Weinberg Flashcards
1
Q
Dominant allele is present but its phenotype is not manifested because of the actions of other genes within the genome
A
Incomplete penetrance
2
Q
Neutral mutation
A
Change in DNA sequence that has no effect on phenotype, including mutations that have no effect on protein structure
3
Q
Genetic element that is present in the gene pool of a species in multiple variant forms; have small or no effect on phenotype or evolutionary fitness
A
Genetic polymorphism
4
Q
Mutation affecting a single DNA nucleotide
A
Point mutation
5
Q
Enzymes involved in DNA replication
A
DNA polymerase III - creates daughter strands
Helicase - unwinds DNA double helix into template strands
DNA primase - synthesizes short RNA primer on lagging strand template to allow DNA polymerase to synthesize Okazaki fragment
6
Q
Deviations from normal chromosome number
A
Aneuploidy
7
Q
Mutation that strikes the genome of a cell outside the germ line; such a mutation cannot be transmitted to the next organismic generation
A
Somatic mutation
8
Q
Covalent attachment of a carbohydrate side chain, usually a covalently linked branched network of monosaccharides, to a second molecule, like the side chain of an asparagine residue of a protein
A
Glycosylation
9
Q
Covalent attachment of a phosphate group to a substrate, often the side chain of an amino acid residue (usually serine, threonine, or tyrosine) of a protein
A
Phosphorylation
10
Q
Enzyme that cleaves a protein substrate
A
Protease
11
Q
Process of copying DNA sequences into RNA molecules
A
Transcription
12
Q
What enzymes mediate transcription?
A
RNA polymerases
13
Q
Sequence of protein synthesis
A
DNA —> pre-mRNA transcript —> splicing to remove introns —> export to cytoplasm —> association with ribosomes for translation —> translation to amino acid chains —> folding —> functional protein
14
Q
Portion of a primary RNA molecule that is deleted during the process of splicing
A
Intron
15
Q
Portion of primary RNA transcript that is retained in the RNA product of splicing
A
Exon
16
Q
Triplet codon in the genetic code, often created by a point mutation, that specifies an amino acid residue different from that specified by the codon that it replaces
A
Missense mutation
17
Q
Cell-biological program enabling acquisition by epithelial cells of some of the phenotypes of mesenchymal cells such as fibroblasts
A
Epithelial-mesenchymal transition (EMT)
18
Q
Covalent alteration of a protein occurring concomitantly with or after the initial polymerization of the polypeptide backbone of the protein, including cleavage of the initially synthesized polypeptide and covalent modification of its amino-acid side chains
A
Post-translational modification
19
Q
Polypeptide composed of 76 amino acid residues that undergoes covalent attachment to a substrate protein, often signaling that the resulting protein is destined for degradation
A
Ubiquitin
20
Q
Gene that is used universally in all cells throughout the body independent of their differentiated state and is assumed to be essential for their continuing viability
A
Housekeeping gene
21
Q
Gene that is expressed only in cells of certain individual tissue types
A
Tissue-specific genes
22
Q
Technologies by which systematic analyses are made of large numbers of distinct protein species in a biological sample, such as a cell lysate, or a biological fluid
A
Proteomics
23
Q
Protein that is involved in regulating the transcription of a gene, often by associating with specific sequences in the promoter region of the gene
A
Transcription factor
24
Q
Short (5-10 nucleotide long) oligonucleotide sequence in DNA that is characteristically associated with one or another biological function, including recognition, and binding by sequence specific transcription factors
A
Sequence motif
25
A relatively short sequence of nucleotides near or within a gene to which a transcription factor may bind in a sequence specific manner and in turn influence the transcription of this gene
Enhancer
26
__ consists of a core formed as an octamer of four different histone molecules, each present in two copies
Nucleosome
27
Degree of compaction of chromatin is regulated by __
N-terminal tail of the histone
28
What are the four standard histone species that comprise nucleosome octamers?
H2A
H2B
H3
H4
**H1 is bound to some, but not all nucleosome octamers
29
Histone variant whose phosphorylation occurs in the nucleosomes that flank sites of double-strand DNA breaks, facilitating subsequent DNA repair
H2AX
30
Histone variant that operates specifically to activate genes encoding epithelial functions and to repress those specifying mesenchymal functions, resulting in shifts in transcription that are responsible for programming of malignant cell traits
H2A.Z
31
Most histone modifications affect what residues?
Lysine and arginine
32
Types of histone modifications
Methylation
Acetylation
Phosphorylation
Ubiquitylation
(Less common biotinylation and sumoylation)
33
What enzyme attaches methyl groups covalently to cytosine bases of CpG dinucleotides in DNA
DNA methyltransferases
34
What does CpG mean
Cytosine positioned 5’ immediately before guanine
35
Methylation of CpG dinucleotides generally causes __ of nearby genes
Repression
36
How does methylation occur?
DNA methyltransferase enzymes recognize hemi-methylated (one of teh two strands is methylated) segments of recently replicated DNA and proceed to methylate any unmethylated CpG dinucleotides that are complementary to already-methylated CpGs in the other DNA strand
37
What are microRNAs (miRNA)?
Endogenously synthesized RNA transcribed by RNA polymerase II and processed into 21- to 23-nucleotide-long ssRNA that interferes with translation of an mRNA or causes its degradation
38
What miRNA was found to suppress expression of the ras gene
Let-7
39
Loss of what miRNA processing enzyme has been found to facilitate the formation of tumors in mice and humans?
Dicer
40
What are long non-coding RNAs?
Relatively long (>200-nucleotide) RNA molecules that have no identifiable protein-coding sequences and thus no readily ascertainable functions. Tend to associate with proteins involved in regulating transcription
41
What long non-coding RNA has been found to be correlated with metastatic behavior of human breast and colorectal carcinomas?
HOTAIR
42
What are small circular RNAs?
RNAs created as side products of splicing in the nucleus. Only a tiny subset play functional roles
43
__ is an important tumor suppressing microRNAs
MiR-7
44
Mechanisms that control protein formation/accumulation
1 - promoter-proximal pausing
2 - post-transcriptional processing of pre-mRNA transcripts, including alternative splicing patterns
3 - stabilization or degradation in the cytoplasm of the mRNA product
4 - regulation of mRNA translation
5 - post-translational modification
45
What is the function of a kinase?
To attach a phosphate group to their protein substrate
Specifically they remove the gamma phosphate from ATP and covalently attach the phosphate moiety to a substrate molecule (often but no exclusively proteins)
46
What is a homologous gene?
A gene or characteristics that are similar in related organisms because of shared descent from a common precursor
Also orthologs
47
What are paralogs?
