Gene Expression Flashcards
1
Q
Where is DNA transcribed into RNA?
A
The nucleus
2
Q
Where is RNA processed?
A
The nucleus
3
Q
Where does mRNA exit through?
A
nucleopores
4
Q
Where are ribosomes assembled on mRNA?
A
The cytosplasm
5
Q
Where does translation take place?
A
The cytosplasm
6
Q
What does the SRP do?
A
Directs polypeptides/ribosomes to the ER
7
Q
In which organelle is the signal sequence cleaved?
A
The ER
8
Q
The new protein is synthesized into the lumen of which organelle?
A
The ER
9
Q
From the Golgi Apparatus the newly synthesized protein is moved to a ____, ____, or the ____.
A
vacuole, peroxisome, or plasma membrane
10
Q
Once fused with the plasma membrane, a protein can be released into the ____.
A
cell wall
11
Q
Number of copies of complete genome
A
Ploidy
12
Q
All plant species have at least 1 whole genome duplication event in their evolutionary history. T or F ?
A
True
13
Q
Contains multiple copies of complete genome from a single species
A
Autoploidy
14
Q
Contains multiple copies of complete genome from 2 or more species
A
Allopolylpoidy
15
Q
Loss of DNA segment from chromosome
A
Direct repeats
16
Q
Inversion of DNA segment in chromosome
A
Indirect repeats
17
Q
aka “jumping genes” DNA segment with ability to insert into a new location within genome
A
Transposons
18
Q
The study of changes in organisms caused by modification of gene expression rather than alteration of genetic code itself
A
Epigenetics
19
Q
How many ways can genome duplication occur?
A
Three
20
Q
Chromosomes fail to segregate properly leading to abnormally diploid gametes that fuse to form an allotetraploid plant
A
Meiosis effect
21
Q
Recombination resulting in a gene being separated from its promoter (inactivation) or a gene being placed next to a new promoter (alters gene expression patter)
A
Intramolecular recombination
22
Q
2 classes of transposons
A
Retrotransposons, and DNA transposons
23
Q
The enzyme which synthesizes a DNA copy of a transposon from RNA
A
Reverse transcriptase
24
Q
The enzyme that excises and inserts transposon from DNA into a new place in the genome
A
Transposase
25
What happens when a transposon is inserted into the coding region of a gene?
Gene inactivation, protein aborted or functions poorly
26
What happens when a transposon is inserted near the coding region of a gene?
Gene inactivation by disrupting promoter-gene relationship, altered gene expression due to promoters on transposon
27
Which type of chromatin makes up 10% of genomic DNA, is in a closed state, with methylated and tightly packed histones, and is transcriptionally inactive?
Heterochromatin
28
Which type of chromatin makes up 90% of genomic DNA?
Euchromatin
29
Which type of euchromatin is transcriptionally inactive?
Euchromatin in intermediate state
30
Which type of euchromatin is transciptionally active?
Euchromatin in open state
31
Histone modification associated with gene activation
Acetylation
32
Histone modification associated with gene inactivation
Methylation
33
Enzymes that remove acetate from H3 and H4 lysines
Histone deacetylase
34
Enzymes that transfer acetate from acetyl-CoA to H3 and H4 lysines
Histone acetyltransferases (HATs)
35
Enzyme that adds CH3 group to H3 lysines
Histone methyltransferases (HMTs)
36
Enzyme that removes CH3 groups from H3 lysines
Histone demethylases
37
Enzyme that removes methylated cytosine
Glycosylase
38
Enzyme that adds methyl group to cytosine bases at C5 position
DNA methyltransferase
39
What is it called when the phenotype of 1 parent is always expressed in progeny of successive generations regardless of genetic contribution of the other parent?
Parental imprinting
40
What does the ddm1 mutant refer to?
Mutant with a decrease in dna methylation
41
At which end is the initiation site located?
5' end
42
RNA polymerase acts ___ to ___ on template strand.
3', 5'
43
Nascent RNA chain elongates ___ to ___.
