Archive for October 2018

In the aldol cleavage of Fructose 1,6 bis phosphate to DHAP and GAP, why is there 96% DHAP?

In the aldol cleavage of Fructose 1,6 bis phosphate to DHAP and GAP, why is there 96% DHAP?



Answer: Because DHAP is involved in the uptake of glycolysis NADH electrons into the mitochondrial matrix so they can also be used in ATP production. BUT these are taken up by FADH molecules and so become worth only 1.5 ATP (unlike Krebs Cycle NADHs)

Why does the c ring rotate?

Why does the c ring rotate?



Answer: Each c subunit has a critical aspartic acid residue that when an H+ comes in, causes it to become neutralized and thus want to interact with the hydrophobic membrane. Thus it pulls that c cubunit to the side. This is repeated over and over again. And as the C ring turns it causes the gamma to rotate

Describe how the gamma and beta subunits of ATP synthase interact to allow ATP formation.

Describe how the gamma and beta subunits of ATP synthase interact to allow ATP formation.



Answer: The gamma subunit as it rotates extends into the ring and breaks the symmetry of the hexamer by interacting with a beta subunit and changing the beta subunits conformation. The change in conformation causes the beta subunit to either be in a an open, tight or loose position. ATP is generated from ADP and Pi in the tight conformation and released in the loose conformation.

Describe the experiment used to test the proton-motive force. Draw it.

Describe the experiment used to test the proton-motive force. Draw it.



Answer: Used light sensitive bacteriorhodopsin protein incorporated on one end of a vesicle membrane, ATP synthase on the other. The protein is closed when in the dark. Put a high concentration on H+ ions and ADP + Pi outside the vesicle. Then shine light on the vesicle. They found that the ATP was produced. So the proton motive force is coupled with ATP synthesis.

Describe the action on Complex IV.

Describe the action on Complex IV.



Answer: Cytochrome C Oxidase catalyzes the transfer of electrons from 4 reduced Cyt C molecules to Oxygen. The electrons first reduce Heme a3 and Cub which then bind to oxygen. The oygen will take the electrons from them to form H2O.

What is ubiquinone versus ubiquinol?

What is ubiquinone versus ubiquinol?



Answer:

Ubiquinone is the oxidized form of Coenzyme Q (Q)
Ubiquinol is the reduced form of Coenzyme Q (QH2)

Why does each NADH give 2.5 ATPs but each FADH2 only gives 1.5.

Why does each NADH give 2.5 ATPs but each FADH2 only gives 1.5.



Answer: When FADH2 is taken up by Complex II, it undergoes the same transfer of electrons through iron-clusters and then to Coenzyme Q, and QH2 is formed however, this is all not coupled to a pumping of protons out at this point. (It is only involved in the Q protons while NADH is involved in the Q protons AND the pump at Complex I)


What are the two special things about Complex II.

What are the two special things about Complex II.



Answer: It is the same succinate dehydrogenase from the Krebs cycle. Was the only Krebs Cycle enzyme that was embedded into the mitochondrial matrix. Second special thing--this is where FADH2 enters the electron transport chain.

Describe the flow of NADH's electrons.

Describe the flow of NADH's electrons.



Answer: NADH gives two electrons to FMN, the electrons then travel through a series of iron-sulfur clusters to get to Coenzyme Q. Coenzyme Q accepts the two electrons (and in the process also takes up 2 protons from the matrix to become QH2). All this flow of electrons from NADH to Coenzyme Q is coupled to the pumping of 4 protons out.

Describe the structure of Complex I.

Describe the structure of Complex I.



Answer: It is a Huge complex with 46 subunits. Its structure suggests a piston mechanism that shunts protons across the membrane through 3 separate channels.

What is the respirasome?

What is the respirasome?



Answer: These are Complexes I, II, III, IV that sit on the mitochondrial inner membrane and are involved in the pumping of H+ ions into the intermembrane space

Explain the role of dynein in flagella movement.

Explain the role of dynein in flagella movement.



Answer: Dynein arms reach up to grab adjacent microtubule in doublet. Creates a bending that is used for motion.

What are focal contacts?

What are focal contacts?



Answer: The "feet" involved in cell crawling. This happens if a whole cell needs to move to a diff region. The focal contacts (contain integrin) form as actin polymerizes on the plus end. There is a contraction on the neg end as focal contacts are lost.

What is plectin?

What is plectin?



Answer: Cross links that hold intermediate filaments and microtubules together. Seen on a micrograph.

What is dynein and kinesin?

What is dynein and kinesin?



