Chemical and Physical Biological foundations Score 122

Question 1

What is the equation for buoyant force?

Answer 1

The force of buoyancy is given by Fb = ρfVsubg, and g should not change. The maximum value of V should not either; the object can always be fully submerged, so the maximum value of V is just the total volume of the object. for the maximum buoyant force, the object must be fully submerged

Question 2

How does surface tension effect alveoli?

Answer 2

surface tension is a binding force that resists increase in surface area. Because the alveoli are small wet sacks (roughly spherical), a higher surface tension would make these wet spheres of fluid more difficult to inflate, particularly when they were deflated after exhalation (because a smaller sphere has a higher ratio of surface area to volume).

Question 3

Why could increasing the temperature for a reaction decrease the reaction rate?

Answer 3

Increasing temperature decreases the solubility of gases in liquids. This decreases the concentration of a reactant in the displacement and decreases the rate of reaction. However, the solubility of solids in liquids increases with increasing temperature.

Question 4

How does atomic radius/volume influence electron affinity between atoms?

Answer 4

The smaller atomic volume leads to greater repulsive forces between the existing electrons and the electron being added

Question 5

Why is I2 not likely to undergo a displacement reaction with NaBr?

Answer 5

For nonmetals, reactivity increases with the tendency to gain an electron and follows the electron affinity and electronegativity periodic trends. Reactivity for the halogens decreases down the column, so F2, Cl2, Br2, and I2 are of decreasing reactivity. For this reason, I2 is insufficiently reactive to undergo a displacement reaction with NaBr

Question 6

What is the reaction quotient (Q) equation and it’s relationship to K?

Answer 6

Question 7

Why can delta G not equal K?

Answer 7

ΔG cannot equal Keq. ΔG = ΔG° + RT ln Q, and when the reaction is at equilibrium ΔG°=–RT ln K. This eliminates D.

Question 8

What does the Kreb’s Cycle produce?

Answer 8

The Krebs Cycle produces NADH and FADH2, as well as CO2, which result from oxidation of carbons present on acetyl-CoA

Question 9

Go through full Krebs Cycle

Answer 9

Question 10

What does beta-oxidation produce?

Answer 10

beta-oxidation involves oxidation of acyl-CoA molecules and yields NADH, FADH2, as well as acetyl-CoA as products.

Question 11

Go through beta oxidation

Answer 11

Question 12

Final Products of Beta Oxidation. Numbers example using 18 Carbon starting material.

Answer 12

Question 13

What does the electron transport chain produce?

Answer 13

the electron transport chain does produce ATP as the result of oxidation of electron carriers, but oxidation of those carriers would yield NAD+, not NADH

Question 14

What is Newton’s third law?

Answer 14

His third law states that for every action (force) in nature there is an equal and opposite reaction. In other words, if object A exerts a force on object B, then object B also exerts an equal and opposite force on object A.

Before the throw, the person, sled, and ball all have horizontal velocity. When the person throws the ball upward in her reference frame, she exerts an upward force on the ball. Therefore a downward reaction force is exerted on her by the ball. This downward force cannot provide an acceleration in a horizontal direction (and indeed, it doesn’t provide an acceleration in the vertical direction either because of the normal force from the ground on the sled), so there is no change in horizontal velocity or speed.

Question 15

What must happen for total internal reflection to occur?

Answer 15

Total internal reflection can only happen when the incident medium has a greater index of refraction than the surrounding medium.

Question 16

Explain Snell’s law of refraction

Answer 16

Snell’s law of refraction states that n1sinθ1 = n2sinθ2. For total internal reflection, θ1 = θcritical and θ2 = 90°, which means that n1sinθcritical = n2. The index of refraction of air (n2 in this case) is 1, so immersing the medium in fluid has caused n2 to increase. Since n1 remains constant, the equation tells us that sinθcritical, and therefore θcritical itself, must increase.

Question 17

What is an addition reaction?

Answer 17

Question 18

What is tautomerization?

Answer 18

Tautomerization refers to a rapid equilibrium between structural isomers, often a ketone and its enol form

Question 19

What is esterification?

