Lecture 2: RNA structure and function

Question 1

T/F: RNA opportunistically hybridizes with itself

Answer 1

yes!! loves to form loops, base-pair whenever possible

Question 2

what are the three main differences between RNA and DNA?

Answer 2

1. RNA has a hydroxyl group on the
   2’ carbon of the sugar (ribose)
2. Uracil instead of thymine
3. RNA usually single-stranded

Question 3

T/F: RNA can form short helical regions (hairpin loops)
and some RNAs can fold into complex tertiary structures

Answer 3

true!!

(G = U base pairing plus other interaction form structures)
found in tRNAs, rRNA, ribozymes

Question 4

T/F: tRNA structure is planar

Answer 4

false!! displayed as planar to show structure better but actually super bunched up and twisted irl

Question 5

what are the secindary structures of RNA?

Answer 5

duplexes, hairpins, bulges, internal loops

Question 6

secondary structure of _____ is dominated by the formation of
double helices stabilized by Watson-
Crick base pairs between
complementary stretches

Answer 6

RNA

Question 7

______ in secondary structure of RNA is two sepeereate pieces of RNA base-pairing together

Answer 7

duplexes

Question 8

______ in secondary structure of RNA are small loops, ____ are big loops

Answer 8

hairpins
loops

Question 9

______ in secondary structure of RNA are mismatches of sequence in a larger duplex

Answer 9

gaps (mismatches)

Question 10

the helices of RNA are…. and ____ in length

Answer 10

relatively short and 8-10 bp in length

Question 11

_______ predicts RNA secondary structure

Answer 11

thermodynamics

Computational programs exist to predict lowest free energy structures and base pair probabilities for RNA… this prediction is very difficult though!!

Question 12

it’s energetically _______ as RNA folds into secondary structures

Answer 12

favourable

Question 13

why is it super difficult to predict RNA secondary structure?

Answer 13

we need to surmount activation energies to perform the folding itself… if it’s too hard it won’t do it!!

also hard because there’s many, many different possible conformations oftentimes… even if it’s physically possible to fold we can’t really know if the RNA actually will

Question 14

T/F: RNA folding is the most essential process underlying RNA function

Answer 14

true!!!

Question 15

T/F: While significant progress has been made in understanding the
forces driving RNA folding in vitro, the rules governing
intracellular RNA structure formation remain challenging to
explore

Answer 15

true

Question 16

do RNA adopt complex tertiary structures?

Answer 16

yes!! and act as biological catalysts

some RNA enzymes are ribozymes and have an active site, binding sites for substrates and cofactors

Question 17

ribosomes are….

Answer 17

ribozymes!! RNA world hypothesis… proteins probs developed later but ribozymes survived evolution!

Question 18

T/F: ribozyme function is highly dependent on structure

Answer 18

true!! can do many things but their secondary/tertiary structure is super integral!!

Question 19

________: catalyzes reversible cleavage
and ligation reactions at a specific site within
an RNA molecule. It is one of several
catalytic RNAs (ribozymes) known to occur in
nature (ex., in RNA viruses) It serves as a
model system for research on the structure
and properties of RNA, and is used for
targeted RNA cleavage experiments

Answer 19

hammerhead ribozyme

Question 20

T/F: RNA motif have been used to help with
ensuring the release of the guide RNA
required for CRISPR technology

Answer 20

true

Question 21

_______: a recurrent, conserved structural or sequence pattern in RNA that plays a specific functional or structural role. These motifs are like “building blocks” in RNA molecules that help them fold properly and interact with other molecules (like proteins, DNA, or other RNAs)

Answer 21

RNA motif

ex: enable ribozyme to act as an enzyme

Question 22

what are the three most well-known forms of RNA?

Answer 22

mRNA, tRNA, rRNA
- present in all organisms!

Question 23

________:
accounts for just 5% of the total RNA in the cell.
* most heterogeneous of the 3 types of RNA in sequence and size.
* Carries complimentary genetic code copied, from DNA during
transcription
* Unstable and degraded by RNAses readily.
* May be further processed

Answer 23

mRNA

Question 24

how are eukaryotic mRNA further processed?

