Cell Biology Exam Ii

Front 1

Extra Cellular Matrix

Back 1

-ECM Proteins on basement membrane & around fibroblast cells
-Provides protection, maintains shape, guides cells

Front 2

Collagen

Back 2

-19 types
-made up of 3 proteins (each a hydrophobic alpha helix)
-braided = high tensile strength (found in bones and ligaments)
-1/3 of AA that make it up are proline or hydroxyproline

Front 3

Collagen Fiber

Back 3

made up of several braided rows of collagen

Front 4

Proteoglycans

Back 4

-Protein backbone w/ disaccharide branches
-Disaccharides: Chondroitin Sulfate, Keratin Sulfate, Hyaluronic Acid
-called GAG's -> alternating disaccharides

Front 5

Fibronectin

Back 5

-Homo Dimer (2 identical proteins)
-linked by intermolecular disulfide bridges
-Guide Cells

Front 6

Laminins

Back 6

-Trimer
-Guide Cells (lay down road to follow)

Front 7

Elastin

Back 7

-Found in Dermis (skin springs back after pulled)
-Elastin stretches but is still held together by disulfide bridges

Front 8

Chondrocytes

Back 8

have huge ECM, mostly made of collagen

Front 9

All Proteins Synthesized

Back 9

-in RER->Golgi (o-linked glycolysis)->Plasma Membrane in vesicle->exocytosed to outside

Front 10

Neural Crest Cells Moving

Back 10

follow fibronectin pathways

Front 11

Primordial Germ Cells (PGC) in yolk sac

Back 11

-reproductive cells move to gonads in embryo
-follow on top of laminin pathways

Front 12

Erythroid Cells

Back 12

-early blood cells
-need to get to liver & bone marrow
-follow on top of laminin pathways

Front 13

Lymphoid Cells

Back 13

-Cells of the immune system
-Bone marrow, spleen, lymph nodes, and thymus
-follow on top of laminin pathways

Front 14

Selectins

Back 14

-L: shortest
-E: middle
-P: longest
-N-terminus in cytoplasm; alpha helix through PM; ECM
-Lectin-like domain on end (like to stick to sugars)
-stick to glycoproteins from other PM

Front 15

ICAM

Back 15

-Immunoglobin Cell Adhesion Molecule (Immunoglobin Super Family)
-Change by random mutation and take on new functions

Front 16

Cadherins

Back 16

-Dimers Overlap
-glycoproteins that mediate Ca2+ cell-cell adhesion and transmit signals from the ECM to cytoplasm

Front 17

Integrins

Back 17

-alpha & beta chains

Front 18

Blood Vessel Endothelial Cells

Back 18

have adhesion molecules on them

Front 19

Adhesion Proteins

Back 19

made in ER & brought to PM in vesicles

Front 20

Gap Junction

Back 20

-Sites between animal cells that are specialized for intercellular communication
-PM's come close together & are spanned by very fine strand or pipes that allow passage of small molecules

Front 21

Tight Junction

Back 21

-Specialized contacts that occur at the very apical end of the junctional complex that forms between adjacent epithelial cells
-Adjoining membranes make contact at intermitten points where integral proteins of the two adjacent membranes meet.

Front 22

Desmosomes

Back 22

-Disc shaped adhesive junction containing cadherins found in a variety of tissues where they are located basal to the adherin junctions
-Plaques on the inner surface of PM serve as anchors for intermediate filaments that extend into cytoplasm

Front 23

Adherin Junctions

Back 23

encircle each of the cells near its apical surface, binding that cell to its surrounding neighbors
-held together by calcium dependent linkages

Front 24

Nucleus Characteristics

Back 24

-Eukaryotes: Yes
-Prokaryotes & Mitochondria: No

Front 25

Chromosome Characteristics

Back 25

-Eukaryotes: Many
-Prokaryotes & Mitochondria: One

Front 26

Shape of DNA Characteristics

Back 26

-Eukaryotes: linear w/lots of protein
-Prokaryotes & Mitochondria: circular w/ little protein

