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Midterm > Biochemistry > Flashcards

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

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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
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3
Q

Whats the difference between RNA , DNA polymerase?

A

Rna-starts from zero

Dna-not from zero needs the primer rna

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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)

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5
Q

How much base the E.coli genoum have? How much does it take to replicate all of it?

A
  1. 6x10(6)

- 40min

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6
Q

DNA polymerase in Prokaryotes goes in a speed of?

A

1000 base in a second

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7
Q

The entire human genome is replicated in?

A

8h

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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

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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)

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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
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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
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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

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13
Q

If the helicase in the upper strand means?

A

The synthesis is in the lower strand

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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

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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

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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
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17
Q

Whats the okazaki fragments?

A

Fragments of Dna seperated by primer RNA which form lagging strand

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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

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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)

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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
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21
Q

What the deficiency of DNA polymerase 2 do?

A

no replication and no growth

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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
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23
Q

The new nucleotide binded by the polymerase 3 is linked to its neighbors nucleotide at?

A

OH from 3 end

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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
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25
Q

The enzymes that act on the lagging strand?

A

Ligase, DNA polymerase 1,3

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26
Q

When the DNA replication accours?

A

Inthe S phase

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27
Q

What does bidirectional and semiconservative means?

A

Bi-goes both ways

Semi- compoed of one old and one new strands of Dna

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28
Q

The origin of replication is at?

A

AT rich regions

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29
Q

The origin of replication in E.coli is called?

A

OriC

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30
Q

The bacteria replication can be ….. or ……

A

Unidirectional or bidirectional

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31
Q

At what phase of cell cycle the histone is formed?

A

G1

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32
Q

The DNA polymerase synthesized ….. to replication

A

Prior

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33
Q

Protiens required for dna replication?and what needs energy and whats not?

A

DnaA Atp
Ssb protien no atp
Helicase needs Atp
Topoisomerase 1 no atp 2 needs atp

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34
Q

Direction of dNa replication?

A

The enzymes reades from 3-5 end

The synthesis is from 5-3 end

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35
Q

Whats the RNA primer?how much nucleotides?

A

Short segment of Rna (5-10 nucleotides ) initiat dna synthesis

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36
Q

Whats the main enzyme in Dna replication?

A

DNA polymerase 3

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37
Q

Whats the tertiary structure of dna? And its types

A

Dna winded around basic protiens (histones)
-ve supercoil the dna winded right handed
+ve .. ….. …. Left handed

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38
Q

What corrects the 3 end of histone gene MRna?

A

U7

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39
Q

What distroy the telomeres? And what fixes it?

A
  • Nuclease

- telomeras

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40
Q

The base composition of humanDNA is?

A

30%for both Adinin and thaymin

20% for both cytocin and Guanin

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41
Q

Whats the life spane of mRna?

A

1 houre

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42
Q

What type of RNA that inhibit the transcription?why?

A

MiRNA

-where there’s no need for the protien its stop its synthesis process

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43
Q

Who’s responsible for the UV absorption in the DNA and why?

A

The nitrogen bases due to its aramatic composition

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44
Q

What are the types of DNA deoxyribonucleotides?

A

DGmp,Damp,Dcmp,Dtmp

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45
Q

Whats the unusual bases of tRna?

A

Thymine, dihydrouracil,pseudouridin

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46
Q

What the AuG codon for?

A

Methoinin

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47
Q

Does the base compostion of DNA changes?

A

No its doesn’t change with age or nutritional state or change in environment

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48
Q

Whats the chromatosome? And how much bases it pairs?

A
  • Nucleosomes and H1

- 200

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49
Q

How much does alpha and beta homoglubin have genes in dna?

A

Alpa: 4
Beta: 2

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50
Q

How many types of Trna?

A

60

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51
Q

Whats the sevberg unit and its value and what ut depends on?

A
  • the rate of sedimentation of macromolecules in ultracentrifuge
  • 10-13 second
  • molecular weight,shape,density
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52
Q

Chromosome diameter?

A

7nm

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53
Q

At 5 end RNA is protected by? And the process called?the bond?

A

Cap: 7 methyl guanosin triphosphat

  • caping
  • 5-5 phosphotriester bond
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54
Q

Whats the function of MiRna?

A

Create a non coding RNA to regulate the gene expression

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55
Q

Whats the bond between DNA and histones?

A

Electrostatic bond

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56
Q

Whats the mRna?

A

Gene transcription from dna is due to mrna

-quickly degraded

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57
Q

Whats spilicing and who’s responsible for it?

