Exam 1 Flashcards
What are the classes of functional, non-protein coding sequences
Promotor and enhancer regions (binding sight for TF)
Binding sights that maintain higher order chromatin structures
Regulatory RNAs (micro and long non-coding RNA)
Mobile genetic elements (transposons)
Telomeres and centromeres
What is the difference between euchromatin and heterochromatin
Euchromatin is transcriptively active
Heterochromatin is densely packed
What regulates chromosome separation at metaphase
Kinechtocore complex
Is there a greater or less GC content in bands
Less
What are the two most common forms of DNA variation in the human genome
Single nucleotide polymorphisms and copy number variations
What are SNPs
Variants at single nucleotide positions; almost always biallelic
What is linkage disequilibrium
If you have a neutral SNP but subsequently have a disease-associated gene as a result of physical proximity, the sNP and genetic factor are said to be in linkage disequilibrium
What is the difference between CNV and SNPs
CNVs can be biallelic but can also have complex rearrangements of genomic material with multiple alleles; CNVs also are involved in a greater percentage of coding sequences *indicates involvement in phenotypic diversity
What do chromatin remodeling complexes do
Reposition nucleosomes on DNA, exposing or obscuring gene regulatory elements
What do chromatin writer complexes do
Initiate covalent modifications of histones
Describe histone methylation
Lysine and arginines can be methylated by writer enzymes; can be associated with transcriptional activity or repression based on which histone residue is marked
Describe histone aceytlation
Lysine residues are acetylated by histone acetyl transferase, which opens chromatin ; reversed by deacetylation
Describe histone phosphorylation
Serine residues phosphorylated and depending on the residue, will either open or condense chromatin
Describe DNA methylation
results in transcriptional silencing; regulated by methyltransferases, demethylating enzymes and methylated DNA binding proteins
How many nucleotides are long no coding rNAs
> 200
What is the function of micro RNAs
Modulate the translation of target mRNAs into their proteins; *impt for posttranscriptional gene regulation
What is DICER important for?
Processing miRNAs after transcription; generates mature single-stranded miRNA associated with a multiprotein aggregate called RNA-induced silencing complex
What is the function of rNA-induced silencing complex (RISC)
When the miRNA binds to its corresponding base pairs on target mRNA, it directs the RISC to either induce mRNA cleavage or repress its translation
What is a seed sequence
All mRNAs have this sequence in their 3’ untranslated region (UTR) that determines the specificity of the miRNA binding and gene silencing
What are small interfering RNAs
They serve as substrates for DICER and interact with RISC similarly to miRNAs; used in lab to determine gene function and developing as therapeutic agents for oncogenes
What is XIST
An example of long noncoding RNA; transcribed from X chromosome and then provides repressive cloak over X chromosome and silences gen
Describe how miRNAs are made
Transcribed to a primary RNA which is processed in the nucleus to make pre-miRNA (ssRNA with secondary hairpin loop that form stretches of dsrNA); pre-mRNA exported out of nucleus and DICER trims it in cytoplasm to generate mature ds miRNAs; miRNA then unwinds and the single strands are incorporated into RISC
What are the roles of long noncoding RNA
Facilitate TF binding and promote gene activation
Bind TF and prevent gene transcription
Histone and DNA modification can be directed by binding of them
Can stabilize secondary or tertiary structures that influence chromatin structure
What are the functions that all differentiated cells must perform
Protection from environment, nutrient acquisition, communication, movement, renewal of senescent molecules, molecule catabolism, energy generation
What is the importance of isolating cellular functions
If there are degredative or hazardous enzymes, can keep in certain organelles without risking damage to other cellular machinery; also allows for unique IC environments that will allow maximum functionality of certain enzymes
Where are proteins that are destine for the plasma membrane or points beyond made
RER and modified in Golgi
Where are proteins intended for the cytosol made
Free ribosomes
Where are SERs abundant
Gonads and liver; used for steroid hormone and lipoprotein synthesis as well as modification of hydrophobic compounds into water soluble compounds for export (ie Metabolism of drugs)
What do peroxisomes do
Breakdown fatty acids, generating hydrogen peroxide
What is the cytoskeleton important for
Determining polarity of the cell; important in epithelium to determine apical and basal part of cell
What is the purpose of phosphatidylinositol on the inner cell membrane
Can be phosphorylated and serve as an electrostatic scaffold for intracellular proteins; or polyphosphoinositides can be hydrolyzes by phospholipase C to generate second messengers
What does phosphatidylserine do
On the inner membrane where it confers a negative charge involved in electrostatic protein interactions; when it flips to extra cellular surface (occurs in cells undergoing apoptosis), it signals phagocytes to eat the cell; *in platelets is a cofactor for blood clotting
Where are glycolipids and sphingomyelin normally expressed
On extracellular surface; glycolipids (especially ones with terminal sialac acids that confer negative charge) are impt for cell-cell/matrix interactions (including inflammatory cell recruitment and sperm-egg interactions)
What do integral membrane proteins contain on their cytoplasmic side?
Positively charged amino acids; anchors the protein to the negatively charged hydrophilic heads of the phospholipids
What does glycosylphosphatidylinositol do?
Anchors protein on the extracellular surface
Which two proteins are found mostly extracellularlly
Phosphatidylcholine and sphingomyelin
Which two proteins are mostly found on the inner membrane
Phosphatidylethanolamine and serine
Glycolipids are only found on which surface
Outer; contribute to glycocalyx
What do channel proteins create
Hydrophilic pores
What kind of transporter is multidrug resistant protein
ATPase; pumps polar compounds out of cells * cancer cells resistant to treatment
Loss in the ability to generate energy in a cell leads to what?
Osmotic swelling
What are caveolae
Invaginations of cell membrane that participate in endocytosis of small molecules
What is transcytosis
Movement of material from apical to basal side of cell; plays a role in increased vascular permeability during healing wounds and tumors
What are caveolae associated with
GPI linked molecules, cAMP binding proteins, SRC family kinases, and folate receptor
What are the main functions caveolae-mediated endocytosis are involved in
Regulate signaling and adhesion by internalizing receptors and integrins
Which two cellular processes begin at the clathrin coated pit
Pinocytosis and receptor mediated endocytosis
What are two examples of molecules that use receptor mediated endocytosis
Transferrin and LDL; in the environment of the lysosomes, they release iron and cholesterol and are then recycled back to membrane
What are actin microfilaments
Form from G-actin -> noncovalently polymerize into F-actin that intertwined to form ds helices that forms a polarity
What are intermediate filaments useful for
Can be used to determine origins for poorly differentiated tumors;
Lamin: nuclear lamina of all cells (mutations involved in MD and premature aging - progeria)
Vimentin: mesenchymal cells (fibroblasts, endothelium)
Desmin: m cells
Neurofilaments: axons
Glial fibrillary acidic protein: glial cells
CYtokeratins: distinct varieties (acidic type I and neutral/basic type II)
What is the overall function of intermediate filaments
Do not actively reorganize; are important for allowing cells to bear mechanical stress; major structural proteins of skin and hair
What are microtubules
Diverse of alpha and beta tubules; defined polarity; - side embedded in microtubule organizing center near the nucleus where it is associated with centrioles; + end elongates or recedes in response to stimuli by adding or subtracting tubulin; act as connecting cables for proteins that use ATP to move vesicles or other molecules
What are the two kinds of microtubues
Kinesins: anterograde - to + transport
Dyneins: retrograde + to - transport
Also participate in sister chromatid separation during mitosis; have also adapted to form cilia in sperm and bronchial epithelium
What are tight junctions made up of
Occludin, claudin, zonulin, and catenin
What are the two types of desmosomes
Between cells: spot desmosomes or macula adherens
Between cell and ECM: Hemidesmosomes
What proteins are involved in desmosomal junctions
Cadherins; in belt desmosomes E cadherin - associated with actin (influence shape and motility) in spot desmosomes Demogleins or desmocollins associated with intracellular intermediate filaments; in hemidesmosomes integrin
What are focal adhesion complexes
Localized at hemidesmosomes; include proteins that can generate intracellular signals when cells are subjected to increased shear stress (ie: endothelium or cardiac myocytes)
What forms gap junctions
Connexons; important in cardiac tissue (permits uniform contraction); permeability of junctions is decreased by low intracellular pH or increased calcium
What is the function of chaperon molecules
Keep proteins in the ER until folding is complete
What is the ER stress response
If you have an overload of misfolded proteins t hat need to be degraded, ER cant handle it, which triggers apoptosis
The Golgi apparatus modified proteins from ______ conformation to ______
Cis; trans
What is the difference in function between the cis Golgi and the trans golgi
