Chemical and Physical Foundations of Biological Systems Flashcards
1
Q
How does the primary structure of a protein form?
A
The amino-terminus of one amino acid attacks the carboxy-terminus of another.
2
Q
Why might polarized light be used to determine whether a sample is composed entirely of Glycine?
A
Because glycine is not optically active (no chirality).
3
Q
How would you go about making a nitrile group more reactive?
A
Attach an electron withdrawing group to the carbon of the nitrile group (becomes -C=N+).
4
Q
What type of lens would be appropriate for correcting hyperopia (farsightedness)?
A
Convex. Light is being focused behind the retina, need it to converge more quickly.
5
Q
Which type of lens will make light converge? Which will make light diverge?
A
Convex lenses converge light while concave lenses diverge light.
6
Q
For a converging lens, at what distance from the lens will the image be real?
A
At any distance outside the focal length.
7
Q
Will real images formed by a converging lens be inverted or right-way-up?
A
Inverted.
8
Q
What is the simplest way to differentiate α-D-glucose and β-D-glucose?
A
Recognize that the OH on the anomeric carbon (hemiacetal carbon) will have opposite conformations.
9
Q
How would we determine the mass percent composition of an element in the product of a reaction?
A
Starting moles are irrelevant. Figure out the reaction and then divide the atomic mass of the desired element by the total mass of product.
10
Q
When an acyl halide reacts with a primary alcohol, what functional group is formed?
A
An ester. Try to draw it out if you’re confused!
11
Q
What is an acyl halide?
A
Basically a carboxylic acid but replace the OH with a halogen (ex. Cl-).
12
Q
How many neutrons and protons are in ¹⁴C? What about ³⁴P?
A
¹⁴C: 8 neutrons, 6 protons
³⁴P: 19 neutrons, 15 protons
13
Q
How many reactant molecules are involved if a reaction follows second order kinetics?
A
- # of reactant molecules is = order the reaction follows.
14
Q
How many reactant molecules are involved if a reaction follows third order kinetics?
A
- # of reactant molecules is = order the reaction follows.
15
Q
if ΔG > 0, the reaction is _______.
A
Nonspontaneous.
16
Q
If the potential energy of the products is greater than the potential energy of the reactants, we say that the reaction is ________.
A
Endothermic.
17
Q
If a reaction proceeds spontaneously to the right, Kᴇǫ must be ______.
A
Greater than 1.
18
Q
What is meant by an element’s “oxidation number”?
A
Oxidation numbers must be balanced in a neutral molecule (ex: O = -2, H = +1, Cl = -1, N = -3, etc.)
19
Q
For use in titration, a triprotic acid with multiple acidic protons can _________.
A
Act as a buffer over several pH ranges.
20
Q
If a lever with varied weights on each side is in static equilibrium, what must be true?
A
The torque on either side is equal, therefore the weights can not be positioned at equal distances from the fulcrum.
21
Q
Which amino acids have hydrophobic side chains? Which ones are amphipathic? Which have hydrophilic side chains?
A
HPhobic: Gly, Ala, Val, Leu, Ile, Pro, Phe (GAVLIPF)
APathic: Met, Trp, Tyr, Lys (MWYK)
HPhilic: Ser, Thr, Cys, Asn, Gln, His, Arg, Asp, Glue (STCNQHRDE)
22
Q
Are charged molecules more, or less soluble in water than neutral molecules?
A
Charged molecules are more soluble in water than neutral molecules.
23
Q
What factors contribute to a molecule having a high melting point?
A
Larger size (increased dispersion forces) and capability for dipole-dipole interactions.
24
Q
In thin-layer chromatography, is a molecule more or less likely to have a high Rғ (greater relative movement) if it is more polar?
A
More polar molecules tend to be stationary, having a relatively lower Rғ than molecules which are less polar.
25
How is the equivalence point of a titration determined?
