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PH1123 Microbiology > Unit 3 > Flashcards

Unit 3 Flashcards

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1
Q

what is the endoplasmic reticulum?

A

single compartment from the outer layer of nuclear envelope into the cytoplasm

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2
Q

what is the most extensive organelle, making up 50% of the plasma membrane?

A

endoplasmic reticulum

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3
Q

what is the sarcoplasmic reticulum

A

endoplasmic reticulum of striated (heart) and skeletal muscle

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4
Q

describe the structure of the endoplasmic reticulum

A

interconnected array of tubules and cisternae with a single lipid bilayer

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5
Q

what are the types of ER

A

rough

smooth

sarcoplasmic

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6
Q

what’s the difference between rough and smooth ER

A
  • ROUGH
    • has ribosomes
    • makes proteins
    • protein sacs bud off as transport vesicles to golgi apparatus for processing and then sent to plasma membrane or another organelle
  • SMOOTH
    • no ribosomes
    • makes lipids
    • carbohydrate metabolism
    • detoxification of natural metabolism products/ products and drugs
    • found abundantly in the liver
    • regulates calcium concentration in muscle cells for contraction
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7
Q

which organ produces most proteins?

A

liver

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8
Q

what are the subunits of RER?

A
  • small ribosomal subunits: read RNA
    • large subunits: join amino acids to form a polypeptide chain
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9
Q

what cells secrete so many proteins?

A

b-lymphocytes secrete antibodies

beta cells of the pancreas, produce hormones

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10
Q

what is glycosylation?

A

addition of a sugar molecule.

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11
Q

which organelle recognizes destination label attached to polypeptide and amino acids?

A

rough endoplasmic reticulum

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12
Q

list the functions of both the RER & SER

A

RER:

  • protein manufacture
  • protein targeting

SER

  • drug detoxification
  • steroid production
  • calcium storage and release
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13
Q

How does RER produce proteins?

A

via ribosomes in a process known as translation

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14
Q

how does the RER target proteins?

A

by a signal sequence at their amino (N) terminus that is often aa(15-60), which enables cellular transport machinery and correct positioning of the protein inside the cell

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15
Q

how does the SER produce lipids?

A

via enzymes embedded in the membrane of the SER, which form the lipids of membranes

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16
Q

how does the SER eliminate drugs?

A

it has CYP450 enzymes, which have a role detoxification of xenobiotics, cellular metabolism and homeostasis.

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17
Q

define sarcomere

A

complicated unit of striated muscle tissue

or

repeating unit between Z lines

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18
Q

what are skeletal muscle composed of?

A

muscle fibers aka myofibers

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19
Q

how does SER regulate calcium storage and release

A

Calcium is pumped into the SER by active transport and released in response to hormonal signals. This is particularly important in muscle cells where the SER is so prominent it has a special name, the sarcoplasmic reticulum.

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20
Q

make 4 notes on the golgi apparatus

A

1- flattened membrane enclosed disc-shaped-sacs

2- located near the nucleus

3- cis face (entry) trans face (exit)

4- proteins arrive to it in transport vesicles

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21
Q

what happens to transport vesicles upon their arrival at the golgi apparatus?

A

they fuse with golgi, where they are processed, then pinch off through the trans face and move to fuse with plasma membrane

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22
Q

where is golgi found abundantly?

A

in secretory cells, like antibody secreting plasma b cells

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23
Q

what is exocytosis?

A

process by which vesicles release their contents into the cell’s exterior

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24
Q

what’s the difference between a constitutive secretory pathway and a regulated secretory pathway?

A

constitutive: secretory vesicles transport soluble proteins that are released from the cell continually

whereas, regulated pathway, secretory vesicles store soluble proteins for when they are needed just like in mast cells which produce histamine

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25
Q

what are the functions of golgi apparatus?

A
  • secretory pathways
  • lysosome formation
  • protein modification and sorting
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26
Q

how does the golgi apparatus forms lysosomes? and provide an example

A

by the fusion of vesicles that have budded off from the trans-Golgi. The sorting system recognizes address sequences in the hydrolytic enzymes and directs them to growing lysosomes

example: mannose-6-phosphate label is added to proteins destined for lysosomes and packaged into vesicles that bud off from trans golgi

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27
Q

provide an example how how golgi is involved in protein modification and sorting

A

it is involved in post translational modification, for instance, addition of carbohydrates or phosphorylation of oligosaccharides

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28
Q

the golgi apparatus modifies lipids and proteins to produce

1-

2-

3-

A

1- glycolipids

2- glycoproteins

3- proteoglycans

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29
Q

what are the 3 types of golgi vesicles?

