Chem/Phys

Reaction rates

2A + B <--> 2C + B. Which cannot be mechanism for rate-determining step of this rxn? A) A molecule of A collides with molecule of B B) A collides with another A C) B collides with another B D) 2 A collide with a B <-- Passage: Slower step follows 2nd order kinetics --> only involve 2 reactant molecules

Monosaccharide

As glucose, a reducing sugar, is oxidized during Fehling's rxn, how is eq btwn hemiacetal D-glucose and linear D-glucose shifted? --> there is shift favoring replacement of linear form of glucose ring and linear forms of glucose are in eq initially. But only lienar for can undergo oxidation --> as fehling's rxn progresses, more of linear form gets consumed --> eq rxn between linear and ring form to shift toward linear glucose glycosidic bond: O of hydroxyl group acts as a nucleophile and attacks anomeric C of a hemiacetal sugar, like glucose, resulting in formation of an acetal-glycosidic bond. This is analogous to synthesis of DNA, wehre secondary amine of nitrogenous base like cytosine forms a bond to anomeric C of deoxyribose.

Membrane components

Certain species dramatically lower their body T in response to seanson, env changes. During cold weather adaptation process, the cell membranes of these animals would be expected to incorportae: dec amounts of palmitic acid and inc amounts of linoleic acid

Mechanical Equilibrium

Humans head weights 4.8kg and its center of mass is 1.8 cm in front of spinal column joint. If trapezius muscle inserts 1.1cm behind spinar cord joint, how much downward force does it need to exert in order to maintain eq? --> (4.8kg)(9.8m/s^2)(0.018m) = F*(0.011m) --> F = 77N

Ideal Gases

Inhalation facilitates venous flow towards the right atrium by expanding thoracic cavity and inducing a decrease in cavity pressure This is how - pressure breathing works. In same way air will rush into lungs as a result of decreased pressure, so too will venous blood rush into cavity w/ less pressure than the area that came before it

Complex carbohydrate

Key diff in results was that Benedict's test before hydrolysis with maltose was + (w/ sucrose was - ) This proves that maltose contains a free hemiacetal group. (Maltose is disaccharaide but it differs from sucrose in that it is reducing sugar. Maltose-made up of 2 glucose, only 1 of the units is a glucoside, other subunit is present in hemiacetal form --> it can mutarotate) alpha 1,4-glycosidic --> lengthening glycogen alpha 1,6-glycosidic --> branching glycogen

Quantum mechanical model of atoms

Paramagnetic atom exhibit a response to magnetic fields

Reaction of Phenols

Quinone --> Hydroquinone ; Quinone gains 2 electrons and 2 protons --> since 2 protons (positive) are added, 2 electrons (negative charges) must be gained by quinone to be neutral hydroquinone

Organic molecules

Steric congestion tends to promote SN1 type mechanisms. SN1 rxn proceeds by way of mechanism in which leaving group dissociates in a kinetically slow step, producing planar carbocation which is then rapidly attacked by nucleophile

Rutherford, Planck, and Bohr

When light is absorbed by chlorophyll in plants, it is always true that: e- are excited to a higher E level --> It is always true that when an atom absorbs E, its e- move from their ground state to a higher excited state Which quantum # best describes an atomic orbital's overall size?: n -> Principal quantum number, n, provides info about size of orbital (l, azimuthal or angular momentum quantum # designates shapes of orbital, not size)

Amino Acinds Found in Proteins

Which is NOT characteristic associated with peptide bonds (very stable at physiological conditions -->low reactivity) ? : A) Resonance B)High reactivity <-- C) Planar molec. Geometry D) Partial double bond character

enolate chemistry

Which is true of acetone?: It exists as a pair of tautomers, of which the keto form predominates ( acetone exists in two forms, with keto form predominating. This is bc C-O double bond (the carbonyl bond) is much stronger than C-C double bond; acetone is polar but aprotic - no H attached to electronegative atons(FON). unstable to participate in H bonding)

Le Chatelier's Principle

assuming equivalent experimental V and tissue types, which of following would most likely cause aggregation to occur more quickly?: a larger quantity of dissociated cells --> aggregation of cell parts is essentially a chem rxn. Having more dissociated cell will be like having more reactants and will push rxn to occur quicker and more just like Le'Chatelier's principle

water

ion product < Ksp unsaturated solution (no precipitation occurs) ion product = Ksp saturated solution solution at equilibrium (no precipitation) ion product > Ksp supersaturated solution (precipitation occurs) good buffer has a pKa within 1 pJ unit of desired experimental conditions adding salt reduces vapor pressure of liquid. As solute conc is inc, rate at which water molecules can break through liquid surface dec. Boiling point is defined as T at which VP = atmosphoric P. Dec in VP makes BP more difficult to achieve, resulting in higher BP --> COLLIGATIVE PROPERTIES!: special set of chem properties depend on # of solutes particles present, rather than what kind of solutes they are - 1)VP reduction 2)BP elevation 3)Freezing point reduction 4)Osmotic pressure for most substances, liquid becomes more dense as average KE (T) dec, and solid is more dense than liquid due to close-packing solid-state structurs, resulting in formation of solid at bottom of liquid. BUT, solid water is less dense than liquid form at 0C. -->water molecule is bent, with bond angle ~104.5degree. this, combined with degree of H bonding that occur betwen water molecules, yeilds a solid crystalline structure with relatively large amounts of empty space. ("close packing in solid state implies that solid is more dense than liquid --> opposite). indicators function in acid-base titrations to identify, via color change or similar mech, that an expected pH, and this titration endpoint, has been reached. In order to function in this way, an indicator must undergo color change near desired pH. This occurs bc of reversible change in protonation states of indicator. it is desirable then that the pKa of chosen indicator to be ithin +/- unit of target pH. for titrations performed in the study of acetic acid, weak acid, and NaOH, strong base ,endpoint of titration will occur as pH <7. air is bubblied through distilled water. Soln will have pH: <7, bc CO2 undergoes hydrolysis --> air contains elemental N as its major component, but elemental N is essentially inert and is neither an acid nor a base. CO2 can undergo hydrolysis rxn in liquid water to make Carbonic acid, weak acid that produces a soln whose pH <7 benzene, aromatic hydrocarbon, is very stable (inert) in presence of acids and bases and will not react with reagents BP of liquid is T at which vapor P of liquid = surface P. normal VP is 1atm P. vapor P of liquid inc with inc T. Hence, BP of liquid dec as P on surface dec. if a leak develops in apparatus, surface P will inc as will BP surfactants are amphipathic molecules (containing both hydrophilic and hydrophobic regions) that reduce surface tension of liquid. ex) pulmonary surfactant, which reduces surface tension in alveoli, allows them to remain inflated when lung is compressed during respiration / detergents, amphipathic structure allows them to denature proteins (ex. SDS) or solubilize lipids --> During inspiration, contraction of diaphragm and internal intercostal muscles leads to expansion of thoracic cavity and a dec in intraplueral P. this - pressure, relative to atmospheric P at entry of upper airway ,generates airflow through respiratory tree and to its terminal extension - alveoli. elastic recoil force of airway and surface tension of water lining the airway oppose expansion of alveoli due to influx of atmospheric P. Pulmonary surfactant adsorbs to air-water0alveoli interface, reducing surface tension and total force resisting expansion. this inc pulmonary compliance - measure of lung V change at given P of inspired air - and decreases work required to expand lungs at given atmospheric P

nerve and endocrine

majority of steroid hormones have names that end in :-one," "-en," or "-ol" --> ex)terpenes, altosterone, estrogen

separation and purification methods

reverse-phase high performance liquid chromatography (HPLC) : polar mobile phase and non-polar stationary phase One method of isolating polypeptides and proteins from aqueous extracts is freeze drying. Aqueous soln of polypeptide or protein is frozen. What procedure can be used to remove water from frozen sample?: sublimation under reduced pressure -->only sublimation of water under reduced pressure (distillation under reduced pressure) will keep mixture cold and will maintain protein in its native state carboxylic acid group, if deprotonated, will be musch more soluble in water than aldehyde group. --> careful extraction with dilute weak base (such as soln of sodium bicarbonate) would separate these two molecules. More polar a compound is, higher its solubility in aq soln Boiling chips - provides nucleation sites or places to start forming bubbling for liquids when transitioning from liquid to gas during boiling; boiling occurs when Pvap=Patm. Typically, we boil substances by inc T, thereby inc Pvap. Alternatively, however, we lower BP by reducing Patm, which can be accomplished through Vacuum distilation - used when components have very high BP and would otherwise be difficult to distill air bubbles break the surface tension of liquid being heated and prevent superheating and bumping in distillation, component with lower BP boils off first, leaving remaining components in original flask. As with forms of chromatography, increasing column length will enhance resolution of column, leading to more completion fraction. this is bc material of matrix provides physical means of separating proteins. if proteins come in contact with longer length of matrix, diff in retarding forces experienced by proteins will have greater cumulative influence on migration of proteins, lengthening diff in their retention times. Anionic peptides bind to ANION-EXCHANGE COLUMNS. Strength of binding depends on overall charge of peptide (lower magnitude elute at lower salt conc) A protein w/ which properties will most likely have largest - net charge at pH 7?: A protein that binds to anion-exchange column at pH 7 and requires a high conc of NaCl for elution -->a protein w/ low pI would be - charged at pH 7. this protein, being anionic, would bind to anion exchange column. largest - net charge implies presence of large quantity of - charged aa, allowing protein to bind tightly to column. high conc of NaCl would be required for elution. SDS-PAGE conditions denature protein and eliminate quaternary structure Homodimer - both preservation and disruption of quaternary structure results in a single gel band --> subunits of dimer are same molec weight. both native PAGE and SDS-PAGe result in single gel band Lowest molecular weight and weakest intermolecular forces substance --> migrate fastest and be first peak in gas chromatograph (gc) trace from gas-liquid chromatography Eluting strength depends on how strongly a compound adsorbs onto adsorbent. since typical adsorbents are polar, eluting strength increases with increasing solvent polarity. (ex. methanol is more polar than pentane and therefore has greater eluting strength)