5', 3'
44
The region of DNA that is not transcribed into RNA and controls transcription of transcribed region by regulating assembly of transcription initiation complex (TIC) at TATA box
Promoter regions
45
A primer is not required to initiate the synthesis of RNA. T or F ?
True
46
Where do nuclear RNAPs bind to initiate the synthesis of RNA?
To the promoter on the TATA box
47
What is the transcription initiation complex composed of ?
RNAPII and 7 TFs
48
What are the 5 TFs common to all 3 RNAPs ?
TFIIB, TFIIE, TFIIF, TFIIG, and TFIIH
49
Where is the TATA box located in comparison to the transcription start site (how many bps away, upstream or downstream) ?
About 25 bp upstream
50
What is the TFIID complex composed of?
1 TBP (TATA-box binding protein) and 8 TAFs (TATA-box additional protein factors)
51
What does TFIIA do?
Binds to TFIID complex and releases inhibitor from complex
52
What does TFIIF do?
Binds to RNAPII
53
What do TFIIE, TFIIH, and TFIIJ do?
Position RNAPII at start site
54
What does TFIIH do?
Phosphorylates RNAPII
55
Regulatory elements that control transcription of a gene
cis elements
56
Proteins (often dimers) that bind to cis elements
Trans-acting factors (aka transcription factors)
57
pgs 53
-56 for methods to study cis-trans interactions
58
Key structural features of helix-turn-helix TF motif
2 alpha helices separated by a turn, function as dimers
59
Key structural features of helix-loop-helix TF motif
Short helix connected to longer helix by loop, function as dimers
60
Key structural features of zinc finger TF motif
Various structures coordinated by Zn, function as monomer or dimers
61
Key structural features of leucine zipper TF motif
Alpha helix of 35 AA; every 7th AA= Leu, dimerizes along hydrophobic surface
62
Key structural features of basic zipper TF motif (most common among plants)
Variation of Leu Zipper with other hydrophobic AAs in place of Leu, dimerizes along hydrophobic surface
63
How many RNAPs do plastids contain ?
2; E.coli RNAP and Bacteriophage-like RNAP
64
What subunits is the E.coli type RNAP made of ?
4 subunits: 2 alpha, beta prime and beta;
| 1 regulatory unit: sigma
65
Where are the core subunits encoded?
in the plastid genome
66
Where is the regulatory subunit encoded?
in the nucleus genome
67
Where is bacteriophage-like RNAP encoded?
in the nucleus
68
Clusters of 2 or more genes transcribed by RNAP from single promoter
Polycistronic transcription units (PTUs)
69
Plastids adjust number of active promoters depending on stimuli. T or F?
True
70
What is the function of the 5'-cap (m7Gppp)?
Required for exit from the nucleus, increases efficiency of translation initiation (ribosome loading), and protects against degradation prior to translation
71
Addition of 5'-cap is done by....
Addition of guanosine to nascent mRNA, then methylation of guanosine at position N7
72
What is the function of polyadenylation ?
Protects against exo-RNase degradation prior to translation, role in initiation of translation
73
Addition of poly-A tail is done by...
a signal sequence in 3'-UTR (AAUAAA), downstream sequence cleaved by endonuclease, 20-250 adenosines added to 3--end by poly-A polymerase),
74
What is the function of RNA splicing ?
Removal of introns from pre-mRNAs and pre-tRNAs , the release of rRNAs from pre-rRNAs
75
Where are introns located ?
In nuclear genes, chloroplast genes, and mitochondria genes
76
How are introns classified?
By structural features and splicing mechanism
77
What are the splice sites for pre-mRNA introns?
5' splice site (donor site): 5'-GU
| 3' splice site (acceptor site): 3'-AG
78
Where does the branch site structural element bind?
To the 5'-end of intron during excision (about 40 nt from 3' splice site)
79
spliceosome assembly
slide 82
80
initiation of splicing
slide 83
81
completion of splicing
slide 84
82
How do self-splicing introns that form ribozymes work?