A
  • exocytic vesicles (constitutive)
  • secretory vesicles (regulated)
  • lysosomal vesicles
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30
Q

differentiate the 3 golgi vesicle pathways

A

exocytic vesicles → continual/constitutive extracellular release (plasma b cells)

secretory vesicles → regulated, stored until signalled for extracellular release (neurotransmitter release from neuron)

lysosomal vesicle → has degradative enzymes for proteins/ribosomes (digestive proteases)

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31
Q

what is cell cycle?

A

The cell cycle consists of a series of steps during which the chromosomes and other cell material double to make two copies.

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32
Q

which phase makes most of the cell cycle?

A

interphase G1, the cell grows physically and increases the volume of both protein and organelles.

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33
Q

briefly explain the phases of cell cycle

A

Initially in G1 phase, the cell grows physically and increases the volume of both protein and organelles. In S phase, the cell copies its DNA to produce two sister chromatids and replicates its nucleosomes. G2 phase involves further cell growth and organisation of cellular contents. M phase, is the mitosis phase where cell actively divides

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34
Q

at what level of the body do drugs function?

A

cellular

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35
Q

what are the principles of drug action?

A
  • act at specific receptors (internal/external)
  • interfere with physiological or biochemical processes of pathogen/body
  • bind to a single type of receptor
  • enter cells by diffusion though membrane
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36
Q

what are the three types of diffusion used by drugs to enter the cell?

A
  • facilitated diffusion
  • active transport
  • pinocytosis
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37
Q

what types of drugs are there, based on the responses they produce?

A
  • agonist, bind to receptor to stimulate a response
  • antagonist, block receptors to prevent unwanted response (killing pathogens by producing unwanted response)
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38
Q

what is the mechanism of action of penicillin/vancomycin/cephalosporins

A

disrupt formation of cell wall

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39
Q

what is the mechanism of action of sulfonamide/trimethoprim

A

inhibits folic acid metabolism, thus preventing growth

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40
Q

what is the mechanism of action of tetracyclines/streptomycin/chloramphenicol/erythroycin?

A

bind to 70s ribosome, blocking protein synthesis

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41
Q

what is the mechanism of action of polypeptide antibiotics

A

interact with phospholipids and disrupts outer membrane

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42
Q

what is the mechanism of action of quinolones?

A

affects DNA formation

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43
Q

what is the mechanism of action of rifampin

A

affect mRNA formation

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44
Q

what is the general mechanism of action of anticancer drugs

A

interferewith DNA replication, translation and protein synthesis and folding in ER, protein glycosylation in Golgi, and metabolic activity in mitochondria

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45
Q

what is the mechanism of action of the anticancer drug, tamoxifen?

A

induces gonadotrophin release by occupying estrogen receptors in the hypothalamus, thereby interfering with feedback mechanisms

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46
Q

what is a cytoskeleton

A

dynamic, 3D structure that fills the cytosol

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47
Q

what is the difference of cytosol and cytoplasm?

A

Cytosol is known as the matrix of the cytoplasm. It surrounds the cell organelles in eukaryotes. In prokaryotes, all the metabolic reactions occur here. Thus, we can infer that while cytosol is the fluid contained in the cell cytoplasm, cytoplasm is the entire content within the cell membrane

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48
Q

what is the difference between cytoskeleton and cytoplasm?

A

The cytoplasm consists of everything inside the cell membrane of the cell, excluding the nucleus in a eukaryotic cell. The cytoskeleton is a cellular “skeleton” that criss-crosses the cytoplasm.

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49
Q

what are the three cytoskeleton filaments?

A

microfilaments

microtubules

intermediate filaments

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50
Q

what is the composition of the cytoskeleton?

A

protein polymers, that are made up of identical subunits that allow rapid reorganization

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51
Q

how are the different filaments of the cytoskeleton formed?

