Exam 3 Flashcards
(401 cards)
1
Q
Microfilaments (actins)
A
• support/organize plasma membrane
• Cell shape and division and motility
2
Q
Microtubules (tubulins)
A
• organize cytoplasm
• Intracellular transport
• Cell division
• Cilia/flagellae motility
3
Q
Intermediate filaments (IF proteins)
A
• strengthen cytoplasm/tissues
• Support nucleus
• Epidermal appendages (hair/nails)
4
Q
Actin
A
• medium sized globular proteins (45kDa)
• Six actin gene, including muscle (alpha-actin) and non-muscle (beta and gamma-actin) subtypes
5
Q
Tubulin
A
• medium sized globular protein (55kDa)
• Two dozen tubulin genes, alpha, beta, and gamma subunits
• expressed in all cells especially neurons
• binds and hydrolyzes GTP—>GDP
• interacts with motor proteins 
6
Q
Basic building subunits of microtubules
A
Heterodimers of Alpha-beta tubulin
7
Q
Intermediate filament proteins
A
• 50-200kDa
• 70 gene products categorized into six sub-families
• present in tissue specific manner
8
Q
Monomers of intermediate filament proteins
A
Long, linear molecules that assemble during polymerization like threads forming a rope
9
Q
Tubulin polymers
A
Tubules formed from Proto filaments that display chemically different ends (polar) 
10
Q
Types of actins
A
Muscle— skeletal, cardiac, smooth
Cytoplasmic —beta and gamma cytoplasmic
11
Q
Types of tubulins
A
• alpha tubulin, 8 genes
• Beta tubulin, 10 genes
• Gamma tubulin, 2 genes
12
Q
IF proteins subfamilies
A
- Acidic keratins
- Neutral/basic keratins
- Vimentin, desmin, GFAP
- Neurofilament IF proteins
- Lamins
- Lens-specific beaded IFs
13
Q
polarized polymers are formed by:
A
Actin and tubulin
- subunits are easily added to the plus end, and removed from the minus end 
14
Q
Actin and tubulin as nucleotide-binding proteins
A
ATP/GTP and ADP/GDP respectively
ATP and GTP binding stabilize the polymers, and ADP and GDP destabilize the polymers
15
Q
Dynamic instability
A
The rapid cycling between microtubule polymerization and depolymerization that occurs continuously in cells 
16
Q
Actin polymerization is initiated by:
A
1.) Formin (parallel bundles)
2.) Arp complexes (branching networks)
17
Q
Tubulin polymerization is nucleated by:
A
1.) Ring complexes containing gamma tubulin (TURCs)
2.) Alpha and beta tubulin bind to form a heterodimer
3.) Alpha subunit bind to TURC’s beginning the formation of a microtubule (at - end)
4.) TURCs in centrosome
18
Q
Major phosphorylation sites in an intermediate filament protein (lamin)
A
PSer-22
PSer-392
PSer-628
19
Q
IF proteins regulated by:
A
Phosphorylation —> Depolymerization
Dephosphorylation —> Polymerization
20
Q
Taxol (paclitaxel)
A
A clinically useful drug that works by stabilizing microtubules, thereby interfering with mitotic spindle function in dividing cells. Used to treat some types of cancers
21
Q
Where is actin cytoskeleton?
A
Localized near plasma membrane, including forming specialized arrays at cell—cell and cell—ECM junctions
22
Q
Functions of microfilaments
A
• support an organization
• cell—cell adhesions at adheren junctions 
• cell—ECM adhesion at focal contacts
• regulate gene expression
23
Q
Actin and myosin interaction
A
Muscle of the cell
• Controls cell shape
• Drives cytokinesis during cell division
• Drives cell motility
24
Q
Proteins that link microfilaments to the plasma membrane
A
1.) talin
2.) catenins
3.) dystrophin
4.) ERM proteins
25
Myosin
Motor proteins associated with Actin cytoskeleton
26
Type II myosin
Conventional, they can form bipolar filaments through ability of their long tails to wrap around each other and an anti-parallel orientation
This allows them to pull microfilaments past each other (contraction)
27
Other types “ unconventional” myosin
Act as monomers or dimers. Do not form bipolar fibers, but bind to different types of cargoes in the cytoplasm
Participate in vesicular trafficking, and interact with Rab small GTPases
28
Steps of myosin activation
1.) ATP hydrolysis, conformational changes
2.) binding of ATP releases a myosin head from a microfilament
3.) Hydrolysis to ADP plus Pi “cocks” the head, which reattaches to microfilament
4.) Pi released, confirmational change that pulls the microfilament—tightly bound 
29
Myosin in the absence of ATP
Heads cannot be displaced from tightly binding actin, resulting in rigor mortis 
30
 Rho family of G-proteins
Promotes stress fiber formation (parallel) 
31
Rac family of G-Proteins
Promotes lamellipodia formation (peripheral MF network stabilized with filamin)
32
Cdc42
Promotes filopodia formation (parallel microfilament bundles stabilized with cross-linking proteins that support fingerlike cell extensions)
33
Focal adhesion
Contains integrins, microfilaments, linking proteins, focal adhesion kinases
Play Central roles in adhesion and cell motility. Communicate status of attachment to ECM
34
Microvilli
• Increase the absorptive area of the plasma membrane
• are supported by a core bundle of actin microfilaments, but are non-motile
• Prominent in intestinal epithelial
35
Adherens junctions
1.) Cadherins: IMPs that adhere to each other in the presence of Ca2+
2.) linking (anchor) proteins: alpha and beta-catenins.  Can travel into the nucleus, and function as transcriptional regulators
36
Sub-plasma membrane-associated microfilaments
• physically support the plasma membrane
• Interact with IMP’s and linking proteins
37
Actin and muscular dystrophy
Distroglycan complex: IMPs
Dystrophin: linking protein
ECM: laminin and collagen
^^ Mutations in these proteins (esp. dystrophin) weakens the muscle cell membrane leading to cell death
38
Centrosome 
- the microtubule organizing center (MTOC)
- Nucleates and organizes microtubules
- Located near nucleus and Golgi apparatus
• composed of a pair of centrioles
39
Pericentriolar materials (PCM)
Amorphous material surrounding centrioles. Contains TURC‘s which nucleate microtubule polymerization
40
Three forms of centrosomes
1.) MTOCs
2.) Basal Bodies
3.) Spindle Poles
41
Centrosome: Basal bodies
Specialized centrioles that arise through repeated duplication of centrosome centrioles
Migrate to apical (top) region of a cell and nucleate microtubules extension that form cilia and flagellae
42
Centrosome: spindle poles
Duplicated centrosomes that nucleate the spindle apparatus in dividing cells
43
Primary Cilium
One per cell, non-motile, 9+0 axoneme, Sensory and signaling functions, formed when cells stop dividing, important in early development
44
Polycystic kidney disease and obesity causes:
Deficits associated with primary cilium
45
Microtubule structural proteins
• MAP1,2,4
• Tau
• Plectin
46
Microtubule motor proteins
• Dyneins
• Kinesins 
47
Alzheimer’s disease and TAU
TAU hyper phosphorylation is linked to its condensation into neurofibrillary tangles— Aggregates are toxic to brain cells
48
Dyneins
Move cargo towards the (-) end of MTs
Drives ciliary and flagellar motility
49
Kinesins
Move cargo toward the (+) end of MTs
50
Kartagener’s Syndrome (ciliary dyskinesia)
Cilia and flagellae are immotile due to mutations in dynein 
51
Blistering diseases originate due to:
1.) Auto antibodies produced against normal desmosomal and hemidesmosomal proteins
2.) mutations in IF proteins or other hemi/desmosomes
52
Pemphigus (bullous pemphigus)