Electronic structure

# of incident photons affects only # of e-, not their E. e- E depend on photon E, cathode work function, and potential diff between cathode and anode The onlt effect of photon freq has on the ejected e- is on its KE. Photon E = cathode work function + e- KE. # of e- ejected (current) depends on # of incident photons

forces and acceleration

..it is moving to the LEFT at 100 microm/s before...5 sec after..it is moving to the right at 200 microm/s.. The avg acceleration of cell is: (200- -100)/5 = 600 microm/s^2 As skydiver approaches a constant (terminal) velocity, his acceleration will start to approach 0, and then will increase sharply as he touches the ground

1st law of thermodynamics

A sample of 2-methylnaphthalene is placed in bomb with a heat capacity of 1620 J/Celciues. Bomb is submerged in calorimeter containing 2 kg of water. If temperature of water increases by 2 degree celcius when the sample is ignited, what is heat released in Joules?: The calorimeter is a closed system, so no heat leaves the system and qr=qw+qb. Since q=mc*deltaT, the eq becomes: qr=mbcb*deltaT+mwcw*deltaT. Since bomb and water have same change in T, factor out deltaT and obtain: qr=(mbcb+mwcw)*deltaT --> qr=(1620+2*4190)*2 During adiabatic process, there is no transfer of heat; expansion of parcel causes a decrease in temperature A combustion engine in a production plant is in contat with a coil of pipes carrying water that functions to cool engine. The water is converted to stream and flows through a long vertical pipe to be released into atmosphere. Heat is transferred from engine to atmosphere primarily by: CONDUCTION THEN CONVECTION The body loses E via all three forms of heat transfer: conduction(skin causes a change in T of air and sweat as result of direct contact), convection(as sweat evaporates heated air convects away from skin), radiation(all objects above absolue zero emit radiation)

distillation

After mixing Compound C with water in Test 1, student wishes to separate mixture. Best method for separating mixture is: Extraction, bc compound C and water will be in separate phases (filration is used to separate a solid from a liquid, and so isn't useful when separating two liquids compound with lower BP --> distill first

DNA structure

After using Sanger method of DNA seq, used gel electrophoresis and got a single dark band. Which is most likely source of error? --> Dideoxynucleotides were omitted from reaction mixture --> absence of dideoxy nucleotides, DNA Pol will replicate the entire template and this produce complete copies - all of same length Which statement about NAD is true?: NAD is composed of 2 nucleotides joined by their phosphate groups. ( NAD+ is oxidized form of NAD and acts as an oxidizing agent (becomes reduced), while NADH is reduced form of NAD and acts as a reducing agent (becomes oxidized). Just like nucleotides in nucleic acids, nucleotides in NAD are joined through their P groups, not ribose) Adenosine once attached to P group becomes nucleotide, whereas nucleosides don't have P group attached. Both nucleotides and nucleosides have base attached to ribofuranose via glycosidic linkage Hydrogen bond acceptors are N and O: A contains 1 donor and 1 acceptor T contains 1 donor and 1 acceptor G contains 2 donors and 1 acceptor C contains 1 donor and 2 acceptors

Reactions of alcohols

All rxns will lead to formation of aldehyde EXCEPT: A) Ethanoyl chloride + H2, Pd-BaSO4+quinoline -> (lindlar reagent-like catalyst --> aldehyde) B) 1-butanol + PCC -> (primary alcohol oxidize-- aldehyde) C) 2-propanol+KMnO4 -> (oxidation of 2ndary alchohol-->ketone) D)Ethyne+dicyclohexylborane+H2O2 -> (anti-markovnikov addition of water to terminal carbon --> trautomerize to aldehyde)

subatomic particles

Although MRI relies on signals from H bc of its abundance in body, other elements can be imaged with MRI. Which are most likely to be good candidates for MRI imaging?: I) 13C II) 14C III) 31P IV) 32P --> Hydrogen nucleus has a magnetic moment, to interact with magnetic field, nuclei must have a magnetic momentl they must have odd number of neutrons + protons. --> isotones that can be imaged by MRI are the ones with odd atomic masses In order for fission to occur, E must be supplied to nucleus to initiate for rxn. This E comes from KE of particle that is used to bombard the nucleus. In order for this KE to be transferred to nucleus, particle must be able to get within close proximity to it. Protons would not work well bc being + charged themselves, they would experience repulsion from + charged nucleus. On the other hand, neutrons don't experience electrostatic repulsion from nucleus

Properties of Acids and Bases

As O2 is consumed underwater, body also produces CO2. This has effect of --> decrreasing pH of blood (inc. CO2--> inc. H2CO3 in bloodstream --> dec. pH in blood) Carbonic acid is physiological buffer. The deltapKa/degree Celcius for carbonic acid has been calculated as -0.009. based on this info, which is always true about dissociation of carbonic acid?: enthalpy change > 0 --> Since deltapKa/degree celcius is -, that means temperature increases; the pKa of carbonic acid decreases. Since pKa get smaller, Ka gets larger, more dissociation at higher T. For eq, that means that rxn is shifted to right, away from reactants, rxn must require heat, which means it is endothermic and has a positive change in enthalpy; dissociation involves breaking bonds --> endothermic Weakest conjugate base --> strongest acid (acids that has e-withdrawing substituent on alpha C tend to be stronger, since dissipation og e- density has a stabilizing effect on carboxylate anion that will be formed if proton dissociates. Likewise, acids with e-donating alpha substituents tend to be weaker. liquid water will always have some ions in soln. dissociation constant eq is H2O --> H+ + OH-, Keq=10^-14. this makes conc of hydrogen and hydroxide ions 10^-7 M each in soln, regardless of any other conditions

fluids of physiology

As bradykinin is released from neotatal lungs, dec in cross-sectional area of ductus arteriosus: inc R, and so blood flow dec through ductus arteriosus --> as ductus arteriosus constricts, blood has a diff path that it is able to take (it can remain in pulmonary artery). So it is perhaps useful to think of circulatory system as a circuit. Where there is greater resistance there is less current. As tube gets thinner its R goes up, and less fluid will flow through it, as long as there's another path Which woud NOT be observed in patient with reduced intravascular volume status?: A) Decreased urine volume B)Dry mucous membranes C) Vasoconstriction D)Decreased urine osmolarity --> in attempt to raise blood volume and P, water will be reabsorbed from kidneys. this will lead to decreased urine output and higher urine osmolarity. (Urine volume would be low bc body;s homeostatic mechanisms will work to minimize fluid loss; mucous membranes will experience loss of water in attempt to raise BP and V; lowered BV will result in lowered BP, and so to increase BP, blood vessels will undergo vasoconstriction) a typical systole/diastole reading (in mmHg) is 120/80. diastolic blood pressure is much lower than systolic BP bc: heart exerts no force on blood during diastole. --> when muslces of heart relax as they do during diastole the heart is not exerting any force on blood inc P in lungs (pulmonary hypertension) inc P that the heart is working against, while keeping V the same. This inc amount of work that heart has to do. The work can be calculated as area under curve for PV graph. Since P inc and V remains the same, work must increase. an astronaut on Earth notes that in her soft drink an ice cube floats with 9/10 of its volumne submerged. If she were instead in lumar module parked on Moon where the gravitation F is 1/6 that of Earth, ice in same soft drink would float: with 9/10 submerged -->floating ice cube implies that its weight is balanced by bouyant force on it. Wice= mg = r(fluid)*V(submerged)*g --> both weight and bouyant force are proportional to g, making the numerical value of g irrelevant to V of ice cube that is submerged

Mechanical Equilibrium

Assume human arom has mass of 4.5kg in baseball player, and that it is distributed half in hand, half in shoulder. If length from shoulder to hand is 0.8m, tension exerted by arm as it reaches maximal velocity is most nearly: 40kN --> a uniform circular motion problem, centripetal force is provided by tension in arm. Since half of weight is in hand, mass is 2.25 kg. The radius is provided, velocity must be calculated. At 24 rpm(passage), hand is traveling at [(24)(2)(pi)(0.8)]~120m/s --> F=mv^2/r --> F=(2.25)(120)^2/0.8 =40000N