A

by polymerisation of a distinct type of protein subunit

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52
Q

provide an example of a drug that targets the ER/Golgi complex

A

rapamycin (sirolimus), used as a prophylactic treatment in kidney allograft recipients

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53
Q

what does rapamycin target in the ER/Golgi complex?

A

serine-threonine-protein kinase mTOR/T cells

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54
Q

what is the structure and function of microtubules?

A

hollow tubes made up of alpha and beta tubulins that are a part of the cytoskeleton

they provide proper shape and keep organelles in place

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55
Q

what class of drugs are colchicine and paclitaxel?

A

microtubule drugs

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56
Q

what are the classes of microtubule drugs?

A
  • tubulin binding
  • microtubule-stabilizing
  • microtubule-destabilizing
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57
Q

what is the mechanism of action of tubulin binding drugs?

A

inhibit microtubule dynamics that are required for DNA segregation and cell division

indication: cancer

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58
Q

what is the mechanism of action of microtubule stabilizing drugs?

A

prevent the dissociation of tubulin subunits and block mitosis which stabilizes GDP bound tubulin

indication: breast cancer/ovarian cancer

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59
Q

what is the mechanism of action of microtubule destabilizing drugs?

A

promote disassembly of microtubules, causing a change in organelle location and blocks wbc migration thus reducing inflammation

indication: inflammatory conditions (arthritis/gout)

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60
Q

what is the significance of lipids in the cell membrane?

A

they provide good drug targets (receptors/channels/receptors)

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61
Q

draw the phospholipid bilayer (plasma membrane)

A
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62
Q

what are the 4 different endocytic pathways?

A
  • budding
  • fission
  • fusion
    • direct transport
63
Q

TRUE OR FALSE:

lipids in the plasma membrane have asymmetrical organization

A

TRUE

64
Q

give 5 examples of lipids in the plasma membrane

A

phosphatidylethanolamine

phosphatidylserine

phosphatidylglycerol

phosphatidic acid

phosphatidylcholine

glycolipids

cholesterol

65
Q

what is the function of endocytosis?

A
  • uptake of extracellular nutrients (iron-transferin/fat-ldl/oncogenic signaals-cancer)
  • cell recovery (protein/lipids)
  • cholesterol homeostasis (LDL receptor)
66
Q

what is the extracellular pH

A

7.4

67
Q

what is anaemia and haemochromatosis?

A

anaemia: lack enough healthy red blood cells to carry adequate oxygen to your body’s tissues
haemochromatosis: an inherited condition where iron levels in the body slowly build up over many years

68
Q

what is the function of iron in cells? how does it enter the cell?

A
  • carry oxygen in the hemoglobin of red blood cells throughout your body so your cells can produce energy.
  • heme synthesis, which forms haemoglobin, a protein found in red blood cells.
69
Q

what is the epidermal growth factor, and what does it do?

A

common mitogenic factor that stimulates the proliferation of different types of cells, especially fibroblasts and epithelial cells. EGF activates the EGF receptor (EGFR/ErbB), which initiates, in turn, intracellular signaling.

70
Q

1- what is EGF internalization?

2- what is the major mechanism by which EGF internalization is carried out?

A
  1. Activated EGF (epidermal growth factor) receptors are removed from the cell surface via endocytosis and subsequent degradation in the lysosome.
  2. clathrin-mediated endocytosis (CME), whereby the receptor is removed from the surface via clathrin-coated pits and then routed to the early endosomes
71
Q

which digestion product do these proteins carry

beta globulins

alpha globulins

albumin

A

beta globulins → cholesterol/triglycerides

alpha globulins → phospholipids

albumin → free fatty acids (FFA)

72
Q

fats being hydrophobic, they need specialized transport by _______

A

lipoprotein complexes

73
Q

plasma lipids are transported to become:

A

1- soluble

2- recognizable

74
Q

cholesterol/triglycerides/phospholipids are carried as complexes along with proteins known as _______

A

apoproteins

75
Q

what are the 3 apoproteins?

A

APO E

APO C

APO B

76
Q

what is the function of LDL

A

Low-density lipoproteins (LDL) carry cholesterol from the liver to the rest of the body.