Affects outer layers of skin, auto antibodies to Desmosomal desmogleins 
Blisters are easily ruptured
53
Pemphigoid (bullous pemphigus)
Effects lower layers of skin (junction of epi-dermis and dermis)
Autoantibodies produced against: ColXVII, BPAG2/BP180, and dystonin (BPAG1/BP230)
Stiff blisters that do not break open easily
54
Epidermolysis bullosa Simplex
EBS — caused from loss of function mutations in keratin
55
Nuclear lamina functions
• Physical support for the nuclear envelope
• interconnects nucleus with cytoskeleton and ECM
• organize chromatin
• cell differentiation
• cell cycle and apoptosis
• gene expression
56
Progeria
Disease of accelerated aging Caused by perturbations in lamin farensylation 
57
Penicillin and penicillin related compounds
Contain thiazolidine ring, beta-lactam ring, And a variable side chain that dictates it’s microbicidal activity
58
How penicillin works:
Beta lactam ring Affects penicillin binding proteins by blocking transpeptidation
59
Naturally derived penicillins
Penicillin G
penicillin V
60
Penicillinase-sensitive penicillins
Amoxicillin, ampicillin
61
Penicillinase-resistant penicillins
Dicloxacillin, nafcillin, oxacillin
Do NOT need to pair with beta lactamase inhibitors
62
Antipseudomonal penicillins
Piperacillin, Ticarcillin
High resistance to drugs
63
Beta lactamase inhibitors
1. Clavulnic acid
2. Sublactam
3. Tazobactam
They bind to and inactivate the beta lactamases to protect the penicillin drugs
64
Cephalosporin drugs
Contain beta-lactam ring, broad-spectrum and resistant to Penicillinases, Commonly given via IV, fewer allergic reactions
65
First generation cephalosporin drugs
• Good against gram positive cocci and a few Gram negative
1. cefazolin
2. Cephalexin
66
Second generation cephalosporin drugs
More broad spectrum than first generation, can target more Gram negative bacteria
1. Cefaclor
2. Cefoxitin
3. Cefuroxime
67
Third generation cephalosporin drugs
Broad spectrum with especially well developed activity against enteric bacteria that produce beta lactamases
1. Cefotaxime
2. Ceftadime
3.  Ceftriaxone— Crosses BBB
68
Fourth generation cephalosporin drugs
Broad-spectrum for both gram-positive and gram-negative with increased activity against pseudomonas and gram-positive organisms
1. Cefapime
69
Fifth generation cephalosporin drugs
Broad gram positive and gram-negative coverage including MRSA but not pseudomonas
1. Ceftaroline
70
Carbapenems
Have beta lactam ring, used in the hospital setting when other antibiotics aren’t working (side effects: G.I. distress, skin rash, CNS toxicity)
1. Doripenem
2. Ertapenem
3. Imipenem
4. Meropenem 
71
 Cilastatin + imipenem why?
To block renal hydropeptidase in order to decrease the inactivation of the drug in the renal tubules
72
Non-beta-lactam cell wall targeting drugs
Bacitracin (streptococci/staphylococci), isoniazid (Mycobacterium TB), Vancomycin (Staphylococcal infection), fosfomycin (phosphoric acid agent)
73
Bacitracin
Narrow spectrum antibiotic produced by a strain of the bacterium bacillus subtilis
Combats superficial skin infection by streptococci and staphylococci
74
isoniazid
Bacteriocidal to mycobacterium TB, But only against growing cells
75
Vancomycin
Narrow spectrum antibiotic most effective in treating staphylococcal infections in case of penicillin resistance or allergy
76
Fosfomycin
Phosphoric acid agent effective as alternate treatment for urinary tract infections caused by enteric bacteria
77
Oxazolidinones (Linezolid)
• 50S subunit inhibitor
• Bacteriocidal/bacteriostatic
• Inhibits protein synthesis by binding to the 50S subunit, preventing the formation of initiation complex
78
Oxazolidinones are used against:
Gram-positive bacteria including MRSA and VRE (Vancomycin resistant enterococci) 
79
Side effects of Oxazolidinones 
Bone marrow suppression (thrombocytopenia), peripheral neuropathy, and serotonin syndrome
80
Resistance to Oxazolidinones
Resistance via a point mutation in the ribosomal RNA
81
Aminoglycoside drugs
• 30 S subunit inhibitors
• Bacteriocidal
• Irreversible inhibition of the initiation complex through binding of the 30S subunit. Can cause misreading of the mRNA
• Requires oxygen for optic. Drugs ineffective against anaerobes

82
Types of aminoglycoside drugs
1. Amikacin
2. Gentamicin
3. Neomycin
4. Streptomycin
5. Tobramycin
83
Side effects of the aminoglycoside drugs
Nephrotoxicity, neuromuscular blockade, ototoxicity, teratogen (pregnant women) 
84
Resistance of aminoglycoside drugs
Resistance via bacterial transferase enzymes that inactivate the drug by acetylation, phosphorylation, or adenylation 
85
Aminoglycoside drugs used against
• severe gram-negative rod infections
• Synergistic with beta lactamases
86
Tetracycline drugs
• 30 S Subunit inhibitors
• bacteriostatic

• binds to the 30 S subunit and prevents the attachment of aminoacyl tRNA in the A site
87
Types of tetracycline drugs
1. Doxycycline
2. Minocycline
3. Tetracycline
88
Side effects of tetracycline drugs 
G.I. distress, discoloration of teeth and inhibition of bone growth in children, photo sensitivity, NOT used during pregnancy
89
Resistance of tetracycline drugs
Resistance via decreased uptake or increased efflux out of the bacterial cells by plasmid-encoded transport pumps
90
Macrolide drugs 
• 50S subunit inhibitors
• bacteriostatic
• inhibit protein synthesis by blocking translocation, bind to the 23S rRNA of the 50S ribosomal unit : bind to E site
91
Tetracycline drugs used against
Borrelia burgdorferi, mycoplasma pneumoniae, Rickettsia, and chlamydia
92
Macrolide drugs used against
Atypical pneumonia’s, sexually transmitted infections, gram-positive cocci, and Bordetella pertussis 
93
Side effects of macrolides 
G.I. motility issues, arrhythmia caused by prolonged QT interval, acute cholestatic hepatitis, rash, eosinophilia, theophylline serum increase, Inhibition of cytochrome P450
94
Types of macrolides
1. Azithromycin
2. Clarithromycin
3. Erythromycin
95
Chloramphenicol
• 50 S subunit inhibitor
• Blocks P site, blocks peptidyl transferase
• Bacteriostatic
96
Chloraphenicol used against:
Meningitis, and rocky mountain spotted fever
Has limited use due to toxicities, continued use in developing countries because of low cost
97
Chloraphenicol side effects
Anemia, aplastic anemia, grey baby syndrome
98
Chloramphenicol resistance
Resistance via plasmid-encoded acetyltransferase that inactivates the drug
99
Clindamycin
• 50 S subunit inhibitor
• Bacteriostatic
• Blocks peptide transfer and translocation at the 50 S ribosomal unit
100
Clindamycin used against: 
Anaerobic infections, aspiration pneumonia, lung abscesses, and oral infections
Group A strep infections
101
Clindamycin side effects
C. Diff, Fever, diarrhea
102
Clindamycin VS metronidazole
Clindamycin treats infections above the diaphragm, well metronidazole treats anaerobic infections below the diaphragm
103
Dalfopristin/quinupristin
Mechanism:
Combined action is bactericidal for some organisms. Binds 50 S to inhibit translocation
Spectrum:
Reserved for infections caused by multiple drug resistant gram-positive bacteria. Not a first line of treatment
104
Resistance of  Dalfopristin/quinupristin
• Ribosomal methylation prevents binding of drug to its target.