Front 27

Division Characteristics

Back 27

-Eukaryotes: Mitosis
-Prokaryotes & Mitochondria: Fission

Front 28

Organelle Characteristics

Back 28

-Eukaryotes: Yes
-Prokaryotes & Mitochondria: No

Front 29

Ribosome Size Characteristics

Back 29

-Eukaryotes: 80s
-Prokaryotes & Mitochondria: 70s

Front 30

rRNA Characteristics

Back 30

-Eukaryotes: 28s, 18s
-Prokaryotes & Mitochondria: 23s, 16s

Front 31

Porin Characteristics

Back 31

-Eukaryotes: Yes
-Prokaryotes & Mitochondria: Yes

Front 32

Muscle Cells

Back 32

-have a high # of mitochondria per cell
-neurons & sperm also have a high # of mitochondria (ATP for movement)

Front 33

Porins

Back 33

-have no selectivity (just have to be small enough to fit through)
-regulation takes place in the PM

Front 34

Glycolysis

Back 34

2 pyruvic acids, 2 ATP, 2 NADH
-ATP for work
-pyruvic acid-> high potential for energy

Front 35

Ensymes in Krebs Cycle

Back 35

8 -> 4 from nucleus, 4 from mitochondria

Front 36

Protein Target Sequence

Back 36

8-10 extra AA that act as shipping address for protein

Front 37

No Target Sequence

Back 37

goes to cytoplasm

Front 38

Mitochondrial Location Signal (MLS)

Back 38

goes to mitochondria

Front 39

Nuclear Localization Signal (NLS)

Back 39

goes to nucleus

Front 40

RER Location Signal (RLS)

Back 40

goes to RER

Front 41

Peroxisome Location Signal(PLS)

Back 41

goes to peroxisome

Front 42

Direction ATP Synthase Spins

Back 42

clockwise

Front 43

Porphyrin Ring

Back 43

light absorbing "head" of molecule

Front 44

Chlorophyll a

Back 44

absorbs blue (430nm) & red (670nm)

Front 45

Chlorophyll b

Back 45

absorbs blue (470nm) & red (650 nm)

Front 46

Antennae Pigment Molecules

Back 46

catch photon and send signal inward through vibration which passes energy on until it reaches the reaction center (Mg2+ ion)

Front 47

electrons reduce NADP+ ->
NADPH through

Back 47

FD (faradoxin)

Front 48

light energy knocks 2e- off of PS II which goes to a receptor and then through

Back 48

Electron Transport Chain

Front 49

How is e- replaced in PS II

Back 49

light causes photolysis of H2O which replaces the e-

Front 50

NADPH & ATP build up in the stroma

Back 50

used to build carbohydrates through carbon fixation

Front 51

Mitochondria Proton Pumps

Back 51

-3 proton pumps
-Complexes I, III, & IV

Front 52

Chloroplast Proton Pumps

Back 52

-1 proton pump
-Cyt b6/f

Front 53

Secreted Proteins

Back 53

-Protein Hormones, Insulin, LH, FSH, GH
-Protein Growth Factors

Front 54

ECM Proteins

Back 54

-Collagen, Fibronectin
-Laminin, Proteoglycan

Front 55

Integral Membrane Protein

Back 55

-stays in membrane as an alpha helix
-Selectins, ICAM's, ETC
-Na+/K+ pump
-CFTR
-Glycophorin A

Front 56

Transport of Vesicle

Back 56

1)Coat Protein put on Vesicle
2)Protein Motor Delivers vesicle
3)Vesicle Tethered to membrane
4)Docking: v-snares & t-snares
5)Vesicle membrane fuses w/ target

