Biochemistry Flashcards
1
Q
Requirements of DNA replication?
A
-tamplet old ssdna
-primer RNA
-protiens
dna a
Ssbinding protien
Dna helicase
Topoisomerase
-enzymes
Primase
DNA polymerase in euck alpha beta gama delta ë
DNA polymerase in pro 1 2 3
-substrate
Deoxynucleoside triphosphate
2
Q
Steps or replication of Dna synthesis?
A
- separate two strands by DnaA the comes SSB protien the comes the helicase
- synthesis of Rna primer
- synthesis of new DNA
- removal of rna primers and replace it with DNA
3
Q
Whats the difference between RNA , DNA polymerase?
A
Rna-starts from zero
Dna-not from zero needs the primer rna
4
Q
The unwinding of DNA in prokaryotes and eukaryotes sites?and why?
A
- Pro-at single site called origin of replication
- Euk-at multiple sites for rapid replication of long Dna many origin of replication (replicators)
5
Q
How much base the E.coli genoum have? How much does it take to replicate all of it?
A
- 6x10(6)
- 40min
6
Q
DNA polymerase in Prokaryotes goes in a speed of?
A
1000 base in a second
7
Q
The entire human genome is replicated in?
A
8h
8
Q
Formation of replication fork?
A
After the unwinding of Dna it form v shaped ative site for the synthesis
-it moves through the whole dna during synthesis
9
Q
Neck in the replication form means? And gap?
A
Neck:two nucleotides not connected with a bond
Gab: there is no nucleotide(space)
10
Q
Whats the Dna A and its function? And formed of?where it starts?
A
Makes the first separation in DNA bind to nucleotides sequences AT rich regions
- 20to50 monomers
- needs Atp
11
Q
Whats the SSB protien?function?mechanism of its binding?
A
- Binds to the single strand after it’s separate
- bind one of them followed by the rest of them
- protect the ssdna from nuclease
12
Q
Whats the helicase?where is it binded?from where it begins?
A
It binds to the ssdna near the replication fork and pass to the neighbors to dustruct the bonds and unwind the dna
-needs Atp
13
Q
If the helicase in the upper strand means?
A
The synthesis is in the lower strand
14
Q
Whats the Dna topoisomerase?
A
Remove the supercoils during the unwinding of dna and makes swivels between the seperated and not separated strands
15
Q
Types of topoisomerase and thier charecters?
A
Topo1:cut one strand
-No Atp required its uses the energy from cleavage of diester bond to resael the strand
-it have nuclease and ligas activities
-relax -ve super coils in E.coli and -ve or +ve in eukaryotes
Topi2:cut two strands
-need atp
-Dna gyrs topo 2 of bacteria relax -ve supercoil to circular Dna by Atp hydrolysis
16
Q
Leading strands? Lagging?
A
- coppied in direct of the advancing replication fork synthesized continuously
- coppied in the direction away from replication fork synthesized discontinuously
17
Q
Whats the okazaki fragments?
A
Fragments of Dna seperated by primer RNA which form lagging strand
18
Q
Whats the primase?what does it make?
A
Specific Rna polymerase enzyme from Rna primer
-makes hybrid duplux of Dna temple and Rna temple
19
Q
DNA polymerase 1 composition ? Where it works?its function?and activity?
A
Have 1 polypeptide
-remove rna primers and replace it with Dna
-heve 3-5 exo nuclease for hydrolysis of base mismatch (one nucleotide)
-have 5-3 exonuclease for removal of rna primers “excision”
-have proofreading function
•in lagging strands)
20
Q
DNA polymerase 2?
A
- Repair the newly synthesized dna
- doesn’t involve in the replication process
- have proofreading fucntion3-5 exonuclease
- no exision activity
21
Q
What the deficiency of DNA polymerase 2 do?
A
no replication and no growth
22
Q
DNA polymerase 3?
A
Have 10 subunits
- The alpha subunit catalyst for bond formation between nucleotides
- the main enzyme in replication
- have proofreading function but not excsion function
- recognizes the Rna primers uses to dna synthesis
- needs Rna primer as acceptor for the first deoxynucleotide
23
Q
The new nucleotide binded by the polymerase 3 is linked to its neighbors nucleotide at?