Answer 24

guanosine cap and poly-A tail, both impart stability to the mRNA

Question 25

______: ' the smallest of the 3 types of RNA, possessing around 75-95 nucleotides. * main function is the transfer of amino acids during protein synthesis. * _____- also act as adapters in the translation of the genetic sequence of mRNA into proteins. Thus, they are also called adapter molecules.

Answer 25

tRNA

Question 26

T/F: Each amino acid has at least one corresponding tRNA

Answer 26

true!! some of them are shared, because of the third-base wobble and multiple codons (61) for only 20 essential aa!

Question 27

______: RNA component of the ribosome, which is essential for protein synthesis in all living organisms. * is the predominant RNA in most cells, composing around 80% of cellular RNA. * Ribosomes are approximately 60% rRNA and 40% protein by weight.. Two subunits, the large ribosomal subunit (LSU) and small ribosomal subunit (SSU).

Answer 27

rRNA

Question 28

what are the three rRNAs of prokaryotes?

Answer 28

23S and 5S in large subunit 16S in small subunit

Question 29

T/F: The prokaryotic ribosome contains around 50 ribosomal proteins

Answer 29

true!!

Question 30

T/F: Eukaryotic ribosomes and rRNAs are larger and more polymorphic than those of prokaryotes

Answer 30

true! In yeast, the LSU contains the 5S (different from prokaryote 5S), 5.8S and 28S rRNAs

Question 31

Ribosomal RNA genes (rDNA) genes are important to a cell and while always present, mutate slowly over time... why do we use them for phylogeny?

Answer 31

because they are pretty highly conserved so we can trace back lineage... and they're in everything!!

Question 32

_____ are Useful as “molecular clocks” – how much they differ between organisms is related to how long ago two organisms

Answer 32

rRNA 16S subunit

Question 33

________ is starting to replace traditional rRNA gene sequencing (like 16S rRNA in bacteria) for phylogenetic and taxonomic analysis because it provides much more comprehensive, accurate, and high-resolution data

Answer 33

Whole genome sequencing (WGS) looks at millions of genes, rather than just one functional AND evolutionary analysis less prone to error cheaper

Question 34

what is the ITS region?

Answer 34

the two internally transcribed spacers including the 5.8S gene

Question 35

T/F: in the ITS region, the 18S, 5.8S, and 28S rRNA genes transcribed as a unit by RNA polymerase I

Answer 35

true

Question 36

Sequence comparison of the ITS region is widely used in taxonomy and molecular phylogeny because of several favorable properties... what are they?

Answer 36

1. It is routinely amplified →small size associated 2. It is easy to detect even from small quantities of DNA due to the high copy number of the rRNA clusters. 3. It has a high degree of variation even between closely related species. This can be explained by the relatively low evolutionary pressure acting on such non-coding spacer sequences

Question 37

T/F: ITS sequences evolve more rapidly than the highly conserved rRNA genes. This makes them useful for distinguishing: Closely related species Fungal and plant species Even strains within species

Answer 37

true!!

Question 38

what are the other types of RNA specific to eukaryotes?

Answer 38

snRNA (SNurps) regulatory: miRNA and siRNA lncRNAs

Question 39

_____ is involved in the processing of pre-messenger RNA (pre-mRNA) into mature mRNA. They are very short, with an average length of only 150 nucleotides

Answer 39

snRNA

Question 40

where is snRNA found?

Answer 40

in the nucleus- forms the spliceosome that splices RNA (binds to introns and splices them out)

Question 41

miRNA and siRNA both...

Answer 41

regulate gene expression

Question 42

________ (21-22 nt) is found in eukaryotes: * function via base-pairing with complementary sequences within mRNA molecules. * Thus, mRNA molecules are silenced, by one or more of the following processes: (1) Cleavage of the mRNA strand into two pieces (2) Destabilization of the mRNA through shortening of its poly(A) tail (3) Less efficient translation of the mRNA into proteins by ribosomes

Answer 42

miRNA

Question 43

what is the main difference found between miRNA and siRNA

Answer 43

where they come from! miRNA encoded in the genome siRNA come from outside the cell (viruses, synthetic, etc.)

