Finals ugh Flashcards
(377 cards)
1
Q
What is saccharyomyces cerevisiae
A
A single celled eukaryote model organism
2
Q
What type of organism is extracellular matrix special to
A
Animal cells, other organisms have other stuff
3
Q
What is a lysosome, what type of organisms have this
A
It is a compartment that degrades cellular components no longer needed, exclusive to animal cells
4
Q
What are three things not present in animal cells and what do they do? Are they only present in plant cells
A
Cell walls, which protect against mechanical stress and shape the cell. Vacuoles, with a type of degradation and another for storage. Chloroplasts for photosynthesis. Not only plants, some cells are neither plants nor animals
5
Q
WHat is a cytoplasm
A
Contents of the cell outside the nucleus, includes everything like organelles and ribosomes, cytoskelly
6
Q
What is the cytosol
A
Aqueous part of the cytoplasm not including membrane bound organelles, but does include ribosomes and cytoskelly
7
Q
What is the lumen
A
Inside the organelles, it is the space in between two nucleic membranes, and the entirety of the shit inside a mitochondria
8
Q
What do membranes do (6 things)
A
Compartamentalization, scaffolding for biochem activities,act as a semipermeable barrier, transport solutes, respond to exernal signals, and facilitate interactions between cellS
9
Q
Why is a membrane fluid and mosaic
A
Because of the mobility of lipids and some of the proteins, because of the different lipids and proteins
10
Q
What does the hydrophilic head and hydrophobic tail make the phospholipid overall
A
Amphipathic
11
Q
What different lipids are the membranes made of
A
phospholipids, sterols, and glycolipids
12
Q
What is a phospholipid’s polar head made of
A
A molecule such as choline and serine (can be different groups, including amino acids and other non-amino acids) and phosphate, both of which are negatively charged.
13
Q
What connects the hydrophilic head to the hydrophobic tail
A
Glycerol
14
Q
What is a sterol made of
A
A hydrophilic head of an OH and a hydrocarbon tail that’s nonpolar. Only one tail, not two.
15
Q
What is a glycolipid made of
A
A hydrophilic head that connects with two hydrocarbons. It has one tail, like sterols
16
Q
What is a membrane phospholipid with a glycerol group called
A
Phosphoglycerides
17
Q
How many carbons are the hydrocarbon tails on a phospholipids and what are the two types
A
They can be 14-24 carbons and is saturated or unsaturated. Unsaturated does not maximize the number of Hs, because it has a double bond
18
Q
What is phospatidylcholine and where is the choline
A
The choline is above the phosphate and it is the head group
19
Q
Draw the phosphate and glycerol structures
A
refer to notes
20
Q
What happens when phospholipids spontaneously self associate into bilayers in aqueous environments?
A
Free edges are eliminated, and you get self sealing containers
21
Q
What is the minimum diameter of a phospholipid compartment
A
25 nm
22
Q
What are liposomes
A
Artificial lipid bilayers. (Just know following) Used to study lipid properties, membrane properties, drug dicovery
23
Q
What happens when a cell membrane is pierced
A
The membrane will reseal, it can be deformed without breaking it, and has structure with fluidity
24
Q
How can phospholipids move
A
Diffuse laterally (switch places with neighbors often, you can also go up and down slightly), rotate (spin wheee), flex (wobbling), and flip flopping, but very very rare, and it is spontaneous
25
Why do you need to regulate cell membrane fluidity
For the function of things like membrane proteins, which are used for transport, enzyme activity, and signaling.
26
What influences membrane fluidity
Temperature, the colder the less fluid. Composition: the more cis double bonds, the more fluidity because the less tight the packing. The shorter the hydrocarbon tails, the more fluid because the lipid tails interact less (it's like thinner fabric, such as 涤纶 as opposed to denim). It allows for more flexion and more rotation. And lipid composition, such as cholesterol in animal cell membranes stiffens the membrane and decreases water permeability
27
What are the types of sterols in animal and plant cells
Animals have cholesterol, plants have plant sterols and some cholesterol
28
How much of the plasma membrane by weight are sterols
20%
29
How does the sterol decrease mobility of the phospholipid tails and make it less permeable to polar molecules
It has a rigid planar ring structure which acts like a wedge (creates big hydrophobic region)
30
What is the nonpolar hydrocarbon tail of a sterol made of
The same shit as that of a phospholipid (chemically equivalent)
31
What does a scramblase and where is it.
Scramblases are phospholipid translocators and they quickly flipflop phospholipds to the other layer RANDOMLY. This is beccause phospholipid synthesis happens by adding phospholipids to the cytosolic side, and you need a scramblase to even it out. in golgi membrane
32
Why do membranes retain orientation
To avoid moving the membrane glycoprotein to the wrong side.
33
What side is phosphatidylserine on
Cytosolic
34
What does a flippase do
It flips specific phospholipids to the cytosolic leaflet using ATP (for example phosphatidylserine to the cytosolic side). Some can bind cytosolic proteins at the plasma membrane.
35
How are glycolipds and glycoproteinns formed
Adding sugar groups to lipids and proteins on luminal face of the golgi, and it will end up on the plasma membrane inside some organelles.
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Which side of the bilayer can cholesterol be
Any
37
What are the four types of membrane proteins
Transmembrane, monolayer associated, lipid linked, protein attached
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How are lipid linked membrane proteins held onto the lipid bilayer
The lipid is in the bilayer but the protein is not.
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How are protein attached membrane proteins attached to the bilayer
Associate with membrane or integral membrane protein noncovalently
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How much mass of animal membrane is from membrane protein
50%
41
How many times can a transmembrane protein pass through the lipid bilayer
Once or more
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What is the part embedded in the membrane for a monolayer associated protein
Amphipathic alpha helix
43
How do you extract integral membrane proteins? Which are the three integral membrane protein types
Detergents to destroy the lipid bilayer. THe three types are transmembrane, monolayer associated, and lipid linked
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What can peripheral membrane proteins attach to to hold it into place, and how to extract
Its bound to other proteins or lipids by noncovalent interactions. It only needs gentle extraction methods (lipid bilayer intact)
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Why are transmembrane proteins amphipathic
The aqueous domains have AA side chains that are polar, vice versa for membrane spanning domains
46
How many amino acids in a membrane spanning alpha helix, why do they look like that
20, its so the peptide bonds are hydrophilic and bind to itself , leaving hydrophobic side chains on the outside
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What are the types of membrane spanning domains
Multiple alpha helices, with amphipathic nature so the hydrophilic faces in, and beta barrels like porin proteins in bacteria. It is a rigid channel that doesn't undergo conformational changes and let small nutrients, metabolites, and inorganic ions through
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What is the job for a single pass membrane spanning protein
receptor
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Multipass membrane spanning proteins are:
amphipathic
50
Can you orient transmembrane proteins any way you want
no, orientation needed for function
51
How does x ray crystallography work
x ray hits protein crystal and the diffracted beams show a diffraction pattern that allows you to calculate structure. You get a graph of hydropathy index on the y axis, amino acid number on the x, with 0 being N terminus or C terminus (can be switched around). The higher the peak the more hydrophobic. You can see the 20-30 hydrophobic amino aicds that span membrane as alpha helix
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What is the hydrophilicity properties of the alpha helix of a monolayer associaited membrane protein
hydrophilic on one side, hydrophobic on the other
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Which side (extracellular or cytosolic) are lipid linked membrane proteins added on
The protein could be synthesized on the ER side or the cytosolic side. If it is synthesized from the ER side, there will be a GPI anchor which then ends up on the cell surface. If it is synthesized on the cytosolic side by cytosolic enzymes. then the protein will be directed onto cytosolic side
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54
How do detergents work
The hydrophobic region interacts with the hydrophobic parts of the phospholipids and proteins, forming a liquid detergent micelle. Detergents also form detergent micelles by themselves in water to make the hydrophobic heads face out. You can also have a water soluable protein lipid detergent complex where everything is mashed together
55
How do you get only the protein of interest in a bilayer to study it
You get the membrane proteins solubilized with detergent, then get rid of the lipid detergent micelles and add phospholipids with detergent. Remove detergent and proteins will join with membrane. Lipids allow normal protein structure and function and proteins diffuse faster in artifical membrane
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What is a membrane domain
functionally and structurally specialized region in the cell membrane or organelle, that has specific proteins, Tight junction connect cells to adjacent ones and proteins cannot go past that
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What is lateral diffusion of membrane proteins and what is used to study it
It is moving left and right. Not always can proteins diffuse laterally. You study with FRAP
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How does FRAP work
proteins bind to GFP, which is a green fluorescent protein covalently attached, and then you incubate. photobleach with lazer, and the unbleached will move around and migrate in.
