Final exam

Question 1

What are the qualifications of the cell theory?

Answer 1

1) All living organisms are composed of one or more cells. 2) cells are the basic unit of structure, function and organization in all organisms. 3) cells come from pre-existing cells.

Question 2

What parts make up a phsopholipid?

Answer 2

hydrophilic head (polar head group, phosphate, glycerol), hydrophobic non-polar neutral fatty acid

Question 3

What is amphipathic?

Answer 3

Hydrophobic and Hydrophillicn parts.

Question 4

How impermeable is the phospholipid membrane?

Answer 4

selectively permeable

Question 5

What kind of molecules are impermeable?

Answer 5

large uncharged, polar molecules, glucose, sucrose. or charged molecules, H+, Na+, HCO3-, Ca2+, Cl-, Mg2+, K+

Question 6

What kind of molecules are freely permeable?

Answer 6

O2, CO2, N2

Question 7

what kind of molecules are slightly permeable?

Answer 7

small, uncharged polar molecules, H2O, glycerol

Question 8

What is the second law of thermodynamics and how does it apply to cell membranes?

Answer 8

In the universe, or any closed system, the degree of disorder or entropy always increased. With hydrophobic molecules ordered water no longer forms cages of ordered molecules around the hydrophobic molecules and is instead more disordered because it doesn’t have to interact which has a higher entropy than hydrophobic molecules disordered.

Question 9

What movements can phospholipids do?

Answer 9

lateral diffusion, flexing with the tails extending wider, rotation.

Question 10

What movement can phospholipids not do?

Answer 10

flip layers unfavorable even for short period to have opposite interactions of hydrophilic and hydrophobic, usually done by proteins flipases.

Question 11

what is Fluorescence recovery after photobleaching, FRAP?

Answer 11

fluorescent labeled lipids are shot with a high-powered laser that is turned off. Those areas recover fluorescence because of lateral diffusion but those molecules are still present elsewhere over time and you wouldn’t be able to eventually detect that there was bleaching.

Question 12

What does saturated vs. unsaturated fatty acids mean?

Answer 12

saturated- less molecular space, stiffer, make tails longer less fluid make tighter with cholesterol by packing in between empty spaces to counteract warm temps.
unsaturated- one or more double bonds forming kink/branches/shorter reducing tendency of hydrocarbon tails to interact with one another, cannot pack as tightly, more space fluid counteract cold temperatures

Question 13

What are the acidic amino acids?

Answer 13

Aspartic acid (Asp, D), glutamic acid (Glu, E) have negative charges gave up hydrogens

Question 14

What are the uncharged polar side chains?

Answer 14

Aspargine (Asn, N), Glutamine (Glu, Q), Serine (Ser, S), Threonine (Thr, T), Tyrosine (Tyr, Y)

Question 15

What are the non-polar side chains?

Answer 15

Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Proline (Pro, P), Phenylalanine (Phe, F), Methionine (Met, M), tryptophan (Trp, W), Glycine (Gly, G), Cysteine (Cys, C)- disulfide bonds can form between two side chains

Question 16

What are the basic amino acid side chains?

Answer 16

Lysine (Lys, K), Arginine (Arg, R), Histidine (His, H), positive charges gained proton

Question 17

What alpha-helix is most favorable?

Answer 17

right handed, with a hydrogen bond between every 4th amino acid and lining up backbone hydrogen bonded to itself and hydrophilic parts shielded from outward hydrophobic lipid environment. R groups stick outward around helix usually similar kinds stick out on similar sides. and it is extremely favorable for 2-3 alpha helices to wrap around each other forming a coiled-coil with all of the non polar side chains on one side and are inward. N-H and C=O H-bond interactions. make up secondary structure.

Question 18

What are beta-sheets and what form do they take that is most favorable?

Answer 18

hydrogen bonds between segments of chain lying side by side put side outward and anti-parallel align the best. N-H and C=O H-bond interactions. stick out from sheet up and down. make up secondary structure.

Question 19

what are dimers?

Answer 19

two identical folded proteins that are symmetrical held together by identical bonding site

Question 20

how can proteins be held into lipid bilayer?

Answer 20

transmembrane- extend through bilayer, part on either side. peripheral- most in cytosol, amphipathic alpha helix on the surface of it. outside bilayer could be either side and is held on by one or more covalently attached lipid groups and/or non-covalently attached to other proteins,

Question 21

what is the structure of an amino acid or protein?

Answer 21

N-terminus, alpha carbon w/side chain, and carboxyl group which is deprotonated and the nitrogen acidic under standard conditions. group peptide bond of carbonyl and nitro planar due to resonance

Question 22

why are protein conformations favorable?

