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
2
Q
How do the proteins know where they’re going?
A
SORTING SIGNALS aka SIGNAL SEQUENCES
3
Q
Where do sorting signals aka signal sequences occur?
A
Occurs in the primary & secondary structures of polypeptides
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
5
Q
What if a protein doesn’t have a protein signal?
A
By default, remain in the cytosol
6
Q
Cytosol
A
contains many metabolic pathways
protein synthesis
cytoskeleton
7
Q
Nucleus
A
contains main genome
DNA and RNA synthesis
8
Q
ER
A
synthesis of most lipids
synthesis of proteins for distribution to many organelles and to the plasma membrane
9
Q
Golgi apparatus
A
modification, sorting, and packaging of proteins and lipids for either secretion or delivery to another organelle
10
Q
Lysosomes
A
intracellular degradation
11
Q
Endosomes
A
sorting of endocytosed material
12
Q
Mitochondria
A
ATP synthesis by oxidative phosphorylation
13
Q
Chloroplasts
A
ATP synthesis and carbon fixation by photosynthesis
14
Q
Peroxisomes
A
oxidation of toxic molecules
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
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
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)
18
Q
BASIC AMINO ACIDS
A
lysine & arginine
19
Q
NLS (Nuclear localization signals) receptors use what?
A
GTP hydrolysis
20
Q
Mitochondria & Chloroplast Import
A
Proteins have signal sequence (ss)
Organelles membrane localized RECEPTORS
Transmembrane TRANSLOCATOR COMPLEX
21
Q
How are proteins transferred across the mitochondrial membrane?
A
UNFOLDED
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
23
Q
What kind of alpha helix does the mitochondrial signal sequence have?
A
An amphipathic (polar & nonpolar)
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”
25
How are the proteins that are being made directed for translocation into the ER?
By SIGNAL RECOGNITION PARTICLE (SRP) and the SRP receptor & translocation channel
26
What are the first two steps of ER import?
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
27
How are proteins modified in the ER & golgi?
Through glycosylation
28
Glycosylation
Where a carbohydrate to a macromolecule, such as a protein & lipids
Glycosylation is done by oligosaccharide protein transferases by a HIGH energy bond
29
Disulfide bond formation is also catalyzed in the ------
ER
30
What is the function of Chaperone proteins?
They make sure the proteins are properly folded and inserted in the membrane
31
What is the orientation of plasma membrane proteins dependent on?
On their synthesis & trafficking history
PROPER INSERTION OF THESE PROTEINS IS ESSENTIAL FOR THEIR FUNCTION
32
Which terminal signal sequence in many secretory proteins cleaved and how are they cleaved?
N-terminal are cleaved off by a signal peptidase
33
Stop transfer & stop transfer sequences inserts what into the ER membrane for single and multipass transmembrane domain proteins?
Hydrophobic transmembrane helices
34
Name an example of a multipass ™ (transmembrane) protein
bacteriorhodopsin
35
The unfolded protein response (UPR) pathway
is an example of a signal pathway that helps cells maintain quality control over protein folding & biogenesis by INCREASING chaperone activities
36
Name the disease that is caused by the fact that quality control at the ER chaperones is extremely stringent (tight)
cystic fibrosis (CF)
CF variant proteins can be slightly misfolded & misfolded proteins are rapidly degraded regardless of whether they are at all functional
37
How are vesicles made and how do they know where to go?
Vesicle transport
Vesicles move soluble and membrane-associated proteins between cellular compartments
38
Secretory pathway
“Forward” flow: ER→Golgi→Plasma Membrane→Lysosome
“Retrograde” flow: Golgi→ER “retrieval”
39
Endocytic pathway
Flow: plasma membrane→endosome→lysosome→plasma membrane
40
How are vesicles formed and targeted?
By the action of protein coats
41
Protein Coats
Coats serve to deform membranes so that they can be “pinched off” by dynamin: GTP hydrolysis
42
What is responsible for targeting & fusion specificity of vesicles to their destination membrane?
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
43
What is the key sorting station as is the endosome?
TRANS face of the golgi
44
2 golgi derived pathways to the plasma membrane
constitutive & regulated
45
Constitutive secretion pathway
unregulated exocytosis
46
Regulated secretion pathway
regulated exocytosis are made to wait for a signal to fuse
47
Another experimental approach that has been key to working out the secretory & endocytic pathways has been a
genetic one using temperature sensitive mutants
Using reconstituted protein sorting in cell extracts in vitro (complementary to genetics)
48
Endocytosis of specific proteins, ligands, hormones & biomolecules can be ------
receptor-mediated
Early endosome is like the in that it is a sorting point for different destinations
49
Lysosomal function is important to ----
Lysosomal function is important to sphingolipid degradation
Problems in these different enzyme functions cause lysosomal storage diseases
50
Protein staining reveals several structural filaments present in eukaryotic cells
Three filament systems make up the cytoskeleton of eukaryotic cells
Intermediate filaments
Microtubules
Actin filaments
51
Intermediate filaments
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
Intermediate filaments --> Cytoplasmic
Keratins in epithelia
Vimentin: in connective tissue, muscle cells,& glial cells
Neurofilaments in nerve cell
Nuclear lamins in all animal cells
53
Nuclear lamins
Nuclear lamins: provide strength, support, and integrity to the nuclear membrane
Regulated by phosphorylation & dephosphorylation
54
What is the disease that is caused by mutations in the lamin A gene→causing premature aging?