• Enzymes inactivate the drugs.
• Efflux proteins that pump them out of the cell.
105
Macrolides/ clindamycin relation to dalfopristin/quinupristin
Cross resistance. Resistance to one of these drugs is equal to resistance to all of these drugs
106
Side effects of  Dalfopristin/quinupristin
High incidence of althralgias, Inhibits CYP3A4 and is likely to have significant drug interactions
107
Drugs you not use with newborns
Chloramphenicol
108
Drugs you do not use in children
Tetracyclines
109
Drugs you do not use during pregnancy
Tetracycline, aminoglycosides, clarithromycin, chloramphenicol, etc.
110
Adjust drug based off of elderly renal function
Beta lactams, aminoglycosides
Half-life of these drugs will be increased, retention of drugs increases
111
Seizures caused by:
Beta lactams, mostly carbapenems
112
Hepatotoxicity Caused by:
Rifampin
113
Nephrotoxicity via:
Impenems, Aminoglycosides, vancomycin
114
 Ototoxicity caused by:
Aminoglycosides, vancomycin
115
Anemia caused by:
Chloraphenicol
116
Arthralgia caused by:
Dalfopristin/quinupristin
117
Superinfection caused by:
Clindamycin, third generation cephalosporin, ampicillin
118
Causes disulfiram reaction when taken with alcohol:
Second generation cephalosporin with methylthiotetrazole groups
119
Aminoglycoside + penicillin synergy
Penicillin increases permeability of cell membranes increasing the ability of amino glycosides to enter the cell
120
Vancomycin + aminoglycoside combination drug
Each alone have some nephrotoxicity. If given together you get marked renal impairment
121
Penicillin + tetracycline
79% mortality for pneumococcal meningitis
122
Folic acid synthesis and reduction inhibitors
1. Sulfadiazine
2. Sulfamethoxazole
3. Sulfisoxazole
4. Trimethoprim
Cause sensitivities in bacteria that need to synthesize their own dihydrofolic acid
123
Sulfonamides
• bacterial static
• Competitive inhibitors if dihydropternoate synthase resulting in a disruption of folic acid synthesis
• Inhibits bacterial growth by decreasing nucleotides
124
Sulfonamide resistance
Comes from altered enzyme, decreased uptake, or increased PABA synthesis
125
Sulfonamide side effects:
Nausea, vomiting, diarrhea, rash, fever, headache, depression, jaundice, hepatic necrosis, drug induced lupus, and serum sickness-like syndrome
126
Sulfonamides and G6PD
Sulfonamides can cause a deficiency in G6PD, leading to acute hemolytic anemia
127
Sulfonamide competition with bilirubin
Competitive inhibitor for bilirubin binding sites on plasma albumin, may increase fetal blood levels of unconjugated bilirubin —kernicterus 
128
Sulfonamides and warfarin
Sulfonamides displays albumin binding sites for warfarin, increasing the effective activity of the displaced drug
Anticoagulant dosage should be reduced during sulfonamide therapy
129
Major uses for sulfonamides:
• CNS and ocular toxoplasmosis
• Infection by nocardia bacteria
• Malaria
• UTIs
• Otitis media
130
Trimethoprim
• bacteriostatic
• Inhibits bacterial dihydrofolic reductase (downstream)
• inhibits purine and DNA synthesis
131
Major uses for trimethoprim
Primary use is for the prevention of recurrent, uncomplicated urinary tract infections
132
TMP + SMX
Trimethoprim + sulfamethoxazole 
Bacteriocidal = static + static
• High degree of synergistic activity by inhibiting same pathway
133
Types of Quinolones
1. Ciprofloxacin
2. Enoxacin
3. Gemifloxacin
4. Levofloxacin
5. Moxifloxacin
6. Nalidixic acid
7. Norfloxacin
7. Ofloxacin 
134
Quinolone drugs
• Bacteriocidal
• Inhibit the enzymatic activity of topoisomerase class enzymes: DNA gyrase and topoisomerase IV
• Promote the cleavage of DNA in these enzyme DNA complexes
• Cannot be taken with antiacids
135
Quinolones are used against:
Aerobic gram-negative bacilli, Particularly members of the family enterobacteriaceae 
136
What drug is strong enough to use against pseudomonas (P. Aeruginosa)?
Levofloxacin 
137
Side effects of quinolones
G.I. side effects, confusion, CDF, yeast infection, cartilage damage, arthropathy
tendinitis in those older than 60 also taking prednisone
138
Metronidazole
• Bacteriocidal
• Inert, activity is determined by the capacity of susceptible organisms to activate the drugs once it enters the cell via passive diffusion
139
Metronidazole used against:
Anaerobic infections, bacterial septicemia, CNS infections, bacterial vaginosis, acne rosacea
140
Disulfuram reaction with alcohol + metronidazole 
Disulfiram ethanol reaction due to increased serum acetyl-aldehyde
Metronidazole blocks aldehyde dehydrogenase, inhibiting the oxidation of acetylaldehyde
^^^ hangover feeling results
141
Rifampin
• Bacteriocidal
• Find bacterial RNA polymerase at the active Center, blocking the elongation of mRNA
142
Rifampin used against:
Active TB, asymptomatic carriers of Neisseria meningitidis 
143
Side effects of rifampin
Induction of cytochrome P450, leading to organ rejection, loss of seizure control, and risk of pregnancy if on birth control
144
Mitochondria DNA is hypermutable
• not bound to histones in a chromatin structure
• Exposed to higher concentrations of ROS
• Balanced by copy number genes, heteroplasmy
145
MtDNA copy number can be affected by:
Metabolic state, hormones, and drugs
146
TCA cycle functions:
• oxidized two carbons from acetate to CO2
• Make NADH, FAD2H, and GTP
147
PDH and the TCA cycle occur in:
The mitochondria
148
Glycolysis occurs in:
Cytosol
149
Inherited point mutations in MPC1 can cause:
Lactic acidosis and hyper pyruvatemia (pyruvate—> lactate dehydrogenase)
150
Four subunits of PDH
E1: pyruvate decarboxylase, TPP
E2: Transacetylase, Lipoate and CoA
E3: dihydrolipoyl dehydrogenase, FAD,
NAH+
X:
151
PDH Kinases 
Inhibits: pyruvate, ADP
Activates: Hypoxia, acetyl-CoA, and ADH, ATP
152
PDH phosphatase
Activated by calcium
153
PDH regulation
Phosphorylation and dephosphorylation of serine residues on E1 alpha subunits
154
Key regulator of the TCA cycle
Isocitrate dehydrogenase is the key rate limiting enzyme in the TCA cycle
155
Positive deltaG reactions in the TCA cycle
 citrate—aconitase—> isocitrate
Malate—malate dehydrogenase—> oxaloacetate 
156
Build up of citrate leads to what other metabolism?
Fatty acid, cholesterol synthesis
157
Buildup of Malate leads to what other metabolism?
Gluconeogenesis
158
Citrate synthase
Hydrolyzes the thiolester bond of acetyl Coa to join acetate and oxaloacetate forming citrate
Tricarboxylic acid
159
Aconitase 
Catalyze is a two step isomerization to convert citrate to isocitrate producing Intermediate aconitate 
160
Isocitrate dehydrogenase (IDH3)
Catalyzes oxidative decarboxylation for TCA cycle, producing CO2.