Genes or patients that are related to another gene or protein through evolution from a common ancestral precursor
Ex: the c-myc, N-myc, and L-myc genes in the mammalian genome are paralogs due to their descent from a common ancestral gene
48
What enzyme is capable of making a DNA complementary copy of an RNA molecule using the RNA molecule as a template
Reverse transcriptase
49
Neoplastic growth forming at one site in the body, the cells of which derived from malignancy located elsewhere in the body, such as the site of primary tumor formation
Metastasis
50
Tumor growing at the anatomical site where tumor formation began and proceeded to yield this mass
Primary tumor
51
Any of a series of pre-malignant, non-invasive growths in various epithelial tissues, many of which have the potential to further to carcinomas
Adenoma
52
The majority of human tumors arise from __
Epithelial tissues
53
The specialized extracellular matrix that forms a sheet separating epithelial from stromal cells or endothelial cells from pericytes
Basement membrane (aka basal lamina)
54
Meshwork of secreted proteins, largely glycoproteins and proteoglycans, that surrounds most cells within tissues and creates a structural scaffold in the intercellular space
Extracellular matrix
55
Cancer arising from epithelial cells
Carcinoma
56
Innermost layer of cells in an early embryo, which in chordates serves as precursor of the gastrointestinal tract and associated tissues, including the lungs, liver and pancreas
Endoderm
57
Outermost layer of cells in an early chordate embryo that gives rise to the skin and nervous system
Ectoderm
58
Middle layer of cells in an early chordate embryo lying between the ectoderm and endoderm, which is the precursor of mesenchymal tissues, including connective tissues and the hematopoietic system . Ovaries originate from this layer
Mesoderm
59
Some epithelial sheets serve largely to seal the cavity or channel that they line to protect the underlying cell populations. Tumors that arise from epithelial cells forming these protective cell layers are termed __
Squamous cell carcinomas
Epithelial cells lining the skin (keratinocytes) and most of the oral cavity spawn tumors of this type
60
Epithelial cell type found in a variety of epithelial tissues, notably the skin. These cells are named after the cytokeratins that they express, which form key components of the cytoskeleton of the cells.
Keratinocytes
61
Tumor derived from secretory epithelial cells
Adenocarcinoma
62
Tumor derived from mesenchymal cells, usually those constituting various connective, tissue cell types, including fibroblasts, osteoblasts, endothelial cell precursors, and chondrocytes
Sarcoma
63
Referring to tissue, composed of cells of mesodermal origin, including fibroblasts, smooth muscle cells, endothelial cells, and adipocytes
Mesenchymal
64
Mesenchymal cell type that is common in connective tissues and in the stromal compartment of epithelial tissues and is characterized by its secretion of collagen
Fibroblast
65
Mesenchymal cell type related to fibroblasts that constructs mineralized bone through the deposition of a collagenous matrix and apatite (calcium phosphate) crystals
Osteoblasts
66
Hematopoietic cells derive from the __
Mesoderm
67
Malignancy of any of a variety of hematopoietic cell types, including the line is leading to lymphocytes and granulocytes, in which the tumor cells are non-pigmented and dispersed throughout the circulation
Leukemia
RBCs are pigmented so don’t get called leukemia
68
Solid tumor of lymphoid cells
Lymphoma (usually in LNs)
69
Nonepithelial tumors arising from cells that form various components of the central and peripheral nervous systems
Neuroectodermal tumors
Includes gliomas, glioblastomas, neuroblastomas, schwannomas, and medulloblastomas
70
Melanomas derive from melanocytes, which arise from a primitive embryonic structure termed the __
Neural crest
71
Small-cell lung carcinomas (SCLCs) secrete ___ in response to neuronal signaling
Biologically active peptides
These tumors contain cells having many attributes of neurosecretory cells. It appears these tumors originate in endodermal stem cell populations of the lungs that have shed some of their epithelial characteristics and acquired others that are characteristic of a neuroectodermal lineage
72
Transition by a cell from one differentiation lineage into other phenotypic state characteristic of cells from another, distinct differentiation lineage
Transdifferentiation
Usually irreversible
73
Benign tumor formed by embryonic stem cells in which a wide variety of differentiated cell types are formed
Teratoma
74
Reversion of a more differentiated cell to the phenotype of a less differentiated cell, such as its stem cell precursor
Dedifferentiation
75
Having a tissue and cellular architecture lacking the differentiated characteristics of an identifiable tissue-of-origin or tumor type
Anaplastic
76
A tumor, often a metastasis, whose histopathological appearance does not permit a determination of its tissue-of-origin within a patient
Cancer of unknown primary
77
Accumulation of excessive numbers of normal-appearing cells within an otherwise normal-appearing tissue
An increase in the size of a tissue or organ, usually due to increased cell number rather than increase size of constituent cells
Hyperplasia
78
Replacement within a tissue of cells of one differentiation lineage by cells belonging to another lineage that are not normally encountered there (invaders present in the wrong location that often appear completely normal microscopically)
Metaplasia
79
Where is metaplasia most frequent
Epithelial transition zones
80
Metaplasia in which squamous epithelium of the esophagus is replaced by secretory epithelial cells of a type normally found in the stomach
Barrett’s esophagus
81
A pre malignant tissue composed of abnormally appearing cells forming tissue architecture that deviates from normal
Dysplasia
82
A tumor, usually presumed to be pre malignant, protruding into the lumen of an organ, such as gut or bladder, often equated with an adenoma
Polyp
83
Benign, adenomatous proliferation of epithelial cells; term often used to describe benign lesions of the skin
Papillomas
84
A genetic alteration that is present in the genomes of all the otherwise-heterogenous neoplastic cells within a tumor and is indicative of their shared descent from a common ancestral cell; such mutations are associated with the trunk of a branched tree drawn to depict graphically the evolutionary history of these cells from their common ancestor
Truncal
85
The Philadelphia chromosome results from a translocation of what two chromosomes?
9 and 22
The translocation is reciprocal (there is a loss and a gain by both chromosomes) but the sizes of the exchanged parts are unequal so resulting chromosome 22 is truncated
86
The Philadelphia chromosome is present in the leukemia cells of most __ patients
Chronic myelogenous leukemia (CML)
87
Describe the Ames experiment
Mutated Salmonella are used because they cannot grow in selective media that lacks histidine
Mutagens/carcinogens are introduced
If colonies develop it means the bacteria mutated to a genotype that can grow in the absence of histidine
88
Chemical compound that is relatively nonreactive chemically but can be converted into a highly reactive carcinogen, usually through metabolic processes
Procarcinogen
89
A chemical compound that is able to directly contribute to the induction of cancer without further chemical modification
Ultimate carcinogen
90
Agent that furthers progression of multi-step tumorigenesis by nongenetic mechanisms, notably those involving inflammation and/or mitogenesis
Tumor promoters
91
Name the ten properties of transformed cells
1. Altered morphology
2. Loss of contact inhibition
3. Anchorage independence
4. Immortalization
5. Reduced requirement for exposure to mitogenic growth factors
6. High saturation density
7. Inability to halt proliferation in response to deprivation of growth factors
8. Increased import of glucose
9. Glycolysis in presence of oxygen
10. Tumorigenicity
92
Ability of a gene to concomitantly induce a number of distinct alterations in a cell
Pleiotropy
93
What oncogenes are associated with HPV?
E6 and E7
94
What virus is associated with development of Burkitt’s lymphomas in young children in Equatorial Africa and New Guinea, and nasopharyngeal carcinomas in SE Asia?
Epstein-Barr virus (herpesvirus)
95
The __ gene of HPV produces a product that represses transcription of viral oncogenes, and this gene is discarded/disrupted during chromosomal integration.
E2
(Disruption allows active transcription of the E6 and E7 oncogenes)
96
A genetic element, implicitly formed of dsDNA, that exists in a cell, often over multiple cell generations, but is not physically linked via covalent bonds to the cell’s chromosomal DNA
Episomes
97
The dsDNA copy of a retroviral genome that is the product of reverse transcription
Provirus
98
Process through which an RNA template is copied into complementary DNA
Reverse transcription
99
Class of viruses that use a reverse transcriptase enzyme to copy its genomic single-strand RNA into double-strand DNA that serves as a template for transcription of viral mRNA and progeny viral genomes
Retrovirus
100
What are some examples of retroviruses?
RSV
HIV
Avian leukosis virus (ALV)
Murine leukemia virus (MLV)
101
What is the function of the enzyme integrase?
To integrate an episomal DNA (such as retroviral DNA genome) into host-cell chromosomal DNA
102
What gene encodes integrase?
pol
103
What gene contains all the viral transforming functions of RSV?
src
104
Avian leukosis virus is src-___ while RSV is src-____
Negative; positive
105
What is the definition of an oncogene?