Gibbs Free Energy

Assume that aggregation will happen at any T. this process will most likely result in: a dec in enthalpy and inc in entropy --> aggregration will happen at any T means that it is always a spontaneous rxn. --> rxn always ahs a - Gibb's free energy

ideal gases

At constant P, the ratio between V expansion of a mole of gas w/ a high Cp to that of a mole of gas with a low Cp for a given heat inpull will be: LESS THAN 1 --> given Q=nCp*deltaT, a gas with a high Cp will have a smaller change in T for a given Q than a gas with low Cp. Change in T is directly proportional to change in V at constant P (Charles' Law) --> gas with high Cp will expand less than a gas with a low Cp, and ratio of this expansion will be <1 If Gamow bag at 4000 m is inflated to pressure 0.15atm above ambient pressure, the partial pressure of oxygen inside the bag is: 0.15 atm -->from figure in Passage, atmospheric pressure at 4000m is ~0.6atm. According to stem, Gamow bag is inflated to 0.15 atm above atmospheric pressure, so pressure inside the bag is 0.75atm. the footnote at bottom of Passage says to assume that the mole ration of N:O is 4:1, so mole fraction of oxygen is 1/(1+4)=1/5=0.2. by Dalton's law, partial pressure is Xoxygen*Ptotal = 0.2*0.75atm = 0.15atm

Nuclear Rxns

Beta and Gamma radiation differ - Beta particles will be deflected in magnetic field while Gamma rays will not Beta particles have - charge. They are electrons and will be deflected by magnetic b/c they are charged. Gamma rays are high E photons lacking any charge --> They will not be deflected in magnetic field or e- field precisely b/c they are uncharged Half life of 32-P is 14.28 days. What fraction of initially pure sample will have decayed after 28.56 days? After 2 half-lives (28.56 days), 3/4 of the sample will have decayed (1/2 then 1/4 => 3/4) 90 38 Sr decays by emitting an alpha particle to form a stable isotope of krypton, 86 36 Kr. If after 19 hrs 75% of sample has decayed, what is half life of reaction?: 9.5 hours --> after one half-life, 50% of sample will remain. After two half-lves, 50% * 50% or 25% of sample will remain; if 25% of sample remains then 75% of sample has decayed --> since two half-lives have passed in 19hours, half-life must be 19 hours/2 = 9.5 hours half life Q: how much it has form? = how much it will decay? gamma radiation is strong enough to cause molecular electronic transitions by exciting e- to higher E levels in molecular orbitals. this indicates that the radiation can either excite or eject e- (depending on its E) and can create free radicals (atoms with unpaired valence e-) while beta decay does cause nuclear transmutation of protons to neutrons (beta-plus) or neutrons to protons (beta-minus), atomic mass lost in these processes is negligible. This means that whether after one or five half-lives, ATOMIC MASS will be same in both cases (atomic mass is NOT % of certain isotope that is left after radioactive decay) Shorter wavelength Electromagnetic radiation (such as gamma rays) carries much more E than longer wavelength EMR (like radio waves). Closer an e- is to nucleus, harder it is to eject. bc sp-hybridized orbitals have most s character among sp, sp2, and sp3, they contain e- that are hardest to eject photon energy must be larger than bond E in order to break the bond KE of photoelectron = hf - work function E of electromagnetic radiation is directly proportional to # of photons, and intensity of electromagnetic radiation is defined as E emitted per unit. Thus, intensity is directly proportional to # of photons emitted

Resistance

Blood pressure is greater in systemic circulation and blood flow rate is same for both pulmonary and systemic circulation Pulmonary circulation is much shorter than systemic - resistance is also much less, analogous to resistance formula (R=rho*L/A). Compound with the fact that right ventricle (which feeds pulmonary circulation) generates less force than left ventricle (which feeds systemic circulation) Since Pressure=F/A, pulmonary pressure < systemic. Since pulmonary & systemic are connected in SERIES, flow rate (analogous to current) must be equal Suppose an individual with dry skin has come in contact w/ a high-voltage DC circuit. In an attempt to resuce him, another person, with wet skin, makes contact with the first, forming a parallele connection. Then the amount of time require for 10C of charge to exit the power source will: DECREASE For may applications, it is necessary for physioloogists to approxiamte R of human body. In order to measure this, a physiologist might aska willing subject to : hold a positive terminal of a known V source with one had and - terminal with other hand, while physiologist measures the current --> In order to determine R of human body, a known voltage can be applied and current can be measured The first person acts as a resistor w/ resistance 10^4 ohm. If 2nd person latches on to the first, he too would be a resistor - one that has been added in parallel. 2nd person has wet skin --> have lower resistance. Adding resistors in parallele acts to decrease the overall R of circuit --> if R dec, total current passing through circuit inc --> since circuit is change in charge/change in time, inc in current means less time will be required to pass the same amount of charge

The Chem of Groups

CO2 --> CO + [O] CH4 + 2[O] --> CH2O + H2O Atomic oxygen is extremely reactive, and not found in any sig. quantity on Earth's surface bc it is a free radical - unpaired e- in outer orbital More shielding by material corresponds to higher absorption coefficient. Shielding properties of material depend on both atomic weight (higher weight, better shielding) and density of material (denser, better the shielding). So, reason that gold has lower atomic weight than lead but is better shield (higher absorption coefficient) is bc it is denser than lead. mistakely adds NaOH insteaad of HCl to metal-containing flask. Whar are results of exp?: No rxn takes place since elemental iron will not react with aqueous bases without O2 gas --> Iron will not react with water without addition of oxygen, which oxidizes iron (forming rust). In absence of oxygen or acid, elemental iron will not react to form any products and no reaction will take place

Regulation of enzyme activity

Calcium ion can bind to delta subunit of phosphorylase b kinase, activating it. The kinase is then able to convert glycogen phosphorylase b to glycogen phosphorylase a. with lab equipment that does not have ca, such as centrifuge, this process will not occur and no glycogen phosphorylase a will be isolated

Tertiary and Quaternary Protein Structure

Disruption of B12-protien complex primarily inovlves breaking of H bonds (Passage: VB12 protien bonds are disturbed by stomach acid --> denaturation --> Loss of quaternary/tertiary/ 2ndary structure ----> Disruption of H bonds) If only structural zinc-protein interactions are distrupted in zinc-binding enzyme, Vmax for enzyme would most likely: decrease bc the conformational stability of protein is compromised --> Although P2 in Passage describes that structural zinc binds outside of active site, this doesn't mean it will not affect the function of enzyme. by destabilizing the tertiary structure of enzyme, Vmax is almost certainly going to be altered Disulfide bond forms only between cystiene: 2RSH --> RS-SR +2H+ + 2e- (Hydrogens are product of disulfide bond formation, thiol groups must be oxidized) Tertiary or quaternary structure maybe determined by disulfide bonds, but disulfide bonds do not contribute to primary or secondary structure

Electrical circuits

Electric field lines exit from positive and enter - charges. The axon is negatively charged, extracellular soln has 0 net potential. A charged particle ACCELERATES in E field. The e- starts with a velocity that inc as it approaches the anode through vacuum The motion of - charged particle after it has been injected between plates of charged, parallel-plate capacitor? -->Opposites attract, so - charged particle will move toward + plate. Bc there is constant force qE on particle, it will accelerate toward + plate Potential E of oscillatory motion is 1/2kx^2 where x is displacement. Where max displancement occurs --> max electrical PE two plates of capacitor collect charges of opp sign. As more charge arrives it is harder and harder to fill plates until finally an eq occurs as capacitor discharges the V across it falls, thus to maintain a constrant current, R must proportionately reduced. I=V/R--> to keep I fixed ,R falls with V the capacitor charges up and stores E in E field between places. E sotred is 1/3C*V©^2, where V© is V across capacitor. Battery is source of E for circuit and thus is store of E. Unit of Power = Watt = J/s = ft*lb/s = kg*m^2/s^3

