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BIOCHEMISTRY > BIOCHEMISTRY- Molecular > Flashcards

BIOCHEMISTRY- Molecular Flashcards

1
Q

In in which form does the DNA exist in order to fit in the nucleus?

A

Condensed, chromatin form

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2
Q

How many times does the negatively charged DNA loops around the positively charged histone octamer?

A

Twice

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3
Q

What does the negatively charged DNA loops around the positively charged histone octamer form?

A

Nucleosome bead

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4
Q

From which amino acids does the histones are rich?

A

Lysine and arginine

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5
Q

Which histone is the only one that isn´t in the nucleosome core?

A

H1

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6
Q

How are the main compounds that manage the stabilization of the chromatin fiber?

A

H1 binds to the nucleosome and to Linker DNA

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7
Q

In which phase does the DNA condenses to form chromosomes?

A

In mitosis

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8
Q

In which phase does the histones and DNA synthesis?

A

During S phase

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9
Q

What is the difference between Chromatin and HeteroChromatin?

A

HeteroChromatin= Highly Condensed

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10
Q

Is the Heterochromatin active?

A

No, it´s transcriptonally inactive, sterically inaccessible

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11
Q

What´s the difference between Heterochromatin and Euchromatin?

A

Euchromatin is less condensed, transcriptionally active, sterically accessible

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12
Q

What happens to the transcription when the DNA is Methylated at CpG islands?

A

Represses transcription

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13
Q

Which template strand is methylated in DNA reparation?

A

Cytosine and adenine

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14
Q

What does the DNA methylation allows?

A

Allows mismatch repair enzymes to distinguish between old and new strands in prokaryotes

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15
Q

So… what´s the difference when the histones are methylated in comparison to DNA methylation?

A

Usually reversibly represses DNA transcription, but can activate it in some cases

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16
Q

Usually reversibly represses DNA transcription, but can activate it in some cases

A

Relaxes DNA coiling, allowing for transcription

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17
Q

Which nucleotides form the Purines?

A

Adenine and Guanine

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18
Q

How many rings does the purines have?

A

2 rings

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19
Q

Which is the mnemonic for PURines?

A

PURe As Gold

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20
Q

Which nucleotides form the pyrimidines?

A

Cytosine, Thymine, Uridine

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21
Q

How many rings does the pyrimidines have?

A

1

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22
Q

This nucleotide has a methyl…

A

Thymine

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23
Q

What happens when the cytosine has a deamination?

A

It makes Uracil

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24
Q

Which nucleotide is found in the RNA and not in the DNA?

A

Uracil

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25
Q

This nucleotide is present in the DNA instead of the Uracil, which is present in the RNA…

A

Thymine

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26
Q

Which are the three aminoacids necessary for the purine synthesis?

A

Glycine
Aspartate
Glutamine

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27
Q

Which bond is stronger between GC bond or AT bond?

A

GC bond is stronger

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28
Q

What kind of bond does each nucleotide has with another nucleotide?

A

Hydrogen bond

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29
Q

How many H bonds does G-C have?

A

3

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30
Q

How many H bonds does A-T have?

A

2

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31
Q

What is the conformation of the nucleoside?

A

Base + Deoxyribose

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32
Q

Which are the components for the Nucleotides?

A

Base + deoxyribose + phosphate

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33
Q

In every nucleotide what kind of bond do they have between each other?

A

3´- 5´phosphodiester bond

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34
Q

In the novo purines synthesis, what is the process to form one?

A

Start with sugar+ phosphate

Then add the base

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35
Q

What is the process to synthesis from novo a pyrimidine?

A

Make a temporary base
Add sugar + phosphate
Modify base

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36
Q

Which one it´s an example of a temporary base?

A

Orotic acid

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37
Q

This enzyme it´s responsible for the conversion from ribonucleotide to deoxyribonucleotide…

A

Ribonucleotide reductase

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38
Q

Which ones are the two metabolic pathways that the Carbamoyl phosphate is involved?

A

De novo pyrimidine synthesis

Urea cycle

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39
Q

In the nucleotide synthesis, which enzyme does the Leflunomide inhibits?

