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FMS Week 1 Flashcards

1
Q

Ataxia telangiectasia

A

Results from mutations in ATM gene, spider veins, loss of motor control, immunodeficiency, sensitivity to radiation

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2
Q

Neurofibromatosis

A

Inherited cancer syndrome caused by mutation in NF1 gene

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3
Q

DNA polymerase δ

A

Leading and lagging strand synthesis and base excision repair

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4
Q

XPC

A

NER gene, xeroderma pigmentosum assoc.

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5
Q

GEF

A

A GTP meditator for G-proteins

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6
Q

What is the second step of RNA modification?

A

The RNA is cleaved at the polyA signal, the tail is synthesized by polyA polymerase, PABPN1 (poly A binding protein 1) stops synthesis at 200-300bp

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7
Q

what are the similarities of the 2 apoptosis pathways?

A

they both activate the same effector caspases

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8
Q

mutation in mismatch repair gene (MMR)

A

Lynch syndrome, most commonly results in hereditary non-polyposis colon cancer (HNPCC)

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9
Q

2 types of anchoring junctions

A

adherens junctions and desmosomes

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10
Q

aflatoxins

A

carcinogens from peanut/grain mold

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11
Q

what is the biggest difference between dephosphorylation and GTP hydrolysis?

A

GTP hydrolysis is not mediated by an enzyme

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12
Q

Bloom syndrome

A

results from mutation in BLM gene of homologous recombination, short stature, narrow face with prominent nose, skin-sun sensitivity, facial rash, immunodeficiency, cancer, possible mental retardation

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13
Q

translation initiation

A

40s subunit joins mRNA at 5’ region, scans for the first start codon in the proper context, 60s subunit joins and translation begins

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14
Q

carcinogens from charred meat

A

heterocyclic amines

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15
Q

aneuploidy

A

less or more than an exact multiple of the haploid set of chromosomes

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16
Q

erythromycin

A

binds to the 50s subunit and inhibits translocation (prokaryotes)

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17
Q

what type of molecules are second messengers?

A

small molecules that aplify the signal of the first messenger (ligand)

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18
Q

1000-fold increase of skin cancers, “children of the night”

A

Xeroderma pigmentosum

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19
Q

where does DNA methylation occur?

A

C-G adjacent basepairs

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20
Q

JAK-STAT Pathway

A

cytokines bind receptor, JAKs phosphorylate each other, JAK binds and activates STAT through phosphorylation, STAT (complex) is a transcription factor

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21
Q

cycloheximide

A

inhibits translocation (blocks translational elongation)(eukaryotes)

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22
Q

What is PTEN?

A

PTEN inhibits PIP2 to PIP3 secondary messaging, indirectly leading to promotion of apoptosis (AKT indirectly leads to degradation of p53) and inhibition of cell growth

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23
Q

Werner Syndrome

A

results from mutations in WRN gene of homologous recombination and DNA replication, short stature, premature aging, cancer

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24
Q

CNV

A

copy number variants

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25
Q

CDKN2 family

A

bind and inhibit only D-CDK4/6 (restriction point)

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26
Q

What effect do Xrays have on DNA?

A

strand breakage

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27
Q

tight junction

A

seals gaps between epithelial cells

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28
Q

what is myc?

A

a transcription factor for cyclin D

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29
Q

receptor of RAS-MAPK

A

tyrosine kinase

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30
Q

ATM gene

A

gene associated with homologous recombination in double-stranded breakage

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31
Q

how do hydrophillic signals act?

A

surface receptors trigger signal transduction through to effector proteins that can act both inside and outside the nucleus

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32
Q

what facilitates phosphorylation?

A

ATP (to ADP) and a protein kinase

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33
Q

XPA

A

NER gene, xeroderma pigmentosum assoc.

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34
Q

DNA mismatch repair

A

Guided by mismatch proofreading proteins cut out segment of strand with “nick” so that DNA pol can resynthesize

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35
Q

prophase

A

chromosomes condense, mitotic spindle forms, nucleus disassembles, chromosomes begin attaching to mitotic spindle

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36
Q

metaphase

A

chromosomes line up

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37
Q

cytokine

A

small proteins that stimulate differentiation/proliferation of immune cells

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38
Q

Bad

A

apoptotic sensor

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39
Q

FANC

A

interstrand DNA crosslink repair gene, assoc. w/ fanconi anemia

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40
Q

pemphigus vulgaris

A

blistering disease caused by autoantibodies to desmosomal proteins

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41
Q

DNA polymerase ε

A

Leading strand synthesis and base excision repair

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42
Q

7-TM receptor

A

large serpentine domain that is usually coupled to large G-protein

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43
Q

membrane-mediated signalling

A

signals communicate through the membranes of adjacent cells

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44
Q

what family is p16?

