DLA 3a- Transcription Flashcards
1
Q
What is the central dogma?
A
The information that is contained in the DNA is transcribed to mRNA by RNA polymerase
mRNA is translated to protein by ribosomes
2
Q
Outline RNA transcription in Prokaryotes and Eukaryotes
A
- DNA transcribed via RNA polymerase to mRNA
- mRNA translated to proteins via ribosomes
NB: tRNA and rRNA are involved in the processing in the mRNA
3
Q
How is the catalytic activity of RNA polymerase similar to that of DNA synthesis?
A
- Phosphodiester bond formation between nucleotides and pyrophosphate is released
- DNA is used as the template
4
Q
What are the differences between Catalytic Activity of RNA polymerase and DNA synthesis?
A
-RNA polymerase has helicase activity
-the nucleotide triphosphate (NTP) used as substrate are different
Thymine base in DNA is replaced with Uracil to be complementary to Adenine in RNA synthesis
The sugar of RNA is ribose sugar and not deoxyribose
No primer is required to initiate synthesis
5
Q
In bacteria, a single RNA polymerase is composed of…
A
The core polymerase and sigma factor
6
Q
What is the sigma factor in RNA polymerase?
A
It enables the RNA polymerase to recognize promoters
7
Q
Describe the 3 different RNA polymerases in Eukaryotes
A
- RNA polymerase 1: 5.8S, 18S, and 28S rRNA genes
- RNA polymerases 2: all protein-coding genes (mRNA), lnc -RNAs and some snRNAs
- RNA polymerase 3: tRNA genes and some snRNAs
8
Q
What does the r in rRNA mean?
A
Ribosomal
9
Q
What does the t mean in tRNA?
A
Transfer
10
Q
What does “lnc” mean in lnc-RNA?
A
Long non-coding
11
Q
What does the “Sn” mean in snRNA?
A
Small nuclear
12
Q
What is the -10 region in prokaryotic gene?
A
The pribnow box
13
Q
What region does RNA polymerase bind to for a prokaryotic gene?
A
The promoter region
14
Q
Describe where the ignition and termination of RNA synthesis occurs
A
- Initiation of RNA synthesis at the beginning of the gene at +1
- RNA polymerase releases the RNA transcript after the terminal signal
15
Q
What is the -35 region in prokaryotic genes?
A
The -35 region
16
Q
Where does mRNA transcription begin?
A
At +1 base pair
17
Q
Where is the promoter region in the prokaryotic genes?
A
The conserved regions at -35 and -10 base pairs
18
Q
What are the subunits of RNA polymerase?
A
The core enzyme and the sigma subunit
19
Q
What is the function of Holoenzyme RNA polymerase for prokaryotic RNA polymerase?
A
It binds to prokaryotic DNA and scans till it recognizes the promoter sequence
20
Q
Describe the functioning of prokaryotic RNA polymerase
A
- At the promoter sequence, RNA pol. unwinds the helix to expose the template strand
- Requires all 4 NTOs as substrate( A,U,C,G)
- RNA polymerase will then synthesize in the 5’ to 3’ direction reading the template strand from 3’ to 5’
- Elongation of the RNA occurs
- RNA pol. will stop at the termination signal
21
Q
Which DNA strand serves as the template for RNA ?(both prokaryotes and eukaryotes)
A
Template strand/ anti-sense strand / non-coding strand
22
Q
How can the template/ antisense strand be identified?(both prokaryotes and eukaryotes)
A
Read in 5’ to 3’ direction
23
Q
What is the Un-used/ non transcribed DNA strand called ? (both eukaryotes and prokaryotes)
A
Non-template strand/sense strand/ coding strand
24
Q
Why does the RNA polymerase have helicase activity?
A
RNA pol. has helicase activity to open up a double helix
25
A DNA strand is as follows:
3’. TACCGACGGT 5’
What will be the resulting RNA strand of transcription?