Cells latch onto these particles and extract fat and cholesterol from them.

carries 70% of body’s cholesterol

77
Q

what is APO B protein

A

primary lipoprotein that is the structural backbone of LDL, synthesized in the liver where it interacts with other molecules to form VLDL

78
Q

what is are the properties of VLDL?

A
  • triglyceride rich
    • LDL precursor
79
Q

what is hypercholesterolemia?

A

overproduction or overclearance of APO B, increasing the deposition of cholesterol in the endothelium leading to cardiovascular disease or atherosclerosis

80
Q

what are the 3 lipoproteins?

A
  • VLDL
  • LDL
  • LPa
81
Q

define autophagy

A

degredation of old and damaged organelles in membrane in the lysosome

82
Q

what’s the difference between retrograde transport and anterograde transport?

A

When substances are going toward the axon tip, it is known as anterograde transport, and when they are going toward the cell body, it is known as retrograde transport

83
Q

provide notes about insulin

A

Insulin is a peptide hormone

produced by beta cells of the pancreatic islets encoded in humans by the INS gene.

It is considered to be the main anabolic hormone of the body.

84
Q

what is the mechanism of action of insulin

A

Insulin helps keep the glucose in blood within a normal range. It does this by taking glucose out of the bloodstream and moving it into cells throughout the body.

85
Q

how is insulin produced in the body?

A

When you digest your food, carbohydrates convert to glucose. The glucose is directed into your bloodstream, which causes your blood glucose levels to rise. This is what sends the message to your pancreas to produce insulin, which instructs your cells to absorb the glucose traveling through your bloodstream

86
Q

give one example for a direct membrane traffic disease and an indirect one

A
  • direct: neimann pick type c (lysosomal storage)
  • indirect: cystic fibrosis (CFTR traffic)
87
Q

1- what is the function of CFTR?

2- what happens to CFTR in cystic fibrosis patients?

A

1- regulating the proper flow of chloride and sodium (a component of salt) in and out of the cell membranes in the lungs and other organs

2- CFTR transport is blocked in the endoplasmic reticulum

88
Q

differentiate eukaryotic and prokaryotic cells

A
89
Q

why do cells need endocytosis?

A

because molecules required for cell function are polar and large and can’t diffuse through the hydrophobic portions of the plasma membrane by passive diffusion

90
Q

what are the types of endocytosis?

A
  • pinocytosis
  • receptor mediated (clathrin mediated)
  • phagocytosis
91
Q

what is pinocytosis?

A

when small vesicles take dissolved material in liquids.

e.g. saprophytic fungi

92
Q

what is clathrin mediated endocytosis?

A

a vesicular transport event that facilitates the internalization and recycling of receptors engaged in a variety of processes, including signal transduction (G-protein and tyrosine kinase receptors), nutrient uptake and synaptic vesicle reformation.

e.g viruses → LDL uptake (coated vesicle)

93
Q

what is phagocytosis?

A

ingestion of bacteria or other material by phagocytes and amoeboid protozoans

94
Q

what are the steps of phagocytosis?

A

1- engulfment

2- phagosome formation

3- digestion in phagolysosome

4- expulsion of undigested materials

95
Q

phagocytosis acts on particles that are bigger than _____ nM

A

250 nM

96
Q

what are the cells that are capable of phagocytosis?

A
  • neutrophils
  • monocytes
  • macrophages
  • mast cells
  • dendritic cells
97
Q

what is the difference between phagocytosis/endocytosis/autophagy?

A

phagocytosis: external pathogens
endocytosis: receptor recycling
autophagy: excess/old organelles

98
Q

what are the symptoms of dysfunctional mitochondria

A
  • profound weakness
  • encephalopathy
  • seizures
  • liver failure
  • poor growth
  • neurological symptoms
  • muscle weakness
99
Q

what is the site of oxygen utilization?

A

peroxisomes

100
Q

why are peroxisomes so named?

A

because they contain one or more enzymes that use oxygen to remove hydrogen from organic substrates in oxidative reactions hat produce hydrogen peroxide

RH2+O2→ R + H2O2

101
Q

what is the function of endosomes?

A
  • regulation of cell surface protein expression
  • internalization of nutrients
  • uptake and digestion
    • exploit pathogens
102
Q

which organelle produces lysosomes?

