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Noorda FOM > FOM Module 0-2 Review > Flashcards

FOM Module 0-2 Review Flashcards

1
Q

2nd messenger IP3 is terminated by

A

Phosphotase

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2
Q

What does Gq GPCR do

A

Activates phospholipase C-beta leading to increase in IP3 and DAG which activates PKC

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3
Q

Enzymes involved in histone acetylation

A

Histone Acetyltransferases (HATs): Add acetyl groups
Histone Deacetylases (HDACs): Remove acetyl groups

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4
Q

Mutation in ABCC2 causes

A

Dubin-Johnson syndrome

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5
Q

2nd messenger PIP2 precursor is

A

PI-4-P

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6
Q

Antiviral drug that treats HIV/AIDS

A

Zidovudine
(3-azido-2’3’-dedeooxythymidine)

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7
Q

What drugs inhibit DNA synthesis (S phase)

A

5-Fluorouracil
Hydroxyurea
Methotrexate

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8
Q

What protein is affected by Pertussis toxin

A

Gi

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9
Q

What does cyclophosphamide do

A

DNA alkylation leading to cross linking (stops polymerization)

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10
Q

2nd messenger DAG is released by

A

Phospholipase C

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11
Q

Disease relating to trinucleotide translation repeats (specifically CAG)

A

Huntington disease

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12
Q

What does Botulinum C3 protein do to the cell

A

Inactivates Rho proteins, leading to the disassembly of actin fibers and disruption of actin cytoskeleton organization. This effect impairs various cellular processes, including cell shape, motility, and division

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13
Q

What do GEF’s (Guanine nucleotide Exchange Factors) do

A

Activate GTPase by removing GDP (inactive) and adding GTP

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14
Q

What disease comes from mutation in ATP7A

A

Menkes disease (kinky hair)

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15
Q

When is glucose diffused through active transport (sodium-dependent glucose transporters (SGLT))

A

During periods of fasting when glucose is low in the intestines

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16
Q

Ligand for serine/threonine pathway

A

TGF-beta

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17
Q

Enzymes involved in histone methylation

A

Histone Methyltransferases (HMTs): Add methyl groups
Histone Demethylases (HDMs): Remove methyl groups

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18
Q

Mutation in what transporter causes Menkes disease (kinky hair disease)

A

ATP7A

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19
Q

Key characteristics of RNA polymerase II

A

Recognizes TATA and CAAT
Requires transcription factors
Essential for transcription and RNA processing

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20
Q

Is DNA repair active/not active, and which mechanism, in S phase

A

Active, Mismatch Repair (MMR)

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21
Q

What does ABCA1 do

A

Removes cholesterol from cells

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22
Q

What do mitomycin C antibiotics do

A

Cross links DNA

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23
Q

What does an adaptor protein do

A

Bind specific amino acid sequences for insulin signaling (SH2, SH3)

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24
Q

What carbohydrate compounds are elevated in Gaucher disease

A

Glucocerebrosides

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25
Q

What protein is affected by Botulinum C3 protein

A

G12

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26
Q

Initial intracellular substrate in RTK (insulin) pathway

A

IRS-1

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27
Q

How does DNA methylation affect gene expression

A

Associated with gene repression and DECREASED
transcription

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28
Q

Is DNA repair active/not active, and which mechanism, in G1 phase

A

Active, Nucleotide Excision Repair (NER)

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29
Q

Ligands for integrin pathway

A

Fibronectin
Vitronectin
Collagen
Laminin

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30
Q

What glucose active transporter (SGLT) also actively transports bile acids and fat-soluble vitamins, and is the mutation site for Crohn’s disease?

