Term
| Describe a function of the nucleus |
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Definition
-regulate activity of the cell
-carried out by production of proteins
-intermediary molecule is needed because DNA doesn't leave nucleus |
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Term
| Why is RNA a good intermediary molecule? |
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Definition
-degrades quickly so it is short lived
-enables the nucleus to have more control over protein synthesis |
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Term
Describe the following contributions to the discovery of RNA by the following:
1. Volkin and Astrachan
2. Spiegelman |
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Definition
1. used 32P to show burst of RNA after viral infection
-the labeled RNA degraded quickly
2. demonstrated that the RNA matched the viral genome but not the host (E. coli) |
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Term
| Describe the Central Dogma |
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Definition
Replication
-ensures the perpetuation of genetic info from generation to generation
Control of Phenotype
1. Transcription/Reverse Transcription
-gene expression
2. Translation
-proteins |
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Term
Describe the 5 major types of RNA
1. mRNA
2. tRNa
3. rRNA
4. snRNA
5. miRNA |
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Definition
a. codes for proteins
b. structural and enzymatic component of ribosomes
c. imports amino acids to ribosome
d. forms with proteins used for RNA processing (spliceosomes)
e. used to block the expression of mRNA |
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Term
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Definition
| region of genome that codes for a protein |
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Term
| Describe the similarities/differences of DNA replication and Transcription? |
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Definition
Similarities
1. synthesis occurs in 5-->3 direction
2. reads 3-->5
3. occurs in the nucleus
Differences
1. ribonucleoside triphosphates instead of deoxy
2. one strand of DNA is used as template
3. RNA chains can be initiated without a primer
-no 3' OH needed |
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Term
| Describe the subunits of RNA polymerase |
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Definition
1. alpha are involved in assembly
2. beta contains RNA nucleotide binding region
3. beta prime contains DNA template binding region
4. sigma recognizes promoter sites
-only needed for initiation |
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Term
| Describe Initiation- 3 parts |
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Definition
1. Binding to the promoter region
-sigma unit recognizes this
2. unwinds the two strands of DNA locally
3. forms bonds for the first 8-9 RNA nucleotides
-sigma is then released |
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Term
| Describe the promoter region in Prokaryotes |
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Definition
*promoters are on the Nontemplate strand
-35 sequence
TTGACA
-sigma binds here (recognition sequence)
-10 sequence
TATAAT
-AT rich region facilitates unwinding
5-9 bases upstream is normally a purine (A or G) where transcription begins |
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Term
Describe the following sigma factors
70
54
32
23 |
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Definition
70- normal
54-nitrogen metabolism
32- heat shock
23- viral infection |
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Term
| Describe Elongation in Prokaryotes |
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Definition
1. sigma is released
2. DNA unwinds and rewinds
3. 2,400 nucleotides/min
-slower than DNA replication
*RNA/DNA hybrid= 2-3 nt
*Bubble= 18 nt |
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Term
| Describe Rho Independent Termination |
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Definition
1. G:C rich region followed by Ts (nontemplate)
2. G:C region forms hairpin structure
-bases pair up with each other forming hairpin
3. places tension on the RNA strand
4. polymerase cannot bring back the RNA to the pore
5. breaks off at the T rich region because of the weak bond |
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Term
| Describe Rho Dependent Termination |
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Definition
1. Rho binds to C rich region of 50-90 bp long
2. Rho binds to mRNA 5-->3
3. catches up to RNA poly and RNA chain pulls chain free
*does not bind until the ribosomes have fallen off the CDS region |
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Term
Describe Transcription in Eukaryotes
Polymerases |
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Definition
1. produces rRNA (besides 5s)
-promoter region is typically bipartite and GC rich
(-180 to -105; -45 to 20)
2. produces nuclear pre-mRNAs
-total sensitivity
-TATA box
*codes for proteins
3. produces tRNAs, 5s mRNA, other small RNAs
-promoters are downstream of TSS
-bind and come backwards |
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Term
Describe Transcription in Eukaryotes
RNA Poly 2 Initiation- Transcription Factors (first part) |
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Definition
1. TF2D
-contains Tataa Binding Protein (TBP)
-binds to promoter which is TATAA box (-30 of TSS)
(5-->3 on nontemplate)
2. TF2A
3. TF2B
-directs orientation
-directs distance/starting point
*all bind to the TATA box |
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Term
Describe Transcription in Eukaryotes
RNA Poly 2 Initiation- Transcription Factors (second part) |
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Definition
4. TF2F
-binds with RNA poly 2
-initiates unwinding of DNA
5. TF2E
-binds downstream of TSS
6. TF2H
-helicase activity: allows DNA to bubble
-takes phosphate off ATP |
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Term
Describe RNA processing
7-methly guanosine cap |
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Definition
*added to the 5' (front) end when mRNA is 30 nt long
a. initiation of translation
b. protects growing mRNA strand
-messes up RNA digesting enzymes |
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Term
| Describe the parts of RNA processing |
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Definition
1. 7 methyl guanosine cap
2. Poly A tails
3. Splicing
4. RNA editing |
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Term
Describe RNA processing
Poly A tails |
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Definition
*added to the 3' end
1. cleavage of 3' end occurs 11-30 nt downstream from AAUAA sequence and upstream from GU rich near the end
2. Poly A polymerase adds polyA tails (about 200 nt long)
*requires specificity component that binds to AAUAA, stimulatory factor that binds to GC, endonuclease, and poly a polymerase
a. protects processed mRNA from degradation
b. aids in transport to cytoplasm |
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Term
Describe RNA processing
Splicing
1. Endonuclease and ligase |
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Definition
1. occurs on tRNA
-shape driven
-requires endonuclease to cut
-ligase restores bond |
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Term
Describe RNA processing
Splicing
2. Self-splicing |
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Definition
2. occurs on rRNA
-shape driven
-no enzyme invovled
-rRNA cuts itself
-two exons are close to each other
-requires guanine with 3' OH
-two phosphoester bond transfers
*reversible-not protected at head and tail |
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Term
Describe RNA processing
Splicing
3. Spliceosomes |
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Definition
3. occurs on pre-mRNA
-complex RNA/protein structures= spliceosomes
-protein driven
-occurs during transcription |
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Term
| How would you locate an intron on pre-mRNA? |
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Definition
conserved sequenced that is 30 bases upstream from 3' end of the intron
5' GT....UACUAAC....AG 3'
*the third A is always there |
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