Lecture 13 Flashcards
1
Q
what are the steps involved in the flow of genetic information (from gene to protein)
A
- transcription: the process of synthesizing RNA from a DNA template
- translation: the process of synthesizing protein from an RNA template
2
Q
compare DNA and RNA
A
DNA:
- Bases include: A, T, C, G
- contains 2’ hydrogen
- linear polymer
- usually double stranded
RNA:
- bases include: A, U, G, C
- contains 2’ hydroxyl
- linear polymer
- almost always single stranded
3
Q
What is the difference between between the sugar in RNA and DNA
A
- DNA has deoxyribose sugar
- RNA has ribose sugar
4
Q
RNA can form …
A
non conventional base pair interactions that allow for the ability to adopt a variety of shapes
5
Q
what does transcription produce
A
- transcription produces an RNA transcript that is complementary to the template strand except it uses uracil instead of thymine
6
Q
what are the similarities between transcription and DNA replication
A
- DNA needs to be unwound
- one DNA strand acts as a template
- NTPs (instead of dNTPs) are added one at a time in a 5’ to 3’ manner
7
Q
what are the key differences between transcription and DNA replication
A
- the newly synthesized RNA is displaced and DNA reforms a double helix
- RNA molecules are much shorter
- RNA polymerase catalyze the polymerization instead of DNA polymerase
- uses NTPs instead of dNTPs
- can start RNA chain without a primer
8
Q
gene expression
A
- includes the process of transcription and/or translation
9
Q
what is mRNAs function
A
code for proteins
10
Q
RNA polymerase
A
- several RNA polymerase can be working on the same gene at the same time
11
Q
what is the general sequence of events of transcription in bacteria
A
- RNA polymerase binds tightly to a promoter: a specific sequence immediately upstream from transcription start site (where RNA transcription begins)
- double helix is opened, transcription begins using one strand as a template
- transcription stops when RNA polymerase encounters a specific sequence known as the terminator (stop site)
- RNA and RNA polymerase dissociate from the DNA
12
Q
the bacterial promoter
A
- both promoter and and terminator have conserved sequences
- the numbers represent the nucleotide position relative to the first nucleotide transcribed
- the promoter has conserved sequences at -10 and -35 regions
- these regions are bound by a subunit of the RNA polymerase know as the sigma factor
13
Q
how does bacterial RNA polymerase correctly bind to RNA
A
- a single RNA polymerase transcribes the major RNAs in bacteria
- RNA polymerase posses a sigma factor which recognizes where to begin transcription
- the sigma factor bind to -10 and -35 regions in only one direction ensuring RNA polymerase binds in one orientation
14
Q
what five ways does eukaryotic transcription differs from prokaryotic transcription
A
- has a greater number of RNA polymerase (3)
- requires general transcription factors
- has a more elaborate control mechanism
- has to take DNA packing into account
- processes mRNA
15
Q
what genes are transcribed by RNA polymerase II
A
- all protein coding genes, miRNA genes, plus genes for non coding RNA (those in spliceosomes)
16
Q
in bacteria what 2 things are needed to initiate transcription
A
- RNA polymerase
- sigma factor
17
Q
what do eukaryotes require to allow transcription to occur
A
- they require a large number of accessory proteins that are known as transcription factors
- transcription factors help to position RNA polymerase, separate the DNA, and initiate transcription
18
Q
describe the general sequence of events for general transcription factors
A
- TFIID binds to the TATA box found within the promoter
- other transcription factors assemble the transcription initiator complex
- TFIIH contains a kinase domain which phosphorylates c-terminal domain of the RNA polymerase, allowing the RNA polymerase to clear the promoter
- the other transcription factors dissociate
- when transcription is complete c-terminal domain is dephosphorylated
19
Q
what the TATA box
A
- it is a conserved sequences often used to locate the promoter
20
Q
the TATA binding protein is a
A
subunit of TFIID
21
Q
what does TFIID binding to the tata box do?
A
- helps other general transcription factors to assemble
22
Q
what are the elaborate control mechanisms for eukaryotic transcription
A
- eukaryotic gene expression is controlled by regulatory DNA sequences
- regulatory DNA sequences can be thousands of base pairs away which require the interaction of several proteins and complexes
- this allows eukaryotes to respond to a greater variety of signals
23
Q
how does chromatin condensation affect transcription
A
- unlike bacteria, eukaryotic DNA is packed on nucleosomes
- the chromatin must be modified to allow access by the transcription factors
24
Q
Are transcriptions and translation kept seperate in prokaryotes/eukaryotes
A
- eukaryotes separate transcription and translation thanks to the nucleus
- prokaryotes can begin translating mRNA before it is completely transcribed
25
Eukaryotic mRNA processing
- eukaryotic mRNA undergoes processing before being exported:
- addition of 5' cap
- polyadenylation
- splicing of introns
- processed RNA is exported from nucleus to cytoplasm
26
What is RNA capping
- addition of the 5' cap increases stability of mRNA and helps with its export to the cytoplasm
- the cap is an atypical methylated guanine nucleotide linked to the RNA using an unusual linkage (5' to 5')
27
what is polyadenylation
- adds a series of repeating adenine nucleotides to the 3' end of the molecule
- also increases stability of mRNA and helps with its export to the cytoplasm
28
what is splicing
- in eukaryotes, immature mRNA contains intervening, non coding sequences (introns) that interrupt coding sequences of a gene (exons)
- the introns must be removed before translation and this is achieved through a process known as splicing
29
when does RNA processing occur
- during or shortly after transcription
30
the proteins that perform capping, splicing and polyadenylation associate with
- phosphorylated c-terminal domain (CTD) of RNA polymerase II
31
Why must introns be removed
- intron must be removed because an error of one or two nucleotides can shift the reading frame of the resulting mRNA molecules and change the protein it encodes
32
in general how is splicing carried out?
- splicing is carried out by small nuclear ribonuleoproteins (snRNPs) which contain both RNA and protein
- the RNA component is a small nuclear RNA (snRNA) which performs majority of the catalysis
- several snRNPs work together to form a complex known as the spliceosome
33
what are the general steps in splicing
step 1: adenine attacks the 5' splicing site and cuts the sugar phosphate backbone of the RNA
step 2: the 5' end cut of the intron becomes covalently linked the 2'-OH and forms a branched structure
the 3'-OH end of the exon sequence joins to the start of the next exon sequence and then introns are released in the form of al lariat structure which is further degraded
34
What is alternative splicing
- it allows many different products to be produced from a single gene
35
putting specific axons together can form a _________
modular "machine"
36
how is mRNA exported
- export is mediated by the nuclear pore complex
- mRNA must be bound to specific proteins including : poly-A-binding proteins, a cap-binding complex and proteins that bind to mRNA that have been appropriately spliced
37
mRNAs degradation
- mRNAs are eventually degraded in the cytosol by nucleases, specifically ribonuclease
38
The half life of mRNA
- the half like of mRNA is from minutes to hours depending on the species and specific mRNA
- it is also affected by the 3' untranslated region of the mRNA that its between the end of the coding region and the poly-A tail
