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Onc Boards > Weinberg > Flashcards

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

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2
Q

Neutral mutation

A

Change in DNA sequence that has no effect on phenotype, including mutations that have no effect on protein structure

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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

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4
Q

Mutation affecting a single DNA nucleotide

A

Point mutation

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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

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6
Q

Deviations from normal chromosome number

A

Aneuploidy

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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

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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

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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

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10
Q

Enzyme that cleaves a protein substrate

A

Protease

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11
Q

Process of copying DNA sequences into RNA molecules

A

Transcription

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12
Q

What enzymes mediate transcription?

A

RNA polymerases

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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

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14
Q

Portion of a primary RNA molecule that is deleted during the process of splicing

A

Intron

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15
Q

Portion of primary RNA transcript that is retained in the RNA product of splicing

A

Exon

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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

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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)

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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

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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

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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

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21
Q

Gene that is expressed only in cells of certain individual tissue types

A

Tissue-specific genes

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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

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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

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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

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25
Q

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

A

Enhancer

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26
Q

__ consists of a core formed as an octamer of four different histone molecules, each present in two copies

A

Nucleosome

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27
Q

Degree of compaction of chromatin is regulated by __

A

N-terminal tail of the histone

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28
Q

What are the four standard histone species that comprise nucleosome octamers?

A

H2A
H2B
H3
H4
**H1 is bound to some, but not all nucleosome octamers

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29
Q

Histone variant whose phosphorylation occurs in the nucleosomes that flank sites of double-strand DNA breaks, facilitating subsequent DNA repair

A

H2AX

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30
Q

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

A

H2A.Z

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31
Q

Most histone modifications affect what residues?

A

Lysine and arginine

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32
Q

Types of histone modifications

A

Methylation
Acetylation
Phosphorylation
Ubiquitylation
(Less common biotinylation and sumoylation)

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33
Q

What enzyme attaches methyl groups covalently to cytosine bases of CpG dinucleotides in DNA

A

DNA methyltransferases

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34
Q

What does CpG mean

A

Cytosine positioned 5’ immediately before guanine

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35
Q

Methylation of CpG dinucleotides generally causes __ of nearby genes

A

Repression

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36
Q

How does methylation occur?

A

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

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37
Q

What are microRNAs (miRNA)?

A

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

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38
Q

What miRNA was found to suppress expression of the ras gene

A

Let-7

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39
Q

Loss of what miRNA processing enzyme has been found to facilitate the formation of tumors in mice and humans?

A

Dicer

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40
Q

What are long non-coding RNAs?

A

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

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41
Q

What long non-coding RNA has been found to be correlated with metastatic behavior of human breast and colorectal carcinomas?

A

HOTAIR

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42
Q

What are small circular RNAs?

A

RNAs created as side products of splicing in the nucleus. Only a tiny subset play functional roles

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43
Q

__ is an important tumor suppressing microRNAs

A

MiR-7

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44
Q

Mechanisms that control protein formation/accumulation

A

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

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45
Q

What is the function of a kinase?

A

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)

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46
Q

What is a homologous gene?

A

A gene or characteristics that are similar in related organisms because of shared descent from a common precursor

Also orthologs

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47
Q

What are paralogs?

A

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

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48
Q

What enzyme is capable of making a DNA complementary copy of an RNA molecule using the RNA molecule as a template

A

Reverse transcriptase

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49
Q

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

A

Metastasis

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50
Q

Tumor growing at the anatomical site where tumor formation began and proceeded to yield this mass

A

Primary tumor

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51
Q

Any of a series of pre-malignant, non-invasive growths in various epithelial tissues, many of which have the potential to further to carcinomas

A

Adenoma

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52
Q

The majority of human tumors arise from __

A

Epithelial tissues

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53
Q

The specialized extracellular matrix that forms a sheet separating epithelial from stromal cells or endothelial cells from pericytes

A

Basement membrane (aka basal lamina)

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54
Q

Meshwork of secreted proteins, largely glycoproteins and proteoglycans, that surrounds most cells within tissues and creates a structural scaffold in the intercellular space

A

Extracellular matrix

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55
Q

Cancer arising from epithelial cells

A

Carcinoma

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56
Q

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

A

Endoderm

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57
Q

Outermost layer of cells in an early chordate embryo that gives rise to the skin and nervous system

A

Ectoderm

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58
Q

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

A

Mesoderm

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59
Q

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 __

A

Squamous cell carcinomas

Epithelial cells lining the skin (keratinocytes) and most of the oral cavity spawn tumors of this type

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60
Q

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.

A

Keratinocytes

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61
Q

Tumor derived from secretory epithelial cells

A

Adenocarcinoma

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62
Q

Tumor derived from mesenchymal cells, usually those constituting various connective, tissue cell types, including fibroblasts, osteoblasts, endothelial cell precursors, and chondrocytes

A

Sarcoma

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63
Q

Referring to tissue, composed of cells of mesodermal origin, including fibroblasts, smooth muscle cells, endothelial cells, and adipocytes

A

Mesenchymal

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64
Q

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

A

Fibroblast

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65
Q

Mesenchymal cell type related to fibroblasts that constructs mineralized bone through the deposition of a collagenous matrix and apatite (calcium phosphate) crystals

A

Osteoblasts

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66
Q

Hematopoietic cells derive from the __

A

Mesoderm

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67
Q

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

A

Leukemia

RBCs are pigmented so don’t get called leukemia

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68
Q

Solid tumor of lymphoid cells

A

Lymphoma (usually in LNs)

