Applied Biochemistry - RNA Structure, Synthesis, and Processing

What are the three major types of RNA in the process protein synthesis?

rRNA, tRNA, and mRNA

What is ncRNA?

Non-coding RNA

What is the size of prokaryotic rRNA?

5S, 16S, 23S

What is the size of eukaryotic rRNA?

5S, 5.8S, 18S, 28S

What is rRNA?

Ribosomal RNA

How much of the total cell RNA is rRNA?

80%

What is a ribozyme?

RNA with catalytic activity

What is the smallest type of RNA?

tRNA

What percentage of total cell RNA is made up of tRNA?

15%

Which type of RNA contain a high percentage of unusual/modified bases?

tRNA

What is this part of tRNA?

3’-End CCA

What is this part of tRNA?

Site of amino acid attachment

What is this part of tRNA?

TΨC loop

What is this part of tRNA?

Variable loop

What is this part of tRNA?

Anticodon

What is this part of tRNA?

Anticodon loop

What is this part of tRNA?

D loop

What is this part of tRNA?

Complementary base pairs

What is this part of tRNA?

5’ end

What diseases are associated with a mutation in lysine tRNA?

Myoclonic epilepsy with ragged red fibers (MERRF) and mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS)

What disease is associated with mutations in leucine tRNA?

Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS)

What is MERRF?

A disorder that affects skeletal muscle structure and function (myopathy)

What is MELAS?

A disorder that affects the brain, nervous system, and muscles

What percentage of total cell RNA is made up of mRNA?

5%

What is mRNA?

Messenger RNA

What is the function of mRNA?

Coding RNA that carries genetic information from DNA for use in protein synthesis

What is the name of an mRNA that carries information from more than one gene?

Polycistronic

Where is polycistronic mRNA found?

Prokaryotes, mitochondria, some viruses, and chloroplasts

What is the name of mRNA that carries information from only one gene?

Monocistronic

Where is monocistronic mRNA found?

Eukaryotes

What is the S in the measurement of rRNA?

the Svedberg unit for sedimentation rate

What are the sizes of rRNA species encoded by miochondrial DNA?

12S and 16S

How many types of tRNA molecules are there?

At least one type for each of the 20 amino acids

What is the structure of tRNA?

Cloverleaf

Label this part of mRNA.

5’ end

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5’ end

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Poly-A tail

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3’-Untranslated region

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Coding region

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5’-Untranslated region

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Cap

What is RNA polymerase?

A multisubunit enzyme that recognizes the promoter region at the beginning of DNA to be transcribed and makes an RNA copy

In what direction is RNA synthesized?

5’→ 3’

Label this section of prokaryotic RNA polymerase.

Holoenzyme

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Core enzyme

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Omega

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Beta and beta prime

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Alpha

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Sigma

What components make up the core enzyme of RNA pol?

Alpha, beta, and omega

What component makes up the RNA pol holoenzyme?

Sigma

Which part of the core enzyme is required for enzyme assembly?

Alpha and omega

Which part of the core enzyme is required for template binding?

Beta prime

Which part of the core enzyme is required for 5’→ 3’ polymerase activity?

Beta

What part of the core enzyme of RNA pol lacks specificity?

The core enzyme

What is the function of the holoenzyme of RNA pol?

Recognizing promoter regions on DNA

What are the three phases of transcription?

Initiation, elongation, and termination

What happens in the initiation of transcription?

The RNA pol holoenzyme binds to the promoter region of DNA.

What are consensus sequences?

Calculated sequences of the most frequent residues at certain positions

What is the -35 sequence?

The initial point of contact for the holoenzyme, about 35 bases to the left of the start of transcription

What is the pribnow box?

A consensus sequence at -10 which is the site of melting/unwinding of a short stretch of DNA to make a transcription bubble

Label this section of the prokaryotic promoter region.

-35 sequence

Label this section of the prokaryotic promoter region.

TTGACA

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~19 base pairs

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TATAAT

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Pribnow box

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~7 base pairs

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Start of transcription

Label this section of the transcription bubble.

Negative supercoils

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Template strand

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Nontemplate strand

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RNA polymerase

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3’ end of RNA being elongated

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Positive supercoils

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RNA-DNA hybrid helix

Label this section of the transcription bubble.

RNA

What happens in the elongation phase of protein synthesis?

RNA polymerase synthesizes RNA sequences longer than 10 nucleotides in length.  The core enzyme moves along the template strand acting as its own sliding clamp. 5’ → 3’ direction

What makes RNA pol different from DNA pol?

RNA pol does not require a primer and does not have 3’→ 5’ exonuclease domain, therefore more errors