RNA Flashcards
(76 cards)
1
Q
transcription
A
- RNA synthesized from the template DNA strand in a 5’ to 3’ direction.
- The coding strand is complementary to the template strand and shows what the RNA will look like, aside from having thymadine instead of uradine
2
Q
messenger RNA
A
- longest chains of RNA
* nucleotides specify amino acids that are used to make proteins
3
Q
ribosomal RNA
A
forms ribosomes (site of protein synthesis in cells)
4
Q
transfer RNA
A
- transfers amino acids to proteins
* important for translation
5
Q
micro RNA (miRNA)
A
- target mRNA molecules -> bind via base pairing -> remove poly-A tail -> mRNA degradation by endonucleases
- block translation into protein
6
Q
small interfering RNA (siRNA)
A
- regulate gene expression
* cause degradation of mRNA
7
Q
small nuclear RNA (snRNA)
A
splicing of pre-mRNA
8
Q
RNA polymerase
A
- synthesizes RNA from DNA template by binding to promoter region and opening double helix
- does NOT require a primer
- requires transcription factors (proteins)
9
Q
types of RNA polymerase
A
Eukaryotes:
•RNA polymerase I -> most rRNA (5.8S, 18S, and 28S)
•RNA polymerase II -> mRNA
•RNA polymerase III -> rRNA (5S) and other RNAs
Prokaryotes have only 1 RNA polymerase that is a multisubunit complex
10
Q
alpha amanitin
A
- powerful inhibitor of RNA polymerase II
- from death cap mushroom (amanita phalloides)
- liver failure
11
Q
Rifampin
A
- inhibits bacterial RNA polymerase
* used for tuberculosis
12
Q
actinomycin D
A
•used in chemotherapy to inhibit RNA polymerase -> blunts replication of cancer cells
13
Q
promoters
A
- DNA regions that are not transcribed
- bind to RNA polymerase and transcription factors
- binding to RNA polymerase opens double helix
14
Q
common eukaryotic promoters
A
- TATA box (TATAAA, binds esp TFIID)
- CAAT box (CCAAT)
- GC box (GGGCGG)
15
Q
Enhancers
A
- DNA sequences that increase rate of transcription
- can be upstream or downstream from gene
- bind to transcription factors called activators -> stabilize transcription factors/ RNA polymerase
- b/c DNA coiling, can be geometrically close to gene while many nucleotides away
16
Q
Silencers
A
- DNA sequences that decrease rate of transcription
- can be up- or downstream of gene
- binds transcription factors called repressors -> prevent RNA polymerase binding
17
Q
untranslated regions
A
- 5’ end -> upstream coding sequence and recognized by ribosomes to initiate translation
- 3’ end -> found after stop codon; importation for post-translational gene expression
18
Q
significance of introns and exons
A
- Eukaryotic DNA has introns and exons that are transcribed into RNA within the nucleus
- before exiting nucleus the introns are cut out of the RNA
- only the exon portions enter cytoplasm to be translated to protein
- histone genes don’t have introns
19
Q
heterogeneous nuclear RNA (hnRNA)
A
=pre-mRNA
•the initial transcript that is modified in nucleus to become mRNA
20
Q
key modifications to mRNA before it leaves nucleus
A
- 5’ capping
- splicing out of introns
- 3’ polyadenylation
21
Q
5’ capping
A
- addition of 7-methylguanosine to 5’ end soon after transcription begins
- distinguishes mRNA from other RNA
22
Q
RNA splicing
A
- occurs during trancription
- removal of introns
- introns always have 2 nucleotides at either end: 5’ = GU and 3’ = AG
23
Q
snRNPs
A
= small nuclear ribonucleaoproteins
•short RNA polymers with proteins
•RNAs have high content of uridine (U-RNA)
•5 U-RNAs: U1, U2, U4, U5, U6
24
Q
spliceosome
A
= snRNPs + mRNA
•intron portion of mRNA forms loop called “lariat”
•lariat is released, then exons are joined
25
anti-SM (anti-smith)
* antibodies against proteins in snRNPs
| * seen in lupus
26
anti-RNP
* antibodies against proteins in U1 RNA
* strongly assoc with Mixed Connective Tissue Disease
* also seen in lupus and scleroderma
27
alternative splicing
