Cell Biology - BIOB10 (post midterm)

Unfolded Protein Response

If there is a large amount of unfolded/misfolded proteins accumulating in the ER, cells have a plan of action called … (3)

Chaperones, proteases

Unfolded Protein Response (UPR):

What 2 things are made more?

Degrade

Unfolded Protein Response (UPR):

More proteases are made to … defective proteins

Decreased

Unfolded Protein Response (UPR):

Translation of new proteins not involved in UPR is …

(increased or decreased)

Chaperones

Unfolded Protein Response (UPR):

Activation on UPR is based on … binding to sensors decreasing

Decreasing

Unfolded Protein Response (UPR):

Activation of UPR is based on chaperones binding to sensors …

(increasing or decreasing)

Increases

Unfolded Protein Response (UPR):

There is less binding of chaperones to sensors because binding to misfolded proteins …

(increases or decreases)

Native form

Some genetic diseases have mutation leading to the expression of a mutant protein, which means they cannot fold properly into … (2)

Destroyed

When a mutant protein is recognized by the quality control pathway in the ER, it is … which loses protein & protein function in the cell

Cystic fibrosis

An example of a ER protein folding disease (2)

Vesicular

Transport of proteins via intermediates

Vesicles

Dynamic organelle involved in selective transport of proteins/materials

Bud

Vesicles … off donor compartment

Coat

Budding vesicles have a … of soluble proteins assembling on the membrane of donor compartment

Cytosolic

Budding vesicles have coat of soluble proteins on donor compartment.

Where are these soluble proteins from? Lumenal or cytosolic

Coat proteins

Proteins that mechanically force the membrane to curve and form a budding vesicle (2)

Cargo

Vesicles:

What protein is needed to go from donor to target?

COP II

Vesicle budding + Coat Proteins:

Vesicles that transport proteins forward from ER to Golgi (anterograde)

COP I

Vesicle budding + Coat Proteins:

Transport proteins backwards from Golgi to ER (retrograde)

Clathrin

Vesicle budding + Coat Proteins:

Any transport from the Golgi onwards is done by …

COP II

Vesicles: COP II, COP I, or clathrin?

Transport from ER to Golgi

COP I

Vesicles: COP II, COP I, or clathrin?

Transport proteins from Golgi to ER

Clathrin

Vesicles: COP II, COP I, or clathrin?

Protein sorting to plasma membrane, lysosomes, endocytosis, etc.

6

Clathrin Coat Proteins (vesicle budding):

Clathrin has # proteins

Triskelion

Clathrin Coat Proteins (vesicle budding):

Clathrin has 6 proteins total that form a … structure.

Basket

Clathrin Coat Proteins (vesicle budding):

The Clathrin triskelions come together to form a … around vesicle

Adaptor proteins

Clathrin Coat Proteins (vesicle budding):

What binds to clathrin to form the inner coat between vesicle and clathrin shell? (2)

Inner coat

Clathrin Coat Proteins (vesicle budding):

Adaptor proteins bind to clathrin to form the … (2) between vesicle & clathrin shell

Phosphoinositides, PI

Clathrin Coat Proteins (vesicle budding):

Adaptor proteins form inner coat.

What binds specific adaptor proteins based on phosphorylation of inositol sugar at 3’, 4’, and 5’ position? (1,1)

Phosphorylation, inositol

Clathrin Coat Proteins (vesicle budding):

PI (phosphoinositides) bind specific adaptor proteins based on … of their … sugar at 3’, 4’, 5’ position

Different

Clathrin Coat Proteins (vesicle budding):

Different organelles have … PIPs (phosphoinositidyl phosphates)

(different or same)

Phosphoinositide, cargo receptor

Clathrin Coat Proteins (vesicle budding):

Adaptor protein binds to a … head group and to a … (2) to enhance binding to plasma membrane

Fission

Vesicle budding depends on membrane …

Dimeric membrane bending proteins

Clathrin Coat Proteins (vesicle budding):

Membrane curvature where adaptor proteins assemble (4?)

Fission, dynamin

Clathrin Coat Proteins (vesicle budding):

Severing the vesicle from donor compartment is done by … proteins, specifically …

Dynamin

Clathrin Coat Proteins (vesicle budding):

What is the specific fission protein severing vesicle from membrane?

Neck

Clathrin Coat Proteins (vesicle budding):

The way dynamin severs vesicle from membrane is it creates a collar around the … of budding vesicle

GTP

Clathrin Coat Proteins (vesicle budding):

Dynamin (severs vesicle from membrane) is a … binding protein (acronym)

GTP hydrolysis

Clathrin Coat Proteins (vesicle budding):

Dynamin creates a collar around the neck of the budding vesicle. What is the actual mechanism that does the severing? (2)

Coat recruitment GTPases, Rab proteins, SNAREs

Vesicles are mediated by 3 proteins that control movement & fusion

Coat recruitment GTPases

Targeted vesicle transport (3):

Initiates coated vesicle formation (3)

Rab proteins

Targeted vesicle transport (3):

Directs vesicles

SNAREs

Targeted vesicle transport (3):

Docking & fusion

Pinched

COP II vesicle transport:

Once the entire coat is assembled, the vesicle is … off

Sar1, COP II proteins

COP II vesicle transport:

GTP hydrolysis occurs once vesicle leaves ER which releases 2 things

Cargo receptor

COP II vesicle transport:

Proteins that are fully/partially exposed on the lumenal surface of COP II vesicles

Rab

Rab or SNARE proteins [vesicles]:

