Chem 481 Test 3

No not really. It only stores information.

The portion of DNA that contains the information of a functional biological product.

Nucleotides.

• 1. Nitrogenous Base.
• 2. Pentose (b-D-ribofuranose derivative).
• 3. Phosphate.

• Purine,
• DNA,
• Deoxyadenosine

• Purine,
• DNA,
• Deoxyguanosine

• Pyrimidine,
• DNA,
• Deoxycytidine

• Pyrimidine,
• DNA,
• Deoxythymidine

• Purine,
• RNA,
• Adenosine

• Pyrimidine,
• RNA,
• Cytidine.

• Pyrimidine,
• RNA,
• Uridine.

Pyrimidine.

• Purine.
• 

The deoxythymidine has a methyl group on it's pyrimidine ring at position 5 that is not present in uridine. This could potentially end up keeping the DNA in the nucleus whereas RNA would be free to pass through.

2' hydroxyl.

The sugar-phosphate backbone. The oxygen in the phosphate and in the sugar are able to form hydrogen bonds.

• 5'-3'.
• The phosphate is at the 5' and the sugar's 3' carbon sits at the 3' end.

• Phosphodiester linkage.
• P-O-C(5')-C(4')-C(3')-O-P

280nm. This is because of the aromatic amino acids Trp, Phe, Tyr.

260nm.

Yes, the Purines and Pyrimidines as well as the sugars are turned so that their rings lie over each other like stacks of coins. This allows for extensive pi stacking between polymers.

Intercalators have aromatic structures that fit in between the stacked sugars and nitrogenous bases to induce variations in the energy associated with the placement of each monomer. They can be carcinogenic when it becomes more energetically favorable for a different base to replace the original base.

• B form.
• You can clearly see the major groove and the minor groove.

They are not especially relevant as biological molecules, but they are possible structures, and may have applications in nano-technology.

• 1.It can have both information storing properties, and enzymatic properties.
• 2. Its single stranded nature allows for structural flexibility and altering base pairing interactions.

• 1. mRNA
• 2. tRNA
• 3. rRNA

It can dimerize adjacent pyrimidine pairs through a forbidden Diels-Alder reaction.

It is involved in regulatory methylation at nucleophylic positions.

• Adenosine 5'-Triphosphate.
• 

Energy doesn't come from breaking ATP, The energy payoff comes from ADP being stabilized by water.

• Target genes are excised with a restriction enzyme.
• The same restriction enzyme also cuts a bacterial plasmid.
• The target gene and the plasmid join with sticky ends, and then a 2nd type of enzyme seals the two together.
• Bacteria can now express the target gene.

Plasmid.

Yes.

• Origin of replication
• antibiotic resistance
• restriction sites.

Type 2

Restriction enzymes that cut DNA as specific sites.

About 4-6bp

True.

It reseals sticky ends by reforming the phosphodiester bonds.

After a restriction cut, they are the few base pairs that protrude. They are complementary to any other cut made by that enzyme.

Insertion of the modified plasmid into bacteria.

• The bacteria overproduce the product.
• Inclusion bodies are formed.
• The celles lyse.
• product is purified through affinity collumn.

• A=0.1
• T=0.1
• G=0.4
• C=0.4

• Take 280/260, and compare this value to a chart.
• This value will correspond to a F value, and to a proportion of nucleic acid at that value.
• Multiply the A₂₈₀ by the F value to find protein concentration in mg/ml.
• The percentage of DNA at that reading is available on the chart.

The number of cis-double bonds. The more it has, the lower it's melting point.

• Increase fluidity.
• (less side chain interactions)

It is amphipathic, and helps butter be more soluble.

Sphingolipid

• 18 Carbons
• cis double bond from C9-10

That counting backwards the first carbon that has a double bond is carbon 3.

• This type of lipid has 3 fatty acid chains all held together with an 3ester (acyl) lincages to a common 3 carbon backbone.
• 

• A base (like NaOH) would have to be used to cleave the 3 ester bonds:
• 
• 
• 

The trans-fats are not easily metabolized. This is why they have such long shelf lives. The bacteria that would spoil them cannot metabolize the trans double bond quickly enough and they die.