A

CDKN2

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45
Q

2 ways splicing can regulate translation

A

alternative introns/exons, differential splice sites within an intron

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46
Q

cyclin-CDK G2/M transition (entry to mitosis)

A

A-CDK1

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47
Q

what is the biggest difference between dephosphorylation and GTP hydrolysis?

A

GTP hydrolysis is not mediated by an enzyme

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48
Q

carcinogens from peanut/grain mold

A

aflatoxins

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49
Q

Ras

A

small G-protein, activated (GTP) through tyrosine-kinase complexes

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50
Q

what are the 2 pathways of apoptosis?

A

Intrinsic (mitochondrial) and extrinsic (death receptor)

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51
Q

what is a procaspase?

A

an inactive caspases that cleave eachother to activate, then cleave executioner caspases to activate them in a cascade

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52
Q

snRNPs

A

guide splicing process, make up the splicosome

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53
Q

Xeroderma Pigmentosum

A

high risk of all skin cancers, results from mutation in any XP gene (NER gene): XPA, XPC, ERCC2, ERCC4, ERCC5

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54
Q

actin-linked cell matrix junction

A

actin anchors to extracellular matrix (basal lamina). basal “adherens”

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55
Q

What are the pro-apoptotic sensors and what do they do?

A

Bad, Bim, Bid, Puma, and Noxa. They are BH-3 only proteins. They sense cellular stress/damage and take out the anti-apoptotic regulators to start apoptosis.

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56
Q

receptor of PI3K-AKT pathway?

A

receptor dimers with intrinsic kinase domains or that bind intracellular kinases

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57
Q

direct ligation

A

DNA-protein kinase and Ku allign dsDNA breaks, usually results in bp deletions

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58
Q

Restriction point pathway

A

Growth factors trigger signalling pathway that upregulates myc (cyclin D transcription factor), cycD activates CDK4/6, D-CDK4/6 phosphorylates Rb, inactivated Rb (hyperphosphorylated) no longer inactivates E2F, freed and activated E2F is transcription factor for S phase genes such as cyclin A

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59
Q

WRN

A

gene involved in homologous recombination and DNA replication, codes for a DNA helicase

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60
Q

Bcl-XL

A

anti-apoptotic regulator

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61
Q

BRCA1/2

A

gene associated with homologous recombination in double-stranded breakage

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62
Q

non-homologous end joining

A

resects ends to uncover 2-3 nucleotide micro-homology

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63
Q

fragile-X syndrome

A

caused by nucleotide expansion mutations

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64
Q

RAS-MAPK pathway

A

growth factors bind receptor, Ras is activated by GTP exchange factor (GEF), Ras activates (p) Raf, Raf activates (p) Mek, Mek activates (p) Erk (MAPK). Erk phosphorylates target proteins including transcription factors such as Myc

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65
Q

membrane-mediated signalling

A

signals communicate through the membranes of adjacent cells

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66
Q

ERCC2

A

NER gene, xeroderma pigmentosum assoc.

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67
Q

GPCRs

A

large G-proteins

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68
Q

how to hydrophobic signals act?

A

the enter the plasma membrane and bind with receptors in the cytoplasm, then move into the nucleus

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69
Q

myotonic dystrophy

A

caused by nucleotide expansion mutations

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70
Q

euchromatin

A

more relaxed chromatin, more transcriptionally active

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71
Q

what is p53?

A

a tumor supressor gene that is involved in the restriction point pathway, DNA damage checkpoint pathway, and the apoptosis pathway

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72
Q

cAMP-PKA pathway

A

Peptide hormone is ligand for 7TM receptor, which activates adenylate cyclase, which activates (p) cAMP, which removes inhibitor on protein kinase A (PKA), PKA enters the nucleus and activates transcription factors

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73
Q

receptor of JAK-STAT

A

cytokine receptor coupled to JAK

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74
Q

steroid receptors

A

gene-specific transcription factors that are activated by hormone binding

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75
Q

how does methylation deactivate genes?