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69
Q

Nonepithelial tumors arising from cells that form various components of the central and peripheral nervous systems

A

Neuroectodermal tumors

Includes gliomas, glioblastomas, neuroblastomas, schwannomas, and medulloblastomas

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70
Q

Melanomas derive from melanocytes, which arise from a primitive embryonic structure termed the __

A

Neural crest

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71
Q

Small-cell lung carcinomas (SCLCs) secrete ___ in response to neuronal signaling

A

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

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72
Q

Transition by a cell from one differentiation lineage into other phenotypic state characteristic of cells from another, distinct differentiation lineage

A

Transdifferentiation

Usually irreversible

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73
Q

Benign tumor formed by embryonic stem cells in which a wide variety of differentiated cell types are formed

A

Teratoma

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74
Q

Reversion of a more differentiated cell to the phenotype of a less differentiated cell, such as its stem cell precursor

A

Dedifferentiation

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75
Q

Having a tissue and cellular architecture lacking the differentiated characteristics of an identifiable tissue-of-origin or tumor type

A

Anaplastic

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76
Q

A tumor, often a metastasis, whose histopathological appearance does not permit a determination of its tissue-of-origin within a patient

A

Cancer of unknown primary

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77
Q

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

A

Hyperplasia

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78
Q

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)

A

Metaplasia

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79
Q

Where is metaplasia most frequent

A

Epithelial transition zones

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80
Q

Metaplasia in which squamous epithelium of the esophagus is replaced by secretory epithelial cells of a type normally found in the stomach

A

Barrett’s esophagus

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81
Q

A pre malignant tissue composed of abnormally appearing cells forming tissue architecture that deviates from normal

A

Dysplasia

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82
Q

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

A

Polyp

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83
Q

Benign, adenomatous proliferation of epithelial cells; term often used to describe benign lesions of the skin

A

Papillomas

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84
Q

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

A

Truncal

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85
Q

The Philadelphia chromosome results from a translocation of what two chromosomes?

A

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

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86
Q

The Philadelphia chromosome is present in the leukemia cells of most __ patients

A

Chronic myelogenous leukemia (CML)

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87
Q

Describe the Ames experiment

A

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

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88
Q

Chemical compound that is relatively nonreactive chemically but can be converted into a highly reactive carcinogen, usually through metabolic processes

A

Procarcinogen

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89
Q

A chemical compound that is able to directly contribute to the induction of cancer without further chemical modification

A

Ultimate carcinogen

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90
Q

Agent that furthers progression of multi-step tumorigenesis by nongenetic mechanisms, notably those involving inflammation and/or mitogenesis

A

Tumor promoters

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91
Q

Name the ten properties of transformed cells

A
  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
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92
Q

Ability of a gene to concomitantly induce a number of distinct alterations in a cell

A

Pleiotropy

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93
Q

What oncogenes are associated with HPV?

A

E6 and E7

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94
Q

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?

A

Epstein-Barr virus (herpesvirus)

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95
Q

The __ gene of HPV produces a product that represses transcription of viral oncogenes, and this gene is discarded/disrupted during chromosomal integration.

A

E2

(Disruption allows active transcription of the E6 and E7 oncogenes)

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96
Q

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

A

Episomes

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97
Q

The dsDNA copy of a retroviral genome that is the product of reverse transcription

A

Provirus

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98
Q

Process through which an RNA template is copied into complementary DNA

A

Reverse transcription

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99
Q

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

A

Retrovirus

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100
Q

What are some examples of retroviruses?

A

RSV
HIV
Avian leukosis virus (ALV)
Murine leukemia virus (MLV)

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101
Q

What is the function of the enzyme integrase?

A

To integrate an episomal DNA (such as retroviral DNA genome) into host-cell chromosomal DNA

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102
Q

What gene encodes integrase?

A

pol

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103
Q

What gene contains all the viral transforming functions of RSV?

A

src

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104
Q

Avian leukosis virus is src-___ while RSV is src-____

A

Negative; positive

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105
Q

What is the definition of an oncogene?

A

Gene that can transform cells from a normal to a neoplastic state

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106
Q

What is the definition of a proto-oncogene?

A

Normal cellular gene that, upon alteration by DNA-damaging agents or viral genomes, can acquire the ability to function as an oncogene

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107
Q

____ is a ___ and plays a role in the normal life of chickens, but ___ is a ___ and causes cell transformation because of RSV integration

A

c-src; proto-oncogene
v-src; oncogene

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108
Q

What oncogene is found in feline leukemia virus and what does it cause?

A

fes; feline sarcoma virus

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109
Q

What viruses carry H-ras and K-ras?

A

H-ras = Harvey sarcoma virus
K-ras = Kirsten sarcoma virus

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110
Q

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

A

Insertional mutagenesis

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111
Q

What is the Cag pathogenicity island?

A

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

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112
Q

T/F: CagA function is required even after tumors develop in gastric carcinoma cases

A

FALSE - it’s a “hit and run” oncoprotein

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113
Q

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

A

Transfection

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114
Q

What compound in coal tars is a potent carcinogen and mutagen

A

3-methylcholanthrene (3-MC)

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115
Q

erbB-related gene erbB2 is also known as as what

A

neu or HER2

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116
Q

Increases in gene copy number of HER2 of ___ are associated with decreased survival in human breast cancer

A

> 5

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117
Q

the gene whose amplification is thought to be causal in fostering tumor development

A

Driver

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118
Q

nearby flanking genes that “may go along for the ride” but are mechanistically unimportant in tumor development; genes altered by passenger mutations

A

Passenger

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119
Q

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

A

Tumor suppressor gene

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120
Q

What mutation of H-ras proto-oncogene led to activation of the oncogene?

