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Cell Bio Exam 2 Flashcards

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1
Q

Describe the path that proteins take from synthesis to secretion.

A

Proteins are synthesized in the endoplasmic reticulum by ribosome. They are processed in the Golgi complex, and then secreted in vesicles.

This process has constitutive and regulated components

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2
Q

What is the endocytotic pathway?

A

The trafficking of materials into the cell via endosomes.

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3
Q

What signals vesicles to move from one location within the cell to another?

A

The bilipid membranes of vesicles are studded with proteins that bind to other proteins to relay the vesicle from one place to another

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4
Q

Why is yeast a good model organism for studying trafficking?

A

Yeast cells are very large in size, making it easier to look at the vesicles inside the cell.

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5
Q

Describe the Pulse-Chase technique

A

Cells to be studied are incubated with a radioactive amino acid (pulse). The proteins being synthesized during the pulse will contain labeled amino acids. The labeled AAs are then removed from the nutrient source and replaced with non-radioactive AAs (chase).

The cells are fixed at various time points to see the movement of the proteins through the cell.

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6
Q

Describe the movement of labeled proteins seen using the pulse-chase technique

A

Labeled proteins are seen closer and closer to the plasma membrane as time goes on.

ER –> Golgi –> Vesicles

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7
Q

What is Green Fluorescent Protein?

A

GFP is a fluorescent tag that can be fused to target protein. This is done by transforming the organism of interest.

Fluorescent microscopy can be used to visualize the tagged protein moving through the cell.

The protein is isolated from a jellyfish

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8
Q

What is a temperature-sensitive mutation, and how is it useful for studying trafficking?

A

A conditional mutation that produces the mutant phenotype in one (restrictive or non-permissive) temperature range and the wild-type phenotype in another (permissive) temperature range.

If the protein accumulates in the ER at restrictive temperatures, then the mutation alters the AA sequence required for the protein to leave the ER

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9
Q

What is a microsome?

A

small vesicles that still contain transmembrane proteins that were part of the original ER and Golgi

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10
Q

How can antibodies be used to study ER and Golgi microsomes?

A

Different microsomes have different protein compositions, and thus different epitopes. Antibodies can be generated against these proteins, and then used to co-stain whole cells as endomembrane markers.

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11
Q

Describe a 2-fusion protein method for staining learning whether or not a protein is located on the endomembrane.

A

The target protein can be tagged with GFP, and the endomembrane can be tagged with RFP.

Where these two tags overlap will fluoresce yellow, indicating the presence of the target protein on the membrane

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12
Q

What is the significance of the KDEL sequence found on Protein Disulfide Isomerase (PDI)?

A

This is a highly conserved AA sequence found at the carboxy terminus of PDI.

This AA sequence is necessary for ER retention and sufficient to reduce the secretion of proteins from the ER.

Thus, this sequence traps proteins that are not supposed to be secreted from the ER inside the ER.

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13
Q

What is Mannosidase II a maker for?

A

Mannosidase II is a marker for the Golgi apparatus.

It is a 135 kD protein located on the luminal side of the Golgi mebranes.

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14
Q

What structures does the Lgl1 protein co-localize with?

A

The ER and the Golgi

Detected using GFP and RFP overlaping as yellow signal

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15
Q

How do proteins get from the ER to the golgi?

A

Via a process called “Vesicle Budding”

Little membrane bound vesicles are pinched off from the ER membrane in a budding process.

This vesicle then fuses with the membrane of the Golgi Apparatus

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16
Q

If a yeast cell has a mutation resulting in faulty vesicle budding, where will proteins accumulate?

A

They will accumulate in the ER becasue the cannot leave through the budding process.

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17
Q

If a yeast cell has a mutation resulting in faulty vesicle fusion, where will the proteins accumulate?

A

They will accumulate within the cell. They will properly leave the ER, but will not be able to enter the Golgi Apparatus

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18
Q

What are the two types of endoplasmic reticulum? What makes them different?

