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Spring Sophomore Year > Cell Bio Exam 3 > Flashcards

Cell Bio Exam 3 Flashcards

1
Q

3 major pathways in eukaryotic cell for protein trafficking: all from cytoplasm to destination

A

Transport through nuclear pores (to nucleus)

Transport across membranes to chloroplast, mitochondria & peroxisomes

Transport by vesicles from ER to Golgi

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2
Q

How do the proteins know where they’re going?

A

SORTING SIGNALS aka SIGNAL SEQUENCES

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3
Q

Where do sorting signals aka signal sequences occur?

A

Occurs in the primary & secondary structures of polypeptides

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4
Q

What is a common required feature of sorting and trafficking processes to move proteins across the membrane to deform & separate or fuse membranes?

A

They require ENERGY input

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5
Q

What if a protein doesn’t have a protein signal?

A

By default, remain in the cytosol

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6
Q

Cytosol

A

contains many metabolic pathways

protein synthesis

cytoskeleton

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7
Q

Nucleus

A

contains main genome

DNA and RNA synthesis

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8
Q

ER

A

synthesis of most lipids

synthesis of proteins for distribution to many organelles and to the plasma membrane

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9
Q

Golgi apparatus

A

modification, sorting, and packaging of proteins and lipids for either secretion or delivery to another organelle

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10
Q

Lysosomes

A

intracellular degradation

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11
Q

Endosomes

A

sorting of endocytosed material

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12
Q

Mitochondria

A

ATP synthesis by oxidative phosphorylation

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13
Q

Chloroplasts

A

ATP synthesis and carbon fixation by photosynthesis

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14
Q

Peroxisomes

A

oxidation of toxic molecules

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15
Q

What are the 2 suspected origins for the evolution of internal membrane compartments?

A

Plasma membrane invaginations: endomembrane system

Endosymbionts: mitochondria & chloroplasts
Double membrane & own genome
Anaerobic pre-eukaryotic cell→ early aerobic eukaryotic cell

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16
Q

Endosymbiosis theory is supported by several observations

A

Organelles have circular chromosomes (like bacteria)

Organelle genes are more similar to bacterial genes than to those found within the nucleus

During the evolution of mitochondria and chloroplasts, most genes have been lost or transferred to the nucleus

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17
Q

Nuclear Transport Steps

A

Nuclear pore complexes: allows proteins & mRNAs to traffic across the nuclear membrane

Nuclear localization signals (NLS): “nuclear” proteins associate with NLS receptors which MOVE THE CARGO ACROSS the nuclear membrane in GTP dependent manner

Nuclear export signals (NES)

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18
Q

BASIC AMINO ACIDS

A

lysine & arginine

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19
Q

NLS (Nuclear localization signals) receptors use what?

A

GTP hydrolysis

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20
Q

Mitochondria & Chloroplast Import

A

Proteins have signal sequence (ss)

Organelles membrane localized RECEPTORS

Transmembrane TRANSLOCATOR COMPLEX

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21
Q

How are proteins transferred across the mitochondrial membrane?

A

UNFOLDED

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22
Q

How do the signal sequences get removed in Mitochondria & chloroplast import?

A

SIGNAL PEPTIDASES - this is unlike nuclear localization where shuttling can occur

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23
Q

What kind of alpha helix does the mitochondrial signal sequence have?

A

An amphipathic (polar & nonpolar)

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24
Q

ER import vesicle traffic

A

Signal receptor recognition particle (SRP), SRP receptor

ER: first decision point for protein destinations

Vesicle traffic: coats & SNARES

Glogi: the major destination point for paths→”bus station”

Endosome = the other major: “bus station”

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25
Q

How are the proteins that are being made directed for translocation into the ER?

A

By SIGNAL RECOGNITION PARTICLE (SRP) and the SRP receptor & translocation channel

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26
Q

What are the first two steps of ER import?

