Chapter 3 Flashcards
What is one major structural difference between RNA and DNA?
2’ hydroxyl on sugar
This refers to the presence of a hydroxyl group (-OH) on the 2’ carbon of the ribose sugar in RNA, which is absent in DNA.
Which base is found in RNA instead of Thymine?
Uracil
Uracil (U) replaces Thymine (T) in RNA.
What is the typical structural form of RNA?
Single stranded
RNA is generally single-stranded, whereas DNA is typically double-stranded.
What are the eight major types of RNA?
- Ribosomal RNA (rRNA)
- Messenger RNA (mRNA)
- Transfer RNA (tRNA)
- Small nuclear RNA (snRNA)
- Small nucleolar RNA (snoRNA)
- MicroRNA (miRNA)
- PIWI-interacting RNAs (piRNAs)
- Long noncoding RNA (lncRNA)
These different types of RNA play various roles within the cell.
What are two key points for understanding RNA function?
- RNA can form complementary base pairs with other nucleic acids.
- RNA can interact with proteins: Ribonucleoprotein (RNP) particles.
These interactions are crucial for many cellular processes.
How can RNA serve as a scaffold?
RNA can serve as a scaffold upon which proteins can be assembled.
An example includes the signal recognition particle.
Can RNA be catalytic?
Yes, RNA can be catalytic - ribozyme.
Ribozymes are RNA molecules that can catalyze chemical reactions.
What constitutes the primary structure of RNA?
A chain-like molecule composed of subunits called nucleotides joined by phosphodiester bonds.
Each nucleotide consists of a ribose sugar, a phosphate group, and a nitrogenous base.
What are the common bases found in RNA?
- Adenine (A)
- Guanine (G)
- Cytosine (C)
- Uracil (U)
These bases are fundamental to RNA structure and function.
What is the secondary structure of RNA characterized by?
The folding of an RNA chain into a variety of structural motifs.
This includes structures like bulges, base-paired helices, and hairpin loops.
What type of double helix does base-paired RNA adopt?
A-type double helix
The presence of the 2’-OH group in RNA hinders the formation of a B-type helix.
What are noncanonical base pairs?
Base pairs that differ from Watson-Crick pairing.
They can widen the major groove and enhance accessibility to ligands or proteins.
What role do noncanonical base pairs play in RNA?
- RNA self-assembly
- RNA-protein interactions
- RNA-ligand interactions
These interactions are essential for the proper functioning of RNA.
True or False: Chemical modification of RNA bases does not affect their hydrogen bonding characteristics.
False
Chemical modifications can change how RNA bases interact with each other.
Fill in the blank: ‘tRNA looks like Nature’s attempt to make RNA do the job of a ______.’
protein
This quote by Francis Crick highlights the functional similarities between tRNA and proteins.
What is the role of Transfer RNA (tRNA) during translation?
tRNA is a critical link between codons carried on mRNA and the amino acid carried by the tRNA.
What are the two main structural forms of tRNA?
Cloverleaf secondary structure and L-shaped tertiary structure.
What is the function of the anticodon loop in tRNA?
It directs binding of the tRNA to the codon through base pairing.
Name three general principles of tRNA structure.
- Modified bases
- tRNA loops each have a separate function
- Coaxial stacking of stems
What is the significance of modified bases in RNA?
More than 100 modified bases exist in RNA, affecting hydrogen bonding characteristics.
Which modified nucleoside was the first to be identified in tRNA?
Inosine (I).
What is the function of the T-loop in tRNA?
Recognition by the ribosome.
What is the function of the D loop in tRNA?
Recognition by the aminoacyl tRNA synthetases.
What role does the anticodon loop play in tRNA function?
It base pairs with the mRNA codon.
How do base-paired stems in tRNA contribute to its structure?
They are involved in long-range interactions with other stems.
What is the A-type helical arm formed by in tRNA?
The 7 bp acceptor stem stacks on the 5 bp T stem.
What are common tertiary structure motifs in RNA?
- Pseudoknots
- A-minor motifs
- Tetraloops
- Ribose zippers
- Kink-turns
What is the significance of RNA folding?
RNA folding is based on hydrogen bonding and base stacking.
True or False: RNA can develop several unique structures like DNA.