A

SLC10A2

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31
Q

Where is the Prader-Willi gene located

A

Chromosome 15q11-13

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32
Q

Where is the Angelman syndrome gene located

A

Chromosome 15q11 (ubiquitin-protein ligase E3A (UBE3A))

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33
Q

What is xeroderma pigmentosa

A

Extreme sensitivity to UV light due to thymidine dimers not being removed by NER leading to severe sun-induced skin damage, basal cell carcinoma, squamous cell carcinoma

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34
Q

What does ELISA give you

A

Detection and quantification of specific proteins

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35
Q

What to use Western blot to find

A

Molecular weight
Presence or absence of a protein
Posttranslational modification of a protein (ug to ng)

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36
Q

What is Hartnup disease

A

Inability to reabsorb neutral amino acids

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37
Q

Function of RNA polymerase III

A

Synthesize tRNA
Synthesize 5S rRNA
Synthesize sn/snoRNA

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38
Q

2nd messenger DAG target is

A

Protein kinase C (PKC)

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39
Q

2nd messenger calcium target is

A

Calmodulin (CaM)
Calpain
Others

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40
Q

What causes Angelman syndrome

A

Fathers gene is silenced by DMAT and mothers gene has been deleted

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41
Q

What causes Beckwith-Wiedemann syndrome

A

Fathers gene deleted and mothers gene silenced by DMAT

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42
Q

What does diphtheria toxin do to the cell

A

Inactivates EF2 leading to decreased protein synthesis and causes cellular damage, contributing to the pathology

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43
Q

What drug inhibits microtubule formation in prophase

A

Vincristine

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44
Q

What is ataxia telangiectasia

A

Rare mutation of ATM gene resulting in nervous and immune deficiencies, ataxia (difficulty with coordination and balance), and clustered spider veins on skin and eyes

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45
Q

What is key in determining Dubin-Johnson syndrome

A

Hyperbilirubinemia

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46
Q

Where is RNA polymerase I active

A

Nucleolus

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47
Q

How is histone acetylation clinically significant

A

Acetylation can lead to oncogene activation or tumor suppressor gene repression.
Dysregulation in histone acetylation linked to Huntington disease.
HDAC inhibitors (vorinostat) used in cancer treatment

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48
Q

What mutation in the beta-globin gene leads to sickle cell anemia

A

Glutamate to valine on position 6 (E6V)

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49
Q

How do anthracyclines fight cancer

A

Disrupt DNA structure and function (intercalation)*
Inhibit topoisomerase II*
Generate ROS
Alkylize DNA
Introduce apoptosis

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50
Q

When do you use Restriction fragment gel electrophoresis

A

Check DNA for point mutations causing or deleting enzyme cutting sites

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51
Q

What mutation in the beta-globin gene leads to hemoglobin E (Hb E)

A

Glutamate to lysine at position 26 (E26K)

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52
Q

What is histone acetylation

A

Addition of acetyl groups (COCH3) to lysine residues in histone tails

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53
Q

When do you use microarrays

A

Gene expression profiles and genetic variations
Identify genetic biomarkers associated with diseases

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54
Q

Platinum based chemotherapy drugs for testicular, ovarian, bladder, and lung cancers

A

-platins
(Cisplatin
Oxaliplatin
Carboplatin)

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55
Q

What does SLC6A19 do

A

Encodes sodium-dependent neutral amino acid transporter B-OAT1

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56
Q

When is cytosine arabinoside an inhibitor

A

During S-phase DNA synthesis

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57
Q

2nd messenger calcium precursor is

A

Stored calcium

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58
Q

When do you use Real-Time PCR

A

Real time amplification of DNA using florescent probes

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59
Q

When do you use Western blot

A

Following SDS-PAGE for specific antibody labeling (qualitative)

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60
Q

Is DNA polymerization active/not active in G2 phase

A

Not active

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61
Q

Mutation in ABCA1 causes

A

Tangier disease

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62
Q

Molecular switch in RTK (insulin) pathway

A

Ras GTP -> GDP (inactive)
Ras GDP -> GTP (active)