A
  • Cuting the introns from the HnRna and leaving the exons

- due to snRna

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58
Q

What does the DNaA form ?

A

-ve and positive (more) supercoil

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59
Q

The relaxing Dna called?and the complicated?

A
  • Euchromatin

- heterochromatin

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60
Q

Dna length is ?

A

2m

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61
Q

Whats the modification that happens to tRna after transcription?

A
  • 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
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62
Q

Why does DNA doesn’t undergoes with mutation?

A

Presence of Thaymin instead of uracil

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63
Q

How much chromosomes are in the dna?

A

26 pairs (46)

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64
Q

How is the DNA is stable?

A

Due to the absence of O in C2 of the sugar

- decrease the hydrolysis of 3-5phosphodiester bond

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65
Q

What forms the Ribosomes and its sedimentation rate in humans?

A

rRna small 18s - larg 28s 5.8s 5s
Small subunit 40s
Larg subunit 60s
Together 80s

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66
Q

What connects the two double strands of DNA?

A
  • Hydrogen bonds between the nitrogen baded

- Hydrophobic vander waals between the staked bades

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67
Q

How is the DNA loosened from the Histones?

A

By acitylation of histones

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68
Q

Whats the DNA? And whats the bonds that links it?

A

Linear polymer of deoxyribonecleoside mono phosphate / covelant bond called 3-5phophodiester bond

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69
Q

Why the thymin is important for the cancellation of dna mutation

A

The C5 is in no way can be changed like in uracil

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70
Q

What separates the two strands of dna (protein)?

A

DnaA

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71
Q

Where the breackig of DNA accoures in replication ?

A

In weak places like between A,T due to the non covelant 2 hydrogen bonds

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72
Q

Where does the acceptor arm of tRna terminats?

A

On C,C,A

73
Q

What causes the rethatosis?

A

The snRNA cut the wrong bases along with introns

74
Q

Where the hydrogen bond is formed in DNA and where its doesn’t get formed?

A

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
Q

How much bases in the nucleosomes?

A

146

76
Q

Whats the half life of insulin?

A

6 mins (decrease half of the insulin per 6minuts)

77
Q

Whats the DNA denaturation? And what happens to the bonds?

A

Separate of double helix by breaking the H bond between bases by heating or increas ph
-the phosphodiester bond is not broked

78
Q

Whats the Tm and its value?

A

The point where half of the DNA helix is melted

-90cْ

79
Q

Histones have no tail to protect it but it have?

A

U7 of snRna

80
Q

How is the dna and histones get attached?

A

Dna is -ve histones is +ve

81
Q

The distance spance by one turnin DNA?

A

34Aْ

82
Q

The distance between two bases in the strand of DNA is

A

3.4 Å

83
Q

Whats the Renaturation of DNA?

A

Reasociation of two strands together Annealing

84
Q

What are the bases at the 3 end of tRna?

A

C,c,A

85
Q

The two strands of DNA are not identical but complimentary to each other due to?

A

Base pairing

86
Q

Where does the hexokinase exist and how much exons it have?

A

Liver,pancreas,thyroid gland

-10 exons

87
Q

The sum of purin risidus equals

A

Sum of pyramids risidues A+T=G+C

88
Q

Whats the quaternary structure of DNA?

A

-Combine DsDna with proteins(dnaA) and RNA(in transcription)

89
Q

Where is the absorption of UV is the most in DNA?

A

In single stranded Dna in denature state

90
Q

Whats the RNA and what links it?

A

Single strand ribopolynucleotides linked by 3-5phosphodiester bond

91
Q

What are the types of RNA?

A 
MRna
rRna
TRna
SnRna
MiRna
92
Q

Whats the difference between the A,B,Z types of DNA?

A 
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
Q

How much nucleotides the tRna have?

A

74-95

94
Q

What gene that have no HnRna as a precursor for its MRna?

A

Gene for Histones synthesis

95
Q

What are the parts of chromosomes?and which one have the genes?

A
  • Centromeres in the center(no genes)
  • Telomeres in the periphery (on its later part)
  • two chromatides (sisters)
96
Q

What the anticodon arm in tRna ?

A

Three base sequences that connect to Mrna in protein synthesis

97
Q

How much genes in the DNA of nucleus?

A

20,000to30,000

98
Q

What are the measurements of BDNA in nm?

A

3.4nm in each turn
2nm in diameter
0.34nm space between bases

99
Q

What are the enzymes that loosen the DNA from Histones?

