BIO 211 Lecture Notes - Lecture 1: Phagocytosis, Carbohydrate, Mitophagy

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fuchsiacoyote139

30 May 2018

School

Drexel University

Department

Bioscience & Biotechnology

Course

BIO 211

Professor

Dr.Stanford

For unlimited access to Class Notes, a Class+ subscription is required.

Prior to Week 1 Class 1 – pp. 695-710. Can skip sections on “Phosphoinositides mark

organelles and membrane domains,” “Not all transport vesicles are spherical.”

Know

• Which compartments vesicles can move between in a eukaryotic cell

o Er, golgi, late endosome, lysosome, early endosome, recycling endosome,

secretory vesicles

• The types of coat proteins and what type of transport they are used for (i.e., COPII coated

vesicles are typically trafficked from the ER to the Golgi)

o Clathrin coated

▪ Transport from plasma membrane and between endosomal and golgi

compartment

o COP-I coated

▪ Bud from golgi compartments

o COP-II coated

▪ Bud from ER compartments to golgi

• The components that make up coated vesicles

o Cargo – membrane components and soluble luminal molecules carried by

transport vesicles

o Cargo receptors

▪ Transmembrane receptors that capture soluble cargo molecules inside

vesicle

o Coat proteins

▪ Drive pathway of vesicles

o Adaptor proteins

▪ Form a discrete inner layer of coat between clathrin cage and membrane

▪ Bind clathrin coat to membrane and trap transmembrane proteins

▪ Basically package selected transmembrane proteins and their

corresponding proteins into clathrin coated transport vesicles

o Coat-recruitment GTPases

• What dynamin is, and what role it plays in cells

o Soluble cytoplasmic protein, at the neck of each bud

o Has a PI(4,5) and P2 binding domain

▪ Tethers protein to membrane

o And GTPase domain

▪ Regulates rate at which vesicles pinch off from the membrane

• The role of coat-recruitment GTPases

o Control assembly of clathrin coasts on endosomes and COPI and COPII coats on

Golgi and ER membranes

• What NSF is, and what role it plays in cells

o Catalyzes disassembly of SNAREs

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o Hexameric ATPase

o Uses energy of ATP hydrolysis to unravel interactions between SNAREs

Understand

• The basic goals and principles of intracellular vesicular traffic

o To move molecules for use in biosynthetic pathways

• What the default pathway is for a protein that is initially folded in the ER, but has no

other signal sequences

o Secretory pathway to end up at plasma membrane

• The functions of coat proteins

o to direct vesicles to the appropriate destination

o inner layer – concentrates specific membrane proteins in a specialized patch to

bring about a vesicle membrane

o outer layer – assembles into basketlike lattice that deforms patch to shape the

vesicle

• How coated vesicles form

o Bud off from specialized coated regions of membranes

o Clathrin

▪ Each subunit has 3 large and 3 small polypeptide chains that form

triskelion

▪ Triskelion assemble into basketlike framework to make coated pits (buds)

on cytosolic side of membranes

▪ BAR domains bind and impose their shape on membrane via electrostatic

interactions with lipid head groups

• That vesicles are uncoated before they fuse with their target membrane

• How coat assembly is controlled, including how coat-recruitment GTPases are regulated

o Active – GTP; inactive – GDP

o Guanine nucleotide exchange factors activate proteins (GDP→GTP)

o GTPase activating proteins inactivate proteins (GTP→GDP)

o Types of GTPases

▪ ARF - Control assembly of COPI and clathrin coats at Golgi

▪ Sar1 - Control assembly of COPII at ER

• What tethering is and how Rab proteins are involved in tethering

o Tethering is attachment to a membrane of organelle or transport vesicle – Rab5

o Rab proteins and Rab effectors direct vesicle to specific spots on the correct target

membrane

• The role SNAREs play in membrane fusion and why they need to be pried apart after

fusion

o SNARE proteins and regulators mediate the fusion of lipid bilayers

o V-snares → vesicle membranes

▪ Single polypeptide

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o T-snares → target membranes