IDH1 in the cytosol and IDH2 in the mitochondria catalyze the same reaction but use NADP+/NADPH
161
Alpha ketoglutarate dehydrogenase
Catalyzes the final oxidative decarboxylation. At this point to carbons are released as carbon dioxide
162
Succinate thiokinase 
Cleaves the thioester bond linking succinate and CoA— exergonic.
Uses cleaving energy to phosphorylate GDP to GTP
163
Succinate dehydrogenase
Oxidizes succinate to introduce double carbon, reducing FAD in the process
Is part of complex II of the electron transport chain, transferring e- from FAD2H to coenzyme Q
164
Mesenchyme
A part of the mesoderm of an embryo which develops into connective tissue/cartilage/bone/Lymphatic vessels, blood vessels
Appears at every stage of animal life
165
Mesoderm
One of the three germ layers in the embryo of a Metazoan animal.  located between ectoderm and endoderm.
Gives rise to connective tissue, bone, cartilage, muscle, blood, blood vessels, lymphoid organs, pericardium, notochord, Kidney, gonads
166
Components of connective tissue proper
Extra cellular matrix
- Fibers
- Ground substance
Cells
167
What are ECM fibers?
Collagen, elastic fibers, reticular fibers
168
What is ECM ground substance?
Glycosaminoglycans (GAGs), proteoglycans, glycoproteins, integrins 
169
Physical characteristics of collagenous fibers
• 1-20 nm in diameter
• comprised of smaller fibrils
• Irregular, undulating shape
• Inelastic
• Forms gelatin in boiling water
• Leather industry: tanning process
• Stains with acid dyes (pink in H&E)

170
Most common amino acids in collagen
Lysine, proline, hydroxyproline, hydroxylysine
171
Collagen synthesis
1. Alpha chains (in golgi and ER)
2. Procollagen (In secretory vesicle)
3. Tropocollagen macromolecule (outside of cell)— assembles into fibrils
172
Type I collagen
Ordinary connective tissue (loose and dense) and bone
173
Type II collagen
hyaline collagen
174
Type III collagen
Loose connective tissue, blood vessel wall, skin, liver, long, support for lymphoid tissue
175
Type IV collagen
Basement membranes, network forming
176
Type V collagen
Widespread
177
Type VII collagen
Anchoring filaments attach basal lamina to underlying connective tissue
178
Where do collagen fibers originate from?
Fibroblasts
179
Elastic fibers
- thinner than collagen
- May reach 10 to 12 mm in length in elastic ligaments
- branch freely
- Highly refract tile, yellowish
- May be in arterial walls (fenestrated)
180
Elastic fibers staining
Orcein, resorcin-fuchsin, aldehyde-fuchsin
— relaxed elastic fibers have a wavy appearance in H&E sections
181
Chemical composition of elastic fibers
1. Elastin: Amorphous component
— High proline, glycine, valine
— Desmosine and isodesomosine amino acid cross-links

2. Fibrillin: microfibrillar component
— Cysteine
— marfan’s syndrome & aged skin
182
Origin of elastic fibers
Fibroblasts, smooth muscle cells
183
Reticular fibers (type III collagen)
- small (0.03-0.04mm)
- Stained by silver or PAS stains
-  more carbohydrate dense
- Located in muscle cells, nerves, epithelial structures, glandular organs, lymphatic tissues, red bone marrow, skin, liver, lungs 
184
Origin of reticular fibers
Fibroblasts, reticular cells
185
Amorphous intracellular substance (Ground substance) 
• viscous solution <—> Thin gel
• Homogeneous and transparent
• significant amount of bound water, GAGs, proteoglycans and proteoglycans aggregates
186
Glycoproteins definition
Mostly protein and are glycosylated with monosaccharides or disaccharides in the ER and Golgi
• Secreted or integrated into the membrane
• Laminin in fibronectin are secreted from cells into the ECM

187
Glycosaminoglycan (GAGs) definition
Polysaccharides produced by processing enzymes in the Golgi and outside the cell
• Often sulfated to produce a negative charge
188
Proteoglycans definition
Heavily glycosylated proteins and are primarily composed of polysaccharide/carbohydrate
• Aggregates of a core protein produced in the ER and glycosylated with GAG’s in the Golgi
• Polysaccharide component of proteoglycans and GAGs attract water, and act well as lubricant or shock absorbers
189
Hyaluronic acid (Non-sulfonated GAG)
• very viscous insulation
• High molecular weight
• Alternating glucosamine and glycouranate units
• accounts for many of the physical characteristics of ground substance (Barrier to bacteria and present in synovial joints)

190
Fibronectin
• glycoprotein
• Soluble (hepatocytes): in blood plasma
• insoluble (fibroblasts): in ECM
• Organize cellular matrix, barn to different macromolecular species
191
Laminin
• confined to basement membrane (lamina densa)
• Structural and adhesive functions
192
Origin of laminin
Epithelial and smooth muscle cells
193
Connective tissue cells
1.) fibroblast
2.) Mesenchymal cells and pericyte 
3.) fat cell
Visitors from the blood: Macrophage, plasma cell, mast cell, lymphocytes, Eosinophil, neutrophil
194
Fibroblasts
Most common CT cell
Large, oval nuclei, distinct nucleolus, basophilic cytoplasm, abundant RER and ribosomes, enlarged Golgi, numerous cytoplasmic vesicles with fine threads

195
Function of fibroblasts
Production of connective tissue fibers, production of amorphous intracellular substance (ground substance) 
196
Scurvy
• generalized degeneration of connective tissue
• Deficiency in vitamin C
• Necessary for conversion of proline to hydroxyproline
• Cannot form hydrogen bonds to join alpha chains
197
Ehler’s Danlos syndrome
• short stature, stretchable skin, hyper mobility
• Cannot Cleve N-terminus of procollagen to create tropocollagen
• Mutations in collagen or processing in the face
198
Osteogenesis imperfecta: brittle bone disease
Abnormal production of collagen I
199
Mesenchymal cells
•Relatively primitive, undifferentiated cells
• along blood vessels, especially capillaries
• Functions: Precursor of fibroblasts, Fat cells, mast cells, smooth muscle cells, Endothelial cells
200
Fat cells
• Occur singly or in small groups in loose CT
• large masses in adipose tissue
• Undifferentiated mesenchymal cells
201
Macrophages
Monocyte: in blood
Macrophage: in tissue
Capable of ameboid movement— Moves to site of inflammation

202
Plasma cells
• produce antibodies
• Not comment except for in connective tissue of the digestive tract, greater omentum, reticular connective tissue of blood forming organs
• Numbers increase in areas of chronic inflammation
• Derived from activated B lymphocytes
203
Mast cell
• present in most loose connective tissues
• Originate from hematopoietic stem cells (Bone marrow)
204
Mast cells contain granules of:
1. Heparin
2. Histamine
Function: degranulate to mediate information in allergies and anaphylaxis
205
Loose areolar CT
• Arranged irregularly, appears cobwebby, understained spaces due to ground substances
• made of fibroblasts, macrophages, fibers (Mostly collagen), amphorous ground substance
206
Dense, irregular CT
• constituent fibers irregularly arranged
• Made of fibers (Coarse collagenous fibers), cells (Fibroblasts and macrophages), ground substance
207
Dense regular CT
• Two forms: collagenous and elastic
• lined up in parallel, well suited for withstanding tension in one direction
•  fibroblast is the major cell between the fibers
• Poor blood supply = injury slow to heal
208
Adipose tissue
• many fat cells, arranged in groups or lobules.
