Molecular Cell Bio Exam 2

Front 1

Phospholipid Bilayer

Back 1

- hydrophobic inside (non-polar, cytoplasmic)
- hydrophilic outside (polar, exoplasmic)

Front 2

Phospholipids

Back 2

- phosphoglycerides (glycerol based, in cytoplasmic layer, phosphatidyl choline, serine, inositol, 2 fatty acids)
- sphinogolipids (sphingosine based, long, sphinomyelin, found in animals only, 1 fatty acid)

Front 3

Glycolipids

Back 3

- carbohydrate and a lipid
- serve as cell markers
- more on exoplasmic layer

Front 4

Lipids

Back 4

- fatty acids
- 12-20 Carbons long
- length determines thickness in turn saturation

Front 5

Saturated Fatty Acid

Back 5

- no double bonds
- myristic, stearic, palmitic

Front 6

Unsaturated Fatty Acid

Back 6

- mono (1 double bond, oleic acid)
- poly ( more than 1 double bond, linoleic, linolenic, arachidonic)
- cis (fluidity) and trans (fats) bonds

Front 7

Sterols

Back 7

- 4 Carbon rings and -OH group
- rigidity buffers against over fluidity (hydrocarbon structure) and rigidity (cold temps)
- animals; cholesterol
- plants; phytosterol
- fungi; ergosterols
- bacteria, mitochondria, chloroplasts; hopanoids

Front 8

Membrane Fluidity

Back 8

- rotational movements (around own axis)
- lateral diffusion (along membrane)
- transverse diffusion (back and forth exoplasmic to cytoplasmic layers with enzyme help)

Front 9

Changing Fluidity

Back 9

- cold temps cause rigidity
- membrane receptors don't function properly
- decreases fatty acid length, increases double cis bonds
- hibernating animals help by increasing ratio of unsaturated fatty acids to saturated fatty acids

Front 10

Integral Proteins

Back 10

- amphiphatic
- monotopic goes through exo or cytoplasmic
- transmembrane goes through both
- anion, aquaporins

Front 11

Peripheral Membrane Proteins

Back 11

- exo or cytoplasmic
- do not penetrate bilayer
- form non covalent bonds w/ polar or integral protein on exoplasmic phospholipid
- cytochrome C

Front 12

Lipid Anchored Protein

Back 12

- cyto or exoplasmic
- covalently bonded to fatty acid chains and glycosyl phosphatidyl inositol

Front 13

Membrane Sugars

Back 13

- on glycolipids and glycoproteins
- forms glycocalyx around cell

Front 14

Glycocalyx

Back 14

- cell markers (prevents autoimmune disease, transplant rejections, signals damage cell to destruct; cancer)
- cushions cell

Front 15

Isolating Membrane Proteins

Back 15

- Peripheral by change in pH or concentration of salt
- integral by using sodium dodecyl sulfate (anionic detergent (adds negative charge to proteins) and a surfactant to keep alveoli fluid for gas exchange) to dissolve lipids
- PAGE gel separates by protein size

Front 16

Simple Diffusion

Back 16

- direct, unaided across bilayer don concentration gradient, exergonic, Delta G < 0
- rate of diffusion not saturable
- if H2O it's osmosis

Front 17

Facilitated Diffusion

Back 17

- aka passive transport
- requires transport proteins (symporters, antiporters (anion exchanger), uniporter (glucose)) that bind, change shape and transport to other side
- movement down electrical concentration gradient
- Delta G < 0, exergonic
- no directionality

Front 18

Movement of Glucose

Back 18

- down gradient
- inside cell glucose is converted to blu-6-p

Front 19

Anion Exchanger

Back 19

- antiporter facilitated diffusion
- CO2 in blood moves into RBC via plasma
- inside cell, CO2 is converted to H2CO3 by carbonic anhydrase
- decreases CO2, increases drive for CO2 into cell

Front 20

Ion Channels

Back 20

- facilitated diffusion
- highly specific to ion
- 4 types: ligand gated, voltage gated, mechanosensitive and non-gated

Front 21

Porins

Back 21

- facilitated diffusion
- barrels through membrane filled with H2O
- allow passage of small sugars

Front 22

Aquaporins

Back 22

- facilitated diffusion
- move H2O
- in plants to increase turgor pressure, prevent wilting
- in kidney tubules for thirst, decrease bp, bv triggering vasopressin increasing aquaporin

Front 23

Active Transport

Back 23

- movement against/ up gradient
- delta G > 0, endergonic
- requires energy or coupling
- direct coupling (ATP driven Na/K pumps)