Front 57

Lysosome

Back 57

breaks down material using hydrolysis; contains hydrolytic enzymes

Front 58

Endocytosis

Back 58

1)Phagocytosis
2)Pinocytosis
3)Receptor-mediated

Front 59

Phagocytosis

Back 59

brings in big molecules

Front 60

Pinocytosis

Back 60

brings in lots of small molecules

Front 61

Cytoskeleton

Back 61

1)Microtubules (hollow)
2)Intermediate Filaments (solid)
3)Microfilaments (solid)
4)Protein Motors

Front 62

Mirotubules

Back 62

-Hollow; 24nm diameter

Front 63

Intermediate Filaments

Back 63

-solid; 10nm diameter
1)Keratin (skin, nails)
2)Vimentin (liver celss)
3)Desmin (muscle)
4)Neurofilaments (neuron axons)
5)Lamins (inside nucleus)
6)Plectin
7)Spectrin (RBC->strengthens RBD membrane)
8)Dystrophin (muscle cells-> reinforces muscle cells)
9)Nexin (cilia & flagella-> keeps it from bending too far)

Front 64

Microfilaments

Back 64

-solid; 8nm diameter
-actin (globular actin to/from filamentous actin)
-myosin: II is most common in muscle cells

Front 65

Protein Motors

Back 65

1)Kinesin (+) moves toward + end
-Kinectin
2)Dynein (-) moves toward - end

Front 66

Intermediate Filament Assembly

Back 66

1)Monomer (N->C)
2)Dimer: 2 monomers braided
3)Tetramer: Dimer align a little off center with alternating N->C then C->N
4)IF structure: tertamers organized into intermediate filament

Front 67

1)Mitochondrial, Chloroplast, & Prokaryotic Ribosome size
2)Eukaryotic Ribosome size

Back 67

1)70s
2)80s

Front 68

1)Products of Glycolysis that enter mitochondria
2)Electrons from 2 NADH cross the two membranes via

Back 68

1)2 pyruvates
2)glycerol-3-phosphate

Front 69

In Krebs Cycle (TCA) the enzyme ______ catalyzes the conversion of Succinate to _______ and this enzyme is also part of the ETC

Back 69

1)Succinyl-CoA synthase
2)Succinate Dehydrogenase

Front 70

Two Krebs Cycles produce ______ and _______ that contain high energy electrons that pass onto the ETC

Back 70

1)6 NADH
2)2 FADH2

Front 71

When proteins are imported into a mitochondria they must first be unfolded in the cytosol by _____ and then refolded in the matrix by ______

Back 71

1)Hsp70
2)Hsp60

Front 72

The first step of the Calvin Cycle in chloroplasts involves the bonding of one carbon from CO2 to a molecule of _______ by the enzyme _________

Back 72

1)RuBP
2)RuBP carboxylase

Front 73

N-linked glycosylation of a protein starts in the lumen of the RER. The barbohydrates are first assembled on a _______ molecule and then they are transferred to the R-Group of the AA _______ at the N-terminus of the protein

Back 73

1)lipid carrier
2)asparagine

Front 74

Vesicles heading to the PM have ______ protein coating their outer surface and these vesicles also have ______ to trap them at the PM

Back 74

1)none
2)v-snares

Front 75

Microtubules are composed of ________ heterodimers that are added to the growing end or the _______ (other designation) end of the tubule

Back 75

1)alpha & beta tubulin
2)plus end

Front 76

The sperm flagellum bend due to the protein motor called ______. The microtubules are prevented from continuously sliding past each other by ______ protein.

Back 76

1)Dynein
2)Nexin

Front 77

Matrix

Back 77

Mitochondria Cytoplasm

Front 78

ETC (mitochondria)

Back 78

in cristae of mitochondria

Front 79

sperm entering egg

Back 79

-only nucleus of sperm enters egg leaving mitochondria behind
-all mitochondria DNA comes from mother

Front 80

Prep for Krebs (TCA) Cycle

Back 80

-Pyruvate naturally flows from cytosol to mitochondria (higher concentration outside than in)
1)Enzyme->Pyruvate decarboxylase strips CO2 off
2)NAD+ reduces to NADH
3)Coenzyme A attatches to form Acetyl CoA (using enzyme transferase