A

Golgi

103
Q

what are the hydrolytic enzymes of lysosomes?

A

lipases

nucleases

carbohydrases

proteases

104
Q

how are lysosomal diseases caused?

A

deficiency of an enzyme required for lipid and glycoprotein metabolism, for example resulting in gaucher’s disease

105
Q

what is ambroxol indicated for and what is its mechanism of action?

A

it is indicated for parkinson’s, it increases the activity of glucocerebrosidase (enzyme replacement therapy)

106
Q

what causes neurodegenerative disease?

A

accumulation of misfolded proteins in the cytosol and nucleus

107
Q

what causes neurodegenerative disease?

A

accumulation of misfolded proteins in the cytosol and nucleus

108
Q

what enzyme is accumulated in huntington’s disease?

A

polyQ

109
Q

what protein is misfolded in familial amyotrophic lateral sclerosis?

A

superoxide dismutase 1

110
Q

what protein is misfolded in

1- alzeheimer

2- parkinson’s

3- spongiform encephelopathies

4- familial amyloiditic polyneuropathy

A
  1. amyloid beta peptide
  2. alpha synuclein
  3. prion proteins
  4. tranthyretin
111
Q

what is the main function of the mitochondria?

A

cellular respiration, convert energy usable by cells (ATP)

112
Q

why does excercise increase the number of mitochondria?

A

because cells adapt to higher demand of energy

113
Q

what are the main regions of the mitochondria

A
  • outer membrane
  • intermembrane space
  • inner membrane
  • matrix
114
Q

what is the function of the inner membrane of the mitochondria?

A

form cristae that increase surface area thus enhance ATP production (high demand mitochondria = more cristae)

115
Q

what is the function of the intermembrane space of mitochondria?

A

it has cytochrome C which is a component of electron transport chain across inner membrane

apoptosis

116
Q

what enzymes does the matrix of the mitochondria have?

A

krebs cycle, pyruvate oxidation, and other enzymes that encode tRNA/ (37genes)

117
Q

what are plasmids?

A

small ring shaped DNA molecules containing a few genes

118
Q

what is the function of plasmids?

A
  • fertility: transfer genetic material
  • resistance: from antibiotics
  • degredative: digestion of organic compounds
    • virulence: turn bacterium to pathogen
119
Q

what are the mechanisms by which plasmids transfer genetic material? (horizontal gene transfer)

A
  • transformation
  • transduction
    • conjugation
120
Q

which bacteria produces insulin?

A

E.coli

121
Q

what chemical reactions take place in the cytosol?

A
  • early nutrient breakdown
  • glycolysis
  • protein manufacture
  • signalling transduction
122
Q

what’s the difference between endothelium and epithelium?

A

epithelial cells line both internal surfaces and external surfaces of the body whereas endothelial cells line the internal surfaces of the components of the circulatory system.

123
Q

describe the two regions of the phospholipid bilayer in terms of permeability

A

polar molecules: ions, peptides, charged drugs

Apolar: glucose, fats, uncharged drug

124
Q

a solution that has the same solute concentration as compared to another one is known as

A

isotonic solution

125
Q

the main cause of the resting membrane potential

A

differential distribution and relative permeabilities of NA & K ions

Also think of important solutes: Glucose etc . Extracellular Concentration of Calcium is 1.5-2.0mM Massive difference between intracellular and extracellular calcium

126
Q

what is responsible for 1/5 of the cell’s energy expenditure?

A

ATPase

127
Q

what is the function of ATPase?

A
  • ATPase helps maintain resting potential,
  • effect transport, and regulate cellular volume.
  • It also functions as a signal transducer/integrator to regulate MAPK pathway, ROS, as well as intracellular calcium. In most animal cells, the Na+
128
Q

what are the membrane proteins?

A

intrinsic, such as ion channels, receptors for neurotransmitters, pumps and transports (CFTR)

extrinsic, such as recognition and adhesion molecules

129
Q

what’s the difference between an ion pump and an ion channel?

A

ion pumps actively transport ions against a concentration gradient, while ion channels allow ions to passively flow down a concentration gradient.

further reading: Ion channels versus ion pumps: the principal difference, in principle | Nature Reviews Molecular Cell Biology

130
Q

define ion channels

A

Ion channels are water-filled pores that allow ions to cross the membrane and move DOWN their concentration gradient.

