Exam 3 Flashcards
What components of a cell make up the highest percentage of cell volume?
Cytosol and mitochondria
In liver and pancreatic cells, the membrane of what organelle as 15X the surface area of the plasma membrane and why?
The endoplasmic reticulum, because these cells specialize in protein and lipid synthesis
What is responsible for the topological equivalence of cell organelles?
Constant endocytotic fusion and budding between specific membrane structures
Nuclear pore diffusion
What are the three fundamental mechanisms for moving proteins between cell organelles?
Gated transport
Transmembrane transport
Vesicular transport
Which of the protein moving mechanisms requires that topological equivalence?
Gated transport and vesicular transport
Which of the protein moving mechanisms requires unfolding and re-folding of the protein?
Transmembrane transport
What are signal sequences, and where are they attached?
Amino acid sequences at the N-terminals of proteins that are recognized by transport proteins that move proteins across compartments
What is the name for the signal sequence that is on nuclear proteins?
“Specific nuclear localization signal sequences” (NLSs)
What makes up the nuclear pore?
Made up of nucleoporins that are groups of proteins with octagonal symmetry. There are small aqueous channels.
What are the two kinds of nuclear receptor proteins? Where do they bind?
Nuclear import receptor proteins that recognize nuclear localization signals
Nuclear export receptor proteins that recognize nuclear export signals
Both bind to both the signal sequence and nucleoporins
What is the energy source that helps get proteins across the nuclear pore? What are the two kinds? Which is inside and which is outside?
The GTPase Ran protein (or RAN) does this. It has the two forms of RAN-GAP (outside) and RAN-GEF (inside). RAN-GAP hydrolyzes GTP, and RAN-GED catalyzes the binding of GTP to RAN
What is an example of the regulation of nuclear transcription factors? How does it work?
The NF-AT protein regulates the activation of white blood cells. Dephosphorylation of NF-AT by calcineurin causes a conformational change that exposes the nuclear import sequence
What kind of translocation of protein occurs at the mitochondria? Why is it called this?
Post-translational translocation. This is because proteins are mostly translated after they are in the mitochondria
What is the integral membrane unit that deals with protein entrance into the mitochondria, and what are the common subunits in it and what are their functions?
The complex is a protein translocator
Outer-membrane complex: TOM
Inner-membrane complexes: TIM23 and TIM 22
Folding helpers: HSP70 (folding) and HSP90 (folding)
What are two things that can effect where a mitochondrial protein ends up?
Stop transfer sequence and OXT complex
What is the smooth ER often responsible for?
Lipid synthesis and calcium storage
What method can separate rough and smooth ER?
Sucrose gradient centrifugation
What kind of translocation of protein occurs at the rough ER? Why is it called this?
Co-translational translocation. This is because proteins are translated while they are entering the ER.
What recognizes the signal sequence on something that should be sent to the ER, what does it do, are where does it take it?
This sequences is recognized by “SRP” (signal recognition particle) and temporarily stops protein synthesis
This SRP tag allows this complex (which is made up of SRP, ribosome, nascent polypeptide) to bind to SRP receptor on ER surface
What catalyzes the formation of di-sulfide bridges in the ER lumen?
PDI
How are misfolded proteins recognized in the ER, and how are they dealt with?
Oligosaccharides on unfolded proteins are markers that allow recognition my enzyme glucosyl transferase. Then chaperonin calnexin helps with folding. The glucose tag is removed by glucosidase.
What is the retorotranslocation and what happens?
This is when a protein is exported from the ER because it just will not fold correctly. A protein ubiquitin is bound to the target which is then degraded by proteases
Where are phospholipids made, and what enzymes help with the membrane formation process?
They are made on the cytosolic side of ER membrane, and scramblease helps get it to the lumen side and flipase to make the membrane assymetrical
Where do GPI anchors originate?
This connection is made in the ER lumen
What is the sleeping sickness parasite and what does it do?
Trypanosomes – they shed a coat of GPI anchors so the cell cannot be recognized by white blood cells
What components of the cell take part in vesicular transport?
ER, golgi, vesicles, and plasma membrane
What are the 3 major targeting coats?
COPI, COPII, and Clathrin
What are the three components of a clathrin coat?
Clathrin, transmembrane cargo receptor protein, adaptor proteins
How can phospholipids help capture cargo?
Phospholipids with inositol head-groups have domains that can bind to specific cargo
What controls the pinching off of membrane?
The protein dynamin
What proteins regulate coat assemble and vesicle stability?
Arf and Sar-1
Sar-1 binds to budding vesicles and binds GTP which activates coat assembly
What proteins regulate vesicle docking and targeting?
SNARE proteins seem to have a central role in specifically catalyzing the fusion of vesicles with the target membrane
Rabs seem to work with other proteins to regulate initial docking and tethering of vesicle to target membrane
How was the golgi complex discovered?
Staining cells with silver nitrate applied to tissues soaked in osmium and bichromate
Where to the cis and trans faces of the golgi face?