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What does faster recovery indicate for diffusion coefficient in FRAP
The fluorescence recovery rate indicates rate of protein diffusion, quicker recovery is quicker diffusion coefficient
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What types of proteins can you use for FRAP
cytosolic and membrane
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How can you tell a protein does not diffuse laterally? How to tell if it is slower
If the recovery for FRAP does not really get back to the original point, it does not diffuse. If it does but the slope is less, its slower
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What is the difference between artifical bilayers and cell membranes
Artifical bilayers are impermeable to most water soluble molecules, but cell membrans allow membrane transport proteins to facilitated transport specific molecules through passive diffusion or active transport.
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What molecules are permable across artificial/nonartificial bilayers without proteins
Small nonpolar are highly permeable, small unchareged but POLAR are slightly permeable. Larger uncharged polar molecules are very very slightly permeable, ions don't get through
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Why are small nonpolar molecules permeable
For cell respiration
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What does it mean for something to be permeable across a membrane
It can move via simple diffusion across, high concentration to low (down gradient). More hydrophobic/nonpolar diffuse faster
66
What do transmembrane proteins transport and how. How do cell membranes differ in transmembrane proteins
Polar and charged molecules like ions, sugars, amino acids, nucleotides, various cell metabolites. Each transport protein is selective and transport a specific class of molecules. Different cell membranes have a different complement of transport proteins
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How does a channel protein transport
It selects based on size and electric charge. It binds weakly to transported molecule and does not change in conformation during transport. They are hydrophobic pores that allow diffusion, and the channel is opened up to let stuff through
68
How does a transporter protein transport
Binds strongly to transported molecule, does change in conformation a lot and moves shit by changing shape. The solute fits into binding site and has specific binding of the solute
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What are passive transporters
Simple diffusion, channel proteins (aka channel mediated), and transporter mediated transport. Transporters can be passive or active.
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What is active transport
A transporter pump that moves up the concentration gradient and needs energy
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What forms the electrochemmical gradient
The concentration gradient, membrane potential. The concentration gradient usually wins, for example when concentration pushes the positive charged ions out but outside is also positively charged. If the concentration gradient and membrane potential work in the same way, then it goes really fast
72
Are channels or transporters faster
Channels
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How do channel proteins select what to bring through
Ion size and electric charge, most are selective. The dehydrated K+ ion will go through because water does not go through
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What organisms have ion channels
Almost everyone, animals, plants, microorganisms
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What is the difference between non gated and gated ion channels
Non gated are always open. They are still selective on what to move out though. It has a major role in generating membrane potential in plasma membrane across cells. For example K+ moves out of the cell to generate resting membrane potential in animal cells.
76
Explain the electrochemical gradient for K+
The extracellular space is positively charged but has a lesser concentration
77
What are gated ion channels, are they common
They are the most common and need a signal to open
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What are the types of gated ion channels
Mechanically gated, you need stress. LIgand gated (need ligand like neurotransmitter, it can be extracellular ligand or intracellular). And Voltage gated, that needs a change in voltage across membrane
79
How does transporter mediated diffusion behave in terms of speed, compared to simple diffusion
Transporter mediated goes quick then simple goes slow.
80
When a transporter protein is in the transition state with a substrate in the middle, what can happen
It is reversible. It can puke the substrate back out to the original side. If more solute outside, the solute binds more to the transporter facing outside, and thus more goes in
81
What does a glut uniporter do
It transports glucose down the concentration gradient in either direction, in or out. It is reversible, but always down. Passive transport
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What are examples of active transport and the energies used
Gradient driven pump with one solute down gradient to provide energy to move the second against the gradient. No ATP needed here.
ATP driven pump that use ATP hydrolysis to move solute against gradient
Light driven pump in bacteria
83
What is the difference between a symport and antiport and what is the similarity
They both use free energy from one solute to move the other AGAINST the gradient. Symport is in the same direction, antiport is in opposite directions
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What is the difference between uniport, symport and antiport
Uniport does not need extra energy source and is not a pump. Symports and antiports are pumps are are active.
85
How does the Na+ glucose symporter transport stuff
Na is moved down gradient as energy to move glucose up. There are random oscillations between conformations. It aims to make glucose high in cytosol. Conformational changes only occur after both sites are occupied, not one. You get Na easily because there's a lot but you need to wait for glucose. Then once both are attached they are both puked out to the other side
86
How does the Na+ H+ antiporter function
Na+ is moved down electrochemical gradient to provide energy for H+ to move against. This is because cytosolic pH needs to me baintained, but there is excess H+ in the cytosol. H is moved out of the cell to reduce acidity
87
Why do you need a Na+ - K+ pump
Because the Na+ glucose and Na+ H+ transporters all move Na+ in, down the gradient. If this keeps up you're going to have a shit ton of Na+ inside and the gradient is going to be gone
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What are types of ATP driven pumps
P-type pumps that needs to be phosphorylated during the cycle, ABC transporter, and V-type pump
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What is an example of a p type pump
The Na+ K+ pump that moves both against electrochemical gradients. 3 Na+ out, 2 K+ in. Na+ gradient is used to transport nutrients like glucose and maintain pH
90
Describe the pumping cycle of the Na+ K+ pump
3 Na bind on cytosolic side, then it gets phosphorylated, and the Na get thrown to the extracellular side. The K+ binds and it is dephosphorylated, pump returns to original and K+ is puked into cytosolic side and it can now continue
91
What p type pump do plants have instead of the Na+ K+ one?
H+ pump that creates a membrane potential, it is different from the one on the vacuoles and lysosomes in animals. The one in ORGANELLES is a V type, the one in the MEMBRANE is p type
92
What is an ABC transporter
it uses 2 ATP to pump small molecules across cell membrane
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What is a v type proton pump
Uses ATP to pump H+ into organelles to acidify lumen, in lysosomes and plant vacuoles. V type pumps move H+ against electrochem gradient
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What is the difference between F-type ATP synthase and V-type proton pump.
The F-type ATP synthase is structurally related but goes in opposute direction. Instead of on the lysosome and plant vacuole, it is on the mitochondria, chloroplasts and bacteria. F-type ATP synthase make atp and uses the gradient to do so. It is reversible and depends on ATP concentration and H+ electrochemical gradient.
