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Biol 413 > chapter 9,11, 12, 13 > Flashcards

chapter 9,11, 12, 13 Flashcards

1
Q

how are antibodies used to visualize specific proteins within cells and tissues

A
  • primary antibody binds to target protein (antigen A); secondary antibody (marker-coupled) recognizes primary antibody
  • immunofluorescence; immunohistochemistry; western blotting

allows us to amplify signal because proteins can be very small. Multiple secondary antibodies can recognize a primary antibody to amplify signal

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2
Q

fluorescent microscope

A

LED light source
1. filters light before it reaches specimen
2. filters light obtained from the specimen and passes only wavelengths emitted when dye fluoresces

fluorescence- a physical property of an object absorbing light at one wavelength and then reemitting it at another

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3
Q

light microscope

A
  • uses optical diffraction
  • can resolve details 0.2 um apart
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4
Q

fluorescent vs light microscope sample prep

A

fluorescent: fixation, permeabilization, and specific fluorescent labeling to visualize target proteins
light: minimal preparation; can use live samples

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5
Q

advantages of fluorescent and confocal microscope

A

fluorescent: high specificity; mutliple labeling; dynamic (live cell) imaging
confocal: excludes out-of-focus light; laser light source; create 3D images

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6
Q

bright-field microscope
dark-field microscopy
phase-contract microscope

A

bright-field: light passing through a cell in culture forms the image directly
dark field: exploits the fact that light rays can be scattered in all directions by small objects in their path
phase-contrast: increase phase differences so that the waves are more nearly out of phase

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7
Q

how does electron microscope work?

A
  • can visualize atoms
  • uses a beam of electrons instead of visible light to illuminate a specimen, allowing for much higher resolution imaging than light microscopes.
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8
Q

superresolution light microscopy methods

A
  1. SIM
  2. STED
  3. PALM/STORM
  4. TIRF
  5. light sheet microscopy
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9
Q

single molecule localization microscopy

A

to determine the precise localization of specific molecules
* stimulated emission depletion microscopy
* PALM;STORM

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10
Q

TIRF

A
  • total internal reflection fluoresence
  • useful to image single molecules located near cell’s surface
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11
Q

light sheet microscopy

A
  • another form of confocal
  • lazer comes at an angle and sends out thin sheet of light
  • useful to image large tissue structures
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12
Q

TEM

A
  • reads passage of e- through the sample
  • used to create electron-microscope topograms
  • gives narrow image
  • Provides high-resolution images of internal structures (up to atomic resolution).
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13
Q

SEM

A
  • to obtain images of surfaces
  • for when don’t want to section things
  • detects e- scattered/emitted from specimen’s surface
  • has greater depth of field than TEM
  • it is usually smaller, cheaper, and simpler
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14
Q

what does EM tomography do?

A
  • to study larger structures with same resolution as SEM
  • specimen tilted to maximum of 60° to allow imagingn form multiple angles and give 3D reconstruction
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15
Q

TEM vs SEM specimen prep

A

TEM- requires thin sectioning, fixation and staining to visualize internal structures
-SEM- conductive coatings and surface cleaning

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16
Q

TEM sample prep

A

glutaraldehyde- fixative that cross-links proteins
osmium tetroxide- binds and stabilizes lipid bilayers and proteins
uranium and lead- staining tissue to visualize specific cell components

tissue stained with electron-dense materials, which adhere to the cells but dont target a specific protein

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17
Q

cryo-EM

A
  • specimen is rapidly frozen and imaged of all orientations without further processings
  • can determine structure of macromoecules without need to crystalize
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18
Q

rank ease of passage of molecules through the membrane

A
  1. hydrophobic molecules (gases, steroid hormones)
  2. small uncharged polar molecules (H2O, urea, glycerol, NH3)
  3. large uncharged polar molecules (glucose, sucrose)
  4. ions
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19
Q

channel vs transporter

A

channel- allow specific solutes to pass; faster transport rate; weaker binding to affinity to solutes; passive only
transporter- bind to solute and undergo conformational changes; may be passive or active (pumps)

