Chapter 3

Question 1

What makes a molecule polar?

Answer 1

Carries a charge

Hydrogen binding capabilities

Question 2

How many different ways can a peptide of three amino acids be formed? How about 100 amino acids?

Answer 2

3- 8000 ways

100- 1.3x10^130 ways

Question 3

Do all amino acids have a chiral carbon and stereoisomers?

Answer 3

All of them except glycine

Question 4

What is the basic common structure of all amino acids?

Answer 4

COO-
               |
  H3N+-C- H
               |
              R
They all have a carboxyl group, amino group (H3N+), an alpha carbon (chiral center), and a R group which is where amino acids differ

Question 5

How can you determine which amino acids weigh more than others?

Answer 5

The complexity and size of their side chains

Question 6

What is post translational modification?

Answer 6

Where certain amino acids can be covalently modified after their incorporation into a protein
Can change the properties of the residue to influence activity of the protein
Example is phosphorylation

Question 9

What are the five groups of amino acids?

Answer 9

Non-polar aliphatic
Aromatic
Polar, uncharged
Polar, positively charged
Polar, negatively charged

Question 10

What are the 5 polar, uncharged amino acids?

Answer 10

Serine, threonine, cysteine, asparagine and glutamine

Have hydrogen bond capabilities but no charge

Serine and threonine can undergo kinase-meditated phosphorylation of their hydroxyl Group

Question 11

How does cysteine help stabilize structures of proteins?

Answer 11

It can form disulfide bonds when the two sulfur hydrogen compounds on the amino acid lines up

Question 12

What are the 3 positively charged amino acids?

Answer 12

THEY HAVE THE POTENTIAL TO CARRY CHARGES, they won’t always carry them

Lysine, arginine, histidine

Lys and arg always carry a +1 net charge and physiological pH

Histidines imidazole (circle group) has pKa near physiological pH so fraction of them will have +1 charge while most will have 0

Question 13

What are the 2 negatively charged amino acids?

Answer 13

Aspartate and glutamate carry net charge of -1 at physiological pH

Both have carboxyl groups in side chains

Flavour enhancers

Question 14

What are the 7 non polar, aliphatic amino acids?

Which one is found at the turns of polypeptides?

Answer 14

Glycine, alanine, proline, valine, leucine, isoleucine, and methionine

Proline in combination with glycine turns amino acids

Question 15

What are the 3 aromatic amino acids?

What could be considered the fourth?

Answer 15

All these have circle groups on side chains
Phenylalanine, tyrosine, tryptophan
Histidine also has a circle

Question 16

What does amphoteric mean?

Answer 16

Can act as both weak acids and bases

Amino acids ionize in aqueous solution and are amphoteric

Question 17

What is a zwitterion?

Answer 17

The diplomat ion of an amino acid

When it carries a negative and positive charge in one molecule

Question 18

What are the two groups that accept and donate protons that ever amino acid has and what are their relative pKa?
(There is also a third)

Answer 18

The carboxyl group pKa~ 2.0
The amino group pKa ~ 10.0

There is also the side chains of triprotic amino acids that can donate and accept protons
pKa is in between 10 and 2

Question 19

What are the 7 triprotic amino acids?

Answer 19

Lysine, Arginine, histidine, asparangine, glutamine, cysteine, tyrosine

Question 20

What is the isoelectric point (pI) of an amino acid?

Answer 20

The pH at which the net charge on the molecule is equal to zero

You take the max pH that has zero and minimum pH that has zero and add them then divide by two

Question 21

When the pH is above the pKa is the protonated or unprotonated form dominating?

Answer 21

The unprotonated form dominates
(NH2, COO-)
More negative

Question 22

How do you draw titration curves for diprotic amino acids?

Answer 22

With the given pKa values for the carboxyl and amino group, you can draw the titration line on a graph and flatten the line out at that point,
Then with the given pH you draw a line to the graph to determine which protonated or unprotonated compounds you use

All diprotic aminos will have similar titration curves

See chapter 3 titration curve examples

Question 23

How do you find the net charge of an amino acid from a titration chart?

Answer 23

You use the titration chart to draw the amino acid then add up the charges and then the charges go down by 1/2 per section
I II III IV
+1 +1/2 0 -1/2

Question 24

How do you draw the titration curve for triprotic amino acids?

Answer 24

Same as diprotic just with an extra side chain buffering region inbetween the carboxyl and amino group buffering regions

See examples on chapter 3 titration curves

Question 25

How do you know which element gets the hydrogen when protonating the side chain of a triprotic amino acid?

Answer 25

There should be only one element that can accept a hydrogen due to not having full bonds

Question 26

How can you compare the pKa’s of side chains of triprotic acids from smallest to largest?

Answer 26

The bigger the side chain, the bigger the pKa

Question 27

What are petite bonds?

Answer 27

Are formed by condensation reactions (loss of water molecule, or dehydration synthesis)
Between the carboxyl of one amino acid and the amino group of the other
(Take the O from carboxyl group and 2 H’s from H3N)

Question 28

Do the amino acid flash cards

Answer 28

IN BACKPACK

Question 29

When connecting amino acids by a peptide bond what double bond shows resonance?

Answer 29

The oxygen double bonded to the carbon has resonance with the nitrogen now bonded to the same carbon

Question 30

What are the three advantages of creating biomolecules as polymers of smaller, simpler building blocks?

Answer 30

1. Simplicity of chemistry- one reaction for polymerization, one for degradation
2. Recycling- biomolecules can be digested back into component building blocks (reusable)
3. Diversity- cast number of molecules of varying lengths and sequences

Question 31

What compose peptide chains? How do you write out peptide chains?

Answer 31

Amino acid residues

You use the one letter code of amino acids in a sequence
Ex: Tyr-Gly-Gly-Phe-Leu
YGGFL

Question 32

What are host defence peptides and retro-inverso peptides?

Answer 32

Host defence- used to help kill off germs and protect against future bacteria
Retro inverso- isomers in which the sequence in reversed and D-amino acids are employed