95
How do transport proteins regulate critical cellular processes
Transcellular transport of glucose by transporters and generate membrane potentials
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What do epithelial cells do
Line intestines, surfaces, cavities and organs.
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Where are the glucose Na+ transporters in epithelial cells
The apical domain
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Describe the gut and lining cell concentrations of glucose
The intestine lumen has a low glucose concentration, the cytosol of the epithelian cell has a high glucose concentration, and the extracellular fluid on the basolateral cell has low glucose concentration. So you are moving glucose from low to high concentration.
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What is the lateral domain and basal domain of a epithelial cell, adn what is the extracellular fluid.
Lateral domain is the side of the cell with the tight junctions, basal is the part facing basal lamina, which faces the extracellular fluid (bloodstream)
100
What are the two functions of tight junctions
Stop stuff (like glucose) from going between cells, so it goes all into bloodstream. Restricts membrae proteins
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What proteins are on the apical and basolateral plasma membranes?
Apical: Na+ glucose symporter. Basolateral: GLUT2 uniporter, and Na+ K+ pump.
102
Where is membrane potential used, what is it.
It is the difference in electrical charge across membrane (not concentration). Used by gradient driven pumps to carry out active transport and electrical signalling.
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How do animals generate membrane potential
K leak channels get K outside due to less K existing outside (it all got pumped in by Na+ K+ pump). However, leaking out makes the outside positive and creates a membrane potential. When the channel is open, and a shit ton of positive charge is present outside, K will not leak even if it wants to due to concentration because the positive is there and its homophobic
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How much does K leak channel and Na+ K+ chennels contribute to the membrane potential
K leak is most, Na+ K+ only 10%
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Why is the outside of cells positive
Because there is a net 1 positive ion pumped out for the Na+ K+ pump, and K+ also flows out from high to low concentration. This forms a -20mV to -200 mV equilibrium for animal cells, depending on state of membrane's ion channels and concentrations
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What is equilibrium for membrane potential
It is the resting membrane potential
107
Why are you going insane
Because i'm hyperfixating like a bitch and i have the neurodivergent urge to shake my leg and kiss evil men gently on the forehead
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What does the negative resting membrane potential mean
It's from the perspective of the inside, the inside is more negative
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What ions are common and which are uncommon in extracellular space
Na+, Cl-. Low K+
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What ions are common and uncommon in the cytosol
Low Na+, Cl-, high K+. High amounts of cells fixed anions, like nucleic acids, proteins, cell metabolites
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What does the H+ pump do for plants and why
It brings H+ outside and creates a membrane potential of -120 to -160. Used by gradient driven pumps to carry out active transport, for electrical signalling and pH regulation
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What does the endosome do
Sort ingested (endocytosed) stuff and recycle it
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What does the peroixome do
destory toxins, lipids/fatty acids with hydrogen peroxide. performs oxidative reactions
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What does the Golgi do
modifies proteins and lipids for secretion or other organelles
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What does the ER do
makes lipids, reuptakes and releases Ca2+, makes new membrane, makes steroid hormone, rough ER makes proteins
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How much volume does the cytosol occupy and what does it do
It occupies half the volume, the other half is organelles. It degrades proteins and synethesizes them, has many metabolic pathways and houses the cytoskeleton which holds organelles in place and direct vescicles driven by proteins that use ATP hydrolysis.
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How do cells differ in terms of intracellular compartments
The volumes will be different for different cell types
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What is a hepatocyte and what membrane type does it have more
It detoxifies and has more smooth ER for phospholipid synthesis and detoxification.
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How much of the membrane is ER
50%
120
What does the Rough ER do and what type of cell has a lot of it
It makes membrane bound ribosomes, synthesis of soluble proteins and transmembrane proteins for the endomembrane. Soluble proteins are often secreted
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What is the definition of an organelle
Discrete structure or subcompartment of a eukaryotic cell specialized to carry out a particular function. Can be isolated with differential centirfugation
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What are some membrane bound organelles and what are some not membrane bound ones
Membrane bound: nucleus, endoplasmic reticulum, golgi. Not: nucleolus, centrosome
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How are proteins sorted
mRNA arrives in cytoplasm and if the protein made from that mRNA has no sorting signal, then it will stay in the default location, the cytosol. If there is a sorting signal, the signal is called the signal sequence and is a couple of specific amino acids that's part of the protein. It is encoded for by RNA and DNA
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How are proteins sorted to different organelles
There is a specific sequence on each cell that tells proteins to go to the nucleus, mitochindria, ER, peroxisomes, etc. They are recognized by sorting receptors that take proteins to their destination.
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How are nuclei signal sequences different
They are kept instead of removed once arrived, like other organelles. This is because the membrane is gone during cell division
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What is the difference between post translational and co translational sorting
Post translational is when proteins are fully synthesized before sorting. Co translational is when proteins have an ER signal sequence and gets put into the ER as it is being synthesized. They are all nuclear encoded
127
How do proteins go into the nucleus
It enters folded and only if it has a nuclear localization signal. It is fully synthesized then sorted. The nuclear localization signal is detected by the nuclear import receptor then younked through, and the sorting receptor leaves once done. There is a high concentration of Ran-GDP in the cytosol and Ran-GTP in the nucleus. GTP is hydrolyzed to move the protein
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What is an example of a protein that needs to enter the nucleus
transcription activators, which are needed for eukaryotic transcription
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How are proteins moved into peroxisomes
The same as nucleus, post translational and folded. They are fully synthesized and have a 3 amino acid signal sequence
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What does the perixomal import receptor do
It escorts the protein in and comesout
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How are proteins sorted into the mitochondria and plastids
Unfolded by chaperones and using ATP, signal is cleaved after entering.
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Where do most proteins for the mitochondria come from
the nucleus even though it has its own genomes and ribosomes
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Who unfolds proteins for mitochondria import
Cytosolic hsp70 chaperone proteins
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Where is the signal for mitochondria sorting proteins
N terminus
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How are proteins sorted into the ER
There is a hydrophobic ER signal sequence (8 or more hydrophobic AAs). Once in the ER, it will not reenter the cytosol because it is transported by the vescicle. You need proteins in the ER to go to the endomembrane system, which includes things like the ER, golgi, endosomes, and lysosomes
136
How does cotranslational translocation happen in the ER
Insertion happens as translation continues, you need ER attached ribosomes, and there is no additional energy needed for it. The elongation of polypeptide pushes it in.
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What kind of proteins enter the ER
soluble proteins for secretion or lumen of endomembrane, and transmembrane which are embedded in the membrane
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What is the first thing synthesized for an ER protein
ER signal sequence
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What happens after the ER signal sequence emerges
SRP (signal recognition particle) recognizes the ER signal and ribosome, then the complex goes to the SRP receptor, opens the translocon, and proton synthesis continues. Translocon is closed before this. The ER signal sequence is cleaved by signal peptidase. Protein released, translocon closes. The soluble protein stays in the lumen of an organelle (needs membrane bound organelle) or is secreted
140
What happens to the methionine and ER signal sequence once the protein is made
It is cleaved and degraded in the membrane, because it is hydrophobic
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How do single and double pass proteins get embedded in the ER membrane
Translocation stops when the stop transfer sequence gets noticed. Translation may continue to finish the protein. Then signal peptidase cleaves the ER signal sequence for single pass and translocon closes. For double pass, both start and stop transfer sequences are released into the lipid bilayer as membrane spanning alpha helices.