Answer 22

combined water entropy but alone a positive delta g because water could make some of those interactions with the protein but combined with the non-covalent bonds make negative delta H to create negative delta g

Question 23

what are the non-covalent bonds?

Answer 23

electrostatic- polar/charged interaction. hydrogen bond-polar uncharged. van der waals- uncharged non-polar electron cloud fluctuations.

Question 24

What are some things that occur in tertiary and quaternary structure?

Answer 24

tertiary- van der waals, electrostatic interaction, hydrogen bonding of protein itself. disulfide bonds between cysteine residues stabilizing structure.
quaternary- van der waals, electrostatic interaction, hydrogen bonding between proteins, disulfide bonds between cysteine residues stabilizing structure.

Question 25

Describe the structure of the antibody?

Answer 25

Two light chains, and 2 heavy chains with carbohydrate attached. 2 variable and 2 constant, sections per chain, pair of beta sheets, variable regions vary in sequence with hyper variable loops. Each arm has four domains. each variable domain has 3 and 5 beta sheets with disulfide bond. Two constant heavy chains that make up the bottom portion and the inside of the antibody with a variable domain on the end of the heavy chain. Opposite that is the constant domain of the light chain connected to the constant chain of the heavy chain via a sulfide bond. The two variable chains of the heavy and light chain connect to antigen binding site. Disulfide bonds are found throughout. 2 identical antigen-binding sites.

Question 26

what is the function of the chaperone protein?

Answer 26

provides a chamber in which a protein can fold without other proteins interacting to form aggregate/amyloids usually from B-strands, allowing them more time to fold properly.

Question 27

what are protein domains?

Answer 27

conserved part of a given protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. they are genetically mobile units, once existed as independent proteins

Question 28

what encompasses Protein degradation?

Answer 28

a proteasome breaks down a protein even if it is still unfolded, or folded, by engaging a catalytic site to break done peptide bond separating amino acids.

Question 29

How do antibodies work?

Answer 29

once ligand binds to B cell with that antibody on its surface enlists ER to make many more and secrete them externally forming aggregates and links the antigens and they are either ingested by phagocytic cells or special proteins in blood kill the bacteria or virus.

Question 30

Why are the variable regions important?

Answer 30

2 antigens, hinge regions fleible more variable to allow arms to move and bind to 2 antigens at the same time and bind to many different kinds of antigens.

Question 31

What is immunofluorescence microscopy?

Answer 31

you use fluorescence antibodies and have to kill cells. 1) fix and permeabilize cells. 2) add antibodies and incubate wash away anything not tightly bound. shows localization places

Question 32

What is immunoblotting (western blotting)?

Answer 32

1) make a cell lysate
2) treat sample with amphipathic detergent (SDS page) coating proteins causing them to become unfolded by interacting with hydrophobic groups not allowing them to react with eachtoher and have negative charge. the bigger the protein the bigger the charge. break disulfide bonds by reducing agent. insert into gel and it moves down gel the smaller the protein the faster it migrates through. called SDS-polyacrylamide gel electrophoresis 3) transfer proteins to filter paper which shows every protein that the cell is expressing with different sizes and some positions relate to one another. 4) add fluorescent antibodies
5) see by fluorescent detection the fluorescent proteins only seeing where the protein with that particular antibody is which is degraded within the phagocyte

Question 33

What is immunoprecipitation (affinity purification)?

Answer 33

is the technique of precipitating a protein antigen out of solution using an antibody that specifically binds to that particular protein. This process can be used to isolate and concentrate a particular protein from a sample containing many thousands of different proteins. Immunoprecipitation requires that the antibody be coupled to a solid substrate at some point in the procedure.Antibodies that are specific for a particular protein (or group of proteins) are immobilized on a solid-phase substrate such as superparamagnetic microbeads or on microscopic agarose (non-magnetic) beads. The beads with bound antibodies are then added to the protein mixture, and the proteins that are targeted by the antibodies are captured onto the beads via the antibodies; in other words, they become immunoprecipitated.

Question 34

What is feedback inhibition?

Answer 34

mechanism of down-regulating enzyme activity by the accumulation of a product later in the pathway and large quantities of final products accumulate resulting in product bind to earlier enzyme slowing down catalytic activity limiting further substrates emerging from the reaction. negative regulation-preventing an enzyme from acting. positive regulation- activity stimulated by regulatory molecule product in one branch stimulates activity of an enzyme in another pathway.

Question 35

Describe allosteric regulation?

