Gene Expression Flashcards
0
Q
DNA to RNA
A
Transcription
1
Q
DNA for the synthesis of another identical DNA.
A
Replication
2
Q
RNA to protein or AA
A
Translation
3
Q
RNA to DNA because of retro virus
A
Reverse transcription
4
Q
Largely dictates the physical observable characteristic of an organism which is known as phenotype
A
Genotype
5
Q
Characteristic of an organism
A
Phenotype
6
Q
Refers to a change in the DNA
A
Mutation
7
Q
Result from different kinds of mutation
A
Disease
8
Q
DNA structure
A
Double helix
2 anti parallel strand
9
Q
Bond that keeps the 2 anti parallel strands together
A
H bond
10
Q
Stacked at the center of the DNA
A
Base
11
Q
Back bone of DNA
A
Sugar and phosphate
12
Q
3 form of DNA
A
B
A
Z
13
Q
Tall and slender
It is where enzymes will attach during replication and transcription
Right handed
A
B form
14
Q
Form seen in a solution with higher salt concentration or with alcohol added
Short and stout
A
A form
15
Q
Longer than B form
Seem to zigzag
A
Z form
16
Q
A molecule made up of repeating sub units
A
Polymer nucleotides
17
Q
Nucleotides linked by
A
Phophodiester bond
18
Q
Each nucleotide is made up of?
A
Bases
Deoxyribose
Phosphate
19
Q
H bonded with each other
Attached to the sugar
A
Bases
20
Q
Attached to the PO4
A
Deoxyribose
21
Q
Sugar
Has 5 carbon
A
Deoxyribose
22
Q
Used to distinguish it from the carbons of the base
A
Primes
23
Q
Attachment of bases by glycosidic bond
A
C1
24
Contains a hydroxyl functional group 3' ends
C3
25
Contains hydroxyl group
Called the 5' end of the sugar
Always contain a PO4
C5
26
Mitochondria
| Prokaryotic DNA bacteria
Closed circular
27
Eukaryotic DNA
Linear
28
Linear DNA ends are referred to as
Telomeres
29
Telomeres shorten after each round of
Replication
30
Linker part of the DNA
Linker histone
31
Associates with the linker part of the DNA
H1
32
Will form the octameric core
H2A
33
Nucleosome
H4
34
Size of DNA that wounds around Histone
150 bp
35
Size of linker DNA
50bp
36
DNA that is further compacted
Nucleosome
37
Is the nucleosome
30 nm fiber
38
30 nm fiber will be packaged into a lampbush or test tube brush appearance
700 nm scaffold
39
Packaging ratio during interphase
1000
40
Packaging ratio during mitosis
10,000
41
The lampbrush in turn will be packaged into a
Chromosome
42
Central part of the chromosome
Centromere
43
Ends of linear chromosome
Telomere
44
1 chromosome =
1 DNA molecule
45
In the nucleus of human cell, it contains how many molecules of DNA
46
46
Refers to all the DNA present in human cell
Genome
47
DNA present in the nucleus
Nuclear genome
48
DNA present in the mitochondria
Mitochondrial genome
49
Portion of the nuclear DNA that can be potentially transcribed into RNA
Gene sequences 30%
50
The remaining 70% of nuclear genome do not code for anything. They are just there as
Spacers
51
Gene sequences 30%
10 % codes for protein
| 90% codes for RNA
52
Apparent when the chromosome is stained
Extragenic DNA
53
Usually contain active genes
| Referred as euchromatin
Light staining areas
54
Usually contain junk DNA
| Referred as heterochromatin
Dark staining areas
55
DNA polymerization proceeds in
5' to3' direction
56
DNA polymerization, complementary DNA acts as
Template
57
DNA polymerization, acts as co factor
Magnesium
58
Enzyme that catalyze the synthesis of phosphodiester bond
DNA polymerase
59
It will determine the sequence of the new strand
Template
60
Bond formation between P and OH and cleavage of the diphosphate
Nucleophillic attack
61
The oxygen would launch a nucleophillic attack as a result there is formation of
Phosphodiester bond
62
Why do we say that the DNA grows in the 5' to 3' direction?
You can always add only in the 3' end
63
Synthesize primers?
Primase
64
To provide 3'OH to initiate DNA synthesis
Primers
65
Without primers
DNA polymerase cant start its activity
66
Responsible for removal of primers
| Take over DNAsynthesis by inserting 5' to 3' polymerase function
DNA polymerase 1
67
Utilizes energy from ATP
| Synthesize a phosphodiesterbond to make it a one continous strand without breaks
Ligase
136
Unwinding and primer formation
Initiation
137
Formation of daughter DNA strands
Elongation
138
Will separate the 2 strands
Helicase
139
Keeps the 2 strand apart from each other
Single strand binding protein
140
Primary responsible for the synthesis of leading strand
DNA polymerase 3
141
Synthesis of leading strand
Requires primers
5'to3' direction
Synthesis is continous
DNA grows towards the direction of the replication pork
142
Synthesis of the lagging strand
Requires multiple primers
5' to 3'
Discontinuous resulting to the formation of okazaki fragments
DNA goes away from the replication fork
143
Enzyme responsible for initial synthesis of the okazaki fragment
DNA polymerase 3
144
Remove primers
DNA polymerase 1
145
Connect adjacent okazaki fragments after the primers have been taken out
Ligase
146
Mechanism that make sure that the replication porks meet at the other end simultaneously
Termination utilization substance
147
Difference between eukaryotic and prokaryotic DNA replication
Prokaryotic- single origin
- DNA polymerase 2 creates both strands
- supercoiling
Eukaryotic- multiple origin
- DNA polymerase alpha for leading strand and delta for lagging strand
- supercoiling and telomere shortening
148
Problem associated primarily with prokaryotic replication
Supercoiling
149
Solution for supercoiling
Topoisomerase
150
Problem associated with linear DNA replication
Telomere shortening
| Because there is no 3' for OH no attachment site
151
Solution for telomere shortening
Telomerase
152
How do we solved that 3 overhand
T loop, dahil sa telomerase
153
It synthesize DNA utilizing an RNA template
hTRT human telomerase
154
New strand is longer than the original one. Extra sequences have been introduced.