Energy

Entire systemic circuit: small bump - steep drop - steep climb back What is root mean square speed of As4 particle as it is sublimed? (assume at high T arsenic acts like an ideal gas; Boltzmann constant, KB, can be approximated as 1.4*10^-23 J*K^-1) and kinetic energy of gas is equal to 3/2KB*T --> Boltzmann constant relates particle activity and T. 3/2kB*T = 1/2mv^2 --> molecular weight ~0.3 kg/6.02*10^23 --> velocity is ~270m/s as a cyclist rides down a hill without pedaling, which best represents relationship between his lost U and his K gained?: U>K --> in ideal system, total mechanical energy, sum of potential and kinetic energy, is conserved. Cyclist in this Q is not in ideal system. he must contend with non-conservative forces like wind resistance, which reduce amount of K he can develop from a given loss of U. Consequently, not all of lost U is converted into K how many molecules of NADH would be produced by complete beta-oxidation of stearic aid, 18 carbons, into acetyl-CoA? --> 8: each iteration of beta-oxidation reduces the carbon chain by two atoms, produces 1 NADH. The eighth oxidation, of a C4 acid, produces two molecules of acetyl-CoA --> 8 rounds of beta-oxidation are needed, so only 8 molecules of NADH will be produced

thermodynamics and bioenergetics

G=-RTlnKeq --> Keq=e^(-G/RT)

fluids and gases

Hb dissociation curve at high altitude has distinct shape from that at atm pressure. Which explains this shape?: Homotropic regulation by oxygen occurs --> sigmoidal shape of curve implies that as each O binds to Hb, affinity of Hb for O goes up. Homotropic regulation is when molecule serves as substrate for its target enzyme, as well as regulatory molecule of enzyme's activity. O2 is homotropic allosteric modulator of Hb. four subunits of Hb actually bind to oxygen cooperatively, meaning binding of O to one of 4 subunits will increase likelihood that remaining sites will bind with O as well. --> cause sigmoidal curve fluid pressure changes with depth are assumed to be linear. Which explains why this does not hold true for atm Pressure changes?: the V of mass of air is not constant --> hydrostatic pressure for liquids is linear bc as depth changes, density of liquid remains constant. Gases, however, have densities that change according to forces applied to them. gases are compressible while liquids and solids are not with decreasing T, air is able to hold less H2O. since colder air can hold less total H2O, same relative humidity would result in less total water in air --> In most cases, solubility of ionic substances in water inc with T, while opposite pattern is observed for gases. Bc higher T provides gases with more KE that they can use to escape solution. Pressure favors the solubility of gases too 100kPa = 100000Pa = 100000 N/m^2 = 10^5 N/m^2 --> 100J/L * (1000 L/m^3_ = 10^5 J/m^3 = 1-^5 Nm/m^3 = 10^5 N/m^2 ------> 100 kPa is equivalent to 100 J/L constricted arteries may collapse under P from outside arteries. This can be explained by: necessary inc in fluid velocity through constricted arterial sections causing a corresponding drop in fluid pressure --> According to continuity eq, v inc as A dec. inc v dec P. if P inside artery drops far enough, it may fall below pressure outside artery, causing it to collapse from external P when surgeons cut into artery, blood will shoot out of body as result of BP. That pressure is converted to KE causing blood to move rapidly as it exits body The work done by gas relies on any change in volume of container that is holding it. Without the container changing volume, the gas is not doing any work

Current

If neuron is 1st measure at resting potential but later found to require app of +3mA of current to return to -60mV/ Which explains neuron's net ion flow between 2 measurements? --> + ions flowed out of cell (applied current is + into cell, so cell is -. axon becomes more - when + ions leaves cells or - ions come into cell) According to Passage, when current of 70mA passes through heart, it will cause: the heart to acquire an irregular rhythm, resulting in improper blood flow When a battery, resistor, and capacitor are connected in SERIES, the initial voltage on capacitor is zero and as charge accumulates, V rises towards V of battery - rise is asymptotic Passage: 70mA current causes more damage to cardiac tisuse than a current in excess of 1A. A current of 70mA will cause the heart to contract irregularly, resulting in improper blood flow.

Acid-Base Chem of Amino Acids

In Ion-exchange chromatography, Amino acid will be eluted most efficiently if its pI is: Lower than pH of sodium acetate solution (IEC is based on diff degrees of binding to negatively charged beads. Thus, + molecules will bind to greatest extent, neutrol will be bind, - will actually be repelled by beads. pH that are lower than pI will favor binding, since molecules will be +, while pH that are close to or higher to pI will discourage binding, since molecules will be neutral or -.) aspartic acid will not show any buffering capacity at physiological pH, bc at that pH there won't be any mixture of weak acid/base conjugate pair of aspartic acid (hallmark of buffer). That is, at pH=7.4, only one form of aspartic acid is present (protonated amino group, deprotonated carboxyl and side chain groups) Use of HISTIDINE tagging and nickel column is form of AFFINITY chromatography

Absorption and Emission of Light

In MRI, hydrogens in tissue are subjected to a magnetic field. In response, the protons emit radio freq radiation, which is imaged as a bright area. Which tissue is LEAST likely to show up as a bright region in an MRI scan? : A) Kidney B) Eyes C) Femur D) Bicepts --> Since MRI relies on imaging of protons, brightness is proportional to # of protons, this Q is asking which tissue is likely to not have very many protons. Mosy protons in biological tissues arefound in water, it is asking which tissue has the lowest water content. --> Soft tissues like internal organs (kidney), eyes, and muscles will have higher water content than bonds like femur. In a strongly acidic soln (such as one with pH ~0), gentian violet will be yellow, that means it reflects yellow light and absorbs purple/indigo light. The wavelength of purple light is 400-430 nm. In soln with a pH of 3 (where [H+] = 0.001 M), gential violet will be purple. that means that it reflects purple light, which has a wavelength of 400-430 nm and therefore a freq (c=fㅅ) of 698-850 THz. pH affects the absorption and there is change between 0 and 3, indicating there is acidic group with pKa between 0 and 3. light with wavelength 200nm is UV light; illuminating DNA with UV light is likely result in destruction of that DNA. in any case, light in visible spectrum is required to visualize gentian violet inc degree of conjugation --> dec in E diff between MO involved in electron excitation --> change in absorption Attenuation = weakening of signal. Sound E is attenuated as it passes through body bc parts of signal are reflected, scattered, absorbed, refracted, or diffracted. Amplification does opposite of attenuation; it makes signal stronger The freq used in ultrasound must be greated than: 20kHz. -->ultrasound is defined as sound w/ freq above human range of hearing ("ultra" = "above"). Human range of hearing is 20Hz~20kHz. Anything greater than 20kHz qualifies as ultrasound

Amino Acids Found in Proteins

In a neutral soln, region of protein has a solvation sheel with hydrogen of water directed towards the protein. Which is likely to predominate in segment?: Glutamic acid and aspartic acid --> since H are directed towards the protein, it can be reasonably concluded that region is predominant;ly - charged. -->-charged aa Similar to D and L conventions for naming carbohydrate stereoisomers, D and L conventions for naming stereoisomers of amino acid indicate ONLY configuration of groups about alpha C. D or L designation does not give any indication about which direction compound rotates plane-polarized light (determined experimentally). R and S conventions, which are also concerned with describing configuration of groups about central atom (alpha C) can be applied to amino acids. --> L-alanine could also be called (S)-alanine reactive side chains must be protected by DIFFERENT protecting groups to prevent unwanted side reactions

Electrochemical cells

In electrochemical cells, salt bridges (release anion and cations into separate half cells to counteract the buildup of charge created by current flow) prevent charge build up in galvanic cells Derivatives of phosphatidic acid, such as phosphatidylinositol, are found in myelin sheath that surrounds neurons. --> poor conductors, which help myelin speed up action potential transmission ( Myelin surrounds axons and helps speed up action potential transmission. It acts like an insulator, swathing the axon so that action potential only needs to "refresh" itself at nodes of Ranvier) Tetrodotoxin acts by not allowing sodium to pass into nerve cells through their channels. --> there would be no action potential at poisoned region of membrane (since it is blocking influx of sodium, membrane potential will not change and thus there will be no action potential to trigger a change in membrane potential) What could account for difference in capacitance per area between myelinated axon and unmyelinated axon?: In unmyelinated axons, lipid bilayer is thinner --> Presence of myelin sheath effectively increases thickness of lipid bilayer by factor of 200, which increases d, distance between two "plates" of capacitor, to 1 micrometer. For any capacitor, increasing distance between plates decreases capacitance (C=permittivity*A/d) in electrochemical cell, oxidation occurs at anode and reduction occurs at cathode. During oxidation process, electrons are released to surroundings, the electrons then can be used to reduce at cathode. --> electron flow from anode to cathode myelination exists to inc membrane resistance to ion leakage, allowing ions to travel farther. However, bc nodes of ranvier contain additional sodium channels that open to propagate the wave of depolarization, their absence would result in wave dying before it reached axon terminal --> no nodes of ranvier, individual sodiaum ions would travel farther but depolarization would not reach axon terminal A biomedical engineer attempts to recharge a Ni-Cd hearing-aid battery using a Zn-HgO cell. if reduction potential at anode of Zn-HgO cell is -0.762, and fully charged Nu-Cd battery has V of 1.4V, reduction potential at cathode must be: greater than 0.638V --> the rxn that is being used to recharge battery must have a V greater than battery's original charge --> Ered,cathode - Ered,anode > Eoriginal --> Ered,cathode>Eoriginal+Ered,anode --> Ered,cathode>1.4V+(-0.762V) --> Ered,cathode must be > 0.638V

vectors and scalars

In exhibition, fastest recorded pitcher was playing against a batter 60feet from pitching mound. If ball was thrown horizontally and took 0.4 sec to reach home plate, what was its vertical velocity as it passed over home plate?: bc ball is thrown horizontally, inital vertical velocity is 0m/s. Assuming air resistance is negligible, only force acting on ball while it is in flight is gravity. --> V=V0+at --> V=(0m/s)+(10m/s^2)(0.4m/s) = 4m/s