A

HAT [histon acetyletransferas]

HDAC [histone deacetylase]

100
Q

The supporting protein links the fibrils of selenoid to form?

A

Fiber

101
Q

What forms the Ribosomes and its sedimentation rate in prockaryot?

A

Small unit 30s (16s rRna)

Larg unit 50s (23s 5s rRna)

102
Q

The increase of UV absorption in the single stranded dna is called?

A

Hyperchromicity of denaturation

103
Q

Whats inside the double stranded DNa and out side?

A

Inside:hydrophobic Nitrogen base

Outside (backbone):sugar and phosphate

104
Q

How dow the bacteria protect its dna from viruses?

A

Methylation of adinin by endonuclease activity(restricted)

105
Q

What are the nucleoprotiens?examples

A

Proteins + nucleic acid

  • ribosomes
  • chromosomes
106
Q

What part of Histones is rich in lysin and which in arginin?

A

Lysin:h2a h2b
Arginine: h3 h4

107
Q

Core of nucleosomes is?

A

Histones

108
Q

The arms of tRna?

A 
D arm
TçC (thymine,pseudouridin,cytosin)
Anti codon
Acceptor arm
Extra arm (long 20 bases-short 3 bases)
109
Q

Diameter of nucleosomes?

A

10nm

5 for each histone

110
Q

What are the sizes of major and minor grooves in double helix of DNA?

A

Major:1.2
Minor:0.6

111
Q

Where does the RNA exist? %

A

Ribosomes and ER 50%
Cytoplasm 25%
Mitochondria 15%
Nucleus 10%

112
Q

What shape of DNA in bacteria?

A

Closed circular

113
Q

How many times dna winded around the histones and what does it form?

A
  • two times

- nucleosomes

114
Q

At 3 end the RNA protected by? How much?and the enzyme called?

A

Tail:polyadinin

  • 45-200 adinin
  • adinin polymerase
115
Q

Who’s responsible for the tailing of mRna?

A

U4 U6

116
Q

Each histone is formed of

A

H1 H2A H2B H3 H4

117
Q

Chromosomes formed of?primerly

A

Dna , histones, basic proteins+acidic proteins

118
Q

How much mitochondrial dna synthesize protiens?

A

13 enzymes

119
Q

Where is the DNA is located in the cell and its %?

A

Nucleus:99%
Mitochondria:1%

120
Q

The maximum point of UV absorption in DNA is at

A

260 nm

121
Q

How much nucleotides the SnRna have?

A 
U1 165
U2 188
U3 216
U4 139
U5 118
U6 106
122
Q

The bases of DNA summation is

A

A=T

G=C

123
Q

Whats the secondary structure of DNA and who discovered it?

A

Double helix

-watson and crick

124
Q

What rearrange the DNA after the work of DnaA!

A
  • ve and +ve supercoil cancel each other

- toboisomeras enzyme

125
Q

What causes the tight coiling of DNA{enzyme}

A

HDAC Histones deacylation

126
Q

During the replication what part of dna forms +ve super coil?

A

The open part that got opened by DnaA

127
Q

The complementary base pairing in DNA is done by?

A

G=C by three H bonds

A=T by two H bonds

128
Q

The coiling of two DNA strands gives?

A

Minor and major groves as binding sites for the enzymes and regulatory protiens

129
Q

What forms the selenoid ? And whats the selenoid diameter?

A
  • 6 nucleosomes

- 30nm

130
Q

What part of RNA is rich in uracil?and its type

A

SnRNA

-U1-U6

131
Q

The selenoid is stablizes by

A

H1 histon

132
Q

Whats forms the backbone and the inside of RNA?

A

Backbone:sugar and phosphate
Inside: C A G U

133
Q

What shape of DNA presents in the eukaryotic cells mitochondria?

A

Circular

134
Q

How many types are there in DNA and from where originate?

A

A,b,c,d,e right handed
z left handed
-formed by changing the humidity of DNA

135
Q

The base pairing in each turn in double strand DNA is

A

10.4

136
Q

The separation of DNA doubled helix do at what temperature?

A

And a melting temperature called Tm

137
Q

What type of DNA exists in the Body?

A

Bdna

138
Q

The DNA under the physiological conditions it forms?

A

Right handed double helix (BDNA)

139
Q

Whats does DNaA needs to work?

A

ATP

140
Q

The width of DNA double helix is?

A

20Å

141
Q

Number of base pairing in the whole dna of the cell?

A

7x10(9)

142
Q

The linkage of pseudouridin?