A

attracts histone deacytylases (HDAC), compacts histones around promoters

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76
Q

mitotic/spindle assembly checkpoint

A

Mad2 recruited to kinetochore, Mad2 inhibits APC/C (an ubiquitin ligase), mitotic proteins and cyclins (A&B) cannot be degraded by 26S, and the cell cycle is arrested in mitosis until securin can restore loose chromatids

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77
Q

steroid receptors

A

gene-specific transcription factors that are activated by hormone binding

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78
Q

cytokine

A

small proteins that stimulate differentiation/proliferation of immune cells

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79
Q

HNPCC

A

“Lynch syndrome”, colorectal cancer, MMR mutation: MSH2/3/6, MLH1, PMS1/2

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80
Q

NF1

A

a gene that accumulates regulates Ras when growth factor is not present to initiate it

81
Q

desmosomes

A

connects intermediate filaments between cells

82
Q

what activates apoptosis?

A

caspases (cysteine proteases that cleave proteins after aspartic residues)

83
Q

CDKN1 family

A

CKI family that inhibits multiple cyclin-CDK complexes, broad spectrum

84
Q

streptomycin (aminoglycosides)

A

inhibit initation and cause misreading of mRNA (prokaryotes)

85
Q

Beta-thalassemias

A

mutation in Beta-globin subunit of hemoglobin caused by mutation in promoter, often the result of splice-site mutations

86
Q

what facilitates dephosphorylation?

A

protein phosphatase

87
Q

chemokine

A

agent that attracts motile cells through receptor mediated signalling

88
Q

first messenger of cAMP-PKA pathway

A

peptide hormones (epinephrine etc.)

89
Q

Proofreading

A

3’ to 5’ exonuclease activity of DNA pol

90
Q

Neurofibromatosis

A

Inherited cancer syndrome caused by mutation in NF1 gene

91
Q

Telomerase

A

synthesizes incomplete 5’ ends of the lagging strands, levels are mostly high in rapidly dividing cells (embryos and cancer)

92
Q

CKIs

A

cyclin-dependent kinase inhibitors, sterically inhibit

93
Q

IP3-PKC pathway

A

Receptor activates large G protein, which activates phospholipase C, which cleaves PI4,5P2 to IP3 and DAG. IP3 binds to SER Ca channels to release Ca. Ca binds to PKC which has bound to DAG, activating the complex, PKC complex phosphorylates many substrates including nuclear transcription and cytoplasmic regulatory proteins

94
Q

Describe a SINE

A

Short interspersed nuclear elements, non-coding DNA, use rev transcriptase from LINES, most common are ALU repeats

95
Q

RISC

A

RNA-induced silencing complex, pairs miRNAs with compliments on mRNA for possible translational repression and rapid/eventual degredation

96
Q

PI3K-AKT pathway

A

ligand binds receptor, facilitates phosphorylation of PIP2 to PIP3, PIP3 stimulates PDK1, which activates AKT(PKB) through phosphorylation, AKT(PKB) is a master regulator for cell growth and against programmed cell death

97
Q

what is p53s role in the restriction point?

A

p53 is a growth inhibitor that upregulates p16 and inhibits the restriction point pathway, leaving Rb in a hypophosphorylated state (bonded to E2F)

98
Q

iPSC

A

induced pluripotent stem cells

99
Q

MCL1

A

anti-apoptotic regulator

100
Q

differences between apoptosis and necrosis

A

necrosis is pathological rather than physiological, membranes break up, contents may leak out and cause inflammation.

Apoptosis is physiological [programmed cell death, cell shrinks intact, contents may be released in apoptotic bodies

101
Q

What does the Bcl-2 family do?

A

They control mitochondrial outer membrane permeability (MOMP)

102
Q

paracrine signalling

A

signaling molecules that act on nearby cells

103
Q

Which type of nucleotide is more at risk to DNA damage due to metabolism?

104
Q

chemokine

A

agent that attracts motile cells through receptor mediated signalling

105
Q

heterochromatic

A

more condensed, repressed chromatin

106
Q

First messenger of RAS-MAPK

A

growth factors

107
Q

Large Heterotrimeric G-Protein Function

A

Ligand stimulates alpha subunit, which can then leave rest of complex to activate an effector molecule, hydrolyzing GTP so the subunit can return to the complex

108
Q

MLH1

109
Q

adherens junctions

A

connects actin filaments between cells

110
Q

Bim

A

apoptotic sensor

111
Q

chloramphenicol

A

inhibits the peptidyl transferase activity of the 50s ribosomal subunit (prokaryotes)

112
Q

PCNA

A

proliferating cell nuclear antigen, “sliding clamp”, inhibited by p21 so that DNA pol cannot stay attached

113
Q

GAP

A

A GTPase activating protein, indirectly results in GTP hydrolysis

114
Q

how does acetylation activate genes?