Answer 35

allosteric regulation is mediated by protein conformational changes, allosteric regulators are often products of other chemical rxns in the same biochemical pathway, allosteric regulation can be used for positive and negative regulation of enzyme activity is not limited to enzyme as the subject to this form of regulation. effector binding influencing site on opposite side of protein altering the function of the functional site. can distort/inhibit or open up site/activate

Question 36

what dies a kinase do?

Answer 36

enzyme that covalently adds a phosphate group to a protein “phosphorylation” transferring the terminal phosphate group of ATP to a hydroxy group on a serene, threonine, or tyrosine side chain.

Question 37

what does a phosphatase do?

Answer 37

removal of a phosphate from a protein “dephosphosphorelation.” can stimulate or inhibit

Question 38

what does ubiquitin addition do?

Answer 38

covalent addition of a ubiquitin to a lysine forming an isopeptide bond, a small polypeptide, to a protein is post-translational ubiquitylation on leading to their degradation by the proteasome with ubiquitin conserved

Question 39

how are proteins regulated?

Answer 39

1. Control amount of protein
   à Regulate synthesis (transcription, translation) and/or
   degradation/ubiquitylation.
2. Control activity of protein
   à Regulate localization, enzymatic function, ability to interact with binding partners, … allosteric regulation

Question 40

what is a lysozyme?

Answer 40

enzyme that severs polysaccharide chains of bacterial cell walls.

Question 41

how does an enzyme lower activation energy?

Answer 41

forms multiple non-covalent bonds that hold substrate so the shape is favorably distorted for the bond to easily break and held close to two acidic amino acids greatly reducing the activation energy to be done and it forms a template or mold of strategic amino acid placement that bring the reactant together in proper orientation by altering distribution of electron in substrate, driving it toward the transition state. increase local substrate concentrations, create the induced fit to strain bonds and are not changed

Question 42

what is a conformational change?

Answer 42

most proteins and other molecules are not stuck in one absolutely static 3D structure. instead they usually have two or more forms that are very similar but not identical induced by ligand or post-translation molecule. A conformational change is the change of a protein from one three dimensional structure (“conformation”) to another subtly different structure, often (1) accompanied by a change in function/activity of the protein and (2) triggered by a post-translational modification or the binding of a ligand.

Question 43

What is the SRC kinase regulation by tyrosine phosphorylation.

Answer 43

it is a regulatory receptor that when ATp bound to one sight the other is in a conformation that it cannot be bound and the kinase is off and vice versa turns it on.

Question 44

What is the evidence for the formation of the ER and nuclear membrane?

Answer 44

Plasma membrane invagination likely explains the origin of the secretory organelles (ER, Golgi, lysosomes, endosomes). membrane contiguous with outer plasma membrane then became separated and membrane proteins are delivered from one compartment to another by a budding vesicle. From ER to golgi, endosomes, and lysosomes and to the cell exterior and membrane

Question 45

what is the evidence for the endosymbiotic theory?

Answer 45

The “endosymbiotic theory” provides the best explanation for the origin of the mitochondria and chloroplast. ate another prokaryotic cell and kept it while it lost some of its DNA but kept its surrounding membrane, some DNA, makes some of own proteins, doesn’t easily exchange contents. many of their functions could be carried out at the plasma membrane but better optimize energy with increase surface area,

Question 46

what is the default localization of proteins?

Answer 46

cytosol?

Question 47

what organelles use gated transport?

Answer 47

nucleus transports between topologically equivalent compartments through selective gates

Question 48

what organelles used transmembrane transport?

Answer 48

cytosol- peroxisomes, plastids, mitochondria, endoplasmic reticulum. transport between topologically distinct compartments, across a lipid bilayer.

Question 49

what organelles use vesicular transport?

Answer 49

ER-golgi, endosomes, lysosome, and cell exterior via secretory vesicles. transport between topologically equivalent compartments via membrane-enclosed transport intermediates.

Question 50

what is needed for protein transport?

Answer 50

1) signal sequence, 2)machinery to recognzie/transport bearing sequence,
3) directionality knowing when to pick up/drop off
4) energy source

Question 51

where are steroid hormone synthesize?

Answer 51

Smooth ER

Question 52

Where are secreted proteins modified?

Answer 52

golgi

Question 53

where is there a breakdown of lipids and toxic molecules?

Answer 53

peroxisom

Question 54

where is there degradation of worn-out organelles macromolecules and particles by endocystosis

Answer 54

lysosome

Question 55

what do proteins undergo when entering ER?