Cis faces ER. Trans faces plasma membrane
What vesicle coat is on vesicles going from the ER to golgi
COPII
What is the name of the sequence that says a protein should leave the ER for the golgi
Exit signals
What is the sequence that says that some proteins should go back to the ER?
KDEL
List 4 functions of the golgi
Newly synthesized membrane, secretory, and lysosomal proteins leave ER and enter cis face of golgi
As proteins pass through golgi stack to trans face, they are modified
A protein’s length may be trimmed by a proteolytic enzyme
Amino acids may be modified
Carbohydrate of glycoproteins are modified in stepwise enzymatic reactions which helps create the highly glycosylated proteins used to form the cell coat and extracellular matrix
At the trans face, the proteins are sorted and target for delivery by vesicles for their destined location
What are the two hypotheses for transport though golgi
Vesicular transport model and cisternal maturation
What is proteolytical processing and what is its purpose?
Many hormones and neuropeptides are made as inactive protein precursors and proteolysis activates the active molecule. These cleavages begin in the trans golgi network and continue in secretory vesicle
What does it mean for a cell to be polarized?
This means it has distinct plasma membrane domains
What distinguishes proteins that are destined to be in the basolateral membrane? What recognizes this and where are they sorted?
These proteins have sorting signals in their cytoplasmic tails, and these amino acid sequences are recognized by coat proteins which sort them into appropriate vesicles in the trans golgi network
What are 3 types of endocytosis?
Phagocytosis, pinocytosis, and receptor mediated endocytosis
What signal tells a cell that it should engage in phagocytosis?
Receptor proteins (Fc receptors) are activated, usually by antibody molecules with an Fc region
What is an example of receptor mediated endocytosis?
LDL uptake that will turn into cholesterol.
What are the three possible fates of receptor proteins that undergo endocytosis?
Recycled to plasma membrane
Different plasma membrane domain (transcytosis)
Degraded in lysosomes
What are the sources of “stuff” for lysosomes?
Endocytosis, autophagy, and phagocytosis
Describe the process of targeting proteins to lysosomes.
Proteins destined to the lysosome have M6P markers that are added to N-linked oligosaccharides as the pass through the cis golgi network. The M6P groups are recognized by transmembrane M6P receptor proteins, which are present in the trans Golgi network. The receptor proteins bind to adaptor proteins (adaptins) in assembling clathrin coats. The clathrin-coated vesicles deliver their contents to a late endosome and then to a lysosome
Why aren’t H’s stripped from hydrocarbons directly combined with oxygen for energy? Describe why not and explain what does happen and why.
This would release too much energy at once. The H’s are passed from molecule to molecule with higher electron affinity so energy is released slowly in packets, which is more useful for the cell.
What is the first molecule that accepts electrons from NADH, and what catalyzes this transfer?
Coenzyme Q (ubiquinone). This is catalyzed by NADH dehydrogenase
What is common between electron transport chain carriers?
Electron transport chain carriers are mostly small molecules or atoms imbedded in prosthetic groups within proteins
What are the 5 types of electron carriers in the electron transport chain?
Flavoproteins, cytochromes, copper atoms, ubiquinone, iron-sulfur protein complexes
What are the three major electron transfer complexes?
NADH dehydrogenase complex, cytochrome b-c complex, cytochrome oxidase complex
What happens to the free energy released from the electron transport chain?
The free energy lost by the electrons in these complexes is taken up by the surrounding proteins in the complex and is coupled to the pumping of protons out of the matrix, across the inner mitochondrial membrane.
What is the potential difference in the inner mitochondrial membrane?
160 mV
How can you visualize the concentration gradient in the inner mitochondrial membrane?
You can treat the mitochondria with a lipid soluble, positively charged, fluorescent dye, the dye accumulates in the negatively charged matrix and makes the mitochondria fluoresce brightly
What is the “proton motive force”?
A force created by both the pH gradient and the potential difference – an electrochemical gradient down which protons can diffuse back into the matrix.
How can protons get back into the mitochondrial matrix?
Through ATP-synthase (this is an F-type pump)
What is DNP, and what does it do?
Di-nitrophenol binds protons and shuttles them back into the matrix, across inner mitochondrial membrane, and down proton gradient, rather than allowing the protons to go through ATP-synthase. The free energy generated is lost as head and not used to make ATP
What are the components of ATP-synthase and what do they do? How has this been shown experimentally?
F0 stalk crosses the inner mitochondrial membrane. F1 spherical ATP-ase fragment sticks out into the matrix
Removal of the F1 sphere eliminates ATP synthesis and renders the inner mitochondrial membrane leaky to protons. This is because it essentially is an open tube allowing leakage
Literally, how does ATAP-synthase synthesize ATP? How many are made?
The rotation of the stalk drives the subunits of the F1 head through a series of conformations that successively bind ADP and Pi, combine them to make ATP, and release the ATP. It takes 12 protons to drive one revolution of the, rotor, creating three ATP molecules from each of the three ADP binding sites on the F1 head - one ATP per 4 protons transferred to the matrix
What are three methods of using proton gradients to drive ATP synthesis?