Cis can recycle proteins back to ER
Trans sends them to other organelle or to be released
Which cells have abundant golgi
Goblet, bronchial epithelium, plasma
Where are lysosomal enzymes made
ER; then tagged with a mannose-6-phosphate residue in the golgi; allows it to be delivered to lysosomes
What is heterophagy
Lysosomes fuse with endosomes or phagosomes to degrade internal contents; end products are either released into cytosol or discharged into ECM via exocytosis
What is autophagy
Senescent organelles or denatured proteins are targeted for lysosomes driven degradation by encicircling them with double membrane derived from the ER and marked by LC3 proteins; can be activated by nutrient depletion or intracellular infections
Describe the process of proteasome degradation
Cytosolic proteins are tagged with ubiquitin as a result of extrinsic mechanical or chemical stress via E 1,2,3 ubiquitin ligases
Mitochondrial disorders can be ________
Autosomal, X linked or maternally inherited
What is the intermembrane space of the mitochondria
Site of ATP synthesis
What does the oxidation of sugar drive in the mitochondria
H+ pump that drive H+ out of the matrix into the intermembrane space; as the H+ flow back down their gradient, the energy released is used to make ATP
What is the Warburg effect
Since pure oxidative phosphorylation doesn’t leave any carbon to make lipid or proteins, rapidly growing cells upregulate their glucose and glutamine uptake and decrease their ATP production/glucose; intermediates of TCA cycle are used to make proteins
Describe the process of necrosis
External cellular injury causes formation of mitochondrial transition pores, allowing dissipation of the proton gradient and therefore no ATP is generated and cell dies
How do mitochondria take part in apoptosis
Intrinsic pathway; if mitochondria damaged or cell cannot make survival proteins, mitochondria become leaky and let out cytochrome c -> activates caspases
What is unique about NO as a ligand
It can diffuse into adjacent cells
What molecules bind to RTK
Insulin, epidermal growth factor, and platelet derived growth factor
What is the notch receptor
Recognizes ligand and is cleaved -> enters nucleus and affects transcription
What does activation of the wnt/frizzled pathway lead to
Release of beta catenin which acts as a TF; *LDL related receptors act this way; beta catenin usually ubiquinated - activation of this pathway recruits disheveled protein to disrupt the degredation complex
Explain the RTK pathway
Autophosphorylates which causes bridging protein to put GTP on RAS and activate it -> activates RAF -> phosphorylates MAPK -> phosphorylates transcription factors, generating responses; RAS can also activate PI3K -> Akt -> mTOR
What is the function of adaptor proteins
Modulates cell signaling
What must a TF contain in order to induce transcription
Protein:protein interaction domain that recruit histone modifying agents, chromatin remodeling complexes, and RNA polymerase
Besides proliferation and growth, what else do growth factors initiate
Migration, differentiation, and synthetic capacity
What are epidermal growth factor and transforming growth factor produced by
Macrophages and epithelial cells
Mutations of EGFR1 cause what
Cancers of lung, head and neck, breast and brain
What is overexpresion of the ERBB2 linked to
Breast cancer (HER2)
What is the function of hepatocyte growth factor
Acts as a morphogen embryologically (influences pattern of tissue differentiation), promotes cell migration (scatter factor), and enhances hepatocyte survival
What is HGF produced by
Fibroblasts, non-hepatocyte liver cells, endothelium, and mesenchymal cells
How is HGF activated
Synthesized as pro-HGF, activated by serine professes at site of injury; MET is receptor (RTK)
What is a mutation or overexpression of MET associated with
Renal and thyroid papillary carcinomas
What are the isoforms of platelet derived growth factor
AA, AB, BB: constitutively active
CC and DD: activated by proteolytic cleavage
What produces PDGF
Platelets, macrophages, endothelium, smooth m, tumors
What are the receptors for PDGF
PDGFR alpha and beta (RTK); induce fibroblast, endothelial and smooth m proliferation; *chemotactic
What are the vascular endothelial growth factors
A, B, C, D and placental growth factor
What is VEGF-A involved in
Angiogenesis after injury and in tumors
What are VEGF B and PIGF involved in
Embryonic vessel development
What are VEGF C and D involved in
Angiogenesis and lymphatic development
Where are VEGFs expressed the most
In epithelium cells next to fenestrated epithelium (podocytes in kidney, pigmented epithelium in retina, and choroid plexus in brain)
What is the most important inducer of VEGF production
Hypoxia via pathways that involve hypoxia inducible factor; VEGF causes vascular dilation and increased vascular permeability; also induced by PDGF and TGF alpha
What do VEGFs bind to
RTKs (VEGFR 1 and 2); 2 is found mostly on endothelium and is most important for angiogenesis
What are abs to VEGF used to treat
Tumors especially in renal and colon (decreases vascular supply for growth); also used to treat we AMD
What does increased levels of soluble versions of VEGF1 in pregnant women cause
Preeclampsia
What do released fibroblast growth factors associate with
Heparan sulfate in ECM; released by proteolytic
What do FGFs bind to
FGGR 1-4 (RTK); contribute to wound healing, hematopoiesis, and development; *basic FGF can also do angiogenesis
What other proteins are in the same family as TGFbeta
BMPs, activins, inhibits, mullerian inhibiting substance
Which isoform of TGFbeta is the most widespread
1
What are the TGFbeta receptors
Serine/threonine kinases; induce phosphorylation of smads which form heterodimers with smad4, allowing nuclear translocation and association with DNAbinding proteins to activate or inhibit transcription
What is a pleiotropic agent
An agent that has multiple affects depending on the tissue; TGFbeta is an example
What are the functions of TGFbeta
Stimulates production of collagen, fibronectin, and proteoglycans; inhibits collagen degredation by decreasing matrix metalloproteinase (MMP) activity and increasing activity of tissue inhibitors of proteinases (TIMPs); drives fibrosis in situation of chronic inflammation; anti inflammatory cytokines by inbhiting lymphocyte proliferation
What are the two forms of ECM
Interstitial matrix: space between cells in connective tissue and btw parenchyma epithelium and vascular and smooth m; synthesized. By mesenchymal cells; made up of fibronectin, elastin, collagen, proteoglycans, hyaluronate
Basement membrane: organized interstitial matrix around epithelial cells, endothelial cells and smooth m cells; made up of nonfibrillar type IV collagen and laminitis
What are the components of the ECM
Fibrous structural proteins: elastin and collagen
Water-hydrated gels: proteoglycans and hyaluronan (permit compressive resistance and lubrication)
Adhesive glycoproteins: connect ECM elements to one another and cells
What are fibrillar collagens
Form linear fibrils stabilized by hydrogen bonds; form connective tissue; tensile strength derived from lateral cross linking formed by covalent bonds vis the activity of lysyl oxidase *dependent on vitamin C (children with ascorbate deficiency have skeletal deformities and bleed easily)
What do nonfibril collagens do
Form basement membranes, help regulate collagen fibril diameters or collagen-collagen interactions via fibril-associated collagen with interrupted triple helices (FACITS - type IX in cartilage), or provide anchoring fibrils to basement membrane beneath strat squamous epithelium (Type VII)
Where is elastin most important
Valves, BV, uterus, skin, ligaments
What are elastin fibers made up of
Elastin core with associated mesh work of fibrillin; fibrilllin defect can cause skeletal abnormalities and weakened aortic walls (Marfan)
What do proteoglycans consist of
Glycosaminoglycans (keratan sulfate and chondroitin sulfate) attached to a core protein; these are linked to a hyaluronic acid polymer (hyaluronan)
Do collagen fibers have elasticity
No
Does lysyl oxidase also have an effect on elastin
Yes; cross links them as well, but have hydrophobic segments that form a blob during rest, when stretched, these segments separate but the cross linking keeps the strand in tact
How do proteoglycans form gel like matrix
The negative charge of the sulfated sugars recruit sodium and water
How is bFGF regulated by ECM and cellular proteoglycans
Syndecan has side chains that can bind bFGF that has been released from damaged ECM; it also has a cytoplasmic tail that interacts with the actin cytoskeleton
What are adhesive glycoproteins
Fibronectin and laminin
What are adhesion receptors
Integrins, immunoglobulins, cadherins, and selectins
What does fibronectin do
Provides scaffolding for subsequent ECM deposition, angiogenesis, and reepithelialization
What does laminin do
Connects cells to ECM components such as type IV collagen and heparan sulfate; also modulates cell proliferation, differentiation, and motility
What do integrins do
Allow cells to attach to ECM components such as fibronectin and laminin; on surface of leukocytes essential in mediation firm adhesion at sites of inflammation; attach via tripeptides arginine glycine aspartic acid motif
What are the phases of the cell cycle
G1: presynthetic growth
S: DNA synthesis
G2: premitotic growth
M: mitosis
What is cell cycle progression driven by
Cyclins and cyclin dependent kinases
What happens as the CDK completes its round of phosphorylation
The associated cyclin is degraded and CDK activity abates
What do CDK inhibitors do
Enforce the cell cycle checkpoints by modulating CDK-cyclin complex activity
Which cells do not proliferate
Neurons and cardiac cells
Which proteins selectively effect cyclin CDK4 and CDK6
P15, p16, p18, and p19
Which CDKs regulate the G1 to S transition?