Question 44

explain how miRNA is transcribed and cleaves mRNA

Answer 44

encoded in the genome and transcribed by RNA poly I to pri-miRNA (primary RNA), turned to pre-mRNA then processed by Dicer enzyme grabbed by Risc protein and loaded into the complex The RISC uses the miRNA as a template to recognize complementary sequences in target mRNAs... if it matches a target sequence PERFECTLY the slicer component of RISC will cut the mRNA

Question 45

______: class of double-stranded RNA molecules, 20-25 base pairs in length * It interferes with the expression of specific genes with complementary nucleotide sequences by degrading mRNA after transcription, preventing translation

Answer 45

siRNA

Question 46

_____ is known as short interfering RNA or silencing RNA

Answer 46

siRNA

Question 47

Since in principle any gene can be _______ by a synthetic siRNA with a complementary sequence, siRNAs are an important tool for validating gene function and drug targeting in the post-genomic era

Answer 47

knocked down

Question 48

what are siRNAs currently being used as?

Answer 48

an agricultural tool to silence pathogenic genes in plant pathogens

Question 49

T/F: siRNA is also fed into DICER

Answer 49

true!! and since there's generally always a perfect match it almost always results in knockdown using DICER and RISC

Question 50

_______ is transcribed by cells and usually involves a single strand of RNA that often imperfectly matches targets

Answer 50

miRNA (micro-RNA)

Question 51

_________ is usually synthetic and transfected from outside as intermediates thatmatch targets exactly

Answer 51

siRNA (short/small interfering RNA)

Question 52

T/F: Can be internal: some organisms possess RNA dependent RNA Pol that can create complementary strand, or from repetitive transposable elements (i.e. siRNA... that can then be fed into dicer and risc)

Answer 52

true!! These endogenous siRNAs are often involved in silencing transposable elements, viral defense, or heterochromatin formation

Question 53

there's a group that developed species-specific RNA interference- based control treatments capable of reducing fungal infection... how is this effective in crops and agriculture?

Answer 53

spray siRNA on plants, genes knocked down from virulent fungus which then becomes non-pathogenic!! foliar applications of dsRNAs to the leaf surface that significantly decreased fungal infection and S. sclerotiorum disease symptoms (still hypothetical now but being researched!)

Question 54

_____: 200 nt to ~100 kilobases * function not understood BUT suspected to be regulatory eg.: -molecular sponge to sequester and inactivate repressive RNAs (such as certain siRNAs) ? eg.: - can interact with transcription factors and activate or maybe inactivate DNA regulatory proteins. i.e. cytoplasmic and nuclear effects

Answer 54

lncRNA (long non-coding)

Question 55

_____ can do a bunch of different things simply because they're very large

Answer 55

lncRNA

Question 56

what are the six lncRNA functions?

Answer 56

transcriptional activation " repression enhancer RNA scaffolding protein for chromatin remodeling complexes regulation of RNA splicing sequestration of miRNA

Question 57

what are the forms of RNA specific to prokaryotes?

Answer 57

RsmZ (or A or Y) sRNAs tmRNA

Question 58

_______ is a small regulatory RNA in prokaryotes that helps control gene expression by soaking up (sponging) proteins (CsrA) that would otherwise block translation

Answer 58

RsmZ

Question 59

Bacteria also have ______, which are a miRNA-like mechanism of encoded small ncRNAs that interfere with translation by binding to mRNAs

Answer 59

sRNAs

Question 60

T/F: sRNAs may be cis or trans-encoded

Answer 60

true!! cis are transcribed from the opposite strand of the ORF itself (perfect annealing) while trans-encoded ones are elsewhere on the genome with gene finding mechanisms we keep finding more and more sRNA

Question 61

______: rescue stalled ribosomes

Answer 61

transfer-mRNA (tmRNA)

Question 62

how does tmRNA work? what are the two main steps?

Answer 62

1. a non-encoded alanine is added; 2. the ribosome switches to the mRNA- like domain of tmRNA, thus resuming protein synthesis BUT added sequence is a proteolysis- inducing tag! (i.e. peptide will be degraded)