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KCUMB Molecular Biology > EXAM III Final > Flashcards

EXAM III Final Flashcards

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1
Q

What are two cell phenotypes that cause them to undergo apoptosis?

A
  1. Macrophage activation
  2. DNA fragmentation
  3. A decrease in the nucleus and volume
  4. Less adhesion, smaller cytoskeleton and nuclear envelope
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2
Q

Explain the difference between initiator and executioner caspase

A

Initiator caspase (-8,9) initiates apoptosis by activating the caspase cascade by causing executioner caspase (-3) to actually cleave the downstream targets. (Such as cytoskeleton, inactive endonuclease, proteins, cell adhesion proteins)

Executioner caspase executes apoptosis

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3
Q

Name two ways in which proto-oncogenes become activated to become oncogenes

A
  1. Gene amplification, which causes the overproduction of a normal protein.
  2. Chromosome rearrangement by a nearby regulatory DNA sequence that brings new regulatory sequence that causes overproduction of a normal protein or Creates overactive fusion protein. (I.e. EGF receptor rearrangement can remove the extracellular domain; epidermal growth factor)
  3. Regulatory mutation which causes an overproduction of a normal protein. (I.e. Promoter mutation)
  4. Deletion or point mutation in a coding sequence causing a hyperactive protein in normal amounts (I.e. Ras)
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4
Q

Describe the pathology of cancer and how it goes from benign to malignant

A

A tumor is originally benign. Once it invades a nearby capillary the tumor has become malignant and is capable of entering tissues via the blood vessels. Tumors can also become adhered to the endothelial vessel walls.

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5
Q

Describe polyp and how it develops

A

A polyp is a precursor to colorectal cancer (APC tumor suppressor gene mutation). They normally take about ten years to develop and if left untreated can become malignant and be cancerous. If the polyp is excised, the patient is cured.

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6
Q

Explain how Gleevec is used in the treatment of anti-cancer therapy

A

Gleevec is used in chronic myeloid nous leukemia (via Philadelphia chromosome translocation) and binds to the ATP binding site of BCR/Abl, inhibiting tyrosine kinase activity thereby inhibiting cell proliferation

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7
Q

What are the two forms of cell death?

A
  1. Necrosis - contents spill out

2. Apoptosis - cell death under physiological conditions (programmed; cells shrink and condense)

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8
Q

T/F; Eliminating lymphocytes after destroying and ingesting microbes is an example of apoptosis

A

True

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9
Q

T/F; programmed cell death is important for certain cells such as those that are abnormal, non-functional, or potentially dangerous

A

T

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10
Q

T/F; cytochrome c is a marker of apoptosis

A

True; released from mitochondria

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11
Q

T/F; apoptosis is an extracellular proteolytic cascade mediated by caspases (proteases)

A

False; apoptosis is intracellular

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12
Q

T/F; Cysteine is the active site on caspases

A

True; Cysteine aspartyl specific proteins

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13
Q

T/F; Caspases targets proteins and cleaves them in their sequence where a glycine amino acid residue occurs

A

False; cleaves where there’s an Aspartic amino acid residue

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14
Q

T/F; pro caspase is an inactive precursor of caspase

A

True; this is the primary synthesized version of caspase

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15
Q

T/F; the active form of caspase is a heterodimer

A

True; made up of large and small subunits which forms the heterodimer

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16
Q

T/F; the caspase cascade is reversible

A

False; it’s actually irreversible

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17
Q

Are death receptors involved in the intrinsic or extrinsic pathway of apoptosis?

A

Extrinsic

Intrinsic involves cytochrome c from mitochondria

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18
Q

Explain how decoy receptors work in the extrinsic pathway of apoptosis

A

Decoy receptors contain ligand binding domain (no death domains) which blocks the binding of Fas ligand to the Fas death receptor

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19
Q

Explain how the protein FLIP works in the extrinsic pathway of apoptosis

A

FLIP is a competitive inhibitor to pro caspase-8,10 death effector domain, thereby inhibiting apoptosis

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20
Q

What are some factors that cause activation of the intrinsic pathway of apoptosis?

A

Injury
DNA damage
Lack of oxygen, nutrients
Lack of extracellular survival signals

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21
Q

What is the function of cytochrome c in the intrinsic pathway of apoptosis?

