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Lecture Reviewer Flashcards

1
Q

It explains the flow of genetic materials in organisms.

A

Central Dogma

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2
Q

It uses DNA as a template to produce another DNA.

A

Replication

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3
Q

It uses DNA as the template for the synthesis of an RNA.

A

Transcription

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4
Q

It uses RNA as the template for the synthesis of a protein.

A

Translation

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5
Q

It is an
RNA-driven DNA synthesis.

A

Reverse Transcription

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6
Q

3 major steps in DNA replication, transcription, and translation.

A

Initiation
Elongation
Termination

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7
Q

An enzyme that unwinds the double helix of the DNA and splits it open.

A

DNA Helicase

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8
Q

This enzyme relieves the tightening of the supercoil to prevent DNA damage.

A

Topoisomerase

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9
Q

It stabilizes the unwound DNA, preventing them from re-annealing.

A

Single-strand Binding Protein (SSB)

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10
Q

This enzyme adds a short piece of RNA at the 3’ end of the DNA to serve as a primer.

A

RNA primase

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11
Q

A strand of DNA where the addition of nucleotides is continuous.

A

Leading Strand

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12
Q

A strand of DNA where several RNA primers are required to gradually guide the DNA polymerase.

A

Lagging Strand

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13
Q

It is involved in the initial addition of DNA nucleotides.

A

DNA polymerase ɑ (alpha)

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14
Q

It adds DNA nucleotides to the leading strand.

A

DNA Polymerase ɛ
(epsilon)

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15
Q

It adds DNA nucleotides to the lagging strand, and is also responsible for proofreading and nipping the RNA primer, initiating removal.

A

DNA polymerase δ (delta)

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16
Q

It adds DNA nucleotides to both strands and is only found in prokaryotes.

A

DNA Polymerase III

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17
Q

It detaches the short RNA primer.

A

Flap Endonuclease 1 (FEN1)

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18
Q

It coats the long flap of RNA primer; prevents FEN1, and helps DNA2.

A

Replication Protein A

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19
Q

It cleaves the long RNA primer, making it shorter for final cleaving by FEN1.

A

Dna2 Endonuclease

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20
Q

Short DNA segments that are formed between the RNA primers.

A

Okazaki Fragments

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21
Q

It binds the Okazaki fragments together to form a single continuous DNA strand.

A

DNA ligase

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22
Q

The DNA strand that contains the code is referred to as _______.

A

Sense strand

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23
Q

Its
complementary DNA strand is called _______ and it serves as the template for transcription.

A

Antisense strand

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24
Q

TFIIs that comprise the pre-initiation complex.

A

TFIID, TFIIA, TFIIB, TFIIF

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25
Q

It is the first transcription factor that
binds to the TATA box.

A

TFIID

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26
Q

Once attached, it bends the promoter
by 80o, which helps in the binding of
TFIIA and TFIIB.

A

TATA Box-binding protein (TBP)

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27
Q

It stabilizes TFIID.

A

TFIIA

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28
Q

It interacts with TBP molecule and
recruits the RNA Polymerase II.

A

TFIIB

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29
Q

It assists in the binding of the RNA
Polymerase II on the promoter

A

TFIIF

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30
Q

TFIIs that comprise the open complex.

A

TFIIE, TFIIH

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31
Q

It binds to the pre-initiation complex
and helps the binding of TFIIH.

A

TFIIE

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32
Q

It splits open the promoter.

A

TFIIH

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33
Q

It adds RNA nucleotides to antisense strand.

A

RNA Polymerase

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34
Q

This is the process of modifying
the terminal nucleotide of the
pre-mRNA.

A

5’ capping

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35
Q

It removes terminal phosphate at 5’ end.

A

RNA Triphosphatase

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36
Q

It attaches guanyl phosphate to 5’ end.

A

Guanylyl Transferase

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37
Q

It attaches methyl group to guanine nucleotide.

A

Methyl Transferase

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38
Q

It is the final structure formed at the 5’ end, which protects the pre-mRNA from degradation and is also important for translation.

A

5’ cap or Methylguanosine cap:

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39
Q

It cleaves the pre-mRNA and separates it from the RNA Polymerase II.

A

Cleavage Stimulation Factor (CstF)

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40
Q

Similar to the 5’ end, the 3’ end is also protected.

A

3’ Poly (A) Tail

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41
Q

It recruits Poly A polymerase.

