Ch. 8 Rna Transcription & Processing Pt. 1

Front 1

What are the 5 main ways RNA differs from DNA?

Back 1

1. Uses ribose & not deoxyribose

2. Uses Urasil instead of Thymine

3. Single stranded rather than double stranded

4. Some can function as enzymes (enzymatic). Ex: ribozymes in ribosomes

5. Use NTPs (nucleotide triphosphate) instead of dNTPs (deoxynucleotide triphosphate)

Front 2

What kind of RNA is the intermediate necessary for protein synthesis?

Back 2

Messenger RNA (mRNA).

Front 3

What are functional RNA? (Also known as non-coding RNA)

Back 3

RNA types that play a role without being translated into a protein. All RNA that isn't mRNA is functional RNA.

Front 4

What does Transfer (tRNA) do?

Back 4

It is responsible for bringing correct amino acids to mRNA during translation.

Front 5

Which type of RNA are major components of the ribosomes that guide assembly of amino acid chain?

Back 5

Ribosomal (rRNA)

Front 6

What is snRNA?

Back 6

Small nuclear RNA. Assist in RNA processing events such as the splicing reaction.

Front 7

What is miRNA?

Back 7

Micro RNA. They regulate the translation/amount of protein created by many eukaryotic genes.

Front 8

What is siRNA

Back 8

Small interfering RNA. They inhibit viral infection and spread of transposable elements.

Front 9

Which classes of functional RNA are constitutive? What does this mean?

Back 9

tRNA, rRNA, and snRNA. It means they are continuously synthesized throughout the cell's life because they are always needed.

Front 10

What is the central dogma (Francis Crick, 1978)

Back 10

DNA --> Transcription ---> mRNA ---> Translation ---> Protein

Front 11

What is a DNA sequence that codes for RNA?

Back 11

A gene

Front 12

What are structural genes?

Back 12

Genes that code for mRNA, the intermediate between DNA and proteins.

Front 13

What are non-structural genes?

Back 13

Genes that code for all classes of RNA that aren't mRNA. The RNA is the final product rather than a protein.

Front 14

What is lncRNA? (Also called ncRNA)

Back 14

Long non-coding RNA. Mostly unknown function. Don't code for protein, but may play a role in dosage compensation.

Front 15

What is on the 2' carbon of ribose as opposed to deoxyribose?

Back 15

A hydroxyl (OH) group. Deoxyribose only has a hydrogen on the 2' C.

Front 16

What are the components of a gene?

Back 16

Begins with a promoter followed by the transcription initiation site. Then comes the RNA coding sequence followed by the terminator and termination site.

Front 17

What are the components of mRNA?

Back 17

Untranslated region, translation start, protein-coding sequence, translation stop, next untranslated region.

Front 18

What is the coding strand?

Back 18

The nontemplate strand of DNA. Its sequence matches that of the RNA product molecule.

Front 19

What is the non-coding strand?

Back 19

The strand of DNA that is the template for the RNA transcript. Its code is complementary to the RNA product molecule.

Front 20

In what direction does RNA Polymerase read the template?

Back 20

As in DNA, it reads in. 3' to 5' direction.

Front 21

What are UTRs?

Back 21

Untranslated regions. These are found on either end of an mRNA molecule.

Front 22

What is a codon?

Back 22

A three-nucleotide sequence of RNA that can: 1) code for amino acids beginning with a start codon, or 2) tell translation to stop.

Front 23

Explain how the strands of DNA can be used as templates? For example, is only one strand used?

Back 23

Overall, both strands of a chromosome can be used as a template. Only one strand will be used for any one gene. For that gene, the same strand will always be used.

Front 24

True or false: Genes cannot be in opposite orientations. Explain.

Back 24

False. Because genes are read from 3' to 5', and because DNA strands are antiparallel, the orientation of the gene depends on the orientation of the template strand used.

Front 25

In what direction is RNA synthesized (not read)?

Back 25

Like in DNA, the RNA daughter molecule is synthesized in a 5' to 3' direction.

Front 26

What causes the "Christmas Tree" appearance?

Back 26

Many RNA are transcribed simultaneously from a gene, causing this appearance.

Front 27

What is a promoter?