A

Released from intermediate space of mitochondria and binds to adaptor protein to activate procaspases

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22
Q

Define Apaf1

A

Apoptotic protease activating factor-1; bound by cytochrome c which becomes an apoptosome and activates caspase-9 (initiator caspase_

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23
Q

What are the two types of Bcl2 proteins that control the release of cytochrome c into the Cytosol?

A

Pro-apoptotic = BH3 and BH123 (Bax, Bak)

Anti-apoptotic = Bcl2 (Bcl-XL, BH1234) = located on cytosolic surface and prevents the aggregation of BH123 (active form)

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24
Q

What is the mechanism of BH3 in the intrinsic pathway of apoptosis?

A

Pro-apoptotic and located in Cytosol and inhibits anti-apoptotic Bcl2 protein from inhibiting aggregation of BH123 for the release of cytochrome c

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25
Q

Explain the mechanism of IAPs in apoptosis

A

Inhibitors of Apoptosis bind and inhibit caspases or add ubiquitin to caspases

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26
Q

What it the mechanism of anti-IAPs?

A

Blocks IAPs by neutralizing them and blocking their functions of inhibiting apoptosis

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27
Q

Can excessive Bcl2 cause cancer?

A

Yes, because this inhibits apoptosis which would inhibit DNA-damaged cells from dying allowing them to continuing proliferating

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28
Q

List the 3 classification of cancers

A
  1. Carcinomas - via epithelial cells
  2. Sarcomas - via CT and muscle tissue
  3. Leukemias and lymphomas - via WBCs and their precursors
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29
Q

What is the difference between neovascularization and angiogenesis?

A

Angiogenesis is the formation of blood vessels from PRE-EXISTING VESSELS

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30
Q

What are the two main classes of cancer critical genes that are the genetic causes of cancer when mutated?

A

Tumor suppressor genes (loss of function; recessive) - p53, CKI, Rb

Oncogenes (gain of function; dominant) - Bcl2

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31
Q

Which of the following is not involved in cellular function of oncogenes?

A. Cell cycle proteins
B. Transcription factors
C. Ligands
D. Receptors
E. Nucleus
A

Nucleus

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32
Q

List some examples of the two types of tumor suppressor genes; growth restriction and the maintenance of genome integrity

A

Growth restriction = caspases, Rb, CKI

Maintenance of genome integrity = checkpoint control proteins; DNA repair enzymes/pathways, ATM & ATR (detects DNA damage), Ataxia Telangiectasia

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33
Q

T/F; Cdk and cyclin are proto-oncogenes

A

True; are usually involved in cell proliferation when bound with CKI(p16)

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34
Q

List some functions of p53 in the regulation of the genome

A

Tumor suppressor gene

Cell cycle arrest
DNA repair
Apoptosis
Blocks angiogenesis

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35
Q

List some functions of p53 in the regulation of the genome

A

Tumor suppressor gene

Cell cycle arrest (CKI = p21 = inhibits cell cycle)
DNA repair
Apoptosis (activates BH3, BH123)
Blocks angiogenesis

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36
Q

Define gastrulation

A

The transformation of a hollow sphere of cells into a structure with a gut

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37
Q

Define gene duplication

A

When higher organisms have several homologs of the same gene

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38
Q

List the two classes of proteins most important for the development of organisms

A
  1. Cell adhesion and cell signaling proteins; layering and talking
  2. Gene regulatory proteins (the basis for making organisms different from one another; what allows expression)
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39
Q

Completely undetermined vs. Committed cell fates

A

Completely undetermined cells can change rapidly due to the environment

Committed cells have an idea where they are but can also change with the environment; brain cell that can become microglia, or ependymal, or astrocyte

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40
Q

What is an example of a cell that undergoes long range signaling during inductive signaling during cellular differentiation

A

Morphogens; BMP, Shh

When a substance diffuses through the extracellular matrix

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41
Q

Short range vs. long range signaling

A

Short range = cell-cell contact

Long range = substances diffuse through extracellular environment

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42
Q

Symmetric vs. Asymmetric division

A

Symmetric = daughter cells become different due to environment influences (weak asymmetry)

Asymmetric = granule location within cytoplasm

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43
Q

Define inductive signaling

A

Environmental signals that come from neighboring cells that induce different development patterns in a homogenous group

(short range vs. long range; morphogens)

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44
Q

Positive feedback and lateral inhibition during symmetrical division

A

After daughter cells have begun to undergo asymmetry via environmental signals, positive feedback allows strong asymmetry = all or none and irreversible

Self-amplifying

Allowing cells to have memory

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45
Q

Define morphogen

A

A long range inductive signal that imposes a PATTERN on a field of cells forming gradients of [different] thus allowing for target cells to undergo different developmental pathways

Gradient formed by = Inducer vs. inhibitor

Gradient becomes less the further you remove from a source

46
Q

What two factors are the response to signaling pathways dependent upon during cell differentiation?