Front 24

Indirect Coupling

Back 24

- aka secondary active transport
- transports symporters and antiporters protein
- ex: symport of glucose and amino acids in intestine symport Na & H+ pumps create H+ gradient, movement down its gradient powers movement of sugars

Front 25

Reaction in Chemical Reaction

Back 25

- A + B ---> C
- keq = [C]/([A]*[B])

Front 26

Reaction in Transport

Back 26

- S out <---> S in
- keq = [S]in/[S]out = 1
- at equilibrium
- [S]in < [S]out, Ln < 0 and G < 0, exergonic, spontaneous
- [S]in > [S]out, Ln > 0 and G > 0, endergonic, requires energy

Front 27

Anabolic Pathways

Back 27

- build up
- decrease randomness, entropy
- endergonic
- delta G > 0
- polymerization/elongation of nucleic acid, protein synthesis

Front 28

Catabolic Pathway

Back 28

- break down
- increase randomness, entropy
- exergonic
- delta G < 0
- ATP hydrolysis, glycolysis

Front 29

ATP

Back 29

- primary energy currency
- function to transfer phosphate group
- Glu + ATP ---> Glu-6-P + ADP
- 3 phosphates, ribose, adenine
- 3 high energy bonds
- phosphoanhydride (-7.3), phosphoester (-3.6)

Front 30

Hydrolysis

Back 30

- exergonic
- ATP ---> ADP + Pi or ATP ---> AMP + PPi
- H2O ---> -OH + H+
- increase randomness

Front 31

Oxidation

Back 31

- reduction in biological systems
- transfers electron in pairs or with protons
- exergonic
- dehydrogenation reactions
- ethanol ----> acetaldehyde + 2e- + 2H+

Front 32

Reduction

Back 32

- gain of e- in pairs
- endergonic
- hydrogenation reactions
- acetaldehyde + NADH+ -----> ethanol + NAD+

Front 33

Glycolysis

Back 33

- breakdown, oxidation of glucose to pyruvate
- exergonic
- delta G = -20kcal/mol
- glucose ---> 2 pyruvate + 2 ATP + 2 NADH + H+
- invested 2 ATP
- derived 4 ATP + 2 NADH + 2 H+

Front 34

Glycolysis Steps

Back 34

glucose (w/ ATP---> G-6-P ---> fruct-6-p (w/ ATP/PFK---> fruct-1,6-bis P ---> dihydroxyacetone-p + glycerol-3-p (w/NAD + Pi---> q,3-bisphosphoglycerate (w/ADP---> 3-phosphoglycerate ---> 2-phosphoglycerate ---> phosphoenolpyruvate (w/ATP---> pyruvate

Front 35

Fermentation

Back 35

- absence of O2 when pyruvate is processed
- regenerates NAD+ not ATP
- lactate, ethanol + CO2, acetone

Front 36

Lactate

Back 36

- lactic acid
- built up during strenuous exercise
- later delivered by blood to love/kidneys to be converted to glycolysis by gluconeogenesis
- delta G < 0, spontaneous (-320k/m)

Front 37

Cellular Respiration

Back 37

- aerobic respiration
- maximizes energy yield after glycolysis
- yields more ATP b/c of an external e- acceptor, O2

Front 38

Aerobic Respiration

Back 38

- yields 38 ATP
- oxidation/removal of e- from glucose
- transfers e- to coenzymes
- Pyruvate oxidation, TCA cycle, e- transport system, ATP synthesis
- in mitochondria, chemotrophs and phototrophs

Front 39

Mitochondria

Back 39

- outer: porins
- intermembrane space: H+ gradient
- matrix: pyruvate dehydrogenase, krebs cycle enzymes, mitochondrial DNA

Front 40

Aerobic respiration steps

Back 40

- when O2 is present pyruvate into matrix by translocase, symported with H+
- pyruvate undergoes oxidative decarboxylation by pyruvate dehydrogenase, oxidizing pyruvate, pyruvate decarboxylation and addition of Acetyl CoA, CO2, NADH
- Acetyl CoA adds to oxaloacetate for citric acid
- citric acid is decarboxylated twice forming succinate
- succinate converts to regenerated oxaloacetate

Front 41

5 Oxidation Steps in Aerobic Respiration

Back 41

- pyruvate --> Acetyl CoA (CO2 + NADH)
- 2 at citrate --> succinyl CoA (CO2 + NADH)
- 2 at succinate --> oxaloacetate (FADH + NADH)

Front 42

Decarboxylation

Back 42

- NAD+ --> 1 NADH = 3 ATPs

Front 43

Dehydrogenation

Back 43

- succinate to fumarate
- FAD+ --> 1 FADH = 2 ATPs

Front 44

Pyruvate Dehydrogenase

Back 44

- regulated allosterically
- cues that indicate abundant energy levels NADH, ATP, Acetyl CoA
- cues that indicate low energy levels NAD, AMP, CoA
- decrease ATP, increase TCA

