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cell and molec bio > Bio Test 3 > Flashcards

Bio Test 3 Flashcards

1
Q

Southern Blot

A

DNA is usualy digested with restriction enzymes first. Then, DNA is transferred to a filter for hybridization. Electrophoresis is generally on agarose gel.

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2
Q

Northern blot

A

RNA is on the filter. Agarose gels, usually. Probe as for southern.

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3
Q

Western

A

Protein is on the filter. SDS Polyacrylamide gels. Probe is an antibody to the protein of interest

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4
Q

Probe

A

Labeled nucleic acid complementary to the sequence that we are looking for. Electrophoresis is usually on agarose gel.

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5
Q

Why do we need a blot

A

to see a particular part of the genome, or a particular RNA of protein.

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6
Q

Blotting involves…

A

transfer of the DNA to a nylon or nitrocellulose membrane.

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7
Q

Probing involves…

A

soaking the filter in a solution containing a labeled DNA that is complementary to the gene region that we want to observe

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8
Q

What are antibodies

A

glycoproteins produced by our B lymphocytes, they recognize foreign antigens and are crucial to the immune system

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9
Q

what do we produce antibodies against

A

bacteria, viruses, etc

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10
Q

cytoskeleton

A

cell shape and movement

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11
Q

ex of Organelles

A 
Nucleus 
mitochondria
Chloroplasts 
Peroxisomes
Secratory System
Endocytic system
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12
Q

Secratory system includes…

A

ER, Golgi, Transport vesicles, endosomes, lysosomes, plasma membrane

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13
Q

endocytic system includes…

A

lysosomes and endosomes

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14
Q

cytosol

A

contains many metabolic pathways. Protein synthesis

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15
Q

Nucleus

A

contains main genome; DNA and RNA synthesis

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16
Q

Endoplasmic Reticulum

A

synthesis of most lipids; synthesis of proteins for distribution to many organelles to another organelle

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17
Q

Lysosome

A

intracellular degradation

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18
Q

Golgi apparatus

A

modification, sorting, and packaging of proteins and lipids for either secretion or delivery to another organelle

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19
Q

endosome

A

sorting of endocytosed material

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20
Q

mitochondria

A

ATP synthesis by oxidative phosphorylation

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21
Q

Chloroplasts

A

ATP synthesis and carbon fixation by photosynthesis

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22
Q

peroxisomes

A

oxidation of toxic molecules

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23
Q

Proteins that need to go anywhere in the secratory or endocytic system are synthesized on what?

A

Membrane-bound ribosomes

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24
Q

nucleus structure

A

pore protein and lamins

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25
Q

nucleus proteins coming and going

A

importins and exportins

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26
Q

mechanisms for coming and going of proteins

A

importins, exportins and the GTP binding protein, RAN.

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27
Q

Nuclear envelope

A

two lipid bilayers contiguous with the ER

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28
Q

Nuclear lamina

A

fiborous network of proteins underneath membrane and reaching throughout

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29
Q

nuclear pores

A

complicated protein structures to let molecules in and out of the nucleus

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30
Q

Lamins

A

type of intermediate filamnt present in nucleus inside nuclear membrane

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31
Q

nucleoporins

A

proteins of the nuclear pore

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32
Q

karyopherins

A

importins and exportins for moving proteins and RNAs in and out of the nucleus

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33
Q

G-Proteins

A

Ran is an example of an important type of molecular “switch” involved in many cellular processes

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34
Q

what is the role of the nuclear envelope?

A

seperate the nucleus from the cytoplam

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35
Q

What two membranes does the nuclear envelope consist of?

A

nuclear pore complexes and nuclear lamina

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36
Q

the outer membrane is continuous with what system?

A

ER

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37
Q

the inner membrane includes proteins that bind to what?

A

Nuclear lamina

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38
Q

most molecules that go in and out need to go through what?

A

nuclear pore

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39
Q

How do larger molecules get in and out of the nucleus

A

they need to imported and exported

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40
Q

importins

A

bind the protein to be imported by means of the nuclear localization signal and then brings it to the nuclear pore and then through it.

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41
Q

exportins

A

bind to proteins to be exported from the nucleus using the nuclear export signal located in these proteins. (NLS)

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42
Q

RAN

A

example of a GTP binding protein that is involved in many cellular processes.
Ran binds to GTP and allows cargo to be released. escort the imp out to get another cargo to put it into the nucleus.

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43
Q

Signal recognition particle

A

the complex moves to the translocation channel, where translation of the protein occurs while it is being threaded across the membrane.

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44
Q

signal peptidase

A

remove the signal sequence

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45
Q

anterograde trasnport

A

forward in the ER to Golgi to vesicles to plasma membrane.

