Chapter 10- Dr. Kim

Ribose

deoxyribose

What are the two purine ribonucleotides?

Adenine and Guanine

What are the pyrimidine ribonucleotides?

cytosine and thymine

How many total ribonucleotides found in RNA?

four

U=A or U=G belongs to the ____ ribonucleotides.

purine

Is DNA and RNA composed of nucleotides?

yes

What type of sugar is found in DNA?

deoxyribose

What type of sugar is found in RNA?

ribose

Is there a 2' OH group on Deoxyribose sugar?

No

There is a 2' OH group on ribose sugar.

true

What are the bases associated with DNA?

A, G, C, T

What are the bases associated with RNA?

A, G, C, U

Nucleotides are joined together by phosphodiester bonds in both RNA and DNA.

true

Is DNA double stranded or single stranded?

double stranded

Is RNA double or single stranded?

single stranded

There are many types of secondary structures for RNA.

true

What is the secondary structure of DNA?

double helix

Is DNA stable?

stable

Is RNA stable?

no, it is easily degraded

RNA has a primary and secondary structure.

true

RNA contains ____ in place of thymine.

uracil

How does an RNA molecule form a secondary structure?

RNA molecule folds, owing to hydrogen bonding between complementary bases on the same strand

What kind of base pairing does RNA have?

intramolecular base pairing

What are the components of the 3D rna nucleotide chain?

amino acyl acceptor arm

t-loop

d-loop

anticodon loop

Messenger RNA (mRNA)

intermediate necessary for synthesizing protein (functional product)

What kind of RNA is not easily translated into polypeptides?

Functional RNA

What are the types of functional RNA?

tRNA

rRNA

snRNAs

miRNAs

siRNAs

tRNA

bringing the correct amino acid to the mRNA

rRNA

major components of ribosomes

snRNAs

RNA processing components of spliceosome

miRNAs

regulating gene expression

siRNAs

genome defense

What is transcription the separation of?

DNA double strands

is a primer required for transcription?

No (replication only)

What are three components of transcription?

template DNA, NTP, transcription apparatus

information transfer

through complementary pairing of bases

What is the name of the template strand?

non-coding (non-sense) strand

non-template strand

mRNA sequence

mRNA sequence is the same as the ______ strand

coding/sense

What is RNA transcribed from?

one DNA strand

What end are nucleotides always added to of the RNA molecule?

3' end

Initiation of RNA synthesis does not require a primer.

true

Where does DNA unwind at in the RNA molecule?

at the front of the transcription bubble

What region is the promotor found in?

5' regulatory region

What is name of the site where the first base is transcribed?

initiation site (+1)

What are the core enzymes in the initiation step of prokaryotes?

alpha, beta, beta', theta

Which holo-enzyme is not a core enzyme?

sigma

alpha (core enzyme)

help assembly/ promote interactions with regulatory proteins

Beta (core enzyme)

active in catalysis

Beta prime (core enzyme)

binding to DNA

Theta (core enzyme)

enzyme assembly

What enzyme is known to correct positioning of the holoenzyme, binding to -35 and -10?

sigma

Around what region does the sigma enzyme separate the DNA strands?

-10 region

When does the sigma enzyme dissociate?

after transcription begins

Different sigma factors recognize different sets of _____.

promoters

When is RNA transcription initiated in bacteria?

when core RNA polymerase binds to the promoter with the help of sigma

Many RNAs can be simultaneously transcribed from a ____.

gene

When there is presence of a nucleus, such as eukaryotes, what is the consequence?

separated transcription and translation

What occurs in the nucleus of eukaryotes?

RNA processing

What is the primary transcript in eukaryotes?

pre-mRNA

What is the primary transcript in prokaryotes?

mRNA

Eukaryotic genome is the presence of a ____.

nucleus

RNA polymerase I

large rRNAs

RNA polymerase II

pre-mRNA, some snRNAs, snoRNAs, some miRNAs

RNA polymerase III

tRNAs, small rRNAs, some snRNAs, some miRNAs

RNA polymerase IV

some siRNAs in plants

What are the promoters of genes transcribed by?

RNA polymerase II

Where is the TATA box region?

-30 bp region

TFII

transcription factor of RNA polyermase II

What is the TATA binding protein?

TBP

_____ is apart of the TFIID complex.

TBP

What protein attracts other GTFs and RNA polymerase II?

TBP

PIC

pre-initiation complex

______ + ______= Pre-initiation complex

RNA polymerase II + GTFs

CTD

C-terminal domain of RNA polymerase

What happens with to the interactions with GTFs when phosphorlyated?

the GTFs are weakened

Which of the following is true of RNA compared to DNA?

RNA has a hydroxyl group on 2'-carbon atom of its sugar component

When RNA is transcribed from a gene, which strand of DNA is used?

the template strand

The transcription unit includes three essential regions. What is the proper order of these regions?

promotor, RNA coding sequence, terminator

What would the result be if a specific sigma subunit were mutated?

RNA polymerase would fail to initiate transcription at the promoter specific to the sigma subunit

The bacterial holoenzyme binds to which part of the promoter?

-10 and -35 consensus sequence

In rho-dependent transcription termination, the rho factor binds to _____.

mRNA

In eukaryotes, what initially binds to the TATA box on the DNA template?

TFIID

What is the ribsome binding site on prokaryotic mRNA?

shine-dalgarno sequence

Where is the start codon in prokaryotic transcription?

5' end

Where is the stop codon located during prokaryotic transcript?

3' end

In Eukaryotic transcription, what end does the cap add to?

5' end

Eukaryotic RNA processing is _______.

cotranscriptional

What are the three characteristics of RNA processing in eukaryotes?

capping

splicing

polyadenylation

splicing

removal of introns and joining of exons

polyadenylation

addition of 100s of adenine nucleotides

What does not require a coding sequence and is removed from mature RNA in eukaryotic transcription?

intron

During capping, what is the 7-methyl guanine added to?

5'-5' phosphate

Where is the polyA tail added?

3' end

What are the two functions of CAP?

protects RNA from degradation (increased stability)

required for ribosome binding (translation)

How many total places are there for methylation?

3 places

What are conserved regions related to?

intron splicing

What is the splicing machinery called?

spliceosome (molecular complexes)

What type of RNA is apart of the spliceosome?

small nuclear RNA (snRNA)