Tethering

SNARE

Rab or SNARE proteins [vesicles]:

Docking

SNARE

Rab or SNARE proteins [vesicles]:

Fusion

Rab, GTP

Vesicle tethering is done by … proteins which are small … binding proteins

Lipid

Vesicle tethering: Rab

Associated to membranes by a … anchor

Organelles

Vesicle tethering: Rab

Specific Rab proteins associate with specific …

Cytosol

Vesicle tethering: Rab

Recruit tethering proteins from the …

Positive

Vesicle tethering: Rab

… feedback loop of active Rab5 recruits Rab5 GEFS to make more Rab5s

Fusion

Vesicle docking: SNAREs

Process leads to vesicle …

Vesicle

Vesicle docking: SNAREs

v-SNAREs are on … membrane

v-SNARE

Vesicle docking: SNAREs

SNARE protein on vesicle membrane

Target

Vesicle docking: SNAREs

t-SNARES are on … membrane

t-SNARE

Vesicle docking: SNAREs

SNARE protein on target membrane

Fuse

Vesicle fusion: SNAREs

Interaction between v-SNAREs & t-SNAREs will pull respective membranes together and will … together

Bilayer

Vesicle fusion: SNAREs

SNARE proteins allow for the 2 membranes (vesicle & membrane) will create a new …

NSF

Vesicle fusion:

Once fusion has occurred, unzipping the SNARE proteins require … protein which is ATPase (acronym)

v-SNAREs

Vesicle fusion:

When unzipping SNARE proteins post fusion, … are retrieved and returned to compartment of origin

Fuse, vesicular tubular clusters

After COPII coat is lost, ER derived vesicles … together in … (3)

ER Golgi Intermediate Compartment

ERGIC (expand)

Vesicular tubular clusters

ERGICs are made of … (3)

Retrograde transport vesicles, COPI

If misfolded proteins or ER resident proteins accidentally exit via budding vesicles, they can be sent back via … (3, 1)

Coatomer

Vesicle transport:

COPI coats are recruited as a preassembled complex called …

Signal sequence, C-terminal

How do we know if ER resident protein retrieval is necessary?

Because ER resident proteins have a … (2) on the … of the protein

Nucleus

Golgi Apparatus is located adjacent to the … above the rough ER

Cisternae

Golgi apparatus:

Consists of ribbon-like stacks of membranous …

Functions

Golgi apparatus:

Cisternae are distinct which means they can perform several distinct …

Cis

Golgi apparatus:

Cisternae closest to the ER

Medial

Golgi apparatus:

Middle cisternae

Trans

Golgi apparatus:

Cisternae leading to proteins budding off

Cis to medial to trans

Golgi apparatus:

Protein progression through the golgi networks (… to … to …)

No

Golgi apparatus:

Are there discrete boundaries between different cisternae?

Processed, modified, sorted

What 3 important processes are done in the golgi?

Functional compartmentalization

The fact that proteins are processed, modified, and sorted is seen as … (2) in the golgi

Soluble, aggregates

Golgi:

Proteins are glycosylated for 2 reasons:

1. Keeps intermediates of protein folding … and prevents …

Glycocode

Golgi:

Proteins are glycosylated for 2 reasons:

1. Keeps intermediates of protein folding soluble and prevents aggregates

2. Sequential modification signify progression of protein folding via …

Mannose

N-glycosylation in Golgi:

You will lose an additional 3 … which creates a high-mannose oligosaccharide

GlcNac, mannose

N-glycosylation in Golgi: COMPLEX

Addition of … and trim of 2 …

High mannose oligosaccharide, complex oligosaccharides

Any N-linked glycans going through golgi have 2 fates

O-linked glycosylation

A further Golgi protein modification where sugars are attached to serine or threonine on specific proteins (3)

N-linked, O-linked

Protein modification glycosylation in the golgi (2)

Vesicle transport, stationary cisterna

How does Golgi maintain polarized structure?

Hypothesis 1:

2 names, each cisterna is static so all protein movement through the golgi requires vesicles

Cisternal maturation

How does Golgi maintain polarized structure?

Hypothesis 2: [more accurate, 2]

Cisterna are formed by vesicles from ER

Cis-end to trans-end

How does Golgi maintain polarized structure?

In Hypothesis 2 or Cisternal Maturation Model, cisternal physically move from the (… to …) as they mature

Vesicular tubular cluster

How does Golgi maintain polarized structure?

In hypothesis 2 or Cisternal Maturation Model, it is more accurate because without the … (3), the entire golgi falls apart

Golgins

Cytosolic Golgi proteins forming long tethers to capture vesicles by interacting w/ Rab proteins

Lysosomes

Digestive organelles which break down macromolecules & move products back to cytosol

Acidic

Lysosomes have a highly … environment

Oxidation, lipids

Peroxisomes rely heavily on … to break things down (H₂O₂) and they break down …

Amino acids, nucleotides

Peroxisomes break down lipids.

Lysosomes break down … (2 things)

Glycosylated

The reason why lysosomes don’t eat themselves is because most proteins are …

Phagocytosis, endocytosis, autophagy, macropinocytosis

Lysosomes get 4 major pathways of delivery

Acid hydrolases

Lysosomes are considered bags of … (2) which function in acidic pHs which can break down entire organelles

Proton pumps

The reason why lysosome is hella acidic is because it has a lot of … (2) on the membrane driving H+ into lumen using ATP (low pH)

Into

The reason why lysosome is hella acidic is because hella proton pumps drive H+ … lumen using ATP

(into or out of)