Depends on the relative pH of the acid and the base (ex: stomach acid and NaOH have equivalence ~pH 7)
26
Which nucleotides are purines? Which are pyrimidines?
Purines: AG
Pyrimidines: C(U)T
(U replaces T in RNA)
27
The loss of which bonds is most likely to cause loss of quaternary/tertiary/secondary structure?
Hydrogen bond disruption will cause higher structures to be lost.
28
True or False: enantiomers (L/D-etc) will rotate polarized light in opposite directions and also have different physical properties?
False. Enantiomers have the same physical properties with the exception of polarized light rotation.
29
What must we know ahead of time to use bomb calorimetry to determine bond energies?
A lot (it's inefficient). Reactant mass, reactant heat of formation, temperature of products and reactants, mass of calorimeter, specific heat of calorimeter, mass and specific heat of water in calorimeter, heat of formation of products, etc...
30
How would we calculate the solubility product constant Kₛₚ of a molecule? (think dissolution)
Figure out how many moles of each product are produced per mole of reactant. Describe this as Kₛₚ=(p₁x)ᵖ¹(p₂x)ᵖ² where pₙ is the number of moles of product produced per mole of reactant
31
In Sanger sequencing, lack of dideoxynucleotides would cause what erroneous result on gel electrophoresis?
A single dark band, because without dideoxynucleotides the entire template is replicated and all copies are the same length.
32
If we maintain the volume of air in a container at 3.8L as we increase the pressure from 1 atm to 2 atm, how many moles of air would we need to add to maintain the volume of air in the container?
When pressure doubles, the volume of air in the container will shrink to 1.9L. We must add back the 1.9L of air, but at double the pressure this means we add back double the moles of air, 3.8/22.4.
33
If we have a circuit containing 3 resistors in series and we know the current through the last resistor, how can we determine the current through the first resistor?
In series, the current through each resistor is the same.
34
What is the equation for Ohm's Law?
I = V/(R₁ + R₂)
35
If the applied current is positive into a cell, what is the charge of the cell?
Negative.
36
If a cell has a negative resting potential but is constantly letting positive ions leak in, what must also be occurring?
Positive ions must be getting pumped out.
37
What must we know during a titration if we wanted to assess the concentration of an acid that we would not need if we just wanted to assess the number of moles of acid?
Initial volume of solution is only necessary if we want to get a concentration. Otherwise we can use our titrating base to determine the number of moles of acid.
38
What kind of bonding makes a molecule less soluble in water? What other effect does this have?
Increased intRAmolecular hydrogen bonding makes a molecule less soluble, and also lowers the melting point.
39
What is being lost when proteins lose their secondary, tertiary, or quaternary structure?
Hydrogen bonding.
40
If carbon dioxide is being produced in excess, the pH of blood is _____.
Decreasing. (becoming more acidic)
41
What is required for two molecules to form a hydrogen bond?
1. A hydrogen bond donor ex: N-H or O-H
2. A hydrogen bond acceptor
ex: =O: or N:
(w/ free electrons)
42
What would the pH be of a pool of 0.01M HCL(aq)? How do you determine this?
For strong acids, pH is the exponent of the concentration. So 0.01M = 10^-2M = pH of 2.
43
An element which can act as an electron acceptor should have ______.
High electron affinity.
44
How is the polarity of a molecule associated with its boiling point?
More polar molecules have higher boiling points than less polar molecules.
45
Why might it be necessary to break the surface tension of a liquid during heating?
To prevent superheating of the liquid and allow boiling to occur.
46
What must be true of two identical molecules, on in the (+) configuration and the other in the (-) configuration?
They differ in orientation around a chirality centre. (At least one carbon must be chiral and a stereocentre).
47
The boiling point of a liquid is the temperature at which the vapour pressure equals _____.
The surface pressure.
48
What is Avogadro's number?
6.02*10^23 ions/mol.