Answer: Molecular motors that move vesicles along a microtubule in a cell. Dynein walks towards the neg end, kinesis towards pos

What is treadmilling and catastrophic disassembly?

What is treadmilling and catastrophic disassembly?



Answer:

Treadmilling---plus end is growing at same rate as disassembly on minus end
Catastrophic dissassembly--Accidental loss of the GTP cap

Describe the layers of the gut epithelial cell membrane.

Describe the layers of the gut epithelial cell membrane.



Answer: Apical plasma membrane (nutrient and water intake, secretion regulation), Lateral plasma membrane (cell contact, adhesion and communication), Basal membrane (cell substratum? contact, ion gradient generation)

Give two examples of sentinel cells and how they work.

Give two examples of sentinel cells and how they work.



Answer: They cruise around cells and if they see a problem, they signal. Monocytes will signal for T cells to come while Mast cells signal for MMPs (matrix metalloproteinases)----tumor metastasis?

What is a focal adhesion kinase?

What is a focal adhesion kinase?



Answer: A molecule that is involved in actin signalling to the nucleus. It does this by phosphorylating.

What are integrins?

What are integrins?



Answer: Transmembrane proteins that appear as dimers to which other components of the cytoskeleton are anchored.

What is mTORC1 and mTORC2?

What is mTORC1 and mTORC2?



Answer: Signal molecules involved in regulation of cell growth, metabolism, motility and survival. Absence of mTORC1 in knockout mice produced several issues. Absence of both is embryonically lethal

Why is b-catenin so important in development?

Why is b-catenin so important in development?



Answer: When present (i.e not degraded by Wg pathway), it goes into the nucleus to start a complex for gene expression. When absent (degraded by ubiquitin), gene expression for a lot of genes does not happen in development.

What is Wnt?

What is Wnt?



Answer: An important messenger during development. It binds to frizzled which causes dishevelled to become activated to prevent degradation of b-catenin.

Describe the role of nitric oxide in smooth muscle relaxation in a blood vessel wall?

Describe the role of nitric oxide in smooth muscle relaxation in a blood vessel wall?



Answer: An activated nerve terminal releases acetylcholine which binds and activates NO synthase. The enzyme changes arginine to nitric oxide which can rapidly diffuse across membranes and cause generation of cAMP.

What are 3 roles of epinephrine?

What are 3 roles of epinephrine?



Answer:

Break down of glycogen
Smooth muscle relations (stomach)
Vasodilation (increases blood supply to other tissues)

What is PIP2?

What is PIP2?



Answer: A plasma membrane phospholipid that when hydrolyzed by Phospholipase C, produces IP3 (inositol trisphosphate) a secondary messenger signal transduction molecule. For example, these molecules are part of the signal cascade or epinephrine/norepinephrine causing an end result of Ca2+ release in a smooth muscle cells of blood vessels to produce a dilation.

Give a major role of Protein Kinase A?

Give a major role of Protein Kinase A?



Answer: PKA---Regulates metabolism by turning off and on glycogen production versus breakdown, and glucose synthesis (gluconeogenesis) Is it related to the enzymes of glycolysis like

Give an example of a signal transduction pathway involving cAMP and Protein kinases?

Give an example of a signal transduction pathway involving cAMP and Protein kinases?




Answer: When cAMP is lose in a cell, it cam phosphorylate PK1,which in turn can activate PK2 and result in a cascade of activations with the final activation being of a DNA transcription factor. The transcription factor is caused to lock down on the DNA to signal for transcription to begin.

What are protein kinases?

What are protein kinases?



Answer: Enzymes that modify protein activity by phosphorylating them. They hence regulate a majority of signal transduction pathways.

What is cAMP?

What is cAMP?



Answer: Cyclic Adenosine Monophosphate. Derived from ATP by way of an enzyme called adenylate cyclase which is an integral membrane protein.

Is a second messager molecule in cells used for signal tranduction. It is vital because molecules like adrenaline and glucago cannot pass through the membrane so cAMP conveys their message intracellularly. It also plays an important role in the activation of protein kinases

Describe the signal transduction of epinephrine.

Describe the signal transduction of epinephrine.



Answer: Epinephrine is the ligand. It binds to B-adrenergic receptor which is a transmembrane protein. This activates a trimeric G protein on the cytosolic face which then changes GDP to GTP. The beta and gamma units break off and the alpha plus GTP converts ATP to cAMP .....

Describe the structure of a GCPR

Describe the structure of a GCPR



Answer: 1000 members in family. Long polypeptides that can make 7 passes through the membrane. Variety found in loop regions. Trimeric with alpha, beta, gamma subunits. Has GDP associated in resting state which is exchanged for GTP when signalled.