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46
Q

retrograde transport

A

movment of substance in the reverse of anterograde. Golgi back to ER

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47
Q

Coated vesicles

A

COP for vesicles going from ER to Golgi and back

Clatherine for going to plasma membrane, lysosome, secratory vesicles and in the reverse direction

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48
Q

gathering of proteins to be put into vesicles for transport

A 
Cargo receptor
cargo, with signal to recognize receptor
adaptin, specialized for particular receptors 
clatherine, coting vesicles
dynamin, to pinch the vesicle off
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49
Q

what releases the vesicle at the neck between the donor membrane and the vesicle

A

dynamin

50
Q

v-SNARE’s

A

for membrane fusion

51
Q

t-SNARE’s

A

interact with v-SNARE’s

52
Q

Rab proteins

A

small GTP-binding proteins, similar to the nucler Ran proteins. Give each vesicle type its own identity, marking it for where it should go

53
Q

Describe docking at the target membrane

A

Rab is bound by tethering proteins on the surface. Once there v-SNARE’s and t-SNARE’s can interact, forming coiled-coil protein complexes that bring the membrane into contact.

54
Q

membrane fusion

A

proteins and lipids in the vesicle become part of the target membrane. Soluable material inside the vesicle goes into the new compartment or the outside of the cell.

55
Q

what happens when vesicles arrive at the target membrane

A

vesicles actually move into the cell by means of motor proteins that walk along actin and microtuble filaments.
arrive and fuse
proteins recognize the correct membrane so fusion can be done correctly

56
Q

ER

A

addition of sugars to asparagine residues in proteins
formation of disulfide bonds
protein quality control, destruction of wrongly folded proteins

57
Q

what are the flat-looking membranous structures in the stack of membranes

A

cisternae

58
Q

trans golgi network

A

major branch point for determining ultimate destination: constitutive secretion regulated secretion, movement to lysosomes via late endosomes.

59
Q

Mannose-6-phosphate

A

a signal that the protein should go to the lysosome eventually

60
Q

constitutive secretion

A

for things like normal membrane proteins and lipids of this cell type. Replacements are being made for regular
membrane molecules.

61
Q

regulated secretion

A

Molecules are held in vesicles

until a signal causes them to move to the surface for release. Example: neurotransmitters

62
Q

Endosomal/lysosomal pathway

A

Enzymes like acid hydrolysases normally are found in the lysosome. They are sorted in the TGN to the lysosomal compartment.

63
Q

endocytic system

A

movement of materials into the cell shares some compartment with the secratory system.
Endosomes and Lysosomes

64
Q

Actin

A

the filament that forms all of these networks, branches, crosslinks.

65
Q

SRP

A

starts with a recognition particle. Docked at the ER with srp, so the protein can get to their destination.

66
Q

Endocytosis

A

use clatherin to make the little basket-like structures that form the vesicles.
Going INTO the cell
Step 1: endosome.

67
Q

Endosomes

A

the sorting compartments.

68
Q

early endosomes

A

just beneath PM

69
Q

late endosome

A

closer to the nucleus

70
Q

LDL receptor

A

take up cholesterol-containing particles from the blood.
If the receptor is not functioning normally cholesterol accumulates to very high levels in the bloodstream and forms deposits in the arteries, skin and tendons

71
Q

Receptor-mediated endocytosis, LDL example.

A

low-density lipoprotein.
receptors exist on the surface of some cells
Binding of LDL to receptor triggers formation of clathrin-coated vesicles, vesicles fuse with the endosome, the endosome matures to for lysosome, cholesterol is released into cytosol.

72
Q

Cystic Fibrosis

A

results from probles getting the CF protein to the cell membrane.

73
Q

Intermediate filaments

A

structural support

keratins, filamentous proteins of skin, hair, nails.

74
Q

microtubules

A

chromosomes movement and movement to vesicles and for structure and movement of cilia and flagellae.
-Hollow tubes of proteins that are comprised of alpha and beta tubulin dimers.

75
Q

actin filaments

A

most generally associated with cell movement, cytokinesis, shape changes.

76
Q

What does Coiled-coil mean

A

that they wrap around each other to form strong filaments.

77
Q

Dynamic instability of microtubules

A

GTP-bound form is added at the plus end
GTP is eventually hydrolyed
GDP-bound form is less stable

78
Q

Dynamic instability means what?

A

individual microtibles shrink very rapidly and then grow back

79
Q

How do you stabilize microtubules?

A

by anchoring them to capping proteins in the cell membrane.

80
Q

Actin polymerization

A

Forms thin filaments
Plus and minus end
they are NOT hollow the way microtubules are but they can form different types of networks.

81
Q

What are forms of actin filaments

A

linear
branched
networks
bundles

82
Q

where is cortical actin found

A

just beneath the plasma membrane

83
Q

here are stress fibers found

A

bundles of actin associated with cell movement

84
Q

what do actin bundles form?