A

Cleavage & Polyadenylation Specificity Factor

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42
Q

It adds about 200 adenine(A) residues at the 3’ end of the pre-mRNA giving rise to the Poly (A) Tail.

A

Poly A Polymerase

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43
Q

It binds to the poly A tail to prevent the
degradation of the 3’ end of the pre-mRNA

A

Poly A-binding protein

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44
Q

It is the coding sequence of the Pre-mRNA.

A

Exons

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45
Q

It is the non-coding sequence of the Pre-mRNA.

A

Introns

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46
Q

It is where a newly-made pre-mRNA transcript is transformed into a mature mRNA.

A

Splicing

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47
Q

It cuts off the introns and joins the remaining exons to form the final or mature mRNA.

A

Spliceosome

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48
Q

Three types of RNAs that participate in the process of translation.

A

mRNA (messenger
RNA)
rRNA (ribosomal RNA)
tRNA (transfer RNA)

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49
Q

eIFs that bind to small subunits of the ribosome.

A

elF-1, elF-1A, elF-3

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50
Q

eIFs that bind to 5’ cap and poly A tail, respectively.

A

elf-4E & elF-4G

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51
Q

eIFs that carry mRNA to small subunit of the ribosome.

A

elF-4A & elf-B

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52
Q

eIF that carries initiator met-tRNA to the P site.

A

elf-2

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53
Q

eIF that detaches elF-2 and signals the large ribosomal subunit.

A

elF-5

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54
Q

The site for attachment of tRNA carrying an amino acid.

A

A- site (Aminoacyl Site)

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55
Q

The site where tRNA with an amino acid forms a peptide bond to form an amino acid chain.

A

P-site (peptidyl site)

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56
Q

The site where tRNA with no amino acid exits the ribosome.

A

E-site (exit site)

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57
Q

It binds amino acid to tRNA.

A

Aminoacyl Synthetase

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58
Q

Initial complex is the ______.

A

met-tRNA

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59
Q

It is the transfer of one or more amino acids between peptides.

A

Transpeptidation

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60
Q

It catalyzes the binding of the second amino acid to the first
(methionine) amino acid by forming a peptide bond.

A

Peptidyl Transferase

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61
Q

A process where the ribosome moves to the next codon.

A

Translocation

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62
Q

This is a complete set of relationships among amino acids and codons, which is summarized in a table.

A

Genetic Code

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63
Q

What happens when the ribosome reaches the stop codon?

A

Translation is terminated / stopped.

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64
Q

What are the stop codons?

A

UAG, UAA, UGA

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65
Q

It binds to the stop codon.

A

Cytoplasmic Termination Factor (CTF) / Cytoplasmic Release Factor (CRF)

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66
Q

It binds the amino acid chain to the water molecule, which detaches the a.a. chain from the mRNA.

A

Peptidyl Transferase

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67
Q

In reverse transcription, this is used as a template to synthesize DNA strands.

A

Viral RNA

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67
Q

In reverse transcription, this is used as a template to synthesize DNA strands.

A

Viral RNA

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68
Q

What are steps in reverse transcription?

A

Refer to pp. 15-16 of Module 3.1 / slide 34-38 in PPT of central dogma.

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69
Q

This is a system of genes that regulates gene expression.

A

Operon System

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70
Q

These are adjacent structural genes that code for required proteins.

A

Cistrons

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71
Q

A component of the Operon system that controls transcription.

A

Operator

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72
Q

It promotes RNA Polymerase binding.

A

Promoter

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73
Q

It is a type of inducer operon system.

A

Lactose (Lac) Operon System

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74
Q

How many cistrons does a Lac Operon System have? What are these cistrons?

A

Three (3)

Lac Z (transcribes for galactosidase)
Lac Y (transcribes for lactose permease)
Lac A (transcribes for transacetylase)

75
Q

It is a type of regulatory protein of the lac operon system which binds to the operator gene to turn it off.

A

Lac Repressor

76
Q

It is a molecule that binds to the repressor protein to inactivate it.

A

Lac Inducer

77
Q

It is a type of repressor operon system.

A

Tryptophan (Trp) Operon System

78
Q

How many cistrons does a Trp Operon System have? What are these cistrons?

A

Five (5)

Trp E and Trp D (transcribes for anthranilate synthase)
Trp C (transcribes for indoglycerol phosphate synthase)
Trp B and Trp A (transcribes for tryptophan synthase)

79
Q

It is a regulatory protein that cannot bind to the operator on its own.