What are G proteins and GCPRs?

What are G proteins and GCPRs?



Answer: G proteins and guanine nucleotide binding proteins with GTP as their energy source. Their main function is to serve as signalling molecules (the ligands) in signal transduction cascades. Extracellularly, they bind to G coupled Protein Receptors which are transmembrane proteins that intracellularly activate another G protein which goes on to activate a further cascade of molecules.

What are secondary messenger molecules?

What are secondary messenger molecules?



Answer: They are intracellular molecules that relay an extracellular message given by a ligand on a receptor. The receptor activates the second messenger intracellular which goes on to greatly amplify the message by initiating a signal cascade.

What is signal transduction (3 ideas)

What is signal transduction (3 ideas)



Answer: The use of messenger cascades to transmit a message. The ligand (messenger) and receptor binding follow MM kinetics. Phosphorylation is a common theme.

Describe the 3 types of hormones

Describe the 3 types of hormones



Answer: Autocrine, Paracrine (secreted to work on neighboring cells), Endocrine (secreted into blood for long range action)

Give examples of excitatory neurotransmitters and inhibitory ones.

Give examples of excitatory neurotransmitters and inhibitory ones.



Answer:


E--Acetylcholine, Glutamate, Seratonine
I---GABA, Glycine
Neurotransmitters are natural. But drugs can be made to produce these responses. Eg. Valium is an inhibitory one. Cuases hyperpolarization so AP signal needs to be even stronger for the impulse to propagate (hence less pain felt)

Explain how neurotransmitters excite or inhibit.

Explain how neurotransmitters excite or inhibit.



Answer: Excitatory ones Depolarize by causing Na+ channels to open (so inside becomes more positive then outside). Inhibitory ones Hyperpolarize by opening up Cl- channels (so inside becomes even more negative---by way of becoming even lees positive than it was before)

What are neurotransmitters?

What are neurotransmitters?



Answer: Very small proteins. Chemicals that are kept in vesicles. They travel from presynaptic cell to post synaptic cell and bind to cause a change. Excitatory (hyperpolarize) or Inhibitory (depolarize).

What are glial cells?

What are glial cells?



Answer: A highly complex group of cells in the nervous system. Some are involved in conduction of AP,some for Synapse development and others are phagocytic cells involved in nervous system Immune response

What are astrocytes?

What are astrocytes?




Answer: Involved in the formation of synapses. Control access of blood vessels to the extracellular fluid of the nervous system.

Describe the Nernst equation versus the Goldman equation.

Describe the Nernst equation versus the Goldman equation.



Answer: They are usually made up of identical protein dimers (usually alpha helices) on a membrane that open up to produce a pore and a vestibule in the middle of the membrane. They have a selectivity filter formed by charged residues or an atom like O such that only molecules of the opposite charge will be able to pass through. They pass through by forming transient bonds.

Describe the structure of ion channels.

Describe the structure of ion channels.



Answer: They are usually made up of identical protein dimers (usually alpha helices) on a membrane that open up to produce a pore and a vestibule in the middle of the membrane. They have a selectivity filter formed by charged residues or an atom like O such that only molecules of the opposite charge will be able to pass through. They pass through by forming transient bonds.

What is the Sodium Potassium ATPase for?

What is the Sodium Potassium ATPase for?




Answer: It maintains normal intracellular and extracellular charge distribution for all cells by way of active transport. When it is phosphorylated, it changes conformation to allow 3 NA+ to bind and be released extracellularly. 2 K+ s then load in and are channeled into the cell. This happened as needed to maintain the normal charge distribution. Potassium leak channels also assist in maintaining this.

What is the diff between average velocity and instantaneous velocity? Which is more important? Give the eq for each

What is the diff between average velocity and instantaneous velocity? Which is more important? Give the eq for each



Answer: Average velocity is the change in displacement over a period of time (delta x / delta t). Instantaneous velocity is the displacement for a specific moment in time so a specific time eg. t=5s will be given (delta x /t)

Write out the chart for common angles and their sin and cosines?

Write out the chart for common angles and their sin and cosines?



Answer:


Column 1 (Angles)= 0,30,45,60,90
Column 2 (Sines)= 0 over 2 (0), Square root 1 over 2 (0.5), Sq rt 2 over 2 (0.7), Sq rt 3 over 2 (0.9), Sq rt 4 over 2 (1.0)
Column 3 (Cosines) = Vice Versa

What are the 4 types of motion?

What are the 4 types of motion?



