11.3 Transcription (prokaryotic) Flashcards
1
Q
What is the order of genotype to phenotype
A
Genome to transcriptome to proteome to metabolome
2
Q
What comprises a genome
A
DNA
3
Q
What comprises the transcriptome
A
RNA
4
Q
What comprises the proteome
A
proteins
5
Q
What comprises the metabolome
A
small molecules called metabolites that are used in metabolism
6
Q
What is transcription
A
how dna is converted into rna
7
Q
What are RNAs
A
the molecules that deliver the information from DNA to the cell
8
Q
What comprises a nucleotide
A
A phosphate, a sugar, and a base
9
Q
What is the difference between dna and rna structure?
A
- both made of a phosphate, sugar, and a base
- DNA= deoxynucleic acid
- RNA= ribonucleic acid
- RNA contains ribose sugar w hydroxyl groups at 2nd and 3rd carbon of the ring
- DNA contains deoxyribose sugar, which lacks the hydroxyl group at the 2nd carbon on the ring
10
Q
Where is the nitrogen base on DNA and RNA
A
Attached to the first carbon
11
Q
What are the nitrogenous bases in DNA and RNA
A
- DNA: adenine, guanine, cytosine, and thymine
- RNA: adenine, guanin, cytosine, and uracil
- (T to U)
12
Q
What is the difference between thymine and uracil
A
uracil lacks a methyl group
13
Q
How are the nucleotides linked together in DNA and RNA?
A
- through a phosphate bond to form long chains that forms a spiral
14
Q
What does the phosphate group connect in DNA and RNA?
A
The 5’ sugar of one nucleotide to the 3’ sugar of the next nucleotide in the chain
15
Q
How is DNA held together?
A
the base pairings
16
Q
How many strands are DNA and RNA usually
A
- DNA usually ds
- RNA usually ss (but other structures can form within the single strand)
17
Q
How much of the human genome is transcribed into RNA?
A
5-10%
18
Q
What percent of RNAs contain protein coding sequences?
A
only 2% contain the information to code proteins
19
Q
How many types of RNAs?
A
4
20
Q
What is mRNA?
A
- most famous
- Messenger RNAs
- contain the information to direct protein synthesis
21
Q
What is the central dogma?
A
DNA is converted to mRNA (through transcription) and then mRNA is converted to protein (through translation)
22
Q
What are the 4 types of RNAs?
A
- mRNA (messenger RNA)
- rRNA (ribosomal RNAs)
- tRNA (transfer RNAs)
- ncRNA (noncoding RNAs)
23
Q
What are rRNAs?
A
- ribosomal RNAs
- RNA components of ribosomes, ribozymes involved in protein synthesis
- 80% of cellular RNA (the transcriptome), the most abundent
24
Q
What is tRNA?
A
- tranfer RNAs
- bind amino acids and deliver them to ribosomes to aid in protein synthesis
25
What is ncRNA?
* noncoding RNAs
* involved in gene regulation
* help direct when transcription and translation occur
26
What are the steps of transcription?
1. Initiation
2. Elongation
3. Termination
27
# Transcriptional Initiation (prokaryotic)
What is a promoter?
* A regulatory region of the DNA genome that directs where trancription will begin
* contain recognition sites for RNA polymerase (the enzyme that synthesizes the RNA molecule)
* promoters occur upstream of the transcription start site
28
# transcriptional initation
What is the +1 site?
* The first bp that is read by RNA polymerase
* the beginning of the trancribed region
29
# transcriptional initation
What is upstream and downstream in regards to positions of the genetic code of DNA/RNA
* Relates to the direction that RNA transcription takes place
* upstream refers to the sequences before the transcription start site (minus sign)
* downstream refers to the sequences after the transcription start site (plus sign)
30
# transcriptional initation
In prokaryotes what 2 regions does the core promoter contain?
* 35 element: consensus sequence: 5'-TTGACG-3' (~35 bp upstream)
* 10 element: consensus sequence: 5'-TATAAT-3' (10 bp upstream)
31
# transcriptional initation
What is a consensus sequence?
* the average sequence when comparing a number of similar sequences
* Different promoters will have slightly different sequences
* No promotors may be identical to the consensus sequence
32
# transcriptional initation
What are UP-elements?