Answer 55

moved by protein translocators located in membrane and unfold to get across or not yet created. add disulfide bonds to stabilize when dealing with degradtive enzymes. turned into glycoproteins when they enter by adding oligosaccharide side chain on lumenal side of ER protecting them from degradation holding them in ER till properly folded and guides to organelle by being used as a transport signal. form glycocalyx or a cell-to-cell recognition. if meant to stay in ER first localization signal removed and a later signal added to end

Question 56

explain nuclear import

Answer 56

allows small molecules to go through. has cytolic fibers and a nuclear basket that passes proteins through. proteins need nuclear localization signal, moved through nuclear pores completely formed by karyopherins which bind cargo NPC proteins and Ran-GTP. GAP GTPase activating protein Ran GTP-GDP hydrolysis losing phosphate. GEF guanine nucleotide exchange factor GDP-GTP. Ran-GTP/GDP requires other enzymes. Ran-GTP more abundantly found in nucleus, GEF found in nucleus. Ran-GDP more abundantly found in GAP found in cytosol

Question 57

where is ribosome assembly take place?

Answer 57

nucleolus

Question 58

how would you determine if a nuclear localization is necessary?

Answer 58

get rid of the signal and see where it localizes

Question 59

how would you determine if a nuclear localization is sufficient?

Answer 59

add the signal to a systolic protein

Question 60

What is the mechanism for importing a protein to the ER?

Answer 60

1) SRP binds to ribosomes “co-translational” translating a protein with a N-terminal signal sequence necessary and sufficient and pauses translation.
2) SRP receptor a protein anchored in the rough ER membrane with a systolic domain that recruits SRP and ribosome recruiting it to ER membrane
3) translocon channel- membrane anchored proteins forming aqueous pore in ER membrane and only open when it binds signal sequences and resumes translation
4) signal peptidase a protease that chews off the signal sequence. can have start and stop sequences to allow multi-pass membrane

Question 61

what is the purpose of glycosylation?

Answer 61

help and monitor protein folding in ER, help with protein sorting, protect proteins on surface of cells from digestion. Most ER proteins are glycoslated on cytosolic surface . Mannose timer gives it time to fold and leaves a mannose on if not folded fast after a while a protein acts to take many mannose and glucose off extracting it from ER to be degraded

Question 62

what is the role of membrane vesicle formation?

Answer 62

cargo molecules bind and aggregate and are selected by adaptins bind to specific receptors which receive a clathrin coat and the vesicle is cut off by dynamic and the coating and adaptin coat are released

Question 63

how are cells recognized for their targets?

Answer 63

recognition with Rab proteins recognized by tethering proteins on systolic surface of target with each carrying unique proteins for signals once tethered with tethering proteins the transport vesicle has v-snares which bind to the target membrane’s t-snares docking by coalescing with the lipid bilayer fusing

Question 64

after the ER and golgi what is the default pathway for proteins?

Answer 64

plasma membrane, requires signals to stay in ER, golgi or be transported to lysosome.

Question 65

what are microtubules?

Answer 65

hollow cylinders made of tubulin long and straight have one end attached to centrosome or microtubule organizing center at - end, more rigid ruptured when stretched. rapid disassembly in one location and reassembles, move tracks within cells, organelles, vesicles and cell components. growth at plus end dynamic instability hydrolyze GTP to GDP shortly after added maintain GTP cap. have the largest diameter. GTP. 13 monomeric filament make tube

Question 66

what are actin filament?

Answer 66

helical polymers of protein actin, flexible organized into bundles dispersed throughout cell but mosty highly concentrated in cortex layer of cytoplasm beneath plasma membrane, contractile ring in cytokinesis and contraction of muscles smallest filament . ATP. found at leading edge of movement can stay same length due to tread milling

Question 67

what are kinesins and dyne ins?

Answer 67

kinesins- proteins that move along cytoplasmic micrtubules outward from cells toward plus end. dyneins- move minus end toward cell body

Question 68

What are intermediate filaments and their functions?

Answer 68

rope-like gives mechanical strength much more fluid rope-lie staggered monomers no directionality

Question 69

what are cytoskeletal enzyme developments?

Answer 69

Tubulin=GTpase
Actin=ATPase
both have a plus end and a minus end with growth at plus end not charged

Question 70

describe the structure and function of actin filaments?

Answer 70

assembly and disassembly can happen at both the plus and minus end, but favorability of each is different at each end. Under certain conditions, assembly happens at plus end and disassembly at minus end, Treadmilling by plus end bound to ATP and minus end bound to GDP losing new actin polymerization at the front of the cell

Question 71

what are some cytoskeleton regulator proteins?