131
Q

true of false: Individual ion channels are specific to particular ions, meaning that they usually allow only a single type of ion to pass through them.

A

true

132
Q

what is long q t syndrome

A

Long QT syndrome is an inherited heart problem that affects how your heart beats.

133
Q

what type of receptor is the nicotinic acetylcholine receptor?

A

ionotropic receptor (ligand-gated)

134
Q

what is the mechanism of action of salbutamol?

A

Binding to Beta 2 adrenoceptors results in smooth muscle relaxation and opening of the airways

135
Q

what drug class is salbutamol

A

beta 2 adrenoreceptor agonist

136
Q

true or false

25% of pharmaceutical drugs target receptors

A

true

137
Q

what types of receptors are in the plasma membrane?

A

direct: ionotropic: more than one protein/gene
indirect: intracellular: signal is not membrane limited, signal transduction is slower and needs regulation

138
Q

define a kinase

A

an enzyme that catalyses the transfer of a phosphate group from ATP to a specified molecule

139
Q

what do lipid kinases do?

A

Lipid kinases phosphorylate lipids in the cell, both on the plasma membrane as well as on the membranes of the organelles

140
Q

how does ß-2 receptor – adrenaline M2 Muscarinic Receptor- acetylcholine work

A

β adrenergic receptors are coupled to a stimulatory G protein of adenylyl cyclase. This enzyme produces the second messenger cyclic adenosine monophosphate (cAMP). In the lung, cAMP decreases calcium concentrations within cells and activates protein kinase A. Both of these changes inactivate myosin light-chain kinase and activate myosin light-chain phosphatase. In addition, β2 agonists open large conductance calcium-activated potassium channels and thereby tend to hyperpolarize airway smooth muscle cells. The combination of decreased intracellular calcium, increased membrane potassium conductance, and decreased myosin light chain kinase activity leads to smooth muscle relaxation and bronchodilation.

141
Q

what types of transporters are there?

A

Uniport: Ca2+ pump

Symport: Glucose-Na+ coupled transport in epithelia

Antiport: Na+/K+ pump (ALL CELLS)

142
Q

describe the mechanism of Na+/K+ pump and how it maintains cell membrane potential

A

It accomplishes the transport of three Na+ to the outside of the cell and the transport of two K+ ions to the inside. This unbalanced charge transfer contributes to the separation of charge across the membrane.

In order to maintain the cell membrane potential, cells keep a low concentration of sodium ions and high levels of potassium ions within the cell (intracellular). The sodium-potassium pump mechanism moves 3 sodium ions out and moves 2 potassium ions in, thus, in total, removing one positive charge carrier from the intracellular space.

143
Q

true or false

Ca2+ regulation is achieved by both an antiport and a uniport. As a result intracellular Ca2+ is kept very low (~100 nM).

A

true

144
Q

describe symport action of sodium in the intestine

A

The sodium driven-glucose symporter uses the potential free energy stored in the sodium electrochemical gradient (low sodium concentration inside the epithelial cells) established by Sodium-potassium pump. Therefore, the sodium influx from the lumen to the epithelial cell is coupled with glucose transport.

145
Q

what is apoptosis?

A

programmed cell death

146
Q

what is necrosis

A

Necrosis is the death of body tissue.

147
Q

what are the 2 apoptosis pathways

A

Intrinsic (cell decides) and extrinsic (told by other cells) pathways.

148
Q

true or false

apoptosis is Intimately linked with intracellular Ca2+ and mitochondrial Ca2+ levels

A

true

149
Q

what is the outcome of apoptosis

A

Results in blebbing of the membrane and formation of apoptotic bodies which are cleared by immune cells i.e.macrophages

150
Q

what can cause necrosis?

A
  • hypoxia
  • ischaemia
  • virus
  • poison
151
Q

what is the outcome of necrosis?

A

complete cell death, lysis releases cytotoxic components into the extracellular space which results in inflammation and an immune response.

152
Q

compare and contrast: apoptosis vs necrosis

A
153
Q

what are the main players in apoptosis

A

p53

Bcl-2

caspases

cytochrome c

PH1123 Microbiology (9 decks)

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