A

recruits histone actelation transferase (HAT) to move histones and open gene

115
Q

what facilitates dephosphorylation?

A

protein phosphatase

116
Q

cyclin-CDK at restriction point

117
Q

Ras

A

small G-protein, activated (GTP) through tyrosine-kinase complexes, growth factor initiated protein that is often an oncogene when unregulated

118
Q

Base Excision Repair

A

resects and replaces small lesions (modified bases)

119
Q

translesion DNA replication

120
Q

What are the pro-apoptotic effectors and what do they do?

A

Bax and Bak. They contain BH domains 1-3. They oligomerize to form pores in the outer mitochondrial membrane making it permeable.

121
Q

puromycin

A

causes premature chain termination by acting as an analog of aminoacyl-tRNA (prokaryotes and eukaryotes)

122
Q

ERCC5

A

NER gene, xeroderma pigmentosum assoc.

123
Q

difference between BER and NER

A

NER is for helix distorting adducts and requires removal of large fragment

124
Q

mitogen

A

a growth factor that stimulates proliferation

125
Q

spider veins, sensitivity to radiation, loss of motor control

A

ataxia telangiectasia

126
Q

What is ErbB-2?

A

A RAS-MAPK type growth factor receptor that can be blocked in certain breast cancers

127
Q

what family is p21?

128
Q

gap junction

A

“pipeline” allows passage of small water-soluble molecules between cells

129
Q

integrins

A

allow proteins on outside of cell to sense state of extracellular matrix, connected to actin cytoskeleton

130
Q

Bax

A

pro-apoptotic effector

131
Q

what is the second messenger in cAMP-PKA pathway?

132
Q

cyclin-CDK in S phase (during DNA replication)

133
Q

Interstrand crosslink repair

A

repairs big helix distorting lesions, single nucleotide

134
Q

sequence of splicing

A

Branching nucleotide -OH attacks 5’ splice site, then 3’-OH of removed intron attacks 3’ splice site leaving exons attached and introns in loop structure

135
Q

Describe a LINE

A

Long interspersed nuclear elements, non-LTR, non-viral, retrotransposon, Only line-1 can transpose

136
Q

purpose of JAK-STAT Pathway

A

stimulates blood cell growth and proliferation

137
Q

receptor of IP3-PKC pathway

A

7TM serpentine

138
Q

first messenger of JAK-STAT

A

cytokines (blood cell proliferation factors)

139
Q

purpose of PI3K-AKT pathway?

A

controls cell growth and apoptosis pathways (AKT does through negative control of p53 via MDM2 mediation)

140
Q

mitogen

A

a growth factor that stimulates proliferation

141
Q

cyclin-CDK G1/S transition (beginning of DNA replication)

142
Q

PMS2

143
Q

MSH2/6

144
Q

largest class of genes

A

transcription factors

145
Q

anaphase

A

separation of sister chromatids

146
Q

what protein controls the restriction point?

A

Rb (retinoblastoma protein)

147
Q

first messenger of IP3-PKC pathway

A

selected growth factors, mitogens, immune signals (histamine)

148
Q

DNA polymerase α

A

DNA replication and primer synthesis

149
Q

DNA damage checkpoint pathway

A

cyclin-CDKs activate ATM/ATR, ATM/ATR phosporylate and activate Chk1/Chk2, Chks phosphorylate/inhibit substrates like Cdc25 and p53, Cdc25 can no longer dephosphorylate CDKs leaving them inhibited. P53 upregulates p21

150
Q

Which type of nucleotide is more at risk to exogenous DNA damage?

A

pyrimidines

151
Q

actinomycin D

A

binds to DNA and blocks RNA Polymerase elongation

152
Q

what facilitates phosphorylation?

A

ATP (to ADP) and a protein kinase

153
Q

Noxa

A

apoptotic sensor

154
Q

Bid

A

apoptotic sensor

155
Q

What are the first steps of RNA modification?

A

The 7-MeG cap created by enzymes at the CTD (nose) of RNA Pol II and is added just after RNA Pol II leaves the promoter

156
Q

What disease is caused by mutation in the NF1 gene?