D-CDK 4, 6, and E-CDK2; they do so by phosphorylating the Rb protein
Which cyclins are activated in the S phase
A-CDK2 and ACDK1
Which CDK is essential for the G2 to M transition
B-CDK1
Where are adult stem cells found
In niches; factors and other cells here keep the stem cells quiescent until there is a need for expansion and differentiation
What can be administered to cause release of hemopoeitic stem cells from their bone marrow niches
CSF
What are mesenchymal stem. Cells
Multipotent cells that can give rise to bone, cartilage, muscle and fat; can generate local immunosuppressive environment; thought to be involved in tissue regeneration
What is CRISPRs
Guide RNAs that are used in conjunction with Cas9 to selectively alter or correct DNA sequences
Where are stem cell niches in various tissues
Skin: hair follicles Liver: Hering canals (connect bile ductules to hepatocytes) SI: base of crypt above paneth cells Cornea: limbus Brain: subventricular zone and dentate
What are the adaptive responses
Hypertrophy, atrophy, metaplasia, hyperplasia
What does nutrient deprivation trigger
Autophagy
What is often deposited at sites of cell death
Calcium; pathological calcification
What causes physiologic hypertrophy
Increased workload or hormone-induced (pregnancy)
Describe the pathogenesis of cardiac hypertrophy
Mechanical sensors induce production of growth factors (TGFbeta, IGF1 and fibroblast growth factor) and vasoactive agents; these activate PI3K/ AKT pathway -> activates GATA4, and myocyte enhancer factor 2 (Both TF) which increases production of m proteins responsible for hypertrophy
Switch of contractile proteins during hypertrophy does what?
Ie: in m hypertrophy, alpha myosin heavy chain is replaced by beta, which is slower, but more energetically economical; also evidenced in cardiac m (example: ANP is expressed in both atria and ventricles early in life, but downregulated; cardiac hypertrophy associated with increased ANP in order to reduce hemodynamic load)
What is an example of hormonal hyperplasia
Glandular breast tissue during puberty and during pregnancy
What are examples of pathological hyperplasia
Endometrial, BPH, can be in response to a virus such as HPV
What are examples of physiologic atrophy
Thryoglossal duct, notochord, decrease in size of uterus after birth
What is senile atrophy
Atrophy of the brain caused by decreased perfusion
What is marasmus
Malnutrition
How do chronic inflammatory diseases cause atrophy
Overproduction of TNF decreases appetite and depletes lipids
How can loss of endocrine function lead to atrophy
Some m require hormonal stimulation for normal metabolism (ie: uterus and breast)
How does pressure cause atrophy
Ie: a tumor pressing on a muscle -> decreases blood supply
What cellular changes occur in atrophic mm
Decrease cell size and organelles to reduce metabolic needs, have fewer mitochondria, microfilaments, and RER to achieve new equilibrium
What are lipofuscin granules
Residual bodies left by autophagic vacuoles that resist digestion; cause brown discoloration to the tissue
What is the most common metaplasia
Columnar to squamous (ie: smokers)
What kind of deficiency can lead to induction of squamous metaplasia in the respiratory epithelium
Vitamin A
Where does squamous to columnar metaplasia occur
Barrett esophagus
What is connective tissue metaplasia
Formation of cartilage, bone, or adipose tissue in tissues that normally don’t contain these elements (ie: bone in muscle - myositis ossificans; occurs after intramuscular hemorrhage); less of an adaptive response, more of response to cell injury
What is the mechanism of metaplasia
Reprogramming of stem cells; precursor cells differentiate along a new pathway
A deficiency in what vitamin can cause metaplasia
Vitamin A; also with excess *regulates gene transcription which influences differentiation of stem cells
What are the hallmarks of reversible cell injury
Cell swelling caused by changes in ion concentration and ATP depletion because of reduced oxidative phosphorylation
Is necrosis always pathological
Yes; apoptosis isn’t always
Compare necrosis to apoptosis
Necrosis: swelling, no nucleus, disrupted plasma membrane, enzymatic digestion of cellular contents -> leak out of cell; produced adjacent inflammation, pathological
Apoptosis: cell shrinkage, nucleus is fragmented, intact plasma membrane (but structure different - orientation of lipids), intact cellular contents, no adjacent inflammation, physiologic usually
What features of reversible injury can be seen under the microscope
Cell swelling and fatty change; plasma membrane alterations (blending, blunting, loss of microvilli), mitochondrial changes (amorphous densities), dilation of the ER; intracytoplasmic myelin figures
What is hydropic change or vacuolar degeneration
Under microscope, cell swelling can be viewed as small clear vacuoles which are distended and pinched off segments of the ER
Where are the enzymes that digest the necrotic cell derived from
Lysosomes of the dying cell as well as from the leukocytes that come in as part of the inflammatory reaction
Why do necrotic cells show increased eosinophilia
Because of the loss of cytoplasmic RNA which binds the blue dye and because of the denatured cytoplasmic proteins which binds the red dye
What are myelin figures
Phospholipid masses derived from the damaged cell membranes; they are phagocytosis or further degraded into fatty acids; calcification of these fatty acids can result in production of calcium soaps
Describe the nuclear changes of a necrotic cell
One of three patterns:
Karyolysis: basophils of chromatin fades because of loss of DNA
Pyknosis (also seen in apoptosis): nuclear shrinkage and increased basophilia; chromatin condenses into a mass
Karyorrhexis: pyknotic nucleus undergoes fragmentation
What is coagulative necrosis
Architecture of the dead tissue preserved for a span of a few days; firm texture; denatures enzymes so blocks proteolytic of the dead cells so they persist until leukocytes break them down; localized area is called infarct *ischemia can cause this to all tissues except the brain
What is liquefactive necrosis
Characterized by digestion of the dead cells; transforms tissue into liquid mass; seen in focal bacterial or fungal infections; frequently creamy yellow because of dead leukocytes (pus); *seen with hypoxic death of cells within the CNS
What is gangrenous necrosis
Not a specific pattern of cell death; involves coagualative necrosis and if liquefactive necrosis is also involved can give rise to wet gangrene
What is caseous necrosis
Structureless collection of fragmented or loses cells and granular Debra with distinct inflammatory border; *granuloma
What is fat necrosis
Focal areas of fat destruction usually caused by release of active pancreatic lipases into peritoneal cavity (acute pancreatitis) fatty acids that are produced from this breakdown combine with calcium to produce chalky white areas (saponification)
What is fibrinoid necrosis
Usually seen in immune reactions involving blood vessels; occurs when ab-ag complex deposited on walls of BV; results in bright pink appearance on slides
What effects does mitochondrial damage of
Decreases ATP and increases ROS (causes damage to lipids, proteins and DNA)
What effect does the entry of Ca2+ have in cell death
Increases the permeability of mitochondria by opening the pore and thus decreases ATP generation, and activates multiple cellular enzymes (phospholipases - membrane damage; processes, endonucleases - DNA fragmentation, and ATPases), also directly activate caspases
What are the effects of decreased ATP?
Decreases Na/K pump so cell swells, increase in anaerobic glycolysis (AMP stimulates PFK and phosphorylase)-> decreases glycogen, increases lactic acid (which decreases pH and causes clumping of nuclear chromatin), detachment of ribosomes which causes decreased protein synthesis
What is cyclophilin D
Part of the mitochondrial permeability transition pore (targeted by the immunosuppressive drug cyclosporine)
What is oxidative stress
When production of free radicals outpaces the body’s ability to eliminate them
How are free radicals produced
Reduction-oxidation reactions, absorption of radiant energy, activated leukocytes during inflammation reactions (uses NADPH oxidase), enzymatic metabolism of drugs, transition metals (Fenton reaction), NO can also act as a free radical
What are examples of antioxidants
Vitamins E and A, ascorbic acid and glutathione
What are the enzymes that breakdown H2O2 and superoxide anion
Catalase (peroxisomes)
Superoxidase dismutases
Glutathione peroxidase *Ratio of oxidized glutathione to reduced glutathione is a reflection of oxidative state of the cell
What is lipid peroxidation in membranes
In the presence of O2, free radicals can attack the double bonds of the unsaturated fA of the membrane (specifically OH); this yields peroxides which are also unstable and reactive -> propagation
What are examples of oxidative modification of proteins
Free radicals promote oxidation of amino acid side chains, formation of covalent protein-protein cross links (Disulfide bonds), and oxidation of protein backbone; can damage active sites, disrupt conformation of protein, and enhance degredation of misfolded proteins
What can free radicals do to DNA
Breaks in DNA, cross linking; linked to cell aging and malignant transformation
What does phospholipid breakdown lead to
Accumulation of lipid byproducts -> unesterified free FA, acyl carnitine, and lysophospholipids which are detergents; can also insert themselves into the membrane and alter permeability y
What is the difference between hypoxia and ischemia
During hypoxia, glycolysis can still continue; with ischemia, the delivery of substrates is depleted and therefore glycolysis cannot occur
What is hypoxia-inducible factor 1
Transcription factor that promotes new BV formation, stimulates cell survival pathways, and enhances anearobic glycolysis; deals with hypoxic stress
What can be done to decrease the damage that occurs during ischemia
Transient induction of hypothermia; decreases metabolic demands, decreases swelling, suppresses formation of free radicals, and inhibits inflammatory responses
How does reperfusion injury occur
Oxidative stress: formation of free radicals by damaged mitochondria
Calcium influx exacerbated by reperfusion
Inflammation: neutrophils recruited to reperfused tissue
Activation of complement: IgM deposits in ischemic tissue; when reperfused, activate complement
What are the two ways chemicals can be toxic
Direct
Conversion to toxic metabolites via P450 (ie: acetaminophen)
What are hormone-dependent apoptosis examples
Ovarian follicular atresia during menopause, regression of lactating Breast, endometrial breakdown during menstrual cycle
What kind of infections can elicit apoptosis
Usually viral (HIV, hep, adenovirus); same T cell mediation response as transplant rejection and tumor death
What kind of cell death occurs after obstruction of ducts (ie: pancreas, glands, kidney)
Apoptosis
What are caspases
Cysteine professes that cleave proteins after aspartic residues
What is BCL2 overexpressed in
B cell lymphomas
What are the anti-apoptotic proteins
BCL2, BCL-XL, and MCL1; reside in outer mitochondrial membrane, cytosol and ER membrane; prevent leakage of cytochrome c; stimulated by growth factors
What are the pro-apoptotic proteins
BAX and BAK; upon activation, they oligomerize with outer mitochondrial proteins and promote mitochondrial permeability
What are sensors?