A

Aporepressor Protein

80
Q

It is a non-protein compound that may either come from outside of the cell or a product
of metabolism within the cells.

A

Corepressor

81
Q

What are the 2 types of gene regulation?

A

Prokaryotic gene regulation
Eukaryotic gene regulation

82
Q

These genes may be turned on or off depending on the need of the cell.

A

Facultative Genes

83
Q

These genes are never turned off because they are important for
the maintenance of the cell.

A

Constitutive Genes

84
Q

How does eukaryotic gene regulation occur?

A

Regulation of Transcription Factors
Regulation of Transcription
Regulation AFTER Transcription
Regulation of Translation
Regulation AFTER Translation

85
Q

This regulation ensures that only required transcription factors enter the nucleus and
bind to their respective promoter.

A

Regulation of Nuclear Localization

86
Q

Even if TFs are already inside the nucleus, DNA binding is still regulated in two ways: alteration of DNA-binding domain & multimerization.

A

Regulation of DNA-binding

87
Q

Assuming that the transcription factors were able to bind with the promoter,
transcription will still be regulated by either activators or repressors.

A

Regulation of Transcription

88
Q

It facilitates the binding of transcription factors to the promoter.

A

Enhancer DNA

89
Q

Transcription inhibition may done
in either of these three ways.

A

Repressors may either bind to a:
Promoter - prevents binding of transcription factors
Enhancer - prevents binding of activators
Silencer - loops the repressor towards the promoter

90
Q

Transcription may have occurred
but another mechanism can
regulate gene expression after
transcription.

A

Regulation AFTER Transcription

91
Q

Regulatory proteins bind to the mRNA and tell the spliceosomes where to cut the mRNA.

A

Regulation of mRNA Processing

92
Q

Micro RNAs (miRNAs) are responsible for the life span of mRNAs.

A

Regulation by miRNAs

93
Q

eIFs that participate in the translation are phosphorylated and rendered inactive, thus translation cannot occur.

A

Regulation of Translation

94
Q

Regulation AFTER translation can occur in two ways. What are these?

A

Phosphorylation
Ubiquitination

95
Q

It activates or inactivates translated proteins.

A

Phosphorylation

96
Q

It uses ubiquitin, which binds to proteins and delivers them to the proteasome for degradation.

A

Ubiquitination

97
Q

The expression of the genes involved is pretty straightforward.

A

Qualitative Traits

98
Q

These traits are
controlled by genes with a cumulative effect such that the phenotypes show small, gradual
differences.

A

Quantitative Traits

99
Q

It refers to the proportion of a population that will exhibit a particular trait if the allele is found in their genotype.

A

Penetrance / Quantitative Concept

100
Q

100% of all individuals with the same allele in their genotype expresses the trait.

A

Complete Penetrance

101
Q

Not all individuals with the same allele in their genotype expresses the trait.

A

Incomplete / Reduced Penetrance

102
Q

It refers to the degree of expression of a penetrant gene.

A

Expressivity / Qualitative Concept

103
Q

It is due to an environmental factor but mimics a phenotype.

A

Phenocopy

104
Q

It means that the trait has a genetic basis.

A

Concordance

105
Q

It means that the trait has no genetic basis and is due to an environmental factor.

A

Discordance

106
Q

These are alleles with quantifiable traits and have additive effects to the expression of the trait.

A

Polygenes

107
Q

The distribution of quantitative traits in a population can be analyzed by statistical
methods that compute for the mean, variance, and standard deviation.

A

Analysis of Quantitative Characteristics

108
Q

It is determined by the genes of an individual and the environment.

A

Phenotypic variance

109
Q

Formula for phenotypic variance

A

VP = VG + VE

110
Q

It is determined by incomplete dominance, complete dominance, and gene
interactions and epistasis.

A

Genotypic variance

111
Q

Formula for genotypic variance

A

VG = VA + VD + VI

112
Q

It refers to the percentage of phenotypic variation that is due to genotypic variations.

A

Heritability

113
Q

It is the proportion of the phenotypic variation due to ALL the genetic factors.

A

Broad Sense Heritability (H2)

114
Q

Formula for broad sense heritability

A

H2 = (VG/VP) X 100

115
Q

It is the proportion of the phenotypic variation based on the additive genetic variance.

A

Narrow Sense Heritability (h2)

116
Q

This is the alteration of the phenotype without altering the genotype.