A

The rough and the smooth ER (RER and SER)

The RER has ribosomes and is organized into cisternae. It is continuous with the outer membrane of the nucleus. It is associated with the synthesis of exported proteins.

The SER has no ribosomes and has tubular membrane structure

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19
Q

Is the lumen of the ER made of the same components as the cytosol?

A

No. The ER lumen has a different composition (pH and [protein])

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20
Q

What are the different functions of the smooth ER?

A
  • Storage of Ca2+ ions
  • Synthesis of steroid hormones and cholesterol
  • Detoxify molecules in the liver
  • Hormone synthesis
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21
Q

How are hydrophobic foreign molecules able to be excreted?

A

Cytochrome P450 is an enzyme found in the SER in liver cells that adds oxygen molecules to hydrophobic foreign molecues to make them hydrophilic enough to be excreted

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22
Q

Describe the RER and golgi complexes found in secretory cells.

A

These cells (salivary glands, intestines…etc.) are polar.

They have many secretory vesicles with lots of RER and extensive golgi networks.

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23
Q

What are the functions of the RER?

A
  • Synthesis of exported proteins
  • Initial glycosylation of proteins
  • Folding of polypeptides
  • Recognition and removal of misfolded proteins
  • Assembly of multimeric protein complexes
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24
Q

What is the Signal Hypothesis?

A

Proteins that are supposed to be secreted will have a Signal Sequence (SS) at their N-terminus made up of 5-10 hydrophobic terminus.

A Signal Recognition Particle (SRP) binds the SS once it emerges from the ribosome.

The SRP binds to an SRP receptor on the membrane and a channel called a Translocon

The protein is then translated directly into the lumen of the ER.

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25
Q

What happens in the lumen of the ER?

A

Protein processing begins

Enzymes act to:

  • cleave the signal peptide (signal peptidase)
  • Protein glycosylation begins (oligosaccharyltransferase)
  • Chaperone proteins assist protein folding
  • Intermolecular disulfide bonds are formed (PDI)
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26
Q

Describe how the translocon synthesizes transmembrane proteins

A

2 scenarios depending on which way the N-terminus is supposed to face.

1) if the N-terminus is extracellular, the translocon opens up and expels the peptide into the membrane.
2) If the N-terminus is cytosolic, then it needs to be flipped. Translation pauses as the protein is flipped. The mechanism is unknown.

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27
Q

How are cisternal and exoplasmic orientations related?

A

Cisternal means toward the lumen of the ER/Golgi/vesicle. When a vesicle fuses with the plasma membrane, the cisternal proteins and lipids will become exoplasmic, meaning that it is oriented towards the extracellular side of the cell.

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28
Q

What cellular membrane has the highest concenteration of phosphatidylcholine?

A

The ER membrane has the highest concentration of PC with about 55%

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29
Q

How is membrane asymmetry achieved?

A

Lipid-modifying enzymes can alter lipids directly in the membrane (ex: PI4PK)

Lipid sorting occurs during vesicle budding, determining which lipids are included in the vesicle.

Phospholipid transfer proteins can shuttle lipids from one compartment to another

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30
Q

What is one clinical application of phospholipid transfer proteins?

A

In mice, these proteins have been shown to be highly active in atherosclerosis. Deletion prevents atherosclerosis.

These proteins are thus a potential drug target for treating atherosclerosis.

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31
Q

What is dolichol?

A

A carrier lipid involved in protein glycosylation in the endoplasmic reticulum.

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32
Q

What sugar is always added first during the protein glycosylation in the ER? What happens to it first?

A

GlcNAc. which is then phosphorylated by GlcNAc-1-phosphotransferase.

This can be inhibited by tunicamycin

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33
Q

Describe the protein glycosylation process in the ER.