A

point mutation in teh reading frame from G in proto-oncogene to T in oncogene

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121
Q

Pancreatic carcinoma has a point mutation in which ras gene

A

K ras

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122
Q

Melanoma has a point mutation in which ras gene

A

N ras

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123
Q

Gene notations

A
  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)
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124
Q

What chromosomes are involved in translocations in burkitt’s lymphoma?

A

Chromosomes 2, 14, or 22 and chromosome 8

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125
Q

Why are chromosomes 2, 14, and 22 important in development of Burkitt’s lymphoma? (Aka what do they contain)

A

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

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126
Q

What is the bcr-abl protein

A

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

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127
Q

80% of alveolar rhabdomyosarcomas harbor a translocation that fuses the domains of what two transcription factors

A

PAX3 or PAX7 and FKHR

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128
Q

Name 6 common growth factors

A

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)

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129
Q

An agent that provokes cell proliferation

A

Mitogen

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130
Q

PDGF is a potent stimulator of ___

A

Fibroblasts

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131
Q

EGF causes what

A

Dramatic changes in cell shape
Stimulates proliferation of epithelial cells

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132
Q

What is the universal phosphate donor of the cell

A

ATP

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133
Q

Src operates as what kind of enzyme

A

Tyrosine Kinase

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134
Q

Protein to which one or more phosphate groups have been covalently attached, usually to threonine, serine, or tyrosine residues

A

Phosphoprotein

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135
Q

Src phosphorylates certain ___ residues of its protein substrates

A

Tyrosine

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136
Q

Most phosphoproteins are phosphorylated at __ and __ residues

A

Threonine and serine

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137
Q

Where was the erbB oncogene originally discovered

A

Genome of avian erythroblastosis virus (AEV)

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138
Q

The v-sis oncogene comes from what virus

A

Simian sarcoma virus

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139
Q

What cells does PDGF stimulate

A

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)

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140
Q

PDGF-R is what kind of receptor

A

Tyrosine kinase

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141
Q

Kaposi’s sarcoma is caused by what

A

Human herpesvirus 8 (HHV-8)

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142
Q

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

A

ret

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143
Q

What gene encodes the receptor for hepatocyte growth factor (HGF)

A

met

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144
Q

What mutation in Rottweilers is responsible for their high risk of developing several types of cancer?

A

Mutation in met gene leading to point mutation affecting the juxtamembrane region of Met receptor

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145
Q

Examples of Janus kinases (JAKs)

A

EPO receptor
TPO receptor
Interferon receptor

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146
Q

What protein involved in facilitating endocytosis is overexpressed in a variety of human carcinomas

A

huntingtin-interacting protein-1 (HIP1)

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147
Q

Overexpression of HIP1 prevents endocytosis of a number of cell surface proteins, including ___

A

EGF-R

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148
Q

What protein is a stron promoter of EGF-R endocytosis?

A

cyclin-G associated kinase (GAK)

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149
Q

What protein is responsible for tagging ligand-activated EGF-R via mono-ubiquitylation, causing endocytosis of EGF-R and degradation in lysosomes?

A

c-Cbl

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150
Q

Three types of Hedgehog ligands

A

Desert Hh
Indian Hh
Sonic Hh

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151
Q

G-protein-coupled receptors activate

A

guanosine nucleotide-binding proteins (G-proteins)

These G-proteins switch between a GTP-bound active state and a GDP-bound inactive state

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152
Q

Chemokine receptors are a subset of what receptor type

A

GPCRs

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153
Q
A
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154
Q

Steroid sex hormones, retinoids, and vitamin D are hydro____

A

Phobic

This allows them to readily penetrate the plasma membrane and advance further into the nucleus

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155
Q

Name the parts of a nuclear receptor

A

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

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156
Q

An oligonucleotide sequence in genomic DNA to which hormone-activated nuclear receptors bind

A

Hormone response elements (HREs)

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157
Q

Estrogen receptor binds

A

Estrogen! Aka 17Beta-estradiol or E2

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158
Q

What is tamoxifen

A

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)

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159
Q

Vitamin D ligand has strong effects in normalizing the otherwise highly abnormal stroma of _____ (tumor)

A

Pancreatic adenocarcinomas

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160
Q

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

A

Anoikis

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161
Q

A cell surface tyrosine kinase receptor that recognizes and binds extracellular collagen as its activating cognate ligand

A

Discoidin domain receptors (DDRs)

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162
Q

A heterodimeric cell surface receptor that binds components of the ECM and transmits info about this binding to the cell interior

A

Integrin

The cytoplasmic domain of an integrin may also be coupled with components of the cytoskeleton, thereby linking the ECM to the cytoskeleton

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163
Q

Ras protein functions as a ___ protein

A

G-protein

164
Q

___ distinct ras genes in mammalian cells encode ___ distinct Ras proteins

A

Three; four

K-ras specifies a second protein via alternative splicing of a pre-mRNA

165
Q

What allows Ras proteins to anchor to the cytoplasmic side of the plasma membrane

A

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
Q

Ras has __ activity in that it can bind and hydrolyze (cleave) guanosine nucleotides

A

GTPase

(This is different than Src and erbB)