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What is the difference between N terminal ER signal sequence and Internal ER signal sequence
Both are hydrophobic, but the internal holds the protein in place. It is not removed, and it is NOT at the very end of the N terminus
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In what order do you go through the endomembrane system
In order: er, golgi, endosome/lysosome
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What do intracellular compartments exchange
Exchange lipids and proteins
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What is the secretory pathway
When the ER delivers proteins and lipids to other the outside by exocytosis, or to lysosomes with endosomes
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What is the endocytic pathway
Ingestion and degradation of extracellular shit into the cell via endocytosis
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What is the retrieval pathway
Recycling lipids and proteins for reuse. From the Golgi to ER, for example, if something was supposed to be in the ER but escaped to the Golgi.
148
How are vescicles combined with respective organelles
They are recognized based on proteins on the surface of the vesicle
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What does the RAB and tethering protein do
Initial recognition between vescicle and target membrane. RABs are small GTP binding proteins on transport vescicles and organelles that only fuse with the correct membrane
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What happens once the RAB and tethering protein dock the vescicle
SNAREs loop around complementary SNAREs on the target like twizzlers and displace water. It needs to be very close to fuse. Then the SNAREs are reused
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What are the similarities between constitutive and regulated exocytosis pathways
They both don't need a particular signal sequence (as in amino acid sequence to signify location). Both can have soluable and membrane proteins
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What is unique about constitutive exocytosis pathways
Constitutive is in all eukaryotic cells, that have a continual delivery of proteins to plasma membrane to replenish cell surface proteins or some extracellular matrix/other cell proteins. Also for soluble proteins like collagen. It is general and does not only bring out specific ones
153
What is unique about regulated exocytosis pathways
Regulated secretion in specialized cells, stored in specialized secretory vescicles and you have large quantities. It responds to an extracellular signal which causes vesicle fusion with the plasma membrane. Examples include pancreatic b-cells that release insulin when high glucose.
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Where does translation start for ER proteins
Cytosolic ribosomes. The ER signal sequence directs it to the ER
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How many sacs does the Golgi have
6-8 but sometimes more
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What is the cis trans and medial golgi network and cisterna
Cis is close to golgi, trans is close to cytosol. The network is on the edges, they look like pita with olives, and the cisterna are in the middle, like plain pita
157
Where does protein glycosylation occur, why do you need it
It starts in the ER, a single type of oligosaccharide is attached to many proteins to prevent degredation, or to keep it in ER until folded, to guide to other organelles by being a transport signal. Complex processing happens in the Gongi
158
What is complex protein glycosylation in the Golgi
Depending on the location, different sugar is added. The modifications are for proteins and lipids. Proteins that enter the ER move by transport vescicles or Golgi migrate to catch them. The sugar will face the lumen and may eventually face outside of the cell but NEVER the cytosol.
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What is pinocytosis
Fluid, small moleculess less than 150 nm
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What is phagocytosis
large particles, microorganisms and cell debris larger than 250 nm
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What are the stages of endosomes
Early endosomes come from endocytic vescicles that fuse to form early endosomes, and they mature to late endosomes as they get more digestive enzymes. Lysosomal proteins (hydrolases, H+ pump) keep getting dished out by golgi so it becomes more acidic. Late endosomes mature into lysosomes
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How acidic is a lysosome
5 pH, from V type atpase H+ pump
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What do lysosomes contain
40 types of hydrolytic enzymes that have acid hydrolases like proteases nucleases, lipases, etc. They only function in acidic conditions to protect the cell.
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What is unique about lysosome proteins
Membrane proteins on noncytosolic face are glycosylated for protection. Transport proteins puke out amino acids sugars and nucleotides
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What gives vescicles directionality
Directed movement of transport vescicles, being pulled by motor proteins associated with the cytoskelly
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What is the cytoskelly, what are the funcitons
A network of protein filaments that are highly dynamic and important for structural support (animals have no cell wall) and internal organization (of organelles and vesicle transport). Also for cell division (chromosome segregation and dividing the cell into two). And large scale movements (crawling cell with muscle contraction)
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How thicc are the cytoskelly filaments, what microscopes to use to see
7 to 25 nm. It cannot be seen with the light microscope with 200 nm resolution. Fluorescence microscopes can be used to label the cytoskeleton and you can see them. TEMs are the best and have resolution limit of 1nm.
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Why do microtubules seem thicker than in reality
Because of the diffraction from light microscopy
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How does immunofluorescence microscopy work, what is the purpose
Cells are fixed, it is used to determine location of proteins inside the cell. The primary antibody is used to bind to protein, and secondary binds to protein, and glows because it has a fluorescent marker. It's done this way because it's cheaper
170
What are the three types of cytoskelly and the thicknesses
Actin 7nm, Intermediate filament 10nm, Microtubule 25nm (JUST NEED ORDER NO NUMBER)
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How are the types of cytoskelly different from each other
Different mechanical properties, different protein subunits. But they're everywhere, in all animal cells :3 And all held together noncovalently
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What do intermediate filaments do, and what are the two types
They support the cell to withstand stress when twisted or deformed, because they are toughest and most durable. Cytoplasmic IFs in animal cells are in charge of this strength, and are connected to plasma membrane at desmosomes. Nuclear form nuclear lamina, which is right under the nuclear membrane (plants have different)
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What are the three cytoplasmic IFs
Keratin, which is the most diverse and spans the whole cell, vimentin in connective tissue, muscle and glial. Neurofilaments in nerve cells.
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What happens to nuclear IFs as the cell divides
It disassembles and reforms every division, provides attachment for chromosomes
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How are the monomers for cytoplasmic IF proteins wrapped around each other, what is the monomer like
Monomer has N and C domains that are distinct and unstructured with alpha helical region. Two form a coiled coil dimer with distinct ends, and then eight form a not polar filament. It is a staggered antiparallel tetramer. And then the tetramers form a big bundle and adds to overall, which is not polar
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What are three characteristics of cytoplasmic IF
Tough flexible, and high tensile strength
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What is an epithelium
sheet of cells covering an external surface or lining internal body cavity
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Where are intermediate filaments anchored at
cell-cell junctions (desmosomes) which connect to desmosomes. they don't go through the cell boundaries of course
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What is the purpose of microtubules and what are they involved in
Organizing. Involved in cell organization (vesicle transport, organelle transport, acting as the centrosome in animal cells), forming the mitotic spindle, structural support for cells and flagella/cilia.
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What are microtubules made of
Tubulin, which are long and stiff hollow tubes (basically, microtubules are made of PVC pipe). They are inextensible (you can't stretch a PVC pipe)
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What are the subunits for microtubules
Alpha tubulin and beta tubulin, which stick by noncovalent bonding. The heterodimer is bound to GTP.
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How long do microtubules lat
Not very long, they rapidly disassemble and reassemble
183
Why do you need polarity for microtubules
The polarity is needed to guide directional intracellular transport.
184
How many protofilaments for a hollow microtubule tube
13 parallel ones
185
What are the bonds between individual subunits and between strands, which is stronger
Both noncovalent, the ones between strands is weaker.
186
How do microtubule tubes grow
Only at ends, it's more rapid at the plus end.