A

Insteat of C-N bond it’s bounded by C-C between phosphate and pentos

143
Q

Whats the precursors of MRna?and what is formed of?

A

HnRNA(hetero nucleic RNA)
-formed of exons(coding part)entrons(non coding)
⬇️
Synthesis of proteins

144
Q

How much of the dna genes is repeated?

A

30%

145
Q

The two strands of DNA are arranged in

A

An anti parallel way and wind around each other in the same axis

146
Q

What the telomerase responsible for?

A

Reverse transcription forms the DNA out of RNA

147
Q

What is the primary structure of DNA?and where it starts and end?

A

The base sequence of polynucleotide strand

-from5 end to 3 end

148
Q

Whats the base pairing rule?

A

G pairs with C

A pairs with T

149
Q

What does the melting temperature Tm depend on and how?

A

On the base compostion of the strand
-with⬆️ G and C ⬆️Tm
With ⬆️A and T ⬇️Tm

150
Q

Cutting in the wrong place by SnRna causes?

A
  • Unfunctional protien

- termination of the transcription process

151
Q

The selenoids gathered to form ?

A

Fibril(chromatin)

152
Q

What end of tRna bound to amino asids and with what bond?

A
  • 3end

- ester bond(covelant)

153
Q

Enzymes that synthesis the lagging strand?

A

DNA polymerase 1 and 3

154
Q

Enzymes that synthesis leading strand?

A

DNA polymerase 3 only

155
Q

The bases of the DNA are found in form of?

A

Deoxyribonucleotide (tri)phosphate

156
Q

How does the DNA polymerase 3 works?

A

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
Q

Whats the proofreading of DNA polymerase 1?

A

-goes from 3-5 to detect errors and break only one nucleotides

158
Q

Whats the exonuclease function of DNA polymerase 1?

A
  • Proofreading:3-5 one nucleotide

- exonuclease:5-3 more than one nucleotide

159
Q

Topoisomerase 2 have a name in bacteria?

A

Gyrasw

160
Q

Topoisomerase 2 used for ?

A

Anticancer, Antibiotics

161
Q

How many origin of replication in humans?whay?

A

Multiple origin

-for rapid replication of the tall dna

162
Q

Whats does the polarity of DNA means?

A

Have two ends 3 and 5 one end is phosphate while the other is sugar

163
Q

How much of the dna id coding and how much is uncodding?

A

1-2% coding

99%non coding

164
Q

How much of dna is repeated? And where does it exist?And how much base pairing it have?function?

A

30%
-in centromers or telomeres and randomly distributed
•5-500
-give the genetic print each one have its own repititive sequence

165
Q

How is the Bent Dna is formed?

A
  • 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
Q

How the triple stranded Dna is formed?and what does it give? Named the bond?stability and why?

A

-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
Q

Four stranded DNa formed at? With what bond? Stability?what does it form?

A
  • In areas rich in Guanine like telomeres
  • forms structures called G quartets
  • stable due to the cation in its middle K+
  • hoogsten bond
168
Q

How many strands the four stranded DNA formed of?

A

Only one but bent and coiled many times

169
Q

The four stranded Dna form structures called?

A

-tetraplexus

170
Q

What connects the G quartets in four stranded Dna?

A

Hoogsteen H bond

171
Q

The prokaryotic chromosomes is associated with?

A

Histon-like baic protiens and RNA

172
Q

Who’s responsible for the antibiotics resistance in the bacteria?

A

The plasmid

173
Q

Who unwinds the Dna in replication in eukaryotes?and what protects the ssdna?

A
  • Helicase

- replication protien A(SSB protien)

174
Q

Whats the units of DNA polymerase in eukaryotes?

A
  • alpha: primase activity +Synthesis of DNA
  • beta:repairs
  • gama: for mitochondria
  • delta: as 3 polymerase
  • ebsi: repair
175
Q

How does the delta DNA polymerase works in eukaryotes?

A
  • 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
Q

Enzymes that removes RNA primer in replication in eukaryotes ?

A
  • RNAas H

- flapping endonuclease 1

177
Q

Antibiotics works on topoisomerase 2?

A
  • ciprofloxancin
  • Nalidixic acid
  • Novobiocin
178
Q

Anticancers?

A
  • etoposide
  • adrianmycin
  • Doxorubicin
  • mercaptopurin
179
Q

In photodamage in bent dna it formes? And if didn’t get corrected will cause?

A

Thiymen dimer , xeroderma pigmentosum

Midterm (5 decks)

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