FOM Week 1 Flashcards
1
Q
What is the purpose of the cytoskeleton?
A
Structural strength, transport, movement and directional info
2
Q
What does it mean when a cytoskeleton is dynamic?
A
location and life cycle can alter the protein output and ratios
3
Q
At what end does actin tend to have subunits added to?
A
The plus end, but can have units added to the minus end
4
Q
What important molecule does actin have a binding site for?
A
ATP binds right in the center
5
Q
What are ARPs? What do they do?
A
ARPs for a complex and bind to the minus end of the actin filament, stabilizing it. Filament will then grow rapidly on plus end. They also bind other acting molecules at a 70 degree angle and create a meshwork
6
Q
How do microtubules compare to actin?
A
They are thicker and consist of heterodimers of alpha and beta tubulin subunits 13 protofilaments come together
7
Q
What are the locations of the plus and minus end of a microtubule?
A
Plus end lies in the periphery and the minus end is in the centriole
8
Q
What is the purpose and outcome of the GTP cap on microtubules?
A
GTP cap stabilizes microtubule allowing for growth
9
Q
What happens to a microtubule with a GDP cap?
A
a GDP cap is unstable, the microtubule will begin to shrink GDP encourages curving of the protofilament which can lead to shrinking
10
Q
What can be used to stabilize the minus end of a microtubule?
A
Gamma tubulin
11
Q
What is formin?
A
Dimer that allows actin to grow faster by stabilizing the plus end and adding subunits
12
Q
What is profilin?
A
binds actin to enhance ATP binding and adds actin subunits to the plus end
13
Q
What is cofilin?
A
binds actin and condenses it leading to a shorter and thicker filaments
14
Q
What is a subunit example of a microfilament?
A
actin
15
Q
What are a few subunit examples intermediate filaments?
A
Vimentin (mesenchyme) Glial fibrillary acidic proteins (glia) Neurofilament (neurons) Keratins (epithelia) Nuclear lamin Desmin (muscle)
16
Q
What is a subunit example of microtubules?
A
alpha and beta tubulin
17
Q
What are the common structural properties of fibrillar proteins?
A
Repeating globular subunits and long twisting fibers Building structures for cytoskeleton or ECM Actin tubulin - repeating alpha and beta subunits creating protofilaments
18
Q
What are the common structural properties of integral membrane proteins? What are examples?
A
Surrounded by hydrophobic lipid membrane Inside out distribution of amino acids - hydrophobic amino acids span the membrane and hydrophilic sit outside the membrane Bundles of alpha helicies and beta barrels
19
Q
What are the common structural properties of intrinsically disordered proteins?
A
- Not globular 2. Unpredictable secondary structure 3. No hydrophobic core 4. Long repetitive sequences 5. Appear to fold when binding targets 6. Bind wide range of targets
20
Q
Explain the characteristics of proteins with similar sequences
A
These are homologs Can have as little as 25% of same seq but have similar function Difference in residues lead to individual characteristics
21
Q
What are the functional classes that proteins can share?
A
Chemical Signaling structure transport storage
22
Q
Provide an example of an isoform and explain what it is.
A
Hexokinase (phosphorylates many sugars) vs glucokinase (phosphorylates just glucose) Isoforms have same general function but subtle differences
23
Q
Can proteins share a common ligand? If so explain.
A
Yes Many proteins can bind ATP and have similar binding sites for this to occur
24
Q
What are two common post-translational modifications?
A
Phosphorylation and proteolysis
25
What is phosphorylation
Protein kinase removes a hydroxyl and the addition of a phosphate group. Can activate or deactivate a protein
26
What are the characteristics of proteolysis?
Proteases cleave the phosphate backbone Create a new N and C terminus Irreversible
27
What is a characteristic of protein modularity?
Mix and match of different classes on one polypeptide
28
What is a domain?
A domain is a part of a polypeptide that may have its own specific function Each domain may have its own characteristics and the function of the whole may not be knocked out by deletion of one domain
29
What are the types of folding?
On purpose or accidential
30
What is an example of a protein unfolding on purpose?
Protein digestion in the stomach as well as lysosomal protein degradation
31
What can happen what a protein is accidentally misfolded?
It can be targeted for degradation
32
What is cytoplasmic crowding and what can be a result of it?
The cytoplasm is very crowded and proteins can push up against each other possibly leading to protein unfolding. This can expose hydrophilic sidechains that will glomb to other side chains and aggregate together
33
What factors can cause a protein to denature?
pH, Ionic strength, Pressure, Temp, Urea, Osmotic Pressure
34
What is a pathological result of protein unfolding?
Amyloid formation can occur when unregulated protein aggregation occurs from different native folding
35
What factors can enhance folding?
