Cell Bio_Test2

Front 1

What are endosomes derived from?

Back 1

plasma membrane

Front 2

What's the difference between endosomes and phagosomes?

Back 2

endosomes take in smaller molecules than phagosomes

Front 3

What do endosomes do?

Back 3

act as sorting stations to decide where proteins and molecules go

Front 4

What do lysosomes do? What's their pH?

Back 4

degrade molecules into monomers; 4-5

Front 5

What is the largest set of membranes found in the cell?

Back 5

ER

Front 6

What does the smooth ER do?

Back 6

lipid synthesis, vitamins, detox enzymes

Front 7

What can the rough ER add to the folded protein?

Back 7

disulfide bonds and sugar moieties

Front 8

What are the 3 distinct regions of the golgi? What makes them distinct?

Back 8

cis, trans, medial; different modification enzymes that add different carbs to protein

Front 9

What magnifies the object when using a normal bright-field light microscope?

Back 9

the light and the lens

Front 10

What is the best resolution of a normal bright field light microscope?

Back 10

.2 micrometers

Front 11

What does a phase-contrast microscope involve?

Back 11

the different thicknesses and the refractive index of the cells

Front 12

What is a refractive index?

Back 12

how much the light bends when passing through an object

Front 13

How does thick/thinness relate to bending of light?

Back 13

the thicker the object, the more bending of light

Front 14

What is a phase-contrast microscope good for visualizing? What is it not good for visualizing?

Back 14

eukayotic cells; thick objects

Front 15

What is a differential interference contrast (DIC) microscope good for visualizing? What is it not good for visualizing?

Back 15

outside of cells; inside of cells

Front 16

What does a differential interference contrast (DIC) microscope involve?

Back 16

bends light in order to cast a shadow making the cell appear 3D

Front 17

When is it good to use a fluorescent microscope?

Back 17

when making recombinant proteins

Front 18

Describe the process of making a GFP gene.

Back 18

1. Take geneX and recombine with GFP gene
2. put recombinant in plasmid and put in cell
3. cell creates proteins
4. proteins localize and fluoresce

Front 19

Which fluorescent dye binds to Ca? When bound, what color does it fluoresce?

Back 19

Fura-2; yellow

Front 20

What can be used to separate out fluorescent cells form non fluorescent cells?

Back 20

FACS- fluorescence activated cell sorter

Front 21

What are 3 processes cells can be used to study?

Back 21

differentiation, protein function, transport

Front 22

Where are promotors found? How long are they?

Back 22

less than 200 bp upstream from start site; 10bp

Front 23

Where are enhancers found? How long are they?

Back 23

200bp-50,000bp upstream and sometimes in the intron; 10bp--can be repeated

Front 24

Where are repressors found? How long are they?

Back 24

anywhere; 10 bp

Front 25

What are the two common techniques to identify transcription factors?

Back 25

DNase 1 fingerprinting
EMSA

Front 26

Describe the process of DNase 1 fingerprinting?

Back 26

1. radiolabel upstream of protein binding sequence
2. Add DNase 1
3. run on gel
4. tf leaves gap on the footprint

Front 27

Describe EMSA?

Back 27

1. radiolabel a piece of DNA at a certain length w/ known weight
2. add tf of known weight to a different piece of DNA
3. run on gel
4. bands with tf are shifted upward
5. tells what the tf is

Front 28

Give 4 examples of tf regulation.

Back 28

1. NFAT and AP1 work with each other to transcribe genes
2. homodimers vs heterodimers
3. have to have HNF1 and HNF3 to make TTR gene in liver

Front 29

What promotor does NFAT and AP1 bind to?

Back 29

IL-2 promotor

Front 30

What is the purpose of miRNA?

Back 30

repress translation of specific mRNAs; decreased production of protein

Front 31

What is the purpose of siRNA?

Back 31

cause mRNA degredation

Front 32

What transcribes miRNAs?

Back 32

RNA Poly II

Front 33

What processes pre-miRNA into miRNA?

Back 33

dicer

Front 34

What is the structure of an miRNA transcript?

Back 34

hairpin

Front 35

How does miRNA prevent translation of mRNA?

Back 35

miRNA-Risc complex base pairs to the mRNA but not perfectly, risc remains bound to the mRNA and prevents initiation

Front 36

What are the 3 types of lipids in a biomembrane?

Back 36

phosphoglyceride, sphingolipid, steroid

Front 37

What is a plasmologen and where is it found?

Back 37

phosphoglyceride with ether linkage rather than ester linkage to the head group; in brain and heart

Front 38

How long are fatty acid tails?

Back 38

16-18 carbons

Front 39

What are sphingolipids?

Back 39

phosphopholipids with amide linkage instead of an ester linkage and a sugar head

Front 40

What is a steroid? what does it help with?

Back 40

4-ringed hydrocarbon; altering membrane fluidity

Front 41

What thickens membranes?

