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Biochemistry > Chpt 2 Water (and Buffers and Stuff) > Flashcards

Chpt 2 Water (and Buffers and Stuff) Flashcards

1
Q

How will our class be defining acids as bases?

A

as proton (H+) donors and proton (H+) acceptors

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2
Q

What does it mean when pH = pKa?

A

[HA] = [A-]

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3
Q

What should you expect your solution to be if the pH < pKa (acidic, neutral, or basic solution)?

A

If the pH < pKa, expect sln to have higher concentration of protonated species than acid

Expect acidic solution

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4
Q

What are the 3 ways to make a buffered system?

A
  1. HA + A- (weak thing and its conjugate)
  2. HA + NaOH (weak thing and some strong base)
  3. A- + HCl (weak thing’s conjugate and some strong acid)
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5
Q

what does pKa tell you about a molecule (other than ‘how strong the acid is’)?

A

pKa tells you the pH at which the [acid] = [c. base]

so by extension, pKa also tells you what pH you have to cross before the DEprotonated version of the molecule starts to outnumber the PROtonated version of the molecule

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6
Q

will a strong acid have a high Ka or low Ka?

A

High

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7
Q

will a strong acid have a high pKa or low pKa?

A

Low

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8
Q

Is pH a fixed value or is it based on the concentration of the solution?

A

pH is based on concentration of solution. A concentrated solution of weak acid can actually have a lower pH than a dilute solution of strong acid.

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9
Q

Is pKa a fixed value or is it based on the concentration of the solution?

A

pKa is a fixed value, that is a property of a given molecule

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10
Q

why do we care about aqueous environments in biochemistry?

A

Because aq environments impact the shape of molecules (via intermolecular interactions), and shape of molecules impacts their functions/behavior.

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11
Q

what’s the max number of hydrogen bonds a water molecule can participate in?

A

4

one for each of the two lone pairs and one for each of the two hydrogens

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12
Q

Are water molecules chiral or achiral?

A

achiral

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13
Q

what are the two specific reasons to care about water in biochemistry

A
  1. water can make hydrogen bonds

2. water is an excellent solvent

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14
Q

which electronegative atoms in a molecule (such as N or O) are the proton DONORS in a hydrogen bond?

A

The atom that is covalently bonded to a hydrogen atom

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15
Q

what does the polarity of a hydrogen bond help you to predict?

A

the likelihood that a favorable or unfavorable interaction will occur between molecules

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16
Q

How strong is a covalent bond compared to a hydrogen bond?

A

Covalent bond is 20 times stronger than a hydrogen bond

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17
Q

are hydrogen bonds considered permanent?

A

No. They are constantly being broken and reformed

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18
Q

which bonds are stronger: liner hydrogen bonds or nonliner hydrogen bonds?

A

linear

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19
Q

what does it mean to say that a hydrogen bond is linear?

A

The partial positive charge on the donor molecule is perfectly aligned with the partial negative charge on the acceptor molecule

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20
Q

what percentage of hydrogen bonds are linear?

A

Around 90%

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21
Q

what is the geometry for a water molecule (especially at low temps such as in the case of ice)?

A

tetrahedral

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22
Q

is a tetrahedral water geometry high in energy or low?

A

high

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23
Q

why is the high energy tetrahedral shape of water tolerated?

A

the high energy from the geometry is offset by the low thermal energy involved in maintaining that shape

this shape is most observable in solid ice when particles are not moving

24
Q

What is maximized when water adopts a tetrahedral geometry?

A

hydrogen bonding

25
Q

does hydrogen bonding in water molecules increase with temp or decrease?

A

decrease

more hydrogen bonding occurs as lower temps (when tetrahedral shape is maximized by the solid ice lattice)

26
Q

does entropy in water molecules increase with temp or decrease?

A

increase

liquid and vapor water have much more entropy than solid ice

27
Q

do entropy and hydrogen bonding need to offset one another in water?

