Chapter 13 pt.1

Question 1

Ribozymes

Answer 1

These catalytic RNA molecules can cut out part of their won sequences, connect some RNA molecules together, replicate others, and catalyze the formation of peptide bonds between amino acids

Question 2

What was the RNA hypothesis?

Answer 2

Early in the history of life, RNA probably served both as the original genetic material and as biological catalyst

Question 3

What is the difference between RNA and DNA?

Answer 3

1. RNA has ribose and DNA has deoxyribose
   (The difference arose from the presence/absence of an hydroxyl group)
2. RNA is sensitive alkaline hydrolysis and DNA is more resistant to alkaline hydrolysis
3. RNA is normally found as single-stranded and DNA is normally found as double stranded

Question 4

Explain what RNA secondary strictures are?

Answer 4

They are often hairpin loop/stem-loop structure
They are antiparallel
These secondary structures are formed from hydrogen bonding interactions

Question 5

Ribosomal RNA

Answer 5

Ribosomal protein subunits make up the ribosome

Question 6

Messenger RNA

Answer 6

Carries the coding region for a polypeptide chain from DNA to a ribosome

Question 7

pre-messenger RNA

Answer 7

Intermediate product of transcription and is unique to Eukaryotes only

Question 8

Transfer RNA

Answer 8

serves as the link between the coding sequence of nucleotides in an mRNA molecular and attaches to one particular type of amino acid and helps incorporate that amino acid into a polypeptide chain

Question 9

CRISPER RNAs

Answer 9

It assists in the destruction of foreign DNA molecules and prokaryotes only

Question 10

What are the three things that RNA transcription need?

Answer 10

1. A DNA template
2. The raw material – rNTPs – needed to build a new RNA molecules
3. The transcription apparatus consisting of proteins necessary for catalyzing the synthesis of RNA

Question 11

How does transcription appear under a microscope?

Answer 11

The transcription apparatus appears as a Christmas Tree, where the tree Trunk is equal to DNA and the branches represent RNA, and as the branches increase, it is indicative of transcription completing or going on

Question 12

Explain Transcription

Answer 12

An RNA molecule that is complementary and antiparallel to the DNA template strand is synthesized; the RNA transcript has the same polarity and base sequence as the non-template strand expect that it contains U rather than T; in most organisms, each gene is transcribed from a single DNA strand, but different genes may be transcribed from different strands

Question 13

Template strand

Answer 13

The nucleotide used for transcription

Question 14

Non-template strand

Answer 14

The nucleotide that is not transcribed but is similar in sequence to the transcribed RNA with the U and T replaced

Question 15

Transcription Unit

Answer 15

Is a stretch of DNA that encodes an RNA molecule and the sequences necessary for its transcription

Question 16

What are the three components that make up the transcription unit?

Answer 16

The promoter, an RNA coding-sequence, and a terminator

Question 17

Promoter

Answer 17

Is a DNA sequence that the transcription apparatus recognizes and binds, it indicates which of two DNA strands are the template, direction of transcription, transcription start site, and the first nucleotide to be transcribed

Question 18

RNA coding sequence

Answer 18

A sequence of DNA nucleotides that is copied into an RNA molecule

Question 19

Terminator

Answer 19

A sequence of nucleotides that signal where transcription is to end and part of the RNA coding sequence

Question 20

Describe Transcription Elongation

Answer 20

RNA is synthesized from rNTPs, nucleotides are added one at a time to the 3’-OH group of the growing RNA molecule, two phosphate groups are cleaved from the incoming nucleotide to the growing RNA molecule

Question 21

PPi

Answer 21

Pyrophosphate

Question 22

What are the similarities between replication and transcription?

Answer 22

Nucleotides are always added to the 3’-OH end of the RNA molecule, like DNA molecule in replication, the direction of transcription is from the 5’ to 3’ end, just like DNA replication

Question 23

What are the differences between replication and transcription?

Answer 23

Unlike DNA synthesis, RNA synthesis does not require a primer

Question 24

RNA polymerase

Answer 24

They carry out all required steps in transcription

Question 25

Explain Bacterial RNA polymerase

Answer 25

1. One type of RNA polymerase that catalyzes the syntheses of mRNA, tRNA, rRNA, and Crisper
2. Multimeric protein – multiple protein subunits
3. Made up of 5 subunits: 2 alpha subunits, 1 beta subunit, 1 beta prime subunit, and 1 omega subunit
4. Omega subunit does not participate in transcription, it stabilizes the enzyme
5. The sigma factor directs the binding of the polymerase

Question 26

The sigma factor

Answer 26

It controls the binding of RNA polymerase to the promoter, without sigma, RNA polymerase initiates transcription at random point along the DNA, when it binds to the subunit to forms a holoenzyme

The sigma factor is required only for the promoter binding and initiation; after a few RNA nucleotides have been joined together, sigma usually detaches from the core protein

Question 27

Rifamycin

Answer 27

An antibiotic that targets the RNA polymerase in bacteria

Question 28

RNA polymerase I

Answer 28

Eukaryotic; large rRNAs

Question 29

RNA polymerase II

Answer 29

Eukaryotic; pre-mRNAs, mRNAs

Question 30

RNA polymerase III

Answer 30

Eukaryotic; tRNAs

Question 31

What steps are involved in RNA transcription initiation?

Answer 31

1. The promoter recognition site
2. Formation of a transcription bubble
3. The creation of first bond between rNTPs
4. Escape of the transcription apparatus from the promoter

Question 32

Consensus Sequence

Answer 32

Is the set of the commonly encountered nucleotides usually implies that the sequence that posses considerable similarity; similar location with respect to start site

Question 33

-10 consensus sequence

Answer 33

Pribnow box is often written simply as

5’-TATAAT-3’
3’-ATATTA-5’

Question 34

-35 consensus sequence

Answer 34

5’-TTGACA-3’ , which lies approximately 35 nucleotides upstream of the start site

Question 35

Explain Transcription Process

Answer 35

1. The sigma factor associates with the core enzyme to form a holoenzyme
2. This binds to the -35 and -10 consensus sequences in the promoter
3. The holoenzyme binds to the promoter tightly and unwinds the double-stranded DNA
4. An rNTP complementary to the base at the start site serves as the first nucleotide in the RNA molecule
5. Two phosphate groups are cleared from each subsequent rNTP, creating an RNA nucleotide that is added to the 3’ end of the growing RNA molecule
6. The sigma factor is released as the RNA polymerase moves beyond the promoter

Question 36

What happens at the 5’end?

Answer 36

The RNA molecule contains three phosphate groups

Question 37

Abortive initiation

Answer 37

• Occurs in both prokaryotes and eukaryotes
• Often in the course of initiation, the polymerase repeatedly generates and releases short transcripts, from 2 to 6 nucleotides in length, while still bound to the promoter
• After several abortive attempts, the RNA molecule synthesizes 9 to 12 nucleotides in length, which allows the polymerase to transition to the elongation stage

Question 38

How is the accuracy of transcription maintained?

Question 39

Rho-dependent Termination Process

Question 40

Rho-independent termination Process