* allows many proteins to be made from the same gene by using a different combination of exons for translation
* allows eukaryotic cells to be more advanced and high functioning than prokaryotes
28
splicing errors
* loss of exons, retention of introns/incorrect joining of introns
* beta thalassemia - many mutations, but some involve splice sites
* oncogenesis - many splice site errors described
29
3' polyadenylation
* triggered by polyadenylation signal (AAUAAA) which is followed by 10-30 nucleotides the CA
* once CSF and CstF bind, transcription is terminated
* then poly-A polymerase (PAP) binds and adds ~200 adenosines to the 3' end (poly-a tail)
* NO template
30
Cleavage and polyadenylation specificity factor (CSF)
RNA binding protein that binds to AAUAA (polyadenylation signal)
31
Cleavage stimulation factor (CstF)
RNA binding protein that binds to CA sequence
32
poly-a polymerase (PAP)
the enzyme that binds after transcription has been terminated to add the poly A tails (~200 adenosine nucleotides) and removes part of the mRNA molecule
33
Processing bodies (P-bodies)
* organelles in cytoplasm
* some mRNA with less extensive miRNA binding will be sequestered here so its not translated
* mRNA often degraded, but some evidence shows it may be later translated
34
translation
* mRNA template -> protein
* occurs in cytoplasm on ribosomes
* tRNA brings amino acids to ribosome for protein assembly
35
ribosomes
* some free in cytoplasm, some part of rough ER
* contain rRNA and proteins
* large and small subunits
* size measured in svedberg units
36
svedberg units
* used to measure sized of ribosomes
| * measure of the rate of sedimenation by centrifucation
37
prokaryotic ribosomes
```
•70S ribosomes
•small units is 30S and large is 50S
•small subunit: 16S RNA + proteins
•large subunit: 5S RNA and 23S RNA + proteins
(LOW yield)
```
38
protein synthesis inhibitor antibiotics
* target ribosomes of the size found only in bacteria
| * ie aminoglycosides
39
Eukaryotic ribosomes
```
•80S ribosomes
•small unit 40S and large unit 60S
•small subunit: 18S RNA + proteins
•large subunit: 5S RNA, 28 S RNA, 5.8S RNA + proteins
(LOW yield)
```
40
tRNA
* transfer amino acids to protein chains
* synthesized by RNA polymerase III
* many bases are chemically modified
* cloverleaf shape (secondary structure) b/c base paring within molecule
* 70-90 nucleotides in length (tiny)
41
key portions of tRNA cloverleaf
* anticodon loop
* D loop (part of D arm)
* T loop (part of T arm
* 3' end
42
anticodon of tRNA
* 3 nucleotides on tRNA
* pairs with complementary mRNA
* correct pairing -> correct protein synthesis
43
D loop of tRNA
* contains dihydrouridine
| * recognized by aminoacyl-tRNA synthetase
44
T loop of tRNA
* contins T psi C sequence (TψC)
* T = ribothymidine
* psi = pseudouridine
* C = cytidine
* needed for tRNA ribosome binding
45
3' end of tRNA
* always ends in CCA
| * hydroxyl (OH) of A attaches to amino acid
46
charging of tRNA
* linking of amino acid to 3' end of tRNA
* catalyzed by Aminoacyl-tRNA synthetase
* requires ATP
47
aminoacyl-tRNA synthetase in eukaryotes
in general there is a unique enzyme for every amino acid
48
hydrolytic editing
* aminoacyl-tRNA synthetase can also proofread the amino acid
* if incorrect it hydrolyzes it either from AMP or tRNA
49
protein synthesis direction
new amino acids are added the c-terminus of previos amino acids in protein synthesis
50
ribosome binding sites
* one for mRNA
* 3 for tRNA (they are codons in the mRNA)
* A-site: amino acid binding (anticodon) (3')
* P-site: tRNA attached to growing protein chain
* E-site: exit of tRNA (5')
51
initiation of translation
* begins with tRNA for methionine binding to the P-site at AUG start codon
* usually removed later by protease enzymes
* uses GTP hydrolysis
* in eukaryotes initiation factors are need to help assemble ribosomes and tRNA
