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BIOCHEMISTRY- Molecular/ videos Flashcards

1
Q

What is attached to the last 3’ Carbon of DNA?

A

OH (Hydroxyl)

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2
Q

What is attached to the 5’ Carbon of DNA?

A

Phosphate

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3
Q

What makes the difference between each human DNA?

A

Sequence of Nitrogen bases

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4
Q

Which bond allows Nucleotides to be atteched to each other in the same strand?

A

Phosphodiester bond

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5
Q

What holds together the double stranded DNA?

A

Hidrogen bonds

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6
Q

Which is the DNA tha predominates?

A

B-DNA right handed helix

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7
Q

How many bases are found in each turn of helix?

A

10 bases approximately

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8
Q

What forms chromatin?

A

DNA + Protein

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9
Q

What forms nucleosome?

A

DNA + Histone Octamer

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10
Q

How are DNA and histones stick together?

A

Because histones have positive charges and DNA negative

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11
Q

Which aminoacids are included in Histones?

A

Arginine and Lisine

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12
Q

Where are Barr bodies found?

A

Heterochromatin

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13
Q

Which drugs work at S phase?

A

5’ FU

Methotrexate

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14
Q

Which drugs work at G2 phase?

A

Bleomycin

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15
Q

Which drugs work at Mitosis phase?

A

Paclitaxel, Vincristin, Vinblastine

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16
Q

Drugs non cell cycle specific

A

Cyclophosphamide

Cisplatin

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17
Q

Which Purine has amino group?

A

Adenine

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18
Q

Which enzyme deaminates Adenine to become Guanine?

A

Adenosine deaminase

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19
Q

What is the result of Adenosine deaminase?

A

Form Guanine from Adenosine by deaminating it

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20
Q

Which pyrimidin has amino group?

A

Cytosine

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21
Q

What is the result of cytosine deamination?

A

Uracyl

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22
Q

Which pyrimidine is in both DNA and RNA?

A

Cytosine

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23
Q

What is the difference between Uracil and Thymine?

A

Metil Group

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24
Q

Which drug inhibits thymidilate synthase?

A

5- FU

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25
Q

When does Nucleoside is called Deoxi?

A

When it lacks OH in 2’ Carbon

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26
Q

Which Pentose Carbon is attached to base?

A

1’ Carbon

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27
Q

What is the function of Telomerase?

A

To make telomers in order to degrade DNA

Associated to oncogen cells

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28
Q

Which is the small arm of chromosomes?

A

p (petit), q (long arm)

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29
Q

Main characteristics of synthesis

A

Is always complementary and antiparallel

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30
Q

How is DNA template read by DNA polymerase?

A

3’ —> 5’

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31
Q

Order of DNA and RNA production

A

5’ —> 3’

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32
Q

Does RNA polymerase requires RNA primer?

A

No, just DNA requires RNA primer

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33
Q

Which is the direction of exonuclease repair in proofreading?

A

3’ —> 5’

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34
Q

Does RNA polymerase has proofreading repair of wrong bases?

A

No, just DNA

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35
Q

Which pathology has antibodies against topoisomerase?

A

Scleroderma

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36
Q

Heterochromatin or Euchromoatin…. has dark staining

A

Heterochromatin

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37
Q

Heterochromatin or Euchromoatin… has active genes

A

Euchromatin

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38
Q

Which DNA type is more sensitive to nuclease?

A

the 10 nm

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39
Q

Types of DNA

A

10 nm

30 nm

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40
Q

Proteins included in histone

A

2A, 2B, 3, 4 each double forming the octamers

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41
Q

Which structures form euchromatin?

A

DNA double helix —> 10 nm chromatin —> 30 nm chromatin —> 30 Fibre forms loops attached to proteins

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42
Q

What structure forms heterochromatin?

A

Higher order Packaging (includes all Euchromatin structures)

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43
Q

What is the function of Nucleolus?

A

Formation of Ribosomes

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44
Q

What happens in DNA methylation?

A

Inactive transcription

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45
Q

What happens in Histone acethylation/ Histone phosphorylation?

A

More active transcription, more gene expression

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46
Q

What causes thymine dimers damage?

A

By UV radiation

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47
Q

Which the recognition enzyme for thymine repair?

