BIOL 4004: Cell Biology (Exam 2)

What are the different types of accessory proteins?

1. Nucleation-promoting factors

2. Monomer-sequestering protein (subunit binders)

3. Filament stabilizer

4. Filament destabilizer

5. Bundling proteins (linking proteins)

6. Severing proteins

7. Motor proteins

Nucleation-promoting factors are proteins that aid in the ________, and is deemed a slow and weak process.

aggregation of subunits

Nucleation-promoting factors are proteins that aid in the aggregation of subunits, and is deemed a ________ process.

slow and weak

The 𝛾-tubulin ring complex is a nucleation-promoting factor in microtubules that binds to ________ or ________ for nucleation.

𝛂-tubulin; β-tubulin

The ________ is a nucleation-promoting factor in microtubules that binds to 𝛂-tubulin or β-tubulin for nucleation.

𝛾-tubulin ring complex

The Arp2/3 complex is a nucleation-promoting factor in actin that has ________ subunits that can bind to ________ subunits, found ________ or on an existing actin filament.

two; two actin; near the plasma membrane

The ________ is a nucleation-promoting factor in actin that has two subunits that can bind to two actin subunits, found near the plasma membrane or on an existing actin filament.

Arp2/3 complex

Monomer-sequestering proteins, also known as subunit binders, are molecules that bind to monomers and ________ the binding of subunits to the ________ end.

prevent or aid; +

________, also known as ________, are molecules that bind to monomers and prevent or aid the binding of subunits to the + end.

Monomer-sequestering proteins; subunit binders

Stathmin is a subunit binder protein found in microtubules that binds to ________ and sequesters them, ________ subunit addition in the process; ________ stathmin cannot bind.

two 𝛂/β-tubulin subunits; blocking; phosphorylated

________ is a subunit binder protein found in microtubules that binds to two 𝛂/β-tubulin subunits and sequesters them, blocking subunit addition in the process; when phosphorylated it cannot bind.

Stathmin; stathmin

Profilin is a subunit binder in actin that binds to the ________ end and ________ by increasing the addition of subunits.

+; promotes filament growth

________ is a subunit binder in actin that binds to the + end and promotes filament growth by increasing the addition of subunits.

Profilin

Thymosin is a subunit binder in actin that doesn't bind on the ________ end and ________ by sequestering free actin subunits.

+; blocks filament growth

________ is a subunit binder in actin that doesn't bind on the + end and blocks filament growth by sequestering free actin subunits.

Thymosin

A filament stabilizer helps maintain the ________ and ________ of filaments in cells, preventing their ________ and promoting their ________ by binding to the filaments themselves.

stability; integrity; disassembly; function

A ________ helps maintain the stability and integrity of filaments in cells, preventing their disassembly and promoting their function by binding to the filaments themselves.

filament stabilizer

MAPs are a ________ of filament stabilizer proteins in microtubules, i.e. ________ in neurons.

family; MAP2 and Tau

________ are a family of filament stabilizer proteins in microtubules, i.e. MAP2 and Tau in neurons.

MAPs

Tropomyosin is a ________ filament stabilizer protein in actin that ________ of seven actin subunits.

long; binds and stretches over a distance

________ is a long filament stabilizer protein in actin that binds and stretches over a distance of seven actin subunits.

Tropomyosin

A filament destabilizer is a protein that ________ of filaments by destabilizing their structure, commonly found when a cell is ________ and wants to change ________.

promotes the disassembly; migrating; direction

A ________ is a protein that promotes the disassembly of filaments by destabilizing their structure, commonly found when a cell is migrating and wants to change direction.

filament destabilizer

Catastrophin is a filament destabilizer in microtubules that can bind to and ________ of a microtubule via ________.

bend protofilaments at the + end; depolymerization

________ is a filament destabilizer in microtubules that can bind to and bend protofilaments at the + end of a microtubule via depolymerization.

Catastrophin

Cofilin is a filament destabilizer in actin that increases strain to make filaments ________ by binding to the ________ and increasing ________, making 𝛂-helical turns ________.

brittle; side; pitch; shorter

________ is a filament destabilizer in actin that increases strain to make filaments brittle by binding to the side and increasing pitch, making 𝛂-helical turns shorter.

