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General Pathology Boards - The cell as a unit of health and disease > Overview > Flashcards

Overview Flashcards

1
Q

ENCODE (Ency­clopedia of DNA Elements) project

A

A 2007 initiative to identify all regions of a genome that could be ascribed some function

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2
Q

How much of the genome is devoted to regulating gene expression or has some functional activity - related to gene expression?

A

About 80%

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3
Q

Noncoding regulatory RNAs

A

Approximately 60% of the genome; RNAs that are never translated into protein, but which nevertheless can regulate gene expression through a variety of mechanisms. The two best-studied varieties are micro-RNAs and long noncoding RNAs

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4
Q

P arm of a chromatid

A

The short arm

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5
Q

Q arm of a chromatid

A

The long arm

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6
Q

Enhancers

A

regulatory elements that can modulate gene expression over distances of 100 kB or more by looping back onto promoters and recruiting additional factors that are needed to drive the expression of pre-mRNA species

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7
Q

The _____ sequences are subsequently spliced out of the pre-mRNA to produce the definitive message that is translated into protein

A

intronic

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8
Q

The most common forms of DNA variation in the human genome

A

single-nucleotide polymorphisms (SNPs) and copy number variations (CNVs)

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9
Q

Biallelic

A

only two choices exist at a given site within the population, such as A or T; common in SNPs

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10
Q

linkage disequilibrium

A

where a genetic element is a useful marker of disease, because it is located in close proximity with a genetic element that causes disease

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11
Q

CNVs

A

genetic variation consisting of different numbers of large contiguous stretches of DNA from 1000 base pairs to millions of base pairs

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12
Q

What percentage of CNVs underlie gene-coding sequences?

A

Approximately 50%

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13
Q

Nucleosomes

A

DNA segments 147 base pairs long that are wrapped around a central core structure of highly conserved low molecular weight proteins called histones

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14
Q

heterochromatin

A

cytochemically dense and transcriptionally inactive

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15
Q

euchromatin

A

cytochemically dispersed and transcriptionally active euchromatin

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16
Q

Chromatin writing complexes

A

carry out more than 70 different histone modifications generically denoted as marks . Such covalent alterations include methylation, acetylation, or phosphorylation of specific amino acid residues on the histones.

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17
Q

Chromatin remodeling complexes

A

can reposition nucleosomes on DNA, exposing (or obscuring) gene regulatory elements such as promoters

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18
Q

Histone acetylation

A

Lysine residues are acetylated by histone acetyl transferases (HAT), whose modifications tend to open up the chromatin and increase tran­scription

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19
Q

Histone methylation

A

Both arginines and lysines may be methylated; variable effect on whether this enables or represses gene transcription

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20
Q

Histone H1

A

sits on the 20-80 nucleotide linker DNA between nucleosomes and helps stabilizes the overall chromatin architecture

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21
Q

How long are long non-coding RNAs?

A

> 200 nucleotides in length.

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22
Q

miRNAs

A

function primarily to modulate the translation of target mRNAs into their corresponding proteins. Posttranscriptional silencing of gene expression by miRNA is a fundamental and well-conserved mechanism of gene regulation present in all eukaryotes (plants and animals) .

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23
Q

DICER

A

successive processing of pre-miRNAs by this enzyme generates mature single-stranded miRNAs of 21 to 30 nucleotides that are associated with a multiprotein aggregate called RNA-induced silencing complex (RISC)

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24
Q

RISC MOA

A

Base pairing between the miRNA strand and its target mRNA directs the RISC to either induce mRNA cleavage or repress its translation.

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25
Q

Perfect match between RISC-bound mRNA and miRNA induces

A

Cleavage

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26
Q

An imperfect match between RISC-bound mRNA and miRNA induces

A

Repression of translation

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27
Q

Small interfering RNAs (siRNAs)

A

Synthetic complexes that can bind with RISC for study purposes; under investigation for possible therapeutic use

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28
Q

XIST

A

lncRNA transcribed from the X chromosome that plays an essential role in physiologic X chromosome inactivation

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29
Q

Functions of lncRNAs

A

facilitate TF binding (gene activation)
pre-emptively bind TF binding (prevent gene activation)
May direct acetylases or methylases
May act as scaffolding ot stabilize multi-subunit complexes

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30
Q

New proteins destined for the plasma membrane or points beyond are synthesized in the ___ and physically assembled in the ___

A

RER; Golgi apparatus

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31
Q

proteins intended for the cytosol are synthesized where?