Gene that can transform cells from a normal to a neoplastic state
106
What is the definition of a proto-oncogene?
Normal cellular gene that, upon alteration by DNA-damaging agents or viral genomes, can acquire the ability to function as an oncogene
107
____ is a ___ and plays a role in the normal life of chickens, but ___ is a ___ and causes cell transformation because of RSV integration
c-src; proto-oncogene
v-src; oncogene
108
What oncogene is found in feline leukemia virus and what does it cause?
fes; feline sarcoma virus
109
What viruses carry H-ras and K-ras?
H-ras = Harvey sarcoma virus
K-ras = Kirsten sarcoma virus
110
Alteration of a gene and its function through the integration of a retroviral provirus or transposon into the gene itself or a closely linked chromosomal site
Insertional mutagenesis
111
What is the Cag pathogenicity island?
40-kb stretch of genes carried by some strains of H. Pylori which encode ~30 protein products that enable the insertion of the CagA bacterial protein into cells lining the stomach leading to deregulation of cellular signals and cell-biological changes that can lead to gastric carcinoma
H. pylori infections are common worldwide but only those that harbor the Cag PAI are thought to be highly effective in triggering gastric cancer
112
T/F: CagA function is required even after tumors develop in gastric carcinoma cases
FALSE - it’s a “hit and run” oncoprotein
113
procedure for introducing DNA or RNA molecules into cells which may thereafter be expressed transiently in such cells or, in the case of DNA, stably in such cells
Transfection
114
What compound in coal tars is a potent carcinogen and mutagen
3-methylcholanthrene (3-MC)
115
erbB-related gene erbB2 is also known as as what
neu or HER2
116
Increases in gene copy number of HER2 of ___ are associated with decreased survival in human breast cancer
>5
117
the gene whose amplification is thought to be causal in fostering tumor development
Driver
118
nearby flanking genes that “may go along for the ride” but are mechanistically unimportant in tumor development; genes altered by passenger mutations
Passenger
119
gene whose partial or complete inactivation, occurring in either the germ line or the genome of a somatic cell, leads to an increased likelihood of cancer development; such a gene that is responsible for constraining cell proliferation
Tumor suppressor gene
120
What mutation of H-ras proto-oncogene led to activation of the oncogene?
point mutation in teh reading frame from G in proto-oncogene to T in oncogene
121
Pancreatic carcinoma has a point mutation in which ras gene
K ras
122
Melanoma has a point mutation in which ras gene
N ras
123
Gene notations
1. Nonhuman oncogenes are written as uncapitalized three-letter words in italics (myc), while their protein products are written in roman font with an initial capital (Myc)
2. Human oncogenes are denoted as all caps italics (MYC) and protein products are roman font all caps (MYC)
124
What chromosomes are involved in translocations in burkitt’s lymphoma?
Chromosomes 2, 14, or 22 and chromosome 8
125
Why are chromosomes 2, 14, and 22 important in development of Burkitt’s lymphoma? (Aka what do they contain)
The immunoglobulin heavy-chain gene cluster is found on chromosome 14
The ĸ antibody light-chain gene is located on chromosome 2
The λ antibody light-chain gene is located on chromosome 22
Remember etiologic agents of this disease include chronic infections by Epstein-Barr virus (EBV, a distant relative of human herpesviruses) and by malarial parasites, which appear to contribute to tumor pathogenesis by suppressing the immune response to EBV
126
What is the bcr-abl protein
Product of transcription of translocation between abl gene on chromosome 9 with bcr gene on chromosome 22
Fusion of Abl protein with Bcr protein causes deregulation of the Abl protein and subsequent emission of growth promoting signals
127
80% of alveolar rhabdomyosarcomas harbor a translocation that fuses the domains of what two transcription factors
PAX3 or PAX7 and FKHR
128
Name 6 common growth factors
Platelet-derived growth factor (PDGF)
Epidermal growth factor (EGF)
Transforming growth factor-Beta1 (TGF-B1)
Vascular endothelial growth factor (VEGF)
Insulin like growth factor (IGF)
Fibroblast growth factor 2 (FGF-2)
129
An agent that provokes cell proliferation
Mitogen
130
PDGF is a potent stimulator of ___
Fibroblasts
131
EGF causes what
Dramatic changes in cell shape
Stimulates proliferation of epithelial cells
132
What is the universal phosphate donor of the cell
ATP
133
Src operates as what kind of enzyme
Tyrosine Kinase
134
Protein to which one or more phosphate groups have been covalently attached, usually to threonine, serine, or tyrosine residues
Phosphoprotein
135
Src phosphorylates certain ___ residues of its protein substrates
Tyrosine
136
Most phosphoproteins are phosphorylated at __ and __ residues
Threonine and serine
137
Where was the erbB oncogene originally discovered
Genome of avian erythroblastosis virus (AEV)
138
The v-sis oncogene comes from what virus
Simian sarcoma virus
139
What cells does PDGF stimulate
Mesenchymal cells (fibroblasts, adipocytes, and smooth muscle cells); can also stimulate growth of glial cells
(EGF and related GF ligands are focused mostly on epithelial cells)
140
PDGF-R is what kind of receptor
Tyrosine kinase
141
Kaposi’s sarcoma is caused by what
Human herpesvirus 8 (HHV-8)
142
Mutant alleles of what gene transmitted through the human germ line are associated with a familial cancer syndrome known as multiple endocrine neoplasia types 2A and 2B, as well as familial medullary thyroid carcinoma
ret
143
What gene encodes the receptor for hepatocyte growth factor (HGF)
met
144
What mutation in Rottweilers is responsible for their high risk of developing several types of cancer?
Mutation in met gene leading to point mutation affecting the juxtamembrane region of Met receptor
145
Examples of Janus kinases (JAKs)
EPO receptor
TPO receptor
Interferon receptor
146
What protein involved in facilitating endocytosis is overexpressed in a variety of human carcinomas
huntingtin-interacting protein-1 (HIP1)
147
Overexpression of HIP1 prevents endocytosis of a number of cell surface proteins, including ___
EGF-R
148
What protein is a stron promoter of EGF-R endocytosis?
cyclin-G associated kinase (GAK)
149
What protein is responsible for tagging ligand-activated EGF-R via mono-ubiquitylation, causing endocytosis of EGF-R and degradation in lysosomes?