Answer 19

chemical reaction in which two reactants (typically an alcohol and an acid) form an ester as the reaction product

Question 20

What is saponification?

Answer 20

Saponification is the process of transforming an ester into a carboxylic acid using base, the opposite of ester formation

Question 21

What is a ketone?

Answer 21

Question 22

What is an aldose?

Answer 22

Question 23

What is H2SO4?

Answer 23

Strong acid which is used to protonate instead of oxidize.

Question 24

What is NaBH4 used for?

Answer 24

Reduction

Question 25

What is PCl3 used for?

Answer 25

known to convert carboxylic acids into acid halides

Question 26

What does NaClO3 do?

Answer 26

is a mild oxidizing agent with several oxygen atoms bonded to a highly electronegative Cl atom.

Question 27

The addition of HCl(g) to SO3(g) yields the superacidic compound HSO3Cl(l). The oxidation state of sulfur in this reaction remains unchanged. Why?

Answer 27

The sulfur atom makes a bond with Cl–, but formally breaks half of a double bond with oxygen, leading to no change in the oxidation state. An alternative solution is to assign oxidation states. For SO3, oxygen has an oxidation state of –2 and sulfur has an oxidation state of +6. In HSO3Cl, oxygen has an oxidation state of –2, contributing a total of –6. Chlorine has an oxidation state of –1 and hydrogen has an oxidation state of +1. Therefore, the oxidation state of sulfur remains at +6 in order for the molecule to maintain an overall neutral charge. Also, note that sulfur has 6 valence electrons, so its maximum oxidation state is +6. Since sulfur already has a +6 oxidation state in the starting compound SO3, the oxidation state cannot increase any further

Question 28

In aqueous solutions, HF is a much weaker acid than HCl. However, when combined with Lewis acids, fluorinated systems make much stronger superacids than chlorinated ones. Which of the following best accounts for this phenomenon?

Answer 28

F– forms very stable complex anions through strong bonding to Lewis acids. The same property that makes HF a weak acid in aqueous systems (relative instability of F–) makes it a very strong acid in the Lewis/Brønsted acid partner. F–, being unstable on its own, makes strong bonds to Lewis acids and very stable complex anions.

Question 29

NMR splitting patterns. How do you tell if something will split?

Answer 29

Look at neighboring hydrogens and add one. (n+1)

Question 30

What are characteristics of Gram positive bacteria?

Answer 30

Gram-(+) bacteria have one phospholipid bilayer membrane. Have thick peptidoglycan layer.

Question 31

What are the characteristics of gram negative bacteria?

Answer 31

Gram-(–) bacteria have two phospholipid bilayer membranes and a thin peptidoglycan layer.

Question 32

What is an anionic amino acid?

Answer 32

Residue carrying an overall negative charge.

Question 33

What are the negatively charged amino acids?

Answer 33

Aspartic acid, and glutamic acid

Question 34

What are the polar amino acids?

Answer 34

Serine, threonine, tyrosine, asparagine, glutamine

Question 35

What are the non polar amino acids?

Answer 35

Glycine, alanine, valine, cysteine, proline, leucine, isoleucine, methionine, tryptophan, phenylalanine.

Question 36

What are the positively charged amino acids (basic)

Answer 36

histidine, arginine, lysine

Question 37

What is a methylating agent?

Answer 37

A methylating agent is an alkylating agent that provides a methyl group. As shown in each answer choice, a methyl carbon atom is attached to an electronegative atom, making these methylating agents carbon electrophiles. One way of assessing the electrophilicity of a carbon electrophile is by examining the leaving group ability of the attached electronegative group. Look for a good leaving group!

The tosylate and triflate leaving groups are resonance stabilized, and iodide is stabilized due to the large size of the anion.

allows for a direct comparison as both fluoride and iodide belong to the halogen family. Since iodide is significantly larger than fluoride, the former is more stable.

Question 38

How do salts dissolved in water change pH?