Osmolytes, chaperone proteins, and chaperonins
36
What is an osmolyte and what are some examples of osmolytes?
Component that affects osmosis Amino acids, polyols (glycerol), methylamines (TMAO), Covalent osmolytes
37
What is an example of a chaperone protein and what do they do?
Heat shock proteins Aid in folding new proteins, help in misfolded proteins and transport across a membrane These bind to smaller sections and aid in folding
38
What are the characteristic and functions associated with chaperonin proteins?
Much larget than HSPs barrel structure provides inner cavity for protein folding Cytosolic protein Lid shuts on the proteins Proteins can go through chaperonins multiple until desired folding is achieved
39
What are the major degredative pathways in a cell?
Lysosomes and Proteosome
40
What are the characteristics of a lysosome?
Low pH to unfold protein and acid proteases to degrade the proteins
41
What are the characteristics of a proteosome?
Large cytosolic protein and utilizes ubiquitin tagging
42
How can degradation play a part in a role such as cystic fibrosis?
Mutation leads to slower protein folding, and thus the protein is degraded before it can fold
43
What intermediate filament is characteristic of muscle
Desmin
44
What intermediate filament is characteristic of epithelia?
Keratins
45
What intermediate filament is characteristic of neurons?
Neurofilaments
46
What intermediate filament is characteristic of glia?
Glial fibrillary acidic protein
47
What intermediate filament is characteristic of mesenchyme?
Vimentin
48
What proteins act to stabilize actin bundles?
Fimbrin - tight, doesnt allow myosin to connect creates parallel bundles Spectrin Actinin - allows for myosin creating contractile bundles Filamin dimers- creates and stabilizes actin meshwork
49
Why do so few actinopathies exist? Why do the genetic codes of all actin proteins seem to be so closely related?
Actin is extremely important and most embryos with actin mutations rarely make it past the 16 cell stage
50
What protein can stabilize the minus end of a microtubule?
Gamma tubulin
51
What two microtubule associated proteins play important roles in neurons?
MAP2 and Tau proteins
52
Describe the characteristics of a MAP2 protein?
Binds adjacent microtubules and allows for correct spacing of microtubules
53
What is the tole of Tau proteins?
These bind microtubules and pack them in tighter bundles.
54
What is a Tau tangle and how can it form?
Tau tangles occur when the Tau proteins hyperphosphorylate and begin to create amyloids. They are no longer in contact with the MT. This has been linked to CTE and brain injuries
55
What are the characteristics of epidermis bullosa simplex?
Mutations of keratin 5 and 14 are weak Disruption of basal layer Critical condition leads to infant death
56
What are the characteristics of epidermolytic hyperkeratosis?
Mutation of Keratin 1 and 10 Basal layer unaffected, epidermis affected cause damage to joints
57
What are the characteristics of epidermolytic plantopalmar keratoderma?
Mutation of keratin 9 Disruption of epidermis that is restricted to palms and soles
58
All glands are what?
EPITHELIAL!!!
59
What are the functions of the epithelium
Absorption, secretion, transport, excretion, protection, and sensory reception
60
What are the features of the epithelium?
Connected to each other tightly Lie on a basement membrane Form membranes and glands Have a distinct polarity Line all body surfaces, cavities and tubes
61
What are the three polarities an epithelial cell can have?
Apical (towards the top) Lateral (Sides) Basal (bottom)
62
What are the characteristics of the apical domain?
Microvilli, Cilia, and stereocilia
63
What are characteristics of microvilli and how do we distinguish them?
Microvilli are short projections of the luminal membrane This leads to greatly increased surface area These specialized for absorption Actin core Appear as a brushed border on histology slides
64
What are the characteristics of cilia?
These have a microtubule core Specialize in motility Inserted into the basal bodies Movement is driven by ATP
65
What are main difference between cilia and microvilli
Cilia - microtubule core and aid in movement Microvilli - actin core and aid in absorption
66
What are a few key characteristics of Kartengers Syndrome?
It is a PCD Patients experience situs inversus Possibly caused by the dyenin arms missing from microtubules
67
What are the characteristics of stereocilia?
Very long microvilli Contain long filamentous actin core Facilitates absorption Found in male epididymis
68
What are the characteristics of the Basal Domain?
Basal Lamina/Basement membrane Hemidesmosomes Basal infoldings
69
What are the characteristics and features of the basal lamina?
ECM proteins act as an interface between epithelium and supporting tissues Aid in establishing polarity and growth of the epithelial cells Contains the lamina lucidia and lamina densa
70
What is contained within the basement membrane
Lamina Reticularis
71
What are the characteristics of hemidesmosomes?
