1 DNA to Protein: Transcription to Translation

Question 1

What is the central dogma of molecular biology?

Answer 1

Question 2

How do the phosphodiester linkages in RNA and DNA compare?

Answer 2

• It’s the same!

Question 3

How does RNA compare to DNA?

Answer 3

*

Question 4

RNA 3D structure

How is it maintained?

What does it allow RNA to do?

Answer 4

• RNA can fold into specific 3D structures.
• 3D structures are maintained by conventional base pairing or modified by nonconventional base pairing.
• 3D structure allows RNA to catalyze its own splicing.
• RNA needs correct 3D structure to maintian enymatic function.

Question 5

During Transcription the RNA strand is complementary to the _____ strand but has U instead of T.

Answer 5

• During Transcription the RNA strand is complementary to the template strand but has U instead of T.

Question 6

How do RNA polyermases have the energy for Transcription?

Answer 6

• The incoming nucleosides (ATP, UTP, CTP, GTP) supply energy needed for catalysis from their triphosphate bonds.

Question 7

What is the function of mRNAs?

Answer 7

• Messenger RNAs, code for proteins

Question 8

What is the function of rRNAs?

Answer 8

• Ribosomal RNAs, form the basic structure of the ribosome and catalyze protein synthesis

Question 9

What is the function of tRNAs?

Answer 9

• Transfer RNAs, central to protein synthesis as adaptors between mRNA and amino acids

Question 10

What is the function of snRNAs?

Answer 10

• Small nuclear RNAs, function ina variety of nuclear processes, including the splicing of pre-RNA.

Question 11

What is the function of snoRNAs?

Answer 11

• Small nucleolar RNAs, help to process and chemically modify rRNAs & Spliceosomal RNAs / mRNAs

Question 12

How does RNA Polymerase know where to start/stop?

Answer 12

• Signals encoded in DNA tell RNA polymerase where to start/stop.

Question 13

How is direction of transcription determined?

Answer 13

• The promoter can be on either strand but always goes 3’ → 5’

Question 14

What is the TATA box and what is it’s function?

Answer 14

• 25 nucleotides upstream from the initiation site
• Most important DNA sequence that signals the start of Transcription.

Question 15

What does RNA polymerase I transcribe?

Answer 15

• rRNA genes

Question 16

What does RNA polymerase III transcribe?

Answer 16

• tRNA genes
• rRNA genes
• some snRNA genes

Question 17

What does RNA polymerase II transcribe?

Answer 17

• All protein-coding genes (mRNA)
• snoRNA
• miRNA
• siRNA
• most snRNA
• lncRNA

Question 18

What does the initation of transcription require?

Answer 18

• The initation of transcription requires multiple activator proteins along with proteins that unwind the chromatin.

Question 19

What role do activator proteins play in transcription?

Answer 19

• activator proteins help coordinate the acquisition of the different proteins needed for transcription initialization.
• They also play a role in modifying DNA shape → affects rate of transcription
• *activator proteins can be located 1000s of nucleotides upstream.

Question 20

Supercoiling negative/positive & Topoisomerase

Answer 20

• Negative supercoiling (behind RNA polymerase)
  
  • helix opening facilitated
• Postivite supercoiling (in front of RNA polymerase)
  
  • helix opening hindered
• Specialized proteins (topoisomerase) remove superhelical tension.

Question 21

What is the first modification of Eukaryotic Pre-mRNAs?

Answer 21

• As soon as the mRNA is ~25 nucleotides long it is capped
• RNA Capping

Question 22

How does RNA Capping work?

Answer 22

• 3 enzymes work together
  
  1. Dephosphorylate the 1^st nucleotide
  2. Adda GMP in reverse linkage (5’ to 5’ instead of 5’ to 3’), and
  3. Add a methyl group to the guanosine
  • Sometimes another methyl group is added to the ribose of the 1^st nucleotide
• The cap allows mRNA to be distinguished from noncoding RNAs and is also important for establishing translation.

Question 23

What is Factor VIII and how does RNA Splicing affect it?

Answer 23

• Factor VIII catalyzes one of the steps in the clotting cascade
• When it is mutated or deleted (incorrect splicing), the result is hemophilia.

Question 24

Whats the idea of alternative splicing?

Answer 24

• Primary transcript can be spliced in different ways to produce distinct mRNAs which then give rise to variant proteins.
• Most alternatively spliced proteins (most protein coding genes) contain constituitive elements that are there almost all the time.

Question 25

How do nucleotide sequences signal where splicing occurs?

Answer 25

Question 26

How does the spliceosome produce RNA-RNA rearrangements?

Answer 26

* ATP hydrolysis * exchange of U1 for U6 * exhance allows for the 5' splice site to be read by two different snRNPs, thereby increasing the accuracy of 5' splice-site selection by the spliceosome.

Question 27

What are the two types of splicing errors?

Answer 27

* (A) exon skipping * (B) Cryptic splicing signals are nuelcotide sequences of RNA that closely resembles true splicing signals and are sometimes mistakenly used by the spliceosome.

Question 29

Within the spliceosome. . . What are U1/U2 What is the role of RNA? What is the role of Proteins?

Answer 29

* U1/U2 are ribonucleo complexes * RNA identifies key regions, No catalysis or enzymtic function * Proteins arrange for catalytic activity to splice things out

Question 30

How do Exons and Introns compare in size amoung Eukaryotes?

Answer 30

* Exons are much more similiar in size among eukaryotes than are introns.

Question 31

What proteins identify splice sites? (introns/exons)

Answer 31

* SR proteins identify the exons * hnRNP identify the introns

Question 32

What percentage of mutations cause changes in splice site sequences?

Answer 32

* ~10%

Question 33

How do RNA-processing enzymes generate the 3' end of Eukaryotic mRNAs?

Answer 33

* Consensus sequences (always CA) at the end of the mRNA signal that the mRNA needs to be **clipped**. * The mRNA is further processed and additional proteins add a **Poly A Tail**

Question 34

What is the imporatance of the Poly A tail?

Answer 34

* Protects message * Involved in translation

Question 35

What is the role of the exosome?

Answer 35

1. The exosome is a protein complex that cleans up damaged RNAs before they leave the nucleus * it is rich in RNAses and chops up RNAs for recycling. 2. Extra cellular communication vesical * infuse exosomes with cancer drugs

Question 36

How are Mature Eukaryotic mRNAs selectively exported from the nucleus?

Answer 36

* The mRNA is packaged for transport ot the cytoplasm * Transport of mature mRNA out of the nucleus is carefully managed. * Requires 5' cap to be intact and appropriately attatched.

Question 37

Steps of Transcription

Answer 37

1. **RNA polymerase**, together with one or more transcription factors, **binds to promoter DNA** 2. RNA polyerase creates a **transcription bubble**, which separates the two strands of the DNA helix. * done by breaking H bonds between complementary DNA nucleotides 3. RNA polymerase **adds RNA nucleotides** (which are complementary to the nucleotides of one DNA strand) 4. RNA sugar-phosphate **backbone forms** with assistance from RNA polymerase to form an RNA strand 5. H bonds of the **RNA-DNA helix break**, freeing the newly synthesized RNA strand 6. In eukaryotes **post transcriptional processing** includes polyadenylation, 5' capping and splicing 7. The **RNA** may **remain in the nucleus** or **exit to the cytoplasm** through the nuclear pore complex.