A

1) The first sugar is linked to the cytosolic side of the ER membrane via a high energy pyrophosphate bond.
2) Branched mannose residues are added
3) The glycosylated protein then flips to face the luminal side of the ER
4) More sugars are added inside the ER
5) The finished oligosaccharide is transfered to a Asn residue on a nascent polypeptide as it is synthesized.

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34
Q

What protein is responsible for flipping the DolPP-GlcNAc2-Man5 across the ER membrane?

A

RFT1

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35
Q

What is the function of oligosaccharyl transferase (OST)?

A

It transfers the finished N-glycan structure to an asparagine residue at the Asn-X-Ser/Thr site on the nascent polypeptide.

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36
Q

How are sugars transfered from the cytosol to the ER lumen?

A

They are transfered one at a time from nucleotide activated sugars (ex: UDP) by specific transmembrane antiporters.

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37
Q

In higher organisms, what are the additional carbohydrate modifications that occur in the ER lumen?

A
  1. Glucosidase I and II remove two (of three) Glu residues from the branched mannose complex
  2. Calnexin guides the protein to another glucosidease II, which removes the last Glu
  3. Glycosyl transferase checks for misfolding by looking for exposed hydrophobic residues
  4. GT will keep checking and initiating refolding until it is folded correctly
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38
Q

What is ERAD?

A

ER-associated degradation

This process degrades misfolded proteins inside of proteosomes.

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39
Q

What is the unfolded protein response?

A

Triggered when misfolded proteins back up in the ER.

Misfolded protein sensors are normally kept inactive by binding protein (BiP)

Sensors respond by either:

1) Dimerizing and phosphorylating elF2alpha which stops protein translation
2) Cytosoloic portion of sensor is cleaved and translocated to the nucleus to induce transcription of genes to relieve ER stress

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40
Q

What are transitional elements?

A

Budding vesicles from the ER on their way to the Golgi

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40
Q

Describe the structure of the Gogli Complex

A

Two networks with three levels of cisternae

cis is closest to the ER, medial is central, and trans is the side of release of vesicles

The membrane sacs are supported by cytoskeletal proteins

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41
Q

How do the functions of the different portions of the golgi complex differ?

A

The CGN sorts proteins to return to the ER and those to proceed through the golgi

The TGN sorts proteins into appropriate vesicles for secretion.

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42
Q

List the stains usable for identifying the cis, medial and trans cisternae, respectively.

A

Cis: osmium tetroxide

Medial: mannosidase II antibodies

Trans: Nucleoside diphosphitase antibodies

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43
Q

Where does complex glycosylation occur?

A

In the Golgi complex

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44
Q

What determines the order of sugar attachment in the Golgi?

A

The spatial arrangement of the transferases within the golgi

The amino acid sequence around site of sugar attachment

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45
Q

What are the two models for how materials move through the Golgi?

A

1) Vesicular transport model
2) Cisternal maturation model

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46
Q

What is the difference between the vesicular transport model and the cisternal maturation model?

A

The VTM states that cisternae are immobile and materials move between them by budding.

The CMM states that the cisternae move towards the trans face of the golgi with the lumenal contents maturing along the way.

Research supports the VTM because enzyme contents of individual cisternae appear to be constant

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47
Q

What role doe COP-II play in vesicular trafficking?

A

COP-II is a protein that coats vesicles and signals for anterograde trafficking (ER–>ERGIC–>Golgi)

48
Q

Explain the mechanism of COP-II causing membrane curvature.

A

Guanine exchange factors (GEFs) induce Sar1 (A COP-II protein) to bind to GTP which causes it to insert into the ER membrane. This begins the curvature.

This recruits other COPII proteins leading to further curvature and vesicle formation

49
Q

What role does COP-I play in vesicular trafficking?

A

It is a coating protein that signals for retrograde trafficking

50
Q

Explain the mechanism of COP-I trafficking.

A

They use GTP binding coat protein called Arf1.

Proteins with KDEL sequences indicate that the protein should be returned to the ER.