Link to epithelial cells in the basal lamina Cell to ECM interactions Link to intermediate filament proteins inside the cell
72
What is an integrin?
Transmembrane hemidesmosome linker protein
73
What is bullous phemphigoid
Auto-immune disease that attacks BP230 and BP180 (hemidesmosomes) A blistering disease that results from the splitting of the epithelium from the basal lamina
74
What are basal infoldings?
High concentrations of mitochondria allow for enhanced cellular traffic
75
What are the parts of the lateral domain?
Zonula occludens, Zonula adherens, Desmosomes, and gap junctions
76
What are the characteristics of the zonula occludens?
Block passage of luminal contents between cells Acts as a collar on the apical side of the cell Tight junction proteins made of claudin form sealing strands
77
What are the characteristics of the zonula adherens?
Adherens junction Lateral adhesions between epithelial cells Through the actin cytoskeleton Where the cell membrane interacts with the actin
78
What are the characteristics of desmosomes?
Cadherins and adhesion proteins - join intermediate filament in one cell to another Thought to be a spot weld Meant to withstand a large amount of friction
79
What is pemphigus?
Cells lose contact and blisters are formed Involving cadherins Leading to suprabasal blistering
80
What are gap junctions?
Lateral junctions comprised of two connexons that allow material to pass though
81
What are the characteristics of glands?
They are epithelial cells that have undergone proliferation, migration, and differentiation Specialized to produce fluid secretion Intracellular synthesis of macromolecules Secretory products stored in secretory granules
82
What are characteristics of unicellular glands?
Small dense core of secretory granules Nucleus at the basal section of the cell Synthesize and secrete hormones Intestine and respiratory system involvement (ex goblet cells)
83
What are the types of signaling?
Autocrine, paracrine, endocrine
84
What is autocrine signaling?
self stimulation "cellular masturbation"
85
What is paracrine signaling
Signals sent to a nearby protein
86
What is endocrine signaling?
Signals sent to the bloodstream for distant targets
87
What are the methods of signaling?
Merocrine, apocrine, and holocrine
88
What is merocrine signaling?
Conversion of membrane - exocytosis
89
What is apocrine signaling?
Secretion includes apical portion of the cell
90
What is holocrine signaling?
Involved total loss of the cell
91
What are the types of secretion from glands?
Serous - Enzymatic Mucous - mucins
92
What are current diagnostic limitations DNA sequencing?
Price, Time, cannot predict efforts of all proteins
93
What is fimbrin?
tight, doesnt allow myosin to connect creates parallel bundles
94
What is actinin?
allows for myosin creating contractile bundles
95
What is filamin?
dimers that create and stabilizes actin meshwork sit on top
96
What connect actin filaments in tight bundles, doesnt allow myosin to connect creates parallel bundles
fimbrin
97
What connects actin filaments and allows for myosin to connect creating contractile bundles
actinin
98
What is a dimers that creates and stabilizes actin meshwork sit on top?
filamin
99
Dimer that allows actin to grow faster by stabilizing the plus end and adding subunits looks like a collar
formin
100
binds actin to enhance ATP binding and adds actin subunits to the plus end looks like swinging arms
profilin
101
binds actin and condenses it leading to a shorter and thicker filaments
cofilin
102
What is the primary structure of a protein and what are its implications and what are the main interacting forces in it?
The primary structure is the amino acid sequence, this sequence has a preferred 3D structure and this determines the function of the enzyme. It utilizes peptide bonds that exhibit a partial double bond characteristic
103
What makes up the secondary structure of proteins and what forces are at work?
In secondary structure the appearance of alpha helicies and beta sheets begins to happen. This local folding occurs that is stabilized by H-bonding between N-H and C=O groups
104
What is the tertiary structure of a protein and what are the intramolecular forces that drive it?
Tertiary structure is the 3 dimensional structure of a protein with incorporation of side chain interactions. Disulfide bridges can form. Hydrophonic interactions cause hydrophobic residues to aggregate to the center of the protein away from the aqueous environment. Ionic bonds, H-bonds, and van Der waals forces are also at work.
105
What is quartnerary structure of a protein and how is this differenct then aggregation? What is a homodimer and what is a heterodimer?
Quarternary structure is when a functional protein consists of multiple peptide chains, whereas aggregation is the **unregulated** grouping of unrelated proteins.
Homodimer- 2 of the same polypeptide chains interacting
Heterodimer- 2 different polypeptide chains interacting
106
How can proteins be in motion?
In small proteins side chains can rotate and be flexible.
Larger proteins tend to have hinges that allow them to bend and flex
107
A mutation in this protein leads to Marfan's syndrome
What is fibrillin-1?
Fibrillin-1 forms fibrils in the ECM leading to abnormalities in connective tissue
108
What is a homolog?