A
  1. Cotranslational insertion of signal sequence bearing proteins & into the ER membrane
  2. SRPs associates with the SRP associated with the nascent ss, this stalls the ribosome and aids in docking on the ER membrane at the SRP receptor
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27
Q

How are proteins modified in the ER & golgi?

A

Through glycosylation

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28
Q

Glycosylation

A

Where a carbohydrate to a macromolecule, such as a protein & lipids

Glycosylation is done by oligosaccharide protein transferases by a HIGH energy bond

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29
Q

Disulfide bond formation is also catalyzed in the ——

A

ER

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30
Q

What is the function of Chaperone proteins?

A

They make sure the proteins are properly folded and inserted in the membrane

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31
Q

What is the orientation of plasma membrane proteins dependent on?

A

On their synthesis & trafficking history

PROPER INSERTION OF THESE PROTEINS IS ESSENTIAL FOR THEIR FUNCTION

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32
Q

Which terminal signal sequence in many secretory proteins cleaved and how are they cleaved?

A

N-terminal are cleaved off by a signal peptidase

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33
Q

Stop transfer & stop transfer sequences inserts what into the ER membrane for single and multipass transmembrane domain proteins?

A

Hydrophobic transmembrane helices

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34
Q

Name an example of a multipass ™ (transmembrane) protein

A

bacteriorhodopsin

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35
Q

The unfolded protein response (UPR) pathway

A

is an example of a signal pathway that helps cells maintain quality control over protein folding & biogenesis by INCREASING chaperone activities

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36
Q

Name the disease that is caused by the fact that quality control at the ER chaperones is extremely stringent (tight)

A

cystic fibrosis (CF)

CF variant proteins can be slightly misfolded & misfolded proteins are rapidly degraded regardless of whether they are at all functional

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37
Q

How are vesicles made and how do they know where to go?

A

Vesicle transport

Vesicles move soluble and membrane-associated proteins between cellular compartments

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38
Q

Secretory pathway

A

“Forward” flow: ER→Golgi→Plasma Membrane→Lysosome

“Retrograde” flow: Golgi→ER “retrieval”

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39
Q

Endocytic pathway

A

Flow: plasma membrane→endosome→lysosome→plasma membrane

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40
Q

How are vesicles formed and targeted?

A

By the action of protein coats

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41
Q

Protein Coats

A

Coats serve to deform membranes so that they can be “pinched off” by dynamin: GTP hydrolysis

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42
Q

What is responsible for targeting & fusion specificity of vesicles to their destination membrane?

A

Rabs, tethers, v-SNAREs (v for vesicle) & t-SNAREs (target found on membrane)

Rabs recognize tethers, then v-SNAREs & t-SNAREs drive the fusion reaction & help provide membrane specificity

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43
Q

What is the key sorting station as is the endosome?

A

TRANS face of the golgi

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44
Q

2 golgi derived pathways to the plasma membrane

A

constitutive & regulated

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45
Q

Constitutive secretion pathway

A

unregulated exocytosis

46
Q

Regulated secretion pathway

A

regulated exocytosis are made to wait for a signal to fuse

47
Q

Another experimental approach that has been key to working out the secretory & endocytic pathways has been a

A

genetic one using temperature sensitive mutants

Using reconstituted protein sorting in cell extracts in vitro (complementary to genetics)

48
Q

Endocytosis of specific proteins, ligands, hormones & biomolecules can be ——

A

receptor-mediated

Early endosome is like the in that it is a sorting point for different destinations

49
Q

Lysosomal function is important to —-

A

Lysosomal function is important to sphingolipid degradation

Problems in these different enzyme functions cause lysosomal storage diseases

50
Q

Protein staining reveals several structural filaments present in eukaryotic cells
Three filament systems make up the cytoskeleton of eukaryotic cells

A

Intermediate filaments
Microtubules
Actin filaments

51
Q

Intermediate filaments

A

Most different compared to the others in structure /composition and regulation

Scaffold or networking provide mechanical strength to cells & organelles

Extensive & very stable assembly interactions

52
Q

Intermediate filaments –> Cytoplasmic

A

Keratins in epithelia

Vimentin: in connective tissue, muscle cells,& glial cells

Neurofilaments in nerve cell

Nuclear lamins in all animal cells

53
Q

Nuclear lamins

A

Nuclear lamins: provide strength, support, and integrity to the nuclear membrane

Regulated by phosphorylation & dephosphorylation

54
Q

What is the disease that is caused by mutations in the lamin A gene→causing premature aging?

