Chapter 11 - Non-coding RNA

Question 1

What is so special about ncRNAs and what does it stand for?

Answer 1

Non-coding RNAs and they do not include polypeptides

Question 2

In typical human cells, only ____% of transcription involves the production of mRNAs

Answer 2

20

Question 3

What kinds of molecules can ncRNA bind to?

Answer 3

• DNA or RNA through complimentary base pairing
• Proteins or small molecules with stem-loop structures

Question 4

What does the function of scaffold do for ncRNAs?

Answer 4

Bind to multiple components like proteins (formation of a complex)

Question 5

What does the function of guide do for ncRNAs?

Answer 5

Guides one molecule to a specific location in the cell (guiding a protein to a site on DNA)

Question 6

What does the function of alteration of protein function or stability do for ncRNAs?

Answer 6

ncRNA affects the ability of the protein to be a catalyst, bind to other molecules, or it’s stability

Question 7

What does the function of ribozyme do for ncRNAs?

Answer 7

An RNA molecule that acts like an enzyme (Peptidyl transferase activity of ribosome)

Question 8

What does the function of blocker do for ncRNAs?

Answer 8

ncRNA prevents/blocks a cellular process (blocks the binding of a ribosome, inhibiting translation)

Question 9

What does the function of decoy do for ncRNAs?

Answer 9

Recognize other ncRNAs and isolate them

Question 10

The key difference between a blocker and decoy is…?

Answer 10

What they bind to
- Blocker binds to a non ncRNA molecule
- Decoy binds to an ncRNA molecule

Question 11

What is Telomerase RNA component TERC and what role does it play?

Answer 11

• DNA replication
• Facilitates binding of telomerase to the telomere + acts as a template for DNA replication

Question 12

What is Hox transcript antisense intergenic HOTAIR and what role does it play?

Answer 12

• Chromatin structure + Transcription
• Alters chromatin structure and represses transcription

Question 13

What is microRNA miRNA + small-interfering RNA siRNA and what role does it play?

Answer 13

• Translation and RNA degradation
• Regulate the expression and degradation of mRNA

Question 14

What is RNA component of signal recognition particle SRP-RNA and what role does it play?

Answer 14

• Protein sorting + secretion
• In bacteria, directs the synthesis of some polypeptides to the plasma membrane
• In eukaryotes, directs polypeptide synthesis to the ER

Question 15

What is CRISPR RNA crRNA and what role does it play?

Answer 15

• Genome defense
• Found in bacteria and archaea, guides an endonuclease to foreign DNA

Question 16

What are telomeres?

Answer 16

The ends of linear eukaryotic chromosomes, composed of repeat sequences

Question 17

What is the function of telomeres?

Answer 17

Protect the ends of chromosomes from becoming tangled or broken

Question 18

Some cells that divide rapidly express an enzyme called ________, which adds what to telomeres?

Answer 18

Telomerase, a repeating sequence + extends the telomeres

Question 19

What is the function of telomerase?

Answer 19

Prevents chromosome shortening (attaches many copies of a DNA repeat sequence)

Question 20

Ends of chromosomes cannot be fully replicated by DNA due to two functional constraints, what are they?

Answer 20

• Synthesis in a 5’ to 3’ direction
• Extension of a pre-existing strand

Question 21

What does Telomerase contain?

Answer 21

Proteins and TERC

Question 22

What are the 3 steps of Telomere lengthening?

Answer 22

1) Building of telomerase - TERC acts as a guide
2) Polymerization - TERC has a sequence that functions as a template
3) Translocation - After polymerization, telomerase moves to the new end of DNA

Question 23

How is telomere lengthening catalyzed?

Answer 23

A protein within telomerase that has reverse transcription (RNA – DNA) activity

Question 24

How does HOTAIR regulate transcription?

Answer 24

Forming a scaffold that binds 2 protein complexes and guides them to particular genes

Question 25

Protein complexes _______ modify ________, and these modifications silence target genes

Answer 25

*Covalently* modify **histones**

Question 26

ncRNAs can affect the ability of mRNAs to be _______ or ________

Answer 26

*Translated* or *degraded*

Question 27

What was the goal of the **Fire and Mello** experiment?