49
How would you calculate the number of ions in a sample, given the mass?
Determine the number of moles (mass/molar mass), then multiply by Avogadro's number (6.02*10^23 ions/mol).
50
When exposed to a base, what does red litmus paper do?
Turns blue.
51
When exposed to an acid, what does red litmus paper do?
Stays red.
52
How can electrons in partially filled d orbitals cause a solution to be coloured?
The electrons in lower energy orbitals absorb visible light to move to the higher energy orbitals.
53
Between (CH₃CH₂)₂NH and (CH₃CH₂)₂CH₂, which is more soluble in water? Why?
(CH₃CH₂)₂NH, because it can form H-bonds with water (because of N-H), while (CH₃CH₂)₂CH₂ cannot.
54
Which is more polar, =O or -OH?
-OH
55
What is the Henderson-Hasselbach equation?
pH = pKa + log([conj. base]/[conj. acid])
56
More hydrogen bonding ______ the boiling point of a liquid.
Increases.
57
What trend does atomic radius exhibit moving from left to right across the periodic table? Why?
Atomic radius decreases from left to right. On the right, charges are higher and so draw in peripheral electrons.
58
What is described by first ionization energy?
The energy required to remove an electron from the outer shell of an atom.
59
On the periodic table, which elements have the highest first ionization energies?
The noble gasses, because removal of an electron disrupts a complete shell/subshell.
60
On the periodic table, which elements have the lowest first ionization energies?
Elements which would be left with a complete shell/subshell upon removal of an electron (ex: K+, Na+).
61
Radioactive isotopes of an element exhibit the same chemical behaviour as the stable isotope because _______.
They share an atomic number (electron interactions + bond formation).
62
How is the magnitude of an electric field calculated?
In volts per meter. This is the same units as newtons per coulomb, the standard for electric fields.
63
How do you calculate the frequency of a light wave?
By dividing the speed of light by the wavelength.
64
What wave phase difference corresponds with destructive interference?
A phase difference of 180 degrees would be half of a wave and therefore destructive interference.
65
What equation relates the period and the frequency of a tone?
T = 1/f
66
If the first harmonic of a tone has a frequency of 100 Hz, then the second harmonic has a frequency of ___ Hz.
200 Hz.
67
What force balances the weight of a floating object? What force is more or less irrelevant in this calculation?
The buoyant force provided by the displacement of water balances. Both are proportional to gravity, making it irrelevant.
68
If a beam of light in air shines into a medium with index of refraction >1.0, how are the angle of entry and the angle of incidence (inside the medium) related?
The angle of entry will be greater than the angle of incidence.
69
What equation gives the relationship between voltage, current, resistance, length between electrodes, and the strength of an electric field?
E = ( V - IR ) / L
70
What kinds of particles will be deflected by a magnetic field? How does this affect photons?
Any that are charged. Photons are uncharged, and so are not deflected.
71
Why do animals faint when blood flow to the brain is insufficient?
When an animal is on the ground, blood pressure through the brain can be increased because there is no difference in height between head and heart.
72
Which is positive in electricity, the cathode or the anode?
The anode, it's actually switched for the purpose of electricity (dumb).
73
The more stable the conjugate base, the _____ the _____.
Stronger the acid.
74
A molecule which has more/stronger electronegative groups will have _____ ______.
Increased acidity.
75
Define mutarotation.
The formation of a cyclic molecule from a straight-chain into either of 2 (or more) anomers.
76
What is the calculation for determining the electrostatic force between two ions?
Coulomb's law:
F = ( k (q1) (q2) ) / r^2
where q = (1.6*10^-19C * ion charge)
(+1,+2,-1, etc.)
77
Sound intensity and area are _____.
Inversely proportional.
78
Sound travels fastest in ______. What implication does this have for human hearing?
A solid. The sound actually travels fastest through the ossicles of the ear, rather than the liquid or air mediums.