Answer 71

Nucleation factors: Monomer binding proteins:
Capping proteins:
Other end-binding proteins: Filament stabilizing proteins: Filament severing proteins:
Regulate rate and location of new filament assembly
Regulate availability of free monomers and therefore addition of monomers to filament ends
Prevent filament assembly or disassembly at bound end
May promote filament assembly or disassembly
Bind along length of filaments to promote stability
Create new filament ends for assembly or disassembly

Question 72

How do kinesins work?

Answer 72

on motor protein ADP kinesin ends binding to filament causes ADP to be released and ATP to bind. This causes the zipper to move and bring around the second sub unit adding ATP. ATP-ADP of first subunit previous end then it is repeated.

Question 73

what are the 3 types of energy?

Answer 73

kinetic, potential, and heat

Question 74

what is metabolism?

Answer 74

the sum of the chemical reactions that take place in the cells of a living organism resulting in growth, division, energy production, excretion of waste. etc. =catabolism+anabolism

Question 75

what is catabolism?

Answer 75

reactions that break down larger, high-energy molecules into smaller, low(er) energy molecules. releases energy

Question 76

what is anabolism?

Answer 76

reactions that assemble small molecules(in many cases intermediates/products of catabolism) into macromolecules and biomass requiring energy.

Question 77

what are plants doing in photosynthesis?

Answer 77

capture useful energy emitted by matters as decay, using this captured to temporarily reverse their own increase in energy

Question 78

what are membrane transport proteins?

Answer 78

highly selective for specific molecules and permit molecules to pass through lipid bilayer, going down concentration gradient

Question 79

what is a pore?

Answer 79

a tube-like channel with a group of proteins that are highly selective in the molecules they let pass through the membrane. surface of alpha-helix R groups customized to form channel

Question 80

where do the light and dark reactions occur in a chloroplast?

Answer 80

light rxn in thylakoid and ETC in thylakoid membrane with protons concentrated in the thylakoid lumen
dark run in stroma

Question 81

what happens in the light reactions?

Answer 81

chlorophyll captures sunlight energy by transmitting it to reaction center PSII taking an electron from water and exciting it when reduced hates electrons it picks up and passes it to another molecule with a lower potential ETC extracting as much energy as possible passed from one to another and protons pumped from stroma to lumen . Photosystem receives electrons from plastoquinon excites and gives to NADPH

Question 82

How can cells be ordered?

Answer 82

increase order or decrease entropy of cell by spending energy releasing heat with a net increase in entropy

Question 83

what are the energy intermediates?

Answer 83

Proton Motive Force (PMF) energy as artificial gradient , NADH energy in excited electrons carries 2-3x energy as ATP, ATP energy in chemical bonds high energy phosphate bonds formation of ATP requires energy input and vice versa

Question 84

How is ATP produced?

Answer 84

1. Substrate level phosphorylation (Glycolysis)
   Direct transfer of a high energy phosphate from a phosphorylated
   organic compound to ADP.
2. Respiration-linked phosphorylation (Respiration)
   High energy electrons from organic molecules (ex. glucose) transferred from NADH to an electron transport chain, ultimately generating PMF. Need an electron acceptor. (What do we use?) Energy from PMF then used to drive the enzyme ATP synthase.
3. Photophosphorylation (Photosynthesis)
   Similar to respiration-linked phosphorylation, except the energy to generate PMF comes from light.

Question 85

Why use different energy intermediates?

Answer 85

1. Different amounts of energy
   Choose the carrier that most efficiently captures/distributes energy from/to a particular reaction. (Having only one energy carrier would be like carrying only $100 dollar bills!)
2. Different redox levels
   Utilizing electron carrying energy intermediates (NADH, NADPH, FADH2) vs. non-redox changing energy intermediates (ATP) can allow cells to balance their electrons while capturing/distributing energy.
3. Regulation and specificity
   Allows for sorting of energy/electrons to different pathways serving different functions.

Question 86

what are REDox reactions?

Answer 86

Hydrogen loss is associated with oxidation (electron loss). Hydrogen gain is associated with reduction (electron gain). All half reactions have an individual E’0 value The favorable direction (-∆G) is positive
The unfavorable direction (+∆G) is negative. A more positive E’0 means that reducing the electron acceptor yields more energy.
A more negative value of E’0 means that oxidizing the electron donor yields more energy. farther electrons fall more energy released

Question 87

Explain the oxygen catastrophe.

Answer 87

prior to cyanobacteria all organisms anaerobic and there was little O2 when they evolved O2 was captured by iron to form insoluble iron oxides forming banded iron formations. 1. O2 oxidized methane (a strong greenhouse gas) to carbon dioxide (a weaker one), triggering the Huronian glaciation (Earth = snowball for 300-400 million years).