Front 81

1 Krebs Cycle Products

Back 81

-2 NADH from Pre-Kreb's
-3 NADH from Kreb's w/ potential energy
-1 FADH2 w/ potential energy
-1 ATP can be used for work
(FADH2 < NADH in energy)

Front 82

steps from 1 Glucose molecule

Back 82

1 Glucose -> 2 Pyruvates ->
2 Kreb's Cycles -> [6 NADH, 2 FADH2, 2 ATP] -> with pre-Kreb's = [8 NADH, 2 FADH2, 2 ATP]

Front 83

Some steps in Kreb's

Back 83

Oxaloacetate -> Citrate -> Isocitrate -> a-Ketoglutarate

Front 84

Glycerol Phosphate Shuttle

Back 84

1) 2 NADH from Glycolysis cannot enter mitochondria
2) electrons transfered to Glycerol-3-phosphate
3) goes through porin & transfers electrons to FAD to form FADH2 (using glycerol-3-phosphate dehydrogenase)
4) Total sum of what mitochondria has to work with = 8 NADH, 4 FADH2, 2 ATP -> from one glucose molecule)

Front 85

pH of intermembrane space & matrix of mitochondria

Back 85

intermembrane space: pH 4 (lots of protons -> acidic)
matrix: pH 8

Front 86

Electron Transport Chain (mitochondria)

Back 86

1)NADH transfers 2e- to Complex I (NADH dehydrogenase) which is then passed to FMN and Fe-S, then to Ubiquinone (UQ)
2)FADH2 transfers 2e- to Complex II (Succinate Dehydrogenase) to FAD to Fe-S, then to UQ.
3)UQ carries the electrons to Complex III where they are passed to Fe-S then onto Cytochrome C
4)Cyt C carries the electrons to Complex IV (cytochrome c oxidase)which eventually passes the electrons onto O2 molecules to create H2O
-Complex I brings 4 H+ into the intermembrane space
-Complex III brings 4 H+
-Complex IV brings 2 H+
5)Protons go through ATP synthase -> C rotates causing gamma to turn in bulb made of 3 alpha and 3 Beta subunits) Beta has active site -> Delta anchors bulb to membrane

Front 87

Ubiquinone

Back 87

hydrophobic protein (stays in membrane)

Front 88

Total protons after ETC

Back 88

104 Protons -> (4FADH2 x 6 H+) + (8 NADH x 10 H+)
-Protons cause ATP synthase to spin and drive endergonic reaction (ADP + P = ATP)
-3 H+ go through ATP synthase = 1 ATP) -> about 34 ATP total

Front 89

C Ring

Back 89

composed of 10-14 subunits

Front 90

Binding Change Mechanism for ATP synthesis

Back 90

1)open site takes in ADP + Pi, movement of proton through the membrane induces shift to loose conformation
2)movement of additional proton induces shift to tight conformation
3)tightly bound ADP + Pi spontaneously condense to form ATP
4)movement of proton through membrane shifts it back to open conformation allowing product to be released

Front 91

ATP synthase experiment

Back 91

1)alpha, beta, and gamma added to test tubes in 3:3:1 ratio
2)AA attaches alpha to slide coated with nickel
3)covalently linked actin filament to gamma
4)coated actin with fluorescent antibodies
5)ATP + H20 = ADP + Pi -> filament seen spinning backwards (counter clockwise)

Front 92

Mitochondria Diseases

Back 92

NARP (from mom & dad) & MELAS (mom) -> trouble making ATP causes muscle & neuron problems

Front 93

Distribuition of ATP (mitochondria)

Back 93

38 ATP -> 30 to host cell; 8 to mitochondria

Front 94

Importing Proteins into mitochondria

Back 94

1)Chaperone protein (Hsp 70) unfolds Protein using ATP energy
2)Unfolded Protein binds to receptor and is passed through both membranes (with 8-10 AA as shipping address)
3)Chaperone Proteins mHsp 70 & Hsp 60 fold protein using ATP
4)Targeting sequence in removed and hydrolyzed while the protein goes to Kreb's, ETC, etc.