Back 41

sphingolipids and cholesterol and both

Front 42

What is the normal membrane thickness?

Back 42

3.5-4nm

Front 43

If you want a bendable membrane which phosphoglyceride should it be made of? Which organelle is made up of majority of this?

Back 43

PE; plasma membrane, outer mitochondrial membrane

Front 44

If you want a stiff membrane which phosphoglyceride should it be made of? Which organelle is made up of majority of this?

Back 44

PC; mitochondrial out membrane; ER membrane

Front 45

What do phospholipases do?

Back 45

cleaves phopholipids at head group

Front 46

What are the 3 categories of membrane proteins?

Back 46

integral; lipid bound; peripheral

Front 47

What is the structure of an integral protein?

Back 47

alpha helix 3.5-4 nm; 20-25 aa's; with a cluster of hydrophilic aa's anchored to the polar heads of cytoplasmic side

Front 48

What is a G-protein coupled cell surface receptors?

Back 48

7 membrane-spanning helices wrapping back and forth; mostly hydrophobic except inside pore

Front 49

Describe the structure of aquaporins.

Back 49

composed of alpha helixes that span the membrane and half helixes inside that partially span the membrane and are made of polar aa's

Front 50

What is a less common structure of a porin?

Back 50

multiple beta strands that form a barrel

Front 51

What is the point of photobleaching?

Back 51

to see how fluid a membrane is; more fluid membranes will recover fluorescence faster

Front 52

Describe the process of photobleaching.

Back 52

1. label a protein with GFP
2. bleach the area so flourescence goes away
3. monitor how long it takes for fluoescence to come back

Front 53

Which proteins have limited movement in the lipid bilayer?

Back 53

those anchored to the cytoskeleton

Front 54

Describe a n-terminal acyl anchor. On what side of the bilayer is it found? what is it always attached to? what is it's structure?

Back 54

cytoplasm; glycine attached to membrane; single saturated fatty acid (14-16 carbons)

Front 55

Describe a prenyl anchor. On what side of the bilayer is it found? what is it always attached to? what is it's structure?

Back 55

cytoplasm; cysteine; 3-5 5C isoprene units

Front 56

Which lipid anchored protein can have double anchors?

Back 56

prenyl anchor

Front 57

Describe a GPI anchor. On what side of the bilayer is it found? what is it always attached to? what is it's structure?

Back 57

exterior; fatty acyl tail with phosphotidyl inositol head; series of proteoglycan sugars

Front 58

What is the structure of a glycoprotein?

Back 58

has carbs attached to ser, thre, asparagine oriented out to the exoplasm

Front 59

What distinguishes blood antigens (A,B,O)?

Back 59

terminal sugar group; A has galactosamine; B has galactose; O has none

Front 60

What is K_ow? How do you determine it?

Back 60

octenol water portition coefficient; how lipophilic a molecule is; put octenol and wat in tube and molecule--number of molecules attracted to octenol over # attracted to water

Front 61

What kind of transporters transport glucose?

Back 61

GLUTS uniporters and aquaporins

Front 62

Which GLUT has the highest km for glucose? lowest?

Back 62

GLUT 2; GLUT3

Front 63

What is the structure of GLUT?

Back 63

12 membrane spanning alpha helixes

Front 64

Where are the different GLUTs found?

Back 64

GLUT1: blood cells
GLUT2: liver cells
GLUT3: neurons

Front 65

Describe P class pumps.

Back 65

use ATP to phosphorylate the proteins causing a conformational change

Front 66

Describe V class pumps.

Back 66

hydrolyzes ATP to gain energy for transporting hydrogens

Front 67

Describe F class pumps.

Back 67

hydrolyzes ATP to make ATP for transporting hydrogen across membrane

Front 68

Describe ABC superfamily pump.

Back 68

hydrolyzes 2 ATP for energy to move across 1 large molecule

Front 69

What are the concentrations of potassium inside and outside the cell?

Back 69

inside: 140
outside: 4

Front 70

What are the concentrations of sodium inside and outside the cell?

Back 70

inside:12
outside: 145

Front 71

What are the concentrations of calcium inside and outside the cell?

Back 71

inside:.0002
outside:1.8

Front 72

What are the concentrations of chloride inside and outside the cell?

Back 72

inside:4
outside:116

Front 73

What are 2 examples of p class pumps?

Back 73

Calcium ATPase and Na/K ATPase

Front 74

Where is calcium stored? Where are calcium ATPases found?

Back 74

mitochondria and ER; in muscle cells on the sarcoplasmic reticulum of the ER

Front 75

Where does the calcium binding site face while ATPase is in E1? E2?

