Cell Bio Exam I Review

Front 1

Endosymbiotic Hypothesis

Back 1

1)anaerobic prokaryote takes in small aerobic prokaryote (3 BYA)
2)aerobic heterotropic prokaryote w/ small prokaryote (eventually mitochondria) (2.5 BYA)
3)plasma membrane invagination (2 BYA)
4)proeukaryotic cell w/ precursors to ER & nuclear envelope
5)protist, fungal, & animal cells
6)photosynthetic cyanobacteria -> algal & plant cells

Front 2

Structure of Plasma Membrane

Back 2

-phospholipids
-proteins
-carbohydrates

Front 3

Structure of Cell Walls

Back 3

-proteins
-carbohydrates (polysaccharides)

Front 4

Structure of Organelles

Back 4

-phospholipids
-proteins
-carbohydrates
-some DNA

Front 5

Structure of Cytoskeleton

Back 5

-protein

Front 6

Structure of Ribosomes

Back 6

-protein
-rRNA

Front 7

Switch between monomers and polymers requires?

Back 7

condensation & hydrolysis (taking & giving water molecules to form & break bonds)

Front 8

Carbohydrates

Back 8

(CH2O)n

Front 9

Lipids

Back 9

-triglycerides: glycerol w/ 3 fatty acid hydrophobic tails
-saturated: no double bonds; solid at room temp
-unsaturated: double bonds; liquid at room temp
-steroids: hydrophobic; mostly signaling molecules
-phospholipids

Front 10

Steroid Examples

Back 10

-leydig cells in testes: cholesterol is converted to testosterone using enzymes & a series of conversions
-granulosa cells in ovaries: cholesterol is converted to estrogen after a series of reactions

Front 11

Phospholipid Structure

Back 11

1)polar head (choline & phosphate)
2)glycerol backbone
3)fatty acid chains

Front 12

Difference Between Beta & Alpha Configurations

Back 12

-Beta has OH above plane
-Alpha has OH below plane

Front 13

Glyogen Linkage

Back 13

alpha (1-4) glycosidic linkage

Front 14

Starch Linkage

Back 14

alpha (1-4) glycosidic linkage

Front 15

Cellulose Linkage

Back 15

beta (1-4) glycosidic linkage

Front 16

Polar Amino Acids

Back 16

lycine, arginine, tyrosine, serine, threonine, glutamine

Front 17

Non-Polar Amino Acids

Back 17

leusine, isoleucine, valine, alanine, tryptophan

Front 18

Side Chains w/ Unique Properties

Back 18

glycine, cysteine, proline

Front 19

Primary Protein Structure

Back 19

-N-terminus -> C-terminus
-Amino Acid Sequence
-synthesis of bonding peptides takes place in the RIBOSOME

Front 20

Protein Synthesized in?

Back 20

mitochondria, chloroplast, & cytoplasm

Front 21

Secondary Protein Structure

Back 21

-alpha helix: contains hydrophobic AA; hydrogen bonds that can break to change length of coil (1 helix = 3.6 residues)
-beta pleated sheet: alternates hydrophobic & hydrophilic (lysine->leusine); held side by side by hydrogen bonds
-hair pin loops: covalent bonds of disulfide bridge holds parts of structure together (strong bonds)

Front 22

Tertiary Protein Structure

Back 22

-3-D folding (Native)

Front 23

Quaternary Protein Structure

Back 23

-Protein made up of 2 or more subunits needed together to function properly

Front 24

Chemical Denaturation

Back 24

Urea & Mercaptethanol: denatures proteins; some refold but others are permanently deformed

Front 25

Exergonic

Back 25

Substrate to Product
(with help of enzyme)
energy is released

Front 26

Endergonic

Back 26

Product to Substrate
(requires input of energy from ATP or GTP)

Front 27

Glucose + ATP ->

Back 27

Glucose-6-Phosphote + ADP
with help from hexokinase

Front 28

R-Group determines?