• Cells surrounded by external lamina and fine collagenous, reticular, and elastic fibers
• Very little amphorous ground substance

209
Reticular connective tissue
— Provides a fine fibrillar Network in lymphoid tissues (spleen, lymph node, bone marrow)
— Made of reticular cells and reticular fibers
210
Fumarate hydrotase
Add a proton and hydroxyl from water to fumarate double bond to form Malate
211
Malate Dehydrogenase
Oxidizes Malate hydroxyl to a keto group, producing NAD to NADH in the process
212
Ethanol metabolism produces NADH. In alcohol poisoning:
The massive amount of NADH produced blocks of the TCA cycle. Gluconeogenesis stops, and patients can become hypoglycemic
213
NADH created from beta oxidation and the TCA cycle
NADH from beta oxidation also inhibits TCA cycle and drives Acetyl-CoA towards ketone bodies synthesis
214
Isocitrate dehydrogenase is regulated by:
Ratio of ADP to ATP. ADP increases affinity for substrate (Activator)
215
The TCA cycle is amphibolic:
Catabolic: oxidizes carbons and reduces NAD and FAD for the generation of ATP via e- chain
Anabolic: TCA intermediates are feedstock for other biosynthetic pathways
216
Myoadenylate deaminase deficiency
Inherited mutation in the gene coding for AMPD1 resulting in inactive AMP deaminase.
Exercise intolerance, muscle pain, weakness
217
Intermediates of the TCA cycle affect gene expression through:
1. Histone acetylation and methylation
2. Cytosine methylation
218
Lysine specific demethylase-1 (LSD1)
Transfers electrons from methyl group to FAD, then removes the carbon as formaldehyde 
219
Jumanji Domain demethylases (JHDM)
Use molecular oxygen to hydroxylate the methyl carbon directly. Alpha KG is decarboxylated to succinate 
220
Oxidation of benzopyrene and covalent bonding of DNA
• Benzopyrene is an aromatic polycystic hydrocarbon from cigarettes, oxidized within the cells to become carcinogenic 
221
Transversion
 purine —> Pyrimidine
222
Transition
Purine —> Purine
Pyrimidine —> Pyrimidine
223
Strand directed mismatch repair
- MUTL binds to mismatch base pair, MUTL scans the nearby DNA for a Nick
- MUTL triggers the degradation of the next strand all the way back through the mismatch: Cut by Helicase
- Repair occurs by DNA polymerase and DNA ligase
224
MLH one mismatch repair defect
Common in HNPCC, Common colorectal cancer hereditary genes 
225
Base excision repair
• DNA glycosylase removes deaminated base
• The sugar phosphate is cut out by AP endonuclease And phosphodiesterase
• The gap of a single nucleotide is filled by DNA polymerase and DNA ligase
226
Nucleotide excision repair
• Bulky lesion is recognized
• One cut is made on each side of the Legion by DNA helicase, Removing a portion of the strand
• The DNA polymerase and ligase repair the strand 
227
Xeroderma pigmentosum (XP) 
Genetically heterogeneous, Autosomal recessive disease of defective DNA repair that causes sensitivity to UV radiation, shortened lifespan
Cockayne is a closely related disease
228
Double stranded break repair
• homologous end-joining with RecA/Rad51 — requires BRCA1&2 as accessory proteins (Uses sister chromatid to fill in missing DNA sequence)
• non-homologous end-joining with Ku protein (end joins Resulting in deletion of DNA sequence piece) 
229
p53
Important G1 checkpoint control gene
- 50% of all cancers have a defect in p53 Transcription factor
230
Aneuploidy
Unusual chromosome number, occurs as a result of meiotic or mitotic non-disjunction
1. Meiotic nondisjunction: causes embryonic lethality
2. Mitotic nondisjunction go on a common event in cancer
231
Chronic myelogenous leukemia (CML)
A translocation between chromosomes nine and 22
BRC-ABL: Philadelphia chromosome
232
Mitotic Spindle Checkpoint
Maintains chromosome segregation Fidelity, Aneuploidy is often caused by defects in this pathway
233
Translesion synthesis (TLS)
Damage tolerance process that allows DNA replication machinery to replicate past DNA lesions such as thymine dimers
234
Desmosomes
1. Cadherins (nonclassical)
2. Linking proteins (armadillo proteins: plakoglobin, plankophilin)
3. Keratin IFs
235
Adherens junctions
1. Cadherins (classical)
2. Linking proteins (armadillo proteins: catenin, plakoglobins, vinculin)
3. Actin MFs
236
Hemidesmosomes
1. Integrins, collagen XVII (BPAG2/BP180)
2. Linking proteins (plakins: dystonin, BPAG1/BP230, Plectin)
3. Keratin IFs
4. Basal lamina and ECM
237
Focal adhesions
1. Integrins
2. Linking proteins (vinculin, talin, paxillin)
3. Actin MFs
4. Basal lamina and ECM
238
Restriction enzyme analysis
Restriction enzymes Find DNA at specific sequences, make double stranded cuts and cleave the DNA
Can be used to identify DNA, or recombine DNA (EcoR1) 
239
Visualizing DNA fragments created by restriction enzyme digestion
Gel electrophoresis
DNA is sorted by charge, and by size
240
Southern blotting
A technique to identify a specific region of DNA
Target DNA is identified by size and hybridization to a probe buy artificial complementary base pairing
241
Sanger/Conventional DNA sequencing
Gives exact order of base pairs in a piece of DNA
Region to be sequenced is determined by choice of primer, Fragments of defined the lengths are generated by ddNTPs chain terminators
MOST SPECIFIC WAY TO IDENTIFY DNA
242
Dideoxynucleotide chain terminators
DNA synthesis depends on 3’ OH of final nucleotide
Dioxane nucleotides are chain terminators because they lack 3’OH
243
Polymerase chain reaction (PCR)
PCR amplifies a defined region of DNA— Specificity and amplification
Repeated cycles of in vitro DNA replication
Specificity because region to be amplified is determined by hybridization of short primers
244
Clinical applications of DNA techniques
HPV, BRCA1, BRCA2 identification
245
Northern blotting
The RNA equivalent of southern blotting. Based on DNA to RNA binding, or hybridization, through complementary base pairing
RNA in cell is separated by size, transferred to a membrane, defined piece of DNA or RNA probe binds specifically to target RNA, probe is labeled 
246
RT-qPCR
Adapts PCR to quantitatively measure mRNA levels
All mRNA is converted to cDNA Using specific primers and PCR— fluorescent dye used to tag
Application is proportional to the initial number of mRNAs
247
Ct (cycle threshold)
A measure of mRNA expression. It is inversely related to expression (More mRNA expression, less cycles needed)
248
Microarray analysis 
Global analysis of mRNA levels, Identify all mRNAs that change expression in a disease state
Based on hybridization of cDNA population derived from sample mRNAs to a grid containing known DNAs at specific locations 
249
Array
• DNA Oligos, 25 bases long
• Each oligo sequence matches an mRNA to be analyzed
• Oligos are arranged in grid sequence corresponding to mRNA and location
250
Clinical applications of microarrays
COVID-19 detection — RT-qPCR to detect virus
Remdesivir— treatment for Covid. Analog of the endogenous nucleoside adenosine. Blocks viral reproduction by blocking synthesis of new RNA strand 
251
Antibodies
• Antibodies are proteins made by B cells
• primary antibody targets specific protein
• Secondary antibody for visualization of primary (fluorescent)
252
ELISA— Enzyme linked immunosorbent assay
Used to detect specific protein in a complex mixture
Primary anti- X (what you’re looking for)
Secondary: anti primary
253
COVID-19 rapid antigen test ELISA
If a person has COVID-19 they will make viral proteins. The viral spike protein is abundant and immunogenic— Immobilizes primary antibody onto spike proteins
254
Western blotting
Identifies a specific protein in the complex mix
Target protein is identified by size and specific interaction between antibody and protein 
255
Clinical application of western blotting
Herceptin/trastuzamab as an antibody to HER2 growth factor receptor
— expressed in breast cancers
256
Immune checkpoint blockade
Nivolumb and Pembrolizumab
These antibodies block an inhibitory checkpoint (PD-1-PD1-Ligand) which then releases the patient’s own immune system to attack the tumor.