BAD, BIM, BID, Puma and NoxaRegulate balance between anti and pro apoptotic proteins; BH3 only proteins (only have one of the BH domains of the BCL family)
Describe the intrinsic apoptotic pathway
Cytochrome c binds to apoptosis activating factor 1 (APAF1) which forms an apoptosome; this binds caspase 9 and cleaves adjacent caspase 9 molecules (autoamplification) -> cleaves and activates other caspases
What are Smac and Diablo
Other proteins released from the mitochondria that bind to cytoplasmic proteins that function as inhibitors of apoptosis (IAPs)
What family are the death receptors from
TNF receptor
Where is FasL expressed
On T cells that recognize self antigens and on cytotoxic T cells
Describe the extrinsic apoptotic pathway
FasL binds to Fas and recruits more Fas, which forms a binding site via the death domains for an adaptor protein called FADD; FADD binds to inactive caspase 8 or 10 (in humans) via the death domain; caspase 8’s cleave each other and initiate the pathway
What can inhibit the extrinsic apoptotic pathway
FLIP; binds to proscapsase 8
Describe one of the interconnections between the two apoptotic pathways
In hepatocytes and pancreatic B cells, caspase 8 activates BH3-only protein, BID which feeds into intrinsic pathway
What are the executioner caspases
3 and 6; cleave inhibitor of DNase; also degrade structural components of matrix
What membrane changes occur during apoptosis
Phosphatidylserine flips out to the outer membrane, where it is recognized by macrophages; some are coated by thrombospondin which is an adhesive glycoprotein recognized by phagocytes; can be coated by C1q (complement)
Describe how DNA damage leads to apoptosis
P53 accumulates in cells with DNA damage to arrest cell cycle; if damage is to great to be repaired, p53 initiates apoptosis
What are examples of diseases due to misfolding of proteins
CF, familial hypercholesterolemia, tay Sachs (lack of lysosomal enzyme), creutzfeldt-Jacob disease, Alzheimer’s
What do mutations in Fas or FasL result in
Autoimmune diseases
What happens when cytotoxic T cells are activated
They release perforin; this promotes entry of granzymes which cleave proteins at aspartate residues and activate caspases
Which disorders are associated with increased apoptosis
Neurodegenerative diseases, ischemic injury, and death of virus-infected cells
What is necroptosis
Resembles necrosis by loss of ATP, swelling of cell and organelles, generation of ROS, release of lysosomal enzymes and rupture of the plasma membrane; but it is triggered by programmed signal transduction; HOWEVER it is caspase-independent!
Describe the pathway of necroptosis
TNF binds to TNFR1 which recruits RIP1 and RIP3 (receptor associated kinases) that also contains caspase 8; but caspases are not activated
When is necroptosis seen
Formation of bone growth plate; associated with cell death in steatohepatitis, acute pancreatitis, reperfusion injury, and neurodegenerative diseases; also act as a backup to fight viruses that have caspase inhibitors (cytomegalovirus)
What is pyroptosis
Accompanied by release of IL-1 (induces fever); microbial products activate immune receptors that activate inflammasomes; inflammasomes activate caspase 1 which cleaves a precursor to IL-1; caspase 1 also activates death of cells but unlike classical apoptosis, causes swelling of cells, loss of membrane integrity, and release of inflammatory mediators
What are the different types of authophagy
Chaperone-mediated
Microautophagy (invagination of lysosomal membrane)
Macroautophagy (autophagic vacuole)
What does the elongation and closure of the autophagosome require
Action of ubiquitin-associated conjugation systems, including microtubule-associated protein light chain 3 (LC3); LC3 is a marker to determine if autophagy is occurring
What diseases have autophagy genes been linked to
IBD, neurodegenerative (both accelerated and decreased), cancer, infections diseases
What are the mechanisms of intracellular accumulations
Inadequate removal of normal substances because of defects in mechanisms of packaging and transport (ie: fatty change in the liver)
Accumulation of abnormal endogenous substance as a result of defects in folding, transport, etc (ie: mutation of alpha anti-trypsin)
Failure to degrade a metabolite due to enzyme deficiency (storage diseases)
Accumulation of abnormal exogenous substance because of enzymatic deficiency and transport (carbon accumulation)
What is steatosis
Abnormal accumulation of triglycerides in parenchymal cells
What are xanthomas
Intracellular accumulation of cholesterol within macrophages; clusters of foamy cells in subepithelial connective tissue of the skin and tendons
What is cholesterolosis
Focal accumulations of cholesterol-laden macrophages in the lamina propria of the gallbladder
What is Niemann pick disease type C
Lysosomal storage disease caused by mutations of an enzyme in cholesterol trafficking; results in cholesterol accumulation in multiple organs
What are russel bodies
Produced by ER during synthesis of immunoglobulins; they are eosinophilia inclusions
What does alpha antitrypsin deficiency do
Mutations in the protein cause slow folding which causes a buildup in the ER; causes emphysema
What is alcoholic hyaline composed of
Keratin filaments
What is an example of extracellular hyaline
In HTN, arterioles become hyalinized
Where and when can glycogen accumulations be found
DM in renal tubular epithelial cells, liver cells, beta cells of pancreas and heart m cells
What is the most common exogenous pigment
Carbon; air pollution; taken up by macrophages; blackens tissues of the lungs (anthracosis) and LN
*tattooing also exogenous pigment; dermal macrophages take up pigment
What is lipofuscin
Insoluble pigment (called wear and tear pigment); derived via lipid peroxidation of lipids from membranes; telltale sign of free radical injury; appears as yellow-brown; prominent in heart and liver of aging patients or patients with cachexia; perinuclear intralysosomal location
What is melanin
Pigment formed from oxidation of tyrosine to dihydroxyphenylalanine by tyrosinase; only black pigment (besides homogentisic acid - occurs in patients with alkaptonuria)
What is Hemosiderin
Major storage form of iron; golden yellow-brown granular or crystalline pigment; formed when there is a local (hemorrhage; bruises) or systemic excess of iron (aggregates of ferritin micelles); can be seen in areas of RBC breakdown (bone marrow, spleen, and liver); when systemic deposits in many places -> caused by hemochromatosis (too much iron due to metabolism deficiency), hemolytic anemia, repeat blood transfusions
What are psammoma bodies
Acquisition of outer layers of mineralization during calcification; thyroid cancer (papillary) prone to formation of these
What are causes of hypercalcemia
Overproduction of PTH, resorption of bone tissue (tumors of bone marrow), vitamin D related disorders (sarcoidosis), renal failure (retain phosphate)
What is unique about the common locations of metastatic calcification
All excrete acid and thus have an internal alkaline compartment which predisposes them to calcification; lung, kidneys, gastric mucosa, arteries, pulmonary veins
What is Werner syndrome
Premature aging; defective gene is a DNA helicase; Bloom and ataxiatelangiectasia are similar but with mutation in enzyme responsible for repairing dsDNA
Telomerase is absent in ________
Somatic cells
Besides telomeres, what is also involved in controlling senescence
Activation of tumor suppressor genes, particularly those encoded for by the CDKN2A locus; encores for p16 or INK4a; p16 is at the G1/S checkpoint
What is the effect of rapamycin on cell agin
Inhibits mTOR pathway and increases life span; also promotes autophagy
What are the downstream targets of IGF1
mTOR and AKT
What are surtuins
Family of NAD-dependent protein deacetylases; adapt to bodily functions to various environmental stresses; promote expression of genes that increase longevity
How does caloric restriction increase longevity
Reduces signaling intensity of IGF1 (lower rates of cell growth and possibly reduced damage) and increases sirtuins (activate DNA repair enzymes via deacylation (contained in wine)
What cells are involved in acute respiratory distress syndrome verses asthma
Asthma: eospinophils
ARDS: neutrophils
Are local and systemic signs more prominent in acute or chronic inflammation
Acute
What are the 4 cardinal signs of inflammation
Rumor (Redness), tumor (swelling), calor (heat), and dolor (pain); loss of function also added
What are some endogenous substances that elicit inflammation in excess
Urate crystals, lipid, cholesterol crystals
What are immune reactions
Reactions against self or allergies
Where are cellular receptors for microbes located
Plasma membrane, endosomes, and cytosol
What do sensors of cell damage recognize
Uric acid (DNA breakdown), ATP, reduced intracellular K+; activate inflammasome which produces IL-1; gain of function in these receptors cause autoinflammatory syndromes
What does mannose-binding pectin recognize
Microbial sugars
What is exudation
Escape of fluid, proteins, and blood cells into interstitial tissue
What causes production of transudate
Imbalance in hydrostatic or osmotic pressure that causes fluid to accumulate without changing the membrane permeability; low specific gravity, low protein (mostly albumin), no cellular material
Is pus exudate or transudate
Exudate; rich in neutrophils and microbes
What effect does vasodilation produce during inflammation
Increased blood flow leads to erythema and heat; this in conjunction with the loss of fluid due to increased permeability causes slower blood flow and ultimately stasis/vascular congestion; engorgement of vessels
