Topic 7-1

Question 1

under the microscope, DNA molecules undergoing transcription exhibit:

Answer 1

Christmas-tree-like structures

Question 2

what are the RNA subunits?

Answer 2

rNTPs (ribonucleoside triphosphates)

Question 3

what are the DNA subunits?

Answer 3

dNTPs (deoxyribonucleoside triphosphates)

Question 4

what is the difference between RNA sugars and DNA sugars?

Answer 4

RNA has a hydroxyl group on the 2’ carbon

Question 5

why is RNA more unstable than DNA?

Answer 5

bc of the 2’OH

Question 6

what is the difference between RNA bases and DNA bases?

Answer 6

RNA contains uracil, adn DNA contains thymine

Question 7

true or false: RNA has no secondary structure

Answer 7

false. RNA is single stranded but can contain many types of secondary structure

Question 8

a flexible secondary shape can allow some RNA to act as:

Answer 8

ribozymes/ catalytic RNA

Question 9

what are the four main functions of ribozymes?

Answer 9

1) cut/edit out own sequence
2) connect RNA olecules together
3) replicate other RNA
4) catalyze peptide bond formation b/w a.a.

Question 10

there are many classes of RNA, what are the four that we focus on in this class?

Answer 10

• ribosomal RNA (rRNA)
• messenger RNA (mRNA)
• transfer RNA (tRNA)
• CRISPR RNA (crRNA)

Question 11

what is transcription?

Answer 11

the synthesis of an RNA molecule from a DNA template

Question 12

what are the three major components required for RNA transcription?

Answer 12

• a DNA template
• ribonucleotide triphosphates
• the transcription apparatus (proteins necessary for catalysing the synthesis of RNA)

Question 13

unlike replication, transcription is _________ in what DNA sequences are transcribed

Answer 13

highly selective

Question 14

during transcription, RNA molecules are synthesized in the _______ direction, and is both _______ and _______ to the DNA template strand

Answer 14

5’ –> 3’, complementary, antiparallel

Question 15

a stretch of DNA encoding RNA molecule and sequences necessary for transcription (promoter, RNA coding region, terminator)

Answer 15

transcriptional unit

Question 16

• contains sequences that the transcriptional apparatus recognize and bind
• dictates which DNA strand is the template strand and transcription start site
  these are characteristics of the:

Answer 16

promoter

Question 17

• contains sequences that signal to end transcription
• usually part of the RNA coding sequence and resulting transcript
  these are characteristics of the:

Answer 17

terminator

Question 18

the first nucleotide transcribed is numbered ____ and numbering ___ downstream. nucleotides upstream of the start site are numbered ___

Answer 18

+1, increases, negative

Question 19

RNA polymerase and array of accessory proteins

Answer 19

transcriptional apparatus

Question 20

a large multimeric enzyme (contains several polypeptide chains)

Answer 20

RNA polymerase

Question 21

the core enzyme of RNA polymerase contains these five subunits:

Answer 21

• alpha (2)
• beta
• beta prime
• omega

Question 22

what is the function of the core enzyme of RNA polymerase?

Answer 22

catalyzes addition of rNTPs, thus elongation of RNA molecule

Question 23

different accessory proteins regulate:

Answer 23

special transcriptional functions

Question 24

what are the three main transcriptional stages?

Answer 24

1) initiation
2) elongation
3) termination

Question 25

transcriptional appratus that assembles on promoter and begins RNA synthesis

Answer 25

initiation

Question 26

what are the four main steps of initiation?

Answer 26

1) promoter recognition/ binding 2) formation of transcription bubble 3) creation of first bonds between rNTPs 4) escape of transcriptional apparatus from promoter

Question 27

critical step for regulating selective gene expression (when and how frequent)

Answer 27

promoter recognition and binding

Question 28

the promoter sequence encodes three key pieces of information:

Answer 28

- where to start - which is the template strand - which direction to move

Question 29

set of most commonly encountered nucleotides among sequences with considerable similarity or consensus. similar location w/ respect to start site

Answer 29

consensus sequence

Question 30

most bacterial promoters have two:

Answer 30

consenseus sequences

Question 31

the pribnow (TATAAT) box

Answer 31

located -10 bp upstream of the start site

Question 32

TTGACA promoter

Answer 32

located -35 bp upstream of the start site

Question 33

a bacterial accessory protein that binds to the core RNA polymerase (forming the holoenzyme)

Answer 33

sigma factor

Question 34

stabilizes polymerase binding to proper promoter start sites ensuring initiation of gene transcription

Answer 34

sigma factor

Question 35

true or false: the signma factor is required only for promoter binding and initiation and detaches after a few RNA nucleotides have been added

Answer 35

true

Question 36

the holoenzyme changes structure leading to tighter binding and unwinding of DNA to form the:

Answer 36

transcription bubble (nucleotides -12 to +2)

Question 37

as subsequent rNTPs are added to the RNA molecule, ______ are cleaved in the rxn

Answer 37

two phosphates

Question 38

polymerase changes shape again such that it "lets loose" of consenses sequences in promoter and is free to:

Answer 38

move and transcribe downstream

Question 39

what are the three main processes involved in elongation?

Answer 39

- unwinding DNA at downstream edge of bubble - adding nucleotides to RNA molecule - rewinding DNA at upstream edge

Question 40

DNA _______ ahead of bubble, negative _______ behind bubble

Answer 40

supercoiling, supercoiling

Question 41

likely relieve supercoiling

Answer 41

topoisomerases

Question 42

a "pause" in transcription caused by backbacking, where:

Answer 42

polymerase slides backward along the DNA template

Question 43

transcriptional pausing is important for:

Answer 43

proofreading

Question 44

what are the three main steps of termination?

Answer 44

1) RNA polmerase stops RNA synthesis 2) RNA molecule is released from polymerase and dissociates from DNA 3) polymerase detaches from DNA

Question 45

what are the two major types of termination mechanisms?

Answer 45

rho-dependent and rho-independent

Question 46

genes with the rho-dependent terminator have two features:

Answer 46

- RNA sequence where rho binds, called the Rut (rho utilization) site - terminator sequence causes polymerase to pause (allows rho to advance towards transcription site)

Question 47

the rho protein has ________ activitiy that unwinds the RNA:DNA hybrid thus terminating transcription

Answer 47

helicase

Question 48

genes with the rho-independent terminator have two features:

Answer 48

- inverted repeats - two sections of terminator have complementary (inverted strands) - string of 'A's in the DNA template follows last inverted repreat (string of 'U's in RNA)

Question 49

in rho-independent termination, the string of uracil causes polymerase to pause, allowing ________ to form

Answer 49

the inverted repeat hairpin