257
Next generation sequencing (NGS)
Faster, more information, identify mutations or genetic variants, identify somatic mutations, $1000 per genome, <24hrs 
258
Clinical application of next generation sequencing (NGS)
Finding Somatic mutations— Sporadic cancer develops through acquisition of mutations that provide selective advantage to tumor
Molecular prenatal diagnosis: trisomy 21 
259
RNA interference (RNAi)
Small non-coding RNAs regulate gene expression in the cell through RNA interference — miRNAs (micro) and siRNAs (short interfering) Can target specific mRNAs for degradation
260
Clinical use of RNAi pathways 
Hepatitis B- Thought to work by targeting viral RNA for degradation
261
CRISPR-CAS9
A system for making genomics alterations in DNA and living cells and organisms
• CAS9, endonuclease, sgRNA
Clinically: treating sickle cell disease
262
Complex II (Succinate dehydrogenase) Does not span the inner mitochondrial membrane
No protons are pumped across the inner mitochondrial membrane, making complex II Create less ATP (FAD) 
263
Proton motive force
The combined difference in proton concentration, pH, and difference in charge across the inner mitochondrial membrane
264
12 protons = How many ATP?
3 ATP
4 protons = 1 ATP
265
Chemical uncouplers
Dinitrophenol, salicylate
266
Block complex I, NADH dehydrogenase
Amytal, rotenone
267
Block complex II, Succinate dehydrogenase
Malonate
268
Block complex III, cytochrome b-c1 complex
Antimycin A 
269
Block complex IV, cytochrome C oxidase
Azide, cyanide, CO
270
Block complex V, ATP synthase 
Oligomycin 
271
Blocks DNA pol-gamma, The mitochondrial DNA replication enzyme
AZT (zidovudine) <— anti-retro viral
272
Adaptive thermogenesis in response to cold
• Norepinephrine activates a lipase which forms free fatty acids from triacylglycerol in brown fat cells
• A proton channel called thermogenin (UCP1) activated (proton hole, uncoupled— Dissipates gradient)
^^ Allows fat to be utilized for heat, independently of ATP conception

273
Chemical uncoupler
Dinitrophenol (DNP) 
Carries over proton across gradient
274
Mechanical uncoupling
• Peroxidation (ROS)
• Mitochondrial swelling do the influx of water
• proton leaking through holes in the membrane, cannot maintain sufficient gradient for ATP synthase to function
275
Mitochondrial permeability transition pore (MPTP)
• Between ANT, VDAC, and other proteins
• this nonspecific poor causes depolarization of mitochondrial membrane and disrupts proton gradient
• regulated by cyclophilin D (CD)
• Inhibited by a high electrochemical gradient
• Activated by calcium, inorganic phosphate, and ROS
276
Fasted state dominant hormone
Glucagon
277
Fed state dominant hormone
Insulin
278
Starved state Dominant hormones 
Catecholamines, and glucagon
279
Pancreatic beta cells express what gene?
INS1 gene
• A single large proteins, processed into two chains through the removal of C-peptide. Disulfide bonds link the two peptide chains after C-peptide is removed
280
How is mature insulin stored?
Hexameric crystals stabilized by zinc atoms
281
Insulin release process
Glucose —> ATP —> inhibits K+ outflow —> promotes Ca2+ inflow —> proteins fuse with membrane and insulin is released 
282
Insulin receptor is a:
Receptor tyrosine kinase
• Insulin binding activates a kinase that phosphorylates tyrosine on itself and other proteins which make binding sites and aggregate proteins at the membrane
283
Two main signaling arms from insulin receptor:
Phosphatidylinositol 3-kinase to PKB
Grb2 to MAPK 
284
AKT activation by insulin results in:
Translocation of intracellular vesicles that contain the GLUT4 glucose transporter to the plasma membrane
285
Primary source of energy during fasting
Amino acid synthesis to glucose
286
Primary source of energy in a starved state:
Lipolysis to glycerol to glucose
Avoid proteolysis to preserve body
287
Glucagon signaling a fasted state
Pancreas —> glucagon —> Second messenger cAMP —> Cellular response (Activation of protein kinase A)
288
Where is glucagon stored?
In vesicles within pancreatic islet alpha cells
289
Alpha cell glucagon release inhibited by
1. Insulin
2. GABA
3. Zn 2+
^^^^^^^^ all from beta cell
4 somatostatin from delta-cell 
290
Hormone sensitive lipase (HSL) 
Inhibited by insulin, activated by glucagon
Triggers fatty acid energy synthesis
291
Activation of protein kinase A for glucagon release
Glucagon—> cAMP—> PKA—> use of stored fuel 
292
Positive sense genome
• mRNA, read easily
• The genome is the mRNA, no copy necessary

293
Negative sense genome
• Copying step (opposite) where copy is read
• The genome contains an RNA dependent RNA polymerase, and needs to be copied— Copy is mRNA
294
DNA binding proteins
Interact with DNA in a sequence specific manner
Major group of DNA is the main site of protein binding, inverted repeats frequently are binding site for regulatory proteins by homodimers
295

Operon
Cluster of genes arranged in a linear fashion whose expression is under control of a single operator
Operator is located downstream of the promoter
Transcription is physically blocked when repressor binds to operator
296
Arginine as a co-repressor
Arginine excess binds with repressor and activate it to shut off Gene operator that normally makes more arginine
Low arginine causes the release of arginine to repressor and synthesis begins again
297
Negative control of transcription
Pulls something off to begin transcription
298
Positive control of transcription
Puts something on to begin transcription
299
Quorum sensing
Mechanism by which bacteria assess their population density
• Bacteria can create autoinducer molecule that diffuses freely across cell envelope in response to the presence of other cells of the same species— Allowing for transcription of specific same genes
300
Conjugation as horizontal gene transfer
Direct contact between two cells where DNA transfer occurs— Specifically have plasmids
Example: F plasmid 
301
Transformation as a horizontal gene transfer
Fragments of genomic material floating in space gets up taken by a cell an incorporated into their genome
Homologous recombination
302
Transduction as a horizontal gene transfer
Genomic material from one cell enters another via a viral vector/bacteriophage
303
Competent cells in transformation
Cells capable of taking up DNA and being transformed
Example: Griffiths experiment S and R cells
304
Generalized transduction
DNA derived from virtually any portion of the host genome is packaged inside the mature virion 
305
Specialized transduction
DNA from a specific region of the host chromosome is integrated directly into the virus genome
306
Lytic pathway
1. Viral DNA replicates
2. Coat proteins synthesized; virus particles assembled
3. Cell lysis and viral dumping occurs
307
Lysogenic pathway
1. Temperate virus inserted into host cell
2. Viral DNA is integrated into the host DNA
3. Cell divides, spreading viral and host DNA to the daughter cells
4. When ready, phage DNA circularizes and detaches from host to DNA
5. Detached DNA replicates and the cell lyses

308
Rare event of transduction
When phage DNA attempts to detach, a portion of the host DNA is exchanged for phage DNA causing recombinant DNA that can enter new cells and spread the original host cell’s DNA
309
HFR strains
Cells possessing an integrated plasmid, they cannot transfer the full chromosome plasmid, so they cannot create an F (+) cell from an F (-) cell
310
Conservative transposition
Transposon is excised from one location and reinserted at a second location
One transposon total
311
Replicative transposition
A new copy of transposon is produced and inserted at a second location
To transposons total (after 1 replication)
312
Plasma versus serum
Plasma clots, serum does not
Plasma contains fibrinogen where serum does not (serum’s fibrinogen is in the blood)
313
Lymph fluid
- Lacks erythrocytes and platelets
- less proteins
- More leukocytes
- Clots slowly (Some fibrinogen present)
314
Never let monkeys eat bananas
Differential count for white blood cells (leukocytes)
N-eutrophils
L-ymphocytes
M-onocytes
E-osinophils
B-asophils 
315
Granulocytes
Neutrophils, eosinophils, basophils 
316
Agranulocytes
Lymphocytes, monocytes
317
Thrombocytes
Platelets, derived from megakaryocytes. Platelets release from cytoplasm and have clotting mechanisms