True.
What stabilizes the tetraloop motif?
Base-stacking interactions.
What is the ribose zipper motif’s function?
It stabilizes helix-helix interactions in minor grooves.
Describe the kink-turn motif in RNA.
Asymmetric internal loops embedded in an RNA double helix causing a sharp bend.
What are the three structural levels of RNA?
- Primary: Nucleotides
- Secondary: Stem, loop, bulge, and junction
- Tertiary: Coaxial stacking, pseudoknots, A-minor motifs, tetraloops, ribose zippers, kink-turns
What is the ‘RNA folding problem’?
Large RNAs can adopt many possible structures and may misfold into nonfunctional structures.
What controls the kinetics of RNA folding?
- Specific binding proteins
- Chaperones
What types of proteins assist RNA in achieving its final shape?
- Heterogeneous nuclear ribonucleoproteins for mRNA
- Ribosomal proteins for rRNA
What are RNA chaperones responsible for?
Preventing the formation of misfolded structures or unfolding misfolded RNA.
What is the role of specific RNA-binding proteins?
Stabilize the native structure of RNA.
What is the time frame for tRNA to achieve secondary structure?
Within 10^-4 to 10^-5 seconds.
What is the time frame for tRNA to achieve tertiary structure?
Within 10^-2 to 10^-1 seconds.
How can RNA folding be analyzed?
By hydroxyl radical footprinting assay.
What is the time required for the catalytic center of large catalytic RNA to complete folding?
Several minutes.
What are some uses for RNA in a cell?
- Some RNAs have catalytic activity.
- Some do not require proteins to be present.
- Some require proteins to create additional structures or contacts for binding a substrate.
What technique did Thomas Cech use to study intron splicing in Tetrahymena thermophila?
The ‘R looping’ technique.
What is an intervening sequence (IVS) or ‘intron’?
A sequence that is spliced out in the final 26S rRNA product.
What conclusion was drawn from the in vitro assay of Tetrahymena self-splicing RNA?
The RNA was splicing itself.
What is the classic definition of an enzyme?
A substance that increases the rate, or velocity, of a chemical reaction without itself being changed in the overall process.
What term was coined for naturally occurring RNA enzymes that are self-splicing?
Ribozyme.
What did Sidney Altman and coworkers show in 1983?
Bacterial RNase P is an RNA enzyme that cleaves 5’ leader sequences off of tRNA.
What is RNase P classified as?
A Ribozyme.
How many protein subunits does human H1 RNA associate with?
At least 10 protein subunits.
What does eukaryotic RNase P act as?
A catalytic ribonucleoprotein (RNP).
What do ribozymes catalyze?
A variety of chemical reactions.
What are the two different groups of ribozymes based on size and reaction mechanism?
- Large ribozymes
- Small ribozymes
Name two examples of large ribozymes.
- RNase P
- Group I Intron
What are some examples of small ribozymes?
- Hammerhead
- Hairpin
- Hepatitis delta virus RNA
- Riboswitch
What is the average size of RNA-based genomes?
Approximately 10,000 nucleotides.
How does the mutation rate of RNA-based genomes compare to DNA-based genomes?
1000-fold higher.
What is the fitness trade-off in RNA viruses?
Between replication rate and replication fidelity.
What are the three main categories of eukaryotic RNA viruses?
- Plus-strand viruses
- Minus-strand viruses
- Double-stranded RNA viruses
What is a prominent human pathogen among retroviruses?
Human immunodeficiency virus 1 (HIV-1).
What are viroids?
Plant pathogens whose RNA is the infectious agent and do not encode any protein.
What is the size of a viroid genome?
A single, very small (250 to 400 nt), circular molecule of RNA.
What do satellite RNAs require for replication?
A helper virus to provide RNA-dependent RNA polymerase.
What is the definition of virusoids?
Circular, single-stranded RNA genomes that do not encode any protein.
What is a hypothetical stage in the evolution of life involving RNA?
When RNA both carried the genetic information and catalyzed its own replication.
What processes do proteins and ribonucleoprotein (RNP) particles catalyze today?
- Replication of DNA
- Transcription of DNA into RNA
- Reverse transcription of RNA into DNA
- Translation of mRNA mediated by the ribosome