A

Epigenetic Inheritance

117
Q

These are molecules that alter gene expression.

A

Epigenomes

118
Q

What are the characteristics of an epigenome?

A

Irreversible
Permanent
Reprogrammed

119
Q

It adds a methyl group to turn off transcription.

A

DNA Methylation

120
Q

It is a mechanism where histone tails either promote or prevent transcription.

A

Histone modification

121
Q

It is when non-coding RNAs (ncRNAs) regulate gene expression.

A

Gene silencing

122
Q

This is the transfer of epigenetic genes from parent to offspring.

A

Transgenerational Epigenetic Inheritance

123
Q

This is when one allele prevents the expression of another allele.

A

Paramutation

124
Q

This occurs when one allele is marked for silencing while the other gene is expressed (depending of the sex of the parent where the allele came from) .

A

Genomic Imprinting

125
Q

It balances the expression of the X-linked genes in males and females.

A

Dosage Compensation

126
Q

To balance the expression of X-linked genes in males and females, one of the X chromosomes of the female undergoes ________ and forms a _______.

A

X-inactivation
Barr body

127
Q

This happens when more X-chromosomes from one parent are inactivated than the other.

A

Skewed Inactivation

128
Q

It refers to the inheritance of traits outside of the nucleus.

A

Extranulear Inheritance

129
Q

This is the inheritance of cytoplasmic materials that contain DNA (e.g. mitochondria, chloroplasts).

A

Maternal Inheritance

130
Q

Traits governed by the DNA in the
organelle are all ________
in origin.

A

MATERNAL

131
Q

Phenotype of the offspring depends on the ____________.

A

Phenotype of the mother

132
Q

This is the inheritance of cytoplasmic materials that were synthesized during oogenesis (mRNA, proteins).

A

Maternal Effect Inheritance

133
Q

Phenotype of the offspring depends on the ___________.

A

Genotype of the mother

134
Q

This is the inheritance of the cytoplasm containing infectious particles that previously entered the maternal cell.

A

Infectious Inheritance

135
Q

Give an example of infectious inheritance.

A

Kappa particles turn cell to killer strain.

136
Q

These are abnormalities of the genetic material that give rise to various lethal and non-
lethal disorders.

A

Mutations

137
Q

Mutations are either due to _________ or _________.

A

Intrinsic factors (errors during DNA replication)
Extrinsic
factors (environmental)

138
Q

It is passed on only to the
products of its mitotic cell division giving rise to a localized mutation.

A

Somatic Mutation

139
Q

It can be passed from parent to child and all cells of the child carry the mutation.

A

Germline Mutation

140
Q

It is a condition wherein the cell (or organism) has one complete set of chromosome.

A

Monoploidy (n)

141
Q

It is a condition wherein cell (or organism) has two or more complete sets of chromosomes.

A

Euploidy

142
Q

A type of euploidy with 2 sets of chromosomes, which is normal in most organisms.

A

Diploidy (2n)

143
Q

A type of euploidy with more than two sets of chromosomes, which are normal in plants but abnormal in most organisms.

A

Polyploidy

144
Q

Types of Polyploidy

A

Triploidy (3n)
Tetraploidy (4n)
Hexaploidy (6n)
Octaploidy (8n)

145
Q

It is a condition wherein a cell (or organism) has gained or lost an entire chromosome.

A

Aneuploidy

146
Q

It involves the loss of one chromosome.

A

Monosomy (2n-1)

147
Q

An example for monosomy

A

Turner’s Syndrome (45, XO)

148
Q

It is the loss of a pair of homologous chromosome, which causes the death of the embryo.

A

Nullisomy (2n-2)

149
Q

It is the loss of one chromosome each from two pairs of homologous chromosomes.

A

Double Monosomy (2n-1-1)

150
Q

It occurs when you gain one chromosome.

A

Trisomy (2n+1)

151
Q

Givd an example of a trisomy.

A

Down’s Syndrome (47,+21)
Edward’s Syndrome (47,+18)
Patau’s Syndrome (47,+13)
Klinefelter’s Syndrome (47,XXY) (48,XXXY)(48,XXYY)(49,XXXXY)(50,XXXXXXY)

152
Q

It occurs when you gain one pair of homologous chromosome.

A

Tetrasomy (2n+2)

153
Q

It occyrz when you gain two pairs of homologous chromosomes.

A

Double Tetrasomy (2n+2+2)

154
Q

A mutation due to a missing DNA segment from a chromosome.