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63
Q

What do rifamycin (rifampin/rifabutin) antibiotics do

A

Inhibit RNA polymerase during transcription

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64
Q

Conservative missense

A

Amino acid is changed but to one with similar properties

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65
Q

Okazaki fragments in eukaryotes form when

A

DNA polymerase delta replicates lagging strand, extending RNA-DNA primers synthesized by primase and DNA polymerase alpha

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66
Q

Why use native PAGE instead of SDS

A

To not denature proteins in question (i.e. Separate hemoglobin types)

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67
Q

What samples are used in Western blot

A

Identification of expression of a specific protein in tissue homogenates, cell lysates, serum. For example, to detect anti-HIV antibody in a human serum sample

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68
Q

Function of RNA polymerase I

A

Synthesize 28S, 18S, and 5.8S

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69
Q

2nd messenger PIP2 target is

A

Ion Channel and transporters

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70
Q

Sequence of signal recognition

A

Initiation
Emergence of signal sequence
Binding of signal recognition particle (SRP)
Targeting to ER
Docking and translocation
Protein synthesis and translocation
Completion

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71
Q

What does Southern blot do

A

Detect DNA

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72
Q

What is busulfan used for

A

Chronic myelogenous leukemia

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73
Q

How is histone methylation clinically significant

A

Abnormal methylation patterns seen in tumors (H3K27me3 in polycomb repressive complex).
Also, in neurodevelopmental disorders (KMT2D mutations in Kabuki syndrome).
Epigenetic Therapy: Targeting specific methylation (GSK-J4, activate HMTs)

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74
Q

What does Zidovudine do

A

Inhibits nucleoside reverse transcriptase (prevents replication)

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75
Q

When do you use RT-PCR (reverse transcriptase)

A

Converting RNA to cDNA to detect RNA virus and gene expression

76
Q

What receptors are examples of “other” receptors

A

Integrin

77
Q

Is DNA repair active/not active, and which mechanism, in G2 phase

A

Active, Homologous Recombination (HR) (double strand break repair)

78
Q

Disease relating to protein folding and post-translational processing (CFTR)

A

Cystic fibrosis

79
Q

What does busulfan do

A

Covalently bond DNA (crosslink) G-A and G-G

80
Q

What does ABCC2 do

A

Encodes MRP2 protein which removes conjugated bilirubin from hepatocytes. Liver function remains normal typically

81
Q

How is DNA methylation clinically significant

A

Hypermethylation of tumor suppressor genes (e.g., MLH1 in colorectal cancer).
Aberrant methylation linked to Rett syndrome (mutations in the MECP2 gene, neurological).
DNMT inhibitors (azacytidine) used in cancer treatment

82
Q

What does PCR do

A

Amplifies DNA fragments
Genetic test

83
Q

2nd messenger cAMP is terminated by

A

Phosphodiesterase

84
Q

Where is the Beckwith-Wiedemann gene

A

Chromosome 11p15.5 (CDKN1C, KCNQ1OT1) (H19)

85
Q

2nd messenger cGMP precursor is

A

GTP

86
Q

Mutation in what transporter causes Dubin-Johnson syndrome

A

ABCC2

87
Q

Enzymes involved in DNA methylation

A

NA Methyltransferases (DNMTs): Add methyl groups
Ten-Eleven Translocation (TET) Enzymes: Removes methyl groups

88
Q

What is histone methylation

A

Addition of methyl groups (CH3) to lysine or arginine residues in histone proteins

89
Q

What test result determines Tangier disease

A

No or very little HDL cholesterol

90
Q

What does 5-lipoxygenase make

A

Leukotriene A4 (LTA4) - leukocytes, lungs, heart
LTB4 - neutrophils
LTC4, LTD4, LTE4 - SM contraction, increase vascular permeability

91
Q

How do quinolones and fluoroquinolones work

A

Inhibit bacterial type II topoisomerases (topoisomerase IV and DNA gyrase)

92
Q

When is DNA polymerase active

A

While synthesizing new DNA 5’-3’ (elongation)

93
Q

Chemotherapeutic drug family anthracyclines for leukemias, lymphomas, and breast cancers