167
Q

5 ways Ras is similar to G proteins

A

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
Q

What molecule stimulates the Ras protein

A

GEF (guanine nucleotide exchange factor)

169
Q

GTPase activity of Ras is intrinsic but can also be strongly stimulated by ___

A

GAPs (GTPase-activating proteins)

GAPs increase intrinsic GTPase activity of Ras by as much as 100,000-fold

170
Q

___ mutations in Ras block stimulatory GAPs from interacting with Ras

A

Point mutations (cause amino acid substitutions)

This traps Ras in its activated, signal-emitting state

171
Q

Ras oncoprotein has lost virtually all of its ___ activity

A

GTPase

172
Q

Which codons are typically subject to missense mutations in the ras genes

A

12, 13, 61

12 is most common

173
Q

What is the half life of the Myc protein

A

25 minutes

174
Q

Signal transduction from Myc depends on its __ within a cell, whereas signal transudction with Ras and Src depends on their ___

A

Concentration ; relocalization and structure

175
Q

Domains of Src and function

A

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
Q

What three major downstream signaling cascades radiate from the Ras protein?

A

PI3K
Raf
Ral

177
Q

Raf, once activated, activates another kinase called ___

A

MEK

178
Q

Once activated, MEK phosphorylates what two kinases?

A

ERK1
ERK2

ERK = extracellular signal-regulated kinases

179
Q

ERK1 and ERK2 are considered

A

MAPKs (mitogen-activated protein kinases)

180
Q

What kinase phosphorylates MAPK

A

MAPKK

MEK functions as a MAPKK

181
Q

What kinase phosphorylates MAPKK

A

MAPKKK

Raf is classified as a MAPKKK

182
Q

Serine/threonine kinase phosphorylation leads to ____ whereas tyrosine kinase phosphorylation leads to ___

A

Functional activation

Relocalization of partner proteins

183
Q

What two chromatin-associated proteins are activated by downstream signaling from ERK

A

HMG-14
Histone H3

184
Q

What growth-regulating genes are stimulated as a result of ERK phosphorylation of the Ets transcription factor

A

Heparin-binding EGF (HB-EGF)
Cyclin D1
Fos
P21Waf1

185
Q

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)

A

Fos
Jun

186
Q

PI3K pathway has __ effect

A

Anti-apoptotic

187
Q

___ is a water-soluble carbohydrate molecule (polyalcohol)

A

Inositol

188
Q

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

A

Phosphoinositol (IP3)

189
Q

Phosphorylated inositol is cleaved into what two parts and what are their functions

A

IP3 (phosphoinositol) - second messenger

DAG (diacylglycerol) - stays at plasma membrane and activates kinases (specifically protein kinase C)

190
Q

___ is responsible for attaching a phosphate group to the 3’ hydroxyl of the inositol moiety of membrane-embedded phosphatidylinositol (PI)

A

PI3K (phosphatidylinositol 3-kinase)

191
Q

A specific PI3K phosphorylates ___

A

PI(4,5)P2 aka PIP2

192
Q

PIP2 acquires another phosphate group and becomes ___

A

PIP3 aka PI(3,4,5)P3

193
Q

Akt/PKB is a ___ protein (and what type of kinase)

A

PH-domain containing protein

PH = pleckstrin homology

It is a serine/threonine kinase

194
Q

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)

A

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
Q

PIP3 levels are low in ___ cells and increase after these cells encounter ___

A

Quiescent ; mitogens

196
Q

____ is a phosphatase that reverses the actions of activating kinases like PI3K

A

PTEN

197
Q

PTEN removes the ___ from PIP3

A

3’ phosphate group

198
Q

Functions of Rho proteins

A

Reconfiguration of the cytoskeleton and the attachments that a cell makes with its physical surroundings

199
Q

___ mediate communication between Ras and Ral

A

Ral guanine nucleotide exchange factors (Ral-GEFs)

200
Q

The Ral pathway can activate what two proteins that contribute to Ras-mediated anchorage-independent growth

A

Sec5
Exo84

201
Q

process of JAK/STAT interactions

A

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
Q

What genes are known targets of STATs

A

myc
genes for cyclins D2 and D3 (allows cells to go through growth and division cycles)
Genes encoding Bcl-XL (anti-apoptotic protein)

203
Q

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

A

STAT3

204
Q

Which STAT acts as a tumor-suppressing protein by antagonizing cell proliferation and survival

A

STAT1

205
Q

Three functions of integrins

A

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
Q

Wnt factors act through __ receptors to suppress activity of __

A

Frizzled receptors
Glycogen synthase kinase-3beta (GSK-3beta)

207
Q

In the absence of Wnts, GSK-3beta phosphorylates key proteins to tag them for destruction, including __

A

Beta-catenin

208
Q

Where is Beta-catenin usually found

A

Cytoplasm

209
Q

Three states Beta-catenin exists in

A

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
Q

Cytosolic Beta-date in molecules result after __ are dissolved via endocytosis of ___ molecules

A

Adherens junctions ; E-cadherin

211
Q

Cytosolic Beta-catenin molecules may initially form multi protein complexes with what three proteins

A

Apc (adenomatous polyposis coil protein)
Wtx
Axin

212
Q

Phosphorylation of Beta-catenin by GSK-3beta results in destruction of Beta-catenin by __

A

Ubiquitylation

213
Q

Wnt signal activation has what effect on Beta-catenin

A

Prevents its destruction which leads to increased half-life and increased steady state concentrations

214
Q

GSK-3beta can also phosphorylate __ in the nucleus

A

cyclin D1

215
Q

non-canonical Wnt signaling means the pathways operate independently of __ signaling

A

Beta-catenin

216
Q

The most important non-canonical Wnt signaling pathways involve five RTKs which carry catalytically inactive kinase domains. What are examples?