PROGERIA
55
Intermediate filaments are between microtubules and actin, however, they are
LESS dynamic than either
56
Microtubules
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
Monomer:
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
Both, actin filaments & microtubules monomers bound to ------- will add to the ----- of the filament while ---- bound monomers are ---- from the other end
ATP or GTP
growing end
ADP or GDP
lost
59
Note that addition and loss, Kon and Koff, can happen on both ends of the filament, however
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
How to study inherent aspects of assembly & disassembly of actin & microtubules?
THROUGH KINETICS
61
The concentration of monomers in solution will influence the
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
When the concentration of monomers is such that ASSEMBLY IS EQUAL TO DISASSEMBLY=
CRITICAL CONCENTRATION
63
Nucleation at the centrosome occurs due to what in microtubules?
Gamma-tubulin & associated proteins (called gamma-Turc) that surround the centrioles
64
Gamma Tubulin
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
What are tubulins?
They’re in MICROTUBULES
A protein superfamily
Members are related by evolution through gene duplication & divergence to different but related functions
66
What is the purpose for capping proteins?
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
Example of where microtubules function?
NEURONS, forms tracks for directed vesicles transport by motor proteins
68
Motor proteins
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
MTOCs of cilia & flagella are
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
Cell division & chromosome segregation
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
Pharmacological approaches: antimitotic drugs
Colchicine: monomer binding
Prevents assembly into filament
“CAM”
Taxol: filament binding
Prevents disassembly
“TFD”
72
Which eukaryotic cytoskeletal systems participate in dividing cells?
ALL 3 OF THEM (intermediate filaments, microtubules, and actins).
73
Actin filaments
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
For Actin Motor proteins
myosin
The heads associate with filament & light chains control specific cargo binding
75
Actin filaments are composed of
actin monomers & grow much like microtubules, except ATP is carried by monomers rather than GTP
76
Actin The system equilibrium in the cell is poised for very
rapid polymerization
77
What is the problem with actin?
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
Filament nucleation occurs by
Filaments are constantly being
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
Cell motility
crawling of cells over surfaces is an actin-dependent process- “push & pull” mechanism with three components
80
Push in Actin
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
How are the ARP complexes nucleated new filaments?
Side binding & generation of a “y”shaped branched network
82
Nucleation of new filaments near the leading edge of cell movement by
ARP complex activity balanced with severing/remodeling=highly dynamic structure
83
How does nucleation of new filaments in filopodial extension occurs?
By activity of FORMINS, adding to the (+) end of the filament & pushing the membrane “spike”outward
84
Signaling starts on the exterior of the cell through ----- or growth factors receptors
INTEGRINS
Help out set up focal contacts, which are locations of actin filaments assembly and signal transduction
85
Pull in Actin
Is provided by MYOSINS (motor proteins) associated with actin filaments
86
Myosin move (or move on) the actin filaments
2 main types:
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
Cytokinesis
another contractile function of actin & myosin-II filaments
88
Muscle contraction
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
Motor neurons
Signals→ T-tubule→Action potential→sarcoplasmic reticulum→Ca+2 release→action potential→myofibril contraction
90
Sequence of binding events that regulate contact muscle myosins with actin filament
Myosin-binding site exposed by Ca+2 binds to troponin→tropomyosin movement
91
4 phases
4 phases: G1, S (DNA replication), G2, M (mitosis and cytokinesis)
92
M phase has five stages: mitosis (nuclear division) +cytokinesis (cytoplasmic division)
Prophase
Prometaphase
Metaphase
Anaphase
Telophase
93
Replicated chromosomes exhibit
Cohesins: glue sister chromatids together until they split at anaphase
Condensins: recognize chromosomes into high compact mitotic structure
94
Prophase
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
Prometaphase
NE breakdown, chromosomes associate with spindle
96
Metaphase
Metaphase → congression of chromosomes
Forces from motors & microtubule dynamics balance chromosomes (kinetochores) on the plate (center of areas of spindles)
97
Anaphase
Anaphase → dissolution of sister chromatid cohesion, migration to poles
Forces from motor & microtubules pull chromosomes (kinetochores) to respective poles
98
What are the two phases to anaphase?
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
Telophase
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
Cytokinesis
cytoplasm division by a contractile ring of ACTIN & MYOSIN FILAMENTS
101
All three filament systems are dynamically regulated to accomplish
MITOSIS & CYTOKINESIS
102
Microtubules based MOTOR proteins, kinesins, and dyneins, play important roles in
spindle assembly & attachment & movement of chromosomes
103
Cell cycle cues coordinate the release of sister cohesion during the progression from metaphase to anaphase:
Inhibitory protein (securin) + inactive proteolytic enzyme (separase)--(active APC:anaphase promoting complex) →ubiquitylation & degradation of securin→active seperase→ cleaved & dissociated cohesins in anaphase
104
What is the difference between meiosis I & meiosis II?
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
What are the paired homologous chromosomes in meiosis I called?
BIVALENTS
106
MEIOSIS I
synaptonemal complexes are the sites for enzyme function→creating at least 1 CROSSOVER per pair of homologs
107
When failure to segregate homologs or chromatids in meiosis I or meiosis II its called
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
What helps to maintain diversity of alleles & factors affecting disease loci in diploid individuals
RECOMBINATION & SHUFFLING
109
Omics
parallel analysis across all genes/transcripts/proteins
110
Cellular mechanisms on how cells work & organisms develop
Combinatorial control of gene expression
Actions of signal transduction pathways
Cellular outcomes
111
How do these laws differ?
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
Independent assortment at work can be observed in a dihybrid cross of peas
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