A

PROGERIA

55
Q

Intermediate filaments are between microtubules and actin, however, they are

A

LESS dynamic than either

56
Q

Microtubules

A

Creates polarity in cells/chromosome elements

Arrange & move organelles

Track for vesicle movement by motor proteins

Cell division & motility –> Cilia & flagella

Microtubules + end growth or shrinkage is regulated by GTP bonding & hydrolysis

(+) aka growing ends are oriented toward the cell periphery & away from MTOC (microtubule organizing center)

Organization of the ER & golgi

Responsible of dynamic instability

Individual microtubule ends, unless capped or protected are constantly either growing or shrinking

Alpha-beta tubulin heterodimer –> Protofilament

57
Q

Monomer:

A

filament dynamics of microtubules & actin filaments are regulated by similar activities:

Nucleotide binding and hydrolysis on growing end of the filament

Proteins acting to influence filaments or monomers, e.g nucleators, serving, bundingling, sequestering

58
Q

Both, actin filaments & microtubules monomers bound to ——- will add to the —– of the filament while —- bound monomers are —- from the other end

A

ATP or GTP

growing end

ADP or GDP

lost

59
Q

Note that addition and loss, Kon and Koff, can happen on both ends of the filament, however

A

the “+” or growth favoring end of the filament is where the actin-ATP or tubulin-GTP is found and this end is such that Kon is much greater than Koff, whereas on the other end addition is much less favored or not at all.

60
Q

How to study inherent aspects of assembly & disassembly of actin & microtubules?

A

THROUGH KINETICS

61
Q

The concentration of monomers in solution will influence the

A

RATE OF ADDITION to the growing end

K: is the equilibrium constant for the addition of monomers

Concentration doesn’t influence the off rate
By “off rate”=Koff

62
Q

When the concentration of monomers is such that ASSEMBLY IS EQUAL TO DISASSEMBLY=

A

CRITICAL CONCENTRATION

63
Q

Nucleation at the centrosome occurs due to what in microtubules?

A

Gamma-tubulin & associated proteins (called gamma-Turc) that surround the centrioles

64
Q

Gamma Tubulin

A

Discovered in mold in ohio

Extragenic suppressor of an aspergillus beta-tubulin allele (genetic approach)

It’s different from both alpha & beta, key similarities to beta

Gamma binds alpha like beta does in the protofilament to initiate or nucleate protofilament formation

65
Q

What are tubulins?

A

They’re in MICROTUBULES

A protein superfamily

Members are related by evolution through gene duplication & divergence to different but related functions

66
Q

What is the purpose for capping proteins?

A

They can stabilize the (+) ends from depolymerization to make a stable array of microtubules (like a set of track)

Create polarity in cells

Arranging & moving organelle

67
Q

Example of where microtubules function?

A

NEURONS, forms tracks for directed vesicles transport by motor proteins

68
Q

Motor proteins

A

Motor proteins move cargo (vesicles, other microtubules, organelles, chromosomes) on microtubules in a specific direction

  1. Kinesin: (+) end, forward (KF)
  2. Dynein: (-) end, backward - Coordinated between the outer doublet microtubules
69
Q

MTOCs of cilia & flagella are

A

MTOCs of cilia & flagella are: basal bodies

Functionally and compositionally related to centrioles

In plant cells, there are NO centrosomes & the MTOC are more diffuse, but still shares some components of centrosomes

70
Q

Cell division & chromosome segregation

A

Cell division & chromosome segregation is a highly regulated collaboration of DNA & proteins associated with the microtubules cytoskeleton

Formation of a mitotic spindle begins with centrosome duplication & separation

Changes in microtubules dynamics and distribution are coordinated tightly with the cell cycle

Separation requires motors

Coordination works in part by the cell cycle checkpoints

71
Q

Pharmacological approaches: antimitotic drugs

A

Colchicine: monomer binding
Prevents assembly into filament
“CAM”

Taxol: filament binding
Prevents disassembly
“TFD”

72
Q

Which eukaryotic cytoskeletal systems participate in dividing cells?