The KKXX sequence on the KDEL receptor binds to the COP-I protein, which allows the protein to be returned to the ER.

51
Q

What is clathrin?

A

A coat protein for vesicles between the golgi and the plasma membrane

It is detected on vesicles going to and from lysosomes and endosomes

52
Q

What is the function of endosomes?

A

Part of the endomembrane system that sorts materials that are endocytosed or on their way to the lysosome.

They recycle receptors allowing them to return to their membrane of origin.

53
Q

What is bulk-phase endocytosis?

A

Also known as pinocytosis.

A non-specific method of endocytosis that takes in any molecules/particles near the clathrin coated pit.

54
Q

What is receptor mediated endocytosis?

A

A more specific method of endocytosis than pinocytosis.

Membrane receptors bind ligands. The receptors are bound to adaptor proteins that connect to clathrin.

A clathrin coated pit forms as the membrane is invaginated.

55
Q

What is the difference between an early endosome and a late endosome?

A

Early endosomes sort housekeeping genes from signaling receptors and ligands.

Late endosomes contain the cargo and are found closer to the golgi network.

56
Q

Describe the structure of clathrin.

A

A clathrin triskelion is made of 3 heavy chains and three light chains that assemble into a 3-legged structure.

57
Q

Does clathrin bind directly to transmembrane receptors?

A

NO.

Clathrin binds to adaptor proteins (AP2), which are attached to the cytosolic side of the transmembrane receptors.

58
Q

What are the steps involved with the fusion of a vesicle and a membrane?

A
  1. Tethering: vesicles attach to membrane via Rab proteins
  2. Docking: SNARE proteins (vSNARE in vesicle and tSNARE on membrane) bind to each other
  3. Some signal (often Ca2+) brings vesicle and membrane together
59
Q

What signals enzymes to be transported to the lysosome?

A

A phosphorylated N-acetylglucosamine is added to mannose. The GlcNAc is then removed, leaving just the phosphates.

This addresses the protein for the lysosome

This is proof that GAGs play a signaling role

60
Q

What receptor binds lysosomal enzymes in the golgi?

A

Mannose 6 phosphate receptor (MPR)

61
Q

What is autophagy?

A

the process of digesting old organelles in lysosomes

62
Q

Describe the process of autophagy.

A

1) A double membrane from the ER surrounds an organelle to be digested to form a autophagosome
2) A lysosome fuses with the autophagosome
3) Residual body (remains after digestion) will be either exocytosed or remain as a lipofuscin granule

63
Q

What is a lipofuscin granule?

A

granular yellow-brown pigment granules composed of lipid-containing residues of lysosomal digestion

they are a signal of wear and tear pigments found in liver cells

64
Q

What happens in lysosomal storage disorders?

A

Malfunctioning lysosomes cause lysosomes to build up within the cell.

These are recessive disorders that are fatal

65
Q

What are the main components of the cytoskeleton?

A

Actin, intermediate filaments, and microtubules

66
Q

What are the functions of cytoskeletal filaments?

A

1) Structure and support
2) intracellular transport
3) Contractility and motility
4) Spatial organization

67
Q

Describe the “movement” of microtubules over time.

A

Microtubules elongate and shorten over time. They are dynamic structures.

This behavior is believed to be due to allow the microtubules to search for things within the cells to attach to.

68
Q

What is the typical lifetime of a cytoskeletal microtubule?

A

Only several minutes

“Dynamic instability”

69
Q

Describe the structure of microtubules.

A

They are rigid structures made up of 13 protofilaments of alpha-beta dimers arranged in a circle. These protofilaments are held together via noncovalent forces

Each microtubule has polarity, with the plus end ending in beta and the minus end ending in alpha

70
Q

What are MAPs?

A

Microtubule associated proteins (MAPs) are asymmetric proteins with one end binding to the microtubule and and the other is a short filament.