Stereoisomers

In exp what would happen if only part of rxn mixtures was transferred to volumetric flask? partial transfer of mixture into volumetric flask --> lower conc of products --> observed optical rotation decreases. Since both conc of product & optical rotation decrease, specific rotation remain same Observed rotation would decrease and specific rotation would remain same ( specific rotation = obs. Ratation/(conc of soln*length of tube) Pyrocalciferol and lumisterol are diastereomers that only differ in orientation of their 19-methyl group and 14-hydrogen. Unlike enantiomers, diastereomers have diff chemical and physical properties from each other. enantiomers like (-)-methadone and (+)-methadone do not difer in their physical or chemical properties. They can only have diff physio effects by interacting with stereospecific receptor -a receptor that is itself chiral IF both isomers are formed (such as fumaric and maleic acid formed by dehydration), that means the reaction is NOT stereospecific (only one isomer formed)

Solution Equilibria

In solubility exp , solutes X and Y are introduced into subject's bloodstream. Solubility product constants of X and Y are both determined to be > than their solubility product constants at standard conditions. This is due to effect of temperature! (only T can change Ksp) (common ion efect only affect molar solubility, not solubility product) Physicians recommend drinking more water when one is at risk for kidney stone formation. This measure prevents all categories of stones bc it increases urine volume while HAVING NO EFFECT ON # OF MOLES OF ALL SOLUTES IN KIDNEY (increasing fluid intake increases urine output, but doesn;t change # of moles of ions taken into body. if # of moles of ions stays the same, volume of solution increases, then concentration decreases. Lower concentration of all ions will protect against reahing saturation for all possible solids)

Hydrostatics

In their pure liquid states, which would be more likely to exhibit the greater surface tension: glycerol or phosphatidic acid? -->Glycerol, bc it exhibits stronger intermolecular forces than phosphatidic acid (phosphatidic acid has no protons capable of H-bonding, glycerol can paryicipate in H-bond) Buoyant force acting on object is equal in magnitude to weight of fluid it displaces. Since lower altitude air is more dense, given the balloons are of equal V, a given volume of lower altitude will weigh more. Buoyant force is a function of density of fluid, the volume of object that is submerged, and acceleration due to gravity. Since object is fully submerged (in Q), the volume term is constant. Acceleration due to gravity is also constant. For an ideal fluid, density remains uniform as liquid is considered to be incompressible, this if density of water remains constant at all depths, then buoyant force itself must be constant that is independent of depth. After being completely submerged, a diver decelerates while descending in a pool: kinetic E is dissipated via drag. --> diver's weight does not change during dive, and once completely submerged, buoyant force is constant. Since diver is decelerationg there is net force upward. this could be bc magnitude of buoyany force is greater than diver's weight. inclusion of another force (drag) opposing the direction of motion might provide explanation for this A man on earth weighing 200lb floats with 1/10th of his body above water. this man would NOT float on planet whose gravitational pull is: 1/10g 2g 10g the man would always float --> To float, buoyant force must be equal in magnitude to gravitational force (Fb=Fg) --> rho*v*g =m*g. bc g is present on both sides of eq, it is not a factor in determining the man will float

Nature of solutions

Increasing consumption of dietary calcium has been shown to dec risk of calcium oxalate stone formation, while comsumption of ca supplements has been shown to increase risk. --> supplements are most often taken without food, and dietary calcium can prevent ingested oxlate from being absorbed (both methods of ca ingestion increases ca levels. the diff is therefre likely in amount of oxalate available to form stones. if dietary ca removed oxalate (supplements didn't) then the paradox would be resolved) Any solute in water will affect its boiling point, but only those that become ions in soln will conduct electrical charges. Methanol is freely soluble in water, so it will affect boiling point of water soln. but it does not ionize to any appreciable amount in soln, and thus will not conduct electricity Henry's law: solubility of gas in liquid is proportional to its partial pressure --> Concentration=henry's constant * partial pressure

Enzymes as biological catalysts

Malonyl-CoA is produced from acetyl-CoA through action of acetyl-CoA carboxylase. The byproducts of this rxn are: ADP+Pi -> Since enzymes is a carboxylase, this implies that it adds a CO2 molecule to acetyl-CoA. --> CO2 cannot be byproduct; it must be reactant. Passage: FMN is a cofactor for oxidative enzymes, it is least likely to be a cofactor for an enzyme that is not an oxidoreductase. Enzymes with "oxidase," "reductase," "dehydrogenase," or "monooxygenase" are likely to be involved in redox reactions. Tm = T at which 50% of molecules are denatured or fraction folded is 0.5 A ternary complex can be a complex formed between two substrate molecules and an enzyme. This is seen in multi-substrate enzyme-catalyzed reactions where two substrates and two products can be formed. The ternary complex is an intermediate between the product formation in this type of enzyme-catalyzed reactions. Unfolding of proteins is a cooperative process --> sigmoidal curves If a homogeneous catalyst cannot be separated from products at the end of rxn then the products will be contaminated with catalyst. Grinding heterogeneous catalyst increases amount of catalyst available to rxn and therefore inc its rate

Geometrical Optics

Material with Lowest index of refraction will enable light to travel through it at Fastest speed Myopia (nearsightednesss) - light rays entering eye converge in too short distance (focal length too short --> f adjusted by tensing and relaxing of ciliary muscle. Tensed --> f dec., To increase f, relax ciliary muscle) causing image of object at infinity to be focused within vitreous humor before light reaches retina. --> bc ciliary muscle cannot relax sufficiently Amount of light that eq. humor absorbs would only affect intensity (brightness and dimness) of light that ultimately reaches retina, not the location of image everyone is extremely farsigted in water. Inability to see close objects implies optical power of eye is not great enough to focus incoming light on retina. Light from distant objects arrives nearly parallele and requires less optical power (bending), so tissue must arise from inability to bend incoming light; refractive indices of water and eye;s media are too similar --> expereince a form of hyperopia underwater Angle of refraction can be calculated using Snell's law, however, refraction only occurs when light enters at an angle relative to normal, since light enters normal to boundary, angle of incidence is zero and there is no refraction object distance > focal length --> object is real, it appears behind lens of eye if light is not brought to an exact focus, that means light is spread over an extended area. Angle at which light is refracted by lens is dependent on wavelength, while angle at which light is reflected by a mirror is constant and is not affected by wavelength. Since, for lens, angle of refraction is dependent on wavelength, and since light of diff wavelengths is refracted at diff angles by a lens, when incoming light is bent at slightly diff angles, that causes focal point to become an extended area. on other hand, with mirros, angle at which incident light is reflected is constant, and so all light will be focused at same point

Characteristics of Fluids and Solids

Most evolutionary explanation for fainting when circulation to brain is insufficient? fainting results in reduction of effects of gravity on blood flow to brain According to hydrostatic pressure eq, P=rho*g*z, pressure is proportional to depth or inversely proportional to height. If circulation to brain is insufficient, fainting makes individual collapse to floor. This positions the brain at same height relative to rest of the body, and thus prevents blood pressure in brain from dropping Hydrostratic pressure-that is pressure as a function of depth-is assumed to be linear: P=P0+rho*g*h. this only strictly applies to liquids whose densities are essentially constant. The curve should NOT be linear for gases, bc their density is a function of force applied to them: gases are compressible; According to kinetic theory of gases, mixtures of gases do not behave differently than pure gases; air is mostly nonpolar molecules; low pressures make gases more ideally, not less ideally increasing pressure on eardrum by 35kPa can cause it to burst. How deep would a diver have to dive in fresh water to burst his eardrum?: 3.57m --> hydrostatic pressure is Phydro = rho*g*h. for diver's eardrum to burst, Phydro must equal 35kPa or 35*10^3 kg/m*s^2. --> h=Phydro/rho*g = (35*10^3 kg/m*s^2)/(10^3 kg/m^3)(10m/s^2) = 3.5m

Description and Properties

Most stable conjugare base? A) HOOC-CH2Cl B) HOOC-CH2OCH3 C) HOOC-CH2F <--(has most e-negative group, will have most inductive effect) D)HOOC-CH3 Most stable c base -> strongest acid. Acid strength is increased by inductive effect of e-withdrawing groups on neighboring carbon atoms beta-hydroxyketone, when heated, will undergo dehydration in which a water molecule is eliminated. Driving force for this rxn is formation of C-C pi bond that can be conjugated with carbonyl pi bond. The double bond, therefore, has to be between alpha and beta C, the first and second carbons away from carbonyl carbon.