187
What is dynamic instability for microtubules, how do microtubules grow
The plus ands of microtubules grow and shrink. The free dimers bould to GTP are added to plus end but then b tubulin hydrolyzes to GDP, alpha stays the same. If there is rapid addition of dimers, faster than hydrolysis, there will be a cap of GTP dimers which causes the microtubule to keep growing. Microtubules switch between growing and shrinking fast
188
How do microtubules shrink, and what are the old dimers bound to
If the hydrolysis is faster than the adding of fresh GTP dimers, the GTP cap will be gone and the GDP tubulin at plus end will have weaker binding and the microtubule is peeled away. GDP (the old dimers) dimers bind less tight. Once depolymerization starts, it tends to continue
189
What is a microtubule organizing center
A place where microtubules grow out of, such as the centrosome (not centriole) of animal cells. Minus ends are stabilized here and the centrosome has a g-tubulin which starts the growth. Dynamic instability only happens at plus end
190
When can the minus end of microtubules grow and shit
When its not at a MTOC, but it's less prone
191
What happens to GDP bound dimers that are kicked off
Recycled to make GTP ones
192
Which tubulin dimer easily dissociates, which does not
GDP is easily dissociated, GTP is not
193
What is the goal of a MTOC
nucleating sites for microtubule growth, to start assembling new microtubules. plants don't have centrosomes, they have something else!
194
What is the y-tubulin ring complex for
Used by all organizing centers as an attachment site for ab tubulin dimers
195
How many centrosomes are there in interphase and dividing cells? Why do you need dynamic instability
One for interphase, two for mitosis. You need dynamic instability for remodelling, and microtubules are reorganized into bipolar mitotic spindles
196
What do microtubule associated proteins do
y-tubulin ring complexes and branching proteins nucleate growth of new microtubules. they also promote microtubule polymerization, disassembly, stabilize microtubules (prevent disassembly) by binding to the sides and plus end linking to a cell wall
197
How are microtubules used to transport vesicles to the axon terminal quickly, how are they orientated
Plus ends in one direction (close to terminal). There is a walky guy that brings the vesicles to the terminals, and also towards the cell body
198
What are the motor proteins on microtubules, what direction do they go.
Kinesins go towards plus end, dynesins go towards minus end
199
What are examples of kinesins and dynesins, what do they carry
Kinesins carry organelles, vescicles, macromolecules. an example is kinesin 1, which goes towards axon terminus. Dyneins carry worn out mitochondria and endocytosed material towards minus end to cell body.
200
How do the motor proteins of microtubules and actin move
Heads move along the cytoskeleton with ATP hydrolysis to loosen one, and then bind again. The tails bind cargo. It only goes in one direction (stereospecific) for kinesins and dyneins, and generally go towards plus for actin myosins
201
How are microtubules positioned in a cell and how are organelles positioned by them
Microtubules go from centrosome to cell periphery. The ER is stretched from nuclear envelope to periphery by kinesin 1, which pulls it out like a net. The golgi is near centrosome and is stretched out towards microtubule minus end by dynein
202
What is another name for actin filaments, where are they present
Microfilaments, they are present in all eukaryotes
203
What are actin made of
actin monomers, which are one of the most abundant proteins in all cell types. they are flexible and inextensible, they cannot be elastic but you can stretch them to be longer.
204
What are the motor proteins for actin
myosins
205
What are the functions for actin filament
Stiff and stable structures (microvilli), contractile activity, cell mobility (crawling) and cytokinesis (contractile ring)
206
What is a helical filament
A strand of actin filament made of actin monomers, which are polar by themselves. the two protofilaments twist in a right handed helix and forms a plus and minus end. they are joined by noncovalent interactions
207
Explain why actin filament is polar
Because actin monomers have same orientation and the ends are different. Growth is faster at the plus.
208
What are free actin monomers bound to and what happens when they are added
Free ones are bound to ATP, it is then hydrolyzed to ADP, which reduces the binding strength, promotes depolymerization. If you add monomers fast enough then actin filament will have ATP cap.
209
What are the three phases of actin polymerization
Nucleation, elongation, and steady state
210
What is treadmilling
at the equilibrium phase when you have the same rate of adding and removing subunits. Subunits may move along when treadmilling. You have an equal net addition and removal, and need a constant supply of ATP for this, so you can keep adding ATP bound actin to the plus end while the minus disintegrates. Length appears constant. Microtubules and actin both treadmill, but its most common for actin
211
What is nucleation phase in actin polymerization
Small oligomers form but it's unstable
212
What is elongation in actin polymerization
Some oligomers become more stable and you have fatser filament elongation
213
Cell crawling uses what actin polymerization stage
Cell crawling, assembling at leading edge, disassemble at the back, the push forth
214
Why do you need actin binding proteins and what do they do
They sequester actin monomers to prevent polymerization, promote nucleation to form filaments, stabilize actin filaments (capping), organize filaments by bundling and cross linking, and severing actin filaments.
215
What is the difference in function between actin and microtubules
Actin is for keeping the structure, microtubules move shit around (ie organelles)
216
Which way do myosins tend to move, and what energy do they use
Heads bind, detach, then rebind and go towards the plus end of actin usually. Need ATP
217
What does the tail domain for a myosin 1 do
Binds to cargo like vesicles and plasma membrane to tug the membrane.
218
What do the tails of myosin 2 do and where are myosin 2 activities clearest
They have a dimer of coiled coiled tails. Bipolar myosin 2 for example moves actin filaments in opposite directions to create a contractile force common in muscle contraction and contractile ring.
219
What is an epithelia and what are the two types
THe cells that line external surfaces and organs and internal body cavities (such as the liver, skin, organ lining). Stratefied epithelia is the outer layer of the skin. The simple epithelia is one cell thick
220
Which types of cell junctions hold cells together
tight junctions, adherance junctions, and desmosomes.
221
List the order cell junctions from most apical to most basal lateral
Tight junction, adherens junction, desmosome, gap junction, hemidesmosome
222
What is the extracellular matrix made of
Collagen and laminin
223
What does the tight junction create between cells
Sealing strand (tight junction belt), it prevents tracer molecules from getting to the other side
224
Why do you need a tight junction
To prevent mixing of extracellular environments, water soluable molecules cannot go through. It also prevents mixing of membrane proteins by separating the apical from the basolateral.
225
What proteins are on the apical membrane
Na+ glucose symporter
226
What proteins are on the basolateral plasma membrane
GLUT2 uniporter (puts glucose into the bloodstream) and Na+-K+ pump
227
What are claudins and occludins
Transmembrane proteins needed in tight junctions required for both cells. Extracellular domain in one cell interacts with extracellular domain of another to form occludin-occludin claudin-claudin joints. Basically the things that punch the two cells together
228
What do anchoring junctions do and what are the types
They provide mechanical strength to the epithelium, examples include the adherens junctions, desmosomes. These are cell-cell and link the cytoskeletons of neighboring cells. Another type is cell-ecm, which makes hemidesmosomes and links cytoskelly to the basal lamina. Transmembrane adhesion proteins link these junctions to the cytoskeleton inside
229
What are transmembrane adhesion proteins
they have an extracellular domain that interact with another one on neighboring cell, or the extracellular matrix. Intracellular linker proteins link transmembrane adhesion proteins to cytoskeleton
230
What do adherens junctions form, what is the transmembrane protein that forms it
adhesion belt that encircles inside of the plasma membrane. it uses classical cadherins
231
What do the extracellular and intracellular parts of the cadherin proteins connect with
The extracellular part connects with other cadherins proteins from the neighboring cells. THe intracellular part connects to actin filaments
232
What do desmosomes and hemidesmosomes attach to
Intermediate filaments like keratin filaments, which provide the most structural strength
233
What is the difference between desmosomes and hemidesmosomes
Desmosomes connect to a neighboring cell, hemidesmosomes anchor keratin filaments to basal lamina and look like half a desmosome but it actually is made up of very different proteins
234
What transmembrane adhesion proteins do desmosomes use
Nonclassical cadherin proteins like desmoglein and desmocolins
235
What transmembrane adhesion proteins do hemidesmosomes use
Integrins that bind to laminin in basal lamina
236
How do connexins form a gap junction
Six connexin proteins form a connexon, 2 connexons from a intercellular channel going from one cell to another.