2. Mass extinction of anaerobic life forms (likely the biggest mass extinction ever!)
3. Set the stage for evolution of aerobic respiration ! mitochondria!eukaryotic/multicellular organisms! O2 ultimate oxidizer a lot of energy extracted

Question 88

what happens in the light-dependent and light-independent reactions

Answer 88

1. Generation of ATP and NADPH from radiant energy and electrons from H2O = “Light-dependent” reactions O2 waste on thylakoid membrane with proton concentrated inside lumen. 1st half uses plastoquinone and cytochrome creates PMF second half pumps more with plastocyanin and ferredoxin but ends up on NADPH
2. Construction of sugar from CO2 and H2O using the energy and electrons from the ATP and NADPH produced above = “Light-independent” reactions in stroma. rubsico ribulose bis-phosphate carboxylase adds CO2 to 5 carbon sugar cycle goes through 3x 9ATP and 6NADPH to make 1G3P which is the profit 6CO2+12H2O+energy-C6H12O6+6H2O+6O2

Question 89

where does all of respiration take place?

Answer 89

glycolysis-cytosol NADH, pyruvate and ATP
citric acid cycle- mitochondrial matrix
oxidative phosphorylation- inner membrane of mitochondria generating PMF with concentrated protons in intermembrane space

Question 90

what are the steps in Light dependent reactions

Answer 90

1) generation of high-energy electrons at PSII by light harvested from absorbing chlorophyll a(red) and b(blue)to the reaction center
2) ETC, plastoquinone, cytochrome plastocyanin
3) Generation of PMF cytochrome
4) PMf used to make ATP
5) re-excitement of electrons at PS I
6) ETC and electron donation to generate NADPH by ferredoxin

Question 91

What exactly are components of an ETC?

Answer 91

Elelctron carrier molecules:
Protein components
! “Oxidoreductases”, a subset of which are “cytochromes”
! Cytochromes are pigmented proteins whose absorbance spectrum shifts when there is a change in redox state.
Cofactors
! Small molecules that associate strongly or loosely with the proteins.
! Play critical roles in electron transfer
! Example: Heme in Cytochrome c
! Other examples:
Flavin mononucleotide (FMN) Iron-sulfur clusters Quinones/QuinolsQuinones/quinolsQuinone = oxidized state Quinol = reduced state Hydrophobic cofactors that loosely associate with protein complexes and act as mobile electron/proton carriers.

Question 92

H2O donates electrons to PSII

Answer 92

resting PSII lower and more positive than water no energy required until absorbs light

Question 93

PMF generationin chloroplast ETC?

Answer 93

• Generation of H+ by splitting of H2O in the thylakoid space
• Transfer of H+ by plastoquinone from stroma to thylakoid space
• Pumping of H+ from stroma to thylakoid space by cytochrome b6-f complex
• Consumption of H+ in stroma by production of NADPH
potential-mechanical/rotational energy-kinetic energy

Question 94

organic carbon from CO2 requires

Answer 94

6CO2 18ATP, 12NADH to make C6H12O6

Question 95

describe glycolysis?

Answer 95

1 glucose- energy investment 2ATP once phosphofructokinase enzyme that catalyzes committed step to form fructose 1,6-bisphosphate regulated by ATP allosterically then is cleaved to glyceraldehyde 3-phosphate with energy generated by substrate-level phosphorylation by 6 phosphoglycerate kinase and 10 pyruvate kinase
net 2 ATP and 2 NADH but runs out of NAD+

Question 96

compare and contrast how ATP is made in glycolysis vs. photosynthesis?

Answer 96

1. Substrate level phosphorylation (Glycolysis)
   Direct transfer of a high energy phosphate from a phosphorylated organic compound to ADP.
2. Photophosphorylation (Photosynthesis)
   High energy electrons (originally from H2O) are transferred from PSII to an electron transport chain, which generates a PMF. Energy from PMF then used to drive ATP synthesis by the enzyme ATP synthase.

Question 97

why does fermentation occur?

Answer 97

electrons from NADH are dumped back onto pyruvate yielding lactate a soluble sugar to regenerate NAD+ to keep glycolysis running

Question 98

what is the mitochondrial matrix?

Answer 98

the place where the citric acid cycle occurs

Question 99

what happens in the inner membrane and its space?

Answer 99

concentrated protons with membrane where ETC membranes occur

Question 100

Describe TCA/Krebs/Citric acid cycle.

Answer 100

coenzyme A links glycolysis to TCA cycle by releasing CO2 and creating NADH to form acetyl CoA

Question 101

per pyruvate?