A

-rubicins
(Doxorubicin
Daunorubicin
Epirubicin
Idarubicin)

94
Q

What diseases are cyclophosphamides used for

A

Lymphomas
Leukemias
Breast cancer
Ovarian cancer
Systemic lupus erythematosus

95
Q

Symptoms of Beckwith-Wiedmann

A

Overgrowth and large body size at birth
Macroglossia (large tongue)
Abdominal wall defects (omphalocele, umbilical hernia)
Neonatal hypoglycemia
Increased risk of developing childhood cancers
Ear creases or pits
Hemi-hyperplasia (one side of the body is larger than the other)

96
Q

What does Gs GPCR do

A

Stimulates adenylate cyclase boosting cAMP and activating PKA

97
Q

What causes Prader-Willi syndrome

A

The fathers gene is deleted and the mothers gene is silenced by DMAT

98
Q

2nd messenger cAMP precursor is

A

ATP

99
Q

What is Menkes disease (kinky hair)

A

Copper deficiency

100
Q

Symptoms of Hartnup disease

A

Light sensitive rash
Ataxia
Neuropsychiatric manifestations

101
Q

What does Pertussis do to the cell

A

Prevents the Gi protein from inhibiting adenylate cyclase, resulting in prolonged activation of adenylate cyclase and increased cAMP leading to whooping cough

102
Q

Quinolone and fluoroquinolone based antibiotics

A

-floxacin
Moxifloxacin
Gatifloxacin
Levofloxacin
Gemifloxacin

103
Q

When do you use qPCR

A

To quantify DNA levels

104
Q

When do you use Southern blot

A

Diagnose patients suspected of having conditions caused by large expansions of tandemly repeated DNA (myotonic dystrophy type 1)

105
Q

What samples are used in IHC

A

Tumor biopsies, tissue necrosis, identification of specific protein in tumor samples

106
Q

Symptoms of Angelman syndrome

A

Severe intellectual disability and developmental delay
Lack of speech or minimal speech development
Ataxia
Frequent laughing and smiling
Widely spaced teeth
Abnormally flat back of the head (microcephaly)

107
Q

What is the fastest receptor signal?

A

Ligand gated

108
Q

What is the mechanism for Non-Homologous End Joining (NHLJ) (double strand break repair)

A

Directly ligates double strand breaks in DNA

109
Q

2nd messenger cGMP is terminated by

A

Phophodiesterase

110
Q

Where is RNA polymerase II active

A

Nucleus

111
Q

Is transcription active/not active in G1 phase

A

Active

112
Q

What does Northern blot do

A

Detects RNA

113
Q

Ligand for RTK pathway

A

Growth factors

114
Q

What mutation in the CFTR gene leads to cystic fibrosis

A

Loss of phenylalanine at position 508 (ΔF508)

115
Q

2nd messenger DAG is terminated by

A

DAG kinase

116
Q

What cell phase is DNA replication

A

S phase

117
Q

What mutation in the beta-globin gene leads to hemoglobin C (Hb C)

A

Glutamate to lysine at position 6 (E6K)

118
Q

What end unit molecules counter each other in the arachidonic acid pathway

A

Thromboxane A2 (TXA2)
(Platelet aggregation, vaso/bronchoconstriction, mobilize intracellular calcium, SM contraction)
Prostacyclin (PGI2) (relaxation, inhibit platelet aggregation)

119
Q

When do you use Sanger Sequencing

A

Identify position as well as nature of the point mutation

120
Q

Is transcription active/not active in G2 phase

A

Active

121
Q

Is DNA polymerization active/not active in G1 phase

A

Not active

122
Q

What does Gi GPCR do

A

Inhibits adenylate cyclase therefore inhibiting cAMP production

123
Q

What do GAP’s (GTPase Activating Protein) do

A

Stimulate hydrolysis converting GTP to GDP (inactivation)