Cofilin

Bundling proteins, also known as linking proteins, ________ together thereby enhancing their ________ and promoting the formation of ________.

bundle filaments; stability; higher-order structures

________, also known as ________, bundle filaments together thereby enhancing their stability and promoting the formation of higher-order structures.

Bundling proteins; linking proteins

MAP2 and Tau are bundling proteins in microtubules that both ________ and ________ specifically in neurons.

stabilize; bundle

________ are bundling proteins in microtubules that both stabilize and bundle specifically in neurons.

MAP2 and Tau

𝛂-actinin is a bundling protein in actin that utilizes a ________, i.e. loose packing due to binding sites being ________ each other.

dimer structure for contractile bundling; far from

crosslinks and spaces filaments out

________ is a bundling protein in actin that utilizes a dimer structure for contractile bundling, i.e. loose packing due to binding sites being far from each other.

𝛂-actinin

crosslinks and spaces filaments out

Fimbrin is a bundling protein in actin that utilizes a ________, i.e. tight packing due to binding sites being ________ each other.

monomer structure for parallel bundling; close to

crosslinks and spaces filaments out

________ is a bundling protein in actin that utilizes a monomer structure for parallel bundling, i.e. tight packing due to binding sites being close to each other.

Fimbrin

crosslinks and spaces filaments out

A severing protein promotes the ________ and ________ of cytoskeletal elements via ________ filaments.

disassembly; reorganization; cleaving

A ________ promotes the disassembly and reorganization of cytoskeletal elements via cleaving filaments.

severing protein

A motor protein uses ________ and converts it to ________ in the form of a ________.

chemical energy via ATP; mechanical energy; large conformational change

A ________ uses chemical energy via ATP and converts it to mechanical energy in the form of a large conformational change.

motor protein

Dyneins are ________ end directed motor proteins in microtubules. Kinesins are ________ end directed motor proteins in microtubules.

- ; +

________ are - end directed motor proteins in microtubules. ________ are + end directed motor proteins in microtubules.

Dyneins; Kinesins

Myosins are ________ end directed motor proteins in actin.

+

________ are + end directed motor proteins in actin.

Myosins

The head/motor domain ________ and ________.

binds; hydrolyzes ATP

The ________ binds and hydrolyzes ATP.

head/motor domain

Dyneins move vesicles ________ along microtubules and are associated with ________ vesicles.

inward; endocytic

________ move vesicles inward along microtubules and are associated with endocytic vesicles.

Dyneins

Kinesins move vesicles ________ along microtubules and are associated with ________ vesicles.

outward; exocytic

________ move vesicles outward along microtubules and are associated with exocytic vesicles.

Kinesins

Eukaryotic cells are ________, meaning that they contain ________ that carry out their own ________ functions.

compartmentalized; membrane-bound organelles; specialized

________ are compartmentalized, meaning that they contain membrane-bound organelles that carry out their own specialized functions.

Eukaryotic cells

All eukaryotic cells have the ________ of membrane-enclosed organelles.

same basic set

All ________ have the same basic set of membrane-enclosed organelles.

eukaryotic cells

The cytoplasm is the area ________, while the term cytosol refers to the area that is inside the plasma membrane but ________.

inside the plasma membrane; outside the organelles

The ________ is the area inside the plasma membrane, while the term ________ refers to the area that is inside the plasma membrane but outside the organelles.

cytoplasm; cytosol

The mitochondria are evolutionarily derived from an ________, containing their own ________ and exist rather ________ from other organelles.

ancient endosymbiotic relationship; genome; independently

The ________ are evolutionarily derived from an ancient endosymbiotic relationship, containing their own genome and exist rather independently from other organelles.

mitochondria

Other than mitochondria, membrane-bound organelles are dynamically related to one another forming the ________.

endomembrane system

Other than ________, membrane-bound organelles are ________ forming the endomembrane system.

mitochondria; dynamically related to one another

________ can move between ________ in different ways, such as gated transport, transmembrane transport, and vesicular transport.