A

Neurofibromatosis

157
Q

DNA methyltransferases

A

copy methylation patterns in newly replicated DNA in mitosis, “cellular inheritance”

158
Q

what is the execution phase of apoptosis?

A

executioner or effector caspases degrade cellular components

159
Q

Friedreich ataxia

A

caused by nucleotide expansion mutations

160
Q

purpose of cAMP-PKA pathway

A

stimulates transcription of specific genes including regulators of metabolic pathways

161
Q

Nucleotide Excision Repair

A

Repairs big helix distorting lesions, single nucleotide

162
Q

first messenger of PI3K-AKT pathway?

A

selected hormones (eg Insulin), growth factors and cell survival ligands

163
Q

Fanconi anemia

A

results from mutations in FANC genes of interstrand DNA crosslink repair, short stature, developmental abnormalities, bone marrow disorders, cancer

164
Q

Bak

A

pro-apoptotic effector

165
Q

alpha-Amanitin

A

toxin from poisonous mushroom Amanita phalloides, inhibitor of RNA pol II

166
Q

What disease is caused by mutation in the NF1 gene?

A

Neurofibromatosis

167
Q

elements of the core promoter?

A

TATA box, initiation site (INR), downstream promoting elements (DPE)

168
Q

What is mTOR?

A

mTOR is activated by AKT. mTOR activates translation by activation the ribosome and inhibiting a translation initiation inhibitor

169
Q

purpose of IP3-PKC pathway

A

activation of calcium stores and PKC, which plays roles in membrane structure change, transcriptional regulation, immune response, and cell growth

170
Q

what is the apoptotic pathway in most mammalian cells?

171
Q

What are the phases of apoptosis?

A

initiation phase and execution phase

172
Q

GEF

A

GTP exchange factor

173
Q

how much of the nuclear genome codes for proteins?

174
Q

endocrine signalling

A

signalling to elsewhere through the circulatory system

175
Q

Puma

A

apoptotic sensor

176
Q

receptor of cAMP-PKA pathway

A

7-TM serpentine

177
Q

telophase

A

mitotic spindle breaks down, two nuclei form, chromosomes decondense, organelles reassemble

178
Q

what disease is caused by autoantibodies to desmosomal proteins?

A

pemphigus vulgaris

179
Q

tetracycline

A

binds to the 30s subunit and inhibits binding fo aminoacyl-tRNAs (prokaryotes)

180
Q

Single stranded breaks

A

PARP (polyADPribose polymerase) senses break and recruits BER enzymes to repair

181
Q

Myc, Max, & Mad

A

Dimer transcription factors, MycMax acts as activator, MadMax acts as repressor

182
Q

acute myeloid cancers, short stature, developmental abnormalities, bone marrow disorders

A

fanconi anemia

183
Q

cytokinesis

A

division of cytoplasm to form 2 new cells (starts in late anaphase and finishes shortly after telophase)

184
Q

ERCC4

A

NER gene, xeroderma pigmentosum assoc.

185
Q

most important difference about meiosis

A

crossover during prophase I

186
Q

Bcl-2

A

anti-apoptotic regulator

187
Q

Homologous recombination

A

Uses homologous sequence as template to repair double stranded breaks and interstrand crosslinks, “staggered”

188
Q

SNP

A

single nucleotide polymorphism, across genome, 2 variants across population

189
Q

What are the anti-apoptotic regulators and what do they do?

A

Bcl-2, Bcl-XL, and MCL1. They contain BH domains 1-4. They keep the outer mitochondrial membrane impermeable.

190
Q

Huntington’s disease

A

caused by nucleotide expansion mutations, autosomal dominant

191
Q

Polycyclic aromatic hydrocarbons

A

mutagen/carcinogen chemicals from smoke and fossil fuels

192
Q

how much of the genome codes for introns?

193
Q

what is initiation phase of apoptosis?

A

initiator caspases become active

194
Q

hemidesmosome

A

anchors intermediate filaments to extracellular matrix (basal lamina). basal “desmosome”

195
Q

cyclin-CDK in mitosis

196
Q

endocrine signalling

A

signalling to elsewhere through the circulatory system

197
Q

short stature, premature aging, cancer

A

Werner Syndrome

198
Q

short stature, narrow face w/ prominent nose, sun-skin sensitivity, butterfly-shaped facial rahs, immunodeficiency, cancer

A

Bloom syndrome

FMS (10 decks)

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