124
Q

What does G12 GPCR do

A

Activates rho proteins (including Ras) and regulates actin

125
Q

What does cholera do to the cell

A

Prolonged activation of adenylate cyclase, increased cAMP levels, and ultimately, the severe fluid and electrolyte loss

126
Q

2nd messenger cAMP target is

A

Protein kinase A (PKA)
Rap GDP/GTP exchange factor (Epac)
Cyclic nucleotide phosphodiesterase

127
Q

Which amino acids are targeted for phosphorylation by kinases

A

Tyrosine
Serine
Threonine

128
Q

Topoisomerase inhibitors

A

Doxorubicin
Etoposide

129
Q

What drug induces DNA strand breaks in G2 phase

A

Bleomycin

130
Q

What are the enzymes that process arachidonic acid

A

5-Lipoxygenase (LOX)
Cyclooxygenase 1 (COX-1)
Cyclooxygenase 2 (COX-2)

131
Q

Mutation in what transporter causes Tangier disease

A

ABCA1

132
Q

How are the DNA strands synthesized

A

Leading is continuous and lagging has Okazaki fragments

133
Q

Diseases associated with Non-Homologous End Joining (NHLJ) (double strand break repair) mutations

A

Severe Combined Immunodeficiency (SCID)
Ataxia telangiectasia

134
Q

Mutation in what transporter causes Hartnup disease

A

SLC6A19

135
Q

How would mutations in the Ras/Raf pathway affect Ras-GTP/GDP

A

Mutation in GAP’s prevent Ras from inactivation (Ras-GDP), causing unmitigated proliferation from MEK/ERK

136
Q

What does Sanger Sequencing do

A

Detects mutations

137
Q

What do COX-1 and COX-2 make

A

Thromboxane A2 (TXA2)
Prostacyclin (PGI2)
Prostaglandins (PGE2, etc.)

138
Q

2nd messenger cGMP target is

A

Protein kinase G (PKG)

139
Q

What is ELISA used to find

A

Detection of HIV antibodies, specific cytokines, biomarkers, others where you want to compare with a normal reference values and need a definitive number (quantitative)

140
Q

Okazaki fragments in prokaryotes form when

A

DNA polymerase III replicates lagging strand, extending RNA primers synthesized by primase, and joined together by DNA polymerase I with 5’-3’ endonuclease and ligase

141
Q

2nd messenger calcium is released by

A

Storage organelles
Cation channels

142
Q

What part of the cell cycle is Homologous recombination (HR) (Double strand break repair)

A

Late S
G2

143
Q

What disease is caused by mutation in SLC6A19

A

Hartnup disease

144
Q

What receptors are examples of enzyme-linked receptors

A

Insulin
Growth factor
Cytokine

145
Q

Diseases associated with Nucleotide Excision Repair (NER) mutations

A

Xeroderma pigmentosa
Cockayne syndrome

146
Q

When does Nucleotide Excision Repair take place

A

G1 Phase

147
Q

2nd messenger cGMP is released by

A

Guanylyl cyclase

148
Q

Is DNA polymerization active/not active in S phase

A

Active

149
Q

2nd messenger PIP2 is released by

A

PIP5 kinase

150
Q

2nd messenger IP3 target is

A

IP3 gated calcium channel

151
Q

What does Restriction fragment gel electrophoresis do

A

Detects genetic variations, mutations
Genetic mapping
Disease diagnosis
DNA fingerprinting

152
Q

When do you use Northern blot

A

Study mRNA levels
Reflective gene expression
Detect splice site errors

153
Q

How does histone acetylation affect gene expression

A

Associated with gene activation and INCREASED transcription

154
Q

What G protein is affected by Cholera toxin

A

Gs

155
Q

What do microarrays do

A

Genomic profiling

156
Q

2nd messenger PIP2 is terminated by

A

PLC/Phosphotase

157
Q

Which protein facilitates correct folding of other proteins

A

Chaperones

158
Q

Diseases associated with HR

A

BRCA1/2-related breast cancer
Fanconi anemia (short stature, Cafe-au-lait spots, thumb and forearm malformations)