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20
Q

Sarcoplasmic reticulum

A

type of ER found in muscle cells

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21
Q

active transport molecules

A

coupled transporter- using favorable gradient to drive unfavorable gradient
ATP-driven pump- ATP hydrolysis to power transport of something against its gradient
light-driven pump- light or redox energy to power transport against gradient (in bacteria, mitochondria, chloroplast)

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22
Q

active or passive?
uniport
symport
antiport

A

both
uniport- moving one solute in either direction
symport- moving 2 solutes in same direction (coupled)
antiport- moving 2 solutes in different direction (exchange) (coupled)

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23
Q

Vmax and Km

A

Vmax- rate at which transporter flips between conformational states
Km- affinitity to solute

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24
Q

gating mechanisms for ion channels

A
  • volatage-gated
  • ligand-gated- extracellular ligand
  • ligand gated- intracellular ligand
  • mechanically gated
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25
Q

Why do some molecules require energy for transport across a membrane, while other do not?

A

Molecules that move against their concentration gradient require energy for transport beause it is less favorable

26
Q

How is an action potential is initiated and terminated at a nerve terminus?

A

Initiated: causes voltage-gated calcium channels to open, allowing calcium ions to influx and trigger the release of neurotransmitters from synaptic vesicles
terminated:by the inactivation of sodium channels and the opening of potassium channels, which repolarizes

27
Q
  • Identify the primary ions and channels involved in each phase of an action potential
A
28
Q

Define the role of inactivation in the action potential. What happens if channels do not inactivate?

A

Inactivation ensures that once an action potential has been initiated, the neuron cannot be continuously depolarized by the influx of Na⁺.

sustained influx of sodium ions, causing prolonged depolarization of the neuron. This could prevent the membrane potential from returning to its resting state.

29
Q

saltatory conduction

A

action potential propagates along myelinated axon jumping from node to node (just from one node of ranvier to another)

30
Q

schwann cells vs oligodendrocytes

A

schwan cells- myelinated axons in PNS
oligodendrocytes- myelinated axons in brain

31
Q

how can an action potential spread along distances?

A

by depolarizing neighboring regions of the membrane

32
Q

what controls direction of action potential propagation?

A

refractory period (Na channels are innactivated, so action potential is pushed to where they are closed)

33
Q

how can some molecules be at equilibrium, across a membrane but not be the same concentration on both sides?

A

electrochemical gradient

34
Q

nucleolus function

A

rRNA transcription and ribosome assembly

35
Q

stress granules functions

A
  • temporary storage, particularly of translation-related components
  • formed in response to specific stress; contain mRNA
36
Q

p-granules functions

A

RNA metabolism and inheritance

37
Q

postsynaptic density function

A

organization of macromolecules in dendrites needed for neuronal transmission

38
Q

difference between a membrane bound organelle and a biomolecular condensate

A

condensates- membraneless organelles; formed from multiple weak interactions between proteins and macromolecules; subcellular organizations where proteins/nucleic acids are assembled into a functional unit; serve as biochemical factories that can form and dissolve PRN

39
Q

Explain liquid-liquid phase separation

A

property of biomolecular condensate
remains liquid but does not dissolve in the surrounding cytosol

40
Q

describe how the topology of intracellular compartments has evolved

A
41
Q

rough vs smooth ER functions

A

rough- translation of ER-destined proteins occurs simultaneously with insertion into ER
smooth- sites for budding and fusing of transport vesicles

42
Q

describe the mechanism that inserts proteins in the endoplasmic reticulum, for both soluble and
transmembrane proteins, naming the key components

A
43
Q

what 2 kinds of proteins are transferred from cytosol to ER?