A

Ror1
Ror2

217
Q

Six dual address signaling pathways that play a role in human cancers

A

JAK-STAT
Wnt-Beta-catenin
NF-kB
Notch
Hedgehog
TGF-Beta

218
Q

The most common form of NF-kB is a heterodimer of what two subunits

A

p65
p50

219
Q

What sequesters NF-kB in teh cytoplasm

A

IkB

220
Q

Describe NF-kB pathway

A

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
Q

What are some signals that can stimulate IKK

A

TNF-alpha
IL-1beta
LPS
ROS
anti-cancer drugs
gamma irradiation

222
Q

What key anti-apoptotic proteins does NF-kB induce expression of

A

Bcl-2
IAP-1
IAP-2

223
Q

NF-kBs function in a mitogenic fashion by inducing expression of __ genes

A

myc
cyclin D1

224
Q

__ is overexpressed in ~30% of human breast cancers and leads to constitutive activation of the NF-kB pathway

A

IKKepsilon

225
Q

What gene that encodes one of the subunits of NF-kB is amplified in ~25% of human diffuse large B cell lymphomas

A

REL

226
Q

T/F NF-kB overexpression is associated with a poor prognosis in a variety of common cancers

A

True

227
Q

What are the ligands of the Notch receptor

A

Jagged-like protein
Notch-like protein

228
Q

Describe Notch signaling cascades

A

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
Q

Notch signaling is important in governing cell __

A

Differentiation

230
Q

Notch can activate what gene

A

Myc

231
Q

Changes to the Notch receptor after binding ligand are REVERSIBLE/IRREVERSIBLE

A

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
Q

Notch signaling operates in an AUTOCRINE/ENDOCRINE/PARACRINE/JUXTACRINE fashion

A

Juxtacrine - two cells are in direct physical contact with one another

233
Q

Overexpression of one or another of the Notch proteins is seen in what cancer types

A

Cervical carcinomas (majority)
Subsets of colon and prostate carcinomas
Squamous cell carcinomas of the lung

234
Q

Increased expression of what two classes of Notch ligands has been found in some cervical and prostate carcinomas

A

Jagged
Delta

235
Q

60% of all human T-cell acute lymphocytic leukemias have constitutively active __

A

Notch

236
Q

Hedgehog (Hh) is the ligand for what receptor

A

Patched (Ptc)

237
Q

Binding of Hedgehog ligand to Patched receptor alters the receptor’s interaction with __

A

Smoothened (Smo)

238
Q

Describe the Hedgehog signaling pathway

A

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
Q

Hh signaling during embryogenesis has been associated with __

A

Development of patterned development in certain tissues as well as commitments to specific cell states

240
Q

Gli was discovered as a highly expressed protein in

A

Glioblastoma

241
Q

Germaine inactivating mutations of the human patched (PTCH) gene cause __ syndrome

A

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
Q

Tumor of cells arising from primitive stem cells in the cerebellum

A

Medulloblastoma

243
Q

50% of sporadic basal cell carcinomas of the skin (which occur due to somatic mutations) carry mutant ___ and __ alleles

A

PTCH1 (encodes patched 1)
SMO (encodes smoothened)

244
Q

Paracrine signaling of Hh has been reported in what tumor type

A

Small cell lung carcinomas

245
Q

TGF-beta and its signaling pathway play major roles in what class of cancers

A

Carcinomas

246
Q

Describe the TGF-beta pathway

A

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
Q

Smad transcription factors recognize and bind only __

A

Tetranucleotide sequence in chromosomal DNA

248
Q

When signaling in the presence of a Ras oncoprotein, TGF-beta may induce __

A

Epithelial-mesenchymal transition

249
Q

T/F: High-level expression of Yap or Taz, especially when present in the nuclei of carcinoma cells, is correlated with aggressive clinical behavior

A

True

250
Q

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

A

Negative feedback

251
Q

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

A

Positive-feedback loop/feedforward mechanism

252
Q

Why is vemurafinib ineffective in shutting down B-raf mutant colorectal carcinoma cells but effective in shutting down B-raf mutant melanoma cells?

A

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
Q

Cell formed when the plasma membranes of two or more cells fuse, initially resulting in a multi-nucleated cell

A

Syncytium

254
Q

Pediatric tumor of the oligopotential stem cells of the retina

A

Retinoblastoma

This tumor arises in the precursors of the photoreceptor cells and occurs in 1 in 20,000 children

255
Q

What two forms does retinoblastoma appear as in children

A

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
Q

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

A

Single random event; two random events

This is Knudson’s “one-hit” and “two-hit” hypothesis

257
Q

Explain the one hit/two hit concept

A

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
Q

Rb is __ at the organismic level and __ at the cellular level (dominant/recessive)

A

Dominant ; recessive

259
Q

On what chromosome is the Rb gene located

A

Chromosome 13

260
Q

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

A

Loss of heterozygosity

261
Q

Ways loss of heterozygosity can occur

A

Mitotic recombination
Gene conversion
Chromosomal deletions
Loss of chromosomes (nondisjunction)
Translocation