Answer: Translational, Rotational, Vibrational, Combination

What is the 5 point Verbal Strategy?

What is the 5 point Verbal Strategy?



Answer:

1) Know your author (you must answer questions from his/her point of view)
2) What is the main idea
3) Look at the answers for hints and use process of elimination
4) Look at the question for a hint
5) Then you may go back to the passage (last resort only!)

How many bonds will carbon, nitrogen, oxygen an hydrogen form and why?

How many bonds will carbon, nitrogen, oxygen an hydrogen form and why?



Answer: Since they have 4, 5, 6, 1 valence electrons and therefore need 4, 3, 2, 1 to reach their octets, the will form 4,3,2,1 bonds...The 1,2,3,4 rule! Any deviations must mean the atoms carry a charge (due to a loss or gain of electrons)

What is meant by hybridization. Use carbon as an example to explain.

What is meant by hybridization. Use carbon as an example to explain.



Answer: The bringing of orbitals together to form a new type of orbital. This has to happen around an atom before it can bond with another atom. All atoms have different types of orbitals for their bonding (valence) electrons eg. Carbon has 1 in the s and 3 in the p (total 4). The s will have a different energy level from the p's and this is NOT OK to allow carbon to bond (all electrons must have same energy level). So by rearrangings (hybridizing) its orbital, carbon forms 4 sp3 ones which will have the same level of energy and thus allow it to bond with other atoms.

What are sigma and pi bonds?

What are sigma and pi bonds?



Answer: The two types of covalent bonds. Sigma--the electron density is shared between the two nuclei. Pi---the elec den is above and below the internuclear region (the second bond of a double bond or second plus third of a triple bond)


Describe the 3 types of major bonds and give examples?

Describe the 3 types of major bonds and give examples?



Covalent--an even sharing due to same elec negativities eg. C-C
Ionic--a transfer of electrons from a less en atom to a more en atom eg Li-F. Ionic bonds are bonds between two opp charged atoms. They are stronger than cov bonds but more easily solvated than cov when in polar solvents (

What the types of 4 structures important on the MCAT?

What the types of 4 structures important on the MCAT?



Answer:


  1. Lewis Dot Structures--A 2D depiction of molecules showing valence electrons (shared and unshared) as dots.
  2. Bond-Line formula---carbons depicted as line, func groups shown but no H's shown,
  3. Fischer Projections---vertical lines are going into the page, horizontal ones come out.
  4. Newman projections---a straight view down the axis on on of the single bonds, the intersecting lines and large circle are carbons.


What does the n, iso, sec and tert mean in naming organic compounds?

What does the n, iso, sec and tert mean in naming organic compounds?



Answer: This method is used to name branched hydrocarbon substituents (not a main chains). If the substituent is a "normal" straight chain it is n eg. n-butyl. However drop the n and name as a butyl group. If the substituent branches into TWO METHYL groups AT THE END of it, then it is an iso eg. isobutyl. It is sec if the carbon connected to the parent is connected to two carbons (but does not form two methyl groups). Tert is if connected to three. Sometimes tert is abbreviated to t. For example
5 t-butyl

Explain how fluorine allows us to put virtually any R on a CNT.

Explain how fluorine allows us to put virtually any R on a CNT.




Fluorine is a good leaving group which can be replaced easily by other functional groups by using standard Grignard reagents (MgBr), alkyllithium reagents (RLi), or alkyl peroxides. In this way it is possible to attach, in principle, any organic compound R to the walls of the CNTs.

For halogenation of carbon nanotubes- this is the halogen of choice - what special property does it offer?

For halogenation of carbon nanotubes- this is the halogen of choice - what special property does it offer?



fluorine - degree of fluorination can be controlled with the temperature of the reaction which can vary from room temperature to 600ºC. Fluorine is a good leaving group which can be replaced easily by other functional groups by using standard Grignard reagents (MgBr), alkyllithium reagents (RLi), or alkyl peroxides.

Two main issues that end up being great for us when trying to surface functionalize carbon nanotubes.

Two main issues that end up being great for us when trying to surface functionalize carbon nanotubes.



1. Surface functionalization always modifies the electronic properties of the material, complicating the characterization. But! This is awesome for sensors because if you can modify conductivity of CNTs by adsorbing molecules on them, they would make an excellent base for a sensor.

2. Issue with the relative inertness of the sp2 bonded graphene sheets that comprise the nanotubes. The curvature of the nanotube puts a relative strain on the sp2 bonds - the ideal geometry would be planar for sp2 carbon. But! This strain increases their reactivity due to increased surface energy.
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