c-Cbl
150
Three types of Hedgehog ligands
Desert Hh
Indian Hh
Sonic Hh
151
G-protein-coupled receptors activate
guanosine nucleotide-binding proteins (G-proteins)
These G-proteins switch between a GTP-bound active state and a GDP-bound inactive state
152
Chemokine receptors are a subset of what receptor type
GPCRs
153
154
Steroid sex hormones, retinoids, and vitamin D are hydro____
Phobic
This allows them to readily penetrate the plasma membrane and advance further into the nucleus
155
Name the parts of a nuclear receptor
DNA-binding domain
Hinge region
Conserved ligand-binding domain
Above three are flanked by variable N’- and C’- terminal domains
Nuclear receptors may remain in the cytoplasm until ligand binding then go to the nucleus, or may be constitutively bound to chromatin
156
An oligonucleotide sequence in genomic DNA to which hormone-activated nuclear receptors bind
Hormone response elements (HREs)
157
Estrogen receptor binds
Estrogen! Aka 17Beta-estradiol or E2
158
What is tamoxifen
Synthetic pharmacological analog of estrogen which can bind the estrogen receptor and inhibit a subset of the normal signaling functions (aka antagonizes actions of estrogen)
Considered a selective estrogen receptor modulator (SERM)
159
Vitamin D ligand has strong effects in normalizing the otherwise highly abnormal stroma of _____ (tumor)
Pancreatic adenocarcinomas
160
Form of apoptosis that is triggered by the failure of a cell to establish anchorage to a solid substrate, such as the extracellular matrix, or by loss of such anchorage
Anoikis
161
A cell surface tyrosine kinase receptor that recognizes and binds extracellular collagen as its activating cognate ligand
Discoidin domain receptors (DDRs)
162
A heterodimeric cell surface receptor that binds components of the ECM and transmits info about this binding to the cell interior
Integrin
The cytoplasmic domain of an integrin may also be coupled with components of the cytoskeleton, thereby linking the ECM to the cytoskeleton
163
Ras protein functions as a ___ protein
G-protein
164
___ distinct ras genes in mammalian cells encode ___ distinct Ras proteins
Three; four
K-ras specifies a second protein via alternative splicing of a pre-mRNA
165
What allows Ras proteins to anchor to the cytoplasmic side of the plasma membrane
C-termini have covalently attached lipid tails composed of farnesyl, palmitoyl, or geranylgeranyl groups (or combos) that enable the Ras proteins to anchor to the cytoplasmic side of the plasma membrane
166
Ras has __ activity in that it can bind and hydrolyze (cleave) guanosine nucleotides
GTPase
(This is different than Src and erbB)
167
5 ways Ras is similar to G proteins
1 - binds a GDP molecule when in its inactive state
2 - jettisons its bound GDP after receiving some stimulators signal from upstream in a signaling cascade
3 - acquires a GTP molecule in place of the recently evicted GDP
4 - shifts into an activated, signal-emitting configuration while binding this GTP
5 - cleaves this GTP after a short period using its own intrinsic GTPase function to go back to the non-signal-emitting configuration
168
What molecule stimulates the Ras protein
GEF (guanine nucleotide exchange factor)
169
GTPase activity of Ras is intrinsic but can also be strongly stimulated by ___
GAPs (GTPase-activating proteins)
GAPs increase intrinsic GTPase activity of Ras by as much as 100,000-fold
170
___ mutations in Ras block stimulatory GAPs from interacting with Ras
Point mutations (cause amino acid substitutions)
This traps Ras in its activated, signal-emitting state
171
Ras oncoprotein has lost virtually all of its ___ activity
GTPase
172
Which codons are typically subject to missense mutations in the ras genes
12, 13, 61
12 is most common
173
What is the half life of the Myc protein
25 minutes
174
Signal transduction from Myc depends on its __ within a cell, whereas signal transudction with Ras and Src depends on their ___
Concentration ; relocalization and structure
175
Domains of Src and function
SH1 domain - catalytic domain
SH2 domain - binds phosphorylated tyrosine (phosphotyrosine) residues, growth factor receptors/other membrane-associated proteins, regulates activity of the Src kinases
SH3 - bind proline-rich sequence domains on partner proteins
176
What three major downstream signaling cascades radiate from the Ras protein?
PI3K
Raf
Ral
177
Raf, once activated, activates another kinase called ___
MEK
178
Once activated, MEK phosphorylates what two kinases?
ERK1
ERK2
ERK = extracellular signal-regulated kinases
179
ERK1 and ERK2 are considered
MAPKs (mitogen-activated protein kinases)
180
What kinase phosphorylates MAPK
MAPKK
MEK functions as a MAPKK
181
What kinase phosphorylates MAPKK
MAPKKK
Raf is classified as a MAPKKK
182
Serine/threonine kinase phosphorylation leads to ____ whereas tyrosine kinase phosphorylation leads to ___
Functional activation
Relocalization of partner proteins
183
What two chromatin-associated proteins are activated by downstream signaling from ERK
HMG-14
Histone H3
184
What growth-regulating genes are stimulated as a result of ERK phosphorylation of the Ets transcription factor
Heparin-binding EGF (HB-EGF)
Cyclin D1
Fos
P21Waf1
185
What two early genes induced by Raf—>MEK—>ERK activate genes encoding transcription factors that associate to form AP-1 (a heterodimeric transcription factor found hyperactivated in cancer cells)
Fos
Jun
186
PI3K pathway has __ effect
Anti-apoptotic
187
___ is a water-soluble carbohydrate molecule (polyalcohol)
Inositol
188
Inositol, once phosphorylated, can be cleaved by phospholipase C to yield __, which can serve as an intracellular hormone/second messenger to carry signals from the plasma membrane to other parts of the cell
Phosphoinositol (IP3)
189
Phosphorylated inositol is cleaved into what two parts and what are their functions
IP3 (phosphoinositol) - second messenger
DAG (diacylglycerol) - stays at plasma membrane and activates kinases (specifically protein kinase C)
190
___ is responsible for attaching a phosphate group to the 3’ hydroxyl of the inositol moiety of membrane-embedded phosphatidylinositol (PI)
PI3K (phosphatidylinositol 3-kinase)
191
A specific PI3K phosphorylates ___
PI(4,5)P2 aka PIP2
192
PIP2 acquires another phosphate group and becomes ___
PIP3 aka PI(3,4,5)P3
193
Akt/PKB is a ___ protein (and what type of kinase)
PH-domain containing protein
PH = pleckstrin homology
It is a serine/threonine kinase
194
Akt becomes tethered to the plasma membrane via its PH domain association with PI3K. Akt then phosphorylates protein substrates that have what effects on the cell? (5)
1 - aiding in cell survival by reducing possibility of activation of apoptosis
2 - stimulate cell proliferation
3 - stimulate increased cell size by increasing protein synthesis
4 - influences cell motility (poorly understood)
5 - influences angiogenesis (poorly understood)
195
PIP3 levels are low in ___ cells and increase after these cells encounter ___
Quiescent ; mitogens
196
____ is a phosphatase that reverses the actions of activating kinases like PI3K
PTEN
197
PTEN removes the ___ from PIP3
3’ phosphate group
198
Functions of Rho proteins
Reconfiguration of the cytoskeleton and the attachments that a cell makes with its physical surroundings
199
___ mediate communication between Ras and Ral
Ral guanine nucleotide exchange factors (Ral-GEFs)
200
The Ral pathway can activate what two proteins that contribute to Ras-mediated anchorage-independent growth
Sec5
Exo84
201
process of JAK/STAT interactions
Ligand binds —> receptor dimerization —> JAK association with each receptor molecule —> JAKs phosphorylate tyrosine residues on cytoplasmic tails of opposite receptor molecule —> STATs bind phosphotyrosine residues —> STAT-STAT dimmers form and migrate to nucleus to function as transcription factors
202
What genes are known targets of STATs
myc
genes for cyclins D2 and D3 (allows cells to go through growth and division cycles)
Genes encoding Bcl-XL (anti-apoptotic protein)
203
Which STAT is known to be constitutively activated in a number of human cancers including melanomas, breast cancer cells, head and neck cancers, glioblastomas, lung cancers, and gastric cancers
STAT3
204
Which STAT acts as a tumor-suppressing protein by antagonizing cell proliferation and survival
STAT1
205
Three functions of integrins
1 - physically linking cells to the ECM
2 - informing cells whether or not tethering to certain ECM components has been achieved
3 - facilitating motility by making and breaking contact with the ECM
206
Wnt factors act through __ receptors to suppress activity of __
Frizzled receptors
Glycogen synthase kinase-3beta (GSK-3beta)
207
In the absence of Wnts, GSK-3beta phosphorylates key proteins to tag them for destruction, including __
Beta-catenin
208
Where is Beta-catenin usually found
Cytoplasm
209
Three states Beta-catenin exists in
1 - bound to cytoplasmic domain of cell-cell adhesion receptors (like E-cadherin)
2 - soluble in cytosol where it has rapid turnover/short lifespan (<20min)
3 - operates in the nucleus as an important component of a transcription factor complex
210
Cytosolic Beta-date in molecules result after __ are dissolved via endocytosis of ___ molecules
Adherens junctions ; E-cadherin
211
Cytosolic Beta-catenin molecules may initially form multi protein complexes with what three proteins
Apc (adenomatous polyposis coil protein)
Wtx
Axin
212
Phosphorylation of Beta-catenin by GSK-3beta results in destruction of Beta-catenin by __
Ubiquitylation
213
Wnt signal activation has what effect on Beta-catenin
Prevents its destruction which leads to increased half-life and increased steady state concentrations
214
GSK-3beta can also phosphorylate __ in the nucleus
cyclin D1
215
non-canonical Wnt signaling means the pathways operate independently of __ signaling
Beta-catenin
216
The most important non-canonical Wnt signaling pathways involve five RTKs which carry catalytically inactive kinase domains. What are examples?
