Chapter 11: The Expression of Genetic Information via Genes II: Non-coding RNAs

The experimental tools to study RNA structure and function are more recently developed than the tools to study ?

Proteins and protein-encoding genes.

In contrast, other genes are transcribed into ?? RNAs (?), RNA molecules do not ??

Transcribed into non-coding RNAs (ncRNAs),

RNA molecules do not encode polypeptides

In typical human cell, only ?% of transcription involves the production of mRNAs.

20% of transcription

Some ncRNAs bind to ? or another ? through ? base pairing.

ncRNAs bind to DNA or another RNA through complementary base pairing.

ncRNAs can also bind ? or ? molecules.

bind proteins, or small molecules

Stem-loop structures may ? or ? proteins or may form a ? site for a small molecule

May bind or scaffold proteins or may form a binding site for a small molecule.

Common functions of ncRNAs include:

(SGARBD)

Scaffold

Guide

Alteration of protein function/stability

Ribozyme

Blocker

Decoy

Scaffold bind to

Multiple components such as proteins, act as scaffold for formation of a complex

Guide: guide one molecule to a

Specific location in the cell, for example guiding a protein to a particular site on DNA

Alteration of protein function or stability: binding of…

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

Ribozyme

RNA molecules with catalytic function, for example peptidyltransferase activity of ribosome

Blocker

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

Decoy

Recognize other ncRNAs and sequester them, preventing them from working

The key difference between a blocker and decoy is what they bind to:

Blocker binds a molecule that is not an ncRNA and a Decoy binds to an ncRNA.

The ends of linear eukaryotic chromosomes have ? composed of repeat sequences.

telomeres composed of repeat sequences.

What protects the ends of the chromosomes from becoming tangled or broken?

Telomeres

Some cells that divide rapidly express an enzyme called ? which adds the repeating sequence and extends the telomeres.

Telomerase.

The ends of the chromosomes cannot be fully replicated by ? polymerase due to its ??

Cannot be fully replicated by DNA polymerase due to its functional constraints: synthesis in a 5’ to 3’ direction and extension of a pre-existing strand

DNA polymerase cant copy the 3’ ends of the DNA and a 3’ overhang is left behind.

The enzyme ? prevent chromosome shortening by attaching many copies of a ? repeat sequence.

Telomerase, DNA repeat sequence.

Telomerase contains both ? and an ? called TERC (???)

Contain both proteins and an ncRNA called TERC (telomerase RNA component)

Telomerase lengthening occurs in 3 steps:

Binding of telomerase

Polymerization

Translocation

Binding of telomerase

Step 1.) TERC acts as a guide that allows telomerase to bind to the complimentary DNA repeat

Polymerization

Step 2.) TERC has a sequence that functions as a template for the synthesis of a 6-nucleotide sequence.

Telomere lengthening is catalyzed by a protein within telomerase that has reverse transcriptase (RNA → DNA) activity

In step 2, telomeres lengthening is catalyzed by a protein with ? that has reverse transcriptase (?→?) activity.

Protein with telomerase, RNA → DNA

Translocation -

Step 3.) Following the polymerization, telomerase moves to the new end of the DNA strand and attaches another 6 nucleotides.

HOTAIR (?????) is an

HOX transcript antisense intergenic RNA, is an ncRNA in humans and other mammals that regulates transcription by forming a scaffold that binds 2 proteins complexes and guides them to particular genes.

The protein complexes ? modify ?, and these modifications ? the target genes.

The protein complexes covalently modify histones, and these modifications silence the target genes.

ncRNAs can affect the ability of ?

mRNAs to be translated or degraded.

In the embryos that received single-stranded RNA, the mex-3 mRNA levels were decreased; in the embryos that received the double-stranded RNA, no mex-3 mRNA was detected → ?? RNA caused the mex-3 to be degraded.

double-stranded RNA

RNA interference is found in

Most eukaryotic species, including animals and plants; 2 source of ncRNA can promote RNA interference

MicroRNAs (miRNAs) are?

ncRNAs that are transcribed from endogenous eukaryotic genes that play key roles in regulating gene expression.