262
Q

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

A

Polymorphism

263
Q

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

A

Restriction fragment length polymorphism

264
Q

DNA methylation only occurs when __ bases are located in a position that is __ to __ bases

A

Cytosine ; 5’ ; guanosines

Aka CpG

265
Q

When CpG methylation occurs in the vicinity of a gene promoter, it can cause __ of transcription of the associated gene

A

Repression

When the methylation groups are removed, transcription of the gene is often de-repressed

266
Q

What enzymes are responsible for methylating CpGs

A

DNA methyltransferases

267
Q

During the early stages of tumor development, global __ occurs concurrently with __ of CpG island

A

Global hypomethylation
Hypermethylation of CpG islands

268
Q

Methylation of CpG islands associated with gene promoter regions leads to __

A

Shutdown of gene expression

269
Q

CpG methylation is effective in shutting down the expression of a gene only if it occurs where

A

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
Q

NF1 acts as a negative regulator of __ signaling

A

Ras

271
Q

T/F neurofibromatosis type 1 is a relatively common familial cancer syndrome occurring in 1 in 3500 individuals worldwide

A

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
Q

The Nf1 gene encodes the protein __ that functions as a __

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
Q

Genetic condition in which the presence of only a single functional copy of a gene yields a mutant or partially mutant phenotype

A

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
Q

T/F Hereditary nonpolyposis colon cancer aka Lynch syndrome is caused by inherited mutations in DNA repair genes

A

True

275
Q

Adenomatous polyposis coil (APC) aka familial adenomatous polyposis (FAP) results from a defect of the __ gene

A

Apc

276
Q

The Apc gene is located on chromosome __

A

5

277
Q

Beta-catenin’s downstream effects target genes that program __

A

Stem cell phenotype

278
Q

The APC protein is normally responsible for negatively controlling the levels of __ in the cytosol

A

Beta-catenin

279
Q

KEAP1 in normal cells acts as a sensor for chemical and environmental stresses and activation of KEAP1 leads to expression of genes encoding __

A

Cellular antioxidants and detoxification enzymes

280
Q

KEAP1 interacts with what transcription factor

A

NRF2

In the absence of oxidative stress, KEAP1 sequesters NRF2 in the cytoplasm and targets it for ubiquitylation and degradation

281
Q

Describe the KEAP1 pathway

A

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
Q

Some cancers mutate Keap1 gene to cause __

A

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
Q

__ and __ (tumor types) were found to have the highest frequency of Keap1 mutations

A

Adenocarcinomas and squamous cell carcinomas of the lungs

284
Q

Tumor suppressor genes are considered ___ genes while DNA maintenance genes are considered __

(Caretaker/gatekeeper)

A

Tumor suppressor genes = gatekeepers

DNA maintenance genes = caretakers

285
Q

Few cancer syndromes are associated with inherited mutant alleles of proto-oncogenes - what are they and what genes are involved

A

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
Q

___ cells exit the cell cycle irreversibly and cannot re-initiate active growth even in the presence of mitogens

A

Post-mitotic

Ex: neurons in the brain

287
Q

DNA synthesis (S phase) usually takes __ in mammalian cells

A

6-8 hours

(But varies depending on cell type)

288
Q

What are the five subphases of M phase

A

Prophase
Prometaphase
Metaphase
Anaphase
Telophase

289
Q

What are the major checkpoints of the cell cycle

A

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
Q

TGF-beta imposes its growth-inhibitory effects only during what periods of the cell cycle

A

Early and mid-G1

Once a cell is in late G1 it is oblivious to anti-mitogenic signals

291
Q

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

A

Restriction point / R point

292
Q

T/F Cancer cells that exhibit anchorage-independence have lost the late G1 checkpoint

A

True

293
Q

Type of serine/threonine kinase deployed by the cell cycle machinery that depends on an associated Cyclin protein for proper functioning

A

Cyclin-dependent kinase

294
Q

CDKs bind __

A

Cyclins

295
Q

Which CDK binds what cyclin

A

CDK2 - cyclin A and cyclins E1 and E2
CDK 4/6 - cyclin D
CDK1 - cyclin A and cyclin B

296
Q

What cyclins and CDKs are active during each step of teh cell cycle

A

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
Q

What enzymes trigger degradation of cyclins

A

Ubiquitin ligases

298
Q

Which type of cyclins are controlled by extracellular signals

A

D type cyclins

299
Q

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

A

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
Q

Name the three other CDK inhibitors besides the INK4 proteins. What do these target?

A

p21Cip1 (aka p21Waf1), p27Kip1, and p57Kip2

These are more wide activity and can target CDK2-E and CDK2-A complexes

301
Q

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

A

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
Q

What mitogens-activated pathway causes phosphorylation of p21Cip1 molecules to promote cell cycle progression

A

PI3K

303
Q

p21Cip1 (aka p21Waf1) and p27Kip1 inhibit what cyclin-CDK complexes but stimulate what cyclin-CDK complexes

A

INHIBIT cyclin E-CDK2 and cyclin A-CDK2

STIMULATE cyclin D-CDK4/6

304
Q

Describe phosphorylation of Rb through the cell cycle

A

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
Q

What enzyme removes phosphate groups from pRb after the cell exits mitosis

A

Phosphatase type 1 (PP1)

306
Q

T/F Retinoblastoma protein is the molecular governor of the R point transition

A

True

307
Q

Tumorigenic retroviruses acquire and exploit __ while DNA tumor viruses have evolved proteins that interfere with the actions of the __