Proteins; compartments

Proteins can move between compartments in different ways, such as ________, ________, and ________.

gated transport; transmembrane transport; vesicular transport

With ________, a protein in its folded state travels through a ________, occurring for proteins targeted to the nucleus.

gated transport; pore

With gated transport, a protein in its ________ travels through a pore, occurring for ________.

folded state; proteins targeted to the nucleus

With ________, a protein in an unfolded state travels through a ________, occurring for proteins targeted to the ER, peroxisomes, mitochondria, and chloroplasts.

transmembrane transport; narrow channel

With transmembrane transport, a protein in an ________ travels through a narrow channel, occurring for ________.

unfolded state; proteins targeted to the ER, peroxisomes, mitochondria, and chloroplasts

With ________, a protein is packaged in a ________, occurring for transport from ER → Golgi, Golgi → lysosomes, and Golgi → plasma membrane.

vesicular transport; membrane vesicle

With vesicular transport, a protein is ________ in a membrane vesicle, occurring for transport from ________.

packaged; ER → Golgi, Golgi → lysosomes, and Golgi → plasma membrane

Sorting signals and sorting receptors ________ to the correct ________, containing one or more traffic signals in their ________.

cellular location; direct proteins; amino acid sequence

________ and ________ direct proteins to the correct cellular location, containing one or more traffic signals in their amino acid sequence.

Sorting signals; sorting receptors

________ perforate the nuclear envelop to make a pore with proteins called nucleoporins.

Nuclear pore complexes

Nuclear pore complexes ________ to make a pore with proteins called ________.

perforate the nuclear envelop; nucleoporins

There are ________ that fold back and meet at the nuclear pore complex.

inner and outer membranes

There are inner and outer membranes that ________ and ________.

fold back; meet at the nuclear pore complex

An ________, called the nuclear localization signal (NLS), ________ to the nucleus.

amino acid sequence; direct proteins

An amino acid sequence, called the ________, directs proteins to the nucleus.

nuclear localization signal (NLS)

Nuclear import receptors bind to both ________ and ________ to direct the protein through the nuclear pore.

nuclear localization signals; nuclear pore complex proteins

________ bind to both nuclear localization signals and nuclear pore complex proteins to ________.

Nuclear import receptors; direct the protein through the nuclear pore

The ________ imposes directionality on transport through nuclear pore complexes via binding of GTP or GDP.

Ran GTPase

The Ran GTPase imposes ________ on transport through nuclear pore complexes via ________.

directionality; binding of GTP or GDP

If ________ is bound to Ran GTPase via the ________, it will want to exit the nucleus.

GTP; Ran-GEF nuclear localization signal within the nucleus

If GTP is ________ via the Ran-GEF nuclear localization signal within the nucleus, it will want to ________ the nucleus.

bound to Ran GTPase; exit

If ________ in Ran GTPase via the ________, it will want to enter the nucleus.

GTP is hydrolyzed to GDP; Ran-GAP protein

If GTP is hydrolyzed to GDP in ________ via the Ran-GAP protein, it will want to ________ the nucleus.

Ran GTPase; enter

Nuclear Import

1. Nuclear import receptor ________ bound to a cargo protein containing a nuclear localization signal.

2. The ________ encounters Ran-GTP in the nucleus, and it binds to NIR.

3. ________ causes the cargo protein to dissociate from the NIR

4. The ________ bound to Ran-GTP exits the nucleus, encounters Ran-GAP, and induces Ran to hydrolyze its GTP

5. ________ unable to bind to the NIR, ________ allowing the NIR to be recycled.

1. enters the nucleus

2. NIR-cargo complex

3. Ran-GTP binding

4. dissociated NIR

5. Ran-GDP; dissociates

Nuclear Import

1. ________ enters the nucleus bound to a ________.

2. The NIR-cargo complex ________ in the nucleus, and it ________.

3. Ran-GTP binding causes the ________ from the NIR

4. The dissociated NIR bound to Ran-GTP ________, encounters ________, and ________

5. Ran-GDP unable to bind to the ________, dissociates allowing the NIR to be ________.

1. Nuclear import receptor; cargo protein containing a nuclear localization signal

2. encounters Ran-GTP; binds to NIR

3. cargo protein to dissociate

4. exits the nucleus; Ran-GAP; induces Ran to hydrolyze its GTP

5. NIR; recycled

Nuclear Export

1. ________ forms a trimeric complex with a ________ containing a nuclear export signal (NES) in the nucleus