A
OH from 3 end
24
Q
Whats Dna ligase?
A
- Seals the dna fragments in lagging strand
- Uses energy from Atp the. Transform it to Amp+pp(in eukaryotes)
- can form the phosphodiester bond by ATP in eukaryotes
25
The enzymes that act on the lagging strand?
Ligase, DNA polymerase 1,3
26
When the DNA replication accours?
Inthe S phase
27
What does bidirectional and semiconservative means?
Bi-goes both ways
| Semi- compoed of one old and one new strands of Dna
28
The origin of replication is at?
AT rich regions
29
The origin of replication in E.coli is called?
OriC
30
The bacteria replication can be ….. or ……
Unidirectional or bidirectional
31
At what phase of cell cycle the histone is formed?
G1
32
The DNA polymerase synthesized ….. to replication
Prior
33
Protiens required for dna replication?and what needs energy and whats not?
DnaA Atp
Ssb protien no atp
Helicase needs Atp
Topoisomerase 1 no atp 2 needs atp
34
Direction of dNa replication?
The enzymes reades from 3-5 end
| The synthesis is from 5-3 end
35
Whats the RNA primer?how much nucleotides?
Short segment of Rna (5-10 nucleotides ) initiat dna synthesis
36
Whats the main enzyme in Dna replication?
DNA polymerase 3
37
Whats the tertiary structure of dna? And its types
Dna winded around basic protiens (histones)
-ve supercoil the dna winded right handed
+ve .. ….. …. Left handed
38
What corrects the 3 end of histone gene MRna?
U7
39
What distroy the telomeres? And what fixes it?
- Nuclease
| - telomeras
40
The base composition of humanDNA is?
30%for both Adinin and thaymin
| 20% for both cytocin and Guanin
41
Whats the life spane of mRna?
1 houre
42
What type of RNA that inhibit the transcription?why?
MiRNA
| -where there’s no need for the protien its stop its synthesis process
43
Who’s responsible for the UV absorption in the DNA and why?
The nitrogen bases due to its aramatic composition
44
What are the types of DNA deoxyribonucleotides?
DGmp,Damp,Dcmp,Dtmp
45
Whats the unusual bases of tRna?
Thymine, dihydrouracil,pseudouridin
46
What the AuG codon for?
Methoinin
47
Does the base compostion of DNA changes?
No its doesn’t change with age or nutritional state or change in environment
48
Whats the chromatosome? And how much bases it pairs?
- Nucleosomes and H1
| - 200
49
How much does alpha and beta homoglubin have genes in dna?
Alpa: 4
Beta: 2
50
How many types of Trna?
60
51
Whats the sevberg unit and its value and what ut depends on?
- the rate of sedimentation of macromolecules in ultracentrifuge
- 10-13 second
- molecular weight,shape,density
52
Chromosome diameter?
7nm
53
At 5 end RNA is protected by? And the process called?the bond?
Cap: 7 methyl guanosin triphosphat
- caping
- 5-5 phosphotriester bond
54
Whats the function of MiRna?
Create a non coding RNA to regulate the gene expression
55
Whats the bond between DNA and histones?
Electrostatic bond
56
Whats the mRna?
Gene transcription from dna is due to mrna
| -quickly degraded
57
Whats spilicing and who’s responsible for it?
- Cuting the introns from the HnRna and leaving the exons
| - due to snRna
58
What does the DNaA form ?
-ve and positive (more) supercoil
59
The relaxing Dna called?and the complicated?
- Euchromatin
| - heterochromatin
60
Dna length is ?
2m
61
Whats the modification that happens to tRna after transcription?
- reduction by adding 2H to uracil in D arm
- methylation of uracil with methyle trasferase at the TûC arm
- form the pseudouridin by isomarase enzyme at the TûC arm
62
Why does DNA doesn’t undergoes with mutation?
Presence of Thaymin instead of uracil
63
How much chromosomes are in the dna?
26 pairs (46)
64
How is the DNA is stable?