Ror1
Ror2
217
Six dual address signaling pathways that play a role in human cancers
JAK-STAT
Wnt-Beta-catenin
NF-kB
Notch
Hedgehog
TGF-Beta
218
The most common form of NF-kB is a heterodimer of what two subunits
p65
p50
219
What sequesters NF-kB in teh cytoplasm
IkB
220
Describe NF-kB pathway
IkB keeps NF-kB sequestered in cytoplasm and inactive --> stimulus triggers phosphorylation of IkB by IKK and it is tagged for destruction --> NF-kB is liberated and migrates to the nucleus to stimulate gene expression
221
What are some signals that can stimulate IKK
TNF-alpha
IL-1beta
LPS
ROS
anti-cancer drugs
gamma irradiation
222
What key anti-apoptotic proteins does NF-kB induce expression of
Bcl-2
IAP-1
IAP-2
223
NF-kBs function in a mitogenic fashion by inducing expression of __ genes
myc
cyclin D1
224
__ is overexpressed in ~30% of human breast cancers and leads to constitutive activation of the NF-kB pathway
IKKepsilon
225
What gene that encodes one of the subunits of NF-kB is amplified in ~25% of human diffuse large B cell lymphomas
REL
226
T/F NF-kB overexpression is associated with a poor prognosis in a variety of common cancers
True
227
What are the ligands of the Notch receptor
Jagged-like protein
Notch-like protein
228
Describe Notch signaling cascades
Ligand binds Notch —> two proteolytic cleavages occur (one in ectodomain and one in transmembrane domain) —> cleavage of transmembrane domain liberates a cytoplasmic protein fragment (NICD) that migrates to the nucleus of target cells and acts as a transcription factor
229
Notch signaling is important in governing cell __
Differentiation
230
Notch can activate what gene
Myc
231
Changes to the Notch receptor after binding ligand are REVERSIBLE/IRREVERSIBLE
Irreversible
This is different from RTKs. Notch can seemingly only fire once and thus relies on its ability to drive multiple cycles of transcription in the nucleus in order to amplify the signal initiated by ligand binding
232
Notch signaling operates in an AUTOCRINE/ENDOCRINE/PARACRINE/JUXTACRINE fashion
Juxtacrine - two cells are in direct physical contact with one another
233
Overexpression of one or another of the Notch proteins is seen in what cancer types
Cervical carcinomas (majority)
Subsets of colon and prostate carcinomas
Squamous cell carcinomas of the lung
234
Increased expression of what two classes of Notch ligands has been found in some cervical and prostate carcinomas
Jagged
Delta
235
60% of all human T-cell acute lymphocytic leukemias have constitutively active __
Notch
236
Hedgehog (Hh) is the ligand for what receptor
Patched (Ptc)
237
Binding of Hedgehog ligand to Patched receptor alters the receptor’s interaction with __
Smoothened (Smo)
238
Describe the Hedgehog signaling pathway
Hh binds Patched receptor —> altered interaction of Patched with Smoothened —> Smoothened and Gli accumulate in the primary cilium —> failure to cleave Gli —> intact Gli protein migrates to nucleus and activates transcription
239
Hh signaling during embryogenesis has been associated with __
Development of patterned development in certain tissues as well as commitments to specific cell states
240
Gli was discovered as a highly expressed protein in
Glioblastoma
241
Germaine inactivating mutations of the human patched (PTCH) gene cause __ syndrome
Goblin syndrome - inherited cancer susceptibility syndrome which involves increased risk of multiple basal cell carcinomas of the skin as well as other tumors (notably medulloblastomas)
242
Tumor of cells arising from primitive stem cells in the cerebellum
Medulloblastoma
243
50% of sporadic basal cell carcinomas of the skin (which occur due to somatic mutations) carry mutant ___ and __ alleles
PTCH1 (encodes patched 1)
SMO (encodes smoothened)
244
Paracrine signaling of Hh has been reported in what tumor type
Small cell lung carcinomas
245
TGF-beta and its signaling pathway play major roles in what class of cancers
Carcinomas
246
Describe the TGF-beta pathway
TGF-beta is activated —> Smad transcription factors are dispatched to the nucleus where they bind DNA and associate with transcription factors to induce gene expression and repression
247
Smad transcription factors recognize and bind only __
Tetranucleotide sequence in chromosomal DNA
248
When signaling in the presence of a Ras oncoprotein, TGF-beta may induce __
Epithelial-mesenchymal transition
249
T/F: High-level expression of Yap or Taz, especially when present in the nuclei of carcinoma cells, is correlated with aggressive clinical behavior
True
250
Regulatory process by which a stimulatory signal upstream in a signaling pathway activates downstream targets that proceed to inhibit the source of the initial upstream signal, thereby reducing further overall signaling
Negative feedback
251
Regulatory process by which an upstream stimulatory signal provokes a downstream target that proceeds to sustain and/or amplify signaling by the initial stimulatory signal
Positive-feedback loop/feedforward mechanism
252
Why is vemurafinib ineffective in shutting down B-raf mutant colorectal carcinoma cells but effective in shutting down B-raf mutant melanoma cells?
A negative-feedback loop in colorectal carcinoma cells. Normally B-Raf signaling activates ERK which acts via negative feedback to suppress signaling by the EGF-R. When B-Raf is inhibited and MEK is shut down, this negative feedback loop no longer operates and EGF-R begins firing and signaling via alternative downstream pathway (Ras-PI3K-Akt-GSK-3beta cascade), driving colorectal carcinoma proliferation and circumventing the actions of vemurafinib.
