Chapter 8 Exam 3

Question 1

What is the core polymerase?

Answer 1

The RNA polymerase core enzyme is composed of multiple subunits and is responsible for synthesizing RNA from a DNA template but cannot initiate transcription on its own.

Question 2

What is the holoenzyme?

Answer 2

The holoenzyme consists of the core RNA polymerase plus a sigma factor.

It is capable of initiating transcription by recognizing the promoter region of DNA.

Question 3

What is a sigma factor?

Answer 3

A sigma factor is a protein that binds to the core RNA polymerase, enabling it to recognize specific promoter sequences on DNA.

Question 4

How is the sigma factor involved in transcription?

Answer 4

It directs the polymerase to the start site of transcription and detaches once transcription begins.

Question 5

What is the purpose of having multiple sigma factors?

Answer 5

Different sigma factors allow bacteria to respond to various environmental conditions by recognizing different promoter sequences and regulating different sets of genes.

Question 6

What is a promoter?

Answer 6

A promoter is a DNA sequence upstream of a gene that signals where RNA polymerase should begin transcription.

Question 7

How are promoters identified?

Answer 7

Promoters are identified by consensus sequences (e.g., -10 and -35 regions) which are conserved motifs recognized by sigma factors.

Question 8

What is a consensus sequence?

Answer 8

A consensus sequence is a sequence of DNA that is recognized by sigma factors.

Question 9

Where are consensus sequences found in DNA?

Answer 9

They are found in promoters.

Question 10

How are consensus sequences related to sigma factors?

Answer 10

Sigma factors bind to specific consensus sequences within promoters, determining which genes are transcribed under specific conditions.

Question 11

How does altering a consensus sequence affect transcription rates?

Answer 11

Mutations or changes in consensus sequences can make promoters stronger or weaker, affecting how efficiently RNA polymerase initiates transcription.

Question 12

What are the three phases of transcription?

Answer 12

Initiation, Elongation, and Termination.

Question 13

What happens in the initiation phase of transcription?

Answer 13

RNA polymerase holoenzyme binds to promoter and begins RNA synthesis.

Question 14

What happens in the elongation phase of transcription?

Answer 14

RNA polymerase synthesizes RNA from the DNA template.

Question 15

What happens in the termination phase of transcription?

Answer 15

Transcription stops at a terminator sequence.

Question 16

What is a transcription bubble?

Answer 16

A transcription bubble is the locally unwound segment of DNA.

Question 17

What enzyme is involved in transcription?

Answer 17

RNA polymerase.

Question 18

What type of coil is introduced during transcription and how is the tension relieved?

Answer 18

Positive supercoils form ahead of the bubble, and DNA gyrase relieves this tension.

Question 19

What are the six classes of RNA?

Answer 19

mRNA, tRNA, rRNA, sRNA (small RNA), tmRNA (transfer-messenger RNA), Catalytic RNA (also called ribozymes)

Question 20

What is the role of mRNA?

Answer 20

mRNA carries genetic code from DNA to ribosome (translated).

Question 21

What is the role of tRNA?

Answer 21

tRNA delivers amino acids to ribosome during translation.

Question 22

What is the role of rRNA?

Answer 22

rRNA is a structural and catalytic component of ribosomes.

Question 23

What is the universal genetic code?

Answer 23

Three nucleotides code for a codon, codons then code for amino acids.

there are 64 codons total with 3 stop codons and 1 start codon

Question 24

What is a codon?

Answer 24

A codon is a three-nucleotide sequence in mRNA that codes for an amino acid.

Question 25

What is an anticodon?

Answer 25

An anticodon is a complementary sequence on tRNA that pairs with codons during translation.

Question 26

What is the start codon?

Answer 26

The start codon is AUG, which codes for N-formylmethionine (fMet) in bacteria.

Question 27

What do the stop codons code for?

Answer 27

Stop codons (UAG, UAA, UGA) signal termination and do not code for amino acids.