Answer 38

The conjugate acid of a weak base will lower the pH, while the conjugate base of a weak acid will raise it. Conjugates of strong acids or bases have no effect on pH. NH4+, the conjugate of the weak base NH3, is acidic. Cl–, the conjugate of the strong acid HCl, will not affect pH. K+ and HSO4– are conjugates of a strong base and strong acid, respectively. Generally this would indicate a neutral salt. However, the HSO4– ion is acidic in its own right and will lower the pH. Na+ is the conjugate of a strong base and HCO3– is the conjugate of a weak acid, so Item III is a basic salt and will raise the pH of the solution.

Question 39

What causes a hydrogen to show up further downstream on NMR?

Answer 39

hydrogen is closest to the electronegative element (chlorine in this case). Therefore, the chlorine will pull the electron density away from the hydrogen, which causes the hydrogen to have a higher chemical shift (be further downfield) than the other hydrogens.

Question 40

What nucleotides have double ring structures?

Answer 40

The purines, adenine and guanine, are double-ring structures.

PUR As Gold

Question 41

What nucleotides have single ring structures?

Answer 41

Pyrimidines. Cytosine and Thymine.

Pyramids CuT

Question 42

Weight of an object equation on a planet.

Answer 42

w = GMm / R2, where m is the mass of the object, M is the mass of the planet or moon and R is the radius of the planet or moon.

Question 43

What is beta-oxidation?

Answer 43

β-oxidation is a series of redox reactions where the acyl compound is oxidized allowing reduction of electron carriers to occur. In a fasted state, the body uses fatty acids to create ketone bodies for fuel, so β-oxidation would be activated to produce the acetyl-CoA molecules needed for ketogenesis. In contrast, in a fed state, fatty acid synthesis would be activated and β-oxidation would be suppressed. H2O is consumed in beta oxidation. The electron carriers that are reduced in beta oxidation move on to produce ATP in the ETC (do not produce acetyl CoA)

Question 44

How does Glucagon influence beta oxidation?

Answer 44

β-oxidation is activated when the body is low on glucose or energy and requires the production of ketone bodies via ketogenesis or ATP via the Krebs Cycle/ETC. Glucagon is one of the hormones released in a starved state and increases beta oxidation.

Question 45

How does insulin affect beta oxidation?

Answer 45

insulin is released in a fed state and results in glycogenesis and lipogenesis, not β-oxidatio

Question 46

How does epinephrine affect beta oxidation?

Answer 46

epinephrine is a peptide released when the body is in greater need of energy in a sympathetic “fight or flight” state. It will induce the activation of β-oxidation to provide additional ATP for the cells

Question 47

What is a reducing agent?

Answer 47

A reducing agent reduces another compound in a reaction and is itself oxidized.

Acyl-CoA would be the compound oxidized due to the loss of electrons during double bond formation, making it the reducing agent.

Question 48

What is an oxidizing agent?

Answer 48

An oxidizing agent oxidizes another compound in a reaction and is itself reduced.

FAD+ is reduced to FADH2 making FAD+ the oxidizing agent

Question 49

What is alpha decay?

Answer 49

Question 50

Beta Decay

Answer 50

In beta decay, an unstable nucleus with too many neutrons attempts to become more stable by converting a neutron to a proton and emitting an electron. The atomic mass stays the same. Thus the atomic number (number of protons) increases by one and the number of neutrons decreases by one.

Question 51

Positron Emission

Answer 51

Question 52

Electron capture (decay)

Answer 52

Question 53

Gamma Emission

Answer 53

Question 54

How to calculate half life

Answer 54

Question 56

Ionization energy periodic trend and what it is

Answer 56

Ionization energy increases up and to the right on the periodic table.

Ionization energy refers to the amount of energy needed to remove an electron from an atom

Question 57

How to can you tell the affinity of a substrate for a protein?

Answer 57

The affinity of a substrate for a protein can be assessed by comparing the Km values for each, which are inversely related to affinity.

the concentration of cation necessary to reach 1/2 Vmax­­ (otherwise known as Km) for sodium is approximately 8 mM whereas for lithium it is 1 mM. As lithium has a smaller Km, the Na+/H+ transporter has a greater affinity for lithium

Question 58

What happens to Vmax and Km for a mixed inhibitor?