237
What can go through a connexon
Connexons are narrow and water filled, allow inorganic ions and small water soluable molecules to pass. The cells are coupled electrically and metabolically, allowing passage of ions and metabolites less tha 1000 daltons, not very selective. Allows cAMP, nucleotides, glucose, amino acids. Does not allow macromolecules, proteins, nucleic acids
238
What closes gap junctions
extracellular or intracellular signals, like dramaticincrease in cytosolic Ca2+, which can be from leaking of Ca2+ from a damaged cell
239
What are things that will close gap junctions
increase in cytosolic Ca2+, from membrane damage which prevents adjacent cells from losing metabolites
240
What are the intercellular junctions in plant cells and how do they differ from gap junctions
Plasmodemata are cytoplasmic channels lined with plasma membrane. They don't have cell junctions because the cell wall provides support. Plasmodemata allow for cell-cell communication and need to cross cell wall and thus are different from gap junctions.
241
What can go through plasmodemata
Sugars, ions, other essential nutrients less than 1000 daltons. Large molecules, such as proteins and regulatory RNAs are controlled by having callose pinch together.
242
What is the structure of plasmodemata
It has a continuous plasma membrane to share phospholids and membrane proteins. It shares cytoplasm and smooth ER
243
Name the cells and ECM from the surface of the aminal tissue to further down
Epithelium, basal lamina, and connective tissue
244
What is the difference between epithelial tissue and connective tissue
Epithelial tissue has close cells while the cells in connective tissue is rarely connected. Cells are attached to each other in epithelial tissue and cells are connected to the matrix in connective tissue. There is a limited ECM (thin basal lamina) for epithelial cells, and they use cytoskelly filaments for resistance. For connective tissue, you are swimming in ECM and ECM provides resistance to mechanical stress
245
What is different for different types of connective tissue, what is the same
ECM composition, all of the tissues have ECM as their primary component.
246
What macromolecules are in the ECM
Glycosaminoglycans (GAGs) and proteoglycans, fibrous proteins (collagens, elastin) and glycoproteins (laminin and fibronectin)
247
What are GAGs
really long linear chains of repeating dissaccharide. It is a sugar and highly negatively charged, and attracts Na+ and water to form hydrated gels to resist compression (water gets ECM matrix and counteracts the pressure of the ECM). most Gags are synthesized inside the cell and exocytosed. It basically takes up a shit ton of room and is jelly like, creating a resilient matrix
248
What can desmocolin and desmogleins bind to
Desmocolins could bind to itself or to a desmoglein, vice versa
249
What is hyaluronan
A simple GAG, which is spun directly from the cell surface by a plasma membrane enzyme complex
250
What is a proteoglycan
A specific type of glycoprotein that's common in jellylike tissue and occupies a lot of room. Glycoproteins have any kind of sugar on them. The sugar chain on a proteoglycan must be a GAG.
251
How many GAGs are typically on proteoglycans?
95% of total weight, a lot. But they can have few or more. This forms gels of different pore size and density to be different in filtering
252
What is collagen a type of, what does it do, and what is the structure
It is a fibrous protein, provides tensile strength, and resists stretching. Collagen has three chains wound around each other, which then forms a fibril, and these fibrils form a very thick collagen fiber (comparable to cells)
253
How is collagen made
Secreted as procollagen by fibroblasts (skin, tendon, connective tissue) and osteoblasts (bone). Procollagen prevents premature forming of collagen, and it is cleaved to form mature collagen
254
How are connective tissue cells that secrete collagen connected to the collagen fibrils
They bind through integrin, which binds on fibronectin that binds to the collagen.
255
What does fibronectin bind to
a domain binds to collagen, another integrin. fully extracellular
256
What does integrin bind to
Fibronectin (extracellular domain) and adaptor proteins which binds to actin filaments, in the intracellular domain.
257
What is elastin
A fibrous protein that gives tissues elasticity and stretches and relaxes like a rubber band. It gives resilience
258
Skin needs to keep its shape. How does the ECM do this
provides strength and prevents tissue from excessive stretching
259
What is the basal lamina
A basement membrane that underlies all epithelia. It is thin, 40-120 nm thick and screted by epithelial cells. It has a feedback loop with the epithelial cell where the cell secrete ECM to be basal lamina, and the basal lamina tells the cell to put the apical side on the opposite, not basal side
260
What does the basal lamina do regarding compartamentalization
It separates epithelia from underlying tissue and prevents fibroblasts (it makes macromolecules and collagen) in connective tissue from interacting. It allows macrophages and lymphocytes (immune cells) through
261
What is the basal lamina organized by and anchored by? Regarding epithelial cells, not connective tissue!
It is held in place, or anchored by hemidesmosomes. It is organized by laminin which interacts the integrins of hemidesmosomes and the type IV collagen of the basal lamina. Laminin is a glycoprotein. Connective tissue has different proteins holding it in place
262
What is different about cell wall as opposed to ECM
More rigid than ECM of animal tissues
263
What are the main components of the plant cell wall and what is the purpose of each
Made of cellulose and pectin. Cellulose provides tensile strength, pectin fills space to resist compression
264
How is cellulose synthesized, rest of cell wall?
It is made at the plasma membrane from a synthase complex that is latched onto the microtubules. Positioning of cytoskelly can determine cellulose location. Other cell wall components are synthesized in golgi, exported by exocytosis.
265
What does agarose gel electrophoresis do
Separate DNA and RNA molecules
266
How is the nuclei separated from organelles and macromolecules
By removing debris then lysing the plasma membrane, filtering, and centrifuging the mixture to separate the soluable and not soluble. The pellet contains the nuclei
267
Why do you need high temperature and detergent to get the nuclear DNA
The detergent and heat denature the proteins and remove them, which isolates the DNA
268
If you look at a bunch of cells divide, what would you notice about the stages of division for the cells
they are all at different stages of division but follow mitosis
269
List the checkpoints of interphase, and the phases
G1, Start transition, S, G2, G2-M transition.
270
What does the G1 phase do? Hint: its what the G1-S checkpoint checks
Check if the conditions are good for cell growth. Checks for nutrients and signal
271
Not all cells in multicellular organisms constantly divide. What type of cell cycles could they have?
Some mature cells don't divide. These are terminally differentiated, include things like nerve cells, muscle cells, red blood cells. Some divide with stimuli, like when damaged liver replace tissue. Some just divide normally like epithelial cells
272
What is G0
There is no cell division, cells are metabolically active. Cells that don't divide are G0
273
What does G2/M transition do
Makes sure Dna is not damaged and fully replicated
274
What is the metaphase to anaphase transition, what is its other name
Spindle assembly checkpoint. Are all chromosomes properly attached to mitotic spindle
275
What does malfunctioning cell cycle checkpoints cause
Cancer lol (chromosome segregation defects)
276
How are the cell cycle checkpoints controlled (what tells it to go and stop)
Cyclin activates specific cyclin dependent protein kinases which then activates specific regulatory proteins. If the CDK is activated, it will progress, and vice versa. CDKs are activated by phosphorylation.
