Ch. 13 - non-coding RNAs

Question 1

history of non-coding RNAs

Answer 1

• ncRNAs were first linked to disease in 2001
• compared to coding RNAs linked to disease in 1909

Question 2

6 main functions of ncRNAs

Answer 2

1. scaffold
2. guide
3. alteration of protein function or stability
4. ribozyme
5. blocker
6. decoy

Question 2

scaffold ncRNA

Answer 2

• bind to multiple components such as proteins, act as scaffold for formation of a complex

Question 3

guide ncRNA

Answer 3

• guide a molecule to a specific location in a cell
• ex: make bind a protein and take it to a specific site in DNA
• must have binding site for both the protein and the DNA

Question 4

ncrNA alteration of protein function or stability

Answer 4

• when the ncRNA binds to protein and can alter the structure
  3 things it may affect:
  1. the ability of the protein to act as a catalyst
  2. the ability of the protein to bind other molecules
  3. stability of the protein

Question 5

ribozymes

Answer 5

ncRNA with catalytic function

Question 6

blocker ncRNA

Answer 6

• physically prevents or blocks a cellular process from happening

Question 7

decoy ncRNA

Answer 7

• recognize other ncRNAs and bind to them, preventing them from working

Question 8

Xist

Answer 8

type of ncRNA
- coats one of the X chromosomes in female mammals and plays a role in its compaction and resulting inactivation

Question 9

HOTAIR

Answer 9

Hox transcript antisense intergenic RNA
- gene located within the HoxC cluster
- contains the antisense from the HoxC genes
- actas as a scaffold for protein complexes that covalently modify histone proteins
- modifications from HOTAIR inhibit transcription, directly or indirectly

Question 10

two ways HOTAIR can inhibit transcription

Answer 10

1. directly inhibiting the ability of RNA polymerase to transcribe the gene
   - can prevent RNA polymerase from forming a pre initiation complex
2. can attract other chromatin-modifying enzymes to the target gene
   - would lead to further changes in chromatin structure that inhibit transcription

Question 11

miRNA

Answer 11

microRNAs
- ncRNAs transcribed from endogenous eukaryotic genes
- play key roles in regulating gene expression, particularly during embryonic development
- partially complementary to mRNAs
- inhibits mRNA in RNA interference (RNAi)

Question 12

siRNAs

Answer 12

small-interfering RNAs
- come from exogenous sources (viruses that infect a cell or from researchers)
- usually a perfect match for mRNA
- degrades mRNA
- plays key role in preventing certain types of viral infections
- also important tool for study molecular biology

Question 13

RNA interference

Answer 13

• found in most eukaryotic species
• can be promoted by miRNAs or siRNAs
• miRNA and siRNA is cut by dicer to a sequence 20-25bp long
• sequence binds with RISC, which inhibits translation or degrades the mRNA

Question 14

RISC

Answer 14

RNA-induced silencing complex
- inhibits translation or degrades the mRNA

Question 15

signal recognition particle (SRP)

Answer 15

• protein-RNA complex that recognized the ER signal sequence of a polypeptide, pauses translation, and directs the ribosome to the ER to complete translation
• type of ncRNA involved in protein targeting

Question 16

two roles of SRP RNA

Answer 16

1. provide scaffold for the binding of SRP protein(s)
2. after SRP binds to the SRP receptor in the ER membrane, it stimulates proteins in the SRP and SRP receptor to hydrolyze GTP
   - allows SRP to release

Question 17

CRISPR-Cas system

Answer 17

• in bacteria and archea
• defends against foreign invaders
• effective against bacteriophages and transposons
• type II is for defense against bacteriophages

Question 18

three phases of CRISPR-Cas

Answer 18

1. adaptation
2. expression
3. interference

Question 19

adaptation in crispr

Answer 19

• occurs after bacterial cell has been exposed to bacteriophage
• Cas1/2 complex cleaves bacteriophage DNA and inserts it into the Crispr gene

Question 20

expression in crispr

Answer 20

• subsequent bacteriophage infection results in the expression phase
• genes encoding pre-crRNA and tracrRNA are transcribed
• complementary base pairing between crRNA and tracrRNA repeats allows formation of the tracrRNA-crRNA complex
• complex binds to Cas9 protein

Question 21

interference in crispr

Answer 21

• ## bacteriophage DNA is destroyed