Mitochondria – oxidative metabolism
Thylakoid membrane of chloroplasts – proton transport during photosynthesis
Light drive proton pump – Bacteriorhodopsin
Where is Bacteriorhodopsin found, and how does it function?
It is an integral membrane protein found in the plasma membrane of certain archeabacteria in salt flats. It is a protein with a small prosthetic group (chromophore) called “retinal” which is embedded in the protein. When retinal absorbs light it has a conformational change that causes pumping of protons out of the cell which makes a proton gradient that ATP-synthase can take advantage of. Used in bacteria under anaerobic conditions.
What are the two main functions of chloroplasts, and where specifically do they occur?
Light reactions in the thylakoid membrane (make ATP) and calvin cycle in the stroma (turn carbon dioxide into sugar)
What wavelengths do chloroplasts absorb?
Blue and red
What can happen when chlorophyll absorbs light and an electron is excited?
Energy can be lost as heat, energy can be transferred by resonance to another chlorophyll molecule electron and associated energy can be transferred to another molecule with higher electron affinity
What actually happens when chlorophyll absorbs light?
An “antennal” chlorophyll in thylakoid membrane absorbs energy and energy is passed through resonance until absorbed by reaction center (P680 in photosystem II or P700 in photosystem I)
What is the final destination of the electrons from photosystem II, and what transfers them there?
Plastocyanin carries the electrons to photosystem I (P700)
What is the name of the complex that P-680 steals electrons from? What specifically has electrons taken from it?
Oxygen evolving enzyme complex. Electrons are taken from Mn.
What takes the excited electron from the reaction center of photosystem II?
Pheophytin
How does Mn compensation for electrons being taken away from it? What are the ratios of this?
Mn steals the electrons from the H atoms in water which. 4 Mn’s take electrons from 2 water molecules, releasing an oxygen molecule and allowing 4 H’s do go into the thylakoid lumen.
Where do the electrons that Mn procures go before photosystem I?
They are received by plastoquinone (Q)
What does P-700 donate high energy electrons to? What does this do with the electrons?
Transfered to A0 which uses the electrons to reduce ferrodoxin
What does ferrodoxin do?
It reduces NADP+ to NADPH
What does the calvin cycle do?
It fixes carbon dioxide into sugar and using the ATP and NADPH made from the “light reactions”
How do LDLs turn into useable cholesterol?
After LDL is brought into the cell, it is delivered to early endosomes, then late endosomes, and then lysosomes. The low pH in the lysosomes, the LDL ester is hydrolyzed into its full cholesterol form which is available for new membrane synthesis
What type of stimuli can cells respond to?
Mechanical, light, heat, chemical
What is signal transduction? How does it become wide spread?
The detection of a stimulus by a receptor protein. The signal from the receptor protein sets off a cascade of signaling proteins and enzymes that cause a widespread cellular response
What is responsible for the amplification of the signal
The second messenger molecules
How are effector enzymes activated?
Phosphorylation of target proteins by activated kinases
Opening or closing of ion channels
Activation of transcription factors
What are some some possible responses by cells to stimuli?
Activation or inhibition of enzymes
Changes in cytoskeletal organization
Changes in ion permeability or activation of ion channels
Activation of gene transcription
Activation of DNA synthesis or mitosis
What are three ways a cell can expose a signal?
Secrete by exocytosis
Diffuse through plasma membrane
Expose to outside of cell but stay attached
How are signaling molecules classified? What class are the majority of signaling molecules in?
Polar or non-polar. Most are polar.
What are the four types of cell signaling? What do they do?
Endocrine - far-reaching Paracrine - local acting Contact dependent - target and signaling cells must be touching Synaptic - like neurons Autocrine - signaling to self
What could happen if a cell is deprived of signals it is supposed to get
Apoptosis
How do acetylcholine effect heart cells, skeletal muscle cells, and salivary gland cells?
Heart - decrease heart rate and force contraction
Muscle - induces contraction
Salivary gland cell - secrete saliva
Where does NO come from and what does it do?
NO comes from endothelial cells surrounding blood vessels and it causes the relaxation of smooth muscle cells that line blood vessels which leads to increased blood flow
How is NO and erection related?
Acetylcholine stimulates calcium which activates NO which diffuses is local endothelial and muscle cells. NO activates enzyme guanylyl cyclase which catalyzes the production of cGMP from GTP. cGMP activates a kinase PKG which leads to muscle relaxation and increased blood flow . Viagra inhibits an isoform of the enzyme phosphodiesterase which is in the penis and destroys cGMP. Thus there is too much cGMP. Other phosphodiesterase isoforms also turn things off in the heat and eye.
What is a common lipid soluble signaling molecule? What does it do? What is the receptor family for these molecules?
Steroid hormones - control function, growth, and differentiation of cells
Nuclear receptor subfamily
What happens when a steroid molecule binds to its receptor?
A conformational change occurs which causes an inhibitory protein to dissociate from receptor and expose a promoter region upstream of a targeted gene
