Biochem Protein Lecture 2

Question 1

What is the Hendersson Hasselbach equation?

Answer 1

pH=pKa + log[A-]/[HA]

Question 2

When the pH of an amino acid is less than the known pKa, which form predominates?

When the pH form of an amino acid is equal to the pKa, what can be said about the amino acid solution?

When the pH of an amino acid is more than the known pKa, which form predominates?

Answer 2

Acid form

Acid and base forms are in equal concentration

Base form

Question 3

The ratio of acid and basic forms of amino acid will be a factor of ____ for each pH unit away from the pKa value

Answer 3

10 (inverse log of 1 is 10)

Question 4

The pH of the α-carboxyl group is

the pH of the α amino group is

Answer 4

about 2

about 9.5

Question 5

Between different amino acids, which varies more in pH, the α carboxyl group or the α amino group?

Answer 5

the amino group (8.8 to 11.0)

note: carboxylic acid group (1.8-2.4)

Question 6

Why are the pKas of the carboxylic groups and amino groups in amino acids lower than the same groups on their own?

Answer 6

Intramolecular forces.

The carboxylic acid group experiences repulsion from the positively charged amino group, lowering the pKa

The amino group H bond is pulled away by the electronegative, depronated carboxyl group, which stabilizes the zwitterion form. Ask why

Question 7

How much more acidic is the carboxyl group of glycine than the carboxyl group of acetic acid?

Answer 7

100X more (2.38pH vs 4.8 pH)

Question 8

If a carboxylic group is further away from the amino group, like β-COOH in aspartate or γ-COOH in glutamate, what happens to the pH?

Answer 8

It increases

Lysine is a good example, the pH of the ε amino group is almost the same as the aliphatic amine

Question 9

The characteristic pH at which the net charge on a molecule is zero is called the

Answer 9

Isoelectric Point (pI)

Question 10

Which form of amino acids predominates, L or D?

Does the other form exist?

Answer 10

L (sugars are D)

Yes but rarely

Question 11

With no ionizable side chains, how is the pI calculated

Answer 11

pI=0.5(pK1 + pK2)

Question 12

When the AA is in its fully ionized form with no net charge, what is this point called

Answer 12

isoelectric point

Question 13

For the negatively charged AAs, how do you calculate the pI?

Generally, pIs for negatively charged AAs will be higher/lower than positively charged AAs

Answer 13

pI=0.5[pKa(Rgroup)+pKa(COOH)]

Lower

Question 14

For positively charged AAs, how do you calculate the pI?

Generally, pIs for positively charged AAs will be higher/lower than positively charged AAs

Answer 14

pI=0.5[pKa(Rgroup)+pKa(NH3)]

Higher

Question 15

For polar uncharged, aromatic, and nonpolar aliphatic groups, how do you calculate pI?

Answer 15

pI=0.5[pKa(COOH)+pKa(NH3)]

Question 16

This method can be used to experimentally determine the pI of AAs

Answer 16

Paper electrophoresis

Question 17

In paper electrophoresis, a piece of filter paper is wetted with buffer solution of known pH and stretched between the two electrode vessels in order to…

Answer 17

Control the pH

Question 18

After wetting the filter paper and stretching it between the two electrode vessels, a drop of amino acid is placed on the paper and the electric current is turned on

If the amino acid is an anion, it will migrate towards the

If its a cation, it migrates towards the

Answer 18

Anode

Cathode

Question 19

Where do AAs come to rest during paper electrophoresis?

Answer 19

At a pH corresponding to the molecules pI (it will have no charge and won’t move)

Question 20

What is glycines charge at any pH above its pI??? Positive or negative?

In this case, it would move towards the cathode or anode in paper electrophoresis?

Answer 20

Negative

Anode

Question 21

Does glycine have a net positive or negative charge at any pH below its pI?

In this case, it would move towards the cathode or anode in paper electrophoresis

Answer 21

Positive

Cathode

Question 22

The further away the pH of an AA is from its pI, the greater/lesser the net electric charge of the AA?

Answer 22

Greater

Question 23

If pH>pI, the molecule is negatively or positively charged?

If pH<pI, the molecule is negatively or positively charged?

Answer 23

Negatively

Positively

Question 24

For all common amino acids except _____ the alpha carbon is bonded to four different groups

The alpha carbon is a ___ center

Answer 24

Glycine

Chiral

Question 25

What are the two common steriochemical configurations of amino acids around the alpha carbon center?

Answer 25

D and L

Question 26

The amino acids found in proteins have an alpha carbon configuration corresponding to ____-glyceraldehyde

Answer 26

L-glyceraldehyde

Question 27

The L configuration of most amino acids corresponds to the R or S configuration in organic chemistry?

Answer 27

S configuration

Question 28

Less common amino acids occur as…

Answer 28

1. constituents of proteins (modiciation of common 2. AA residues following protein synthesis)
2. Free metabolites
3. Hydroxyproline (found in plant cell wall proteins and collagen
4. Hydroxylysine (found in collagen)
5. Methyllysine (constituent of myosin)
6. γ-carboxyglutamate (found in blood clotting proteins prothrombin, and proteins that bind calcium ions)

Question 29

Hydrogen bonds involve two covalently bonded _____ atoms

One of the atoms is covalently bonded to

The other atom interactions with that molecule in this manner

Answer 29

electronegative

Hydrogen

electrostatically

Question 30

In H-bond formation in water, there is a ______ arrangement of the outer shell electron pairs around the oxygen atom, with H atoms at two corners and unshared electron pairs at the other two corners.

What intramolecular force allows for H-bonding?

Answer 30

Tetrahedral

Dipole

Question 31

Each molecule of H2O may be H-bonded to a maximum of ____ other H2O molecules

Answer 31

4

Question 32

Note that AA side chains contain functional groups that can participate in H-bonding.

Can H atoms that are covalently bonded to C atoms participate in H-bonding?

Answer 32

No. C is only slightly more electronegative than H