Lecture 3

Question 1

What are hydrogen bonds?

Answer 1

Electrostatic attractions between a H-bond donor and an acceptor.

Question 2

What is a donor?

Answer 2

Highly polar -OH or -NH groups are good H-bond donors (a H-atom that is covalently bonded to another EN atom)

Question 3

What is an acceptor?

Answer 3

An electronegative atom with available lone pairs of electrons, such as O or N

Question 4

How strong is the hydrogen bond to a covalent bond?

Answer 4

About 5-10% strong, enough to make molecule R1 stick to R2 but not form a permanent link

Question 5

What are H-bonds?

Answer 5

Directional - stronger if donor and acceptor line up with one another.

Question 6

What are the amino acids with positive side chains?

Answer 6

His, Lys, Arg

Question 7

What are the characteristics of positively charged side chains? d

Answer 7

• The side chains contain weak bases that gain H+ (become protonated) and so are positively charged in aqueous solution at neutral pH
• The charge makes them very polar, overriding the non-polar hydrocarbon side chain.

Question 8

What amino acids have negatively charged side chains?

Answer 8

Asp and Glu

Question 9

What are the characteristics of the negatively charged side chains?

Answer 9

They have carboxylic acid groups R-COOH that lose H+ (become protonated) at neutral pH

Question 10

What is COOH deprotonated?

Answer 10

Described as carboxylate groups R-COO-

Question 11

What are carboxylate groups?

Answer 11

Negative and very polar

Question 12

What is the Asp side chain?

Answer 12

-CH2-COO-

Question 13

What is the Glu side chain?

Answer 13

-CH2-CH2-COO-

Question 14

What can amino acids act as?

Answer 14

Acids and Bases

Question 15

What does an acid do?

Answer 15

Donote a proton

Question 16

What does a base do?

Answer 16

Gain a proton

Question 17

What will the acids and bases do?

Answer 17

Gain (protonate) or lose (deprotonate) H+ depending on availability of H+ in solution.

Question 18

What do natural biochemical occur close to?

Answer 18

pH 7

Question 19

What is the equation for how pH express availability of H+:

Answer 19

pH = -log10[H+]

at pH = 7, [H+] = 10-7 M

Question 20

What does the Henderson-Hasselbalch equation relate?

Answer 20

pH, pKa and the state of ionization of a given group.

Question 21

What is the Henderson-Hasselbalch equation?

Answer 21

pH = pKa + log[deprotonated]/[protonated]

Question 22

What do the vast majority of molecules for the a-carboxylate group at pH 7 exist as?

Answer 22

As carboxylate -COO NOT as carboxylic acid - COOH (in deprotonated form)

Question 23

What do the vast majority of molecules for the a-amino group at pH 7 exist as?

Answer 23

As protonated RNH3+ rather than as RNH2

Question 24

What is the correct structure to represent an individual amino acid at neutral pH?

Answer 24

A dipolar ion (zwitterion)

Question 25

What happens when the amino acid is part of a peptide chain?

Answer 25

The a-amino groups and the a-carboxylate groups are linked as uncharged amide (except for the ones at the N and C termini, which are also NH3+ and COO- at pH 7)

Question 26

Which amino acids have ionizable side chains?

Answer 26

There are SEVEN amino acids with side chains that have acid/base properties.

Question 27

What are the amino acids that have acid/base properties for side chains?

Answer 27

Aspartate, Glutamate, Tyrosine, Cysteine, Arginine, Histidine, Lysine

Question 28

What are the side chains of Arg, His and Lys?

Answer 28

Neutral when deprotanted and positive when protonated

Question 29

What does the value of pKa tell you?

Answer 29

Where in the pH scale a group undergoes deprotonation

Question 30

What can a molecule have?

Answer 30

Several ionizable groups, that has its own Pka value dependent on its chemical context.

Question 31

When an amino acid is part of a peptide chain, what will happen?

Answer 31

It will have a slightly different pKa

Question 32

What happens if the pH is one unit or more below the pKa:

Answer 32

The group is fully protonated

Question 33

What happens if the pH is one unit or more higher than pKa?

Answer 33

The group is fully deprotanated

Question 34

What happens if the pH is equal to pKa?

Answer 34

The group is 50% deprotonated and 50% protonated

Question 35

What happens if the pH is less then one unit away from pKa?

Answer 35

Use the Henderson-Hasselbalch equation

Question 36

What can amino acid analysis determine?

Answer 36

Help to determine protein structure

Question 37

What does analysis of amino acids involve?

Answer 37

1.) Separation of a mixture into components 2.) Detection of the components of interest - Can be qualitative (tells you what's present) - Can be quantitivate (tells you how much is present) - Can be preparative (separated components can be recovered for further experiments)

Question 38

Particles of a solid are chosen with a specific property (eg, silica gel)

Answer 38

Known as the stationary phase - polar.

Question 39

Liquid solvent or buffer flows past the particles and is non-polar

Answer 39

Mobile phase

Question 40

Amino acids exchange (partition) between phases

Answer 40

- Polar amino acids P spend more of their time hydrogen bonded to silica and move slowly - Non-polar amino acids N spend more time in solvent, and move almost as fast as solvent

Question 41

What is the highest point reached by solvent?

Answer 41

Solvent Front

Question 42

What do very polar amino acids have?

Answer 42

Low Rf

Question 43

What do non-polar amino acids have?

Answer 43

High Rf - Run with the gel

Question 44

How can amino acids be detected?

Answer 44

Adding ninhydrin which reacts with secondary and primary amines. Alternate is adding fluroscamine, giving yellow fluroscence under UV light.

Question 45

What does Ion exchange chromatography do?

Answer 45

Separates on the basis of charge - Uses charged resins as stationary phase

Question 46

What do cation exchange resins contain?

Answer 46

Negative groups, which bind positive molecules (cations) - Cation Exchange

Question 47

What do anion exchange resins contain?

Answer 47

Negative molecules, which bind negative molecules (anions) - Anion Exchange

Question 48

What is Elution by?

Answer 48

- Competition with a high ion concentration (usually NaCl), which displaces the amino acid from the resin - Changing the pH to alter the charge on the amino acid, so it no longer binds to the resin.