▪ Three proteins

o Need to be disassembled before reuse because they are present as stable

complexes with partner snares

▪ Need to restart process to bring 2 other membranes together

Answer to questions

• Coat formation

o Cargo receptors

o Coat proteins

▪ Clathrin

• Goes from plasma membrane/Golgi to endosomes

▪ COPII

• ER to Golgi

▪ COPI

• Golgi to ER

o Adaptor proteins

o Coat recruitment GTP-ases

▪ Like molecular switch

▪ GTP active; GDP inactive

▪ GTP

• Portion inserted in membrane

• Binding to membrane allows recruitment of the coat proteins

▪ GDP

• Cannot be inserted into membrane

▪ GEF

• Exchange GDP for GTP

• Activates small G protein

▪ GAP

• Exchange GTP for GDP

• Inactivates small G protein

o Coat is resposile for forig esile ad deteriig hat’s iside, after

vesicle formation, coat is removed

• Dynamin

o Involved in pinching off vesicle, not involved in forming coat

• Membrane tethering

o Holding onto vesicle after coat falls off

o Helps vesicle determine what compartment it is supposed to travel to

o Involves Rab proteins

▪ Rab gtp binds to rab effector on membrane

• Membrane fusion

o Involves snares

o Interlock to allow molecules to combine

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Document Summary

Prior to week 1 class 1 pp. Can skip sections on phosphoinositides mark organelles and membrane domains, not all transport vesicles are spherical. Golgi and er membranes: what nsf is, and what role it plays in cells, catalyzes disassembly of snares, hexameric atpase, uses energy of atp hydrolysis to unravel interactions between snares. Inactivates small g protein: coat is respo(cid:374)si(cid:271)le for for(cid:373)i(cid:374)g (cid:448)esi(cid:272)le a(cid:374)d deter(cid:373)i(cid:374)i(cid:374)g (cid:449)hat"s i(cid:374)side, after vesicle formation, coat is removed, dynamin. Involved in pinching off vesicle, not involved in forming coat: membrane tethering, holding onto vesicle after coat falls off, helps vesicle determine what compartment it is supposed to travel to. Involves rab proteins: rab gtp binds to rab effector on membrane, membrane fusion. Prior to week 1 class 2 pp. 710-728 can skip the sections on vesicular tubular clusters mediate transport from the er to the golgi apparatus, proteoglycans are assembled in the.

Related Questions

The vesicles that transport materials from donor membranes to acceptor membranes include:

	1.	COP-II coated vesicles
	2.	COP-III coated vesicles
	3.	COP-I coated vesicles
	4.	Clathrin coated vesicles

2.5 points

QUESTION 11

During skeletal muscle contraction, the roles of ATP include:

	1.	ATP is not required for forming the crossbridges between myosin and actin filaments.
	2.	ATP is utilized as a structural linker to mediate the interaction between myosin and actin filaments
	3.	Hydrolysis of ATP provides energy for myosin head to move along actin filaments and the binding of ATP to myosin head allows the detachment of myosin fromactin filaments.
	4.	ATP binds to actin filaments to drive the power stroke of myosin head.

2.5 points

QUESTION 12

One of the functions of smooth endoplasmic reticulum is

	1.	Synthesizing steroid hormone in the endocrine cells of the gonad and adrenal cortex
	2.	Serves as the starting point of the biosynthetic pathway
	3.	Synthesizing secretory proteins
	4.	Degrading cell debris

2.5 points

QUESTION 13

The function of COP-II coated vesicles is mainly:

	1.	Transporting materials from endosomes to Golgi complex
	2.	Moving materials from the ER to the ERGIC and Golgi complex.
	3.	Transporting materials from Golgi complex back to endoplasmic reticulum.
	4.	Involved in receptor-mediated endocytosis.

2.5 points

QUESTION 14

Which of the following processes is completed in rough endoplasmic reticulum?

	1.	Chaperones help misfolded proteins fold correctly.
	2.	Proteins that target to nucleus are synthesized in rough endoplasmic reticulum.
	3.	O-linked glycosylation occurs in rough endoplasmic reticulum.
	4.	Misfolded proteins are destructed in rough endoplamic reticulum.

2.5 points

QUESTION 15

Kinesin is the motor protein that coorporates with microtubules. It has the following functions:

	1.	It uses GTP as energy source.
	2.	It can hydrolyze ATP and use the energy to drive cargo along microtubules from minus end to plus end.
	3.	It has a globular head that can act as GTPase
	4.	The tail of kinesin is more diverse and binds to cargo

2.5 points

QUESTION 16

For correct segregation and trafficking, lysosomal proteins are tagged in the cis-Golgi with phosphorylated mannose residues, and then the tagged lysosomal enzymes are recruited to clathrin coated vesicles by mannose 6-phosphate receptors.