Back 28

how substrate is oriented in active site

Front 29

Enzyme Mechanism Image

Back 29

1)maintain substrate orentation
2)alter substrate ionic structure
3)exert stress on substrate bonds

Front 30

Enzyme Regulation

Back 30

1)synthesize & degrade enzyme (not efficient)
2)posy-translation phosphorylation (modify enzyme)
3)presence or absence of cofactor (such as Mg2+ ion)
4)protein allosteric actuator (important in mitosis)
5)PH of cellular compartment (changes charge on enzyme)
6)temperature (changes shape and motion of enzyme)(causes hydrogen bonds of a-helix and b-sheets to break)

Front 31

Michaelis-Menten Equation

Back 31

V = Vmax[s/s+km]

Front 32

Michaelis Constant

Back 32

km = s; V = Vmax/2
-if value of km is larger, binding affinity is lower
-if value of km is smaller, binding affinity is higher

Front 33

Stains

Back 33

stick to lipids, proteins, or carbohydrates

Front 34

Antibodies

Back 34

make certain things visible under UV light. antitubulin antibodies make tubulin visible with flurochromes

Front 35

Light Microscope

Back 35

Magnification: 10x - 1000x
Resolution: 0.2um
(visible, UV, confocal scanning laser microscope)

Front 36

TEM

Back 36

Magnification: 1000x - 500,000x
Resolution: 0.002um
-if electron goes through = white; if not = black
1)Fix (preserve) specimen using formaldehyde or gluteraldehyde
2)Wash (Buffer) to get rid of excess preservative
3)Dehydrate using increasing concentrations of alcohol or acetone
4)Embed in plastic
5)Harden & Trim excess plastic
6)Section using ultramicrotome w/ diamond knife
7)Stain with heavy metal
8)Put into TEM

Front 37

SEM

Back 37

1)Fix (preserve) specimen using formaldehyde or gluteraldehyde
2)Wash (Buffer) to get rid of excess preservative
3)Critical Point Dry (freeze dry) sublimation: gas to solid
4)Coat with heavy metal
5)Put in SEM

Front 38

Autoradiography

Back 38

1)Culture medium with radioactive monomer of what you are looking for
2)Fix
3)Wash
4)dehydrate
5)embed in plastic & trim
6)section
7)dip slides into radiation sensitive emulsion in dark room
8)place in dark box to develop until ready for use
-silver grains show up light on film to see if cell was making what you are looking for
-Protein: Leucine
-DNA: Thyamine
-RNA: Uracil

Front 39

Protein Biochemistry/Enzymology

Back 39

1)homogenize (in ice to prevent denaturation)
2)pour homogenate into 2 tubes
3)centrifuge to get pellet & supernatant

Front 40

Sucrose Gradient Centrifugation

Back 40

-centrifuge seperates by size
-in order to seperate components of smae size u need to seperate by density

Front 41

SDS-Polyacrylamide Gel Electrophoresis

Back 41

1)dissolve protein in SDS buffer (has a negative charge & coats protein with negative charge)
2)Heat protein sample to denature
3)Pour gel between glass plates
4)Gel Polymerizes from gel to liquid
5)Load sample and MW markers into reservoirs
6)Electrophoresis protein
7)observe MW (heavier at top lighter at bottom)

Front 42

Plasma Membrane Composition

Back 42

Lipid: 35-40%
Protein: 45-55%
Carbs: 2-10%

Front 43

Plasma Membrane Function

Back 43

-selective permeability
-transport in/out of the cell
-link cytoplasm to ECM
-Enzyme Linked / Receptor Linked

Front 44

Integral Proteins

Back 44

-extracullular domain (polar r-group)
-transmembrane domain (hydrophobic a-helix 12-14 AA)
-cytoplasmic domain (polar r-group)

Front 45

oligiosaccharide

Back 45

several sugars

Front 46

Blood Group Antigens

Back 46

-A, B, AB, O
-have same 5 sugars and membrane lipids & protein
-differ in terminal sugar
-AB can receive any blood, O only O (can't have foreign material)

Front 47

Fluorescence Recovery After Photobleaching

Back 47

1)Stain protein with antibody (red fluorochrome)
2)Wash away unbound antibody
3)select target area
4)"Zap" with a soft laser
5)Bleaches Flurochrome antibody from red to no color
6)observe with UV microscope
7)Recovery (do colored proteins move back into uncolored space)