They act as spacers, stabilizing the microtubules

71
Q

What does Colcemid do?

A

It binds to the plus ends of microtubules, preventing polymerization. This leads to destruction of the shape of the cell.

72
Q

What is microtubule nucleation?

A

The de novo formation of microtubules that occurs at centrosomes.

requires gamma tubulin

73
Q

What is an MTOC?

A

microtubule organing center

MTOCs consist of two centrioles at right angles to each other and an amorphous material called pericentriolar matrix (PCM)

Centrosomes are a type of MTOC

74
Q

What does the PCM consist of?

A

gamma tubulin, pericentrin and ninein

75
Q

What is the function of a centrosome?

A

it nucleates microtubules using gamma-tubulin with the minus end embedded in the PCM

76
Q

What is the energy source for microtubule assembly? How is this molecule used?

A

GTP binds to beta-tubulin

GTP is NOT hydrolyzed upon polymerization, but after incorporation into a polymer

77
Q

When is GDP released from a microtubule?

A

GDP is released after depolymerization

78
Q

What is γ-TuRC?

A

γ-Tubulin Ring Complexes

γ-TuRC’s are the templates for microtubule polymerization

γ-tubulin only binds to alpha tubulin, thus establishing the polarity of the microtubule

79
Q

What features distinguish mother and daughter centrioles from each other within centrosomes?

A

The mother centriole is distinguished by the presence of distal and subdistal appendages.

80
Q

What role does ninein play in the organization of centrosomes?

A

A portion of the γ-TuRC is docked at the mother centriole by ninein. The microtubules formed from this γ-TuRC are quickly captured by the anchoring complex, stabilizing the centrosome.

81
Q

Are microtubules always attached to MTOCs?

A

No. They can be severed from the MTOC and travel elsewhere.

82
Q

What is Katanin?

A

A microtubule severing protein made up of two subunits (p60 and p80).

83
Q

How do microtubules assist intracellular motility?

A

Microtubules are the tracks used by motor proteins to move vesicles, organelles, and molecules from one place to another within the cell

84
Q

A molecule is moving anterograde. Is it moving towards the nucleus or away from the nucleus?

A

Anterograde is the movement from the cell body toward the end of a process.

85
Q

In a neuronal axon, which end of the microtubule is facing the cell body?

A

The minus ends (alpha) are near the cell body.

The plus ends (beta) are near the synapse.

86
Q

What can molecular motor proteins bind to?

A

They bind microtubules and and cargo simultaneously

87
Q

How do motor proteins transport cargo?

A

The motor portion has an ATP binding domain that advances by one tubulin dimer with the hydrolysis of ATP to ADP and Pi

88
Q

Describe the structure of the kinesin superfamily of motor proteins.

A

They are made up of two heavy chains and two light chains.

The heads (on the heavy chains) have ATP binding domains. And they “walk” along the microtubules.

The tail binds to the cargo

89
Q

What is the length of a kinesin “step”?

A

8 nm, which is equivalent to the length of a tubulin dimer.

90
Q

What are dyneins and what do they do?

A

Another molecular motor protein.

Dyneins use the powerstroke ATP hydrolysis mechanism just like kinesins, but they cause RETROGRADE transport.

91
Q

What is Dynactin?

A

an adaptor protein specific for cargo

assists anterograde (kinesin) and retrograde (dynein) transport

92
Q

If a vesicle is bound to dynein, can it also be bound to kinesin?

A

Yes, cargo can be bound to both dynesin and kinesin, although only one of the motor proteins will be active at a given time.

93
Q

What are flagella? How do they function?

A

Hairlike projections from the cell surface that assist in locomotion.

They become rigid during the power stroke, but flexible in the recovery stroke.

94
Q

How do the sizes of cilia and microvilli compare?

A

Cilia are MANY times larger than microvilli.

95
Q

Describe the structure of a cilium.