* additional regulatory sequences that are sometimes found upstream of the core promoter
* no consensus sequences, are very variable
* can be 40 to 250 bp upstream
* typically not essential, do not exist for every gene, but will decrease transcription levels dramatically if mutated
33
# transcriptional initation
What is RNA polymerase (RNAP or RNApol)
* the enzyme that builds RNA chains
* large enzyme that has many, many subunits that help with its various activities
34
# transcriptional initation
What is sigma factor?
* a subunit of RNAP that has two domains that recognizes and binds directly to -35 and -10 elements
35
What does the alpha factor subunit of RNA polymerase do?
* has long flexible "antena" that will reach out and bind to the UP elements
36
# transcriptional initation
Why do bacteria cells produce many different versions of sigma and alpha factor?
* help to recognize and bind to specific promoter sequences and UP elements
* helps cells be selective about which RNAs they are goint to produce at a given time
* offers 1 level of gene regulation
37
# transcriptional initation
What are helix-turn-helix structures?
* in sigma factor, the helix-turn-helix domain binds to the major groove near the -10 element and bends the dsDNA
38
# transcriptional initation
What happens as a result of the tension caused by RNAP?
* the dsDNA begins to separate at the AT-rich -10 element
* this allows RNAP to "see" the +1 site and initiate RNA transcription
39
How many strands of DNA is transcribed?
* Only one strand
* The DNA strand that is transcribed is called the template strand
40
What direction does RNAP build nucleotides?
* 5' to 3', same as DNA poly
* so the 3' to 5' DNA strand is the template strand for RNA transcription
41
What is the first nucleotide of an RNA usually?
* An A (adenine) that is built from the T on the DNA strand on the template strand
* This t is located around 10 bp downstream (+) of the -10 element
42
# Elongation
What happens once RNAP is bound to the promoter?
* Initiation is complete and elongation can begin
* RNAP builds RNA in 5' to 3' direction
* RNA synthesis is complementary and antiparallel to the template strand
43
Does RNAP need a primer?
no, it can build a chain immediately
44
What happens as RNA pol moves off the promoter sequence?
Sigma factor is lost
45
RNAP structure during elongation
* RNAP holds the DNA double stranded chain like a fist sliding up a rope
* There are channels where the dsDNA enters and exits, and a channel where the ribonucleotides enter
* the center has subunits that act as a helicase to separate the dsDNA and as a chaperone to help refold the DNA into double strands after it has been transcribed
46
Where does the new RNA chain emerge from?
* It emerges from the RNA exit channel
47
When does termination of RNA occur?
* when a terminator sequence has been transcribed
48
What is the terminator sequence?
* contains an inverted repeat (a palindrome that reads the same forwards as backwards)
* this causes a stem/loop structure to form in the ssRNA molecule, which is important for the mechanisms of transcription termination
49
What is the p-independent termination mechanism for transcription?
* RNApol transcribes the sequences within the termination sequence
* the RNA forms a stem loop structure within the RNA exit channel of RNA polymerase
* this is too bulky for the exit channel, and the RNA poly begins to dissociate, it is pushed off the dsDNA chain, ending transcription
50
What is the ro dependent mechanism of termination?
* some termination sequences produce an RNA whose stem loop structure isn't stable
* these transcripts require additional help for termination
* a rut sequence, which occurs before the terminator sequence is transcribed
* a small molecule called rho then recognizes and binds to the rut sequence on the rna. rho can move up the RNA faster than RNA can synthesize RNA, so it "catches up" to Rna polymerases and pushes up agains the exit channel, causing the emerging RNA to stall.
* this gives time for the stem loop structure some time to form
* once the stem loop is formed, RNApol falls off the strand
51
ro dependent termination
* transcription proceeds past a rut sequence
* rho factor, an RNA-binding protein w helicase activity, binds to the rut transcript
* rho factor catches up to RNAP and causes a stem-loop structure to form on the RNA within the exit channel- dislodging RNA pol
52
Is transcription continuous?
* yes
* once RNAP has moved off the promoter, a new RNAP can bind and initiate a 2nd transcript
* RNA strands closer to the promoter are shorter, farther are longer