A

On free ribosomes

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32
Q

SER

A

Abundant in gonads and liver; steroid hormone and lipoprotein synthesis, as well as for the modification of hydrophobic compounds (for example, drugs) into water-soluble molecules for export

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33
Q

3 sites of catabolism within the cell

A

Lysosomes
Proteasomes
Peroxisomes

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34
Q

intracellular organelles that contain degradative enzymes that permit the digestion of a wide-range of macromolecules, including proteins, polysaccharides, lipids, and nucleic acids

A

Lysosomes

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35
Q

a specialized type of “grinder” that selectively chews up denatured proteins, releasing peptides. In some cases the peptides so generated can be presented in the context of class I major histocompatibility molecules

A

Proteasomes

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36
Q

play a specialized role in the breakdown of fatty acids, generating hydrogen peroxide in this process.

A

Peroxisomes

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37
Q

shuttle internalized material to the appropriate intracellular sites or direct newly synthesized materials to the cell surface or targeted organelle

A

Endosomal vesicles

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38
Q

Power cell via oxidative phosphorylation, production of ATP
Site of heme synthesis
Can initate and regulate apoptosis

A

Mitochondria

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39
Q

Phosphatidylinositol

A

on the inner membrane leaflet can be phosphorylated, serving as an electrostatic scaffold for intracellular proteins; alternatively, polyphosphoinositides can be hydrolyzed by phospholipase C to generate intracellular second signals like diacylglycerol and inositol trisphosphate.

40
Q

is normally restricted to the inner face where it confers a negative charge involved in electrostatic protein interactions; however, when it flips to the extracellular face, which happens in cells undergoing apoptosis (programmed cell death), it becomes an “eat me” signal for phagocytes. In the special case of platelets, it serves as a cofactor in the clotting of blood.

A

Phosphatidylserine

41
Q

important in cell-cell and cell-matrix interactions, including inflammatory cell recruitment and sperm-egg interactions.

A

Gycolipids

42
Q

phosphatidylcholine and sphingomyelin are overrepresented in the ____ leaflet, and phosphatidylserine (negative charge) and phosphatidylethanolamine are predominantly found on the ____ leaflet

A

outer; inner

43
Q

have one or more relatively hydrophobic α-helical segments that traverse the lipid bilayer. Integral membrane proteins typically contain positively charged amino­acids in their cytoplasmic domains, which anchor the proteins to the negatively charged head groups of membrane phospholipids.

A

Integral or transmembrane proteins

44
Q

Insertion into the membrane may occur through ______ anchors on the extracellular face of the membrane.

A

glycosylphosphatidylinositol (GPI)

45
Q

Glycocalyx

A

The extracellular face of the plasma membrane that is diffusely studded with carbohydrates, not only as complex oligosaccharides on glycoproteins and glycolipids, but also as polysaccharide chains attached to integral membrane proteoglycans.

46
Q

Lipid bilayers are impermeable to

A

passage of polar molecules of greater than 75 daltons in mass, even those that are only slightly larger, such as glucose. Lipid bilayers are also impermeant to ions, no matter how small, due to their charge and high degree of hydration

47
Q

channel proteins and carrier proteins may be used for transport of

A

low molecular weight species (ions and small molecules up to approximately 1000 daltons)

48
Q

___ are used when concentration gradients can drive the solute movement. ____ are required when solute is moved against a concentration gradient.

A

Channels; carriers

49
Q

endocytose extracellular fluid, membrane proteins, and some receptor bound molecules (e.g., folate) in a process driven by caveolin proteins concentrated within lipid rafts ( potocytosis

A

Cavelolae

50
Q

Phagocytosis

A

non-clathrin-mediated membrane invagination of large particles—typically by specialized phagocytes (e.g., macrophages or neutrophils).

