Lecture 2: Central Dogma

Question 1

What is the sequence for the flow of information?

Answer 1

DNA -> RNA -> Protein

Question 2

DNA replication is semidiscontinuous. What does this mean?

Answer 2

•The leading strand copies continuously
•The lagging strand copies in segments (Okazaki fragments) which must be joined

Question 3

DNA Polymerase I

Answer 3

•abundant but not ideal for replication
•Rate (600 nucleotides/min) is slower than observed for replication fork movement
•Has low processivity
•Its primary function is in clean-up

Question 4

DNA Polymerase III

Answer 4

The principal replication polymerase

Question 5

DNA Polymerase II, IV, V

Answer 5

Are involved in DNA repair

Question 6

DNA Pol a

Answer 6

•Used to make primers for Okazaki fragments
•Has primase but no 3’ -> 5’ proofreading

Question 7

DNA Pol e

Answer 7

•Used in leading strand synthesis

Question 8

DNA pol g

Answer 8

•Used in lagging strand synthesis
•Comparable to bacterial DNA Pol III
•Has 3’ -> 5’ proofreading

Question 9

What are the final steps in the Synthesis of the Lagging Strand?

Answer 9

•DNA ligands makes a bond between a 3’-OH and a 5’-PO4
•5’-PO4 must be activated by attachment of AMP
•3’-OH nucleophile attacks this phosphate, displacing AMP

Question 10

Uracil
Basic site
8-Oxoguanine
Single-Strand break

Answer 10

•Base-Excision repair (BER)

Question 11

(6-4)
Bulky adduct
CPD

Answer 11

•Nucleotide-excision repair (NER)

Question 12

Interstate cross-link
Double-strand break

Answer 12

•Recombinational repair (HR, EJ)

Question 13

A-G Mismatch
T-C Mismatch
Insertion
Deletion

Answer 13

Mismatch repair

Question 14

A-G Mismatch
T-C Mismatch
Insertion
Deletion

Answer 14

Mismatch repair

Question 15

What is the end replication problem?

Answer 15

•Leading strand is synthesized to the end of the chromosome
•Lagging strand utilizes RNA primers which are removed
•The lagging strand is shortened at each cell division

Question 16

What is the solution to the End Replication problem?

Answer 16

•Telomeres

Question 17

Messenger RNAs

Answer 17

•Encode the amino acid sequences of all the polypeptides found in the cell

Question 18

Transfer RNAs

Answer 18

•Match specific amino acids to triplet codons in mRNA during protein synthesis

Question 19

Ribosomal RNAs

Answer 19

•Are the constituents and catalytic appropriate amino acids

Question 20

MicroRNA

Answer 20

•appears to regulate the expression of genes, possibly via binding to specific nucleotide sequences

Question 21

What are the E. coli Promoters?

Answer 21

•Consensus sequence
•rrn B P1
•trp
•lac
•recA
•araBAD

Question 22

RNA Polymerase I

Answer 22

•synthesizes pre-ribosomal RNA (precursor for 28S, 18S, and 5.8 rRNAs)

Question 23

RNA Polymerase II

Answer 23

•is responsible for synthesis of mRNA
•very fast (500-1000 nucleotides/sec)
•Specifically inhibited by mushroom toxin a-amanitin
•Can recognize thousands of promoters

Question 24

RNA Polymerase III

Answer 24

•Makes tRNAs and some small RNA products

Question 25

What RNA Polymerase does Plants have?

Answer 25

•Plants appear to have RNA polymerase IV that is responsible for the synthesis of small interfering RNAs

Question 26

What has their own RNA polymerase?

Answer 26

Mitochondria

Question 27

Promoters recognized by Eukaryotic RNA Polymerase II

Answer 27

•Various regulatory sequences •TATA box •lnr

Question 28

Transcription at RNA II Promoters

Answer 28

1. Pol II is recruited to the DNA by transcription factors 2. The transcription bubble forms 3. The CTF is phosphorylation during initiation. The polymerase escapes the promoter 4. Transcription elongation is aided by elongation factors after TFIIE and TFIIH dissociate 5. Elongation factors dissociate. The CTD is dephosphorylated as transcription terminates, a process facilitated by termination factors

Question 29

Maturation of mRNA in Eukaryotes

Answer 29

1. Transcription and 5’ capping 2. Completion of Primary transcript 3. Cleavage, Polyadenylation, and splicing

Question 30

What is the function of tRNA in translation?

Answer 30

•Deliver the amino acids corresponding to each codon within the mRNA sequence.

Question 31

How many genetically encoded amino acids are there?

Answer 31

•20

Question 32

Four letter code in groups of two

Answer 32

•insufficient (16)

Question 33

Four-letter code in groups of three

Answer 33

•Sufficient (64)

Question 34

What direction is the genetic code written?

Answer 34

5’->3’ direction

Question 35

First Codon establishes

Answer 35

The reading frame

Question 36

If reading frame is thrown off by a base or two, what happens?

Answer 36

All subsequent codons are out of order

Question 37

Initiation codon

Answer 37

AUG

Question 38

Termination Codon

Answer 38

•UAA •UGA •UAG

Question 39

Stages of Protein synthesis

Answer 39

1. Activation of amino acids 2. initiation of translation 3. Elongation 4. Termination and Ribosome recycling 5. Folding and Post-translational processing

Question 40

Activation of amino acids

Answer 40

•tRNA is aminoacylated

Question 41

Initiation of translation

Answer 41

•mRNA and aminoacylated tRNA bind to ribosome

Question 42

Elongation

Answer 42

•Cycles of aminoacyl-tRNA binding and peptide bond formation….until a STOP codon is reached

Question 43

Termination and ribosome recycling

Answer 43

•mRNA and protein dissociate, ribosome recycled

Question 44

Folding and post-translational processing

Answer 44

•Catalyzed by a variety of enzymes

Question 45

Termination initiation and Elongation in E. Coli

Answer 45

1. RNA polymerase core bonds to the DNA promoter 2. Transcription bubble forms 3. Transcription is initiated 4. Promoter clearance is followed by elongation 5. Elongation continues. S70 dissociates, and is replaced by NusA 6. Transcription is terminated. NusA dissociates, and the RNA polymerase is recycled

Question 46

Three rules of DNA Replication

Answer 46

1. DNA replication is semiconservative 2. DNA replication is bidirectional 3. DNA replication is semicontinuous

Question 47

Semiconservative

Answer 47

Each strand serves as a template for replication. The 2 new strands are composed of one new strand and its template (old strand)

Question 48

Bidirectional

Answer 48

Replication occurs in both directions from a starting point, sometimes called the origin

Question 49

Three stages of DNA Replication

Answer 49

1. Initiation 2. Elongation 3. Termination