Front 45

Fat Catabolism

Back 45

1) hydrolysis of triglycerides (TG + H2O --> glycerol --> glycerol-3-p --> dihyrdoxyacetone-p)
2) glycerol is converted to a compound that can enter the citric cycle
3) beta oxidation produces Acetyl CoA, enters the citric cycle

Front 46

CoA Depletion

Back 46

- can be limiting step
- incomplete fat catabolism
- increases ketone bodies, decreases blood pH
- fruity breath, hyperventilation

Front 47

Protein Catabolism

Back 47

- stored as muscles, not as energy source
- during starvation it can be broken down for energy
- proteolysis by proteases, oxidative deanimation of amino acid to keto acids

Front 48

Oxid Deanimation

Back 48

- amino acid to keto acids

Front 49

Transamination

Back 49

- keto acids to amino acids

Front 50

Glyoxylate Cycle

Back 50

- plants only
- acetyl CoA --> sugars by gluconeogenesis
- seed generation

Front 51

Electron Transport System

Back 51

- transfer of e-'s from carriers
- exergonic
- 10 H+ are moved for ever pair of e- transferred to complex 1-3

Front 52

Complex 1

Back 52

- NADH dehyrogenase complex
- e-'s from NADH to CoEnzyme Q
- 4 H+
- used by NADH

Front 53

Complex 2

Back 53

- Succinate CoEnzyme Q Cytochrome oxidoreductase
- e's from succinate to FAD+ to CoEnzyme Q
- used by FADH

Front 54

Complex 3

Back 54

- Coenzyme A cytochrome C oxidoreductase
- e-'s from CoEnzyme Q to Cytochrome C
- 4 H+
- used by NADH, FADH

Front 55

Complex 4

Back 55

- Cytochrome C oxidase
- e-'s from Cytochrome C to O2
- 2 H+
- used by NADH, FADH

Front 56

ATP Synthase

Back 56

- ADP + Pi --> ATP
- 1 ATP produced per 3 H+ moved down gradient
- 10 H+ rotate f0/f1 (H+ channel/ATP synthase) complex changing formation of 3 enzyme active site to catalyze 3 ATPs

Front 57

2 NADH Need To Be Transferred into mitochondria to ETS by

Back 57

- liver/hear/kidney: e- from NADH to Malate into matrix into TCA cycle (3 ATPs)
- muscle/brain: e- to glycerol-3-p into intermembrane space to FADH to FADH2 (2 ATPs)

Front 58

Photosynthesis

Back 58

- conversion of light energy to chemical energy
- conversion of inorganic C to organic C
- use light energy to drive anabolic reactions
- two parts: energy transduction reaction and carbon assimilation/fixation

Front 59

Energy Transduction Reaction

Back 59

- pigments absorb light
- transfer e- to chlorophyll a (aka P680)
- e- lost in transfer is replenished by photolysis
- excited e-'s in P680 --> pheophytin --> plastoquinone --> cyctochrom B6/f --> plastocyanin --> PS I (P700 reaction center) --> ferredoxin --> NADP --> NADPH (for calvin cycle)

Front 60

Carbon assimilation/fixation

Back 60

- CO2 to triose (3 carbon sugar)
- occurs in stroma
- CO2 by simple diffusion adds to ribulose 1.5 bis P making 2 of 3-phosphoglycerate with ATP and NADPH to glyceraldehyde-3-p
- trioses moves to cytosol for sucrose formation or stays in stroma making starch to be used for glycolysis

Front 61

Chloroplasts

Back 61

- conduct photosynthesis
- outer memb: highly permeable
- inner memb: selectively permeable barrier
- contains thylakoid (sacs, grana) and connected
- H+ pumped into lumen of thylakoid, enters stroma for ATP synthase

Front 62

Photosynthesis Pigments Have

Back 62

- porphyin group (large multi C-N ring)
- phytol (hydrocarbons anchoring pigments
- Mg2+ (makes charge across ring)
- photon E excites e- in pigments

Front 63

Pigment Absorption

Back 63

- chlorophyll a and b at blue and red but reflect green
- accessory pigments (phycobillins) absorb at blue but reflects red

Front 64

1 triose =

Back 64

9 ATPs, 6 NADPHs and 3 turns of the calvin cycle

Front 65

Rubisco Activation

Back 65

- activase clears active site
- cleaves phosphates from rubisco active site to activate rubisco
- inhibited when increase ADP, phosphate stays, rubisco inhibited, decrease calvin cycle
- increase ATP, actives active to cleave phosphate to increase calvin cycle

Front 66

Rubisco Carboxylase

Back 66

- rib 1.5 bis p + CO2 ----> 2 of 3 phosphoglycerate used in calvin cycle

Front 67

Rubisco Oxygenase

Back 67

- rib 1.5 bis p + O2 ---> phosphoglycolate used in glycerinate + 2 phosphoglycerate used in calvin cycle

Front 68

Endomembrane consists of..