Replication slippage example huntingtons disease
155
Change in nucleotide sequence
Mutation by UV light
156
Happens on the 3rd base of the codon
Usually codes for the same amino acid
Least dangerous
Silent mutation
157
Change in the base, change in the amino acid
Missense mutation
| Sickle cell anemia
158
Amino acids become stop codon
Nonsense mutation
| Most severe
159
Opposite of nonsense mutation
| Stop codon to an amino acid
Readthrough mutation
160
Type of mutation
Substitution
Deletion
Insertion
161
A deletion mutation can result to frameshift with removal of
1,2 or 4 amino acids
No frameshift if the removal of 3 bases or any multiples of 3
162
Consequences of mutation
Disease
Silent- if mutation happen in the spacer DNA
Evolution
163
DNA repair system
Base excision
Nucleotide excision
Mismatch repair
164
Damage base
AP site
165
Recognize AP site and remove its base
DNA glycosylase
166
Removes AP site and neighboring nucleotides
AP endonuclease
167
Involved in removing damaged nucleotides
UvrA
UvrB
UvrC
168
Mismatch repair is very expensive. Enzyme involve
Helicase 2
SSB protein
DNa polymerase 3
Ligase
169
Synthesis of RNA utilizing DNA as the template
Transcription
170
Not all forms of DNA can be transcribed, only certain stretches and this called
Gene
171
Enzyme used in transcription
RNA polymerase
172
Synthesis of RNA 3 major steps
Initiation
Elongation
Termination
173
Works to inhibit the RNA polymerase
Rifampisin
174
Initial binding site for RNA polymerase
Promoter region
175
Parts of the gene that being transcribed
Promoter region
Informative sequence
Terminator sequence
176
Other name for promoter region
Tata box
Pribnow box
GC box
Hogness box
177
This is the actual transcription site, ito talaga yung itatranscribe
Informative region
178
2 strand from DNA
Template
| Coding strand
179
When the RNA polymerase has reached this region of the gene, transcription has to end
Terminator sequence
180
Allows hairpin loop formation on mRNA
GC rich region
181
RNA polymerase with sigma factor locate promoter region
Closed promoter complex
182
RNA polymerase will also act as helicase, the 2 strand separated is now called
Open promoter complex
183
When RNA polymerase locate the first base it will now
Start synthesize RNA
184
While the polymerase unwinds the DNA, after the DNA has been used as template, there is an
Automatic rewinding
185
In the RNA, the sequence will be CG,CG,CG which has what is known as
Self complimentarity
186
Remember, in the terminator sequence, the sequence is
GC,GC,GC
187
There will be hair pin loop formation
Poly A for DNA
| Poly U for RNA
188
Alternative ending, a protein which comes in and separates the RNA from DNA template
Rho Factor
189
Transcription in eukaryote
3 types of RNA polymerase
Not just promoter region
RNA Is not ready for use
Transcription and translation not coupled together
190
Eukaryotic transcription
Code for RNA and protein as well
These are sequence that are transcribe and translate
Exons
191
Eukaryotic transcription
Code for RNA but do not code for protein.
Transcribe but not translate
Introns
192
Eukaryotic transcription
Types of RNA polymerase
RNAP 1,2,3
193
Eukaryotic transcription
Transcribe all ribosomal RNA with the exception of 5S
RNAP 1
194
Eukaryotic transcription
Transcribes mRNA
RNAP 2
195
Eukaryotic transcription
Transcribe tRNA including 5S
RNAP 3
196
This will render the gene silent and cannot be expressed
Methylation of CpG islands
197
Example of how activators and repressors work together to control expression of the lactase gene
Lac operon
198
DNA is released so that it is not anymore lightly packed
Acetylation of nucleosome
199
Smallest
Adaptor molecule
T loop
tRNA
200
Complimentary to the codon in mRNA
Anti codon loop
201
Where amino acids are artached
Acceptor arm
202
Largest
Most abundant
Found in ribosome
Ginger like
rRNA
203
Has P site, A site and mRNA bunding site
Small ribosomal sub unit
204
The one where it has the enzyme peptidyl tranferase
Large ribosomal sub unit
205
tRNA
RNA
AA
P site
M ribosomal binding site
A site
206
The synthesis of protein utilizing as mRNA as template
| Begins at the start codon and ends when the stop codon reached
Translation
207
Template that determines the sequence of the amino acids
mRNA
208
The one that brings the amino acid there
tRNA
209
It is where it will all.
| It is ribosomes catalyzes peptide bond formation
rRNA