A

ALL 3 OF THEM (intermediate filaments, microtubules, and actins).

73
Q

Actin filaments

A

Filament structure & dynamics

Control cell shape, movement membranes

Cell motility

Tracks for vesicle movement by motor proteins

Creates polarity in cells (like microtubules)

Force generation (muscles, dividing cells)

Found throughout the cell, they are most prevalent areas of the cell periphery

74
Q

For Actin Motor proteins

A

myosin

The heads associate with filament & light chains control specific cargo binding

75
Q

Actin filaments are composed of

A

actin monomers & grow much like microtubules, except ATP is carried by monomers rather than GTP

76
Q

Actin The system equilibrium in the cell is poised for very

A

rapid polymerization

77
Q

What is the problem with actin?

A

Much more actin in cells than needed, so the problem is not availability, but how to keep it out of filaments-solution is monomer sequestering (thymosin & profilin) & filament capping

78
Q

Filament nucleation occurs by

Filaments are constantly being

A

Filament nucleation occurs by Arp complex or formin activity which is locally stimulated/regulated

Filaments are constantly being remodeled by severing (gelsolin) and further addition & branching

79
Q

Cell motility

A

crawling of cells over surfaces is an actin-dependent process- “push & pull” mechanism with three components

80
Q

Push in Actin

A

Lamellipodia & filopodia are extended from the cell body; integrins help provide “traction” by adhesion to substrates

The pushing is controlled by signaling from the outside of the cell to key Rho GTPase polarity & signaling proteins

They control regulators by the actin cytoskeleton (ARP, other filament regulators)

81
Q

How are the ARP complexes nucleated new filaments?

A

Side binding & generation of a “y”shaped branched network

82
Q

Nucleation of new filaments near the leading edge of cell movement by

A

ARP complex activity balanced with severing/remodeling=highly dynamic structure

83
Q

How does nucleation of new filaments in filopodial extension occurs?

A

By activity of FORMINS, adding to the (+) end of the filament & pushing the membrane “spike”outward

84
Q

Signaling starts on the exterior of the cell through —– or growth factors receptors

A

INTEGRINS

Help out set up focal contacts, which are locations of actin filaments assembly and signal transduction

85
Q

Pull in Actin

A

Is provided by MYOSINS (motor proteins) associated with actin filaments

86
Q

Myosin move (or move on) the actin filaments
2 main types:

A
  1. Myosin I: vesicle & membrane movements
  2. Myosin II: sliding/contraction in muscles, cytokinesis contractile ring, trailing end migrating cells

Structure of a sarcomere: ATP is consumed by each myosin head as it moves along the actin filament

87
Q

Cytokinesis

A

another contractile function of actin & myosin-II filaments

88
Q

Muscle contraction

A

Involves rapid & dynamic control of contacts between myosin filaments & actin filaments in ordered structure called sarcomeres

Two types span the space between Z discs:
Thick filaments (myosin filaments)
Thin filaments (actin filaments anchored to Z disc)

89
Q

Motor neurons

A

Signals→ T-tubule→Action potential→sarcoplasmic reticulum→Ca+2 release→action potential→myofibril contraction

90
Q

Sequence of binding events that regulate contact muscle myosins with actin filament

A

Myosin-binding site exposed by Ca+2 binds to troponin→tropomyosin movement

91
Q

4 phases

A

4 phases: G1, S (DNA replication), G2, M (mitosis and cytokinesis)

92
Q

M phase has five stages: mitosis (nuclear division) +cytokinesis (cytoplasmic division)