What are the mechanisms of increased vascular permeability
- Contraction of endothelial cells causing increased interendothelial spaces (elicited by histamine, bradykinin, leukotrienes; *immediate transient response)
- endothelial injury -> necrosis
- transcytosis: increased transport of fluid and protein; VEGF can stimulate channels to open
What causes late appearing sunburn
Delayed prolonged leakage from contraction of endothelial cells
What is lymphangitis verses lymphadenitis
Swelling of Lymphatics versus LN
What causes lymphadenitis
Hyperplasia of lymphoid follicles
What is margination
Because of stasis caused by inflammatory reaction, there is a decrease in shear stress and leukocytes travel along the endothelial surface
What are the ligands for selectins
Sialylated oligosaccharides bound to mucin-like glycoprotein backbones
Describe how rolling of the leukocytes is initiated
TNF and IL-1 act on the endothelial cells of postcapillary venules to induce expression of selectins (L and E; and their ligands); histamine and thrombin also stimulate the redistribution of P-selectin from its intracellular stores in the granules (Weibel-Palade bodies); low affinity interactions and as a result, “roll”
Describe how adhesion is mediated
TNF and IL-1 induce endothelial expression of ligands for integrins, mainly VCAM-1 (ligand for beta integrin VLA-4) and intercellular adhesion molecule 1 (ligand for beta 2 integrins LFA-1 and Mac-1); leukocytes express integrins at low affinity state, but chemokines bind to endothelial proteoglycans which then bind to leukocytes and activate them to higher affinity state
What is diapedesis
Migration of leukocytes through the endothelium
What is the function of CD31 or PECAM-1
Adhesion molecules present in intercellular junctions between endothelial cells that help migration of leukocytes
What are some chemoattractants
N-formymethionine, C5a, IL-8, arachadonic acid metabolites (leukotriene B)
What does binding of chemotactic agents do to the leukocytes
Initiations GPCR response -> increase calcium and activate GTP of Rac/Rho/cdc42 family -> polymerization of actin (moves to front, myosin moves to back); causes migration of leukocytes towards chemoattractants
What is unique about the inflammatory reaction of pseudomonas
Neutrophils are constantly recruited for several days
What are the phagocytic receptors
Mannose, scavenger, and opsonins (IgG abs, C3b, and lectin)
What is phagocytosis dependent on
Polymerization of actin filaments
What is the respiratory burst
In neutrophils, the activation of NADPH oxidase to oxidize NADPH and reduce oxygen to superoxide anion
Describe how ROS kill microbes in a phagocyte
Phagocyte oxidase components from cytosol move to membrane and form full complex with membrane components; O2 is converted to H2O2 spontaneously, which is then converted to OCl2 by myeloperoxidase (MPO); OCl2 destroys microbes by halogenation (the halide binds to cellular constituents) or oxidation or proteins and lipids (lipid peroxidation); deficiency in MPO doesn’t effect susceptibliliy to infection
What anti-oxidants do cells contain to protect them from ROS
Glutathione peroxidase and catalase (convert H2O2); superoxide dismutase, transferrin, ceruloplasmin
How is NO produced
From arginine via nitric oxide synthase
What are the types of NO
ENOS, nNOS (expressed at low levels; involved in vascular tone and NT); iNOS - involved in microbial killing; induced when macrophages and neutrophils activated by cytokines or microbes
How is NO involved in microbial killing
In macrophages, it reactions with superoxide anion to produce peroxynitrite which attacks the microbe
What are the two types of neutrophilic granules
Specific or secondary: contain lysozyme, collagenase, gelatinase, lactogen Ron, plasminogen activator, histaminase, and alkaline phosphatase
Azurophil or primary: contain myeloperoxidase, bactericides factors (defending and lysozyme), acid hydrolyzes, and proteases (elastase, cathepsin G, proteinase 3)
What do acid vs neutral proteases do
Acid: degrade bacteria and debris within phagolysosomes because of acidic environment
Neutral: degrade extracellular components; tissue destruction that accompanies inflammatory process; can also cleave C3 and C5, yielding anaphylactic is
What does neutrophil elastase do
Combat bacterial infections
How are the harmful aspects of the granules controlled
Anti proteases in serum *antitrypsin (inhibits elastase).
What are neutrophil extracellular traps
Fibrillar networks that provide a high concentration of antimicrobial substances at sites of infection and prevent their spread by trapping them; consist of chromatin that bind granule proteins; nuclei of neutrophils lost which lead to death of the cells; the nuclear chromatin in NETs is believed to act as an antigen in autoimmune diseases such as lupus
Which T cell is involved in acute inflammation
T17; lack of this causes cold abscesses (no heat production in the inflammatory response)
What termination mechanisms are illicited by the inflammatory response
Switch in type of arachadonic acid metabolite produced from proinflammatory leukotriends to antiiinflammatory lipoxins
What are the most important mediators of inflammation
Vasoactive amines, lipid products (prostaglandins and leukotrienes), cytokines, and complement
What are the plasma derived mediators
Complement; produced in liver
What are the vasoactive amines
Histamine and serotonin
Is serotonin a vasoconstrictor or dilator
Constrictor
What are leukotrienes and prostaglandins produced from
Arachadonic acid
What are eicosanoids
Arachidonic acid derived; synthesized by cyclooxygenases (which generate prostaglandins) and lipoxygenases (which produce leukotrienes)
What inhibits phospholipases
Steroids
What do prostacyclin, thromboxane A2, and PGD/E do?
Prostacyclin: vasodilation, inhibits platelet aggregation
Thrombosane: vasoconstriction, promotes platelet aggregation
PGD/E: vasodilation, increased vascular permeability
What is the difference between COX-1 and 2
COX-1: produced in response to inflammation and expressed in most tissues where it serves homeostatic function
COX-2: inducedby inflammatory stimuli and generates prostaglandins, low or absent in most normal tissues
Where is PGI2 (prostacyclin) made
Endothelium
What does a thrombaxane/prostacyclin imbalance cause
Thrombus formation in coronary and cerebral vessels
What is the major prostaglandin made by mast cells
PGD2
What does 5-lipoxygenase do
Converts arachidonic acid to 5-hydroxyeicosatetraenoic acid (5-HETE) -> precursor for leukotrienes and chemotactic for neutrophils
What do the cysteinyl-containing leukotrienes do
LTC#: vasoconstriction, bronchospasm (asthma), and increased permeability; more potent than histamine
What do lipoxins do
Suppress inflammation by inhibiting recruitment of leukocytes; require two cell populations for their synthesis - neutrophils and platelets
How do COX inhibitors work
Acetylating cyclooxygenases
Why can selective COX-2 inhibitors be dangerous
Would block the formation of PGI2 (vasodilator and inhibitor of platelet aggregation) while leaving the COX-1 mediated production of thromboxane in tract
What is the benefit of ingesting fish oil?
The polyunsaturated fats in fish oil are poor substrates for conversion to active metabolites by cyclooxygenases and lipoxygenase; better substrates for production of anti inflammatory lipid products
How does TNF and IL-1 activate leukocytes
TNF: augments responses of neutrophils to other stimuli and stimulates activity of macrophages by inducing production of NO
IL-1: activates fibroblasts to synthesize collagen; also stimulates Th17 responses
What are acute-phase responses involved in
Fever and sepsis
What can prolonged production of TNF lead to
Cachexia; TNF promotes lipid and protein mobilization by suppressing appetite
Which interleukins are important players in chronic inflammation
IL-12, IFN-gamma, IL-17
What are the different chemokines
CXC: ie: IL-8 (affects neutrophils, but not monocytes or eosinophils)
CC: MCP-1, MIP, and RANTES (regulated and normal T-cell expressed and secreted) -> attract monocytes, eosinophils (eotaxin specifically) basophils and lymphocytes; not potent attractors of neutrophils
C: specific for lymphocytes
CX3C: fractalkine; monocytes and T cells
How do chemokines assert their actions
GPCR; used as coreceptors for HIV
What effect does TNF have on the heart and skeletal m
Low output; insulin resistance
What are homeostatic chemokines
They organize cell types such as T and B cells in the spleen and LN
How is the classical pathway triggered
Fixation of C1 to IgM or IgG that has combined to an antigen
How is the alternative pathway triggered
Microbial surface molecules, complex polysaccharides, cobra venom, or other substances in the absence of antibody
How is the lectin pathway triggered
Plasma mannose-binding lectin binds to carbs on microbes and directly activates C1
Describe the complement pathway
C3 convertase is activated which splits C3 to C3a and C3b -> C3b attaches to the microbe and also to previous fragments to form C5 convertase -> cleaves C5 to C5a and C5b -> C5b attaches to the microbe and binds C6-C9 to form the MAC which lyses the microbe
What do C3a and C5a do
Stimulate histamine release from mast cells; C5a chemotatic for neutrophils, monocytes, eosinophils, and basophils; C5a also activates lipoxygenase pathway
How does MAC work
Makes cells permeable to water and ions and results in lysis
What causes hereditary angioedema
Deficiency in C1 inhibitor
What do decay accelerating factor (DAF) and CD59 do?