277
What does s phase do to chromosomes
replicate them and decondense them, cohesins hold the sister chromatids together
278
When is centrosome duplication started and done
Starts in G1 ends G2
279
What do the chromosomes look like at the end of G2
REplicated chromosomes that are dispersed and tangled
280
What happens to the chromosomes in prophase
Chromosome condensation, sister chromatids get slightly peeled waay from each other. Condensins condense the DNA.
281
Which parts of mitotic chromosomes have cohesins and which have condensins
The centromere has cohesins, the rest has condensins
282
How are microtubules positioned in a non-dividing cell
Microtubules are arranged in a radial pattern with the plus ends facing out and minus on MTOC (centrosome
283
What does prophase do to the mitotic spindle
Dissassembles and reassembles them to form a mitotic spindle, and uses the duplicated centrosomes made in interphase
284
How are centrioles positioned in the centrosome and why are there two
Placed perpendicular. There are two because one is used as a template for the other, semiconservatively.
285
What does the sentrosome matrix do to keep the microtubules stable
y-tubulin ring complexes to assemble new microtubules
286
How are centrosomes duplicated in the cell cycle
Started in G1 and end G2
287
When does mitotic spindle assembly start
Prophase (M phase, mitosis)
288
Explain how the mitotic spindle forms and what it looks like once its done
It is formed by microtubule dynamics, which means you need to take apart the microtubule then reassemble. Once done, it there will be an array of microtubules that extend out ofrom the centrosomes and the centrosomes become the spindle poles.
289
What is a spindle pole
Centrosome which has microtubules that radiate to form the mitotic spindle
290
When does nuclear envelope breakdown happen, what happens right before it
End of prophase, right before prometaphase. It happens after mitotic spindle assembly
291
What is the nuclear lamina made of and what is its structure
Intermediate filaments which creates a meshwork of interconnected nuclear lamin protein. Forms a two-dimensional lattice on inner nuclear membrane
292
What does an interphase nuclear membrane have (e.g. inner and outer membrane)
Nuclear pore, lamins (nuclear lamin proteins are also known as nuclear intermediate filaments), DNA
293
How do you break down the nuclear envelope
Phosphorylation of lamins and nuclear pore proteins causes the nuclear envelope to turn into small membrane vesicles
294
What happens to the nuclear envelope, mitotic spindle and kinetochore microtubules in prometaphase
Nuclear envelope is disassembled, mitotic spindle assembly can be completed, kinetochore microtubules attach onto chromosomes and movement begins
295
Name the three types of mitotic spindle microtubules and what they do
astral microtubules position the mitotic spindle and are scooched around by cytoplasmic dynein. non-kinetochore microtubules are cross linked, connected by kinesin and other microtubule proteins to move shit around later. kinetochore microtubules are attached to duplicated chromosomes to spindle poles
296
How are kinetochores connected to microtubules
Kinetochores, at the centrosomes, connect to one spindle for each chromatid. Both microtubules must attach in a way that generates equal tension on both sides. Also the kinetochores attach onto the plus end of the kinetochore and that exposed plus end allows growing and shrinking of chromosome movement
297
What is a metaphase plate
equator of the spindle, smack dab in the middle of the cell
298
What is tubulin flux and why do you need it
You add tubulin to the plus and remove from the minus end, so the length DOES NOT change. this is so you can maintain the length of the microtubule and keep the chromosomes in place so you don't proceed in the cycle before you check your work
299
What must happen before anaphase starts
all the chromosomes need to be aligned on metaphase plate
300
How are sister chromatids separated in anaphase
Separase activated and the cohesin complex becomes cleaved
301
What happens in anaphase a
Kinetochore microtubules shortened (loss of tubulin from both MINUS AND PLUS) and chromatids pulled apart
302
What happens in anaphase b
Spindle poles move outward by kinesin(act on nonkinetochore microtubules to slide them closer to the centrosome) and cytoplasmic dynein (attached on plasma membrane, move along astral microtubules to pull poles apart)
303
What is interdigitation
when the nonkinetochore microtubules in anaphase b are overlapped
304
What happens in telophase
Chromosomes at each spindle pole, mitotic spindle disassembles, nuclear envelope reassembles, chromosomes decondense, mitosis is done, constractile ring starts to form
305
How does the nuclear envelope reassemble in telophase
Dephosphorylation of nuclear pore proteins and lamins allows reassembly to rebuild nuclear envelope and lamin. The nuclear pores restore localization of cytosolic and nuclear proteins and condensed chromosomes decondense
306
How does cytokinesis happen in animal cells
Actin and myosin filaments form a contractile ring that creates a cleavage furrow midway between spindle poles and you get two daughter cells with own nuclearus. Then the interphase microtubules reform in daughter cells and that's the end of m phase
307
What happens to the actin and myosin for the contractile ring at the beginning and end of mitosis
Beginning: disassemble (makes cell round to prepare for division). End: form contractile ring that brings cell membrane in and contractile ring becomes smaller
308
What is common between mitotic spindle and contractile ring
Both disassemble rapidly after doing job
309
What is different for plant mitosis
No centrosome (something else)
310
What is different for plant cytokinesis
No contractile ring, instead you have vescicles, microtubules, actin which forms a phragmoplast and that makes a cell plate. The nuclear envelope reassembles and chromosome decondenses like in animals but the cell plate is unique. It is a transient membrane compartment from the fusing of vescicles.
311
What happens to the cell plate in G1 for plants
It matures into plasma membrane and cell wall
312
How many cells are made in meiosis and what type
4 haploid cells
313
How many cells made in mitosis and what type
2 diploid cells
314
How are chromosomes lined up differently for mitosis and meiosis
For mitosis, chromosomes are lined up unpaired. Meiosis pairs homologous and are segregated into two daugher cells with the two chromatids still attached to each other (for first cell division)
315
How many rounds of DNA replication for mitosis and meiosis
both only once
316
How many cell divisions for mitosis and meiosis
for mitosis, one round, meiosis has 2.