Kinematics and force

Newton's third law: F(A on B) = -F(B on A); 1st law: inertia. Fnet=0 at eq; 2nd law: force. Total sum of forces acting on object is equivalent to its mass times its acceleration --> Fnet=ma 50kg child is riding on a playground merry-go-round. If radius of circular path of merry-go-round is 5m and freq is 0.1hz. What is force required to keep child on ride?: 0.1Hz--> period is 10s. Speed is 2*pi*r/T = 2(3.14)(5)/10 = 3.14m/s --> Fc=mv^2/r = (50)(3.14)^2/(5) = 100N Passage: Fapplied is increased until gurney moves. --> while Fapplied is less than its max, gurney is not moving. Here, Fnet=0N. --> Fnet=ma --> a=Fnet/m=0 What is mechanical advantage of using ramp, as opposed to lifting gurney straight up: one form of mechanical advantage represents an ability to move a load (do work) using less force than simply lifting the load directly. For inclined plane, this advantange is represented using formula: MA = hypotenuse/height (sin-1). we are told ramp makes 30degree angle with ground --> side ration of x: x*sqrt(3): 2x --> MA=2x/x=2 in order for gurney to slide down the ramp, force pulling it downward (mgsin*theta) must be greater than static frictional force (mu(s)*F(N)=mu(s)*mgcos*theta). Net force one each gurney is thus Fnet = mgsin*theta - mu(s)*mgcos*theta. --> since net force is equal to product of mass and acceleration, rewrite this eq as ma=mgsin*theta - mu(s)*mgcos*theta, wehre a > 0 means gurney will slide down ramp. mass of gurney present in all terms and can be canceled --> it is not a factor in whether the gurney slides. thus, both gurneys (200kg and 50kg) have equal likelihood of slipping down ramp, regardless of fact they have diff total masses period T and freq f of tone are related by T=1/f. if first harmonic has freq of 100hz, then second harmonic ahs freq of 200hz. Period corresponding to 200 second harmonic is 1/200s^-1 = 0.005s object moves at constant speed--> net force on object - 0. in horizontal direction the sum of forces must be 0.

Fluid Dynamics

One artery branches into several arterioles, which further branches out into millions of capillaries The capillaries have a NET greater x-sectional area than arteries, blood flows slower through capillaries (continuity eq: A1*V1 = V2*V2) A patient's max BP(systolic) is 113 mmHg and min(diastolic) is 60mmHg. If his total peripheral R is 20.5 mmHg*min/L, what's diff in his cardiac output between systolic and diastolic pressure? --> BP = cardiac output * total peripheral R --> diff in cardiact output = (Psystolic - Pdiastolic)/R = 2.59 L/min If elastic component of models were removed, which would be true of viscous component? --> Rate of flow would be proportional to pressure difference between adjacent locations until flow became turbulent ( Poseuille's law relates viscosity, pressure differences, and radius of tube to flow of material. It is often seen in biological systems as related to blood flow. There's a direct relationship between pressure diff and flow, and exponential relationship between radius and flow, and inverse relationship between viscosity and flow) Based on Venturi effect, if kidney stone is partially blocking one ureter, how are velocity and hydrostatic pressure of urine affected as it passes through point of blockage? --> Velocity increases and hydrostatic P decreases ( A partial blockage will effectively dec the cross sectional area of ureter. According to Venturi effect, V will increase to maintain continuity and hydrostatic P will decrease to conserve mechanical E.) Norepinephrine causes constriction of blood vessels. If a certain blood vessel is constricted to half of its diameter yet maintains same pressure gradient, according to poiseulle;s law, volumetric flow rate is expected to: DECREASE BY A FACTOR OF 16 --> Q=deltaP*pi*r^4/8*mu*L

Chemical kinetics

Overall rate of rxn (at all substrate and enzyme conc) is proportional to conc of ES complex Slower step of 2 in Passage: The ES breaks down, forming same free, initial enzyme and product in slower second step --> rate-deternmining step --> conc of ES is proportional to rxn rate bc it is compound that reacts in 2nd step (rate determining step) Arrhenius eq describes rate of rxn, this depends on Ea, T, gas constant, and pre-expontential const A. rate of Rxn will be highest when there is lowest Ea --> k=Ae^(-Ea/RT) (lower Ea, greater exponent, greater rxn rate) Km values can be used to represent measure of binding affinity of an enzyme for particular substrate. Expression for Km is same as dissociation constant under conditions where product formation is rate-limiting step. ratio of Kcat to Km is measure of catalytic efficiency Kcat ~ catalytic turnover Km ~ substrate binding Kcat - used to describe rate-limiting step of catalysis under SATURATING conditions of substrate Induced-fit model of enzyme catalysis states that active site of enzyme changes shape upon substrate binding and only proper substrate causes a change that initiates catalysis protein contains 4 disulfide bonds. in order to break these bonds, need to add a minimum of: 4 moles of NADH for each mole of protein --> each mole of NADH can reduce a mole of disulfide bonds. since protein has 4 disulfide bonds, 4 moles of NADH are needed Phosphoryl transfer from kinases comes from GAMMA-Phosphate of ATP

Covalent Bonds

Phenylalanine hydroxylase (PAH - convert phenylalanine to tyrosine) on phenylalanine results in --> conservation of stereochemistry, since primary chiral center is not altered ( no chiral centers) Based on Passage, when glutamate interacts with zing, glutamate is acting as LEWIS BASE.--> P3 describes glutamate as an e- donor coordinating with Zn2+. An e- donor is Lewis base Since electrical conductivity is related to ability of material to conduct an electric current, materials with free electrons are better conductors. In graphite, each C is covalently bonded to 3 other atoms: since C is tetrahedral, this leaves a "sea" of free electrons that can conduct electricity. By contrast, in diamond, each C is covalently bonded to four other atoms, leaving no free electrons. --> C atoms in graphite are arranged in fused aromatic rings, while those in diamond are arranged in tetrahedral lattice --> diamond is an excellent insulator while graphite exhibits conductive properties

Peptide Bond Formation and Hydrolysis

Primary structure of protein is formed when N-terminus of 1 aa attacks C-terminus of another --> H bonding between C and N terminus account for Secondary structure such as alpha and beta sheets, not primary structure only a reducing agent could disrupt disulfide bond

primary and secondary protein structure

Proline prevents alpha-amine N from participating in H-bonding. --> Proline decreasese stability of beta-pleated sheets (beta-pleated sheets are stabilized by H-binds between amine and carboxyl groups of component amino acids of polypeptide chain. Since proline doesn't have H on alpha amino group in peptide group, it can't participate in H-bonding scheme, and would destabilize 2ndary structure) effect on AchE of a temperature much higher than 42 degree in C?: SECONDARY AND TERTIARY STRUCTURE BREAKDOWN ONLY -->increasing T will denature protein. Above 42 C it can be seen that protein has lost functionality which implies that tertiary structure is gone. As T increases, there will be complete denaturation resulting in protein losing its secondaray and tertiary structure and resulting in random coil proinsulin must undergo cleavage by protease, resulting in 2 smaller units that become functional insulin. Protease's action represents modification of proinsulin's: primary structure --> bc sequence of aa is altered, this constitutes a modification of proinsulin's proinsulin's primary structure

Electromagnetic Spectrum

Radio waves have frequencies ranging from 10kHz too 100GHz: Radio waves have smallest frequencies and longest wavelengths of all waves in electromagnetic spectrum. --> radiowaves have longer wavelengths than gamma rays and lower frequencoes than X-rays. AM radio waves have lower frequencies than FM radio waves. X-rays are typically designed as those electromagnetic waves between about 0.01 nm and 1nm. Which energies might an x-ray photon have?: 10keV --> E=hc/ㅅ, (given hc=1240nm) --> E=1240/ㅅ --> 0.01nm: 1240/(0.01) = 124,000eV or 124keV ; 1nm: 1240 eV --> any photon between 1240 eV and 124keV are X-rays When a fluoresecnt molecule absorbs blue light, it will emit light with: longer wavelength and lower E than that of blue light --> Fluorescence is emission of light by a substance that has absorbed light: the electrons of molecule relax to their ground state by emitting a photon of light, after being excited to a higher quantum state bu absorbed light. Therefore, it must be true that the emitted light has lower than that of absorbed light

Kinetics and bioenergetics

Rate of cation formation through deprotonation is directly related to E required to deprotonate the compound. More E required, slower the rate. Stabilizing effects of substituents can be determine dfrom relative stabilization energt (RSE). The more - the RSE, greater stabilization.: NO2> OCH3> CH3 >H > F Positive control - control group that is not exposed to exp treatment but that is exposed to some other treatment that is known to produce expected effect (ex: using known inhibitor is an ex of comparing expected effects of this inhibitor to those of analog treatment).; Negative control - control group that is not exposed to exp treatment or to any other treatment that is expected to have an effect Passage: cephalosporins bind irreversibly to active site of PBP. Of inhibitor types given (competitive, noncompetitive, uncompetitive, suicide inhibition), Suicide inhibition acts as irreversible enzyne inhibitor, it occurs when enzyme binds the inhibitor (Structurally a substrate analogue) and forms irreversible complex with it, usually through covalent bond. this can involve inhibitor being chemically modified by enzyme during normal course of catalysis to produce reactive group that is specifically responsible for formation of irreversible inhibitor-enzyme complex Conversion of pyruvate to glucose requires its initial conversion into oxaloacetate, in rxn catalyzed by pyruvate carboxylase in mitochondria. Oxaloacetate (OAA) is then decarboxylated and phosphorylated by cytosolic or mitochondrial forms of phosphoenolpyruvate carboxylkinase (PEPCK). after transport of either OAA in form of malate or PEP directly from mitochondria, remainder of gluconeogenesis takes place in cytosol PRoduction of PEP,glucose, and fructose 6-phosphate by gluconeogenesis-specific enzymes that bypass irreversible steps of glycolysis push equilibrium of reversible enzymes that function both in glycolysis and gluconeogenesis in direction of glucose production Efficiency = work output/work input.