A

un1. soluble proteins: transferred completly to the Er lumen; destined for secretion out of cell or lumen of another organelle (not mitochondrion or plastid)
2. transmembrane: partly dislocated into ER, embedded in membrane; destined to reside in ER or membrane of another organelle or plasma membrane

both initally directed to ER by ER signal sequence

44
Q

ER signal sequence vs ER retention sequence

A

signal: N-terminal stretch of hydrophobic amino acids
retention: C-terminus (KDEL amino acids)

45
Q

Explain how ER-designated proteins are recognized and transported

A
46
Q

Describe the types of modifications proteins undergo in the ER and how this would affect their function

A

formation of disulfide bonds- stabilize protein structure, only for proteins that are going to be secreted or
have extracellular facing domain
* glycosylation - for proteins that face the extracellular side to provide the carbohydrate layer; aids with folding of proteins such as in case of calnexin

47
Q

Explain the molecular basis for cystic fibrosis

A

mutation in chloride transporter channel causes slight misfolding, which causes protein retention in the ER and degradation. Otherwise, the protein could be funcitonal if reached the membrane

disease is because channel cant fold it property

48
Q

Compare and contrast the transport to mitochondria and chloroplast

A

mitochondria primarily relying on an electrochemical proton gradient across their inner membrane while chloroplasts utilize ATP and GTP hydrolysis for import into their stroma and thylakoid lumen respectively

49
Q

Name the key proteins involved in mediating mitochondrial transport

ADD MORE

A

HSP70- cytosolic chaperone that prevents aggregation and incorrect folding in cytosol (coats to make sure it is still unfolded)
Mia40- oxidizes cysteines and prevents protein from sliding back through TOm and promotes S-S bond formation

50
Q

Name different compartments of mitochondria and chloroplasts and describe how proteins can be transported into each of the compartments

A
51
Q

Describe the nuclear pore

A
  • “gates” through which membranes of the nucleus that allow movement of molecules in both directions
  • small molecules can freely diffuse through nuclear pore but large molecules like proteins and RNA cannot pass without appropriate sorting signal/modificaitons
52
Q

explain what are signal sequences and their function

A
  • needed to pass through nuclear pore
  • short stretch of lysines/arganinines (positive charges)
53
Q

Diagram the Ran GTP/GDP cycle

A
54
Q

compare nuclear import and export, how are they similar

A

Ran GTP increases affinity to cargo when export
changing the concentrations changes the direction of transport

55
Q

Compare and contrast the different transport systems between ER, mitochondria, chloroplast and nucleusx

A
56
Q

List the different secretory pathways and give example of secretory cells

A

COP2 coated vescicles: package and move collagen fibers = make long vesicles (ER –> golgi)
COP1: golgi –> ER
clathrin: princh from plasma membrane

57
Q

Diagram protein movement in the Golgi

A
  • Cis –> trans
  • proteins travel through cisternae by vesicular transportor by golgi cisternae themselves which migrate thourhg staacks
  • forward pathway: ER to golgi
58
Q

Explain the difference between phagocytosis and pinocytosis

A

phagocytosis: cellular eating; occurs in specialized cells that digest large molecules
pinocytosis: ingestion of fluid and small molecules; all eukaryotic cells all of the time

59
Q

Explain receptor-mediated endocytosis, for instance of cholesterol

A

phosphorylation to turn on/off transport signals
binding to anchoring proteins that localize compartments
1. cell bound to SREBP when dont need cholesterol. WHen found in environment because high cholesterol.
2. packaged into vescile and sent to golgi
3. released transcription regulatory protein into cytoplasm
4. goes into nucleus and makes cholesterol biosynthesis enzymes

60
Q

Explain the difference between endosomes, late endosomes, and lysosomes

A

endosomes- large network of membrane tubes and vesicles that sort molecules
early endosomes- just beneath plasma membrane; pH 7
late endosomes- closer to the nucleus; lower pH; involved in final stages of sorting and processing

lysosomes- contain hydrolytic enzymes that digest macromolecules; lumen is acidic for enzymes

61
Q

autophagy vs mitophagy

A

autophagy- digestion of organelles by cell itself (signal: mTOR complex)
mitophagy- selective destruction of mitochondria (PINK1 and parking promote ubiquinations)

Biol 413 (4 decks)

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