Due to the absence of O in C2 of the sugar
| - decrease the hydrolysis of 3-5phosphodiester bond
65
What forms the Ribosomes and its sedimentation rate in humans?
rRna small 18s - larg 28s 5.8s 5s
Small subunit 40s
Larg subunit 60s
Together 80s
66
What connects the two double strands of DNA?
- Hydrogen bonds between the nitrogen baded
| - Hydrophobic vander waals between the staked bades
67
How is the DNA loosened from the Histones?
By acitylation of histones
68
Whats the DNA? And whats the bonds that links it?
Linear polymer of deoxyribonecleoside mono phosphate / covelant bond called 3-5phophodiester bond
69
Why the thymin is important for the cancellation of dna mutation
The C5 is in no way can be changed like in uracil
70
What separates the two strands of dna (protein)?
DnaA
71
Where the breackig of DNA accoures in replication ?
In weak places like between A,T due to the non covelant 2 hydrogen bonds
72
Where does the acceptor arm of tRna terminats?
On C,C,A
73
What causes the rethatosis?
The snRNA cut the wrong bases along with introns
74
Where the hydrogen bond is formed in DNA and where its doesn’t get formed?
Between the purin and pyramids only
- between two purins theres no space for it to be form
- between two pyramids its to far to it to be formed
75
How much bases in the nucleosomes?
146
76
Whats the half life of insulin?
6 mins (decrease half of the insulin per 6minuts)
77
Whats the DNA denaturation? And what happens to the bonds?
Separate of double helix by breaking the H bond between bases by heating or increas ph
-the phosphodiester bond is not broked
78
Whats the Tm and its value?
The point where half of the DNA helix is melted
| -90cْ
79
Histones have no tail to protect it but it have?
U7 of snRna
80
How is the dna and histones get attached?
Dna is -ve histones is +ve
81
The distance spance by one turnin DNA?
34Aْ
82
The distance between two bases in the strand of DNA is
3.4 Å
83
Whats the Renaturation of DNA?
Reasociation of two strands together Annealing
84
What are the bases at the 3 end of tRna?
C,c,A
85
The two strands of DNA are not identical but complimentary to each other due to?
Base pairing
86
Where does the hexokinase exist and how much exons it have?
Liver,pancreas,thyroid gland
| -10 exons
87
The sum of purin risidus equals
Sum of pyramids risidues A+T=G+C
88
Whats the quaternary structure of DNA?
-Combine DsDna with proteins(dnaA) and RNA(in transcription)
89
Where is the absorption of UV is the most in DNA?
In single stranded Dna in denature state
90
Whats the RNA and what links it?
Single strand ribopolynucleotides linked by 3-5phosphodiester bond
91
What are the types of RNA?
```
MRna
rRna
TRna
SnRna
MiRna
```
92
Whats the difference between the A,B,Z types of DNA?
```
A: right handed A:26 in diameter
B: right handed B:20 in diameter
Z:lift handed. Z:18 in diameter
——————————————————-
A:11 base pairing A:2.6 b/n bases
B:10.4. B:3.4
Z:12. Z:3.7
—————————————————-
A:C3 endo. A:Anti glycosidic bond
B:C2 endo. B: Anti
Z:c3 for purin. Z:anto for pyramids and
C2 for pyramids. Syn with purin
```
93
How much nucleotides the tRna have?
74-95
94
What gene that have no HnRna as a precursor for its MRna?
Gene for Histones synthesis
95
What are the parts of chromosomes?and which one have the genes?
- Centromeres in the center(no genes)
- Telomeres in the periphery (on its later part)
- two chromatides (sisters)
96
What the anticodon arm in tRna ?
Three base sequences that connect to Mrna in protein synthesis
97
How much genes in the DNA of nucleus?
20,000to30,000
98
What are the measurements of BDNA in nm?
3.4nm in each turn
2nm in diameter
0.34nm space between bases
99
What are the enzymes that loosen the DNA from Histones?
HAT [histon acetyletransferas]
| HDAC [histone deacetylase]
100
The supporting protein links the fibrils of selenoid to form?
Fiber
101
What forms the Ribosomes and its sedimentation rate in prockaryot?
Small unit 30s (16s rRna)
| Larg unit 50s (23s 5s rRna)
102
The increase of UV absorption in the single stranded dna is called?