Back 75

E1: cytosol
E2: SR lumen

Front 76

Describe the process of calcium transportation across the sarcoplasmic membrane using calcium ATPase

Back 76

1. calcium in cytosol binds to binding sites on the E1 ATPase
2. ATP binds to binding site
3. ATP phosphate phosphorylates aspartate on pump
4. charged aa's close to calcium move away from Ca creating low affinity
5. ATPase changes to E2
6. releases Ca
7. pump dephosphrylates and goes back to E1

Front 77

Describe the process of sodium and potassium transportation across the cell membrane using Na/K ATPase

Back 77

1. E1 has binding sites inside the cell w/ high affinity for Na
2. 3 Na binds to site
3. ATP binds to site and phosphrylates aspartate
4. conformational change to E2 with K binding sites outside cell
5. release Na outside cell
6. 2 K bind to site
7. dephosphorylates and goes back to E2--> releases K

Front 78

What is the purpose of v class pumps?

Back 78

acidifies intracellular organelles like lumen in stomach

Front 79

What are the 2 domains in a ABC family pump?

Back 79

transmembrane--transport
cytosolic--hydrolyzes ATP

Front 80

A defect in which ABC pump causes cystic fibrosis?

Back 80

CFTR

Front 81

Are potassium channels gated or nongated? sodium channels?

Back 81

nongated; gated

Front 82

What is the charge differential of a cell?

Back 82

-60 mV; slightly negative inside

Front 83

Describe the structure of a potassium channel in bacteria.

Back 83

made of 4 subunits with a vestibule filled with water and ions in the middle; there is a specific amino acid sequence: gly-tyr-gly on selectivity filter
Na is smaller than K and doesn't fit as well

Front 84

Describe the action of a Na glucose symporter.

Back 84

symporter is in outward conformation and moves 2Na+ down concentration gradient into cell and l glucose up concentration gradient into cell

Front 85

Where is the ER signal sequence located on a polypeptide? Describe its structure.

Back 85

n terminus; 16-30aas with a hydrophobic core led by 3 charged aa's

Front 86

What is the signal recognition particle called in mammals?

Back 86

p54

Front 87

What does an SRP bind to?

Back 87

hydrophobic groove of SRP binds to hydrophobic core sequence of ER signal sequence and the large ribosomal subunit

Front 88

What is the translocon of the ER?

Back 88

Sec61

Front 89

What is the orientation of the n terminus and c terminus in type 1, 2, 3 integral membrane proteins inserted into the ER?

Back 89

type 1- n is in lumen, c in cytosol
type 2- n is in cytosol, c in lumen
type 3- n is lumen, c in cytosol

Front 90

What is the orientation of the n terminus and c terminus in type 4 A and B integral membrane proteins inserted into the ER?

Back 90

A- n in cytosol
B- n in lumen

Front 91

What are the 4 main modifications that proteins undergo in the er?

Back 91

glycosylation
disulfide bond formation
quaternary structure
proteolytic cleavage

Front 92

During glycosylation in the ER, O linked oligosaccharides are added to which amino acids? How many sugars are attached?

Back 92

serine, threonine; 1-4; less common

Front 93

During glycosylation in the ER, N linked oligosaccharides are added to which amino acids? How many sugars are attached?

Back 93

asparagine; large branching; more common

Front 94

What forms the disulfide bonds in the polypeptide in the ER?

Back 94

PDI

Front 95

Which organelle targeting sequence is located in the c terminus?

Back 95

peroxisome

Front 96

Describe the mitochondria targeting sequence.

Back 96

20-50 aas that forms amphipathic alpha helix--one side positive and one hydrophobic

Front 97

What keeps the precursor protein targeted for the mitochondria from folding?

Back 97

Hsc70

Front 98

What is the mitochondria outer membrane translocon called? inner membrane?

Back 98

TOM 40; TIM 20/17

Front 99

What is the receptor protein on the mitochondria called?

Back 99

TOM 20/22

Front 100

Decribe the structure of proteins targeted for the inner mitochondrial membrane via path a. path b? path c?

Back 100

A- STS in middle
B- Oxa-1 targeting sequences
C- mitochondrial targeting sequences within protein

Front 101

What is the peroxisome targeting sequence? Describe its structure.

Back 101

PTS1; ser-lys-leu at the end

Front 102

What is the nucleus targeting sequence? Describe its structure.

Back 102

NLS; 7 basic aas at end primarily lysine

Front 103

What is the movement of COP1? COP2? Clarthrin?

Back 103

COPI- cis golgi to ER
COPII- ER to cis golgi
clatherin- trans golgi to endosomes or plasma membrane to endosomes

Front 104

What kind of sorting signal does COPII have? What is its GTP binding protein?

Back 104

diacidic (asp-x-glut); Sar1

Front 105

Describe COPII assembly,

Back 105

GDP Sar1 binds to Sec 12 on ER membrane--> replaces GDP with GTP--> tail embeds in membrane; Sar1 brings coat proteins Sec23/24 ; diacidic signal on Sec24 binds to cargo

Front 106

What kind of sorting signal does COPI have?

Back 106

KDEL;