A

Spatial and time

47
Q

Define growth cone

A

An irregular, spiky enlargement at the tip of an axon/dendrite that crawls thru surrounding tissue, trailing the axon or dendrite behind; developing axon-specific proteins forming an axon

Located within the dendrite but doesn’t move; the axon is what moves

48
Q

What dictates growth cone behavior? What senses the ECM environment?

A

Its cytoskeletal machinery (filopodia and lamelopodia) containing actin filaments that assemble and disassemble by the action of Rho and Rac monomeric GTPases

Membrane receptors sense the ECM environment

49
Q

What are two factors that determine the movement and behavior of growth cones? Give some examples

A

ECM environmental sensed by membrane receptors; homophilic cell adhesions via Ig Superfamily and cadherins

Chemotactic factors via neighboring cells; Slit, Semaphorin, and Netrin

50
Q

List the 3 chemotactic factors involved in growth cone migration and what type of neuron expresses the receptor?

A

Attractant = Netrin

Repulsive = Slit & Semaphorin

Commissural neuron contains the Netrin receptor

51
Q

Explain the pathway of the guidance of a commissural neuron

A

Commissural axon grows out towards the attractant Netrin with its receptor towards the midline which is then repelled against the midline via Slit (floor plate midline) and Semaphorin (wall of neural tube) with its roundabout receptors and makes its way towards the brain

Makes a 90 degree turn away from the floor plate

ECM Ca2+ entry allows for growth cone movement

Non-commissural neurons don’t contain the receptor and migrate towards the floor plate

52
Q

Define neurotrophic factors; what is its role in axonal/neuronal growth? What phase?

A

Factors that are needed for survival released by the target cells that determine where synapses are formed (i.e. Nerve growth factor NGF)

Those that don’t receive enough signals die

PHASE II

53
Q

What are the 2 rules that synaptic remodeling is dependent upon in retinal/tectal neurons? Race Relations

A
  1. Axons from cells in different regions of retina that are excited at DIFFERENT cells compete for tectal neurons
  2. Axons from neighboring sites excited at the SAME TIME work together to retain and strengthen synapses with tectal neurons

PHASE III

54
Q

What two factors does activity-dependent synaptic remodeling depend upon?

A
  1. Electrical activity
  2. Synaptic signaling

PHASE III

55
Q

Synaptic remodeling is based on __________

A

Functional activity

56
Q

Layer of skin containing fatty subcutaneous tissue ______

A

Hypodermis

57
Q

Layer of skin rich in collagen, providing toughness, containing loose & dense connective tissue _______

A

Dermis

58
Q

Layer of skin made up of epithelial cells, forming the outer covering of the skin, creating a water barrier and is continuously repaired and renewed ___________

A

Epidermis

59
Q

Skin cells turn over every 30 days by virtue of the presence of stem cells in the basal layers is dependent upon ______

A

Integrin

60
Q

This layer of the epidermis forms the waterproof barrier and is the boundary between outer dead and inner metabolically active cells

A

Granule cell layer

61
Q

The epidermis is a ________ layer made of ____________

A

Stratified; keratinocytes

62
Q

The ________ layer of the epidermis is attached to the basal lamina and are the only dividing cells

A

Basal cell layer

63
Q

This layer of the epidermis contains numerous desmosomes that attach tufts of keratin filaments

A

Prickle cells

64
Q

The outermost layer of the epidermis is the _________ which are flattened dead cells that are densely packed with keratin containing no organelles

A

Squame

65
Q

List the epidermal layer of cells from innermost to outermost

A

BBPGK

  1. Basal lamina
  2. Basal layer
  3. Prickle layer
  4. Granule cells
  5. Keratinized
66
Q

T/F; epidermal cells undergo change in gene expression while moving up the cellular layers of the skin