Answer 58

Mixed-type inhibition is characterized by a decrease in maximal reaction rate (Vmax) and a variable change in Km, depending upon the inhibitor in question

Question 59

What does an unchanged Vmax and an increased Km indicate?

Answer 59

Competitive inhibition

Question 60

The standard reduction potentials (E°) of Cl2 and Na+ are 1.36 V and –2.71 V respectively. What is the standard free energy change in the following reaction (F = 96,485 C/mol e–, 1 V = 1 J/C)?

Cl2 + 2Na → 2NaCl

Answer 60

The solution requires the formula ΔG° = –nFE°. By summing the voltages for the oxidation of Na (2.71 V) and the reduction of Cl2 (1.36 V) we arrive at a total voltage change for the reaction of +4.07 V. Since E° is positive, the answer must be negative (eliminate choices A and B). Substitute +4.07 volts into the equation, using an approximate value of F ~ 105:

ΔG° = –(2)(105)(4) = –8 × 105 J.

-772 kJ/mol

Question 61

What does secondary and tertiary structure depend on?

Answer 61

Secondary and tertiary protein structure largely depends upon the formation of weak interactions including both hydrogen bonding and Van der Waals forces. Formation of these interactions will release energy resulting in a negative ΔH . The folding process occurs spontaneously in order to reach an energy minimum and having multiple potential final folded products would likely not result in a functional protein. Burial of polar amino acids in what is most frequently a nonpolar interior would significantly decrease the stability of the folded state

Question 62

Compare euchromatin with heterochromatin

Answer 62

Since DNA is largely negatively charged due to the many phosphate molecules in its nucleic acid backbone, the histones, which allow DNA to be tightly condensed, would contain many positively charged amino acids, such as arginine and lysine. Euchromatin is loosely condensed, relative to heterochromatin, to allow a high transcriptional activity. It has greater transcriptional activity compared to heterochromatin. Both transcription, as well as eukaryotic chromosomes, are found inside the nucleus.

Question 63

What does DNA ligase do?

Answer 63

The Okazaki fragments produced during DNA replication must be joined by DNA ligase with the formation of a phosphodiester bond

Question 64

What does topoisomerase do?

Answer 64

DNA topoisomerases create cuts at portions of the DNA helix to remove supercoils created during replication

Question 65

What creates the RNA primer for DNA replication?

Answer 65

The enzyme responsible for creating the RNA primer is RNA primase

Question 66

What does telomerase do?

Answer 66

Telomerase adds DNA to the 3’ ends of DNA strands to prevent degradation.

Question 67

What needs to happen for delta G to definitely be negative while looking at a phase diagram during the transition from globular to native state?

Answer 67

For the free energy of transformation (ΔG) to definitively be a negative quantity, the combination of pressure and temperature must be located in a section of the phase diagram where only the native state is indicated. The coordinates for choice B are on an equilibrium line, meaning that the free energy of transformation between the two phases is zero

Question 68

What type of solvent is benzene?

Answer 68

Not very polar

Question 69

What is the energy equation for photons?

Answer 69

E = hf = hc / λ, as energy decreases, wavelength increases.

(Planck’s constant h = 4.14 × 10–15 eV·s.)

Question 70

What does prolactin do?

Answer 70

Prolactin triggers milk production.

Prolactin is released by the anterior pituitary shortly after childbirth (when levels of estrogen and progesterone drop and release the inhibition on prolactin), and again each time the infant nurses. Its function is to stimulate production of breastmilk

Question 71

What does oxytocin do for milk?

Answer 71

oxytocin triggers milk ejection.

Oxytocin is the primary hormone functioning during childbirth; it stimulates the strong uterine contractions necessary to expel the baby from the uterus. It also stimulates the contraction of other reproduction smooth muscle, such as the milk ducts in the mammary glands; this facilitates milk ejection