Chapter 11: Gene Expression - Non-coding RNAs

Question 1

What are non-coding RNAs?

Answer 1

RNA molecules that do not encode polypeptides; only 20% of transcription involves the production of mRNAs; 80% of transcription involves non-coding RNAs; can affected the ability of mRNA to be translated or degraded

Question 2

Why were ncRNAs discovered more recently than other macromolecules?

Answer 2

The experimental tools used to study RNA structure and function are more recently developed than the tools to study proteins and protein-encoding genes

Question 3

How do ncRNAs interact with other molecules?

Answer 3

1. Can bind to DNA or other RNA through complimentary base pairing
2. Can bind to proteins or small molecules

Question 4

What are the common functions of ncRNAs?

Answer 4

1. Scaffold
2. Guide
3. Alteration of protein function or stability
4. Blocker
5. Decoy
6. Ribozyme

Question 5

What occurs during ncRNA scaffolding?

Answer 5

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

Question 6

What occurs during ncRNA ribozyme activity?

Answer 6

RNA molecule with catalytic function, like the peptidyltransferase activity of ribosome

Question 7

What occurs during ncRNA blocking?

Answer 7

The ncRNA physically prevents or blocks a cellular process from happening, for example, blocks the binding of a ribosome, thereby inhibiting translation.

Question 8

What occurs during ncRNA decoying?

Answer 8

ncRNAs that recognize other ncRNAs and sequester them, preventing them from working

Question 9

What occurs during ncRNA guiding?

Answer 9

ncRNAs guide one molecule to a specific location in the cell, for example, guiding a protein to a particular site on DNA

Question 10

What occurs during ncRNA protein alteration?

Answer 10

binding of ncRNA can affect the ability of the protein to be a catalyst, the ability of the protein to bind to other molecules, or the protein’s stability

Question 11

What is the difference between blockers and decoys?

Answer 11

Blockers bind to non-ncRNA molecules; decoys bind to other ncRNA molecules

Question 12

What are telomeres?

Answer 12

The ends of linear eukaryotic chromosomes that have repeating sequences

Question 13

What is the function of telomeres?

Answer 13

Telomeres protect the ends of the chromosomes from becoming tangled or broken

Question 14

What is telomerase?

Answer 14

Enzyme that adds the repeating sequences and extends telomeres

Question 15

Why is telomerase important?

Answer 15

The ends of chromosomes cannot be fully replicated by DNA polymerase due to functional constraints

Question 16

What is the structure of telomerase?

Answer 16

Proteins and an ncRNA called telomerase RNA component (TERC)

Question 17

What are the steps to telomere lengthening?

Answer 17

1. Binding of telomerase
2. Polymerization
3. Translocation

Question 18

What occurs during the binding of telomerase?

Answer 18

TERC acts as a guide that allows telomerase to bind to the complimentary DNA repeat

Question 19

What is polymerization?

Answer 19

Telomeres are lengthened using TERC as a template; polymerization is catalyzed by a protein in telomerase that is capable of reverse transcriptase

Question 20

What is translocation?

Answer 20

Telomerase moves to new end of DNA and adds six new nucleotides

Question 21

What is HOTAIR (Hox transcript antisense intergenic RNA)?

Answer 21

An ncRNA that plays a role in regulating transcription by forming a scaffold that binds 2 protein complexes and guides them to particular genes; modify histones which can silence target genes

Question 22

What are miRNA (micro RNA)?

Answer 22

ncRNAs that are transcribed from endogenous eukaryotic genes; partly complementary to their mRNA targets; regulates 60% of human-protein coding genes

Question 23

What are siRNA (small-interfering RNA)?

Answer 23

ncRNAs that come from exogenous sources; come from researchers or viruses; perfectly complementary to mRNA targets

Question 24

What was discovered in the Fire and Mello experiment?

Answer 24

Double-stranded RNA caused the mex-3 mRNA to be degraded

Question 25

What is RNAi (RNA interference)?

