Topic 2

Question 1

Protein Sequences

Answer 1

• determines how a protein folds
• determines how 2 proteins interact
• one codon change= mutation of the sequence

Question 2

Protein Shape

Answer 2

• shape of a protein can often tell you about its function

Question 3

Proteins are Polymers of Amino Acids

Answer 3

• depending how monomers are linked together can change the protein

Question 4

Generic Structure of an Amino Acid

Answer 4

1. carboxylate group
2. side chain
3. amino group

Question 5

Side Chain

Answer 5

• changing the side chain will change from one amino acid to another
• if the side chain is glycine, this molecule will be symmetrical (achiral)

Question 6

Amino Group

Answer 6

• all amino acids except for glycine have a chiral structure
• only L-forms of amino acids can be used to make a protein

Question 7

How Amino Acids are Linked

Answer 7

• linked via condensation reactions

Question 8

Condensation Reactions

Answer 8

• removal of a water molecule
• very specific
• requires lots of enzymes
• when the water molecule is removed, it creates a peptide bonds

Question 9

Peptide Bonds

Answer 9

• very strong
  -covalent
• bond forms between an amino group of one AA and a carboxyl group of another AA

Question 10

Residues

Answer 10

• Amino acids that are connected by peptide bonds
• START: N-terminus (amino group)
• END: C- terminus (carboxyl group)

Question 11

When Naming From a Structure

Answer 11

1. determine peptide bond
2. determine n-terminus
3. determine c-terminus
4. look at side chains and determine what is what

Question 12

A PKA Value

Answer 12

• describes an acid’s tendency to ionize

Question 13

Lower PKA

Answer 13

• higher tendency to ionize
• stronger acid (lower affinity for proton)

Question 14

Higher PH

Answer 14

• lower concentration of Hydrogen molecule

Question 15

Smaller PKA

Answer 15

• larger Ka value

Question 16

Ka Value

Answer 16

• acid dissociation constant

Question 17

Structures and Abbreviations of the 20 Amino Acids

Answer 17

• see notes

Question 18

pH= pKa

Answer 18

• 50% deprotonated
• 50% protonated

Question 19

pH= pKa +1

Answer 19

• 90% deprotonated
• 10% protonated

Question 20

pH = pKa - 1

Answer 20

• 10% deprotonated
• 90% protonated

Question 21

pH = pKa + 2

Answer 21

• 99% deprotonated
• 1% protonated

Question 22

pH = pKa - 2

Answer 22

• 1% deprotonated
• 99% protonated

Question 23

Calculating Net Charge

Answer 23

• see notes