DAF prevents formation of C3 convertase and CD59 inhibits formation of MAC; both of these are linked to the membranee by a glycophosphatidyl (GPI) anchor -> deficiency leads to excessive complement activation and lysis of RBCs -> causes paroxysmal nocturnal hemoglobinuria (PNH)
What does platelet activating factor do
Platelet aggregation, vasoconstriction, bronchoconstriction, and at low concentrations: vasodilation and increased venular permeability
What activates protease activated receptors (PARs)
Thrombin
What are kinins
Vasoactive proteins derived from kininogens by activation of kallikreins; bradykinin is one product (vasodilation, smooth m contraction, pain when injected) - short lived because inactivated by kininase
What is serous inflammation
Transudate in spaces created by cell injury, peritoneum, pleura, or pericardium; produces an effusion (ie: blister from a burn or viral infection is serous)
What is fibrinous inflammation
Develops when vascular leaks are large or there is a local procoagulant stimulus; fibrinogen leaks out of blood; characteristic of meninges, pericardium, and pleura; can be resolved by fibrinolysis and cleared by macrophages; if not removed, can stimulate in growth of fibroblasts and lead to scarring (can lead to obliteration of pericardial space)
What is purulent inflammation
Also called suppurative; production of pus (neutrophils and liquefied debris of necrotic cells, most often those that underwent liquefactive necrosis); example is appendicitis; also abscesses (central region of necrotic leukocytes and zone around it of neutrophils then around that, zone of vasodilation and fibroblastic proliferation)
When does scarring occur
After substantial tissue destruction, when inflammatory injury involves tissues that cannot regenerate, or where there is abundant fibrin exudation that cannot be cleared
Why is atherosclerosis considered chronic inflammation
Caused by excessive production of cholesterol which causes inflammation
Where are macrophages derived from
Hemopoetic stem cells in bone marrow; embryonic yolk sac and fetal liver
What are sinus histiocytes
Macrophages in the spleen and LN
Describe the classical macrophage activation pathway
Induced by microbial products, T-cell signals (IFN-gamma), or by foreign substances; these activated macrophages produce NO and ROS and upreguate lysosomal enzymes as well as IL-1, 12, 23 and chemokines
Describe the alternative macrophage activation pathway
Induced by cytokines other than IFN-gamma (such as IL-4 and 13); secrete growth factors that promote angiogenesis, activate fibroblasts, and stimulate collagen synthesis (produce TGF-beta, IL-10)
What are the subsets of CD4+ T cells and what do each produce
Th1-> IFN-gamma
Th2-> IL-4, 5, and 13; activate eosinophils and alternative macrophage pathway (allergic reaction and parasites)
Th17-> IL-17; induce secretion of chemokines that recruit neutrophils
What are tertiary lymphoid organs
In chronic inflammation, lymphocytes, antigen-presenting cells, and plasma cells cluster together; seen in synovium of patients with rheumatoid arthritis and hashimoto thyroiditis
What do eosinophilic granules contain
Major basic protein: toxic to parasites and causes lysis of mammalian cells
What receptor do mast cells have?
FceRI (binds Fc portion of IgE abs); involved in both acute and chronic inflammation
What is the purpose of granulomatous inflammation
Granuloma formation is an attempt to contain a microbe that is difficult to erradicate; strong activation of Tcells which causes activation of macrophages; these macrophages may develop abundant cytoplasm (called epithelioid cells); they can also fuse and form giant cells
What are the different types of granuloma
Foreign body: absence of Tcells; macrophages are supposed to the surface of the foreign body and do not recruit anything
Immune granuloma: induce persistent T cell response
*either IL-4 or IFN-gamma transform cells into epithelioid and giant cells
What conditions display granulomatous inflammation
Crohns, sarcoidosis, tuberculosis (granuloma referred to as tubercle), leprosy, syphilis, cat-scratch disease
What are the main mediators of acute phase response
IL-1, 6, TNF, and type I interferon
What are the exogenous vs endogenous pyrogens
LPS: exogenous; IL-1 and TNF endogenous
How is fever induced during the acute phase response
LPS stimulate leukocytes to produce IL-1 and TNF which activates cyclooxygenases to convert AA to prostaglandin
What are the acute phase proteins
C reactive protein, fibrinogen (both stimulated by IL-6) and serum amyloid A protein (stimulated by Il-1 or TNF); act as opsonins
What is fibrinogens action as an acute phase protein
Binds RBCs and causes them to form stacks called rouleaux that sediment more rapidly; measure sedimentation rate to determine inflammatory response
What can overproduction of acute phase proteins cause
Secondary amyloidosis; elevated CRP increases risk of MI; also can cause anemia because hepcidin is increased during the acute phase response (this depletes iron availability)
What is the difference between bacterial and viral infections in terms of leukocytosis
Bacterial: causes neutrophilia
Viral: causes absolute increase in lymphocytes (lymphocytosis)
*some infections are associated with decreased white cells (leukopenia; ie: typhoid fever, rickettsiae)
What are the characteristics of acute phase response
Fever, acute phase proteins, leukocytosis, increased pulse and BP, decreased sweating, rigors (shivering), chills, anorexia, somnolence, malaise
What does sepsis cause
High cytokines in the blood -> disseminated intravascular coagulation, hypotension shock, insulin resistance
What is “organization”
When fibrosis develops in a tissue space occupied by an inflammatory exudate (ie: organizing pneumonia)
What are labile tissues
Continuously dividing; hematopoietic (bone marrow), surface epithelium (skin, oral cavity, vagina, cervix), epithelial of exocrine organs, epithelial of GI tract, uterus, and Fallopian tubes, and transitional epithelium of urinary tract
What are stable tissues
Cells of these tissues are in G0; limited profilerating during normal state, but can proliferate in response to injury; parenchyma of liver, kidney, and pancreas, endothelial cells, fibroblasts, and smooth m *impt in wound healing; limited capacity to regeneration (except liver)
What are permanent tissues
Terminally differentiated and nonproliferative; neurons and cardiac (therefore no regeneration, just scar)
What stimulates cell proliferation
Growth factors from macrophages (release blocks and increase production of proteins to continue cell cycle) and signals from integrins
How is hepatocyte proliferation induced
Stages: 1st -> priming stage: TNF induces IL-6 production by kupffer cells and act on hepatocytes to make them compentent to respond to growth factor signals
2nd -> growth factor phase: HGF and TGF alpha act on hepatocyte to stimulate metabolism and entry of cells into cell cycle; then nonparenchymal cells (kupffer, endothelial, and stellate) replicate
3rd-> termination phase: hepatocytes return to quiescence TGFbeta likely involved
How does liver regeneration from progenitor cells work
*occurs where proliferative capacity is impaired (ie: chronic liver injury) progenitor cells located in canals of herring
What are the steps in scar formation
Angiogenesis: newly formed vessels are leaky becomes of incomplete junctions and VEGF increases vascular permeability (reason there is still edema in healing wounds)
Formation of granulation tissue: migration of fibroblasts, depostition of CT, and vessels and leukocytes form granulation tissue (pink, soft granular appearance)
Remodeling of connective tissue: dense collagen
Describe the steps of angiogenesis
-vasodilation in response to NO and increased permeability due to VEGF
-separation of pericytes from abluminal stuffs and breakdown of basement membrane (allows formation of vessel sprout)
-migration of endothelial cells to injury
-proliferation of endothelial cells (FGF-2) just behind the tip of the migrating cells
-remodeling into capillary tubes
Recruitment of periendothelial cells (perictyes for small; smooth m for larger vessels)
-suppression of endothelial proliferation and migration; deposition of basement membrane
What do angiopoietins 1 and 2 do
Cause detachment of the pericyte so the vessel can grow; Involved in structural maturation of new vessel; Ang 1 interacts with RTK on endothelial cells called Tie2 which stabilizes vessel
What do PDGF and TFG beta do in the stabilization process of angiogenesis
PDGF recruits smooth m and TGF beta suppresses endothelial proliferation and migration and enhances production of ECM proteins
What is the function of notch signaling in angiogenesis
Notch signaling cross talks with VEGF; this regulates sprouting of new vessels, ensuring that new vessels have proper spacing to supply healing wound
What is the role of matrix metalloproteinases (MMPs) in angiogenesis
Breakdown the basement membrane so new sprout can grow
Is production of TGFbeta increased or is the latent form activated in tissue repair
Latent form activated
What is the function of TGF-beta in tissue repair
Migration and proliferation of fibroblasts, increased synthesis of collagen and fibronectin, and decreased degradation of ECM by inhibiting metalloproteinases
What contributions to the contraction of a scar
Fibroblasts acquire features of smooth m and are called myofibroblasts
What are examples of MMPs
Collagenases, gelatinases, stromelysins
What are TIMPS
Tissue inhibitors of MMPS
What are ADAMs
A disintegrin and MMP; anchored to plasma membrane and cleave extracellular domains of cytokines and growth factors
What are factors that can impair healing
Infection, diabetes, nutritional status (vitamin D deficiency inhibits collagen synthesis), glucocorticoids (inhibits TGF beta; may be desired in something line a cornea infection - don’t want opacity of scar); mechanical factors (increased torsion), poor perfusion, foreign bodies
What is healing by first intention
If the injury only involves the epithelial layer, mechanism of repair is epithelial regeneration; ie: surgical incision; first a clot forms which acts as a scaffold and also attracts neutrophils, within 1-2 days cells start to proliferate and meet in the midline beneath surface scab, day 3 -macrophages come and granulation tissue produced; by day 5, neovascularization is complete and fibroblasts recruited by PDGF, EGF, TGF beta, FGF, IL-1 and TNF; continued collagen accumulation (blanching begins)
What is healing by second intention
Large wounds, abscesses, ulceration, and ischemic necrosis; fibrin clot is larger, more exudate and necrotic debris, larger amount of granulation tissue formed; first, matrix containing fibrin, fibronectin, and type II collagen is formed; in two weeks this is replaced by matrix composed of primarily type I collagen; converted to pale, avascular scar with spindle-shaped fibroblasts, elastic tissue; *wound contraction
What is fibrosis
Excessive deposition of collagen
What are important activators of fibrosis
Cell death and production of ROS
What can inadequate formation of granulation tissue or a scar lead to
Wound dehiscence (rupture of wound; most frequently after abdominal surgery) and ulceration (inadequate vascularization during healing)
What is exuberant granulation
Consists of formation of excessive granulation tissue which protrudes above the level of the surrounding skin and blocks reepithelialization (proud flesh); must be removed surgically
What are desmoids/aggressive fibromatoses
Rare incisional scars/traumatic injuries that are followed by exuberant proliferation of fibroblasts that recur after excision; these neoplasms lie in the interface between benign and malignant
Where are contractures more likely to form
Palms, soles and anterior aspect of thorax
What is the difference between inflammatory and non-inflammatory edema/effusions
Inflammatory: infection; exudate
Non-inflammatory: transudate; heart failure, liver failure, renal disease, nutritional disorders
What causes an increase in hydrostatic pressure
Decrease in venous return (DVT, CHF) or arteriolar dilation (heat, neurohumoral dysregulation)
What is nephrotic syndrome
Albumin leaks into the urine; causes decreased osmotic pressure; reduces volume and renal perfusion, causes secondary hyperaldosteronism
What are the categories of edema
Increased hydrostatic pressure, decreased colloid pressure, lymphatic obstruction, sodium retention (renal insufficiency), inflammation
What causes elephantiasis
Parasite filariasis; obstructive fibrosis of lymphatic channels and LN
What is dependent edema
Distribution depends on gravity (legs when standing, sacrum when recumbent) *subcutaneous edema
Where does edema caused by renal insufficiency show?