Answer 25

A type of mRNA silencing that is done by miRNA or siRNA; process found in most eukaryotic species

Question 26

What were the attributes of the control group in the Fire and Mello experiment?

Answer 26

A lot of green

Question 27

What were the attributes of the experimental group with mex-3 antisense DNA?

Answer 27

A little green

Question 28

What were the attributes of the experimental group with double-stranded RNA (mex-3 sense and antisense RNA)?

Answer 28

No green

Question 29

How does miRNA/siRNA degrade or inhibit mRNA activity?

Answer 29

1. First synthesized as primary-miRNA in the nucleus 2. miRNA folds into a hairpin 3. miRNA is cleaved to form a precursor-miRNA and moved out of the nucleus 4. precursor-miRNA and precursor-siRNAs are recognized by dicer in cytosol 5. The dicer further cuts the precursor-miRNA/siRNA down and becomes double stranded 6. The double-stranded miRNA/siRNA associates with a protein to make a protein complex and become single-stranded 7. Then the single-stranded miRNA/siRNA binds to an mRNA and prevents translation

Question 30

What is RISC (RNA-induced silencing complex)?

Answer 30

A complex consisting of miRNA or siRNA and proteins; mediates RNA interference

Question 31

What is SRP (signal recognition particle)?

Answer 31

A complex of protein and ncRNA that directs proteins to a particular location to carry out their functions; particle usually means a complex between proteins and RNA

Question 32

What are the two key roles of SRP?

Answer 32

1. Provides a scaffold for the binding of proteins 2. Alters the structure of the proteins to enhance their GTPase activity

Question 33

What are the steps to protein targeting?

Answer 33

1. SRP binds to an ER signal sequence and causes translation to pause as a polypeptide is being synthesized by a ribosome 2. SRP binds to an SRP receptor in the ER membrane, which is located next to a channel; proteins within the SRP and SRP receptor have to bind to GTP 3. SRP and the SRP receptor hydrolyze their GTP, releasing SRP and allowing translation to resume, with the protein traveling into the ER through the channel

Question 34

What is the CRISPR-Cas system?

Answer 34

A system that provides defense against bacteriophages and transposons; three types: type I, type II, and type III

Question 35

What are bacteriophages?

Answer 35

Viruses that infect bacteria

Question 36

What does CRISPR-cas type 2 contain?

Answer 36

1. Crispr gene with repeats interspersed 2. Gene that encodes tracrRNA 3. Protein-encoding CRISPR associated genes (Cas genes)

Question 37

When is the adaptation phase?

Answer 37

A piece of bacteriophage DNA is inserted into the Crispr gene; occurs after the bacterial cell has been exposed to a bacteriophage

Question 38

What is tracrRNA?

Answer 38

An ncRNA with a region that is complimentary to the repeat sequences of pre-crRNA

Question 39

What is the expression phase?

Answer 39

A subsequent infection triggers the expression phase; Crispr, tracr, and cas9 genes are transcribed; the tracrRNA guides the tracrRNA-crRNA complex to bind to a cas9 proteins

Question 40

What are the three stages of gene defense?

Answer 40

1. Adaptation 2. Expression 3. Interference

Question 41

What are defective miRNAs associated with?

Answer 41

Nearly all forms of human cancer and bad plant health; various ncRNAs are associated with neurological disorders and cardiovascular diseases; seed development, growth, and stress response

Question 42

What is the interference stage?

Answer 42

Resembling the process of RNA interference, the tracrRNA-crRNA-Cas9 complex bind to the bacteriophage's DNA and the Cas9 protein cleaves it

Question 43

What are the roles of ncRNAs in human disease?

Answer 43

Abnormal expression levels of certain miRNAs are found in nearly all forms of human cancer; various ncRNAs are associated with neurological disorders and cardiovascular diseases

Question 44

What are the roles of ncRNAs in plant health?

Answer 44

Abnormalities in ncRNAs play essential roles in seed development, plant growth, and stress responses