5’ AUGGCUGCCA’3
26
Explain the termination of Prokaryotic Transcriotion
- DNA sequence at the end of the gene contains inverted repeats
- When the DNA is transcribed to single stranded RNA, it will form complimentary bond to itself and then firm a hairpin loop
- At the end of the hairpin loop are many consecutive U pairs on the RNA(weak A-U pairing)
- Energy of making the hairpin loop will dissociate the RNA from the DNA template
27
What is the purpose of Rho proteins?
Sometimes these specific proteins assist the RNA to dissociate from the DNA template
28
What is a ORF(Open reading frame)?
This is DNA information that will first be transcribed to RNA and next directly translated in to protein
29
Most times a single gene on the prokaryotic mRNA is ...
Transcribed to a single mRNA
30
When a single gene of a prokaryote being transcribed to a single mRNA it has...
One open reading frame / one ORF
31
Explain the function of the information comprising an open reading frame/ ORF
- the information comes 3 base pairs at a time, called a codon
- Each codon will be translated to an amino acid by the ribosome, to be discussed later
- Starting from start codon AUG, 3 base pairs at a time, all the way to the stop codon
- There is one universal start codon but three universal stop codons
32
What are polycistronic genes?
When there are multiple genes expressed from one promoter region
33
Sometimes mRNA have ...
Polycistronic genes under the control of one promoter
34
Describe the pattern of ORF, RBS and promoters for polycistronic genes
- On a polycistronic genes there are multiple genes for one promoter
- each gene has its own ribosome binding site(RBS) as well as its own unique open reading frame (ORF)
35
Prokaryotic Transcription and Translation happen ________________ in cytosol
Simultaneously
36
What happens to mRNA processing enzymes in Eukaryotic mRNA Transcript ?
- RNA polymerase 2 has mRNA processing enzymes attached to the C-terminal tail
- These processing enzymes are transferred to the RNA as it is being synthesized
37
What are transcription factors?
Proteins bind to these elements and regulate the transcription of a gene
38
What is the approximate position of the element-GC box (eukaryotic mRNA) transcript?
-70 to -200
39
What is the approximate position of the element- CAAT box( eukaryotic mRNA transcript)?
-60 to -100
40
What is the approximate position of the element -BRE (eukaryotic gene)?
-35
41
What is the approximate position of the TATA box(eukaryotic gene)?
-25 to -30
42
What is the approximate position of INR(initiator box)(eukaryotic gene )?
+1
43
Explain the beginning events of eukaryotic mRNA transcription
- RNA pol. 2 binds to the core promoter, “initiation”
- Transcription start site +1
- RNA polymerase continues to synthesize the gene “ELONGATION”
- Synthesis of 3’end processing signature sequence AAUAAA signals the beginning of termination to RNA polymerase
44
What are the Core Promoter(Basal Regulatory Elements)?
The TATA Box
INR (initiator element)
45
What are the proximate,y regulatory elements ?
The GC Box
CAAT box
46
What is TF II D?
TF II D: transcription factor II D
Subunit of TF II D is TBP: TATA Box protein
47
What is the function of TF II D?
One of the many transcription factors which help coordinate the binding of RNA polymerase
48
What is RNA pol. 2?
The isoforms that synthesizes mRNA, always in the 5’ to 3’ direction
49
What is AAUAAA?
The polyadenylation signal recognized by 3’ processing enzymes
50
When does RNA polymerase fall off DNA?
RNA polymerase eventually falls off the template after synthesizing AAUAAA sequence
51
What are the 3 basic modification of eukaryotic mRNA after transcriotion?
- The addition of a 5’ cap
- Splicing our intervening regions from the gene
- the addition of poly A tail
52
Where is eukaryotic mRNA. transcribed by RNA polymerase?
In the nucleus
53
What are the functions of a 5’ cap in post-transcriptional
- The cap stabilizes the mRNA and protects the 5’ end from nuclear attack
- Facilitates transport from nucleus to cytosol
- Cap is required for the initiation of translation of mRNA into protein
54
How is the addition of 5’ cap executed?
Post-translational modification to 5’ end is the addition of a
7-methylguanosine (m7G) cap
55
Describe the discovery of the addition of 5’ cap
-Groups led by Aaron Shatkin , James Darnell and many others discovered that shortly after the first few bases pairs of mRNA is synthesized, the cap is added by the coordinated activity of atleast 4 enzymes
56
What are eukaryotic genes interrupted by?