A

Prophase
Prometaphase
Metaphase
Anaphase
Telophase

93
Q

Replicated chromosomes exhibit

A

Cohesins: glue sister chromatids together until they split at anaphase

Condensins: recognize chromosomes into high compact mitotic structure

94
Q

Prophase

A

Prophase → sister chromatids condense

Spindle assembly

Kinetochores interact with kinetochore microtubules that are parallel to interpolar microtubules in the spindle

Microtubules interacting protein complexes build at centromeres

ASTER (unattached) microtubules position the spindle in many cells

95
Q

Prometaphase

A

NE breakdown, chromosomes associate with spindle

96
Q

Metaphase

A

Metaphase → congression of chromosomes

Forces from motors & microtubule dynamics balance chromosomes (kinetochores) on the plate (center of areas of spindles)

97
Q

Anaphase

A

Anaphase → dissolution of sister chromatid cohesion, migration to poles

Forces from motor & microtubules pull chromosomes (kinetochores) to respective poles

98
Q

What are the two phases to anaphase?

A

A: chromosomes move apart
- Through the shortening of kinetochores

B: poles (and chromosomes) move apart
- Sliding force between interpolar microtubules from opposite poles to push the poles apart; a pulling force
- Pulls the poles toward the cell cortex→moving the two poles apart

99
Q

Telophase

A

Telophase → NE reassembly, migration of nuclei

Nuclear envelope assembly: dephosphorylation of lamins

Decondensation of chromosomes

Division of the cytoplasm beings with the assembly of the contractile ring

100
Q

Cytokinesis

A

cytoplasm division by a contractile ring of ACTIN & MYOSIN FILAMENTS

101
Q

All three filament systems are dynamically regulated to accomplish

A

MITOSIS & CYTOKINESIS

102
Q

Microtubules based MOTOR proteins, kinesins, and dyneins, play important roles in

A

spindle assembly & attachment & movement of chromosomes

103
Q

Cell cycle cues coordinate the release of sister cohesion during the progression from metaphase to anaphase:

A

Inhibitory protein (securin) + inactive proteolytic enzyme (separase)–(active APC:anaphase promoting complex) →ubiquitylation & degradation of securin→active seperase→ cleaved & dissociated cohesins in anaphase

104
Q

What is the difference between meiosis I & meiosis II?

A

Meiosis I: DNA replication, sisters remain COHESED, while homologous chromosomes segregate

Meiosis II: second round of division, sisters segregate (like mitosis)

Meiosis NON IDENTICAL HAPLOID CELLS
Mitosis genetically IDENTICAL DIPLOID CELLS

105
Q

What are the paired homologous chromosomes in meiosis I called?

A

BIVALENTS

106
Q

MEIOSIS I

A

synaptonemal complexes are the sites for enzyme function→creating at least 1 CROSSOVER per pair of homologs

107
Q

When failure to segregate homologs or chromatids in meiosis I or meiosis II its called

A

nondisjunction and leads to aneuploidy

aneuploidy: the condition of having an abnormal number of chromosomes in a haploid set

Example: down’s syndrome→trisomy for chromosome 21

108
Q

What helps to maintain diversity of alleles & factors affecting disease loci in diploid individuals

A

RECOMBINATION & SHUFFLING

109
Q

Omics

A

parallel analysis across all genes/transcripts/proteins

110
Q

Cellular mechanisms on how cells work & organisms develop

A

Combinatorial control of gene expression

Actions of signal transduction pathways

Cellular outcomes

111
Q

How do these laws differ?

A

The Law of Segregation dictates that when we form
gametes, we separate allele copies so the gametes can be haploid.
Differently, the Law of Independent Assortment states that the separation of each pair of chromosomes is completely independent from the separation of any other pair. They each separate randomly, and the outcome of one separation has no influence over the separation of the other.

112
Q

Independent assortment at work can be observed in a dihybrid cross of peas

A

Independent assortment at work can be observed in a dihybrid cross of peas - the presence of new phenotype combinations indicates the genes for seed shape and color assort independently

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