diffraction

Reducing the width of the aperture in optical microscope --> diffraction becomes more pronounced --> worsened resolution The resolution of an image produced by a fluoresecne microscope is limited by diffraction. The resu=olution CANNOT be improved by: I) decreasing wavelength of light illuminating sample II) inc size of aperture of objective lens III) inc size of aperture of ocular lens ---> Diffraction through a circular aperture, like those in lenses of microscope, can is roughly analogous to diffraction through a single slit. Diffraction is affected by wavelength bc light with longer wavelengts diffracts more (at greater angle) than light with shorter wavemength. therefore, in fluoresecnet microscope, shining light with shorter wavelength on sample will result in less diffraction, and greater resolution. With smaller aperture, the diffracted waves diverges more, and this leads to lower resolution. thus, inc size of aperture through which incident light is passing will indeed improve resolution. incident light is only passing through objective lens, not ocular lens, so changing aperture of ocular lens won't make any diff to resolution of image. (a*sin(theta) = nㅅ)

genetic code

Ribozyme is an RNA molecule that is capable of catalyzing rxns similarly to the way enzymes do. Since ribozymes are composed of RNA, and RNA has phosphodiester bonds in ribose-phosphate "backbone", it will be susceptible to cleavage by phosphodiesterases. Peptides, on the other hand, do not contain any phosphates or phosphodiester bonds, so phosphodiesterase won't be able to cleave enzyme

reactions of carboxylic acids

Small rings (containing less than 5 carbons) are extremely unstable due to both torsional and angle strain. Deacylation of aspirin = simple ester hydrolysis rxn --> hydrolysis rxn requires water is it possible for methanol to react with phenylalanine to form methyl ester in absence of acid?: Yes, but more slowly bc acid plays a catalytic role (this is ex of nucleophilic acyl substitution, specifically esterification) Fisher esterification: carboxylic acid + acid + alcohol = ester A lactone ring is result of condensation of an alcohol group and carboxylic acid group in same molecule - essentially, a cyclic ester amide N of metoclopramide has 3 sigma bonds and a lone pair that participates in resonance with sp2 hybridized carbonyl carbon which involves a pi bond, --> it is sp2 hybridized and planar

Sound

Speed of sound is proportional to sqrt(medium's bulk modulus) --> sound travels fastest in sollid (ossicles = malleus + incus + stapes) How long is third-longest resonant standing wave formed inside auditory canal? About 80% of length of canal (auditory canal--> pipe with one closed end --> only odd harmonics exist --> third-largest wavelength = 5th harmonic --> ㅅ=4L/n = 4L/5 = 0.8L)

Carbohydrate classification

Sucrose can be refined to by I)alpha-D-Glucopyranosyl beta-D-fructofuranoside / III) beta-D-fructofuranosyl alpha-D-glucopyranoside Pyran--> 6-membered ring--> glucopyranose ; furan--> 5-membered ring --> fructofuranose ; prefix for a glycoside = "-osyl" --> glucopyranosyl or fructofuranosyl ; glucoside - alpha linkage, fructoside - beta linkage diff between alpha-D-glucose and beta-D-glucose? --> hemiacetal carbons of alpha and beta-D-glucose have opposite absolute configuration. (both are anomers, differ only in abs. cong at their anomeric C. anomeric C is at center of hemiacetal group whose conf. will determine whether -OH is axial or equatorial in cyclic glucose both are not enantiomers bc enantiomers differ at ALL chiral centers (D,L) but anomers differ at only 1 of chiral centers

oxidation and reduction

The reason that NAD+/NADH do not need to be tightly coupled to an enzyme is that NADH does not react with O2: that single-electron transfers to and from NAD+/NADH produce unstable free radical species. NAD+/NADH will only undergo 2-electron, not 1-electron, transfers, and therefore, NAD+/NADH do not need to be bound to enzymes tocontrol their reactivity with dioxygen. By contrast, FAD/FADH2 reacts very easily with O2: single-electron transfers to and from FAD/FADH2 produce highly stable free radical species known as semiquinones. Therefore, FAD/FADH2 will undergo either 1-electron or 2-electron transfers, and must be bound to enzymes in order to keep them from reacting with O2 Biologists isolate a superoxide dismutase enzyme that is complexed with copper instead of manganese. The scientists hypothesize that, when being reduced by O2-, the oxidation state of Cu will: change from +2 to +1 (only answer that shows reduction exclusively)

signaling lipids

Vitamin D3 is a fat-soluble molecule that comes from a steroid precursor. It is insoluble in aqeous environments despite its polar -OH group (this polar group is heavily outweighted by many C). In order to leave the cell, it needs no channel and cannot be contained by a vesicle, it travels freely through the lipid bilayer. Only way for it to travel through aqeuous environment of blood is attached to a polar molecule, like a protein)

Capacitance and Capacitors

Voltage gated channels only exist in significant quantities where the membrane is unmyelinated.-->capacitance of membrane dec when cell membrane is myelinated Axon can be thought of as a parallel plate capacitor, with cell membrane acting as an insulator between relatively negative side of neurons and relatively positive outside. bc the presence of myelin sheath inc the distance between the two "plates", capacitance is dec according to formula, C=epsilon0*(A/d)

Titration and buffers

When H3PO4 is titrated w/ strong base, which is predominant compound at 3rd equivalent pt? = PO4 3- ( at 1st eq pt, H2PO4 - is predominant ; at 2nd eq pt, HPO4 2- is predominant) In absence of pH meter, which indicator soln is most appropriate for titration of stomach and w/ NADH? --> Stomach produces HCl, strong acid, need an indicator whose eq point pH=7 (phenol red: pH= 6.4-8) A stident is standardizing NaOH using KHP (MW=204). The student dissolves 204.22g of KHP in 50mL of water and then titrates w/ the NaOH of unknown conc. Which is NOT cause faulty results?: A)Using unknown amount of water that was more than 50mL<--. B) Using unknown amount of KHP that was less than 204.22g C)Using indicator that has pKa < pH of eq point D) Using indicator that has pKa> pH of eq point first pKa of carbonic acid is 6.35. in blood that contains twice as much bicarbonate as carbonic acid, what % of hemoglobin is saturated when PO2 is 0.1atm? --> pH=6.35 +log(2) = 6.7. -->with curve specified, find point of intersection in Fig1 in Passage at slightly more than 30% The eq point will be reached when eq of acid (KHP) equal to eq of base (NaOH). This case, eq of acid is known and constant and amount of water does not change the amount of acid present.

Reactivity Principles

When acyl halide reacts with primary alcohol --> An ester forms A chemist wishing to activate a carboxyl group could effectively do so by: Reacting it with SOCl2 --> Peptide bonds form by nuc attack of amino group of an aa on carboxyl group of another. Rxn of thionyl chloride with carboxylic acid substitutes a chlorine atom for the carboxyl hydroxyl group, producing an acyl chloride beta-lactam antibiotics are highly reactive bc of their ring strain: the fusion of beta-lactam ring to a second ring forces the geometry of nitrogen atom to be pyramidal, rather than trigonal planar (which is preferred geometry for an sp2-hybridized atom), which confers higher degree of instability. Having more resonance structures would make a compound more stable and less reactive and the carbonyl having less ketone character (i.e. more amide character via resonance) would mean it is less reactive The carbonyl C of acetyl chloride is more electrophilic than that of acetic acid. The e-withdrawing effects of chloride ion make the carbonyl more electrophilic than acetic acid, making it more susceptible to nucleophilic attack by alcohol

Structural Lipids

Which is true about Phospholipids and truglycerides? --> All triglycerides but not all phospholipids have glycerol backbone Tryglycerides are triesters derived from glycerol and 3 fatty acids of varying degrees of saturation. Phospholipids are similar to truglycerides, but their backbone may or maynot be glycerol Higher degrees of unsaturation would decrease calorie count Sphingolipids generally contain a sphingosine backbone amide-linked to a fatty acid. Sphingoside takes palce of glycerol (which provides backbone for most phospholipids), glycerol is not generally found in sphingolipids A hibernating animal will alter the lipid composition in plasma membranes of its cells in order to try to maintain membrane fluidity when T are low --> animal will replace saturated fatty acids(palmitic acid) with unsaturated fatty acids (linoleic aicd) organic components of compound --> separate from aqueous phases --> solutes confined to it are lipophilic or hydrophobic Liposomes can be difficult to detect since they do not absorb visible light and many molecules absorb UV light. if exp design allowed fluorescent dye to be trapped inside during liposome formation, it would allow their detection by fluorescence spectroscopy

Role of ATP

Which of values obtained from bomb calorimetry constitutes sufficient info to determine bond E of activated glucosamine? Bomb cal. Very insufficient way to determine bond enta=hapies within compound when not starting from standard state. Need: mass of reactant, Hf of reactants, T of products, T of reactants, mass of calorimeter, specific heat of calorimeter, mass of water in calorimeter, specific heat of water, Hf of products, background info on bond E contained within either reactants or products

Atomic Structure and Stoichiometry

cancer is failure of mutated cells to regulate cell division and proliferation in a normal manner. Since regulatory genes and processes are complex, mutations caused may not immediately causes detectable cancer, as mutated DNA will disrupt cell cycle over time. N2 is very inert gas. It makes ~80% of air you breathe, yet has no significant chem rxn with lungs - or with anything other than nitrogen-fixing plants. This info implies that N is very inert (unreactive). --> good artificial atm when working with reagents that might react with O or other gas. in lab conditions N2 can be used as atm to prevent unwanted side rxns Na atoms are larger than Cl atoms because the electron cloud of Cl is pulled in more tightly by the increased number of protons in the nucleus. Na+ ions are smaller thanCl- ions because the Na+ ions have electrons in only two energy levels and Cl- ions have electrons in three levels.