A

host cell proto-oncogenes

Host cell tumor suppressor genes

308
Q

HPV E7 not only sequesters pRB but also __

A

Tags it for ubiquitylation and thus proteolytic degradation

309
Q

DNA tumor viruses bind preferentially to what form of pRB

A

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
Q

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

A

HYPOphosphorylated

Hyperphosphorylated

311
Q

Which cyclin/CDK complex is responsible for initiating pRb hypophosphorylation

A

cyclin D and CDK4/6

312
Q

At the R point, cyclin __ and CDK_ levels increase dramatically and drive pRb hyper phosphorylation

A

Cyclin E and CDK2

313
Q

pRb exercises much of its control of the R point through its effect on what group of transcription factors

A

E2Fs

314
Q

When pRb is in the __ states it binds E2Fs

A

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
Q

E2F family has 8 members. Which members bind DNA directly without an associated DP1 or DP2 subunit

A

E2F7 and E2F8

1-6 bind DP1 or DP2 to form heterodimeric transcription factors

316
Q

pRb functions as a transcriptional repressor via recruitment of _

A

Histone deacetylases (HDACs)

317
Q

What forms of E2F are present in abundance in quiescent cells

A

E2F4 and E2F5

318
Q

General overview of Ras signaling effect on cell cycle

A

Growth factors —> growth factor receptors —> Ras —> cyclins D1 and E —> inactivation of pRb —> activation of E2Fs —> S phase entrance

319
Q

Myc targets the cyclin __ gene and the CDK __ gene

A

D2 ; CDK4

320
Q

TGF-beta

A
321
Q

Two organisms/cells/tissues that share identical genetic background

A

Syngeneic

322
Q

Large tumor (large T) antigen comes from what virus

A

SV40 DNA tumor virus

323
Q

What is Li-Fraumeni syndrome

A

Condition of increased cancer susceptibility that results from point mutations in the p53 gene coding sequence

Germ line mutation

Inherited autosomal dominant

324
Q

What chromosome is p53 gene located on

A

17

325
Q

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

A

Dominant-interfering or dominant-negative

326
Q

P53 mutations are usually ___ resulting in amino acid substitutions (rather than __ which cause termination and degradation of the growing polypeptide chain)

A

usually missense

Nonsense cause termination and (often) degradation

327
Q

What things can cause increases in p53 levels in a cell (stressors)

A

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
Q

Proteins that recognize double stranded DNA breaks work through __ kinase

A

ATM

329
Q

What kinases phosphorylate p53 directly

A

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
Q

Phosphorylation of p53 causes DEGRADATION/STABILIZATION

A

Stabilization - protects it from destruction by Mdm2

331
Q

Ataxia telangiectasia is caused by deficiency of what kinase

A

ATM

332
Q

Single-strand DNA breaks active what kinase

A

ATR

333
Q

Degradation of p53 is regulated by what protein

A

Mdm2 aka ubiquitin ligase

(Reverse is true too - expression of Mdm2 is controlled by p53)

334
Q

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

A

Double minute chromosome

335
Q

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

A

True

336
Q

Steps of Mdm2 inactivation of p53

A

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
Q

Mdm2 often forms heterodimers with what other protein that is thought to be responsible for the ubiquitylation activity

A

Mdm2 (aka Mdm4)

338
Q

T/F Phosphorylation of p53 protects it from degradation by Mdm2/MdmX complexes

A

True

339
Q

Phosphorylation of Mdm2 is caused by what kinase (that also phosphorylates p53).

Does phosphorylation of Mdm2 stabilize it?

A

ATM kinase

NO - causes functional inactivation and destabilization of Mdm2

340
Q

`ARF induces rapid increases in p53 by inhibiting __

A

Mdm2

341
Q

What are the important proteins involved in apoptosis

A

Caspaases 3, 7, 8, 9
Bcl-2 proteins (Bim, Noxa, PUMA)
Apaf-1
p73

342
Q

During apoptosis the “Eat-me” signal is __ and is recognized by __

A

Phosphatidylserine (PS)

Recognized by annexin receptor on phagocytic cells

343
Q

Name the pro-apoptotic and anti-apoptotic Bcl-2 family proteins

A

Pro-apoptotic: Bax and Bak

Anti-apoptotic: Bcl-2, Bcl-XL, and Mcl1

344
Q

Bcl-2, Bcl-XL, and Mcl-1 contain __ BH domains

A

4

345
Q

Name the BH3 only proteins

A

Bid
Bim
Noxa
Bad
PUMA

346
Q

Anoikis is dependent on what BH3 only protein

A

Bim

347
Q

p53 induces expression of which BH-3 only proteins

A

PUMA
Noxa

348
Q

What are the initiator caspases

A

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
Q

What are the executioner caspases

A

3, 6, 7

These caspases are activated by initiator caspases and function to cleave cellular target proteins leading to cell death

350
Q

Death receptors bind what ligands

A

TNF proteins

351
Q

Tsp-1 is a secreted protein that functions in the extracellular space to __

A

Block development of new blood vessels

352
Q

What DNA sequence is repeated in telomeres (g rich strand)

A

TTAGGG

353
Q

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

A

Passenger mutation

354
Q

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

A

Driver mutation

355
Q

What is Peto’s paradox?

A

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
Q

What specific mutagenic agents have been associated with cancer in humans?

