA
Ribosomal, messenger, transfer, small nuclear, small nucleolar, micro, piwi interacting, Long non coding
Most common rna by mass
rRNA
Most common by number
tRNA
RNA primary structure
Chain of nucleotides, flat and straight
Secondary structure (RNA)
Folds of RNA chains into motifs
Common secondary structures of RNA
Bulges, stem, ss hairpin or loop, junction
RNA is what type of helix usually
A type- broad and shallow minor grove and major deep grooves, usually recognized by minor grove
Non cannon base pairs help with
RNA self assembly, RNA protein interactions, RNA Lingand interactions, making groove wider
tRNA
Brings amino acid, has anti codon loop
tRNA secondary structure
Cloverleaf
tRNA tertiary structure
L shaped
Secondary tRNA has
T loop, d loop, anti codon
T loop
Recognized by ribosome
D loop
Recognized by aminoacyl, gets charged
Tertiary structure (RNA)
Interactions between secondary structure domains
Psuedoknot
(RNA3D) Hairpin loop pairs with a complementary sequence outside of loop, coaxial stacking
A minor motif
(RNA3D) Adenosine make contact with the minor grooves
Tetraloop motif
(RNA 3rd)Stem loop stabilized by base stacking ex: UUUU
Ribose zipper motif
(RNA 3) Stabilized helix helix interaction in minor grove hydrogen bonding between 2’ OH and base of another helix
Kink turn motif
Asymmetric internal loop embedded in an RNA double helix, sharp turn on backbone of three nucleotide string
specific binding proteins
Stabilized native structure of RNA
RNA chaperones
Prevent misfolding or unfolding, helps RNA be the right form, unfolds misfolds
Hydroxyl radical foot printing assay
Measures how long an rna takes to fold (by cutting back on with a radical)
Riboenzyme
Ribosome that are self splicing and catalytic
Enzyme
Substance that increases rate of chemical reactions
Many ribozymes are - and use
Metalloenzymes (need metal like mg2+), and use acid base reactions
Large ribozymes
RNase P, group I intron, Group II intron, spliceosome, ribosome
Tertiary structure examples (RNA)
Coaxial stacking, pseuoknots, a minor motifs, tetra-loops, ribose zippers, kink turns
Large catalytic RNA folding time
Several minutes to fold
Small ribozymes
hammer head, hepatitis, delta virus RNA, riboswitch
Eukaryotic RNA virus genomes
Single stranded (+or -/) and double stranded
Euk RNA viruses replicationrequirement
No DNA intermediate, just need cytoplasm,
Euk rna shape
Enveloped or non enveloped
Plus strand
Coding strands
Ex. Hepatitis C, sars-cov-2, foot mouth
Minus strand
Non coding strand, need to make plus strand to start coding
Ex. Rabies, mumps, flu, ebola
Double stranded RNA genome
Has both + -
Ex. Rotavirus
Retrovrirus
RNA tumor virus, pseudo diploid, reverse transcription,
RNA bacteriophage types
Single stranded RNA genome and segmented double stranded RNA genome
Viroid
Just RNA, not encode proteins, plant virus, small circle, just host RNA polymerase
rRNA
an essential component of the ribosome.
mRNA
a copy of the genomic DNA sequence that encodes a gene
product and binds to ribosomes in the cytoplasm.
snRNA
plays a role in pre-mRNA splicing, a process which prepares the mRNA for translation.
snoRNA
plays a role in rRNA processing.
miRNA
post-transcriptional gene regulation; each miRNA binds to a complementary sequence in a target mRNA, usually resulting in gene silencing, by triggering degradation of mRNA or by blocking translation by the ribosome.
lncRNA
gene expression
tetrahymena RNA
using the r looping technique, cech found that an intron was spliced out, in vitro, need gtp and mg
RNase p
true ribozyme
large ribozyme characteristics
self splicing, generate 3’ oh termini
small ribozyme features
sub-viral RNA replication, 5’ OH termini, cyclic phoshate
U-turn.
In the anticodon loop of tRNA, hydrogen bonding of uridine with the phosphate group causes an abrupt reversal or “U-turn”
piwirna
resent in germline cells, 24-31 nucleotides in length, associate with PIWI proteins to
form piRNA-induced silencing complexes which repress transposable elements