Front 95

flow of electrons in photosynthesis

Back 95

1)H20 -> photolysis -> 2e- go to PS II
2)excited by light, 2e- move up to P680
3)go through ETC & back down to PS I, excited by light move up to P700
4)ETC -> NADPH

Front 96

Non-cyclic flow of electrons in chloroplast

Back 96

1) 2H20 donate electrons to PS II
2)PS II passes electrons to PQb & then to the Q cycle (PQH2 & PQ)
3)Electrons then transfered to Fe-S in Cytochrome b6/f
4)electrons transferred to PC (plastocyanin) in lumen
5)PC takes electrons to PS I which then passes them onto ferrodoxin (FD) and then onto 2 NADPH in the stroma
-Light excites both PS II & PS I

Front 97

cyclic phosphorylation

Back 97

1)Absorption of light by PS I excites an electron which is transferred to FD
2)FD -> cytochrome b6/f
3)cyt b6/f -> Plastocyanin (PC) and back to P700
4)during process, cyt b6/f moves protons in to create gradient used to make ATP

Front 98

Summary for 6 Calvin Cycles

Back 98

1) 6 cycles for 1 glucose molecule
2) CO2 & H2O needed or Calvin Cycle stops in their absence
18 ATP; 12 NADPH -> Glucose -> Glycolysis, TCA, ETC -> 38 ATP
(18 ATP to eventually get 38)

Front 99

endomembranes

Back 99

each named for structure -> nuclear membrane, golgi membrane, plasma membrane

Front 100

Antereograde

Back 100

Nucleus -> PM

Front 101

Retrograde

Back 101

PM -> Nucleus

Front 102

Constitutive Secretory Pathway

Back 102

happens all the time

Front 103

Regulated Secretory Pathway

Back 103

Only happens when something needs to be released

Front 104

Pulse-Chase Autoradiography

Back 104

1)incubate tissue for a brief period in radioactive AA (B-islet cells make H-insulin with h-leucine) then wash & transfer to medium containing unlabeled AA ->fix, section, photoemulsion
2)pulse: period radioactive AA are incorporated in protein
chase: period when tissue is exposed to unlabeled medium
3)The longer the chase, the further the radioactive proteins can be seen moving along
RER= 3 mins
Golgi= 20 mins
ECM= 120 mins

Front 105

GFP tagging

Back 105

1)Green Fluorescent Protein DNA fused to DNA encoding protein
2)Causes mRNA to be tagged with GFPmRNA and in turn causes protein to be tagged with the GFP
3)GFP allows the protein to be observed accumulating in the RER where it is made
4)GFP then observed moving onto the golgi, and then to PM
5)Using GFP, synthesis & secretory pathway of a protein can be viewed in a dish

Front 106

Smooth ER

Back 106

store Ca2+ and Enzymes (break down toxic compounds that enter it)

Front 107

glycoproteins

Back 107

made in cytoplasm & RER

Front 108

Synthesis of a membrane bound protein

Back 108

1)ribosome & tRNA create a protein from mRNA starting with signal peptide
2)a SRP protein attaches to the signal peptide which connects to the SRP receptor while the ribosome sits on the translocon
3)SRP is released & signal peptide binds to the translocon
4)Protein then translocates through the translocon
5)BiP acts as a chaperone protein and refolds the protein using ATP
6)Then target sequence is cut off and hydrolyzed as the protein is in the ER lumen
7)If becoming and integral membrane protein, it has a stop-transfer sequence and COOH end is in Cytosol while NH3 is in ER lumen most of the time

Front 109

Glycophorin A

Back 109

through membrane one time & has sugar on it -> C-terminus faces cytoplasm; N-terminus faces lumen of RER

Front 110

Static Model of Golgi

Back 110

vesicles transport between golgi

Front 111

Maturational Model of Golgi

Back 111

cisternae move down while vesicles create new cis-golgi (has retrograde transport as well)