Parts of body containing loose connective tissue - periorbital edema
What is a chylous effusion
Peritoneal effusion caused by lymphatic blockage; only transudate even effusion that isn’t translucent
What can edema lead to
Loss of wound healing function; in pulmonary edema, fluid in alveolar spaces prone to bacterial infection, compromises gas exchange (effusions)
What is the difference between hyperemia and congestion
Hyperemia: active process in which arteriolar dilation leads to increase blood flow (ie: exercise or inflammation), affected tissues turn red
Congestion: passive process resulting from reduced outflow of blood; tissues will be cyanotic, increases hydrostatic pressure -> edema; in chronic passive congestion, can lead to ischemic tissue or hemorrhagic foci due to capillary rupture which can then leave hemosiderin-laden macrophages
What is nutmeg liver
Caused by chronic passive congestion
What occurs in acute vs chronic hepatic congestion
In acute, since the centrilobular area is at the distal end of the vascular supply, it will undergo ischemic necrosis, but the peripheral hepatocytes will only undergo fatty changes
In chronic, the centrilobular regions become red-brown and depressed and are surrounded by uncontested tan liver (nutmeg)
What is disseminated intravascular coagulation (DIC)
Activation of clotting produces bleeding because there is consumption of coagulation factors
Describe the process of hemostasis
Arteriolar vasoconstriction (mediated by endothelin) -> primary hemostasis: formation of platelet plug; vWF and collagen exposed on injured endothelium, which promotes platelet adherence and activation (changes shape to spiky) and release granules (recruits additional platelets which undergo aggregation) -> secondary hemostasis: deposition of fibrin; tissue factor exposed at injury; it binds and activates factor VII -> thrombin generation (cleaves fibrinogen to fibrin -> additional aggregation) -> clot stabilization and resorption; contraction to form permanent plug; t-PA set to limit clotting and resorption
What receptors do platelets contain that bind to vWF
Glycoprotein Ib
What are released in the granules that causes recruitment of more platelets to form th primary hemostatic plug
ADP and thromboxane A2; initiate platelet aggregation through platelet GPIIb-IIIa receptor binding to fibrinogen
What do alpha granules of platelets contain
Have P selection on membrane; contain fibrinogen, factor V, vWF, fibronectin, platelet factor 4, PDGF, and TGF beta
What do dense or gamma platelet granules contain
ADP and ATP, calcium, serotonin, and epi
What is Bernard skulked syndrome
Deficiency of GpIb
When platelets change their shape, what else occurs
Alterations in GpIIb/IIIa that increase affinity for fibrinogen (ADP induces change) and translocation of negatively charged phospholipids (phosphatidylserine) to platelet surface (bind calcium and serve as sites for assembly of coagulation factor complexes)
How does thrombin activate platelets
GPCR called protease activated receptor (PAR), switched on by proteolytic cleavage by thrombin
What is glanzmann thrombasthenia
Deficiency in GpIIb and IIIa
What parts of clot formation are reversible
Initiate aggregation; concurrent activation of thrombin stabilizes platelet plus and promotes irreversible platelet contraction
Describe the intrinsic pathway of clotting
A negatively charged surface converts XII->XIIa, which converts XI->XIa; XIa converts IX to IXa, which binds with VIIIa to activate X to Xa; Xa binds to Va and converts prothrombin to thrombin
Describe the extrinsic clotting pathway
TF binds to and activates VII-> VIIa; TF/VIIa cleaves X to Xa which binds to Va and converts prothrombin to thrombin
Describe how clotting occurs in vivo
Tissue factor activates and binds to VIIa, which cleaves IX to IXa; IXa binds with VIIIa and cleaves X to Xa, which binds with Va and cleaves prothrombin to thrombin
Describe the feedback mechanisms in the in vivo pathway of blood clotting
Thrombin positively feedback on Va, the conversion of XI to XIa, and VIIIa
What factor is prothrombin
2
What is the importance of calcium in the clotting pathway
Binds to gamma carboxylated glutamic acid residues on factors II, VII, IX, and X; these factors use vitamin K as a cofactor and are antagonized by Coumadin
What does prothrombin versus partial thromboplastin time measure
PT: extrinsic pathway
PTT: intrinsic pathway
Deficiencies of which clotting factors are associated with severe bleeding disorders
V, VII, VIII, IX, and X; prothrombin incompatible with life
What occurs in individuals with factor XII deficiency
No bleeding disorder -> often susceptible to thrombosis
Why do people with factor XI not bleed as much
Likely because thrombin can activate XI
How does thrombin stabilize the secondary hemostatic plug
Activates factor XIII, which cross links fibrin
What is thrombin’s action on PARs
Induces platelet aggregation of production of thromboxane A2, activate endothelial cells to express adhesion molecules, t-PA, NO, PGI2, and PDGF
When is thrombin an anti-coagulant
When encountering normal epithelium
How is coagulation limited
Blood flow washes out coagulation factors, negatively charged phospholipids are covered when clot starts to form, factors expressed by adjacent endothelium
Describe fibrinlysis
Plasmin breaks down fibrin and interferes with its polymerization ; *D-dimers (clinical marker of thrombotic state); plasmin is activated from plasminogen by XII dependent pathway (reason its involved in thrombosis if deficient) or by plasminogen activating factors (t-PA - active when bound to fibrin); plasmin is regulated by alpha plasmin inhibitor
What are the antithrombotic properties of endothelium
Platelet inhibitors: release prostacyclin, NO, and adenosine diphosphatase (degrades ADP), endothelial cells can also bind thrombin and alter its activity
Anticoagulant effects: produce thrombomodulin and endothelial protein C receptor (bind thrombin and protein c -> this complex causes a loss of thrombin’s ability to activate coagulation factors and platelets and instead activates protein C (Vitamin K dependent, requires protein S cofactor) that inhibits Va and VIIIa, heparin-like molecules (bind and activate anti thrombin III, which inhibits thrombin, IXa, Xa, XIa, and XIIa), and TF inhibitor (requires protein S)
Fibrinolytic effects: synthesize t-PA
What are the defects of primary hemostasis
Platelet defects or vWdisease; typically form petechiae or purpura; also may have nosebleeds (epistaxis), GI bleeding, or menorrhagia; low platelet counts (thrombocytopenia) -> can lead to intracerebral hemorrhage
What are defects of secondary hemostasis
Coagulation factor defects; bless in soft tissues or joints, bleeding into joints (hemarthrosis); hemophilia; intracranial hemorrhage
What is the virchow triad
Endothelial injury, stasis or turbulent blood flow, and hypercoagulability
What can cause endothelial activation or dysfunction (change to prothrombotic endothelium)
Injury, infection, abnormal blood flow, inflammatory mediation, hypercholesterolemia, or homocystinemia, toxins from cigarette smoke
What procoagulant changes occur to the endothelium during activation
Downregulate expression of thrombomodulin and protein C and TFInhibitor
What antifibrinolytic effects are adopted in the prothrombotic state of endothelium
Secrete plasminogen activator inhibitors (PAIs) which limits fibrinolysis and downregulates expression of t-PA
Describe laminar blood flow
Platelets and other cellular elements flow centrally and plasma flows on the periphery
What are some examples of causes of abnormal blood flow
Ulcerated atherosclerotic plaques, aneurysms (form stasis), MI (noncontractile -> stasis), Afib, sickle cell anemia
What is the difference between primary and secondary hypercoagulability disorders
Primary: genetic
Secondary: acquired
What are the most common primary hypercoagulability causes
Factor V mutation (arg->glu substitution; causes resistance to protein C) and prothrombin mutation (noncoding variant that leads to increased prothrombin)
What can cause elevated homocysteine
Deficiency of cystathione beta synthetase
When must inherited causes of hypercoagulability be considered
In patients younger than 50 who present with thrombosis *even when acquired risk factors are present
How do OCPs or hyperestrogenic states cause hypercoaguability
Causes increase hepatic synthesis of coagulation factors and reduced anticoagulant synthesis
What is heparin induced thrombocytopenia (HIT)