Back 27

A recognition site located upstream of a gene (before the gene's 5' end on the non-template strand) that acts as the binding site for RNA Polymerase.

Front 28

What is a consensus sequence?

Back 28

The most commonly occurring nucleotides that reads the same in most individuals. Promoters are often consensus sequences.

Front 29

What is the initiation site? What is it followed by?

Back 29

Where the first transcribed base is located. Always labeled +1. Everything upstream is labeled negative. Everything downstream is labeled positive.

Followed by a the 5' untranslated region before the protein-coding site starts.

Front 30

What are two common promoter regions in prokaryotes?

Back 30

The -35 and -10 regions.

Front 31

What are the core components of RNA Polymerase?

Back 31

Two alpha subunits, a beta subunit, a beta prime subunit, and an omega subunit.

Front 32

What does the sigma factor do?

Back 32

It identifies the -10 and -35 promoter regions in bacteria, positioning RNA Polymerase at the correct transcription start site. Then it detaches. Also helps separate DNA strands so polymerase can bind more tightly.

Front 33

What is the difference between the RNA Polymerase Holoenzyme and RNA Polymerase?

Back 33

Holoenzyme is when the 5 core units are saturated with sigma factor. Once sigma factor detaches, it is just called RNA Polymerase.

Front 34

What are the specific names of the two alpha subunits?

Back 34

NTD (N-terminal domain) and CTD (C-terminal domain)

Front 35

What is the transcription bubble?

Back 35

The site at which the double helix is unwound so polymerase can transcribe one strand. Rewinds behind polymerase forming the bubble.

Front 36

What is Intrinsic termination in prokaryotes?

Back 36

It is non-rho dependent. A G-C rich hairpin loop forms followed by a string of ~8 U's. Hairpin causes polymerase to pause, allowing the newly created A-U bonds to break and release RNA. This happens because A-T creates a stronger bond than A-U, so the template DNA strand will re-bond with the non-template DNA strand.

Front 37

What is rho-dependent termination in prokaryotes?

Back 37

It requires the rho factor protein. This protein binds the the rho utilization site (rut) upstream of the terminator region and moves toward transcript's 3' end. Termination sequence codes for a hairpin structure, causing RNA Polymerase to pause. Rho then acts as a helicase to break the hydrogen bonds between DNA and RNA.

Front 38

Which of the three RNA polymerases is responsible for transcribing protein-encoding genes in eukaryotes? (mRNA, snRNA, miRNA)

Back 38

RNA Polymerase II

Front 39

What are GTFs?

Back 39

General transcription factors. Six-protein complex that binds to a eukaryotic promoter region to attract and correctly place RNA Polymerase II for transcription initiation.

Front 40

What is the PIC in eukaryotic transcription?

Back 40

Pre initiation Complex. Made up of the 6 GTFs and RNA Pol II.

Front 41

What is the TATA Box in eukaryotes?

Back 41

A DNA sequence common in many eukaryotes located -30 bp upstream of the transcription start site. The TATA binding protein (TBP) GTF binds to the TATA Box, helping PIC correctly find gene promoters.

Front 42

What are the two regulatory transcription factors (RTFs) in eukaryotes?

Back 42

Activators and repressors

Bind to RNA polymerase II when transcription begins.

Front 43

What are the two regulatory elements in eukaryotes? What do they do?

Back 43

Enhancers: DNA sequence that increases transcription if bound by activator proteins.

Silencers: DNA sequences that decrease transcription rate if bound by repressor proteins.

Upstream of TATA box.

Ers ending = DNA sequence

Ors ending = Protein

Front 44

What is pre-mRNA?

Back 44

The primary, unprocessed transcript produced by RNA Pol II. It is modified to make mRNA.

Front 45

What are major differences between prokaryotic and eukaryotic transcription?

Back 45

In eukaryotes, the process happens in the nucleus. Pre-mRNA is then processed before translation in the cytoplasm. Prokaryotic mRNA is not processed.

Front 46

What is the last step in eukaryotic initiation?

Back 46

Carboxy Terminal Domain (CTD) gets phosphorylated.

Front 47

What does endonuclease do during eukaryotic transcription?

Back 47

It cuts RNA transcript ~20 nucleotides downstream of the PolyA signal sequence (a stretch of RNA containing only Adenine bases).