Chapter 13

Question 1

RNA compared to DNA

Answer 1

uracil instead of thymine
ribose sugar
less stable because of -OH at 2’ carbon
usually single stranded

Question 2

what are the benefits of RNA being single stranded?

Answer 2

can form secondary structures
have more diverse functional roles compared to DNA

Question 3

what are some of the different types of RNA and their roles?

Answer 3

ribosomal RNA (rRNA) adds protein in the ribosome
messenger RNA (mRNA) is transcribed from protein coding genes and gets translated
transfer RNA (tRNA) brings amino acids to ribosome during translation of proteins
other small RNAs can process RNA and regulate gene activity

Question 4

stage one of transcription in bacteria (initiation)

Answer 4

RNA polymerases needs sigma factor to bind to the promoter
core RNA polymerase catalyzes addition of nucleotides to RNA
RNA polymerase moves down the gene

Question 5

stage one of transcription in eukaryotes (initiation)

Answer 5

1. core promoter is immediately upstream of gene and is where basal transcription apparatus binds
   -basal transcription apparatus can bring about minimal levels of transcription
2. the regulatory promoter is upstream of the core promoter and is where transcriptional activator proteins bind
   -faraway enhancers cam also bind the TAPs; DNA in between must fold to bring the enhancer close to the gene it regulates
   -transcriptional activators bring about higher transcription levels

Question 6

what is the basal transcription apparatus and what does it do?

Answer 6

accessory proteins, general transcription factors, and RNA polymerase
the transcription factors direct RNA polymerase to the right place in a similar fashion to sigma factors

Question 7

stage two of transcription (elongation)

Answer 7

RNA nucleotides are added in the 5’ to 3’ direction
1. RNA polymerase is on the template strand of DNA and synthesizes in the 5’ to 3’ direction; the transcript is complementary and antiparallel to the template strand
2. coding strand is the same as RNA transcript except the coding strand has T and transcript has U
3. topoisomerase relieves the stress from supercoiling

Question 8

stage three of transcription (termination)

Answer 8

1. RNA polymerase stops its job
2. polymerase, new RNA molecule, and the DNA templar detach from one another
3. in eukaryotes, transcription goes beyond the end of the coding sequence; Rat1

Question 9

anatomy of a gene

Answer 9

1. transcription unit= DNA template + sequences necessary for transcription
2. promoter is DNA sequence bound by transcription apparatus
3. RNA coding region gets transcribed into RNA
4. terminator is sequence of nucleotides that indicates where transcription ends

Question 10

transcription stages condensed

Answer 10

initiation: transcription apparatus recognizes and binds to promoter, transcription bubble forms, the first bonds between rNTPs are made, and the transcription apparatus leaves the promoter
elongation: DNA is threaded through RNA polymerase, and RNA is synthesized in 5’ to 3’ manner
termination: end of transcription unit is recognized, RNA separates from the DNA template

Question 11

sigma factor

Answer 11

required for RNA polymerase to bind to the promoter

Question 12

polycistronic mRNA

Answer 12

multiple genes transcribed together with one terminator

Question 13

acetyltransferases

Answer 13

add acetyl groups to amino acids on the ends of histones and destabilize nucleosome structure to make DNA more accessible

Question 14

chromatin-remodeling proteins

Answer 14

can bind to chromatin and displace nucleosomes

Question 15

transcriptional activator proteins

Answer 15

bind to DNA in regulatory promoters/enhancers and bring about higher transcription levels
-interact with basal transcription apparatus at core promoter
-stimulate the assembly of basal transcription apparatus at start site