The trans-fats represent the low energy product of double bond formation.

• 2 fatty acid tails are ester linked to a 3C backbone. The 3rd carbon is attached to a phosphate, and then to a head group substituent.
• 

They can replace the charged phosphate group with galactose or sulfate groups.

it is a glycerophospholipid with an x group coming off of the phosphate.

• • 

• 1 single fatty acid attached to a Sphingosine backbone with an amide bond. The sphingosine has 1 single polar OH group, and a head group substituent (X group).
• 

The amide bond can come on and off much more easily than the traditional lipid acyl linkage.

sphingolipids.

• They are steroid alcohols with alkyl side chains.
• One one side the polar OH group.
• The 4 fused ring steroid nucleus.
• The alkyl side chain.

They decrease its fluidity, giving it more strength.

arachidonic acid derived eicosanoids are hormones that act locally and induce a specific response in tissues. They're a cause inflamation and clotting.

Yes.

• A
• D
• E
• K

Laser bleaching experiments show the return of fluorescent coated phospholipids, indicating that they have fluidly filled the gap.

Cylindrical diacyl groups provide the correct shape for the bilayer. The head and tail diameters are the same.

30 angstroms.

It depends. There is an exceptionally high amount of protein in the bilayer, and in some cases it can be more present (by mass) than the lipid.

• Liquid-ordered state.
• It cant be too disordered: para-crystalline (gel)
• Or too fluid.

Membranes are asymmetrical, they also catalyze trans-bilayer diffusion.

• Lateral diffusion is side to side and very fast: microseconds.
• Transbilayer is flipflop and very slow: days.

• Flips bound substrates (lipids etc) from outside to inside.
• ATP catalyzed movement.

• Flops bound substrates (lipids etc) from inside to outside.
• ATP catalyzed movement.

• Moves bound substrates (lipids etc) from out to in (flip) or in to out (flop).
• Not ATP catalyzed, just runs on equilibrium constants.

Phosphatidylserine.

• Integral membrane protein.
• They are classified by type.
• The non-polar residues are the transmembrane portions,
• The polar residues are the external portions.

Only the signal molecule fits in it's complementary binding on the complementary receptor. Other signals do not fit.

Enzymes activate enzymes and the number of molecules involved at each step increases geometrically.

Receptor activation triggers a feedback mechanism that either deactivates the receptor, or removes it from cell surface.

When 2 signals have opposite effects, the regulatory outcome is the integrated input from both receptors.

G protein coupled receptors (GPCR)

True.

Release of glucose frome glycogen.

That the receptor protein make 7 transmembrane passes before coupling with the different G subunits.

• Signal binds to receptor.
• G subunits attached to receptor separate.
• 1 subunit moves & is activated by GTP replacing GDP
• Active G subunit attaches to Adenylyl Cyclase
• AC catalyzes formation of cAMP.

Palmitoyl subunit.

cAMP

The gamma phosphate in the new GTP causes a conformational shift that activates the Gprotein. (adducts the 2 side subunits towards the center)

They have intrinsic GTPase properties, continually cleaving the activating phosphate.

• It would remain constantly activated.
• Because it is proto-onco, if it is constantly on cancer would result.
•  

cAMP binds to protein kinase A, releasing the catalytic subunits fromt the inhibitory subunits.

Eventually it is hydrolyzed to 5'-AMP.

1:10,000

• Hormone H binds to receptor.
• Occupied receptor Causes GDP/GTP exchange with attached G_q.
• Active G_q moves to PLC and activates it.

• PIP2 spits to form DAG and IP3.
• PIP2 loses its phosphate and P-attached sugar.
• DAG is glycolipid backbone
• IP3 is P-attached sugar.

It cleaves PIP2 at the phosphate to form PIP and IP3.

cuts right at attached phosphate.

2. DAG and IP3

• Lack Catalytic function
• Bring various protein together.
• Grb2 is an example.

• Both lack catalytic function,
• Both bring various proteins together.

• It is a Liquid-ordered region inside a sea of liquid dissordered phospholipid.
• It can attribute its stability to increased sphingolipid and cholesterol concentration in the region.