Answer 101

1 ATP, 4NADH(1 more turning into acetyl coA(, 1FADHS

Question 102

desctibe ETC in inner mitochondrial membrane

Answer 102

1. donation of high-energy electrons from NADH 2. ETC ubiquinone coenzyme Q, 3. cytochrome c oxidase puts electrons on water pumping protons O2 serves as final electron acceptor
2. generation of PMF
3. PMF used to make ATP

Question 103

What is pyruvate kinase and what does it do?

Answer 103

transfer to ADP of high-energy phosphate group forming ATP completing glycolysis rate-limiting step

Question 104

what is signal transduction?

Answer 104

Signal transduction is the process by which a signal is sensed by a cell and converted into a cellular response.

Question 105

why is cell signaling important?

Answer 105

1. Very important for cell-cell communication in multicellular organisms, also in unicellular organisms that must come together to mate or differentiate
   • Thiscaseinvolvesasignalingcell(generatesasignal) and a target cell (receives signal and implements response).
   • Cells“tell”other cells to do all sorts of things: survive, die (“apoptosis”), divide, differentiate, move, stop moving, alter metabolism, prepare to mate!
   Classic example: Pheromones inducing yeast mating grow towards each other forming shmoo
2. Important for a cell to respond to external conditions • In this case, the signal comes directly from the
   environment.
   à Example: Salt inducing Msn2 stress pathway
3. Important for a cell to respond to internal conditions
   • In this case, the signal originates from inside the cell.
   à Example: DNA damage inducing apoptosis

Question 106

what are the steps in signal transduction?

Answer 106

I. Synthesis/release/transport of the signaling molecule to the target cell
II. Recognition of the signal by the target cell
III. Relay, amplification, integration (survive, grow and divide, differentiate, die), distribution, and modulation of the signal inside the target cell – often called a “signaling cascade” intracellular signaling pathways proteins (molecular switches, GTPases “G” proteins”, phosphoproteins (kinases and phosphatases) and small molecules that work as “second messengers” amplifying signal- Molecules like cyclic AMP (cAMP) or Ca++ that are generated/ released in large amounts in response to an activated receptor and act to quickly and “loudly” broadcast the signal to other parts of the cell.
IV. Delivery of the signal to target protein(s) and execution of the cellular response

Question 107

How do GTPases work?

Answer 107

on GTP bound form undergoes hydrolysis by GAP to GDP off form which exchanges GDP for GTP by GEF

Question 108

How do phosphoproteins work?

Answer 108

Phosphorylation of ATP to ADP by kinase with a molecule with a phosphate attached can be on or off. De phosphorylation by phosphatase with water added and a phosphate group leaving to be on or off

Question 109

what are the functions of ion-channeled coupled receptors?

Answer 109

ions flow through when a signal molecule is bound to the receptor

Question 110

Describe Enzyme-coupled receptors.

Answer 110

Receptor tyrosine kinase: signal molecule forming a dimer activating catalytic domain. Signal binding, receptor dimerization and activation of intracellular kinase domains with “cross-phosphorylation” single pass can’t transmit change across membrane so phosphorylates at multiple tyrosine residues for the recruitment by SH2 domains and activation of signaling proteins especially adaptor protein which is connected to Ras-GEF to activate raw protein for downstream intracellular signaling pathways. activated Ras activate map kinase kinase kinase which phosphorylates and activates…
ex. SRC kinase inactive when one conformation bound to P and on when one unbound and the other bound.
unactivated by
a. digestion of the RTK in lysosomes
b. dephosphorylation by protein tyrosine phosphatases
c. removal of the RTK from the plasma membrane by endocytosis

Question 111

What are protein-coupled receptors?

Answer 111

receptor becomes bound to signal molecule activating G protein which activates enzyme

Question 112

how many responses can one signal induce?

Answer 112

The number of different receptors is even greater than the number of signals that can act on them!
This means that a single signaling molecule can often act on more than one receptor, sometimes from different classes.

Question 113

what signals can go across membrane?

Answer 113

hydrophillic signals cannot diffuse across membrane, steroids etc. can

Question 114

when is a GTP binding protein in the one state?

Answer 114

A GTP-binding protein in the “on” state (bound to GTP) is converted to the GDP-bound “off” state due to GTP hydrolysis.

Question 115

describe the different receptors?

Answer 115

ion-channeled coupled receptors- Cell-surface receptors that alter the membrane potential directly by changing the permeability of the plasma membrane
G-protein coupled receptors-Cell-surface receptors that are (almost) always polypeptides with seven transmembrane domains.
enzyme-coupled receptors- d. Cell-surface receptors that were discovered for their role in responding to growth factors in animal cells.

