L11: Genome Replication and Expression

Question 1

Overview of DNA replication

Answer 1

bidirectional
semi-conservative
strands separate
each strand is a template for the synthesis of a new strand

Question 2

What’s different about DNA replication in eukaryotes and prokaryotes?

Answer 2

Eukaryote- multiple oris

Prokaryote- single ori

Question 3

How is the origin of replication selected in prokaryotes?

Answer 3

Protein DnaA binds and “opens” ori

Question 4

What enzyme catalyzes DNA synthesis in 5’ to 3’ direction?

Answer 4

DNA polymerase

Question 5

What does DNA polymerase need for DNA synthesis?

Answer 5

template
deoxynucleotide triphosphates
primer (usually RNA with 3’ OH group)

Question 6

What enzyme breaks H bonds between DNA strands?

Answer 6

helicase

Question 7

What enzyme underwinds DNA and relieves supercoiling?

Answer 7

Gyrase (topoisomerase)

Question 8

What enzyme lays down RNA primers?

Answer 8

DNA primase

Question 9

What enzyme removes RNA primers and fills in the gaps?

Answer 9

DNA pol I

Question 10

What enzyme is a target for ciprofloxacin antibiotic?

Answer 10

Gyrase

Question 11

How are genetic instructions stored and organized in DNA?

Answer 11

DNA sequence of a gene corresponds to amino acid sequence of protein encoded

Question 12

What enzyme is used for transcription in bacteria?

Answer 12

RNA polymerase

Question 13

What is the target of rifampin (antibiotic)

Answer 13

RNA polymerase

Question 14

What are sigma factors?

Answer 14

proteins that direct core of RNA polymerase to promoters

Question 15

What is sigma^s important for?

Answer 15

stationary phase

Question 16

What are the 3 types of RNA generated by transcription in bacteria?

Answer 16

tRNA
rRNA
mRNA

Question 17

What is tRNA used for?

Answer 17

carries amino acids during protein synthesis

Question 18

What is rRNA used for?

Answer 18

component of ribosomes

Question 19

What is mRNA used for?

Answer 19

template for protein synthesis

Question 20

What are the key features of the structure of RNA (that make it different from DNA)

Answer 20

ribose instead of deoxyribose
uracil replaces thymine
usually single-stranded

Question 21

What is the terminator in transcription?

Answer 21

sequence that signals RNA pol to stop

Question 22

What enzyme opens and unwinds DNA without the need for a primer?

Answer 22

RNA polymerase

Question 23

When does the sigma factor leave?

Answer 23

after transcription is initiated

Question 24

What are the two types of terminators?

Answer 24

Rho-independent transcription termination

Rho-dependent transcription termination

Question 25

What type of nucleic acid is a terminator?

Answer 25

DNA

Question 26

Which type of terminator causes RNA pol to release?

Answer 26

Rho-independent

Question 27

What type of terminator causes RNA pol to pause (initially)

Answer 27

Rho-dependent

Question 28

What does the protein Rho do to stop transcription?

Answer 28

binds to RNA, then moves toward RNA pol and causes release

Question 29

How do bacteria control gene transcription in response to their environment?

Answer 29

two-component signal transduction systems

Question 30

Where does transcription in prokaryotes occur?

Answer 30

cytoplasm

Question 31

Where does transcription in eukaryotes occur?

Answer 31

nucleus

Question 32

What do eukarya need for transcription?

Answer 32

``` RNA polymerase Transcription factors (no sigmas) ```

Question 33

What is the promoter element for transcription in Eukarya?

Answer 33

TATA box

Question 34

What process removes introns?

Answer 34

RNA splicing

Question 35

What modifications need to be made to mRNA in Eukarya?

Answer 35

capping - methylguanosine added at 5' end | Polyadenylation - adenine nucleotides added at 3' end - tail

Question 36

What is translation?

Answer 36

synthesis of polypeptides directed by mRNA sequence

Question 37

What does translation require?

Answer 37

ribosomes | energy in the form of ATP and GTP

Question 38

What are the 2 subunits of bacterial ribosomes?

Answer 38

30S and 50S

Question 39

What type of rRNA acts as a ribozyme

Answer 39

23S rRNA

Question 40

What type of rRNA is capable of peptidyltransferase

Answer 40

23S rRNA

Question 41

What type of rRNA aligns mRNA with the ribosome?

Answer 41

16S rRNA

Question 42

What type of rRNA has a sequence complementary to Shine-Dalgarno sequence of the mRNA

Answer 42

16S rRNA

Question 43

What do ribosomes do?

Answer 43

"read" mRNA as a code

Question 44

code is ____ - multiple codons can encode the same amino acid

Answer 44

degenerate

Question 45

codons are read as a ____ made up of __ nucleotides

Answer 45

triplet, 3 nucleotides

Question 46

How many codons are there?

Answer 46

64

Question 47

How many nonsense codons are there?

Answer 47

3 (stop codons)

Question 48

How many sense codons are there?

Answer 48

61 (specify amino acids)

Question 49

What enzyme attaches an amino acid to the 3' end of the correct tRNA molecule?

Answer 49

Synthetase

Question 50

What is the shape of tRNAs?

Answer 50

clover

Question 51

What is the anticodon?

Answer 51

complementary to codon in mRNA

Question 52

What are the 3 stages of translation?

Answer 52

initiation elongation termination

Question 53

What are the 3 sites on the ribosome?

Answer 53

A P E

Question 54

What occurs during initiation of translation?

Answer 54

AUG codon binds to P site, tRNA attaches Met amino acid

Question 55

What occurs during elongation of translation?

Answer 55

Next tRNA binds to A site, peptide bond forms between P and A site amino acids, everything shifts down and process continues

Question 56

What occurs during elongation of translation?

Answer 56

Next tRNA binds to A site, peptide bond forms between P and A site amino acids, everything shifts down and process continues

Question 57

What occurs during termination of translation?

Answer 57

Any one of the 3 stop codons enters, no tRNAs carry anticodon release factors cleave and release the polypeptide

Question 58

What binds to single-stranded DNA after strands are separated to keep them separated?

Answer 58

SSB proteins (single-stranded binding proteins)

Question 59

What enzyme has 3' -> 5' proofreading activity?

Answer 59

DNA pol III