Chapter 11 Bio190

what can ncRNA’s perform?

diverse cellular roles

• chromatin modification

• genome defense

ncRNAs dominate transcription (80% in human cells)

what molecules ncRNAs bind to?

DNA

RNA

Small molecules

Proteins

This allows ncRNA to affect processes such as DNA replication, transcription and translation (DNA and RNA)

What is the role of tRNA ?

tRNA: can form stem loop structure, act as versatile bidning site

Allos ncRNA to attach to proteins, DNA, mRNA, or small moelcules

Role/function of Scaffold

Some ncRNA’s contain binding sites for multiple components (groups different proteins)

• providing structural support for assembling molecular complexes

Role/function of Guide

Some ncRNAs guide molecule to specific location in a cell

• this function relies on ncRNA having multiple binding site (one for protein and for target site in DNA)

Role/function of Alteration of Protein Function or Stability

When binded to protein, ncRNA can alter proteins structure, which can have many effects

• ability of protein to act as a catalyst

• ability of protein to bind to another molecules (proteins, DNA, RNA)

• stability of protein

Role/function of Ribozyme

function as ribozymes (RNA moelcules with catalytic function)

• Peptidyltransferase, (component of large ribosomal subunit) catalyzed peptide bond formation during translation, in order to grow the polypeptide chain in protein synthesis

Role/function of Blocker

An ncRNA may physically prevent or block cellular process from happening

• IN bacteria, an antisense RNA binds to mRNA and blocks ability of ribosome to binds to mRNA, resulting to inhibiting translation

Role/function of Decoy

Some ncRNA recognize other ncRNAs and isolate themselves, preventing from working

• A decoy can bind to miRNA (different ncRNA), so its unable to carry out its function

What does miRNA role/function?

Critical prost-transcription regulatory serving as a stop sign for protein production.

• miRNA binds to mRNA to block it from reading or destroy it completely

X inactive specific transcript (Xist RNA) - Type of ncRNA

Xist RNA coats one of the X chromosomes in female mammals and plays a role in compaction and resulting inactivation

HOTAIR - Type of ncRNA

HOTAIR alters chromatin structure and represses transcription by guiding histone modifying complexes to target genes

The functions of HOTAIR is to form scaffold and guide

• its role as scaffold is to bind of two proteins complexes that covalently modify histone proteins

• its role as guide to guide these complexes to target gene by bidning to regions near gene that contains many purine (GA)

How can histone modification affect gene transcription?

It inhibits (happens in two ways):

1. Histone modification may directly inhibit ability of RNA polymerase to transcribe target gene (prevent RNA polymerase from forming a preinitiation complex)

Where is HOTAIR found?

Found in humans and other mammals that alter chromatin structure in a way that represses gene transcription

• HOTAIR is located with a cluster of genes called HOXC genes (play a role in animal developement)

tRNA - Type of ncRNA

tRNA molecules recognize mRNA codons during translation and carry the appropriate amino acidr

rRNA - Type of ncRNA

rRNA are components of ribosomes, which are site of polypeptide synthesis

SRP - Type of ncRNA

In bacteria, SRP directs synthesis of some polypeptides to plasma membranes.

In eukaryotes, it directs polypeptide synthesis to the endoplasmic reticulum

crRNA - Type of ncRNA

crRNA, found in bacteria and archarea, guides an endonuclease to foreign DNA (DNA of bacteriophage)

What is the role/function of Telomeres?

Telomeres: short nucleotide sequence that is repeated multiple time

• Specialized form of DNA replication that requires function of ncRNA happen at END OF EUKARYOTIC chromosome

What is function/role of Telomerase?

Telomerase: an enzyme that prevents chromosomes from shortening by attaching many copies of DNA repeat sequence to the 3’ end of chromosomes

• Telomerase contain both protein and ncRNA (TERC)

What does the TERC do for Telomerase?

Acts as a guide and templete

What are the occurring 3 steps of lengthening of telomeres?

1. Binding of Telomerase

2. Polymerization

3. Translocation

How can histone modification affect gene transcription

1. histone modification may directly inhibit the ability of RNA poplymerase to transcribe the target gene

2. rather than direct, histone modification may attract other chromatin modifying enzyme to target gene, leading to further changes in chromatin structure that inhibit transcription