Front 112

COP

Back 112

Coat Protein -> can use trypsin to determine where certain parts of protein are located

Front 113

Clathrin

Back 113

sophisticatedly coating for vesicles carrying dangerous cargo (such as digestive enzymes)
-moves material from the TGN to endosomes, lysosomes, and plant vacuoles
-also endocytosis brings in material to be coated with clathrin and moved to endosome and lysosome (mannose 6-phosphate receptors on PM)

Front 114

COP I

Back 114

move material retrograde from ERGIC and golgi back towards ER and from trans-Golgi back towards cis-Golgi

Front 115

COP II

Back 115

move vesicles from ER forward to the ERGIC and Golgi

Front 116

mannose 6-phosphate

Back 116

found on vesicles going to lysosomes

Front 117

acrosome

Back 117

releases lysosomal enzymes to break through the egg (only situation in which enzymes are released into the body)

Front 118

autophagolysosom

Back 118

self-eating

Front 119

pigment granules

Back 119

surround material if it is very toxic even after being broken down (stays in cell as garbage which builds up over time)

Front 120

chemotaxis

Back 120

cell moving in response to a chemical

Front 121

yolk

Back 121

made in liver -> egg -> taken in by receptors (lysosomes slowly but constantly digest yolk)

Front 122

Cytoskeletal Functions

Back 122

1)Structure & support
2)Intracellular Transport
3)Motility & Contractility: walk across filaments
4)Spatial Organization: holds things in place
-not a static structure (constantly moving)

Front 123

Microtubule

Back 123

-made of alternating alpha & beta tubulin
-one row = protofilament (13)
-has a slow growing end (-) and fast growing end (+)
-polymerize & depolymerize on the (+) end
-MAP2 has hook to connect to other microtubules or actin
-kinesin walks towards positive end skipping only on alphas or betas

Front 124

Kinesin

Back 124

ATP goes through one foot and causes other foot to kick forward
-requires a lot of energy
-holds onto vesicle with arms

Front 125

Dynein

Back 125

-has bigger feet than kinesin
-walks toward (-) end
-If on same protofilament, then they collide until on steps aside onto another protofilament
-Requires GTP to polymerize microtubule
-requires hydrolysis of GTP to depolymerize
-Dynein moves chromatid toward (-) end during anaphase)

Front 126

Interphase

Back 126

-Negative end always faces Golgi during interphase
-vesicle must be tethered before arms release it

Front 127

MTOC

Back 127

Microtubule Organization Center: foundation for growth of microtubules (-) end always points toward MTOC
-part of mitotic spindle

Front 128

Centrosome

Back 128

Has outer A, B, C tubules (A is the only full one) with spindles going towards center

Front 129

Pericentriolar Material (PCM)

Back 129

surrounds centrosomes in MTOC

Front 130

Protofilament Polymerization

Back 130

circle of 13 gamma tubulin laid down as foundation for growth of protofilaments on MTOC

Front 131

Axoneme

Back 131

has 9 outer doublets and 2 inner central tubules connected by radial spokes
-Dynein + ATP = Bend

Front 132

Axoneme Movement

Back 132

-center tubules rotate off center sending signals through radial spokes to outer tubules & dynein causing bending for movement
-Proton pump at base of cilia/flagella pumps protons in, through center microtubules (causing movement), and out at tip -> back to proton pump
-When one side contracts, the other is relaxed to get side to side movement
-hydrolysis brings it back to relaxed position

Front 133

Actin Growth

Back 133

adds onto (+) end and takes off from (-) end
-nucleus held in place by actin

Front 134

Myosin

Back 134

-bends with ATP, and returns to original position after hydrolysis
-grabs towards (+) end of actin and pulls it toward (-) end

Front 135

Myosin Va

Back 135

Kinesin only walks on microtubules, then hands off vesicle to Myosin Va which only walks on actin to bring the vesicle to the PM for exocytosis