Guanosine cofactor attacks 5' splice site, cleavage of 3' splice site, ligation of exons
83
initiation of self-splicing
slide 87-88
84
What functional enzyme do mobile introns contain ?
DNA endonuclease
85
What function do DNA nucleases serve in mobile introns?
Recognize intron-less allele, generate double-strand break near insertion or "homing" site, initiate replicative integration of intron
86
Which group of self-splicing introns have features in common with nuclear pre-mRNA splicing?
Group II
87
What is the difference between Group II self-splicing introns and pre-mRNA splicing?
Group II intron does not form spliceosome
88
Where are Group III self-splicng introns found?
in Euglenoid plastids
89
Are most mitochondrial mRNAs transcribed as monocistronic units or polycistronic units?
Monicistronic
90
5'-end of nuclear mRNA?
5'-cap (m7Gppp)
91
5'-end of chloroplast mRNA?
5'-monophosphate
92
5'-end of mitochondria mRNA?
5'-triphosphate
93
3'-end of nuclear mRNA?
Poly-A tail (-AAAA)
94
3'-end of chloroplast mRNA?
Stem-loop structure
95
3'-end of mitochondria mRNA?
Stem-loop structure
96
What are the precursor sections for nuclear rRNA processing ?
17S, 5.8S, and 25S
97
Which precursor sections H-bond after spacer sequence is removed?
5.8S and 25S
98
Which section of nuclear rRNA is unusual compared to other rRNAs and why?
5S, its transcription is independent of other rRNA genes, requires no processing
99
What is present in most tRNA genes?
introns
100
What are tRNAs encoded by ?
gene clusters
101
How many tRNAs are present in plastids?
30
102
How many tRNAs are present in mitochondria?
16
103
Which organelles have/don't have sufficient tRNA for protein synthesis?
Plastids do, Mitochondria don't
104
What is the minimum requirement for protein synthesis with wobble codons?
23 tRNAs
105
What are the 2 RNA editing mechanisms?
Insertion/deletion and Conversion (modifications, substitution)
106
Purpose for amino acid conversions?
Often to restore highly conserved protein
107
Purpose for ORF conversions?
Can shorten open reading frames, may form new start or stop codons
108
Requirements for mRNA translocation ?
5'-cap
poly-A tail
introns removed
109
Requirements for rRNA translocation ?
PTU cleavage
| introns removed
110
Requirements for tRNA translocation ?
PTU cleavage
| introns removed
111
What are the requirements for gene silencing?
dsRNA, Dicer, RISC (RNA induced silencing complex)
112
What does the dicer do?
cleaves dsRNA into short or small interfering RNAs (siRNAs)
113
Biological roles for post-transcriptional gene silencing
Protection, development , Experimental utility
114
Multiple ribosomes simultaneously translating 1 mRNA
Polyribosomes
115
Requirements for protein synthesis
mRNA, ribosomes, protein cofactors, enzymes, inorganic ions, GTP, tRNAs, and amino acids
116
A site:
aminoacyl-tRNA
117
P site:
peptidyl-tRNA
118
E site:
uncharged tRNA exiting ribosome
119
What enzyme catalyzes the charging of tRNAs ?
tRNA synthetase
120
Components required for initiation?
mRNA, charged tRNA(fmet), small ribosomal subunit, large ribosomal subunit, initiation factors (proteins), GTP
121
A ribosomal binding site in mRNA, generally located around 8 bases upstream of start codon AUG. Initiates protein synthesis by aligning the ribosome with the start codon.
Shine-Dalgarno sequence
122
What does IF3 do?
Binds 30S ribosomal subunit
123
What does IF2 do?
Binds GTP, then binds to 30S ribosomal subunit at the P-site
124
What does IF1 do?
Binds charged tRNA and deliver tRNA to IF2 bound to 30S subunit
125
What is the enzyme that catalyzes polypeptide elongation?
Peptidyltransferase
126
How is the peptide bond formed ?
Dehydration, condensation reaction
127
What activity do intervening protein sequences have?
endonuclease activity