Proteins that carry a similar sequence
109
What side chains in a protein can be phosphorylated?
Serine, tyrosine, or threonine
110
Proteins that are unable to be degraded by the the person are what?
These are allergens, they keep their from even after exposure to the various organs of the body
111
How many aggregated proteins are needed to form an amyloid?
Amyloids consist of at least 21 proteins aggregated together
112
What specific proteins make up amyloids and what are they resistant to?
Trick question: Amyloid protein formation is non-specific. Proteins of different types aggregate together and form extremely stable protein structures. Their stability is demonstrated because they are resistant to proteolysis and autoclave resistant.
113
What are examples of osmolytes?
Amino acids-proline, alanine, and taurine
114
What are the roles of heat shock proteins?
Fold new proteins
Refold misfolded proteins
Transport across a membrane
Control activities of some proteins
115
Why is SDS-PAGE beneficial for integral membrane proteins?
Integral membrane proteins won't work well (or maybe not at all) on native gel electrophoresis (which separates on protein charge, not size), because they are not soluble. The SDS of SDS-PAGE can **solubilize the unfolded forms of integral membrane proteins.**
116
What is the G-actin protein and what is its process?
The G-actin protein is an actin subunit. It has a plus and minus end and will bind to ATP. When the subunit is attached to the actin filament, the ATP will be hydrolyzed to ADP.
117
What is a key feature associated with intermediate filaments?
These will form head to tail coiled dimers
118
What is epidermolysis bullosa and what causes it?
In the skin the predominant intermediate filament is keratin. This keratin is linked to the hemidesmosome, which links the cytoskeleton to the ECM. In this disease the keratin is weakened, but the hemidesmosome is strong. Mechanical stress will cause cells to rupture along the basal edge, leaving some of the cell attached to the basal lamina. It is caused by a mutation in keratin 5 and 14 and pts develope blisters shortly after birth
119
What is epidermolytic hyperkeratosis?
A mutation in keratin 1 and 10, and these are found in the middle of the epidermis. These cells will separate, but the separation will cause the basal cell layer to stimulate the division of basal cells to produce more tissue, thus the term hyperkeratosis.
120
What is epidermolytic plantopalmar keratodema?
A mutation of in keratin 9 gene that damages tissues on the palms of the hands and the soles of the feet. Keratinized skins slough off easier.
121
Fill in this chart
122
What is the ARP complex and what does it do?
Activation of ARP2 and 3 will form a complex that binds to the minus end of actin, stabilizing it and allowing for the rapid growth of actin. Once bound to the actin it can attach to other existing actin molecules at a 70 degree angle, thus forming an actin meshwork.
123
What is formin and how does it relate to cytoskeletal development?
Formin is a dimer that stabilizes the actin bundle making it tighter hugging. It shimmies its way up the actin filament.
124
What is profilin?
The profilin has actin monomers bound to it. Essentially this protein complex will bind actin and then stick it onto the plus end of the actin filament. This allows the very rapid elongation of the actin filament.
125
What is cofilin?
Cofilin is another protein that cells use to modify the actin filament. If cofilin binds to the actin filament the actin filament will rotate in a smaller distance. The distance from one helix to the next is reduced in the presence of cofilin.
126
What are alpha-actinin and fimbrin and what are the differences between the two?
Alpha-actinin is a protein that creates contractile bundles. This has enough space for mysosin II to bind. If the actin filaments are bundled by fimbrin, then there is not enough space for the myosin to bind. This is a way for the cell to control actin myosin interactions.
127
What is filamin and how is it different from ARP?
Filamin is a protein that forms a dimer, and helps to stabilize the actin meshwork. This will provide extra strength to the cell. **This is when the actin filaments weave over eachother not joining side by side actin filaments.**
128
What are the functions of the MAP2 and Tau proteins?
MAP2 will bind to adjacent microtubules and allow a greater distance between microtubules. The binding of tau allows the microtubules to be packed into a tighter bundle.
129
What are the features of microvilli?
They have a core of actin filaments that insert into the terminal web. They increase the surface area of the apical membrane. They are specialized in absorption
130
Hemidesmosomes link the what to the what?
Link the intermediate filament proteins inside the cell to the extracellular matrix proteins of the basal lamina
131
What disease is most likely the cause of this and how does it occur?
Bullous phemphigoid. Auto-antibodies to the BP antigens cause the splitting of the epithelium from the basal lamina. The individual keratinocytes remain attached to each other, but the epithelium splits from the basal lamina
132
What is phemphigus?
autoantibodies for a type of cadherin (desmoglein) protein attack. This causes suprabasal blistering as basal cells remain attached to basal lamina.
133
What are the 3 methods of secretion?
134