51
Q

Pinocytosis of extracellular fluid and most surface receptor-ligand pairs involves ____ . After internalization, the _____ dissociates and can be re-used, while the resulting vesicle progressively matures and acidifies.

A

clathrin-coated pits and vesicles; clathrin

52
Q

Transcytosis

A

transcellular endocytotic transport of solute and/or bound ligand from one face of a cell to another

53
Q

the process by which membrane-bound vesicles fuse with the plasma membrane and discharge their contents to the extracellular space

A

Exocytosis

54
Q

pumps polar compounds (e.g., chemotherapeutic drugs) out of cells and may render cancer cells resistant to treatment

A

MDR; a transporter ATPase

55
Q

How does hydropic degeneration occur?

A

Since the cytosol is rich in charged metabolites and protein species that attract a large number of counterions that tend to increase the intracellular osmolarity, cells need to constantly pump out small inorganic ions (e.g., Na + and Cl −), typically through the activity of the membrane sodium-potassium ATPase, lest they become overhydrated. Loss of the ability to generate energy (e.g., in a cell injured by toxins or ischemia) therefore results in osmotic swelling and eventual rupture of cells.

56
Q

noncoated plasma membrane invaginations associated with GPI-linked molecules, cyclic adenosine monophosphate (cAMP) binding proteins, SRC-family kinases, and the folate receptor

A

Caveolae

57
Q

Internalization of caveolae with any bound molecules and associated extracellular fluid

A

Potocytosis or “cellular sipping”

58
Q

a fluid-phase process during which the plasma membrane invaginates and is pinched off to form a cytoplasmic vesicle

A

Pinocytosis

59
Q

rapidly invaginates and pinches off to form a clathrin-coated vesicle ; trapped within the vesicle is a gulp of the extracellular milieu and in some cases receptor bound macromolecules

A

Clathrin-coated pit

60
Q

Macromolecules that enter the cell via receptor-mediated endocytosis

A

LDL and transferrin to release cholesterol and iron. A defect in transport of LDL is responsible for familial hypercholesterolemia.

61
Q

Nuclear lamins

A

important not only for maintaining nuclear morphology but also for regulating normal nuclear transcription

62
Q

Diseases caused by mutations in lamins

A

certain froms of muscular dys­trophy to progeria, a disease of premature aging

63
Q

anterograde (− to +) transport proteins that use ATP to move vesicles, organelles, or other molecules around cells along microtubules

A

kinesins

64
Q

retrograde (− to +) transport proteins that use ATP to move vesicles, organelles, or other molecules around cells along microtubules

A

dyneins

65
Q

mechanically attach cells—and their intracellular cytoskeletons—to other cells or to the extracellular matrix (ECM).

A

Anchoring junctions (desmosomes)

66
Q

Mechanical adhesion focus between two cells

A

spot desmosome or macula adherens

67
Q

Mechanical attachment point for the cell to the ECM

A

hemidesmosome

68
Q

Broad bands of mechanical attachment points in between cells

A

belt desmosomes

69
Q

E-cadherins

A

Transmembrane adhesion molecules in belt desomsomes

70
Q

Transmembrane adhesion molecules in spot desomsomes

A

desmogleins and desmocollins

71
Q

large (>100 proteins) macromolecular complexes that can be localized at hemidesmosomes, and include proteins that can generate intracellular signals when cells are subjected to increased shear stress, such as endothelium in the bloodstream, or cardiac myocytes in a failing heart.

A

Focal adhesion complexes

72
Q

mediate the passage of chemical or electrical signals from one cell to another

A

communicating/gap junctions

73
Q

reactive SER hyperplasia

A

can be caused by repeated exposure to compounds that are metabolized by the SER (e.g., phenobarbital catabolism by the cytochrome P-450 system)

74
Q

What is the sarcoplasmic reticulum?

A

Specialized SER - responsible for the cyclical release and sequestration of calcium ions that regulates muscle contraction and relaxation, respectively

75
Q

Responsible for sequestering intracellular calcium in the cell

A

SER

76
Q

Lysosomal enzymes are initially synthesized in the ER lumen and then tagged with a _____ residue within the Golgi apparatus

A

mannose-6-phosphate (M6P)

77
Q

In this process…. Through poorly understood mechanisms, obsolete organelles are corralled by a double membrane derived from the endo­plasmic reticulum; the membrane progressively expands to encircle a collection of structures and forms an autophagosome which then fuses with lysosomes and the contents are catabolized.