Melanoma cells don’t express significant levels of EGF-R and cannot compensate for B-Raf inhibition
253
Cell formed when the plasma membranes of two or more cells fuse, initially resulting in a multi-nucleated cell
Syncytium
254
Pediatric tumor of the oligopotential stem cells of the retina
Retinoblastoma
This tumor arises in the precursors of the photoreceptor cells and occurs in 1 in 20,000 children
255
What two forms does retinoblastoma appear as in children
Unilateral retinoblastoma - occurs in children with no family history of the disease; sporadic, treatment is usually curative and these patients have NO RISK of tumors elsewhere in the body b/c of the disease
Bilateral retinoblastoma - familial, occurs in children with a parent who also suffered from and was cure of disease early in life; affects multiple sites in both eyes; removal does not protect these children from an increased risk of osteosarcoma during adolescence and an elevated susceptibility to developing other, nonretinal tumors later in life
256
Knudson’s conclusions about retinoblastoma showed the rate of appearance of familial tumors was consistent with a ___, whereas the sporadic tumors behaved as if __ were required for their formation
Single random event; two random events
This is Knudson’s “one-hit” and “two-hit” hypothesis
257
Explain the one hit/two hit concept
In retinoblastoma, familial retinoblastoma cases result because a child inherits a defective copy of one allele so it only takes one hit to inactivate the remaining wild type allele; this is why they usually get multiple tumors in both eyes (more likely for this event to happen). In the sporadic form, cases have two wild type alleles of the gene and require two separate hits, one after another, to fully inactivate the tumor suppressor function and develop tumors (since this is rare, it’s why they only get one tumor in one eye)
258
Rb is __ at the organismic level and __ at the cellular level (dominant/recessive)
Dominant ; recessive
259
On what chromosome is the Rb gene located
Chromosome 13
260
A genetic event in which one of two alleles at a heterozygous locus is lost; the lost allele may simply be discarded or be replaced with a duplicated copy of the surviving allele
Loss of heterozygosity
261
Ways loss of heterozygosity can occur
Mitotic recombination
Gene conversion
Chromosomal deletions
Loss of chromosomes (nondisjunction)
Translocation
262
A variant genetic allele or phenotype that doesn’t appear to be associated with any pathology and, by implication, is a reflection of normal intraspecies variability and thus normal function
Polymorphism
263
Variation in DNA sequence that can be detected through its effect of allowing or preventing cleavage of a chromosomal DNA segment by a restriction enzyme
Restriction fragment length polymorphism
264
DNA methylation only occurs when __ bases are located in a position that is __ to __ bases
Cytosine ; 5’ ; guanosines
Aka CpG
265
When CpG methylation occurs in the vicinity of a gene promoter, it can cause __ of transcription of the associated gene
Repression
When the methylation groups are removed, transcription of the gene is often de-repressed
266
What enzymes are responsible for methylating CpGs
DNA methyltransferases
267
During the early stages of tumor development, global __ occurs concurrently with __ of CpG island
Global hypomethylation
Hypermethylation of CpG islands
268
Methylation of CpG islands associated with gene promoter regions leads to __
Shutdown of gene expression
269
CpG methylation is effective in shutting down the expression of a gene only if it occurs where
Promoter or other regulatory sequences of the gene
(This is different from methylation of DNA sequences in the body of a gene, including exotic sequences, which seems to have little effect on transcription level)
270
NF1 acts as a negative regulator of __ signaling
Ras
271
T/F neurofibromatosis type 1 is a relatively common familial cancer syndrome occurring in 1 in 3500 individuals worldwide
True - characterized by development of neurofibromas (tumors of the sheaths around axons in the peripheral nervous system). Occasionally, a subclass of these tumors called plexiform neurofibromas can progress to malignant neurofibrosarcomas/malignant peripheral nerve sheath tumors
Patients with NF1 also have increased risk of gliomas, pheochromocytomas, and myelogenous leukemias b/c these tumors involve cell types arising from embryonic lineage
(Neurofibromatosis type 2 develops from mutation of a different tumor suppressor gene than type 1)
272
The Nf1 gene encodes the protein __ that functions as a __
Neurofibromin ; Ras-GAP
Remember Ras-Gaps negatively control Ras activation —> they force it to activate its GTPase activity and convert from active GTP bound Ras to inactive GDP bound Ras
273
Genetic condition in which the presence of only a single functional copy of a gene yields a mutant or partially mutant phenotype
Haploinsufficiency
In Nf1 gene, half-normal dose of neurofibromin to mast cells from a heterozygous mutant leads to development of tumors that is not seen when mast cells are exposed to homozygous wild type cells expressing neurofibromin
274
T/F Hereditary nonpolyposis colon cancer aka Lynch syndrome is caused by inherited mutations in DNA repair genes
True
275
Adenomatous polyposis coil (APC) aka familial adenomatous polyposis (FAP) results from a defect of the __ gene
Apc
276
The Apc gene is located on chromosome __
5
277
Beta-catenin’s downstream effects target genes that program __
Stem cell phenotype
278
The APC protein is normally responsible for negatively controlling the levels of __ in the cytosol
Beta-catenin
279
KEAP1 in normal cells acts as a sensor for chemical and environmental stresses and activation of KEAP1 leads to expression of genes encoding __
Cellular antioxidants and detoxification enzymes
280
KEAP1 interacts with what transcription factor
NRF2
In the absence of oxidative stress, KEAP1 sequesters NRF2 in the cytoplasm and targets it for ubiquitylation and degradation
281
Describe the KEAP1 pathway
ROS/toxic molecules react with cysteine residues in KEAP1 —> KEAP1 releases NRF2 —> NRF2 translocates to the nucleus and joins members of teh MAF transcription factor family and other transcription factors to bind genes whose promoters include antioxidant response element (ARE) sequences
282
Some cancers mutate Keap1 gene to cause __
Chronic upregulation of the NRF2-dependent detoxification pathway
Cancer cells produce lots of ROS so by increasing detoxification pathways they may experience selective advantage
283
__ and __ (tumor types) were found to have the highest frequency of Keap1 mutations
Adenocarcinomas and squamous cell carcinomas of the lungs
284
Tumor suppressor genes are considered ___ genes while DNA maintenance genes are considered __
(Caretaker/gatekeeper)
Tumor suppressor genes = gatekeepers
DNA maintenance genes = caretakers
285
Few cancer syndromes are associated with inherited mutant alleles of proto-oncogenes - what are they and what genes are involved
Costello syndrome - H-ras
Familial GISTs - Kit and PDGFR-A
Hereditary papillary renal cell cancer - Met
Multiple endocrine neoplasia - Ret
Noonan syndrome - PTPN11, K-ras, and SOS
Familial neuroblastoma (ALK)
286
___ cells exit the cell cycle irreversibly and cannot re-initiate active growth even in the presence of mitogens
Post-mitotic
Ex: neurons in the brain
287
DNA synthesis (S phase) usually takes __ in mammalian cells
6-8 hours
(But varies depending on cell type)
288
What are the five subphases of M phase
Prophase
Prometaphase
Metaphase
Anaphase
Telophase
289
What are the major checkpoints of the cell cycle
G1-S: prevents entry into S if genome is in need of repair
During S: slows or pauses DNA replication in response to DNA damage
G2-M: prevents entry into M until DNA replication is complete
DNA damage triggers another checkpoint that blocks entry into M
M phase: block entrance into anaphase until all chromosomes are attached to mitotic spindle
Decatenation: checkpoint in late G2 that prevents entrance into M until the pair of DNA helices replicated in S phase have been disentangled (which requires the active involvement of type II topoisomerases)
290
TGF-beta imposes its growth-inhibitory effects only during what periods of the cell cycle
Early and mid-G1
Once a cell is in late G1 it is oblivious to anti-mitogenic signals
291
Decision-making point in the late G1 phase of the cell cycle at which a cell commits itself to either completing the remaining phases or exiting into G0
Restriction point / R point
292
T/F Cancer cells that exhibit anchorage-independence have lost the late G1 checkpoint
True
293
Type of serine/threonine kinase deployed by the cell cycle machinery that depends on an associated Cyclin protein for proper functioning
Cyclin-dependent kinase
294
CDKs bind __
Cyclins
295
Which CDK binds what cyclin
CDK2 - cyclin A and cyclins E1 and E2
CDK 4/6 - cyclin D
CDK1 - cyclin A and cyclin B
296
What cyclins and CDKs are active during each step of teh cell cycle
Early and mid G1: CDK 4/6 and cyclin D
Late G1: CDK2 and cyclin E
Early to mid S: CDK2 and cyclin A
Mid S through late G2 - CDK1 and cyclin A
Late G2 and M - CDK1 and cyclin B
297
What enzymes trigger degradation of cyclins
Ubiquitin ligases
298
Which type of cyclins are controlled by extracellular signals
D type cyclins
299
CDK inhibitors modulate activity of the cyclin-CDK complexes. INK4 proteins are an example - what are the 4 types of INK4 proteins and which cyclin does the INK4 family target
INK4 proteins: these target CDK4/6 complexes and have no effect on CDK1 or CDK2
In this family there is p16INK4A, p15INK4B, p18INK4C, and p19INK4D
300
Name the three other CDK inhibitors besides the INK4 proteins. What do these target?