Occurs following administration of unfractionated heparin; cause abs that recognize heparin and platelet factor 4 on the surface of platelets and heparin-like molecules on endothelial cells; results in activation, aggregation and consumption; produced prothrombotic state, even in the state of low platelet count
What is antiphospholipid antibody syndrome
Clinical manifestations: thrombosis, repeat miscarriages (failure of placentation)a, cardiac valve vegetations and thrombocytopenia; can cause PE (following LE DVT), pulm HTN (recurrent PE), stroke, bowel infarction, or renovascular HTN; abs target proteins that are induced by phospholipids (beta2 glycoprotein I - associated with endothelial cells and trophoblast and thrombin); false positive for syphilis b/c antigen is embedded in phospholipid
What is the difference between primary and secondary antiphospholipid antibody syndrome
Primary: only exhibit hypercoagulable state; no autoimmune disorders
Secondary: autoimmune disease
What are the lines of Zahn
Laminated formed by pale platelet and fibrin deposits alternating with darker red cell rich layers; only form in the presence of flowing blood therefore, their presence distinguishes antemortem clots from postmortem
What are mural thrombi
Thrombi that occur in the heart chambers or aortic lumen
What is the difference between the contents of arterial thrombi and venous thrombi
Arterial: platelets, fibrin, RBCs and leukocytes
Venous: RBCs and few platelets; *red, stasis thrombi
Describe what a postmortem clot looks like
Gelatinous, dark red portion and yellow chicken fat upper portion; usually not attached to vessel wall
What are vegetation’s
Thrombi on heart valves; bacteria or fungi can adhere to valves and form thrombotic masses (infective endocarditis); nonbacterial thrombotic endocarditis can also develop (LIbman-Sacks in lupus)
What is dissolution of a thrombus
Fibrinolysis; shrinkage and disappearance of the clot; only usually occurs in recent clots
What is a mycotic aneurysm
Infected aneurysm; centers of thrombi can undergo enzymatic digestion by lysosomal enzymes in trapped leukocytes; in the setting of bacteremia they can become infected
What do thrombi of superficial veins predispose individuals to
Vasricose ulcers
Is swelling or pain usually seen with DVTs
No; venous collaterals reduce edema
What do tumors produce that make a hypercoagulable state
TF, factor VIII, mucin (procoagulant); called migratory thrombophlebitis or trousseau syndrome
What are the most likely targets of arterial emboli
Brain, kidneys, and spleen; rich blood supply
What is DIC
Not a disease; complication of large number of conditions; causes widespread thrombi in micro circulation; this uses up platelets and coagulation factors (consumptive coagulopathy) which activates fibrinolytic mechanisms; this can lead to hemorrhagic stroke or hypovolemic shock
What is a paradoxical embolism
When thrombis from venous blood passes into the systemic arterial circulation
What is cor pulmonale
Sudden death, right heart failure caused by emboli obstructing more than 60% of pulmonary circulation
Why does embolic obstruction of medium sized arteries in the lung not cause pulmonary infarction
Supplied by both pulmonary and bronchial arteries (if impeded by left sided cardiac failure, then may occur); embolic obstruction of small arteries also does produce infarction
What is fat embolism syndrome
Characterized by pulmonary insufficiency, Neuro symptoms, anemia, and thrombocytopenia; 1-3 days after injury -> tachypnea, dyspnea, and tachycardia; thrombocytopenia due to platelet adhesion to fat globules
What is decompression sickness
When individuals experience sudden decrease in atmospheric pressure; when air is breathed at higher pressures, increased amounts of gas (nitrogen) are dissolved in the blood; if ascend too quickly, nitrogen comes out of solution and causes “the bends”; causes edema, hemorrhage, and focal atelectasis or emphysema (chokes), chronic form - caisson disease (ischemic necrosis of femoral heads, tibia and humerus)
If a patient survives amniotic fluid embolism, what usually results
Pulmonary edema and DIC; most of the manifestations are caused by activation of coagulation factors and immune s stem agains substances in the fluid (not necessarily obstruction by amniotic debris); caused by either tear of uterine veins or placental membranes
What is present at autopsy of someone who died from amniotic fluid embolism
Squamous cells from fetal skin, lanugo hair, fat from vernix caseosa, and mucin from fetal respiratory or GI tract in pulmonary micro vasculature of the mother
When is venous thrombosis more likely to cause infarction
In organs with a single efferent vein (ie: testis and ovary)
What are the classifications of infarcts
Red: hemorrhagic; occur with venous occlusion (testicular torsion), in loose spongy tissues (lung) where blood can collect in infarcted zone, tissues with dual circulation (lung and SI), in tissues previously congested by sluggish venous outflow, and when flow is reestablished to site of previous occlusion (angioplasty)
White: anemic; occur with arterial occlusions in solid organs with end arterial circulation (heart, spleen, kidney) and where tissue density limits seepage of blood into necrotic area
What is shock
State in which diminished CO or reduced effective circulating blood volume impairs tissue perfusion and leads to cellular hypoxia
What are the types of shock
Cardiogenic: low CO due to infarction, ventricular Arrhythmias, extrinsic compression (tampanade), or outflow obstruction
Hypovolemic: low CO due to low blood volume (hemorrhage or burns)
Shock associated with systemic inflammation: microbes,burns, trauma, pancreatitis; arterial dilation, leakage, venous blood pooling; systemic inflammatory response syndrome
Neurogenic: spinal cord injury
ANaphylactic: IgE mediated hypersensitivity
What most commonly triggers septic shock
Gram + bacteria
What factors play a role in septic shock
Inflammatory and counter-inflammatory responses: downstream of TLRs and GPCR that recognize NOD1 and 2; innate immune cells produce TNF, IL-1,12,18 IFN gamma, and high mobility group box 1 protein (HMGB1); complement cascade (directly and through cleavage of plasmin); microbes can also activate factor XII -> activation of thrombin increases inflammation by activity on PARs; also produce counter-inflammatory (switch between inflammation and immunosuppression - switch from Th1 to Th2)
How does sepsis lead to a procoagulant state
Proinflammatory cytokines increased TF production by monocytes, decrease production of thrombomodulin and protein C; dampen fibrinolysis by increasing plasminogen activator inhibitor 1; vascular leak diminishes blood flow producing stasis and diminished washout; activate thrombin systemically -> in fullblown DIC this is activated so much that uses up all supplies and causes hemorrhage
What metabolic abnormalities are present in septic patients
Insulin resistance and hyperglycemia; TNF, IL-1, glucagon, growth hormone, and glucocorticoids all induce gluconeogenesis and proinflammatory cytokines suppress insulin release while simultaneously promoting insulin resistance (impairing expression of GLUT4); hyperglycemia impairs neutrophil function and cause increased adhesion molecule expression; initial surge of glucocorticoids followed by adrenal insufficiency; increased lactate production
What causes acute respiratory distress syndrome in septic patients
High levels of cytokines diminish cardiac contractility and CO
What do superantigens cause
Toxic shock syndrome; they are polyclonal T lymphocytes activators that induce release of high levels of cytokines that result in hypotension, shock and death
What are the stages of cardiogenic and hypovolemic shock
Non progressive phase: reflex compensatory mechanism activated and perfusion maintained (causes tachycardia, peripheral vasoconstriction, and renal conservation of fluid)
PRogressive stage: tissue hypoperfusion and onset of metabolic imbalances including lactic acidosis
Irreversible stage: after body has incurred cellular and tissue injury so severe that even if hemodynamic effects corrected, survival is not possible
What occurs as sepsis reaches the point of no return
In setting of persistent oxygen deficit, convert to anaerobic glycolysis which produced lactic acid; the decreased pH blunts the vasomotor response causing vasodilation and blood pooling in microcirculation; this worsens CO and puts endothelial cells at risk for anoxic injury with DIC; vital organs begin to fail
What tissue are most effected by shock
Heart, lungs (not in hypovolemic), kidney, adrenals, and GI tract