Back 68

- smooth and rough ER
- golgi apparatus
- endosomes
- vesicles

Front 69

Rough ER

Back 69

- studded with ribosomes
- protein synthesis starts in cytosol continuing in lumen
- sort/tag polypeptides
- modifies translation post electron transport chain
- degradation of misfolded polypeptides

Front 70

Smooth ER

Back 70

- drug detoxification (modifies substance by adding -OH, methyl, acetyl, phosphates)
- alters structure to change substance activity
- solublize to H2) for elimination
- P450, adds -OH, anesthetics, barbiturates

Front 71

Exposure to Barbiturates

Back 71

- increase release of P450
- proliferates SER to improve drug elimination

Front 72

Example of P450

Back 72

- aryl hydrocarbon hydroxylase
- adds -OH to polycyclic hydrocarbons
- increases toxicity
- tobaccos use, increases P450 enzyme

Front 73

Carbohydrate Metabolism

Back 73

- smooth ER
- glycogen to glucose-1-p to glu-6-p to brain/muscles for glycolysis or to glucose to transport out of cell

Front 74

Calcium Stores

Back 74

- modified smooth ER, sarcoplasmic reticulum in skeletal muscles
- stores calcium by Ca-ATPases
- action potential triggers volt gated Ca channels to release Calcium into sarcoplasm for muscle contractions

Front 75

Biosynthesis of Steroids, Lipids, Cholesterols

Back 75

- P450 adds -OH to cholesterol making testosterone/estrogens
- phospholipid exchange proteins transports phospholipids synthesis in RER/SER/golgi through cytosol

Front 76

Golgi Complex

Back 76

- continues protein synthesis by sorting/packaging
- cis (facing nucleus, anterograde flow) and trans (away from nucleus, retrograde)
- materials are transported by vesicles from ER to cis face and from trans face to targets

Front 77

Glycosylation

Back 77

- usually in cytosol during translation to ER to golgi
- addition of common core oligosaccharide
- adds OH and NH2
- proper folding, tagging, marking (ER tagged for return along with sugars)

Front 78

Common Core Oligosaccharides

Back 78

- N-acetylglucosamine and mannose, glucose
- flipped inward
- cleavage of mannose, glucose and other moieties

Front 79

Lysosomes

Back 79

- mannose-6-p binds to receptor by trans face
- fuse with endosomes to from lysosomes when leaving golgi apparatus
- lysosomes have low pH, receptors release mannose-6-p floating free
- works as defense, nutrition and recycling of cell components

Front 80

Transport Vesicles

Back 80

- transport to target along microtubules
- release constitutive or regulated (upon signal)
- polarized
- specific destination associated with SNAREs

Front 81

SNAREs

Back 81

- mediate fusion of vesicles to target membrane
- V: vesicle snap receptors on vesicles
- T: target snap receptors on target membrane
- both are complementary and attach to release contents
- dissociated by NSF and electron transport chain proteins

Front 82

Botulinum

Back 82

- cleaves SNAREs
- stops neurotransmitter release
- causing muscle paralysis

Front 83

Pinocytosis

Back 83

- clathrin independent endocytosis
- retrieval of plasma membrane to ER
- recycles membrane

Front 84

Clathrin Dependent Endocytosis

Back 84

- uses adaptor proteins
- phagocytosis

Front 85

Endocytosis Steps

Back 85

- ligand/substance binds to receptors on exoplasmic membrane
- coated pits signal aggregation of clathrin on cytoplasmic membrane to curve around ligand-receptors
- dynamin closes vesicle into cytoplasm
- coating is released
- vesicle fuses with endosome and either digested/recycled/exocytosed

Front 86

Lysozomal Enzymes

Back 86

- usually work inside but..
- sperm break down protective coat of egg
- leaking cause damage to joint tissue (rheumatoid arthritis)

Front 87

Peroxisome

Back 87

- not part of endomembrane system
- H2O2 metabolism (2 H2O2 ---> 2 H2O + O2)
- detox harmful chemicals (dehydrogenation and transfer H to O2 --> H2O)
- oxidation of fatty acids
- metabolism of nitrogenous compounds (transamination to mitochondria)
- catabolism of abiotic, xenobiotic substances (fuel in body)