159
Q

2nd messenger DAG precursor is

A

PIP2

160
Q

What nuclear enzyme makes rRNA

A

RNA polymerase I

161
Q

How do -platins fight cancer

A

Forming adducts with DNA, distorting helices, which disrupt polymerases, leading to apoptosis

162
Q

What do actinomycin D antibiotics do

A

Prevent RNA polymerase movement along DNA

163
Q

Diseases associated with Base Excision Repair (BER) mutations

A

Colorectal cancer (MBD4)
Gastric cancer (NEIL1)

164
Q

What does a scaffold protein do

A

Coordinate signal transduction pathway by attracting and docking vital pathway proteins by binding more than 3 proteins

165
Q

What drug inhibits microtubule formation in metaphase

A

Taxel’s (e.g. Paclitaxel)

166
Q

Diseases associated with mismatch repair (MMR) mutations

A

Lynch syndrome (Hereditary Nonpolyposis Colorectal Cancer (HNPCC))

167
Q

What protein is affected by Diphtheria toxin

A

Elongation Factor 2 (EF-2)

168
Q

Antibiotics targeting DNA gyrase and topoisomerase IV

A

Quinolones
Fluoroquinolones

169
Q

Symptoms of Prader-Willi

A

Behavioral problems (temper
tantrums, stubbornness,
compulsiveness)
Uncontrolled eating/obesity that can be life-threatening
Infantile symptoms: hypotonia
Poor suck/feeding difficulties
Short stature
Small hands and feet
Hypogonadism

170
Q

Chemotherapeutic drug that disrupts DNA replication machinery

A

Cytarabine

171
Q

What receptors are examples of nuclear receptors

A

Hormone (steroid/thyroid)

172
Q

What does shigella toxin do to the cell

A

Inhibits ribosomes (60S) to prevent protein synthesis

173
Q

What step of synthesis does shigella target

A

Translation

174
Q

What toxins interfere with ADP-ribosylation

A

Cholera
Diphtheria
Pertussis
Botulinum C3

175
Q

RTK-Insulin pathway for gene expression

A

Insulin - receptor - autophosphorylation - IRS-1 phosphorylated - Grb2 - Sos - Ras GTP - Raf-1 - MEK phosphorylated - ERK phosphorylated - ERK enters nucleus - ELK phosphorylated - gene expression

176
Q

RTK-Insulin pathway for GLUT 4

A

Insulin - receptor - autophosphorylation - IRS-1 phosphorylated - Pi3K phosphorylated - PIP2 phosphorylated - AKT phosphorylated - Vesicle forms

177
Q

Integrin pathway for differentiation/adhesion/growth

A

Fibro/vitronectin/collagen/laminin - receptor - Talin/FAK/Paxillin/SRC - Gbr2/SOS - Ras - MAPK - differentiation/adhesion/growth

178
Q

Integrin pathway for morphology/growth

A

Fibro/vitronectin/collagen/laminin - receptor - Talin/FAK/Paxillin/SRC - morphology/growth

179
Q

Integrin pathway for gene regulation

A

Fibro/vitronectin/collagen/laminin - receptor - Talin/FAK/Paxillin/SRC - p130cam/C3G - INK - gene regulation

180
Q

Integrin pathway for invasion/migration

A

Fibro/vitronectin/collagen/laminin - receptor - Talin/FAK/Paxillin/SRC - Pi3K - PIP2 phosphorylated - PDK - AKT - invasion/migration

181
Q

CAG repeats cause

A

Huntington’s

182
Q

CTG repeats cause

A

Myotonic dystrophy

183
Q

GAA repeats cause

A

Friedreich’s ataxia

184
Q

When is transferrin upregulated

A

Intracellular iron low

185
Q

When is ferritin upregulated

A

Intracellular iron high

Noorda FOM (18 decks)

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