Lipid rafts.

An oncogene.

Between 50-70mV

• The Electrochemical gradient: The sum of + or - on both sides of the cell membrane.
• The concentration gradient: how much of a certain molecule is on one side vs. the other.

• 3 Na from Inside bind.
• ATP phosphorylates, opening up to outside
• 3 Na release to outside.
• 2 K from outside bind.
• P dephosphorylates, opening up to inside.
• 2 K release to inside.

• Against Electrochemical gradient.
• AND: against the concentration gradient.

• Against the Concentration gradient.
• AND: With the electrochemical gradient.

• Inside is generally negative.
• Outside is generally positive.

The electrogenic ATPase action moving 3 Na out and 2 K in for every ATP hydrolysed.

They have high concentrations outside of the cell. As they move across the membrane, they decrease the differing charges across the membrane, lowering the membrane potential.

K has a (+) charge and is plentiful inside the (-) cell. As it moves from high concentration to low concentration out of the cell, it removes its portion of (+) charge with it. Leaving a more polarized cell, with a greater membrane potential.

One function of IP3 is to tell the endoplasmic reticulum to release Ca²⁺.

• Ras->Raf->Mek->Erk which is synonymus with
• G-Protein->MapKKK->MapKK->MapK

Sos binds to Ras, causing Ras to release its GDP and bind a new GTP.

Activated Ras binds to Raf (MapKKK). This is the first kinase.

• Ins + InsReceptor=Active Kinase.
• Active InsR phosphorylates Irs-1 at 3 tyr residues.
• Irs-1 moves to adapter proteing Grb2 which simultaniously binds sos and Ras.

Grb 2 is activated by Irs-1 phosphate group. It has binding sites for sos and Ras. (Gef and G-protein)

It moves into the nucleus and phosphorylates transcription factors. The transcription factors do the rest.

Insulin can actually hijack the epinephrine pathway by shutting down the GPCR through multible phosphorylations.

• 0.
• This is because the Concentration gradient and Electrical potential cancel each other out.

• It solves for membrane potential at equalibrium.
• 

Before the calculation, you should be able to say if delta G is going to be + or -, then adjust the in/out to out/in depending on the situation.

8.315 J/mol•K

• Kelvin
• 273+Celcius
• Norm Body temp: 310K

1

96500 J/V•mol

Nerve Cells:

• Voltage Gated Na+ channels allow rapid intake of Na moving down to the synapse,
• At the synapse voltage gated Ca2+ take over.
• Acetylcholine vesicles are induced to exocytose at the secretory synaptic cleft.
• With the rapid influx of + charge, the voltage gated K+ channel releases rapid amounts of K+ from the cell, causing a wave of hyperpolarization.

• At the synaptic cleft acetylcholine is released in vesicles. These travel to the post synaptic neuron and activate Na+/Ca2+ ion channels.
• This propogates the wave to the next neuron.

• The activation gate is held closed by the voltage sensors which are sensitive to the polarized sides of the membrane.
• The channel is opened when the (+) voltage sensors are pushed open by an influx of + charges on the cytosolic side of the membrane (membrane depolarization).
• At a certain point an inactivation gate responds to the changing polarity and shuts down the channel (think of the flushing mechanism of a toilet).

Nerves ion channels would be left open, and overload would occur.

Signal protein binding releases messengers to PIP2->DAG + IP3->ER to release Ca2+. Ca2+ also activates Na+ pump. Depolarizing cell membrane causes rapid exocytosis to afferent nerve fibers.

• 1. 1 bad gene: cell growth turned on (oncogene)
• 2. 2 suppressor genes fail: 1 inhereted, 1 mutated
• 3. Stability genes fail: same as above. Can propogate the 2 problems above.

It is a tumor suppressor gene.

Ions are already moving down their concentration gradients, glucose just tags along the same channel against it's concentration gradient.

Glucose Uniporter Glut2 allows glucose to move down its concentration gradient.

• Asn-Pro-Ala (NPA)
• Arg are also present to keep water from moving backwards.

Single file, being pulled through by hydrogen bond formations.