How light and sound interact with matter

destructive inteference occurs in photodiode detectors when direct and scattered light rays take paths to photocell that differ in phase by: 180 degrees --> phase diff corresponding to half of wave is 180 degree. Half a wave diff in phae between 2 wavs corrsponds to destructive interference inc in distance between radio wave peaks due to jet speed causes received wavelength to be lengthened. --> essence of Doppler effect the Doppler eq for freq is changef/f=-v/c for a given relative v between source and detector. --> freq shift changef depends invesely on speed of wave in medium in which it propagates,c. v of sound is much smaller than that of electromagnetic radiation, so for same relative v the freq and wavelength shifts are much greater for sound than for radio waves receiver is in jet flying alongside another jet that is emitting 2*10^6 Hz radio waves. If jet fly at 268m/s, what is change in freq detected at receiver?: 0Hz --> bc there is no relative motion between jets, there is no freq shift focal length of mirror depends only on radius of curvature. visible light tavels more slowly through an optically dense medium than through a vacuum. -->light is absorbed and re-emitted by atomic structure of optically dense medium an ultrasound exam could show the motion of fetus. To image this motion, ultrasound exam devices requires what minimal info?: speed of sound, freq of sound wave emitted and observed --> Doppler effect relates freq of ultrasound wave as detected by moving detector to freq of wave when source is stationary, speed of source, and speed of detector. three of four quantities involved in effect are required conjugated or aromitic C=C bond: 1580~1610 cm-1 larger set of conjugated double bonds --> more likely be detected (and intensely colored Advantage of Doppler ultrasound technique over standard ultrasound technique is that it also allows: Doppler ultrasound takes advantage of Doppler effect in which a sound wave emitted by, or reflected from a moving object, will change its freq based on relative speed of object, in this case, flow of blood in vessel Which will affect the freq of sound waves traveling through air, as measured by a detector? : I) Surface A of detector II) Speed of source of sound III) Distance from source to detector --> II only --> Doppler effect: speed of both source and detector of wave will influence the perceived freq of that wave. IF fine-tuning of that freq is requireed, experimenters can change the detected freq by moving the source at some constant velocity. SA of detector and distace from source will only affect intensity of wave experienced by that detector When foramen ovale fails to close, it can be diagonosed using an echocardiogram. During sonogram, sound waves enter body and are partially reflected at interface between diff materials. How does speed of sound wave change for diff tissues?: Sound wave will travel faster in muscle than it does in blood --> Sound is mechanical wave, so it relies on molecular collisions of propagation. --> sound travesls fastest in solids (where molecules are closer together), slower in liquids, and slowest in gases --> Sound waves will travel faster through solid phase of muslce than it would through liquid blood. frequency of sound produced in vibrating cords and strings of fixed length is proportional to propagation speed of sound through the cord. in turn, propagation speed of transverse wave (such as sound wave in vocal cords) is directly proportional to tension applied along the cord Wavelength of light absorbed by molecule depend on its structure, so production of variety of structurally related opsins functions to enable detection of diff colors Absorption of UV light by organic molecules always results in electronic EXCITATION. Bond breaking can subsequently result, as can ionization or bond vibration

concentration

disaccharide has molecular formula C12H22O11

Periodic properties of the elements

e- in 1s subshell of which elements experience the greatest effective nuclear charge? A)H B)Na C)Cl <-- D)O Zeff increases from left ro right across periodic table bc of increase in + charge in nucleus. B/c Q asks about 1s e-, shielding effects can be ignored making # of protons the most important factor Experimenters set up protocol to separate Cu+ from Zn2+ in aq soln. Assuming all 3 methods are practical, which could be basis of their separation?: I) Ionic radius II) Electrostatic force III) Nuclear size --> All three. Although they have same # of e-, Cu+ and Zn2+ have diff effective nuc charges bc they have diff nuc charge (# of protons). This results in diff in ionic radius and nuclear size. They will also expereince diff electrostatic force (from some outside electric Field) bc they cahrry diff charges. Sulfur is very unstable in its diatomic state, S2. This differs fromO2 bc: double bond in S2 is longer (as one descends a group in periodic table, atomic radius inc and Zeff dec. Due to larger electron cloud (more inner e-) the S to S bond needs to be longer Which has smallest ionic radius?: O2- F- Na+ Mg2+ <-- smallest atom will be one with most protons energy of DNA synthesis is stored in phosphate bonds of dNTPs. Sulfate can make similar bonds but it is not used in same way, why?: S is more electronegative than P resulting in weaker bond to O --> Since diff in electronegativity are key to bond strength, P being less electronegative will give stronger bond to O than S will. Which element would be best to use the plates of a defibrilaator?: A) F B) P C) Pb D) Au<- --> Elements w/ metallic character are best for conducting electricity and lowering resistance to help shock better. Gold, appearing farthest towards the lower left, will be best option for creating plates of debibrillator.

nucleophilic acyl substitution rxns

partial transesterification of triacylglycerol can result in formation of 'diols'. these compounds could also be described as: monoesters of gllycerol --> the diol formed would be remains of triglyceride after 2 fatty acid residues have been removed. The term "diol" would therefore refer to glycerol with 1 remaining fatty acid attached to it, and so could be described as monoester of glycerol SN2 requires a good nucleophile (ex: methoxide ion) Acyl chloride is the most reactive of various kinds of carboxylic acid derivatives, certainly more so than corresponding carboxylic acd. This is bc the Cl is much better leaving group than OH- and is therefore more easily displaced by nuc attack of amino group

intermolecular forces

proline is extracted from txn mixture, which type of intermolecular forces are lifely present In proline soln? --> H bonds, Ion-dipole forces (proline is easily ionizable), Dispersion forces, dipole-dipole forces Primary amines act as H bond donors and hydrogen bond acceptors (lone pair on N is capable of accepting H) order of inc melting point?: urea, glucose, lactose --> at fiven T, molecules with low MP will be liquid, while those with high MP will be solids. Urea,glucose,and lactose are solids at room T, and MP will correlate with molecular weight: lactose is greater than glucose which is grewater than urea. Water is liquid at room T and so has the lowest MP myelin is 80% lipids, --> lipids are mainly held together by london dispersion forces Melting point range includes T when first crystal of compound starts to melt and T when compound is entirely melted. For pure compound, MP range is narrow. Therefore, MP determination is sometimes used to identify unknown pure compound. But presene of impurities in compound lowers and broadens MP range.

denaturation

shorter bonds means stronger bonds, which would tend to make correctly folded protein more stable relative to misfolded protein. But relative stability of misfolded protein does not give any indication that the protein is actually misfolded

coloumb's law

since with electroperception, e- are flowing from area of high e- density to area of low e- density, electric field is created around fish. Since electric fields rely on generation of electric currents, electric fields from biological sources will not be able to form where resistivity of medium is high (air). Therefore, generation of electric fields from biological sources is limited to environment where conductivity is high and resistivity is low (aquatic env)

work

the BP in a capillary bed is essentially 0, allowing blood to flow extremely slowly through tissues. What is work done on 200cm^3 of bloopd against gravity to bring it to capillaries of brain, 50cm above the heart?: 1 J ---> the work done against gravity is simply change in gravitational PE=mgh. mass of blood is its density times its volue, and change in height is 50cm or 0.5m/ Approximating mass of blood at 1g/cm3 gives: (0.2kg)(10m/s^2)(0.5m) = 1 J Electric shock plates ares sometimes used to restore natural rhythm of heart attach victim. Shock plates are run off a 10V battery and draw current at a constant 30A. If each shock draws 300J of electrical E, what is duration of shock?: 1sec --> P=IV --> P=(30)(10)=300J/s. Since P=E/time, time=E/P = (300J)/(300J/s) = 1sec Mechanical work by elastic force: W=k*x^2/2 = Fx/2 (graphically, it is area under force-extension graph)

gas movement

the density of human body can be calculated from its weight in air, Wair, and its weight while submersed in water, Ww. Density f human body is proportional to: Wair/(Wair-Ww) --> Archimedes' principle, ratio of density of an object to density of fluid it is submersed in is equal to ratio of weight of object in air to diff of submersed weight and weight in air.

protein isolation

when quaternary structure of a protein is lost, these conglomerates separate into their individual component proteins. It is evident that each of these components will be smaller than conglomerate and will tuse run through gel filtration column slowly. the smaller proteins will enter porous beads while larger conglomerate (non-denatured protein) would run rapidly column. --> non-denatured protein would elute first