A

Autophagy

78
Q

How are sensecent organelles or denatured proteins targeted for autophagy?

A

LC3 proteins (microtubule-associated protein 1A/1B-light chain 3).

79
Q

What does the inner membrane of the mitochondrion contain?

A

enzymes of the respiratory chain folded into cristae

80
Q

What happens in the intermembrane space of the mitochondrion?

A

site of ATP synthesis

81
Q

studded with porin proteins that form aqueous channels permeable to small (

A

Outer mitochondrial membrane

82
Q

How are mitochondria stimulated to trigger necrosis of the cell?

A

External cellular injury (toxin, ischemia, trau­ma) can damage mitochondria, inducing the formation of mitochondrial permeability transition pores in the outer membrane. These channels allow the dissipation of the proton potential so that mitochondrial ATP generation fails and the cell dies.

83
Q

transcription factors that are activated by lipid-soluble ligands that can easily cross the plasma membrane

A

Intracellular receptors

84
Q

Examples of receptor tyrosine kinases (RTKs)

A

receptors for insulin, epidermal growth factor, and platelet derived growth factor

85
Q

Review - Wnt, Frizzled, Dissheveled

A

Nor­mally, β-catenin is constantly targeted for ubiquitin-directed proteasome degradation. However, Wnt binding to Frizzled (and other co-receptors) recruits yet another intracellular protein ( Disheveled ) that leads to disruption of the degradation-targeting complex. The stabilized pool of β-catenin molecules then translocates to the nucleus, where β-catenin forms a transcriptional complex

86
Q

produced by macrophages and a variety of epithelial cells, and are mitogenic for hepatocytes, fibroblasts, and a host of epithelial cells.

A

EGF and TGF-a

87
Q

produced by fibroblasts and most mesenchymal cells, has mitogenic effects on hepatocytes and most epithelial cells, including biliary, pulmonary, renal, mammary,and epidermal. Also acts as a morphogen in embryonic development (i.e., it influences the pattern of tissue differentiation), promotes cell migration (hence its designation as scatter factor ), and enhances hepatocyte survival.

A

HGF

88
Q

receptor for HGF, it has intrinsic tyrosine kinase activity and is frequently overexpressed or mutated in tumors, particularly renal and thyroid papillary carcinomas.

A

MET

89
Q

produced by platelets, activated macrophages, endothelium, smooth muscle cells, and a variety of tumors. Receptors have intrinsic tyrosine kinase activity; induces fibroblast, endothelial, and smooth muscle cell proliferation and matrix synthesis, and is chemotactic for these cells (and inflammatory cells), thus promoting recruitment of the cells into areas of inflammation and tissue injury.

A

PDGF

90
Q

induces angiogenesis by promoting endothelial cell migration, proliferation (capillary sprouting), and formation of the vascular lumen; also induce vascular dilation and increased vascu­lar permeability

A

VEGF

91
Q

VEGF inducers

A

Primarily HIF-1, but also TGF-a and PDGF

92
Q

disorder of inappropriate angiogenesis and vascular permeability that causes adult-onset blindness; treated with anti-VEGF Ab

A

Age-related macular degeneration

93
Q

produced by platelets, endothelium, and mononuclear inflammatory cells; is secreted as a precursor that requires proteolysis to yield the bio­logically active protein. Pleiotropic, but drives scar formation, and applies brakes on the inflammation that accompanies wound healing

A

TGF-β

94
Q

produced by mesenchymal cells (like fibroblasts); present in the spaces between cells in connective tissue, and between parenchymal epithelium and the underlying supportive vascular and smooth muscle structures

A

Interstitial matrix

95
Q

Major constituents of basement membrane

A

amorphous nonfibrillar type IV collagen and laminin

96
Q

On this protein, highly negatively charged sulfated sugars on the “bristles” recruit sodium and water to generate a viscous, but compressible matrix

A

Proteoglycans

General Pathology Boards - The cell as a unit of health and disease (1 decks)

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