Partially complementary to their mRNA targets, estimated that 60% of human protein-coding genes are regulated by miRNAs.

Small-Interfering RNAs (siRNAs) come from

Exogenous sources - viruses that infect a cell or from researchers.

Usually perfectly complimentary to their target mRNA; they play a role in preventing viral infections and are a research tool.

In the nucleus, ? is the first synthesized as a primary-?

miRNA

The primary-miRNA folds into a ? (stem-?) structure

The primary-miRNA is ? to form a precursor-mRNA, which is ? from the nucleus.

The primary-miRNA folds into a hairpin (stem-loop) structure

The primary-miRNA is cleaved to form a precursor-mRNA, which is exported from the nucleus.

Both precursor-miRNA and precursor-siRNAs are recognized by the ? enzymes in the cytosol.

dicer enzymes

The double-stranded miRNA/siRNA associated with proteins to form a complex called the ?

RNA-induced silencing complex (RISC)

The single-stranded miRNA/siRNA is ? to the specific mnRNAs that will be silenced.

Complementary

The miRNA/siRNA acts as a ? for target mRNAs

guide

Proteins need to be directed to a particular location to carry out their functions; this targeting process is facilitated by an RNA-protein complex called the ?

Signal recognition particle (SRP)

In bacteria, SRP is composed of ? ncRNA and ? protein

In eukaryotes, SRP is composed of ? ncRNA and ? different proteins

In bacteria, SRP is composed of 1 ncRNA and 1 protein

In eukaryotes, SRP is composed of 1 ncRNA and 6 different proteins

The SRP RNA has 2 key roles:

The RNA provides a scaffold for the bind of proteins.

After SRP binds to the SRP receptor in the ER membrane, the SRP RNA stimulates proteins within the SRP and SRP receptor to the hydrolyze GTP; in other words the RNA alters the structure of the proteins to enhance their GTPase activity.

Some species of bacteria and Archaea have a system called the ?-? system that provides defense against ? and ?

Some species of bacteria and Archaea have a system called the CRISPR-Cas system that provides defense against bacteriophages and transpoons

The CRISPR-Cas type II system contains:

Crispr gene with repeats interspersed with short, unique sequences called spacers.

A gene that encodes an ncRNA called tracrRNA (pronounced “tracer RNA”)

Several protein-encoding CRISPR-associated genes (Cas genes)

Cirspr gene with repeats interspersed with short, unique sequenced called

Spacers

A gene that encodes an ncRNA called

tracrRNA

The defense occurs in 3 phases:

Adaptation

Expression

Interference

Adaptation occurs

after the bacterial cell has been exposed to bacteriophage

A piece of bacteriophage DNA is inserted into the ? gene

Crispr gene

If a bacterial cell has already been adapted to a bacteriophage, a ?

Subsequent infection will result in the expression phase.

The ? is an ncRNA with a region that is complimentary to the repeat sequencees of the pre-crRNA.

tracrRNA

The tracrRNA acts as a guide that causes the tracrRNA-crRNA complex to bind to a

Cas9 protein

After the tracrRNA-crRNA-Cas9 complex has formed, the bacterial cell is ready to destroy the bacteriophage DNA, this phase is called ?

Interference, because it resembles the process of RNA interference.

After binding, the ? protein cleves the bacteriophage DNA.

Cas9 protein

Abnormal expression levels of certain miRNAs are found in nearly all forms of human ?

Human cancer

Various ncRNAs are associated with ? disorders (? disease) and ? diseases (?)

Associated with Neurological disorders (Alzheimer disease) and cardiovascular diseases (Arrhythmias)

In parallel to the study of human disease, plant biologists are discovering that

Abnormalities in ncRNAs play essential roles in plant health (seed development, growth, stress responses)