Hyperchromicity of denaturation
103
Whats inside the double stranded DNa and out side?
Inside:hydrophobic Nitrogen base
| Outside (backbone):sugar and phosphate
104
How dow the bacteria protect its dna from viruses?
Methylation of adinin by endonuclease activity(restricted)
105
What are the nucleoprotiens?examples
Proteins + nucleic acid
- ribosomes
- chromosomes
106
What part of Histones is rich in lysin and which in arginin?
Lysin:h2a h2b
Arginine: h3 h4
107
Core of nucleosomes is?
Histones
108
The arms of tRna?
```
D arm
TçC (thymine,pseudouridin,cytosin)
Anti codon
Acceptor arm
Extra arm (long 20 bases-short 3 bases)
```
109
Diameter of nucleosomes?
10nm
| 5 for each histone
110
What are the sizes of major and minor grooves in double helix of DNA?
Major:1.2
Minor:0.6
111
Where does the RNA exist? %
Ribosomes and ER 50%
Cytoplasm 25%
Mitochondria 15%
Nucleus 10%
112
What shape of DNA in bacteria?
Closed circular
113
How many times dna winded around the histones and what does it form?
- two times
| - nucleosomes
114
At 3 end the RNA protected by? How much?and the enzyme called?
Tail:polyadinin
- 45-200 adinin
- adinin polymerase
115
Who’s responsible for the tailing of mRna?
U4 U6
116
Each histone is formed of
H1 H2A H2B H3 H4
117
Chromosomes formed of?primerly
Dna , histones, basic proteins+acidic proteins
118
How much mitochondrial dna synthesize protiens?
13 enzymes
119
Where is the DNA is located in the cell and its %?
Nucleus:99%
Mitochondria:1%
120
The maximum point of UV absorption in DNA is at
260 nm
121
How much nucleotides the SnRna have?
```
U1 165
U2 188
U3 216
U4 139
U5 118
U6 106
```
122
The bases of DNA summation is
A=T
| G=C
123
Whats the secondary structure of DNA and who discovered it?
Double helix
| -watson and crick
124
What rearrange the DNA after the work of DnaA!
- ve and +ve supercoil cancel each other
| - toboisomeras enzyme
125
What causes the tight coiling of DNA{enzyme}
HDAC Histones deacylation
126
During the replication what part of dna forms +ve super coil?
The open part that got opened by DnaA
127
The complementary base pairing in DNA is done by?
G=C by three H bonds
| A=T by two H bonds
128
The coiling of two DNA strands gives?
Minor and major groves as binding sites for the enzymes and regulatory protiens
129
What forms the selenoid ? And whats the selenoid diameter?
- 6 nucleosomes
| - 30nm
130
What part of RNA is rich in uracil?and its type
SnRNA
| -U1-U6
131
The selenoid is stablizes by
H1 histon
132
Whats forms the backbone and the inside of RNA?
Backbone:sugar and phosphate
Inside: C A G U
133
What shape of DNA presents in the eukaryotic cells mitochondria?
Circular
134
How many types are there in DNA and from where originate?
A,b,c,d,e right handed
z left handed
-formed by changing the humidity of DNA
135
The base pairing in each turn in double strand DNA is
10.4
136
The separation of DNA doubled helix do at what temperature?
And a melting temperature called Tm
137
What type of DNA exists in the Body?
Bdna
138
The DNA under the physiological conditions it forms?
Right handed double helix (BDNA)
139
Whats does DNaA needs to work?
ATP
140
The width of DNA double helix is?
20Å
141
Number of base pairing in the whole dna of the cell?
7x10(9)
142
The linkage of pseudouridin?
Insteat of C-N bond it’s bounded by C-C between phosphate and pentos
143
Whats the precursors of MRna?and what is formed of?
HnRNA(hetero nucleic RNA)
-formed of exons(coding part)entrons(non coding)
⬇️
Synthesis of proteins
144
How much of the dna genes is repeated?
30%
145
The two strands of DNA are arranged in
An anti parallel way and wind around each other in the same axis
146
What the telomerase responsible for?
Reverse transcription forms the DNA out of RNA
147
What is the primary structure of DNA?and where it starts and end?