2. The trimeric complex ________ in nucleus, with Ran-GTP facilitating the ________

3. The trimeric complex ________, encounters Ran-GAP, and ________

4. Ran-GDP, ________, dissociates from the complex

5. The cargo protein, ________, dissociates from the complex into the cytosol

1. Ran-GTP; nuclear export receptor (NER) and a cargo protein

2. cooperatively binds together; interaction b/t the NER and cargo protein

3. exits the nucleus; Ran hydrolyzes its GTP to GDP

4. unable to bind to the NER

5. unable to bind to the NER in the absence of Ran

Nuclear Export

1. Ran-GTP forms a ________ with a nuclear export receptor (NER) and a cargo protein containing a ________ in the nucleus

2. The trimeric complex cooperatively binds together in nucleus, with ________ facilitating the interaction b/t the NER and cargo protein

3. The ________ exits the nucleus, ________, and Ran hydrolyzes its GTP to GDP

4. ________, unable to bind to the NER, ________ from the complex

5. The ________, unable to bind to the NER in the absence of Ran, ________ from the complex into the ________

1. trimeric complex; nuclear export signal (NES)

2. Ran-GTP

3. trimeric complex; encounters Ran-GAP

4. Ran-GDP; dissociates

5. cargo protein; dissociates; cytosol

Mitochondrial proteins contain a ________ that directs the protein to receptors in the mitochondrial membrane, which either inserts the protein into the ________ or it is ________ via translocation channels.

targeting sequence; outer membrane; transferred across

________ contain a targeting sequence that ________ in the mitochondrial membrane, which either ________ into the outer membrane or it is transferred across via ________.

Mitochondrial proteins; directs the protein to receptors; inserts the protein; translocation channels

Chaperone proteins of the ________ keep mitochondrial proteins in an ________, allowing the polypeptide chain to be ________ in the outer and inner membrane.

hsp70 family; unfolded state; threaded through the channel

________ of the hsp70 family keep ________ in an unfolded state, allowing the polypeptide chain to be threaded through the channel in the ________.

Chaperone proteins; mitochondrial proteins; outer and inner membrane

Contact sites exist in the mitochondrion where the ________, permitting proteins destined for the matrix to ________.

TOM complex is in contact with the TIM complex; move through each channel sequentially

________ exist in the ________ where the TOM complex is in contact with the TIM complex, permitting proteins ________ to move through each channel sequentially.

Contact sites; mitochondrion; destined for the matrix

Mitochondrial Import

1. The ________ remains unfolded in the cytosol due to hsp70, which ________

2. The protein binds to a receptor in the outer membrane

3. The protein is ________ in the TOM complex

4. The protein moves through the TOM complex and then through the TIM complex in the ________, requiring a ________

5. As the protein ________, the signal sequence is cleaved

6. Hsp70 proteins in the matrix continues to ________ as it is transported, with ATP hydrolysis ________

1. protein; hydrolyzes ATP

2. N/A

3. transferred to the channel

4. inner membrane; proton gradient

5. emerges in the matrix

6. keep the protein unfolded; providing energy for import

Mitochondrial Import

1. The protein remains ________ in the cytosol due to ________, which hydrolyzes ATP

2. The protein binds to a ________

3. The protein is transferred to the channel in the ________

4. The protein ________ and then ________ in the inner membrane, requiring a proton gradient

5. As the protein emerges in the matrix, the ________

6. ________ in the matrix continues to keep the protein unfolded as it is transported, with ________ providing energy for import

1. unfolded; hsp70

2. receptor in the outer membrane

3. TOM complex

4. moves through the TOM complex; through the TIM complex

5. signal sequence is cleaved

6. Hsp70 proteins; ATP hydrolysis

The smooth ER has ________ and is the site of ________.

has no ribosomes; vesicle formation

The ________ has no ribosomes and is the site of vesicle formation.

smooth ER

The rough ER ________ and is the site of ________ into the lumen or membrane ________ via these ________.

has ribosomes; protein synthesis; cotranslationally; ribosomes

The ________ has ribosomes and is the site of protein synthesis into the ________ or ________ cotranslationally via these ribosomes.

rough ER; lumen; membrane

As a protein is ________, the signal sequence is cleaved, resulting in a lower mass that can be detected on ________.

imported into the ER; SDS gels