True

False

2.5 points

QUESTION 17

The process that specialized cells, such macrophages, engulf relatively large particles is:

	1.	Called pinocytosis
	2.	Called phagocytosis
	3.	Mediated by COP-II coated vesicles
	4.	Called autophagy

2.5 points

QUESTION 18

Proteins synthesized on rough endoplasmic reticulum and smooth endoplasmic reticulum are imported co-translationally to their destinations

True

False

2.5 points

QUESTION 19

Treatment of cells with a drug that promotes microtubule disassembly disperses Golgi complex into separate stacks of membrane compartments, suggesting that:

	1.	Golgi complex is made of microtubules.
	2.	Microtubules are important for the organization of Golgi complex.
	3.	Microtubules are transported into Golgi complex
	4.	Golgi complex is composed of tubulin proteins

2.5 points

QUESTION 20

Which of the following is correct about signal sequence of a secretory protein?

	1.	It is an âaddress codesâ for protein trafficking pathways
	2.	It is usually located at the C-terminus.
	3.	It targets the ribosome and the protein that is being synthesized to endoplasmic reticulum.
	4.	It is removed in Golgi complex.

apricotgrasshopper117

silverzebra677

1. Name two similarities and two differences between thecellular processes of importing

protein into the ER and importing protein to the nucleus.

2. What proteins are directly involved in the transportation ofcargo in a clathrin-coated

vesicle?

a. Dynamin

b. Adaptins

c. Cargo receptors

d. t SNARES

3. Suppose a cell was treated with colchiine, a drug causingmicrotubule disassembly.

What would happen within the cell? Why?

Suppose there were a genetic defect in the genes that code forkinesins and dyneins.

What would happen within the cell? Why?

4. Which of the following are true about microtubules?

a. They are utilized by the disease causing bacteriaLysteria.

b. Instability in the minus-end of the microtubule is caused bythe hydrolization of GTP.

c. Centrosomes contain binding sites for microtubules composed atype of tubulin ring.

d. Cellular concentrations of tubulin are above the criticalconcentration for plus-end

polymerization.

e. Motor proteins can attach organelles to the microtubules.

5. Indicate which of the following statements are false:

a. Membrane fusion is energetically unfavorable and thusrequires ATP or similar high

energy molecule to occur

b. Clathrin is responsible for capturing specific molecules fortransport in coated vesicle

structures.

c. Receptor proteins that are incorporated into an endosome canbe retrieved back to the

membrane domain it originated from; can return to a new domainof the membrane; or

can enter the lysosome for digestion.

d. Transport vesicles occasionally bud from the trans Golginetwork to fuse with the

plasma membrane in a process called constitutive exocytosis.

e. Most components of the endocytic vesicle membrane eventuallyare returned to the

plasma membrane for reuse.

6. Match the following organelles with their function:

Organelle Bank:

a. Mitochondria

b. Endoplasmic reticulum

c. Nucleus

d. Lysosome

e. Endosome

f. Peroxisome

g. Golgi apparatus

_____ quality control of mRNA

_____ location of oxidative phosphorylation

_____ responsible for detoxifying organic molecules (livercells)

_____ houses and protects genetic material

_____ responsible for modification and sorting of proteins andlipids

_____ location of ATP synthesis

_____ responsible for sorting endocytosed materials

_____ site of degradation and digestion

_____ responsible for oxidizing toxic molecules

_____ location of lipid synthesis

_____ location of hormone synthesis (adrenal cells)

B. Which organelle(s) from the above list communicate(s) withother organelle(s)

through the use of vesicular transport? ________________

C. Which organelle(s) from the above list receive proteins madein the

cytosol?___________________

D. Through which organelle(s) must proteins pass to reach theorganelle(s) which do not

receive proteins made exclusively in thecytosol?______________

E. Entrance into which organelle(s) requires that proteinsunfold and snake through the

membrane? _________________

F. How do organelles maintain their position in the cytosol? Bespecific.

G. Give 2 advantages that eukaryotic cells gain by havingorganelles.

7. Which of the following statements are true regardingactin?

a. They are arranged in a

crimsonwalrus870

BIO 211 Lecture Notes - Lecture 1: Phagocytosis, Carbohydrate, Mitophagy

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