317
In lab 1 what is the difference between refined and basic protocol
The refined removes extra protein with protein precipitation solution
318
When you centrifuge the isolated wheat nuclei, which part will have the DNA
The pellet
319
Where is the DNA after you pipette the supernatant from centrifiguing and use ethanol to precipitate the DNA
The pellet again
320
What is a hypotonic solute concentration
when the solute concentration outside is less than inside
321
What is SDS, what does it do for chromatin
a strong ionic detergent that solubilizes plasma membrane and nuclear envelope and makes chromatin into protein free DNA molecules
322
How do you remove histones from DNA
with a high salt solution, they precipitate out of the solution because protein solubility decreases
323
How is DNA precipitated
through water ethanol hydrogen bonds, neutralizing DNA backbone with Na+ in solution, and the hydrophobic interactions between neutralized DNA and water causes precipitation
324
What does the wheat kernel consist of
The germ that produces the plant, the endosperm which is a food source for the embyo, and the covering layers that protect the grain
325
If you're pipetting 25 microliters with a p200, what should the numbers be
025
326
If you're pipetting 13.0 microliters with a p20 micropipett, what should the numbers be
130
327
For agarose gel electrophoresis, which electrode does DNA and RNA go towards
the positively charged electrode
328
What does the rate of migration of the molecule depend on, which is the most different for DNA
Shape, charge to mass ratio and size. Size is most different for DNA
329
What is sybrsafe
a sensitive stain for DNA that binds to double straned DNA and emits green light
330
What is the PCR process, what do you need
Small tubes of double stranded DNA template, PCR buffer, MgCl2, deoxyribonucleotides and primers are put in a thermal cycler. When denaturing, the tubes are heated to separate DNA template, during annealing, the temperature is lowered so the primers base pair with complementary sequence on template DNA. The synthesis stage is at a medium temperature where the Taq DNA polymerase synthesizes Dna using complementary DNA strand as template
331
what is bioinformatics
an area of science that uses computational approaches to solve biological questions
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What is BLAST
A one against all similarity search algorithm that compares proteins and nucleotides with others. Explores sequence similarity and homology
333
What is MSA
multiple sequence alignment, which can be done for amino acid resigues that seem to perform similar roles. It is considered many against each other, and you compare several defined sequences with each other. Examines sequence homology and conservation
334
Why do you need PCR buffer
it puts the pH at 7.2 which is ideal for Taq DNA polymerase at 72 degrees
335
Why do you need MgCl2 for PCR
You need free divalent cations for thermoostable DNA polymerase activity
336
What is the structure of a primer for PCR
18-20 nucleotudes chemically synthesized with a defined sequence complentary to 3' end of DNA sequence
337
What does it mean when two sequences are homologous
When two sequences share a common evolutionary history
338
For a 14 nucleotide sequence, what is the maximum match score
28, 2 for each sequence you are comparing
339
What is the bit score
a normalized version of the match score independent of the sequence length and database
340
What is the E value
the number of different alignments with scores equivalent or better than a given score that are expected due to chance.
341
A low E value means what
the more significant the score and the more sure you can be that you're looking at homologous sequences
342
What is a p value
the probability of obtaining an alignment with the score or better
343
What is a restriction enzyme or restriction endonuclease
Enzymes that cleave both strands of DNA molecule at specific sites
344
What is a isoschizomer
If restriction enzymes isolated from different organisms recognizes the same sequence and cleaves the same thing
345
How many base pairs do the majority of restriction enzumes recognize
4 or 6 base pairs
346
What is different between CRISPR-Cas9 and restriction enzymes
CRISPR can have RNA templates that can be manipulated to guide cleavage
347
What are recombinant DNA molecules
molecules from more than one source spliced together
348
How do you clone a gene with a restriction enzyme and vectors
Restriction enzymes cut the part of the gene you want then the vector puts the gene into a host (usually bacteria) and then the vector multiplies and the gene is passed onto progeny. Now you have a lot of the DNA
349
What are plasmids
small circular DNA found in bacteria and yeast that multiply independently of the host cell and regulate their own replication
350
Why did you need to compare uncut PCR product and negative control for PCR with the cut products?
To see if the cutting did something, and see if the PCR actually isolated any DNA out
351
How do you do Koehler illumination
Open field iris diaphram all the way, move condenser up using condenser focus knob, close field iris diaphram and rotate condenser focus knobs unil edges of the diaphram are focused. Then open field iris diaphram and stop when the diaphram moves out of field of view.
352
How do you calculate the magnification of an object
Size of image/actual size
353
What is an ocular recticle and what is a stage micrometer
Ocular recticle is the tiny ruler in your microscope's lens. Stage micrometer is a tiny ruler to calibrate ocular recticle
354
What should you see when you look at parameciums eating congo red stained yeast
There will be a clear membrane around vacuole, vacuole will move towards back of paramecium as digestion continues, and congo red may change color as it is a pH indicator. There is a feeding apparatus which is a groove, and cilia carry food particles down oral grove to the middle of paramecium
355
If you see two lines 100 nm apart and the resolution is 200 nm, what will you see
The image will be one solid line
356
What is magnification and resolution
magnification is an increase in size, resolution is the ability to distinguish between closely positioned objects
357
how do you calculate the minimum distance of separation between two objects needed to see tham as two diffferent objects
0.61 lambda / NA. NA is the numerical aperature, which is equal to n sin a, a is the shape of the cone of light entering the objective lens, n is the refractive index of medium between objective and specimen. they won't test n sin a because if they do, nobody will get it right. even my big ass brain can't remember it and i can remember that in 2th grade i said "yunanosaurus" when prompted to give the name of an extinct animal that starts with the letter y
358
What is bright field microscopy
used to look at living cells and fixed tissues (dead by the end of fixing process). Its easy and you can see living stuff if you want. Use koehler illumination, aligned for maximum lighting
359
Phase contrast microscopy
Contrast in wet mounts with unstained and unmounted specimen. Can study living and use two light filters, so the first one blocks all light except perimeter, second blocks all light from perimeter in the mirror image of the first. So only indirect light is shown and it's dark with haloes
360
Normanski imaging
transparent and internal structures, you can see living, phase changes occur when light passes through a sample are converted to higher contrast and you get 3D image without haloes in phase contrast
361
Fluorescence microscopy
labelling and visualization of discrete parts of a cell, you can see parts not visible by regular light and it can be used for living or fixed cells. samples are labelled with fluorescent molecules and the light is filtered. first set of filter filters the light before it reaches the specimen and only lets the wavelengths that excite the dye through. the second set blocks this light and only lets you see wavelengths emitted. you see bright colors with dark background
362
Confocal microscopy
determine cellular localization of organelles, cytoskeletal elements, can trace stationary cells through tissue (not fast ones). it reduces background noise and can be used for living or fixed cells
363
transmission electron microscopy
uses electrons as illumination source, the wavelength of the electrons is much shorter than visible. the achievable magnification and resolution is higher. TEM specifically is used for internal structures and a tungsten filament generates electrons which are focused by electromagnets to a fixed, sectioned, stained specimen. image is captured on film
364
scanning electron microscopy
contrary to transmission, it is used to view external structures closely and to view whole cells. resolution usually not as good as tem, and uses a focused beam of electrons that produce secondary electrons as the beam hits the specimen. deflected electrons are converted into image captured on film
365
What does the diopter adjustment ring do
focuses the eyepiece
366
What does the slide condenser do
lets you switch between various filters in the condenser
367
What does the condenser iris diaphragm do
It determines the aperature of illumination system
368
what does the field iris diaphragm ring do
it is used to exclude extra light and improve contrast
369
how are flagella quickly regenerated for chlamydomonas
the cytoskeleton is dynamic, due to microtubule dynamics, it regenerates quickly
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What is chlamydomonas rheinhardtii a model organism for
study of chloroplasts, flagellar assembly, intraflaggelar transport
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What does cycloheximide do
it inhibits protein synthesis by blocking elongation phase of translation by inhibiting EF2 translation elongation factor
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What is a time course
making a fresh wet mount from each pair's assigned culture every 20 minutes
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Why does cycloheximide stop flagellar regeneration
You need tubulin to make microtubules for flagella, and tubulin are proteins, which are stopped from being created by the EF2 translation elongation factor
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What is a null hypothesis
saying that there is no difference for a certain statistic across two groups. for example, cycloheximide and non-cycloheximide groups do not have a different proportion of flagelled cells
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how do you calculate chi square
(n (f11f22-f12f21 - n/2)^2)/ (C1) (C2) (R1) (R2) refer to lab manual. don't need memorize (i think) but need to know how to use. on page 5-6
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when do you reject H0, your null hypothesis
when the chi squared is greater than the chisquare critical value.
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what does it mean when you fail to reject H0
that there is no difference between the two groups for the characteristic you are analyzing