A

9 microtubule doublets are arranged in a circle, with 2 microtubules in the middle (9+2 array)

The minus ends are embedded into the cell membrane and the plus ends extend to the tip

The peripheral doublets are connected by Nexin spacers.

96
Q

How does the structure of a microtubule doublet differ from the structure of a single microtubule?

A

Microtubule doublets have one complete microtubule, made of 13 protofilaments, and one incomplete microtubule made of 10-11 protofilaments.

97
Q

What do the radial spokes of the cilium do?

A

They connect the outer doublets to the central sheath

98
Q

What is the length of the longitudinal cilium unit that repeats?

A

96 nm

99
Q

What is an axoneme?

A

The inner cytoskeletal structure of a cilium

100
Q

What connects cilia to the cell body?

A

They are connected through the basal body, which is an MTOC similar in structure to a centriole

101
Q

How does intraflagellar transport occur?

A

Materials can move through the space between peripheral doublets and the plasma membrane by kinesin and dynein.

102
Q

What motor protein drives cilia/flagellar movement?

A

Dynein

Axonemal dynein (which is different than cytoplasmic dynein) hydrolyzes ATP causing adjacent doublets to slide relative to each other leading to movement.

103
Q

Describe the structure of actin microfilaments.

A

They are made of globular actin-ATP monomers composed of 4 subdomains

When polymerized, the filaments are polar because each subunit is oriented in the same region.

Polymerized actin is called F-actin, or microfilaments.

104
Q

Describe the assembly and disassembly of actin microfilaments.

A

Dependent on the concentration of actin-ATP monomers.

High [actin-ATP]: elongation at plus and minus end

Lower [actin-ATP]: added more to plus end than minus end

Even lower [actin-ATP]: removed from minus end but added to the plus end

105
Q

What is treadmilling?

A

When the actin microfilament assembly is at steady state, the units are added to the plus end at the same rate that they are removed from the minus end.

This results in the filament “flying” through the cell without changing length.

106
Q

What is the motor protein for actin filaments?

A

Myosin is the only motor that can bind actin.

107
Q

Describe the actin-myosin interaction.

A

The head domain (S1) of myosin binds actin and ATP. Hydrolysis of ATP leads to movement.

Movement always occurs towards the plus end

108
Q

If a vesicle begins traveling along a microtubule, can it switch and travel along actin later?

A

Yes. Vesicles with kinesin motors (for microfilaments) and myosin motors (for actin) can switch from one to the other to keep moving along.

Transport close to the membrane is usually guided by actin filaments.

109
Q

Describe the filaments that Myosin II can form.

A

Myosin II can form biopolar filaments by antiparallel interactions between the tails of the myosin molecules.

This results in the globular heads being aligned on either side of the myosin tail interactions

110
Q

What is a sarcomere?

A

The contractile unit of muscle fibers made up of actin and myosin.

111
Q

What filaments are present in the A band?

A

myosin and actin filaments overlap in the A band

112
Q

What filaments are present in the H zone?

A

Only myosin

This is region between opposing actin filaments.

113
Q

What filaments are present in the I band?

A

Only actin

114
Q

During contraction, which zones of the sarcomere decrease in length?

A

The H zone and the I band both narrow

115
Q

What is titin?

A

The largest protein known. Extends from the Z line to the M band.

Has elastic properties (due to PEVK region) that help prevent the sarcomere from tearing.

116
Q

What is nebulin?

A

A protein found within the thin filament that acts as a molecular ruler.

117
Q

What does tropomyosin and troponin do?

A

Tropomyosin is a filamentous protein that reinforces actin.

Troponin anchors tropomyosin ends to actin.

118
Q

Explain the role that Ca2+ plays in mediating actin-myosin interactions during muscular contractions.

A

Ca2+ binds troponin, which causes a conformational change that moves tropomyosin, exposing the actin-myosin binding sites on actin

The myosin heads can then bind actin and initiate the power stroke–> contraction

Cell Bio (3 decks)

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