79
In a pipe with a closed end, what harmonics are possible?
Only odd harmonics.
80
In an oxidation reaction, how are the electrons moving?
They are taken from whatever molecule is being oxidized.
81
What formula will give you the ΔH of a reaction?
H = Hf(products) - Hf(reactants)
| *remember to multiply values by the number of moles of product or reactant involved!
82
How do you calculate efficiency in physics?
Efficiency = (load*load distance)/(effort*effort distance)
83
What is the purpose of salt bridges? In what types of electrochemical cells are they found?
Important for preventing charge buildup in galvanic cells.
84
In electrolytic cells, what replaces the need for a salt bridge?
The battery maintains current flow instead.
85
What is the equation for specific rotation of a molecule?
Specific rotation = observed rotation / concentration*length of tube
86
What is the difference between a pyranose and a furanose?
```
Pyranose = 6 member ring
Furanose = 5 member ring
```
87
Between the linear and ring forms of glucose, which is able to undergo oxidation?
Only the linear form.
88
What is the Kw (of water) at 25 C and 1 atm?
10^-14.
89
What factor has the greatest effect on the solubility of a solute in the bloodstream?
Only temperature can affect the solubility of something in the bloodstream.
90
During a change in phase, the temperature _____.
Remains constant.
91
Why are anhydrides not soluble in water?
Because of their high reactivity, they reform into carboxylic acids upon contact with water.
92
Which protease preferentially cleaves peptide bonds next to aromatic amino acids?
Chymoptrypsin.
93
If blood pH were to increase, how would breathing rate change? Why?
Exhalation would slow down to keep more CO2 in the body, making the blood more acidic (by forming HCO3-).
94
What does osmotic pressure depend on? What does not affect this?
Depends on the number of particles present, but not their identity.
95
During titration, what is "happening" to a compound at each equivalence point?
At each equivalence point, a proton is getting stripped off.
96
What factor increases the acidity of alpha hydrogens?
Their proximity to electron withdrawing groups.
97
What do oxidoreductases do? What naming convention is often used for these enzymes?
Catalyze oxydation-reduction reactions (transfer of electrons). Often have oxidase, dehydrogenase, or reductase in their names.
98
What do transferases do? What other kind of enzyme is also a member of this category?
Catalyze the movement of functional groups between molecules. Kinases are also part of this group (phosphorylation).
99
What do hydrolases do? What are some common examples of enzymes which fall under this category?
Catalyze the breakdown of a molecule into two parts by adding water. Phosphatases, peptidases, nucleases, and lipases are all common examples of this function.
100
What do lyases do? What other function do they have and what would their naming convention be in that case?
Catalyze the cleavage of a molecule into two products. When acting in reverse to put molecules together they are called synthases.
101
What do isomerases do? What other categories can these enzymes fall under?
Catalyze the rearrangement of bonds within a molecule. Can also be oxidoreductases, transferases, or lyases depending on the mechanism.
102
What do ligases do? What common reaction are they prominently involved in.
Catalyze addition or synthesis reactions, often requiring ATP. Heavily involved in nucleic acid synthesis and repair.
103
Describe competitive inhibition of an enzyme. How can this be overcome?
enzyme substrates from binding. Overcome by adding more substrate so that substrate concentration is higher than inhibitor concentration.
104
Describe non-competitive inhibition of an enzyme.
The inhibitor binds to an allosteric site to change enzyme conformation and make substrate unable to bind.
105
Describe mixed inhibition of an enzyme. Where do they bind?
The inhibitor can bind to the enzyme either before it has bound substrate or after, but has different affinity for each. These bind at the allosteric site.
106
Describe uncompetitive inhibition of an enzyme.
The inhibitor binds to the enzyme at the allosteric site only once the substrate has bound, thereby locking the substrate in place.
107
What impact do competitive inhibitors have on enzyme Km? What about Vmax?