A

Dihydroorate dehydrogenase

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40
Q

What does Leflunomide inhibits the synthesis for?

A

Orotic Acid

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41
Q

This two medicines inhibits the effect of inositol monophosphate (IMP) dehydrogenase in order to form GMP

A

Mycophenolate

Ribavirin

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42
Q

In the conversion from UDP to dUDP which enzyme is inhibited with Hydroxyurea?

A

Ribonucleotide reductase

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43
Q

Which medicine is the 6- Mercaptopurine (6-MP) prodrug?

A

Azathioprine

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44
Q

This medicine and its prodrug inhibit de novo purine synthesis…

A

6- Mercaptopurine (6-MP) and Azathioprine

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45
Q

The 5 –Fluorouracil (5-FU) inhibits the formation of deoxythymidine monophosphate (dTMP) from deoxyuridine monophosphate (dUMP) by inhibiting which enzyme?

A

Thymidilate synthase

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46
Q

This medicines are the responsible for inhibition of the dihydrofolate reductase in the synthesis of Tetrahydrofolate (THF)

A

Metrotrexate
Trimetroprim
Pyrimethamine

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47
Q

If there is an excess of adenosine deaminase deficiency what will happen?

A

There would be an excess of ATP and dATP

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48
Q

What would happen to the ribonucleotide reductase if there is an excess of ATP and dATP?

A

Inhibition of ribonucleotide reductase with imbalance of the nucleotide

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49
Q

What happens to the DNA if there is an excess of ATP and dATP?

A

Prevents DNA synthesis by imbalance of the nucleotide because of the ribonucleotide reductase inhibition

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50
Q

If the DNA synthesis its stop what happens to the lymphocyte count?

A

The lymphocyte count decreases

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51
Q

Which is one of the main causes of the autosomal recessive Severe Combined Immunodeficiency (SCID)?

A

Adenosine deaminase deficiency

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52
Q

In the Lesh-Nyhan syndrome which enzyme is absent?

A

Hypoxanthine –guanine phosphoribosyltransferesa (HGPRT)

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53
Q

If there is an absence of the HGPRT enzyme what happens to the purines?

A

Defective purine salvage

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54
Q

What is the effect of the HGPRT enzyme?

A

Converts Hypoxanthine to Inosinic acid (IMP)

Converts Guanine to Guanylic acid (GMP)

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55
Q

Which are the main findings on the Lesch- Nyhan syndrome?

A 
Hyperuricemia
Gout
Pissed off (agression, self mutilation)
Retardation (Intellectual disability)
DysTonia
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56
Q

What is the treatment for Lesch-Nyhan?

A

Allopurinol or febuxostat (2nd Line)

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57
Q

True or False… each codon specifies 3 aminoacids

A

False, each codon specifies only 1 aminoacid

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58
Q

True or False… Most aminoacids are coded by multiple codons

A

True

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59
Q

Which aminoacids are enconded by only one codon?

A

Methionine and Tryptophan

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60
Q

This aminoacid is encoded just by the codon UGG

A

Tryptophan

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61
Q

AUG is the codon that alone encondes…

A

Methionine

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62
Q

In humans, which is the exception in the genetic code that isn´t conserved throughout evolution?

A

Mitochondria

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63
Q

In the DNA replication, what is the name of the fragments that are discontinuous in the synthesis?

A

Okazaki fragments

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64
Q

What is the difference in the origin of DNA replication between Prokaryotes and eukaryotes?

A

Prokaryotes single

Eukaryotes multiple

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65
Q

Why is so important the replication fork?

A

It´s the Y-shapped region along DNA template where leading and lagging strands are synthesized

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66
Q

Its purpose is to Unwind DNA template at replication fork

A

Helicase

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67
Q

Prevent strands from reannealing

A

Single stranded binding proteins

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68
Q

What is the main purpose for the DNA topoisomerases?