A

Excision endonuclease

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48
Q

When is excision endonuclease deficient in thymine repair?

A

Xeroderma pigmentosum

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49
Q

Which enzymes repair DNA damage?

A

DNA polymerase and DNA ligase

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50
Q

When does Thymine dimer repair occur?

A

During G1

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51
Q

When does Mismatched base repair happens?

A

During G2

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52
Q

Which are the two genes that may be affected in Mismatched repair?

A

hMSH2 or hMLH1

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53
Q

Alternative name for Hereditary Nonpolyposis Colorectal Cancer (HNPCC)?

A

Lynch syndrome, predisposes to cancer

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54
Q

What explains HNPCC?

A

Accumulation of mutations due to defective mismatched repair

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55
Q

When does Cytosine deamination occurs?

A

During G2

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56
Q

What causes Cytosine deamination?

A

Spontaneous Heat

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57
Q

Which enzyme corrects if Uracil is present in DNA?

A

Uracil Glycosylase

AP endonuclase

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58
Q

Clinical manifestations of Xeroderma pigmentosum

A

Extreme UV sensitivity (vampire existanse)
Excessive Freckling
Multiple skin cancers
Corneal Ulcerations

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59
Q

Which is the function of DNA ligase?

A

Reconect Fosfodiester bonds

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60
Q

What is accumulated in cytosine deamination?

A

Uracil in DNA

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61
Q

What is the effect of p 53 in case DNA repair is not done correctly after slowing down DNA repliaction?

A

Induces Apoptosis

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62
Q

Which virus block p53 action?

A

Hepatitis B and HPV

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63
Q

di and tri nucleotide repeats that occur throughout the genome but typically occur in noncoding sequences of DNA

A

Microsatellites

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64
Q

What happens to microsatellites in cells that lack mismatch base repair?

A

Number of microsatellites will differ in the mutated cells (called microsatellite instability)

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65
Q

What does RNA polymerase initially looks for in Transcription?

A

Initially finds and binds to the promoter, not the coding region

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66
Q

Type of RNA that complementes DNA template transcription

67
Q

Does TATA box is in the DNA template or coding RNA?

A

Coding RNA

68
Q

Does the promoter sequense is transcribed?

69
Q

Which RNA polymerase is required in prokaryotic for transcription?

A

Single RNA polymerase (α2ββ’)

70
Q

Types of RNA polymerase in Eukaryotic

A

RNAP 1
RNAP 2
RNAP 3

71
Q

Who are RNAP 1?

A

rRNA. Except 5s rRNA

72
Q

Who are RNAP 2?

A

hnRNA/mRNA and some snRNA

73
Q

Who are RNAP 3?

A

tRNA, 5s rRNA

74
Q

Where is RNA?

75
Q

Which is the only rRNA that does not belong to RNAP 1?

A

5s rRNA, it is RNAP 3

76
Q

What do prokaryotic need to initiate a promoter?

A

Sigma δ (delta)

77
Q

What do prokaryotic require to terminate transcritpion?

78
Q

Drugs that inhibit prokaryotic transcription

A

Rifampin

Actinomycin D

79
Q

In Eukaryotic what inhibits transcription?

A

RNAP 2 inhibited by α amanitin (mushrooms)

Actinomycin D

80
Q

What does rifampin blocks in prokaryotic?

A

RNA polymerase (α2ββ’)

81
Q

When is Rifampin used?

A

For TB and Bacterial meningitis prophylaxis

82
Q

What is formed after trancription?

83
Q

Once mRNA leaves the nucleous, where does it go to translate?

A

Ribosomes, after that the protein is formed

84
Q

Who looks similar to coding DNA sequence?

A

mRNA, but instead of R is U

85
Q

Who is antiparallel to mRNA?

A

Template sequence of DNA

86
Q

Where are untranslated regions found?

A

After promoter and before transcription terminates

87
Q

Which parts of DNA does not contain protein info during the transcription?

A

5’ (UTR) and 3’ (UTR)

88
Q

What is the coding region?

A

Is the part of mRNA that is translated to protein between 5’ UTR and 3’ UTR

89
Q

Characteristics of Prokaryotic mRNA

A

Policystronic
No introns
Tc and TL are coupled

90
Q

Which is the only structure where RNA is read from 5’ –> 3’?