The base sequence of polynucleotide strand
| -from5 end to 3 end
148
Whats the base pairing rule?
G pairs with C
| A pairs with T
149
What does the melting temperature Tm depend on and how?
On the base compostion of the strand
-with⬆️ G and C ⬆️Tm
With ⬆️A and T ⬇️Tm
150
Cutting in the wrong place by SnRna causes?
- Unfunctional protien
| - termination of the transcription process
151
The selenoids gathered to form ?
Fibril(chromatin)
152
What end of tRna bound to amino asids and with what bond?
- 3end
| - ester bond(covelant)
153
Enzymes that synthesis the lagging strand?
DNA polymerase 1 and 3
154
Enzymes that synthesis leading strand?
DNA polymerase 3 only
155
The bases of the DNA are found in form of?
Deoxyribonucleotide (tri)phosphate
156
How does the DNA polymerase 3 works?
It takes the bases with 3 phosphate and break two of them and keep one the store the energy from it and use it to conect the nucleotide to the one next to it
157
Whats the proofreading of DNA polymerase 1?
-goes from 3-5 to detect errors and break only one nucleotides
158
Whats the exonuclease function of DNA polymerase 1?
- Proofreading:3-5 one nucleotide
| - exonuclease:5-3 more than one nucleotide
159
Topoisomerase 2 have a name in bacteria?
Gyrasw
160
Topoisomerase 2 used for ?
Anticancer, Antibiotics
161
How many origin of replication in humans?whay?
Multiple origin
| -for rapid replication of the tall dna
162
Whats does the polarity of DNA means?
Have two ends 3 and 5 one end is phosphate while the other is sugar
163
How much of the dna id coding and how much is uncodding?
1-2% coding
| 99%non coding
164
How much of dna is repeated? And where does it exist?And how much base pairing it have?function?
30%
-in centromers or telomeres and randomly distributed
•5-500
-give the genetic print each one have its own repititive sequence
165
How is the Bent Dna is formed?
- due to the A-tracts od strand replaced by another base
- due to the collapse of the strand into a minor grove in A-tracts
- photochemical damage or mispairing
- due to anticancer agents like (cisplatin)
166
How the triple stranded Dna is formed?and what does it give? Named the bond?stability and why?
-fromed By forming a new H bond in between bases
-like Adinin connected to Two Thiymens
Or Guanine connected to two cytosin
(T-A-T)(C-G-C)
-by hoogesten bond
-not stable due to the negativity of its backbone leads to electrical repulsion
167
Four stranded DNa formed at? With what bond? Stability?what does it form?
- In areas rich in Guanine like telomeres
- forms structures called G quartets
- stable due to the cation in its middle K+
- hoogsten bond
168
How many strands the four stranded DNA formed of?
Only one but bent and coiled many times
169
The four stranded Dna form structures called?
-tetraplexus
170
What connects the G quartets in four stranded Dna?
Hoogsteen H bond
171
The prokaryotic chromosomes is associated with?
Histon-like baic protiens and RNA
172
Who’s responsible for the antibiotics resistance in the bacteria?
The plasmid
173
Who unwinds the Dna in replication in eukaryotes?and what protects the ssdna?
- Helicase
| - replication protien A(SSB protien)
174
Whats the units of DNA polymerase in eukaryotes?
- alpha: primase activity +Synthesis of DNA
- beta:repairs
- gama: for mitochondria
- delta: as 3 polymerase
- ebsi: repair
175
How does the delta DNA polymerase works in eukaryotes?
- it cant detect the DNA to strat the synthesis
- so it need protien called (prolifritve cell nuclear antigen) or clamp
- the protien also need another protien to work and its called(replication protien C) or clamp loader
176
Enzymes that removes RNA primer in replication in eukaryotes ?
- RNAas H
| - flapping endonuclease 1
177
Antibiotics works on topoisomerase 2?
- ciprofloxancin
- Nalidixic acid
- Novobiocin
178
Anticancers?
- etoposide
- adrianmycin
- Doxorubicin
- mercaptopurin
179
In photodamage in bent dna it formes? And if didn’t get corrected will cause?
Thiymen dimer , xeroderma pigmentosum