A

Is to create a single or double stranded break in the helix to add or remove supercoils

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69
Q

This medicine inhibits DNA gyrase (procaryotic topoisomerase II)

A

Fluoroquinolones

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70
Q

Makes RNA primer on which DNA polymerase III can initate replication

A

Primase

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71
Q

TRUE OR FALSE… DNA Polymerase III is only present in eukaryotic

A

False, DNA polymerase III is only present in prokaryotic

72
Q

In which side does DNA polymerase elongates leading strand by adding deoxynucleotides?

A

In the 3´ end

73
Q

Which is the way of synthesis for DNA polymerase?

A

has 5´ ——::-3´ synthesis

74
Q

Its purpose is to proofreads each added nucleotide in the 3´—–::- 5´ activity

A

Exonuclease

75
Q

Its function is to degrade RNA primer and replace it with DNA, just for procaryotic

A

DNA Polymerase I

76
Q

Has same functions as DNA polymerase III but also excercises RNA primer with 5´ ——::-3´ exonuclease

A

DNA Polymerase I

77
Q

What is the function of DNA ligase?

A

IT SEALS. Catalyzes the formation of phosphodiester bond within a strand of double-stranded DNA

78
Q

Joins the Okazaki fragments

A

DNA ligase

79
Q

An RNA-dependent DNA polymerase that adds DNA to the 3´ ends of chromosomes to avoid loss of genetic material with every duplication

A

Telomerase

80
Q

What are two types of mutations for the silent, missense and nonsense severity mutations?

A

Transition and Transversion

81
Q

What happens in the transition mutation?

A

Purine to purine (A to G) or pyrimidine to pyrimidine (C to T)

82
Q

Which is the diferrence with the transversion mutation in comparission with the transition?

A

In the transversion its a change from a purine to pyrimidine or pyrimidine to purine

83
Q

What is the main point in the silent mutation?

A

Nucleotide substitution but codes for same aminoacid

84
Q

In this kind of mutation the nucleotide substitution resulting in changed aminoacid

A

Missense

85
Q

In the sickle cell disease, which kind of mutation can we find?

A

Missense

86
Q

In this kind of mutation we find a nucleotide substitution resulting in early stop codon

A

Nonsense

87
Q

This is the worst type of mutation beacause there is a deletion or insertion of a number of nucleotidesnot divisible by 3, resulting in misreading of all nucleotides downstream, usually resulting in a truncated, nonfunctional protein

A

Frameshift

88
Q

This is an example of a Frameshift mutation

A

Duchenne muscular dystrophy

89
Q

From the less severe mutation to the worst which would be the order

A

Silent, missense, nonsense, frameshift

90
Q

Who are the responsable of the release of the oligonucleotide- containing damage bases on the single strand DNA repair?

A

Specific endonuclease

91
Q

They´re responsable for filling and reasealing the gap that the endonuclase caused on the DNA repair

A

DNA polymerase and ligase respectively

92
Q

On this disease there is a prevention in the repairing of pyrimidine dimers because of ultraviolet light exposure

A

Defective in xeroderma pigmentosum

93
Q

What is the main function for the Base specific glycosylase?

A

Recognizes altered base and creates AP site (apurinic/apyrimidinic)

94
Q

So… in the base excision repair, who manage to remove one or more nucleotides and cleaves the 5´ end

A

AP endonuclease

95
Q

In the base excision repair who cleaves the 3´ end?

A

Lyase

96
Q

What is the importance of the base excision repair?

A

Important in repair of spontaneous/toxic deamination

97
Q

What happens in the mismatch repair?

A

Newly synthesized strand is recognized, mismatched nucleotides are removed and the gap is filled and resealed

98
Q

In which disease can we see the mismatch repair?

A

Defective in hereditary nonpolyposis colorectal cancer (HNPCC)

99
Q

Are the nucleotide excision repair, base excision repair and the mismatch repair; a single or double strand DNA repair?

A

Single strand DNA repair

100
Q

This is an example of double strand repair

A

Nonhomologus end joining

101
Q

On this disease we can find a mutation of the nonhomologous end joining repair

A

Ataxia Telangiectasia

102
Q

Which way is synthesized the DNA?