A

Just in Ribosomes

91
Q

Structure of protein formed after translation

A

H2N (Amino)- Protein - COOH (Carboxyl) terminus

92
Q

In prokaryotic where does Ribosomes binds to mRNA to initiate translation?

A

Shine Dalgarno sequence, ubicated before coding region

93
Q

What are Polycistronic mRNA of Prokaryotic?

A

Various genes that independetly can translate

94
Q

Where does transcription of DNA takes place?

A

After promoter +1

95
Q

Where are promoter found?

A

In coding strand CAAT, TATA

96
Q

In eukaryotic what contains the important encoding region?

97
Q

How do we know is pre-mRNA?

A

Because is contains introns

98
Q

What is needed in Eukaryotes pre mRNA to become RNA?

A

Remove introns

99
Q

Characteristics of Eukaryotic mRNA

A

Monocystronic
Maturation
Tc and TL are not coupled

100
Q

Maturation characteristics of Eukaryotic mRNA

A

Capping
Splicing
Poli- Adenylation

101
Q

What is the splicing of mRNA in Eukaryotes?

A

Removal of introns

102
Q

What is the capping of mRNA of Eukaryotes?

A

Adds a 7 Me- G cap to 5’ of mRNA

103
Q

What is poly A of mRNA of Eukaryotes?

A

Poly A addition to the 3’ end of mRNA

104
Q

When is the cap added to mRNA of Eukaryotes?

A

During Trancription (Co-transcription_

105
Q

When is Poly A addition made in trancritption of Eukaryotes?

A

At the end of transcription (Post-trancription)

106
Q

Who removes the introns of Pre mRNA?

A

Spliceosome (snRNA)

107
Q

Where does pre mRNA becomes mRNA?

A

In the nucleus, after poly A addition to mRNA, it leaves the nucleus

108
Q

In eukaryotes where does ribosome bind to mRNA?

A

To the capping (5’ 7 Me-G), look for the start codon

109
Q

In whom is Alternative splicing specific?

A

For Eukaryotes

110
Q

Example of Alternative splicing

A

Membrane Ig versus secreted Ig
Tropomyosin variants in muscle
Dopamine receptors in brain

111
Q

What does S of Ribosomes mean?

A

Sedimentation Coeficient

112
Q

Which S subunits are found in Prokaryotic Ribosome?

A

30S+ 50 S = 70 S

113
Q

Which S subunits are found in Eukaryotic Ribosome?

A

40S + 60S= 80 S

114
Q

Which Ribosome structure binds to Shine Dalgarno Sequence of mRNA?

A

16 S rNA that belongs to 30 S subunit and starts translation

115
Q

Which Ribosome subunit recognizes 7 Methyl Cap of mRNA in Eukaryotes?

A

18 S RNA part of 40 S subunit

116
Q

What initiates translation in prokaryotes?

A

Binding of 16 S RNA subunit to Shine Dalgarno sequence

117
Q

What initiates translation in eukaryotes?

A

Binding of 18 S RNA subunit to 7 Methyl Cap of mRNA

118
Q

Functions of tRNA

A

Pick up amino acid

Recognize codon on mRNA

119
Q

Who pairs with anticodon of tRNA?

A

mRNA (antiparallel)

120
Q

Who is covalently attached to 3’ end OH of tRNA?

A

Activated aminoacid

121
Q

Who allows the covalent attachement of 3’ end OH of tRNA to Aminoacid?

A

Aminoacyl tRNA synthase

122
Q

Where can Promoter be found in Eukaryotic cells?

A

(-25) TATA and 970) CAAT

123
Q

Where can promoter be found in Prokaryotic?

A

(-10) TATAAT

124
Q

How many codons encode AA?

125
Q

How many codons exist?

126
Q

How many codons are stop codons?

127
Q

Which are the Start codons?

A

AUG in RNA

ATG in DNA

128
Q

Which are stop codons?

A 
UAG= You are gone
UGA= You go away
UAA= You are away
129
Q

Which aminoacid is formed by the first triplete of DNA and RNA?

