Lec 8. Protein synthesis 1. Transcription

Question 1

What are the three steps to transcription?

Answer 1

Initiation, elongation, termination

Question 2

What are the 4 characteristics of a genetic material?

Answer 2

Replication of self, storage of info, expression of info, and variation through mutation

Question 3

What is the central dogma?

Answer 3

DNA to RNA via transcription. RNA to Protein via translation.

Question 4

What enzyme helps DNA go to RNA?

Answer 4

RNA polymerase

Question 5

What enzyme helps RNA translate to Protein?

Answer 5

Ribosome

Question 6

What enzyme helps DNA replicate?

Answer 6

DNA pol

Question 7

What are three exceptions to the Central Dogma?

Answer 7

Reverse transcription (RNA to DNA). RNA virus replication (RNA to RNA) and RNA directed DNA repair (RNA to DNA)

Question 8

Rad52-dependent HR pertains to what exception of the central dogma?

Answer 8

RNA directed DNA repair (RNA to DNA)

Question 9

What are the 5 features of the genetic code?

Answer 9

Continuous, Unambiguous, Degenerate, nonoverlaping, and universal

Question 10

What does it mean that the genetic code is continuous?

Answer 10

Triplet codons are uninterrupted, no breaks between codons, order is colinear (not scrambled)

Question 11

What does it mean that the genetic code is unambiguous?

Answer 11

Each codon specifies a single amino acid

Question 12

What does it mean that the genetic code is degenerate?

Answer 12

Amino acids can be associated with multiple codons

Question 13

What does it mean that the genetic code is nonoverlapping?

Answer 13

in mRNA, each nucleotide is only part of one codon

Question 14

What does it mean that the genetic code is Universal?

Answer 14

Almost all life on earth uses the same code

Question 15

Pertaining to the genetic code being continuous what are two colinear exceptions?

Answer 15

RNA editiing can change the nature of a codon, some ciliates scramble their germline genomes (the chromosomes used to transcribe mRNAs are not scrambled though). Ex Micronucleus gene is scrambled compared to the MACronucleus gene.

Question 16

True or False? Overlapping genes share DNA space and RNA space

Answer 16

False, Overlapping genes share DNA space and not RNA space

Question 17

Transcription and Translation pertaining to Prokaryotes are

Answer 17

Simultaneous and in a single location

Question 18

Transcription and Translation pertaining to Eukaryotes are

Answer 18

sequential and in separate locations

Question 19

What are the 5 steps to transcription?

Answer 19

1. Promoter binding:RNA pol, TF. 2. Transcirption bubble opens. 3. Elongation of RNA strand. 4. Release of RNA strand. 5. Eukaryote complications

Question 20

What are the two sub categories to Eukaryote complications?

Answer 20

1) Post-transcriptional processing: 3’ polyadenylation, 5’ cap, splicing. 2) Compartmentalization: remain in nucleus vs. exit to cytoplasm.

Question 21

What are the three steps to Transcription initiation?

Answer 21

Specific sequences in the DNA are recognized by Transcription Factors (TF). RNA pol II is recruited to the promoter. Phosphorylation of the C-terminal tail of RNA pol II results in transcription factor release.

Question 22

What is the role of the promoter?

Answer 22

Where we start transcription. Start making RNA

Question 23

What are the steps to promoter recognition?

Answer 23

TFIID is recruited first. TBP (TATA Binding Protein) recognized the TATA Box, distorting the DNA helix. TFIID also simultaneously binds the INR (initiator element) and the DPE (Downstream Promoter Element). TFIIB is recruited second. Binds to the BRE (B recognition Element)

Question 24

What is TFIID role in transition initiation?

Answer 24

Predominately binds to DNA. Recognizes promoter.

Question 25

What is TFIIB role in transition initiation?

Answer 25

Binds to BRE element

Question 26

What is TFIIF role in transition initiation?

Answer 26

Stabalizes RNA pol interaction with TBP and TFIIB, helps attract TFIIE and TFIIH

Question 27

What is TFIIE role in transition initiation?

Answer 27

Attracts and regulates TFIIH

Question 28

What is TFIIH role in transition initiation?

Answer 28

Unwinds DNA at the transcription start point. HELICASE.

Question 29

Is TFIID necessary or sufficient to transcription?

Answer 29

Sufficient

Question 30

Is TATA and initiator element necessary or sufficient?

Answer 30

Necessary

Question 31

What 6 things do we need to recruit the pol?

Answer 31

TF, RNA pol, mediator, chromatin remodeling complexes, histone modifing enzymes, and activator protein.

Question 32

What does the mediator do?

Answer 32

hold things together

Question 33

What does the chromatin remodeling complexes do?

Answer 33

Remove add histones

Question 34

What do histone modifying enzymes do?

Answer 34

writers and erasers of histone codes.

Question 35

What does the activator protein do?

Answer 35

Gives specificity and to go on or off.

Question 36

What is fidelity?

Answer 36

How well it does it correctly.

Question 37

Pertaining to elongation fidelity, RNA poymerases dont have what?

Answer 37

Exonuclease domains

Question 38

Does elongation fidelity of transcription have higher or lower fidelity than DNA repair and RT?

Answer 38

Higher

Question 39

Does elongation fidelity of transcription have higher or lower fidelity than DNA replication?

Answer 39

Lower

Question 40

Pertaining to elongation, prokaryotes vs eukaryotes, what is used for helical stress resolution?

Answer 40

Pro: Gyrase. Euk: Topisomerases

Question 41

Pertaining to elongation, prokaryotes vs eukaryotes, what is the gene content?

Answer 41

Pro: Operons: 1 transcript=many genes. Euk: 1 transcript = 1 gene

Question 42

Pertaining to elongation, prokaryotes vs eukaryotes, what is the RNA processing?

Answer 42

Prok: N/A. Euk: Concurrent with transcription

Question 43

What are the three events for termination in transcription?

Answer 43

RNA pol II falls off, RNA trimmed, RNA polyadenylation

Question 44

What are the two models for termination?

Answer 44

Torpedo Model and allosteric model

Question 45

What is the Torpedo model?

Answer 45

Exonuclease XRN2 chews back RNA and kicks off RNA poll II when the 2 proteins collide

Question 46

What is the allosteric model?

Answer 46

PolyA tail on mRNA signals RNA pol II to change shape and fall off

Question 47

What are the two prokaryotic options for termination of transcription?

Answer 47

Dependent on either Rho protein or secondary structure (hairpin).