318
Neutrophil
Multi lobed nucleus, small red and purple granules
First line of defense, most common cell 
2X The size of a RBC
319
Neutrophilic function
1. Chemoattractants cause neutrophils to migrate to sides of infection
2. Phagocytose bacteria, foreign objects, etc.
3. Produce cytokines that attract and modulate other immune cells
320
Neutrophilic Pathogen killing mechanisms
Phagocytosis, degranulation, neutrophil extracellular traps (NETs)
321
Eosinophil
Bi- lobular nucleus, large granules, stains red, Has crystalline sub structure in granules
Destruction of parasitic worms
322
Basophils
Irregular nucleus you can barely see, lots of dark hematoxylin stained granules
Increase for leukemia, chickenpox, small box, sinus inflammation
323
Basophil functions
1. Allergy and Inflammatory response
2. Phagocytosis
3. Release histamine, serotonin, heparin
4. Produce leukotrienes (smooth muscle contraction)
324
Lymphocytes
Large nucleus with hill and valley staining
B lymphocytes, T lymphocytes, natural killer cells
Creates large Buffy region in centrifuge 
325
Monocyte
Kidney bean nucleus, large cell
Second line of defense against invading organisms. The differentiate into macrophages in the connective tissue and other places
326
Chylomicrons
Found in plasma, enable fats and cholesterol to travel in water base solution of bloodstream
327
Hemoconia
Junk in the bloodstream —> Cell debris —> spleen and liver process it out
If hemoconia is high, consider spleen or liver pathology
328
Single cell motility
Important to embryonic development, necessary for immune cells circulation throat body, and would healing
329
Mesenchymal motility
Rac and Cdc42 G proteins promote Acton polymerization at leading edge of the cell
Rho reorganize actin filaments into parallel arrays of stress fibers that connect to focal adhesions— myosin II interacts with actin stress fibers to pull the back end of the cell forward while focal adhesions dissemble
330
Mesenchymal cells motility accompanied by release of proteases at the front of the cell does what?
Allows the front of the cell to digest impeding extra cellular matrix material, thereby allowing the cell to TUNNEL its way through dense ECM
331
Focal adhesions
Provide necessary traction points for mesenchymal motility
Regions were bundles of microfilaments are physically linked with extra cellular matrix through into grins and linking/adapter proteins 
332
Essential driver of cell motility
Rapid assembly and disassembly of focal adhesions. Preventing this freezes motility
333
FAK and Src
Focal adhesion kinases, non-receptor tyrosine kinases that influence three major signaling pathways 
1. Rho/Rac— Cytoskeleton organization
2. MAPkinase— Regulate cell Proliferation and adhesion
3. PI3K/PKB (AKT)— Promotes cell survival
334
Amoeboid motility
Driven by actin myosin contraction
Microfilaments and myosin around cell periphery squeeze the cytoplasm forward— Movement only occurs if there are spaces large enough to accommodate the size of the nucleus/cell 
335
EMT— Epithelial mesenchymal transition
Involves a loss of epithelial characteristics and a gain of mesenchymal characteristics. Interconnected cells in an epithelium can break loose and become motile
336
The hippo pathway
Activated hippo pathway inhibits Yap/Taz which are two related transcriptional regulators That promote cell proliferation and motility
Hippo pathway phosphorylates yap/Taz (with kinases Mst1/2 abs Lats1/2) leading to their ubiquitination

337
Yap/Taz
Transcriptional regulators that promote cell proliferation and motility when they are dephosphorylated 
They can enter the nucleus when dephosphorylated, and bind to an activate TEAD family transcription factors— inhibit apoptosis, promote cell division, promote cell motility 
338
Loss of function mutations in the hippo pathway
Hyperactivate yap/Taz and thereby enhance growth and create unusually large organs
339
Yap is active when:
• ECM is stiff
• Large surface area
• Sparse cells (far away)
• stretched cells
340
Fibroblast activity feedforward loop
Fibroblast activity stiffens the ECM, stimulates Yap, Which further stimulates stiffening, leading to fibrotic diseases
341
Cell density and hippo pathway
Growing tissues reached their appropriate size and cell density, hippo pathway is active to suppress yap and further Proliferation.
A reduction in cell density, like wounds, increase cell spreading and inhibit hippo and activate Yap
342
Actin polymerization when high does what to hippo?
Inhibits hippo, activating yap
Actin in crowded cells is less polymerized which activates hippo
343
Tension promotes what?
Microfilament assembly and myosin association
344
Stretching of a cell promotes what?
Actin polymerization, and therefore inhibiting hippo and activating yap
345
Cytoskeletal generated tension bridging and cell stretching do what for Yap/Taz?