Front 48

Allosteric Inhibitor

Back 48

changes the shape of an enzyme

Front 49

Negative Feedback

Back 49

end product of reaction goes to feedback site to stop production (auto regulation)

Front 50

Pellet Containing Nuclei & Unbroken cells

Back 50

800g for 10 min (gives postnuclear supernatant)

Front 51

Pellet containing mitochondria, lysosomes, & microbodies

Back 51

12,000g for 20 min (gives postmitochondrial supernatant)

Front 52

Pellet containing microsomes (small fragments of membranes)

Back 52

50,000g for 2 hrs (give postmicrosomal supernatant)

Front 53

Pellet containing ribosomes

Back 53

300,000g for 3 hrs (gives postribosomal supernatant)

Front 54

Sucrose Gradient Centrifugation

Back 54

sucrose density gradient with sample at 65,000 for 2 hrs
1)Lysosomes (1.12 g/mol)
2)Mitochondria (1.18 g/mol)
3)Microbodies (1.23 g/mol)

Front 55

Dalton

Back 55

mass of one hydrogen atom

Front 56

Use to find MW after SDS-PAGE

Back 56

Log graph of weight v. distance

Front 57

Most Abundant Phospholipids

Back 57

1)Phosphatidic Acid
2)Phosphatidyl-choline
3)Phosphotidyl-serine
-PC most abundant facing outward
-PS most abundant facoing inward

Front 58

Dynamic

Back 58

lateral movement of proteins and phospholipids in PM. changes shape of membrane (flip-flop takes a lot longer)

Front 59

N-Linked glycosylation

Back 59

takes place in Lumen of RER then goes to plasma membrane
(Asparagine)

Front 60

O-Linked glycosylation

Back 60

takes place in Golgi Apparatus
(Serine or Threonine)

Front 61

Non-ionic detergents

Back 61

solubilize membrane proteins without disrupting their structure

Front 62

Identifying Transmembrane Domains

Back 62

-adding trypsin to intact cell takes off part of protein in ECM
-adding trypsin to permeabilized cell takes off part of protein in cytoplasm
-SDS-PAGE allows us to see the effects of each piece of protein removed (does move down a lot in gel?)

Front 63

Spectrin

Back 63

creates a border & fences in some free moving integral proteins

Front 64

How can you tell if glucose transport is moving in membrane?

Back 64

-find antibody specific to that protein
-FRAP analysis -> lateral movement (restricted to apical surface of PM)

Front 65

Carrier Mediated

Back 65

channel has to change its shape

Front 66

influx

Back 66

into cell

Front 67

eflux

Back 67

out of cell

Front 68

Non-Mediated Channel

Back 68

does not have to change shape

Front 69

Active Transport

Back 69

ATP used to pump against gradient

Front 70

E1

Back 70

channel open to cytoplasm & closed to EC space

Front 71

E2

Back 71

channel open to EC Space & closed to cytoplasm

Front 72

Steps of Na+/K+ ATPase transport

Back 72

1)3 sodium ions enter channel and bind to binding sites
2)ATP is hydrolyzed (supplies 7kCal of energy) & phosphate is transfered to protein
3)Conformation changes from E1 to E2
4)Sodium leaves and Potassium enters the channel & attaches to binding sites
5)Phosphate is lost
6)Channel returns from E2 to E1
7)Potassium enters the cell
(3 Na+ out & 2 K+ in creates a -70mV charge inside the cell
Inside = 10mM Na; 100mM K
Outside = 100mM Na; 10mM K

Front 73

Cystic Fibrosis

Back 73

thick mucous coats lungs where bacteria grows which complicates breathing (also effects pancreas, seminiferous tubules, and fillopian tubes)

Front 74

Healthy Person's Lungs

Back 74

1)cAMP opens active site of PKA
2)Protein Kinase A puts phosphate on 4 serines which pulls the R-group away from the channel (requires 4 ATP)
3)ATP binds to Nucleotide Binding Domain 1 & 2 to move channel open laterally
4)Cl- moves through channel
5)H2O follows and dilutes mucous to get rid of it easier
6)Phosphatase removes phosphates and channel closes again

Front 75

-If channel doesn't open all the way?
-If channel doesn't open at all?

Back 75

-V-max is lowered
-problem with NBD 1 or 2 (no lateral opening)