A

5´—/- 3´

103
Q

Which end bears the triphosphate (energy spurce for the bond)?

A

5´

104
Q

Which one is the way in the protein synthesis?

A

N- Terminus to C-terminus

105
Q

Which way is synthesized the RNA?

A

The same as DNA 5´—/- 3´

106
Q

Which way does the mRNA is readen?

A

5´—/- 3´

107
Q

Who is the the target in the 3´ hydroxyl attack?

A

The triphosphate bond

108
Q

In the protein synthesis, which one are commonly the start codons for the mRNA?

A

AUG (rarely GUG)

109
Q

Who are the main stop codons that are present on the mRNA?

A

UGA
UAA
UAG

110
Q

In the regulation of gene expression, this is the site where RNA polymerase and multiple other transcription factors bind to DNA upstream from gene locus

A

Promoter

111
Q

From which codons is the promoter rich?

A

AT with TATA and CAAT boxes

112
Q

What would happen to the gene transcription if there is a mutation of the promoter?

A

Commonly results in dramatic decrease if gene transcription

113
Q

What is the importance of the enhancer in the Regulation of gene expression

A

Stretch of DNA that alters gene expression by binding transcription factors

114
Q

This is the site where negative regulators (repressors) bind in the Regulation of gene expression

A

Silencer

115
Q

In the eukaryotes how many RNA polymerase exist?

A

3

116
Q

This RNA polymerase does the most numerous RNA

A

RNA polymerase I

117
Q

Which is the most numerous RNA?

A

rRNA

118
Q

Its function is to make the largest RNA

A

RNA polymerase II

119
Q

This is the largest RNA type

A

mRNA

120
Q

From the three types of RNA polymerase this one has the function to make the smallest RNA

A

RNA polymerase III

121
Q

Its the smalles RNA

A

tRNA

122
Q

In the DNA, is the site where the RNA polymerase II opens the DNA

A

Promoter site

123
Q

What does the a-amanitin, found in Amanita phalloides (death cap mushrooms) inhibits?

A

Inhibits RNA polymerase II

124
Q

If ingested, what are the clinical manifestations of the Amanita phalloides (death cap mushrooms)?

A

Severe hepatotoxicity

125
Q

In the prokaryotes, who makes all 3 kinds of RNA?

A

1 RNA polymerase

126
Q

What is the name of the initial transcript in the RNA processing in Eukaryotes

A

Heterogeneous nuclear RNA (hnRNA)

127
Q

What is the result of the modified hnRNA?

A

mRNA

128
Q

What happens in the process in the nucleus following transcription?

A

Capping of the 5´end DNA (addition of the 7-methylguanosine cap)
Polyadenylation of 3´ end
Splicing of introns

129
Q

Where is the site where the mRNA is transcripted?

A

in the nucleus

130
Q

What happens next to the recently form mRNA?

A

Is transported out of the nucleus into the cytosol, where it is translated

131
Q

Where does the mRNA cuality control occurs?

A

cytoplasmatic P bodies

132
Q

What does the cytoplasmatic P bodies contain?

A

exonucleases, decapping enzymes and microRNAs

133
Q

True or false… the Poly-A polymrase requires a template

A

false… the Poly-A polymrase DOESN´T requires a template

134
Q

Which is the polyadenilation signal?

A

AAUAAA

135
Q

What are the components for the spliceosome?

A

Primary transcript
Small nuclear ribonucleoproteins (snRNPs)
Other proteins

136
Q

After the spliceosome is form, what happens next?

A

Lariat-shaped looped intermediate is generated

137
Q

After the lariat is released, what does it removes and what does it join?

A

remove intron and join 2 exons

138
Q

What are the anti Smith antibodies?

A

Antibodies to spliceosomal snRNPs

139
Q

For which disease does the Antibodies to spliceosomal snRNPs or anti Smith antibodies, are highly specific for?

A

SLE

140
Q

Which kind of disease does the Anti-U1 RNP antibodies are highly associated?

A

With mixed connective tissue disease

141
Q

Who contains the actual genetic information coding for proteins… The exons or the introns?