A

Yes

entropy = disorder
hydrogen bonding = order

28
Q

what is caged water?

A

Water with limited ability to move around and make polar bonds with other water (because it is surrounded by non-polar molecules like oil and stuff)

29
Q

does caged water increase or decrease order?

A

caged water increases order (which decreases entropy)

30
Q

why is caged water unfavorable?

A

because it increases order/decreases disorder

31
Q

Is a single hydrogen bond strong or weak?

A

a single hydrogen bond is weak, but they add up when you have lots and lots of them.

32
Q

how are hydrogen bonds represented pictorially?

A

with dotted lines

33
Q

what are 4 common functional groups that have hydrogen bonds?

A
  1. alochol
  2. carboxylate
  3. carbonyl
  4. amine
34
Q

do hydrophobic molecules for favorable or UNfavorable interactions with water molecules?

A

unfavorable

35
Q

will a bunch of oil blobs have more or less surface area than a single oil blob of the same volume?

A

the blobs have more surface area, and this is unfavorable (because more hydrophobic surface area means more caged water)

36
Q

how does caged water ‘take one for the team’

A

by butting up against hydrophobic material so the other water molecules don’t have to

This minimizes unfavorable interactions

37
Q

on what part of cells might we see caged water existing?

A

cell membrane

38
Q

does caged water maximize or minimize hydrogen bonds with itself?

A

maximize. That’s why it’s unfavored; as hydrogen bonding goes up, entropy goes down

39
Q

are amphipathic molecules polar or non polar?

A

they are both.

They have polar regions and not polar regions

40
Q

in an ‘ideal’ amphipathic molecule, what is the ratio of polar and non polar regions?

A

50:50

But most amphipathic molecules will not have such an even split

41
Q

what is the most non-polar substance we talked about in class?

A

wax

42
Q

why do amphipathic materials take on predictable shapes when they’re dropped into water?

A

they’re trying to maximize favorable interactions: polar parts of the molecule want to be close to water molecules and non-polar parts want to be insulated from water molecules

43
Q

what is a micelle?

A

a little blob of non polar material surrounded by caged water

44
Q

what is a bilayer vesicle?

A

a blob of (aq) non polar material that got so big that it’s center filled with water

45
Q

what is a monolayer?

A

A distinct (non-blob shaped) layer between a polar substance and a non-polar substance

46
Q

are aromatic rings polar?

A

no

47
Q

why is an ionic bond ‘stronger’ in water than in organic solvent?

A

In organic solvent, the ionic bond has less polar material to bond with, so it is more likely to just stay with itself

48
Q

how does water impact protein-ligand interactions?

A

in ligand binding, the water between the enzyme and the substrate prevents the enzyme from working on the substrate. The water must be moved out of the way before the bond can happen.

49
Q

in biochem acid base chemistry, what is more important: charge or protonation?

A

protonation

50
Q

what does the term ‘proton jump’ describe?

A

the way that H+ moves from H2O to H2O in order to form the H3O+ (of H+) found in auto-ionized water

51
Q

when do you use the Hasselbalch equation?

A

For buffers only!

52
Q

how will you know if the solutions in question is a buffer?

A

By recognizing if the ingredients are consistent with one of the 3 ways to make a buffer

You will not be explicitly told that the solution is a buffer!

53
Q

what pH range do we accept as a buffer’s working range?

A

+/- the acid’s pKa value

54
Q

what is a buffer range?

A

the range of pH in which a buffer can effectively resist changes to a solution’s pH

55
Q

when you are trying to cancel the log from a buffer calculation, do you use e^ (anti LN) or 10^ (anti LOG)?

A

10^ (anti LOG)!!!!

For the love of GOD stop pushing the wrong button on your calculator!

56
Q

what is the rule for significant figures with logarithms?

A

you need one decimal place for every significant figure

Biochemistry (23 decks)

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