Km increased
| Vmax unchanged
108
What impact do non-competitive inhibitors have on enzyme Km? What about Vmax?
Km unchanged
| Vmax decreased
109
What impact do mixed inhibitors have on enzyme Km? What about Vmax?
Km increases OR decreases
| Vmax decreases
110
What impact do uncompetitive inhibitors have on enzyme Km? What about Vmax?
Km decreases
| Vmax decreases
111
What equation describes Snell's law of refraction?
nₐsinθₐ = nᵢsinθᵢ
| where n are the indexes of refraction and θ is the angle of refraction
112
Why does visible light travel more slowly through an optically dense medium than through a vacuum?
Light is absorbed and re-emitted by the atomic structure of the optically dense medium.
113
What equation describes the pressure at the bottom of a liquid-filled container?
Pressure = density*g*height
114
Between what elements is an ionic bond most likely to form?
Between elements at the extreme right an left of the periodic table, with varying strength depending on vertical and horizontal separation (corresponding to electronegativity).
115
Adding resistors in parallel acts to _____ the overall resistance of the circuit.
Decrease.
116
Where on the periodic table do the best electricity-conducting elements appear?
Closest to the lower left of the metallic elements.
117
How do you calculate blood pressure (BP) from cardiac output (CO) and peripheral resistance (PR)?
BP = CO * PR
118
Most of the protons in biological tissue are found in _____.
Water.
119
log₁₀(1000) = _____ since ____ = 1000.
Log₁₀(1000) = 3 since 10³ = 1000.
120
Intensity = _____ * _____.
Power * Area
121
An electron donor can also be called a _______.
Lewis base.
122
An electron acceptor can also be called a _______.
Lewis acid.
123
When does a colloidal mixture form?
When one substance in insoluble in the other these can separate into layers (ex: oil and vinegar).
124
What acronym can be used to memorize the order of the visible light spectrum, from low to high frequency?
ROYGBIV
| Red, orange, yellow, green, blue, indigo, violet.
125
What alternate units can be used to describe a Watt?
1J/s because a watt is a unit of power which is energy/time.
126
In a gas-liquid chromatograph, what sort of compounds will produce the first peak in a trace?
Ones with the lowest molecular weight and weakest intermolecular forces.
127
Le Chatelier's principle indicates that adding a _____ acid to a _____ acid will _______ the ionization of the _____ acid.
Adding a STRONG acid to a WEAK acid will DECREASE the ionization of the WEAK acid.
128
How would you calculate the index of refraction in a medium given the speed of light both in a vacuum and in the medium.
Ir = V of light in vacuum / V of light in medium
129
The energy of electromagnetic radiation is directly proportional to ______.
The number of photons emitted.
130
The intensity of electromagnetic radiation is defined as ______.
The energy (# of photons) emitted per unit time.
131
Structures composed largely of carbon and hydrogen are often ______ in nature.
Hydrophobic.
132
What is α decay?
a pair of protons and a pair of neutrons (4 particles) leaves the original nucleus.
133
What is β1 decay?
One of the nucleus' neutrons changes into a proton, increasing the atomic number of the element and releasing an electron.
134
What is β2 decay?
One of the nucleus' protons changes into a neutron, decreasing the atomic number of the element and releasing a positron.
135
What is gamma decay?
The nucleus emits radiation (photon) but otherwise keeps the same number of protons and neutrons.
136
Branching occurs through what kind of bond in glycogen?
α-1,6-glycosidic bonds.
137
The amount of dissociation of an acid in water is inversely proportional to _______.
The charge of the acid. The more negative the charge the less dissociation occurs.
138
What is the thin lens equation?
1/object distance + 1/image distance = 1/focal length
139
Describe the "common ion effect".
In an equilibrium formula, adding ions to the right side will cause a shift to the left, as more of that is made to use up the excess ions.
140
Any ray going from a lower refractive index to a higher one should bend _______ the normal.
Towards.