Question 28

What are the two types of transcription termination?

Answer 28

Rho-dependent and Rho-independent.

Question 29

What happens in Rho-dependent termination?

Answer 29

It requires the rho protein to remove RNA polymerase.

Question 30

What happens in Rho-independent termination?

Answer 30

It involves a GC-rich hairpin loop followed by Uracil residues that destabilize the transcription complex.

Question 31

What are some examples of antibiotics that affect transcription?

Answer 31

Rifamycin B blocks transcription initiation; Actinomycin D blocks transcription elongation by binding to DNA.

Question 32

What enzyme attaches the amino acid to tRNA?

Answer 32

Aminoacyl-tRNA synthetase.

Question 33

Where is the amino acid attached on tRNA?

Answer 33

The amino acid is attached to the 3’ end of tRNA.

Question 34

How does the enzyme recognize the correct tRNA?

Answer 34

The enzyme recognizes unique features of each tRNA, including the anticodon.

Question 35

What is the structure of a ribosome?

Answer 35

Ribosome has a large (50S) and small (30S) subunit, containing rRNA and proteins.

Question 36

What are the three binding sites for tRNA in the ribosome?

Answer 36

A site, P site, and E site.

Question 37

What happens at the A site?

Answer 37

It accepts incoming aminoacyl-tRNA.

Question 38

What happens at the P site?

Answer 38

It holds the tRNA with the growing peptide.

Question 39

What happens at the E site?

Answer 39

It is the exit site for discharged tRNA.

Question 40

What are the three steps of translation?

Answer 40

Initiation, Elongation, and Termination.

Question 41

What happens during initiation of translation?

Answer 41

Ribosome assembles on mRNA, with IF3 helping small subunit bind.

Question 42

What happens during elongation of translation?

Answer 42

Amino acids are added to the growing chain.

Question 43

What happens during termination of translation?

Answer 43

Stop codon recognized, peptide released.

Question 44

How are translation factors involved?

Answer 44

Translation factors assist in each phase.

Question 45

Where does the tRNA carrying N-Formylmethionine dock?

Answer 45

It docks at the P site during initiation.

Question 46

How is docking at the P site different from the elongation phase of translation?

Answer 46

During elongation, new aminoacyl-tRNAs enter at the A site.

Question 47

What is responsible for the peptidyltransferase activity of the ribosome?

Answer 47

The 23S rRNA in the large ribosomal subunit (LSU) — it is a ribozyme.

Question 48

What is a release factor?

Answer 48

A release factor binds to the A site of the ribosome when a stop codon is encountered.

Question 49

What does a release factor trigger?

Answer 49

It triggers the release of the polypeptide chain.

Question 50

What are some examples of antibiotics that affect translation?

Answer 50

Chloramphenicol, tetracycline, erythromycin — these target bacterial ribosomes.

Question 51

What is the function of tmRNA?

Answer 51

tmRNA rescues stalled ribosomes on damaged or incomplete mRNAs.

Question 52

What is the role of chaperones in the cell?

Answer 52

Chaperones assist in protein folding.

Question 53

What is the GroEL/GroES system?

Answer 53

It forms a barrel-shaped complex to refold proteins.

Question 54

What is the DnaK/DnaJ system?

Answer 54

It binds to hydrophobic regions and prevents misfolding.

Question 55

How may proteins be modified post-translation?

Answer 55

Proteins can undergo phosphorylation, methylation, acetylation, etc.

Question 56

Do all proteins have the same half-life?

Answer 56

No, proteins have different half-lives.

Question 57

What part of the protein influences its half-life?

Answer 57

The N-terminal amino acid (N-degron) can influence protein stability.

Question 58

What is a protease?

Answer 58

A protease is an enzyme that degrades proteins.

Question 59

Why is protease important for the cell?

Answer 59

It removes misfolded, damaged, or unnecessary proteins, maintaining cellular health.