Question 116

describe what happens when a G-protein coupled receptor is activate

Answer 116

GPCR and heterotrimeric G-protein inactive, alpha bound to GDP. signal molecule bound to activated receptor GPCR changes conformation and binds to hetertrimeric G protein with GDP dissociation functioning as GEF. Alpha subunit exchanged GDP for GTP and disconnect from each other as activated. activating ion channels and adenylyl cyclase that produces second messengers of cAMP or inhibit. cAMP activate PKA gene trascritption

Question 117

important about G-protein coupled receptors?

Answer 117

Over 1000 GPCRs in the human genome!
• Detect photons, odorants, neurotransmitters, hormones, and peptides, among other signals.
• Underlie our ability to sense odor, flavor, and light, as well as our ability to respond to neurological chemicals such as serotonin and hormones like adrenaline.
• Up to half of all drugs mediate their effects by interacting with GPCRs!

Question 118

understanding figures

Answer 118

Over 1000 GPCRs in the human genome!
• Detect photons, odorants, neurotransmitters, hormones, and peptides, among other signals.
• Underlie our ability to sense odor, flavor, and light, as well as our ability to respond to neurological chemicals such as serotonin and hormones like adrenaline.
• Up to half of all drugs mediate their effects by interacting with GPCRs!

Question 119

what does figure 4 show?

Answer 119

a, Tumour formation over time in nude mice injected with M1 and M2 rescue H1299 cells. After 43 days, 3 out of 7 mice injected with M1 cells and 7 out of 8 mice injected with M2 cells formed tumours. b, Mice injected with M1 cells on the left flank and M2 cells on the right flank. The mouse on the left only formed a tumour from the M2 cells. The mouse on the right formed a bigger tumour from the M2 cells than from the M1 cells. c, Dissected tumours from the nude mice. The only three tumours derived from M1 cells are shown (top row), and these tumours were smaller than four of the tumours from the M2 cells (bottom row). d, Mass of the dissected tumours. Each dot represents the tumour mass from one mouse. The blue line indicates the mean tumour mass originating from M1 cells and M2 cells. e, Immunoblotting of tumour lysates originating from M1 cells, M2 cells, or a 50/50 mixture of M1 and M2 cells (M1/M2). The left panel shows lysates from the injected cells. The right panel shows lysates from the dissected tumours. Lysates were immunoblotted with antibodies towards M1, M2, pyruvate kinase (recognizes both M1 and M2), Flag and GAPDH. To determine whether M2 isoform expression is important for tumour cell growth in vivo, we performed xenograft studies using the M1 and M2 rescue cells. Nude mice were injected with 5 million M1 or M2 rescue H1299 cells, and tumour growth was monitored over a 7-week period. As shown in Fig. 4a, mice injected with the M1 cells showed a delay in tumour development as compared with those injected with the M2 cells. Fewer tumours developed from the M1 cells, and those that did were smaller in size (Fig. 4b, c). As judged by total tumour mass, the M2 cells gave rise to significantly larger tumours than the M1 cells (Fig. 4d). Western blot analysis of the developed tumours shows that the Flag-tagged rescue mM1 and mM2 proteins are retained in the tumours; however, endogenous expression of PKM2 returned in both cases (Fig. 4e). No tumours were recovered that solely expressed mM1. To determine whether this was the result of loss of shRNA-mediated knockdown of endo- genous PKM2 or whether it represented a selective growth advantage for cells expressing M2, a 50/50 mixture of the M1 and M2 cells was injected into nude mice. Tumours that arose from the mixture of M1 and M2 cells only retained expression of the Flag–mM2 rescue protein, demonstrating that most of the tumour, if not the entire tumour, was derived from the M2-expressing cells (Fig. 4e). These data show that PKM2 expression provides a selective growth advant- age for tumour cells in vivo.

Question 120

What is the big picture question being asked by this experiment?

Answer 120

Does a particular version of pyruvate kinase favor tumor formation, and exhibit selective growth and an advantage in tumor cells?
What version of pyruvate kinase is important for tumor cell growth and does it have a selective advantage in tumors?

Question 121

what is the experimental design?

Answer 121

If PKM2 is important for tumor cell growth then M2 cells will exhibit higher levels of the formation of tumors, with overall larger and faster tumors formed

Question 122

what are the actual results and interpretations?

Answer 122

M2 cells had a higher percentage of tumors formed and gave rise to significantly larger tumors showing selective growth advantage for M2 cells only retaining expression of the M2 rescue protein showing that most of the tumor if not all of it was from M2-expressing cells.