A

Always Methionine

130
Q

In the missense mutation of Sickle cell anemia which aminoacids are changed?

A

Glutamine—> Valine

131
Q

What explains Nonsense mutation?

A

A codon is changed to a stop codon signal like (UGA, UAG, UAA)

132
Q

What is the result of nonsense mutation?

A

A truncated (shorter) protein. Usually nonfunctional

133
Q

What is the result of missense mutation?

A

Possible decrease in function: variable effects

134
Q

What is the Missense mutation?

A

New codon specifies different aminoacid

135
Q

Example of large segmental deletion

A

α Thalassemia

136
Q

Example of 5’ splice site or 3’ splice site mutation

A

β Thalassemia

137
Q

Triplet repeat expansion diseases

A

Huntignton disease
Myotonic dystrophy
Fragile X
Friedreich’s Ataxia

138
Q

What is the result of Triplet repeat Expansion?

A

Expansions in coding regions cause protein product to be larger than normal and unusable

139
Q

What does Anticipation means?

A

In every generation the disease appear at younger age and severe

140
Q

Which pathologies have tha anticipation phenomenom?

A

Triplet repeat expansion disease

141
Q

What aminoacid is encode by CAG?

A

Gluthamine

142
Q

Which triplet expansion is seen in Huntington disease?

A

CAG (Gluthamine)

143
Q

What determines which aminoacid is attached to tRNA?

144
Q

What is the structure of aminoacids?

A

Amino group + Carboxyl + Functional group

145
Q

What kind of bond is formed between aminoacids to form proteins?

A

Peptide bond, Amino group of one with carboxyl group of the other

146
Q

What is a recombinant DNA?

A

Splicing together DNA from 2 sources (eg. Human DNA and bacterial vector)

147
Q

Types of DNA

A 
Genomic DNA (fragments of entire genome)
cDNA (complementary DNA)
148
Q

After we have the Genomic DNA how is recombinant DNA formed?

A

They are introduce into plasmid, the result recombinant plasmids, then added to bacteria in a process called transfection then the recombinant DNA is formed

149
Q

Which are uses for cloned DNA?

A

Gene therapy

Transgenic animals

150
Q

What is a palindrome?

A

DNA sequence cleaved by a restriction endonuclease

151
Q

What is a exonuclease?

A

Begins at 1 end and cuts PDE bodn to release single nucleotides (Random)

152
Q

Types of exonuclease

A

5’—> 3’ exonuclease (removes RNA primase)–> replace with DNA
3’ —> 5’ exonuclease Exonuclease

153
Q

What is endonuclease?

A

Cleaves internal PDE bond and release restricion fragments (Particular)

154
Q

Sequence reads same backwards and forwards (usually 4, 6, 8 bp)

A

Palindrome

155
Q

What is a Palindrome of DNA?

A

When a DNA is read backward and forward on the opposite strand of DNA
Eg: 5’ GAATTC 3’
3’ CTTAAG 5’

156
Q

What is required for a Replication vector?

A
  1. Ori (origin)–> DNA sequence recognized by bacteria repliaction enzymes
  2. Single side for a given restriction endonuclease
  3. Antibiotic resistance to select for Bacteria that take up vector
157
Q

What is required for expression vector?

A

All replication Vector characterisitcs + Shine Dalgarno sequence + Promoter

158
Q

What is the principle of Retroviral Gene therapy?

A

Take a piece of Virus, replace a therapeutic drug into virus (Replication defective retrovirus), then virus enters human cell, then express its genes into protein (with therapeutic gene)

159
Q

What is ex vivo replacement therapy?

A

Cells modified outside the body then transplanted back in the body

160
Q

In which pathologies is ex vivo replacement therapy used?

A

SCID
Cystic fibrosis
Hyperammonemia

161
Q

Problems in gene ex vivo replacement therapy

A

Targeting the righ tissue
Integrating the gene in cells
Activating the gene
Avoiding harmful side effects (may be toxic or activates autoimmune response)

162
Q

In which form is DNA analized?

A

After restriction endonuclease forming DNA fragments (restriction fragments)

163
Q

Are RNA and protein cut up in order to be analized?

A

False, not cut up and analized directly

BIOCHEMISTRY (12 decks)

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