Midterm 1 recap

Question 1

What is a snare?

Answer 1

family of membrane proteins responsible for selective fusion of vesicles with a target membrane

Question 2

What are transport vesicles?

Answer 2

membrane proteins that carries proteins form one intercellular compartment to another

Question 3

What is vesicular transport

Answer 3

movement of material between organelles via membrane-enclosed vesicles.

Question 4

What are clathrin?

Answer 4

protein that makes up a coat for transport vessicles that bud towards cystolic side of cell from plasma mebrane (inward endoycitic pathway) or golgi apparatus (outward exocytic pathway)

Question 5

What are Rab Proteins?

Answer 5

GTP binding proteins on surface of transport vesicles and organelles

Serves as molecular marker to ensure vesicles fuse with correct membranes

Question 6

What are tethering proteins?

Answer 6

filamentous transmembrane protein involved in docking of transport vesicles to target membranes

Question 7

Explain how transport vesicles are created from receptor-mediated endocytosis

Answer 7

Coat Assembly:
- cargo receptors bind to a molecule which then changes confirmation to also bind to adaptin proteins on cystolic side

Bud formation:
The adaptin protein allows for clathrin proteins to bind to it

Vessicle Formation:
Protein dynamin forms around neck of plasma membrane and through GTP hydrolyis, pinches it off

Uncoating
- clathrin proteins are removed and transport vesicle is able to fuse with membranes of other organelles

Question 8

Role of Adaptin

Answer 8

1. secures clathrin to vesicle
2. selects cargo molecules for transport via trapping the specific receptor proteins and forming a vesicle containing the receptor proteins and their bounded molecules

Question 9

Explain mechanics of Vesicle Docking

Answer 9

Rab and tethering proteins

The GTPases Rab proteins on the vesicles are binded to tethering proteins on the membrane of the organelle destination
(each specific vesicle and membrane have their own unique Rab and tethering protein combo)

Snares
V-snares on vesicle and T-snares on membrane interact to firmly dock vesicle in place.

Question 10

How do snares facilitate the fusing of vesicles to organelle membranes?

Answer 10

• snares wrap around each other and act like a winch, pulling the vesicle towards the membrane protein
• this allows for fusions because the lipid bilayers can get within 1.5 nm from eachother
• also, due to water being in between the vesicle and membranes, random fusion is higherly energetically unfavorable

Question 11

What is receptor-mediated endoycytosis

Answer 11

selective uptake of material in which macromolecule binds to a receptor in plasma mebrane and enters cell in clathrin-coated vesicles

Question 12

What is an endosome (function)

Answer 12

membrane-enclosed compartment through which material ingested by endocytosis passes on it ways to lysosomes

Question 13

Explain how cholesterol from bloodstream is taken up by cells

Answer 13

receptor-mediated endocytosis:
1. cholesterol in blood bind to proteins and from LDL (low-density lipoproteins)
2. LDL binds to LDL receptors (adaptin binds to these receptors on cytosolic side, clathrin binds to adaptin and dynamin hydrolyzes GTP to pinch off a clathrin-coated vesicle)
3. vesicle fuses with endosome
(endosome’s acidic pH separates LDL receptors from LDL)
4. LDL is transferred to lysosome while LDL receptors bud off in vesicles that fuse back to plasma membrane
5. lysosome breaks down LDL via hydrolytic enzymes and cholestrol is released into cytosol to synthesize new membranes

Question 14

Function of Cytosol

Answer 14

contains many methabolic pathways (protein synthesis and cytoskeleton

Question 15

Function of Nucleus

Answer 15

contains main genome, DNA + RNA synthesis

Question 16

Function of mitochondria

Answer 16

ATP synthesis by oxidative phosphorylation

Question 17

Function of Golgi Apparatus

Answer 17

modification, sorting and packaging of lipids for secretion or delivery to organelles such as lysosomes

Question 18

Function of endoplasmic reticulum
(smooth vs rough)

Answer 18

synthesis of lipids (smooth)
synthesis of proteins for distribution to many organelles and to plasma membrane (ER)

Question 19

function of endosome

Answer 19

sorting of endocytosed material

Question 20

function of lysosome

Answer 20

intracellular degradation
(involved in phagoytosis, pinocytosis, and autophagy)

Question 21

function of peroxisome

Answer 21

oxidative breakdown of toxic molecules

Question 22

Desribe the Na+ K+ pump

Answer 22

transfers Na+ against electrochemical gradient (towards high concentration and positive polarity outside of cell)
transfers K+ against chemical gradient (towards high concentration and negative polarity inside of cell)
- brings three Na+ and 2 k+
- uses 30% of totoal ATP consumption

Question 23

What happens during refractory period of nerve conduction

Answer 23

voltage gated Na+ channels
- changes into an inactive conformation (b/c energetically favorable) where Na+ cannot enter or leave cell membrane

K+ leak channels
- becomes depolarized and opens to allow potassium ions to leave the cell membrane thereby bringing cell potential to negative intracellularly

Question 24

What occurs when an action potential reaches presynaptic nerve terminal

Answer 24

1. Ca2+ ion channels on presynaptic membrane depolarized and changes into open conformation (influx of Ca2+ ions)
2. synaptic vesicles are triggered and results in being exocytosed out of presynaptic membrane into synaptic cleft
3. neurotransmitters from synaptic vesicles bind to neurotransmiter receptors
4. transmitter-gated ion channels then undergo conformation change that allows for ion transport (acetylcholine –> excitatory –> Na+ into cell) (norepinepherine –> inhibitory –> K+ out cell)

Question 25

Why are both electrical and chemical signals used during neuronal transmission

Answer 25

electrical signals help propagate nerve impulses from dendrite to axons quickly (action potential moves and is amplified by voltage gated Na+ channels)

electrical signals CANNOT pass synaptic cleft therefore must be converted to chemcial signals (neurotransmitters)

Question 26

what are gamma (y) tubulins?

Answer 26

gamma tubulin ring complexes make up nucleating sites on centrosome matrix

–> where microtubules grow (polymerizes) from alpha to beta (minus to positve side)

Question 27

Compare and contrast microtubules and actin

Answer 27

microtubules
- 13 parallel protofilaments made from tubulin dimers (alpha pos, beta minus)
- grows at both ends but more rapidly on alpha end (dynamic instability powered by GTP)

actin
- grows faster at plus end than minus end
- when there is intermediate concentration of free actin monomers, tread miling occurs (polymerization at plus end occurs at same rate as depolymerization at minus end
- uses ATP for polymerization

Question 28

Describe dynamic instability

Answer 28

controled by GTP hydrolysis

Growing:
rate of GTP hydrolysis is slower than rate of tubulin dimer polymerization

Shrinking
rate of GTP hydrolysis is faster
- protofilaments contianing GDP tubulin peel away + GDP tubulin is released into cytosol

Question 29

How is skeletal muscle contraction triggered and controlled

Answer 29

Trigger:
- T-tubules connect plasma membrane to sarcoplasmic reticulum (specialized ER
- When T-Tubule polarizes –> voltage gated Ca2+ channels open up
- causes conformation change in Ca2+ release channels on Sarcoplasmic reitculum
- Ca2+ released into the cytosol to cause myofibril contraction

Control
troponin: protein complex that includes Ca2+ sensitive protein
initally: tropomyosin binded to actin and troponin complex keeps it there
influx of Ca2+: calcium ions bind to troponin complex –> conformatin chanage on both troponin and tropmyosin
Myosin heads can now bind to actin