p21Cip1 (aka p21Waf1), p27Kip1, and p57Kip2
These are more wide activity and can target CDK2-E and CDK2-A complexes
301
TGF-beta when applied to epithelial cells elicits downstream responses that increase levels of __ which block the formation of cyclin D-CDK4/6 complexes and inhibit those that have already formed
p15INK4B
This may be why TGF-beta inhibits growth during early and mid-G1 but loses most of its power after cells go through the R point
302
What mitogens-activated pathway causes phosphorylation of p21Cip1 molecules to promote cell cycle progression
PI3K
303
p21Cip1 (aka p21Waf1) and p27Kip1 inhibit what cyclin-CDK complexes but stimulate what cyclin-CDK complexes
INHIBIT cyclin E-CDK2 and cyclin A-CDK2
STIMULATE cyclin D-CDK4/6
304
Describe phosphorylation of Rb through the cell cycle
Up phosphorylated during G0/immediately after exiting mitosis
Becomes HYPOphosphorylated during G1
Becomes HYPERphosphorylated as cells advance through the R point and remains that way throughout the remainder of the cell cycle
After cells exit mitosis the phosphate groups are stripped off by protein phosphatase type 1 which helps prompt reentry into the cell cycle
305
What enzyme removes phosphate groups from pRb after the cell exits mitosis
Phosphatase type 1 (PP1)
306
T/F Retinoblastoma protein is the molecular governor of the R point transition
True
307
Tumorigenic retroviruses acquire and exploit __ while DNA tumor viruses have evolved proteins that interfere with the actions of the __
host cell proto-oncogenes
Host cell tumor suppressor genes
308
HPV E7 not only sequesters pRB but also __
Tags it for ubiquitylation and thus proteolytic degradation
309
DNA tumor viruses bind preferentially to what form of pRB
HYPOphosphorylated form
This is present in most of G1 and are the growth-inhibitory forms of pRb; viral oncoproteins ignore the hyperphosphorylated form which has already been inactivated by phosphorylation
310
The _ form of pRb present in early and mid-G1 is actively growth inhibitory, whereas the _ form of pRb present after the R point is inactive
HYPOphosphorylated
Hyperphosphorylated
311
Which cyclin/CDK complex is responsible for initiating pRb hypophosphorylation
cyclin D and CDK4/6
312
At the R point, cyclin __ and CDK_ levels increase dramatically and drive pRb hyper phosphorylation
Cyclin E and CDK2
313
pRb exercises much of its control of the R point through its effect on what group of transcription factors
E2Fs
314
When pRb is in the __ states it binds E2Fs
Unphosphorylated or HYPOphosphorylated
E2Fs are associated with promoters of a number of genes under their control in the early and middle parts of G1; pRb (and its p107, p130 relatives) are bound to the E2Fs to prevent active gene transcription. Once pRb becomes HYPERphosphorylated at the R point they release E2Fs which are then able to stimulate transcription of their associated genes
315
E2F family has 8 members. Which members bind DNA directly without an associated DP1 or DP2 subunit
E2F7 and E2F8
1-6 bind DP1 or DP2 to form heterodimeric transcription factors
316
pRb functions as a transcriptional repressor via recruitment of _
Histone deacetylases (HDACs)
317
What forms of E2F are present in abundance in quiescent cells
E2F4 and E2F5
318
General overview of Ras signaling effect on cell cycle
Growth factors —> growth factor receptors —> Ras —> cyclins D1 and E —> inactivation of pRb —> activation of E2Fs —> S phase entrance
319
Myc targets the cyclin __ gene and the CDK __ gene
D2 ; CDK4
320
TGF-beta
321
Two organisms/cells/tissues that share identical genetic background
Syngeneic
322
Large tumor (large T) antigen comes from what virus
SV40 DNA tumor virus
323
What is Li-Fraumeni syndrome
Condition of increased cancer susceptibility that results from point mutations in the p53 gene coding sequence
Germ line mutation
Inherited autosomal dominant
324
What chromosome is p53 gene located on
17
325
Mutant allele of a gene that, when co-expressed with the wild-type allele of the gene, is able to interfere with the functioning of the latter
Dominant-interfering or dominant-negative
326
P53 mutations are usually ___ resulting in amino acid substitutions (rather than __ which cause termination and degradation of the growing polypeptide chain)
usually missense
Nonsense cause termination and (often) degradation
327
What things can cause increases in p53 levels in a cell (stressors)
x-rays
UV radiation
Chemo drugs that damage DNA
Inhibitors of DNA synthesis
Hypoxia
Increases in ROS
Exposure of cells to nitrous oxide/acidified growth medium
Myc oncogene
High levels of E2F1
Widespread demethylation of DNA
Nucleotide deficits
Blockage of RNA or DNA synthesis
328
Proteins that recognize double stranded DNA breaks work through __ kinase
ATM
329
What kinases phosphorylate p53 directly
ATM (Which then activates Chk2 that can then go on to phosphorylate p53)
ATR (which then activates Chk1 that can then go on to phosphorylate p53)
330
Phosphorylation of p53 causes DEGRADATION/STABILIZATION
Stabilization - protects it from destruction by Mdm2
331
Ataxia telangiectasia is caused by deficiency of what kinase
ATM
332
Single-strand DNA breaks active what kinase
ATR
333
Degradation of p53 is regulated by what protein
Mdm2 aka ubiquitin ligase
(Reverse is true too - expression of Mdm2 is controlled by p53)
334
Chromosome segment that becomes separated from the chromosome in which it normally resides and is able to perpetuate itself as an extra chromosomal particle unlinked to a centromere
Double minute chromosome
335
T/F Mdm2 binds p53 immediately blocking its ability to act as a transcription factor by preventing its interaction with transcriptional cofactors like acetyltransferases and histone methyltransferases
True
336
Steps of Mdm2 inactivation of p53
Binds p53 —> prevents transcriptional cofactor binding so it can’t be a transcription factor (immediate) —> next causes attachment of a ubiquitin moiety and export of the ubiquitylated p53 out of the nucleus to the cytoplasm
In the cytoplasm p53 is polyubiquitylated and degraded
337
Mdm2 often forms heterodimers with what other protein that is thought to be responsible for the ubiquitylation activity
Mdm2 (aka Mdm4)
338
T/F Phosphorylation of p53 protects it from degradation by Mdm2/MdmX complexes
True
339
Phosphorylation of Mdm2 is caused by what kinase (that also phosphorylates p53).
Does phosphorylation of Mdm2 stabilize it?