A

they form the structure of “microvilli”

85
Q

where do networks usually occur?

A

just underneath the plasma membrane

86
Q

three types of motor proteins?

A

Myosins
Kinesins
Dyneins

87
Q

Myosins

A

movement along actin filaments in the plus direction

88
Q

Kinesins

A

movement along microtubules in the plus direction

89
Q

Dyneins

A

movement along microtubules in the minus direction

90
Q

Microtubules organizing centers

A

centrosome is the main one

91
Q

centrosomes

A

near nucleus
organizes microtubules
minus ends are anchored here by the gamma-tubulin complex
plus end go out into the cell

92
Q

Centrioles

A

resemble the MTOC’s at basal bodies.

when present, they exist in pairs and are comprised of tubulin

93
Q

cytoskeleton motor protins

A

“head” is the microtubule-binding portion that includes ATPase to provide energy
“Tail” is everything else: cargo binding, dimerazation, regulation of motor activity.

94
Q

Why are the tail ends different from each other in a motor protein?

A

they bind different cargo, different localization in the cell, and different regulation

95
Q

describe one ATPase cycle

A

ATP binding
hydrolysis
release of ADP and phosphate

96
Q

transport of microtubules in axons

A

plus end of microtubule is in the far end of the axon, minus end is in the cell body.

97
Q

Synaptic vesicles

A

proteins synthesized in cell body need to go all the way to the end of the axon! They use KINESINS for this purpose
anterograde …go toward plus end.

98
Q

What does ATP carry

A

phosphate in a high energy linkage

99
Q

what does NADH carry?

A

electrons and hydrogens for “reducing power”

100
Q

what does Acetyl co-A carry

A

acetyl groups

101
Q

Glycolosis in cytosol

A

glucose is converted to pyruvate.
we gain 2 ATP and 2 NADH per glucose. Pyruvate is formed and goes to the mit.
Pyruvate is oxidized to acetyl coA forming one NADH and releasing one CO2. Goes to TCA cycle.

102
Q

TCA cycle

A

Krebs cycle: acetyl coA from pyruvate is oxidized to CO2, generates one NADH at the beginning.
the reduced forms of NAD and FAD are formed (plus GTP)

103
Q

what is the flow of protons back into the matrix called?

A

ATPsynthase.

104
Q

what does ATPsynthase lead to

A

ATP production

105
Q

What does the transfer of electrons from NADH through electron transport chain lead to?

A

A Protein gradient across inner mit membrane

106
Q

Cristae

A

the folds in the inner membrane of the mitochondrial membrane. This is where electron transport happens. ATP synthase is also in this membrane.

107
Q

inner membrane space

A

protons are pumped to this region forming the gradient that is used for ATP production

108
Q

Pyruvate dehydrogenase complex

A

oxidizes pyruvate to acetyl coA and CO2, CO2 is released.
reaction produces NADH
acetyl coA is the molecule that enters the TCA cycle

109
Q

Fatty acid oxidation

A

lipids and fatty acids are broken down into two-carbon units and enter the TCA cycle as acetyl coA

110
Q

Uses carbon and energy from sugars to produce ATP. Liberates CO2 to the atmosphere from the carbon compound that it is using. Uses O2 as the final electron acceptor following oxidation of sugars.

A

Mitichondria

111
Q

light reactions

A

harvest energy from light to create ATP and NADPH by means of high energy electrons for reduction
-thylakoid membrane

112
Q

dark reactions

A

for capturing CO2 from the atmosphere to create the complex carbon compounds that we need to live
-occur in the stroma

113
Q

chlorophyll

A

light harvesting compound presents in reaction centers that absorbs light

114
Q

photosystem II

A

creates a proton gradient for formation of ATP by ATP synthase.

115
Q

b6f complex

A

this complex pumps protons, contributing to the proton gradient that eventually forms ATP through ATP synthase

116
Q

three phase of the calvin cycle

A

carbon fixation
reduction
regeneration of intermediates

117
Q

carbon fixation

A

CO2 is combined with a five-carbon bi-phosphorylated sugar called 1,5 ribulosebisphosphate, forming an unstable 6-carbon compound.
Enzyme is called “rubisco”

118
Q

reduction

A

Use NADPH and ATP to make glyceraldehyde 3 phosphate. this is used to make glucose in a series of steps that are not part of the calvin cycle

119
Q

Glyceraldehyde 3 phosphate

A

is a triose phosphate and is one of the intermediates in glycolysis
1 is produced for every three turns of the cycle

120
Q

regeneration

A

regenerate the 5 carbon compound ribulose bisphosphate that can accept another CO2.

cell and molec bio (3 decks)

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