A

Tobacco smoke
ultraviolet radiation
aflatoxin B1
ethanol (which becomes mutagenic, following conversion in the liver to acetaldehyde)

357
Q

Hepatitis B virus can function synergistically with what mutagen in compound to increase risk of hepatocellular carcinoma in humans

A

Aflatoxin B1

358
Q

Agent that can act as both an initiator and a promoter of tumor progression

A

Complete carcinogen

359
Q

Cancer cells express high levels of __ which may contribute to their use of glycolysis rather than oxidative phosphorylation

A

GLUT1 - especially carcinomas and hematopoietic tumors

Cancer cells take in large amounts of glucose from the extracellular space

360
Q

High levels of GLUT1 gene expression is driven by what oncogenes and transcription factors

A

myc
ras
src

HIF-1alpha transcription factor

361
Q

What enzyme catalyzes the last step of glycolysis

A

Pyruvate kinase (PK)’

Converts phosphoenolpyruvate to pyruvate

362
Q

What isoform of PK is typically expressed in adult tissues vs. cancer cells

A

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
Q

What enzyme reduces pyruvate to lactate

A

Lactate dehydrogenase-A (LDH-A)

364
Q

__ serves as a precursor source of nitrogen for bases of RNA and DNA

A

Glutamine

365
Q

T/F: Glutamine is an essential amino acid

A

FALSE - considered nonessential because normal cells can synthesize it (but important from extracellular sources is critically important still)

366
Q

T/F: cancer cells require normal amounts of glutamine

A

FALSE: they require A LOT (more than used in making proteins)

367
Q

Stem cells express high levels of what drug pump

A

Mdr1

368
Q

What are the three most important DNA polymerases

A

pol-alpha
pol-delta
pol-epsilon

369
Q

Which DNA polymerase is most important in proofreading

A

pol-delta

370
Q

pol-__ is responsible for leading-strand synthesis at the application fork

A

pol-sigma

371
Q

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

A

Mismatch repair

372
Q

Mutational process in which the immune groups that protrude from cytosine, adenine, and guanine rings of the DNA bases are lost

A

Deamination

373
Q

Deamination of cytosine yields what

A

Uracil

374
Q

Deamination of adenine yields what

A

Hypoxanthine

375
Q

Deamination of guanine yields what

A

Xanthine

376
Q

Deamination of 5-methylcytosine yields what

A

Thymine

377
Q

Point mutation in which one purine base replaces other or in which one pyrimidine base replaces another

A

Transition

378
Q

White mutation in which a purine base replaces a pyrimidine or vice versa

A

Transversion

379
Q

What enzymes help neutralize reactive oxygen species

A

Superoxide dismutase
Catalase

380
Q

Enzymes that covalently link electrophilic compounds, and thus many carcinogens, with glutathione, thereby detoxifying these compounds and preparing them for further metabolism and excretion

A

Glutathione S-transferases

381
Q

What enzyme removes methyl and ethyl adducts from the O6 position of guanine thereby restoring the structure of the normal base

A

O6-methylguanine-DNA methyltransferase (MGMT) aka DNA alkyltransferase

382
Q

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

A

Base excision repair

383
Q

Type of DNA repair in which the initial step involves the excision of nucleotides rather than bases

A

Nucleotide excision repair

384
Q

BER tends to repair lesions in the DNA that derived from __ sources while NER largely repairs lesions created by __ sources

A

BER = endogenous
NER = Exogenous

385
Q

NER is split into what subtypes

A

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
Q

The pattern of inheritance of xeroderma pigmentosa is

A

Autosomal recessive

387
Q

Cockayne syndrome (CS) is a defect of

A

Transcription coupled NER

388
Q

Hereditary non-polyposis colon cancer aka Lynch syndrome results from germ line mutations affecting what proteins

A

Mismatch repair proteins

Specifically MSH2 and MLH1

389
Q

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

A

NBS1

390
Q

Homologous repair occurs when during the cell cycle

A

S and G2

Need a template strand available

391
Q

Non-homologous end joining occurs when during the cell cycle

A

G1

392
Q

A normal or neoplastic tissue, derived from one species that has been implanted into a host animal from another species

A

Xenograft

393
Q

The tumor microenvironment is made of what components

A

Stromal cells
Extracellular matrix

394
Q

Adherens junctions are made up of __ which is replaced by __ during wound healing

A

E cadherin
N cadherin

395
Q

Shifting display of surface cadherins allows epithelial cells to undergo

A

Epithelial to mesenchymal transition

396
Q

What chemokine is expressed by neuroectodermal and epithelial cancer cell types to attract monocytes

A

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
Q

What matrix metalloprotease is prominently involved in cancer progression

A

MMP 9

398
Q

What is the distance oxygen can effectively diffuse through living tissues

A

0.2mm

399
Q

What three mechanisms contribute to high intra-tumoral hydrostatic pressure

A

1 - lymphatic vessel collapse
2 - leaky capillaries
3 - fibroblast contraction

400
Q

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

A

Angiogenic switch

401
Q

monoclonal antibody that binds VEGF-A

A

bevacizumab aka Avastin

402
Q

Epithelial cells undergoing EMT will stop expressing __ and start expressing __

A

Cytokeratin; vimentin

403
Q

Vimentin is a marker of what cell type

A

Mesenchymal

404
Q

What are some EMT-inducing transcription factors

A

Twist
Snail
Slug
Goosecoid
FOXC2
ZEB1
ZEB2
E12/E47
Prrx 1

405
Q

Snail and Slug are TFs that repress transcription of

A

E-cadherin

Onc Boards (4 decks)

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