Allow yap/Taz into the nucleus through pores 
346
TGF beta signaling and ECM stiffness
When ECM is more stiff, LTBP1 and LAP can bind and cause pulling forces that release TGF-beta and allow it to activate SMAD transcription factors
347
Soluble monomeric actin and MRTF
G Actin + MRTF keep MRTF in the cytoplasm by inhibition
When G Actin is pulled away by attention, allowing for Actin polymerization (to F actin) MRTF can enter the nucleus to regulate gene expression
MRTF used for gene survival
348
High amounts of collagen
Higher collagen content increases ECM stiffness which activates yap/Taz, promoting cell proliferation and motility and inhibiting apoptosis
^^ causes tumors in dense breasts
349
Stretch activated ion channels (SACs)
Activated by membrane stretching, membrane deformation, and fluid shear potentially releasing calcium into the cell
 Caveolae can flatten immediately to provide more membrane stretchiness so that the membrane won’t tear— Caveolae stretching signals to the cell 
350
Activation of KlF2
Inhibits motility and proliferation of genes
Turbulent flow inhibits KlF2 expression resulting in plaques from proliferation, ROS generation, and inflammation
351
Hydrophilic signaling molecules
Require cell surface receptors to generate signals inside the cell
352
Hydrophobic signaling molecules
Can diffuse across the plasma membrane and bind to receptors inside the target cell either in the cytoplasm or nucleus
353
Extra cellular signaling pathway
• ligand gated ion channels
• G-protein linked receptors
• Enzyme link receptors
• Proteolysis linked receptors
354
Intracellular signaling pathways
• nuclear hormone receptors
• Nitric oxide and other dissolved gases
355
Other signaling mechanisms
• Gap junction signaling
• Synaptic signaling
356
Examples of a second messengers
• cAMP, cGMP
• IP3, DAG
• Ca2+
They transfer transduction signal to the target proteins
357
Response types to signals
Graded response: the response proportional to the signal
Switch like response: all on or all off
358
Switch like responses are regulated by:
1. Adjusting the half life of a signaling protein
2. Whether multiple subunits cooperate to trigger an action
3. Positive feedback loops
4. Involvement of protein kinases and G-proteins
359
G proteins
Some signaling pathway components can be turned on via G-protein association, which themselves are activated or in activated by GTP or GDP
360
Ways to desensitize a signal molecule
1. Ligand binding to cell surface
2. Ligand induced receptor endocytosis
3. Phosphorylation of receptors or proteins involved
4. Production of an inhibitor that blocks the transduction process
361
Ligand gated ionotropic signaling
Binding of a signaling molecule to an ion channel that opens the channel. Very fast
Examples: GABA, serotonin, vanilloid, Acetylcholine 
362
Ligand gated metabotropic signaling
Activates molecular cascades upon ligand binding, receptors are almost always GPCRs 
Releases G proteins that bind to ion channels and or intermediary effector proteins to open the channels, SLOW
Examples: Glutamate, Epinephrine, acetylcholine, serotonin
363
Voltage gated ion channels
Found in cardiac muscle and neurons, membrane depolarization
364
Mechanically gated ion channels
Associated with sensory functions including hearing, touch, stretch
365
G-protein linked signaling is carried out by the interaction of what two components?
1. G protein coupled receptors (GCPRs)
2. Heterotrimeric G proteins
366
Alpha monomer of a G protein
GTP/GDP binding switch
367
Heterotrimeric G proteins are regulated by:
RGS: regulators of G-protein signaling
They function as GTPase activating proteins (GAP proteins)
368
Activation of G-protein linked signaling 
GPCR binds in active heterotrimeric G-protein complex (acting as GTP exchange factor) Promoting exchange of GDP for GTP, activating the alpha subunit
369
G-protein inactivation
Binding of the activated subunit to target protein stimulates the alpha subunits ability to hydrolyze GTP to GDP, turning it off soon after activating the target protein
370
Three ways G-protein pathway is regulated by GPCR signaling
1. Adenylate cyclase
2. Phospholipase C
3. Rho, Rac, Cdc42 Monomeric G proteins
371
Gs and Gi
Stimulate and inhibit adenylyl cyclase, respectively
This increases and decreases protein phosphorylation, respectively
372
Gq
Phospholipase C, increases protein phosphorylation by PKC, and activates calcium binding proteins by Ca2+ release 
373
G12-13
Stimulate Rac, Cdc42, RhoA :
Rac: lamelipodia formation, actin polymerization, microtubule growth
Cdc42: filopodia formation, cell polarity, microtubule stabilization
RhoA: actin stress fiber formation, Actin filament stabilization, actinomyosin contractility, microtubule stability
374
What is the main target of cAMP?
PKA (protein kinase A)
375
 Calcium is released into the cytoplasm via three main types of calcium channels
1. Voltage dependent calcium channels in the plasma membrane open in response to membrane depolarization
2. IP3-gated receptors/channels allow escape from ER
3.  RYR in the ER translate changes in membrane potential into calcium release from ER
4. NOT RELEASE: SERCA Moves calcium back into ER
376
Receptor desensitization
The decreased responsiveness that occurs with repeated or chronic exposure to an agonist
377
Receptor downregulation
A decrease in the total receptor number due to endocytosis and subsequent degradation of the receptors 
378
Arrestin binds to phosphorylated GPCRs and inhibits signaling by:
• blocking GPCR interaction with G proteins
• Promoting internal sequestration of GPCRs via endocytosis
• Routing GPCRs to protosomes for destruction
379
Arrestin is stimulated by:
GRK (Like PKA and PKC)
380
Glycogen synthase genes
GYS1: muscle
GYS2: liver
381
What is a branching enzyme?
Glycosyl-4,6-transferase cleaves the chain after it hits around 11 glucose molecules, and creates a 1-6-glycostatic linkage
382
Debranching enzyme
Cuts 1,4 bond one unit away from branching point and transfers the short chain to another non-reducing end: 4:4 transferase — glu-1-P
Cuts remaining 1:6 bond to get a glucose molecule
383
Glycogen phosphorylase is activated when:
It is phosphorylated
384
Glycogen synthase is active when:
It is DEphosphorylated
385
GSD0
Glycogen synthase deficiency
GYS2: Liver, fasting ketotic hypoglycemia, small liver
GYS1: Muscle, skeletal and cardiac dysfunction
386
GSD I: Vin Gierke disease
A deficiency in glucose-6-phosphatase
Fasting hypoglycemia, lactic acidosis, Hepatomegaly due to glycogen accumulation, hyper uricemia, hyperlipidemia
387
GSD III: Cori Disease
Deficiency of 1,6-glucosidase activity of debranching enzyme — can’t debranch to give glucose (still makes Glu-1-P)
Fasting hypoglycemia, ketoacidosis, hyper lipidemia, Hepatomegaly
GSDIIIa: Liver and muscle
GSDIIIb: liver only 
388
Is GSDIIIa or a GSDIIIb more severe?
1,6-glucosidase is more severe if it involves both liver and muscle— GSDIIIa
389
GSD IV: Anderson disease
Severe, fatal in infancy: FTT, hepatomegaly, liver failure
Deficiency of branching enzyme 4,6- transferase — Long wavy form of glycogen that cannot be broken down
390
GSD V: McArdle disease
Deficiency of muscle glycogen phosphorylase
Exercise and tolerance, myoglobinuria after exercise, Increased creatine kinase and increased ammonia after exercise
391
GSD II: Pompe’s disease
Deficiency of lysosomal alpha-1,4-glucosidase activity
 — glycogen accumulates in heart and lysosomal tissue. Cardiomegaly 
392
What is only found in the liver?
Glucose-6-phosphatase (removes phosphate to form glucose to be sent to other cells)
GLUT2, Glucokinase
393
Key enzymes in glycogen synthesis
Glycogen synthase
Branching enzyme
394
Key enzymes in glycogenolysis
Glycogen phosphorylase
Debridging enzyme
395
Types of carbon bonds in glycogen
1:4 — linear chains
1:6 — branched points off linear chains
396
Reducing end vs nonreducing end
#1 C is reducing end (ketone)
397
What does glycogen phosphorylase do?
Breaks the 1,4 bonds between glucose units and adds inorganic phosphate to create gluc-1-P to either be used for glycolysis in skeletal muscle, or the phosphorylated to glucose in the liver 
398
GSD VI: Hers disease
Mutations in liver glycogen phosphorylase— opposite of McArdles disease 
399
What controls the phosphorylation state of glycogen phosphorylase?
Hormone glucagon, epinephrine, norepinephrine, cortisol
Phosphorylated by: PKA, glycogen synthase kinase-3 
400
Glycogen phosphorylase
In the Fasted State, glycogen phosphorylase is active promoting glycogen breakdown
401
Glycogen synthase
In the fed state, glycogen synthase is active promoting the creation of glycogen