A

Exons

142
Q

What is the purpose for the introns?

A

Intervening noncoding segments of DNA

143
Q

Where does the introns are intervening in the Cell?

A

Introns stay in the nucleus

144
Q

Does exons stay in the nucleus

A

NO

145
Q

This disease is an example of an abnormal splicing

A

B-thalassemia

146
Q

How many nucleotides does the tRNA have?

A

70-90 nucleotides

147
Q

In the tRNA what is the anticodon end?

A

Is opposite 3´ aminoacyl end

148
Q

This nucleotides are at the 3´end in the tRNAs both eukaryotic and prokaryotic

A

CCA

149
Q

Who is covalently bound to the 3´ end of the tRNA?

A

The aminoacids

150
Q

In the T-arm tRNA structure what does it contains?

A

Thymine
pseudouridine
cytosine

151
Q

Why are the components of the T-arm in the tRNA so necessary?

A

For the tRNA ribosome binding

152
Q

In the tRNA structure what does the D-arm contains?

A

Dihydrouracil residues

153
Q

Why does the dyhidrouracil residues of the D-arm in the tRNA are so necessary?

A

For the recognition by the correct aminocyl-tRNA synthetase

154
Q

Where is the Acceptor stem in the tRNA structure?

A

The 3´ CCA is the aminoacid acceptor site

155
Q

If the aminoacid and tRNA bond is incorrect, what does the aminoacyk tRNA synthetase causes?

A

Bond is hydrolyzed

156
Q

What kind of bond does the aminoacid and tRNA can have?

A

peptide bond

157
Q

Which are the three steps for the protein synthesis?

A

Initiation
Elongation
Termination

158
Q

What happens to the GTP in the phase of initiation in the protein synthesis?

A

Hydrolyzes

159
Q

In the Charging phase of the tRNA, what does the Aminoacyl-tRNA synthetase uses for the matchmaker ?

A

Uses ATP

160
Q

During this phase of the protein synthesis the initiation factors help assemble the 40S ribosomal subunit with the initiator tRNA and are realeased when the mRNA and the Ribosomal 60 S subunit asemble with the complex

A

Initiation

161
Q

Who assembles with the 40S ribosomal subunit in the initiation phase of the protein synthesis?

A

initiator tRNA

162
Q

When does the 40S ribosomal subunit and initiator tRNA are released from the complex during the initiation phase of the protein synthesis

A

When the mRNA and the Ribosomal 60 S subunit asemble with the complex

163
Q

What relationship does the GTP and the tRNA have?

A

The GTP works during the translocation

164
Q

During the elongation phase where does the Aminoacyl-tRNA binds?

A

to A site

165
Q

Who catalyzes the peptide bond formation and transfers growing polypeptide to amino acid in A site in the elongation phase

A

rRNA (ribozyme)

166
Q

How many nucleotides does the ribosome advances in the elongation phase?

A

3 nucleotides

167
Q

Which way does the ribosome advances in the elongation phase?

A

toward 3´ end of the mRNA

168
Q

What is the translocation?

A

When the peptidyl tRNA moves to the P site

169
Q

In which phase of the protein synthesis does the translocation happens?

A

During the Elongation

170
Q

In this phase the completed polypeptide is released from ribosome during the protein synthesis

A

Termination

171
Q

In the posttranslational modifications what is the trimming?

A

Its the removal of N- or C-terminal propeptides from zymogen to generate mature protein

172
Q

Which one is an example of a protein who suffered trimming posttranslational modification?

A

trypsinogen to trypsin

173
Q

Which ones are covalent alterations?

A

phosphorylation, glycosylation, hydroxylation, methylation, acetylation and ubiquitination

174
Q

This kind of proteins are involved in facilitating and/or maintaining protein folding

A

Chaperone protein

175
Q

Give an example of a Chaperone protein

A

In yeast, some are heat shock proteins (Hsp60) that are expressed at high temperatures to prevent protein denaturing/ misfolding

BIOCHEMISTRY (12 decks)

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