Answer 27

Understand how the *experimental injection of RNA* was responsible for the **silencing of mRNA particles**

Question 28

What was the conclusion of the **Fire and Mello** experiment?

Answer 28

*Double-stranded RNA* caused the **mex-3 mRNA to be degraded**, which was then termed **RNA interference (RNAi)**

Question 29

**RNA interference** is found in *most eukaryotic species*, what are the **2 sources** of ncRNA that can promote RNA interference?

Answer 29

1) **MicroRNA/miRNAs**: ncRNAs that are transcribed from **endogenous** eukaryotic genes *(key role in regulating gene expression)* 2) **Small-interfering RNA/siRNA**: come from **exogenous** sources *(viruses that infect a cell or from researchers)*

Question 30

What are the main steps of RNA interference **(hint: there are 6 steps)**?

Answer 30

1) **miRNA is synthesized** 2) primary-miRNA fold into a **hairpin** which then forms a **pre-miRNA** 3) **pre-miRNA or pre-siRNA** are recognized by the **dicer enzyme in the cytosol** and turns them into **double-stranded miRNA or siRNA** 4) miRNA/siRNA associate with proteins to form the **RNA-included silencing complex (RISC)** 5) single-stranded miRNA/siRNA **target** a specific mRNA that **will be silenced** 6) miRNA/siRNA acts as a **guide** for target mRNA, which once bound, mRNA is **inhibited** or **degraded**

Question 31

What is the function of **signal recognition particles**?

Answer 31

An **RNA protein complex** that helps with *directing proteins to a particular location* (**aka a guide**) to carry out their functions

Question 32

What are the **2 key roles** of SRP-RNA?

Answer 32

1) RNA provides a **scaffold** for the *binding proteins* 2) Alters the **structure of the proteins** to enhance their **GTPase activity**

Question 33

Some species of *bacteria and archaea* have a system called the ________ system that provides defense against ______ and transposons.

Answer 33

**CRISPR-Cas** and **bacteriophages**

Question 34

What does the **CRISPR-Cas type II** system contain?

Answer 34

1) Crispr gene with **repeats** distributed with short, unique sequences called **spacers** 2) A gene that encodes an ncRNA called **tracrRNA** 3) Several **protein-encoding CRISPR-associated genes**

Question 35

What are the **3 phases** of defense that occurs in the CRISPR-Cas type II?

Answer 35

**Adaption, Expression,** and **Interference**

Question 36

What happens in the **adaption** phase of CRISPR-Cas?

Answer 36

- Occurs **after** bacterial cell has been **exposed** to a bacteriophage - A **piece of bacteriophage DNA** is **inserted** into the Crispr gene

Question 37

What happens in the **expression** phase of CRISPR-Cas?

Answer 37

- This happens when a bacterial cell has **already been adapted to a bacteriophage** - A **subsequent infection** will occur - tracrRNA acts as a *guide* that causes tracrRNA-crRNA complex to bind to a **Cas9 protein**

Question 38

What happens in the **interference** phase of CRISPR-Cas?

Answer 38

- Bacterial cell is *ready to destroy* bacteriophage DNA - **Called interference because it resembles the process of RNA interference** - After binding, the *Cas9 protein* **splits the bacteriophage DNA**

Question 39

________ ________ levels of certain miRNAs are found in nearly all forms of human _______

Answer 39

*Abnormal expression* and **cancer**

Question 40

HOTAIR is highly expressed in several ______

Answer 40

*Cancers*; like breast cancer, lung cancer, and colorectal cancer

Question 41

Various ncRNAs are associated with _________ disorders and ________ diseases

Answer 41

*Neurological* and *Cardiovascular*

Question 42

What have plant biologists suggested about abnormalities in ncRNAs in plants?

Answer 42

They play essential roles in plant health: - *Seed development* - *Growth* - *Stress responses*