Sequences which do not code for amino acids(introns)
57
How much human genes have introns?
94%
58
What is the average number of introns per genes?
8 introns per gene
59
What happens to introns in RNA processing?
They are removed
60
What are Exons?
The retained genes, the expressed regions
61
What is RNA splicing?
Removal of introns and joining together exons is called RNA splicing
62
The numbers above/below introns and exon sequences indicate...
The number of nucleotides present in various introns and exon sequences
63
Common intron/exon sequences are found at...
The intron/exon boundaries
64
List why do introns exist
1. Some genes can encode for more than one protein product
2. Introns may be important to the evolution of genes
3. Excised introns are generally degraded, some involved in regulation of gene expression
4. Introns can also regulate transcription
65
How can some genes encode for more than one protein product?
- Alternative splicing: different mature mRNA from the same pre-mRNA
- By splicing out introns and lighting together different combinations of exons
66
How may introns be important to the evolution of genes?
- DNA sequences can be moved around the genome
| - Shuffling of exons may yield new genes
67
“Excised introns are generally degraded, some involved in regulation of gene expression” why is that?
-Some introns contain non coding RNA
- liberation of the ncRNA can then interact with other genes and proteins
- inhibition of translation by inhibiting mRNA closed formation loop
- Regulation of splicing to influence mature mRNA product
68
How can introns regulate transcription?
Intronic sequences in the DNA may be cis regulatory elements where transcription factors, such as silencer proteins or enhancer proteins can bind and either upregulate or downregulate transcription respectively
69
What role does RNA polymerase serve in terminating mRNA synthesis in eukaryotic transcription?
RNA pol. synthesizes the mRNA through the polyadenylation signal AAUAAA and eventually falls off the template
70
What proteins are involved in the poly A tail ?
-AAUAAA is recognized by 3’ end processing proteins to cleave the transcript in the 3’ untranslated region
- CPSF( Cleavage and polyadenylation specificity factor )
- CstF (cleavage stimulating factor)
- Cleavage factors
- Poly A polymerase then adds ~ 50-200 A nucleotides to the 3’ end
- Poly A binding proteins bind to the poly A tail
71
What is the purpose of the poly-A tail in the nucleus?
Proteins bound to the poly-A tail are important for export of mRNA from nucleus to cytosol
- include Nuclear poly-A binding proteins PABPN1(Cap binding complex and other proteins not shown, are also required for export
72
What is the purpose of the poly-A tail in cytosol?
Efficient mRNA translation requires a series of protein-mRNA and protein-protein interactions
- Cytosolic poly-A binding proteins PABC1 associate with the poly-A tail
- Proteins binding to the 5’ cap interact with proteins binding to thePoly-A tail
73
Give the order of proteins in the 5’ cap to the proteins interacting with the Poly-A tail
5’ cap -> elF4E -> elF4A -> elF4G -> PABPC1
74
mRNA turn over is an important ______________ of gene expression (making protein)
Regulation
75
What is the over role of the Poly-A tail?
-Many nucleases in cytosol which will degrade mRNA at the poly A tail
76
What are decay rate and half-life used to describe?
Terms used to describe the stability of the mRNA which reflects how long the mRNA can be translated by the ribosome
-Reflects changing environment or developmental cues in the cell
77
Give 2 examples of genes with a long translation window
B-globin, maternal mRNA
78
What is significant about genes with a short translation window?
Genes with a short translation window often respond to external or internal stimuli
-Nutrition, hormonal, temperature, viral infection
79
What is the intermediate product of transcription?
RNA
80
Genetics is the study of...
Heredity and variation
81
What is a gene?
A unit of inheritance
82
What does the term genetics mean?
A sub discipline of biology concerned with the study of heredity and variation at the molecular, cellular, developmental, organisms land population levels
83
A fundamental property DNA’s nitrogenous basesbases that. Is necessary for the double stranded nature is-
Complementary on