A

Deletion

155
Q

It is a deletion in the X chromosome of males where the gene originally
had 1000 kb (kilobases) but the transcribed mRNA only contained 14kb.

A

Muscular Dystrophy

156
Q

A mutation due to a duplicated part of a chromosome.

A

Duplication

157
Q

It is a mutation that occurs when a chromosomal segment breaks at both ends, is inverted
(turned around), and reunites with the rest of the chromosome.

A

Inversion

158
Q

A type of inversion wherein the inverted area includes the centromere.

A

Pericentric Inversion

159
Q

A type of inversion wherein the inverted area does not include the centromere.

A

Paracentric Inversion

160
Q

It is a mutation caused by a change in position of a chromosomal segment.

A

Translocation

161
Q

A type of mutation caused by a change in one base on a DNA strand.

A

Point Mutation / Base Pair Substitution

162
Q

purine replaced with another purine or pyrimidine replaced with another
pyrimidine

A

Transition

163
Q

purine to pyrimidine or pyrimidine to purine

A

Transversion

164
Q

A type of point mutation which does not result in a new amino acid in the protein sequence.

A

Silent Mutation

165
Q

A type of point mutation which results to a new amino acid in the sequence.

A

Missense Mutation

166
Q

A type of point mutation that produces a protein shorter than the required protein.

A

Nonsense Mutation

167
Q

This is a mutation due to the insertion or deletion of one or more bases.

A

Frameshift Mutation

168
Q

Anything with the ability to produce a mutation is called a _________.

A

Mutagenic Agent

169
Q

This involves exposure to radiation.

A

Physical Mutagens

170
Q

It disrupts chemical bonds in the DNA that could lead to single-strand or double-strand breaks.

A

Ionizing Radiation

171
Q

It affects the pyrimidines cytosine and thymine and could either form photoproducts or dimers.

A

Nonionizing Radiation

172
Q

They break the amino group (-NH2) (deamination) of a base transforming the nucleotide into another type of nucleotide.

A

DNA-reactive Agents / Reactants

173
Q

These are chemicals that structurally resemble purines and pyrimidines and may be incorporated into DNA in place of the normal bases during DNA replication.
They cause transition mutations.

A

Base Analogs

174
Q

A pyrimidine analog that resembles thymine.

A

Bromouracil (BU)

175
Q

A purine analog that resembles adenine, which can pair with T.

A

Aminopurine

176
Q

Substances that insert into the DNA strand and can cause frameshift mutation.

A

Intercalating agents

177
Q

Methyl, ethyl, occasionally propyl groups are added to the bases or backbone of DNA that can lead to spontaneous breakdown (deamination) or mispairing of bases

A

Alkylating agents

178
Q

They are also known as jumping genes because these DNA segments can move from their position to another region of the same DNA or region of another DNA.

A

DNA Transposons

179
Q

They insert their genetic material into the host DNA, disrupting base sequences and genetic functions.

A

Virus

180
Q

Helicobacter pylori triggers the formation of reactive oxygen species (ROS) that damage nitrogenous bases of the DNA.

A

Bacteria

181
Q

How does Direct DNA Repair occur?

A

It involves the reversal of damage caused by radiation, a process called photoreactivation, using the enzyme photolyase to catalyze the process in the presence of light.

182
Q

How does Based Excision Repair (BER)
occur?

A
  • a specific glycosylase recognizes and removes a damaged nitrogenous base
  • DNA polymerase adds a new nitrogenous base
  • DNA ligase binds the new base to adjacent bases
183
Q

How does Nucleotide Excision Repair (NER) occur?

A
  • removal of a damaged polynucleotide segment from the affected DNA strand
  • DNA polymerase replaces the removed nucleotides with new DNA nucleotides, using
    the complementary segment as the template
  • DNA ligase binds adjacent nucleotides.
183
Q

How does Mismatch Repair (MMR) occur?

A
  • if complementary base pairs are replaced by a non-complementary pair or by an
    inserted base analog, a mismatch occurs
  • this mismatch must be immediately repaired before the cell enters the division
  • “proofreading” by DNA polymerase during DNA replication detects mismatched
    bases, removes the wrong base, and inserts the correct base.
184
Q

Polynucleotide kinase/phosphatase catalyzes the production of 3’-OH and 5’ phosphate ends to allow both ends to undergo ligation.

A

Repair of DNA Breaks

Molecular Genetics (2 decks)

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