52
N-formylmethionine (fMET)
* initiation codon AUG -> N-formylmethionine (fMET) in bacteria
* fMET in human bodies triggers chemotaxis of neutrophils (innate immunity)
53
elongation of translation
•uses elongation factors -> hydrolyze GTP to GDP
1. charged tRNA binds to A-site
2. amino acid joined to peptide chain (catalyzed by ribozyme activity called peptidyl transferase)
3. ribosome translocation -> protein moved to p-site, a-site now empty, and tRNA in E site, ready to exit
4. tRNA leaves E site
54
elongation factors in eukaryotes
* EF1 and EF2
| * EF2 is the target of bacterial toxins -> inhibit protein synthesis (ie diptheria toxin and eotoxin A)
55
termination of translation
* ends at mRNA stop codon (UAA, UAG, and UGA)
* no tRNA anticodon for these codons -> no amino acid
* stop codon encountered -> releasing factors bind to ribosome -> catalyze addition of water to protein chain (add OH group)
56
posttranslational modification
* create functional protein
| * includes folding and addition of other molecules
57
phosphorylation
* posttranslational modofication
| * amino acid residue phosphorylated by protein kinase enzymes
58
glycosylation
* posttranslational modification
* formation of sugar-amino acid linkage
* N-, O-, C-linked glycosylation (sugar + nitrogen, oxygen, carbon)
* creates glycoproteins
59
hydroxylation
* posttranslational modification
* addition of hydroxyl (OH) groups
* important for collagen synthesis (hydroxilation of proline and lisine residues)
60
methylation of protein
* posttranslational modification
| * addition of methyl (CH3) groups
61
acetylation of protein
* posttranslational modification
| * addition of acetyl (CH3CO) group
62
ubiquitination of protein
* posttranslational modification
* addition of ubiquitin (small protein)
* tags proteins for destruction of proteasome
63
chaperones
* proteins that facilitate folding of other proteins
| * classic example heat shock proteins
64
heat shock proteins
* aka stress proteins
* chaperones that are constitutively expressed, but levels increased with heat, pH shift, and hypoxia
* stabilized proteins/maintain structure
* helps cells survive environmental stress
65
mRNA start codon
AUG -> methionine in eukaryotes
| school starts in AUGust
66
mRNA stop codons
UGA -> u go away
UAG -> u are going
UAA -> u are away
67
RNA stability
* stability/decay affects gene expression
* RNAs have varying half lives
* 3' UTR is important in RNA stability/instability
68
Iron response elements (IRE)
* if low [iron] iron response proteins (IRPs) bind to IREs and repress ferritin translation while promoting transferrin receptor translation
* if high [iron] iron binds to IRPs and releases them from IREs -> ferritin translation occurs and transferrin receptor mRNA degraded
69
nonsense mediated decay (NMD)
•surveillance pathway to reduce errors in gene expression by eliminating mRNA
70
beta-thalassemia
* autosomal recessive inheritance
* anemia with reduced or absent synthesis of beta chains of hemoglobin
* depends on nonsense mediated decay pathway
71
Duchenne muscular distrophy (DMD)
* mutation on dystrophin gene
| * nonsense mutation that causes mRNA decay and loss of functional protein
72
becker muscular dystrophy
•mutation on dystrophin gene, but does not involve a frameshift mutation
73
diamond blackfan anemia
* proapoptotic hematopoiesis, bone marrow failure, birth defects and predisposition to cancer
* cause by mutations in ribosomal proteins
74
treacher collins syndrome
* autosomal dominal craniofacial disorder
| * mutation in TCO1 (treacle) -> role in ribosome biogenesis
75
small nucleolar RNAs (snoRNAs) mutations
mutations can cause prader-willi syndrome
76
chronic lymphocytic leukemia (CLL)
* most common leukemia in adults
| * loss of part of chromosome 13 -> contains gene encoding miRNAs-15 and -16