A

True; occurs at each step of differentiation

Cells will end up undergoing partial degradation which is dependent upon partial activation of the apoptotic machinery

67
Q

Partial degeneration of the epidermal cell layers is dependent upon ________

A

Partial activation of the apoptotic machinery

68
Q

Basal lamina adhesion is mediated via ___________

A

Beta-1 subunit of integrin

69
Q

Stem cells of the epidermis basal layer provide an ________ supply of fresh differentiated cells every ________ days

A

Indefinite; 30 days

70
Q

State 4 characteristics of stem cells

A
  1. Not terminally differentiated
  2. Can divide without a limit
  3. Undergo slow division
  4. Gives rise to 1 stem cell and a terminally differentiated cell
71
Q

T/F; Stem cells are not tissue specific

A

False; tissue specific

i.e. epidermal stem cells, intestinal stem cells, GI stem cells, etc.

Meaning if you relocate them, they will form whats in their memory, not the new location

72
Q

What percentage of daughter cells via stem cells keep their stem cell qualities?

A

50%

73
Q

Define Independent choice of the division of stem cells

A

Division makes 2 identical cells allowing for the environment to influence its outcome

3 outcomes = 2 stem cells, 1 SC & 1 differentiated, both differentiated

i.e. bodily needs

74
Q

During asymmetric division of SC, which daughter cell receives the parental DNA?

A

The new Stem cell

75
Q

Define transient amplifying cells

A

Cells that don’t immediately differentiate; rather they go through division rounds then differentiate

Programmed to divide for a limited number of times once they leave the basal layer

A characteristic of asymmetrical and independent choice division

76
Q

Which stem cell replication contains drawbacks, rendering us unsure of how existing SCs increase their numbers?

A

Asymmetric division

77
Q

Which SC replication is more flexible and explains the sharp increase in SC numbers when needed for repair?

A

Independent choice

Influenced by environment

78
Q

What factor determines whether a SC stays a SC or commits to differentiation?

A

Loss of contact

Beta-1 subunit of integrin

79
Q

What factor controls the number of SCs?

A

Contact with basal lamina

80
Q

_______ of contact preserves SC potential

A

Maintenance

81
Q

What does overactive Shh cause in the epidermis? What about a deficiency?

A

Overactivation causes continuous division even after leaving the basal layer

Def = loss of sebaceous glands

82
Q

What occurs when Wnt is upregulated in the epidermis?

A

Grows extra hair follicles

Def = no hair follicles

83
Q

What does TGF-beta promote in the epidermis?

A

The formation of collagen rich scar tissue

Repairs skin wounds

84
Q

What does Notch signaling pathway inhibit in the epidermal renewal system?

A

Restricts the size of the SC population

Lateral inhibition causes them to become transient amplifying cells

85
Q

Where are sensory neurons located?

A

Ear, eye, and nose via ectoderm

86
Q

Describe the structure of olfactory epithelium

A

Bipolar neuron with dendrites containing modified cilia facing the external environment that detect external stimulus within supporting cells containing a basal end that makes synapses with neurons that relay the sensory info to specific parts of the brain

87
Q

What is located on the free surfaces of cilia on the dendrites of olfactory neurons? What type of receptor is this?

A

Odorant receptor proteins

(olfactory receptors)

GPCR acts via Adenylyl cyclase activating cAMP —> ion channels = Ca2+ —> neuron depolarization —> Glomeruli relay station

88
Q

Odorant receptor genes that are expressed on olfactory neurons respond to how many numbers of odorant classes?

A

One class of odorant (organic small molecules)

The receptor recognizes structural features of the odorant

89
Q

What is the function of glomeruli?

A

Relay stations in the brain where action potentials run through to response to odorant molecules

1800 glomeruli/bulb in mouse brain

Olfactory neurons expressing same odorant receptor are located in diff places in olfactory epithelium but axons all converge on the same glomerulus

90
Q

How often do olfactory neurons regenerate? Where are these SC located?

A

Every month via neural stem cells in the olfactory epithelium = basal SCs in contact w/ basal lamina

91
Q

What is the function of odorant receptor proteins during axonal guidance?

