Chpt 2 Water (and Buffers and Stuff)

Question 1

How will our class be defining acids as bases?

Answer 1

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

Question 2

What does it mean when pH = pKa?

Answer 2

[HA] = [A-]

Question 3

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

Answer 3

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

Expect acidic solution

Question 4

What are the 3 ways to make a buffered system?

Answer 4

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)

Question 5

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

Answer 5

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

Question 6

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

Answer 6

High

Question 7

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

Answer 7

Low

Question 8

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

Answer 8

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.

Question 9

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

Answer 9

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

Question 10

why do we care about aqueous environments in biochemistry?

Answer 10

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

Question 11

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

Answer 11

4

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

Question 12

Are water molecules chiral or achiral?

Answer 12

achiral

Question 13

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

Answer 13

1. water can make hydrogen bonds

2. water is an excellent solvent

Question 14

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

Answer 14

The atom that is covalently bonded to a hydrogen atom

Question 15

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

Answer 15

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

Question 16

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

Answer 16

Covalent bond is 20 times stronger than a hydrogen bond

Question 17

are hydrogen bonds considered permanent?

Answer 17

No. They are constantly being broken and reformed

Question 18

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

Answer 18

linear

Question 19

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

Answer 19

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

Question 20

what percentage of hydrogen bonds are linear?

Answer 20

Around 90%

Question 21

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

Answer 21

tetrahedral

Question 22

is a tetrahedral water geometry high in energy or low?

Answer 22

high

Question 23

why is the high energy tetrahedral shape of water tolerated?

Answer 23

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

Question 24

What is maximized when water adopts a tetrahedral geometry?

Answer 24

hydrogen bonding

Question 25

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

Answer 25

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

Question 26

does entropy in water molecules increase with temp or decrease?

Answer 26

increase liquid and vapor water have much more entropy than solid ice

Question 27

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

Answer 27

Yes entropy = disorder hydrogen bonding = order

Question 28

what is caged water?

Answer 28

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)

Question 29

does caged water increase or decrease order?

Answer 29

caged water increases order (which decreases entropy)

Question 30

why is caged water unfavorable?

Answer 30

because it increases order/decreases disorder

Question 31

Is a single hydrogen bond strong or weak?

Answer 31

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

Question 32

how are hydrogen bonds represented pictorially?

Answer 32

with dotted lines

Question 33

what are 4 common functional groups that have hydrogen bonds?

Answer 33

1. alochol 2. carboxylate 3. carbonyl 4. amine

Question 34

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

Answer 34

unfavorable

Question 35

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

Answer 35

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

Question 36

how does caged water 'take one for the team'

Answer 36

by butting up against hydrophobic material so the other water molecules don't have to This minimizes unfavorable interactions

Question 37

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

Answer 37

cell membrane

Question 38

does caged water maximize or minimize hydrogen bonds with itself?

Answer 38

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

Question 39

are amphipathic molecules polar or non polar?

Answer 39

they are both. They have polar regions and not polar regions

Question 40

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

Answer 40

50:50 But most amphipathic molecules will not have such an even split

Question 41

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

Answer 41

wax

Question 42

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

Answer 42

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

Question 43

what is a micelle?

Answer 43

a little blob of non polar material surrounded by caged water

Question 44

what is a bilayer vesicle?

Answer 44

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

Question 45

what is a monolayer?

Answer 45

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

Question 46

are aromatic rings polar?

Answer 46

no

Question 47

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

Answer 47

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

Question 48

how does water impact protein-ligand interactions?

Answer 48

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.

Question 49

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

Answer 49

protonation

Question 50

what does the term 'proton jump' describe?

Answer 50

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

Question 51

when do you use the Hasselbalch equation?

Answer 51

For buffers only!

Question 52

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

Answer 52

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!

Question 53

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

Answer 53

+/- the acid's pKa value

Question 54

what is a buffer range?

Answer 54

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

Question 55

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

Answer 55

10^ (anti LOG)!!!! For the love of GOD stop pushing the wrong button on your calculator!

Question 56

what is the rule for significant figures with logarithms?

Answer 56

you need one decimal place for every significant figure