ATM kinase
NO - causes functional inactivation and destabilization of Mdm2
340
`ARF induces rapid increases in p53 by inhibiting __
Mdm2
341
What are the important proteins involved in apoptosis
Caspaases 3, 7, 8, 9
Bcl-2 proteins (Bim, Noxa, PUMA)
Apaf-1
p73
342
During apoptosis the “Eat-me” signal is __ and is recognized by __
Phosphatidylserine (PS)
Recognized by annexin receptor on phagocytic cells
343
Name the pro-apoptotic and anti-apoptotic Bcl-2 family proteins
Pro-apoptotic: Bax and Bak
Anti-apoptotic: Bcl-2, Bcl-XL, and Mcl1
344
Bcl-2, Bcl-XL, and Mcl-1 contain __ BH domains
4
345
Name the BH3 only proteins
Bid
Bim
Noxa
Bad
PUMA
346
Anoikis is dependent on what BH3 only protein
Bim
347
p53 induces expression of which BH-3 only proteins
PUMA
Noxa
348
What are the initiator caspases
2, 8, 9, 10
Initiator caspases become activated by upstream activating signals in the apoptotic pathway and function to activate downstream members of the caspase family
349
What are the executioner caspases
3, 6, 7
These caspases are activated by initiator caspases and function to cleave cellular target proteins leading to cell death
350
Death receptors bind what ligands
TNF proteins
351
Tsp-1 is a secreted protein that functions in the extracellular space to __
Block development of new blood vessels
352
What DNA sequence is repeated in telomeres (g rich strand)
TTAGGG
353
Mutation that confers no selective advantage on a cell caring it, but whose presence in a population of cells is increased because it resides in the same genome as other alleles that do indeed confer advantage
Passenger mutation
354
Mutation creating an allele of a gene that is advantageous for the cell that sustains it and results in clonal expansion of the progeny bearing mutant alleles of this gene
Driver mutation
355
What is Peto’s paradox?
Discrepancy that large bodied long lived organisms do not confront greater cancer incidents than corresponding smaller short-lived animals in spite of vast differences in cumulative cell divisions experienced during an average lifetime
356
What specific mutagenic agents have been associated with cancer in humans?
Tobacco smoke
ultraviolet radiation
aflatoxin B1
ethanol (which becomes mutagenic, following conversion in the liver to acetaldehyde)
357
Hepatitis B virus can function synergistically with what mutagen in compound to increase risk of hepatocellular carcinoma in humans
Aflatoxin B1
358
Agent that can act as both an initiator and a promoter of tumor progression
Complete carcinogen
359
Cancer cells express high levels of __ which may contribute to their use of glycolysis rather than oxidative phosphorylation
GLUT1 - especially carcinomas and hematopoietic tumors
Cancer cells take in large amounts of glucose from the extracellular space
360
High levels of GLUT1 gene expression is driven by what oncogenes and transcription factors
myc
ras
src
HIF-1alpha transcription factor
361
What enzyme catalyzes the last step of glycolysis
Pyruvate kinase (PK)’
Converts phosphoenolpyruvate to pyruvate
362
What isoform of PK is typically expressed in adult tissues vs. cancer cells
M1 = most differentiated adult tissues
M2 = cancer cells, early embryonic cells, and rapidly growing normal cells
M2 causes pyruvate to be diverted away from the mitochondria, reduced to lactate in the cytosol, and secreted
363
What enzyme reduces pyruvate to lactate
Lactate dehydrogenase-A (LDH-A)
364
__ serves as a precursor source of nitrogen for bases of RNA and DNA
Glutamine
365
T/F: Glutamine is an essential amino acid
FALSE - considered nonessential because normal cells can synthesize it (but important from extracellular sources is critically important still)
366
T/F: cancer cells require normal amounts of glutamine
FALSE: they require A LOT (more than used in making proteins)
367
Stem cells express high levels of what drug pump
Mdr1
368
What are the three most important DNA polymerases
pol-alpha
pol-delta
pol-epsilon
369
Which DNA polymerase is most important in proofreading
pol-delta
370
pol-__ is responsible for leading-strand synthesis at the application fork
pol-sigma
371
Class of DNA repair processes that depend on proofreading a recently synthesize segment of DNA and removing any misincorporated bases that may have escaped previous correction by DNA polymerase associated proofreading functions
Mismatch repair
372
Mutational process in which the immune groups that protrude from cytosine, adenine, and guanine rings of the DNA bases are lost
Deamination
373
Deamination of cytosine yields what
Uracil
374
Deamination of adenine yields what
Hypoxanthine
375
Deamination of guanine yields what
Xanthine
376
Deamination of 5-methylcytosine yields what
Thymine
377
Point mutation in which one purine base replaces other or in which one pyrimidine base replaces another
Transition
378
White mutation in which a purine base replaces a pyrimidine or vice versa
Transversion
379
What enzymes help neutralize reactive oxygen species
Superoxide dismutase
Catalase
380
Enzymes that covalently link electrophilic compounds, and thus many carcinogens, with glutathione, thereby detoxifying these compounds and preparing them for further metabolism and excretion
Glutathione S-transferases
381
What enzyme removes methyl and ethyl adducts from the O6 position of guanine thereby restoring the structure of the normal base
O6-methylguanine-DNA methyltransferase (MGMT) aka DNA alkyltransferase
382
Form of DNA repair that initially involves cleavage by a repair enzyme of the glycosidic bond between a base and a deoxyribose, leaving behind an abasic nucleotide
Base excision repair
383
Type of DNA repair in which the initial step involves the excision of nucleotides rather than bases
Nucleotide excision repair
384
BER tends to repair lesions in the DNA that derived from __ sources while NER largely repairs lesions created by __ sources
BER = endogenous
NER = Exogenous
385
NER is split into what subtypes
Transcription coupled repair - focuses on template strand, occurs during transcription to prevent stalling of RNA polymerase
Global genomic repair - focuses on non template strand of transcribed genes as well as non transcribed regions of the genome
386
The pattern of inheritance of xeroderma pigmentosa is
Autosomal recessive
387
Cockayne syndrome (CS) is a defect of
Transcription coupled NER
388
Hereditary non-polyposis colon cancer aka Lynch syndrome results from germ line mutations affecting what proteins
Mismatch repair proteins
Specifically MSH2 and MLH1
389
Nijmegen breakage syndrome characterized by a lack of what protein, leading to failure to execute the initial steps of homologous repair so cells are forced to use non-homologous end joining instead
NBS1
390
Homologous repair occurs when during the cell cycle
S and G2
Need a template strand available
391
Non-homologous end joining occurs when during the cell cycle
G1
392
A normal or neoplastic tissue, derived from one species that has been implanted into a host animal from another species
Xenograft
393
The tumor microenvironment is made of what components
Stromal cells
Extracellular matrix
394
Adherens junctions are made up of __ which is replaced by __ during wound healing
E cadherin
N cadherin
395
Shifting display of surface cadherins allows epithelial cells to undergo
Epithelial to mesenchymal transition
396
What chemokine is expressed by neuroectodermal and epithelial cancer cell types to attract monocytes
Monocyte chemotactic protein-1 aka macrophage chemoattractant protein-1 aka MCP-1
In other tumors, VEGF, CSF-1/M-CSF, and PDGF do this
397
What matrix metalloprotease is prominently involved in cancer progression
MMP 9
398
What is the distance oxygen can effectively diffuse through living tissues
0.2mm
399
What three mechanisms contribute to high intra-tumoral hydrostatic pressure
1 - lymphatic vessel collapse
2 - leaky capillaries
3 - fibroblast contraction
400
Shift by a mass of tumor cells from a state in which they are unable to induce neovascularization to one in which they exhibit this activity
Angiogenic switch
401
monoclonal antibody that binds VEGF-A
bevacizumab aka Avastin
402
Epithelial cells undergoing EMT will stop expressing __ and start expressing __
Cytokeratin; vimentin
403
Vimentin is a marker of what cell type
Mesenchymal
404
What are some EMT-inducing transcription factors
Twist
Snail
Slug
Goosecoid
FOXC2
ZEB1
ZEB2
E12/E47
Prrx 1
405
Snail and Slug are TFs that repress transcription of
E-cadherin