A

They allow the growth cone to migrate to and establish connection with the correct glomerulus in the olfactory bulb

92
Q

Hematopoietic stem cells are an example of

Totipotent SCs
Pluripotent SCs
Multipotent SCs

A

Multipotent

Only can give rise to RBCs and WBCs

93
Q

List the 5 sources where we can obtain hematopoietic SCs

A
  1. Fetal liver
  2. Bone marrow
  3. Peripheral blood
  4. Umbilical cord
  5. iPS cells
94
Q

Stromal SCs (from the bone marrow) can give rise to

A

Hematopoietic SCs

Hematopoietic Supportive Stroma

95
Q

Erythroid differentiation is mediated by what hormone?

A

Erythropoietin

96
Q

List the 7 stages involved in erythroid differentiation

A

BPO

  1. CD34+ cells
  2. Proerythroblast
  3. Basophilic Normoblast
  4. Polychomatic Normoblast
  5. Orthochromatic Normoblast
  6. Reticulocyte
  7. Mature RBC
97
Q

At which stage of erythroid differentiation does the cell lose its nucleus/DNA material?

A

Reticulocyte

98
Q

What types of organs/systems can mesenchymal SCs and adipose SCs (adult SCs) give rise to? What is their potential?

A
  1. Bone, fat, cartilage
  2. Muscle
  3. Nervous system
  4. Heart
  5. Vessels
  6. Kidney
99
Q

What two types of mesenchymal SCs have to capability to give rise to chondrocytes, myoblasts, osteoblasts, pancreatic beta-cells and neuronal like cells?

A

BM-derived mesenchymal SCs

Adipose derived mesenchymal SCs

100
Q

What is a bone marrow transplant and why would one utilize it?

A

To transplant and form hematopoietic SCs

There is a lot of research done on transplant outcomes

Lots of info is available about marrow donation experience

101
Q

From whom would an allogenic transplant be most beneficial for a sick patient?

Are the SCs derived from bone marrow or peripheral blood?

A

Brother/Sister

Low chance to match with parents

Via peripheral blood bc easier to collect, more rapid hematopoietic recovery and less cost

102
Q

What are some characteristics of founder SCs?

A
  1. Derived from embryo but are adult SC bc they remain in body as adult
  2. Around in finite/fixed numbers
  3. Go through a fixed number of divisions
  4. Controlled by short range signals
  5. Give rise to transient amplifying cells when generating into an organ/tissue
  6. Pre-determined
  7. Divides into SC & differentiated daughter cell/transit amp cell
103
Q

T/F; transit amplifying cells can give rise to a daughter SC

A

False; continuing rounds of replication give rise to transit daughter SC that will eventually diff once all rounds of division are complete

104
Q

When using RA to manipulate embryonic SCs, what tissues can it give rise to?

A
  1. Neurons (ectodermal)
  2. Smooth muscle cells (mesoderm); + dibutyryl cAMP
  3. Adipocyte; + insulin + thyroid hormone
105
Q

List the three different protocols that are used to differentiate embryonic SCs from undifferentiated SCs

A
  1. Embryoid bodies with no stromal cells or ECM protein medium
  2. Cells diff on stromal cells with embryonic feeders & LIF to initiate diff
  3. Cells diff on ECM proteins

This is done to analyze all three types

106
Q

Which SC type provides a solid theoretical and experimental foundation to solve rejection problems and induce development of specialized cell types?

A

Embryonic SCs

107
Q

What is a common disadvantage between both early and mature SCs?

A

Mature - diff to maintain in cell culture for long periods in lab; limited longevity

Early - difficult to control in lab/ may require many steps to coax into desired cell type

108
Q

Which SC is unlikely to give an immune response? Which one has more likely for immune rejection?

A

No immune response advantage = mature SC

Possible immune rejection = embryonic/early

109
Q

Which SC (early or mature) is easier to extract in lab?

A

Early

Mature = difficult to find and extract from mature tissues

110
Q

What is the main basis for somatic cell nuclear transfer (SCNt)?

A

Nucleus is taken from a somatic cell of a patient and injected into oocyte of a donor replacing the oocyte nucleus

The blastocyst generated from the hybrid oocyte and the embryonic SCs are isolated (ICM)

Done to avoid graft rejection

111
Q

4 genes that induce adult SCs back to ES like cells

A

Oxt 3/4
Sox2
Myc
KIF4

Direct gene expression manipulation

Multipotent —> Pluripotent

KCUMB Molecular Biology (6 decks)

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