AA, Peptides, Proteins

Question 1

Amphoteric Species

Answer 1

Functional group that can act as e- donor or e- acceptor

Question 2

Under these conditions, ionizable group will become protonated.

Answer 2

Acidic Conditions (low pH)

Question 3

Under these conditions, ionizable group will become deprotonated.

Answer 3

Basic (High pH)

Question 4

pKa

Answer 4

pH at which half of the molecules of a species ar deprotonated ([protonated species] = [Deprotonated])

OR

[HA] = [H+]

Question 5

pH < pKa

Answer 5

Majority of species will be protonated

Question 6

pH > pKa

Answer 6

Majority of species will be deprotonated

Question 7

Each _______ proton will have its own pKa.

Answer 7

ionizable proton (important for polyprotic species)

Question 8

pKa for cabroxylic group

Answer 8

~2

Question 9

pKa for amino group

Answer 9

~9-10

Question 10

Molecule with a positive and negative charge, but is electrically neutral.

Answer 10

Zwitterion

Question 11

AA with non-ionizable side chains will be _______ charged under acidic conditions and _______ charged under basic conditions. Also under normal physiological conditions, these types of AA will exist as _________.

Answer 11

1. Positively
2. Negatively
3. Zwitter Ions

Question 12

What is the isoelectric point?

Answer 12

Point at which AA is electrically neutral

Question 13

When pH is close to pKa, solution will act as a _______.

Answer 13

Buffer

Question 14

The titration curve is nearly ______ flat at pKa values and _______ flat at pI value of an AA.

Answer 14

1. horizontally
2. Vertically

Question 15

How do you calculate pI point of an AA with no ionizable R-group/side chain.

Answer 15

Average the pKa values of the values of the amino and carboxyl group.

(pI = (pKa₁ + pKa₂)/2)

Question 16

How do you find the pI point for acidic AA?

Answer 16

Average pKA values between R-group and Carboxyl Group

(add them then divide by 2)

Question 17

How do you find pI point for basic AA?

Answer 17

Average pKA values between R-group and Amino Group

(add them then divide by 2)

Question 18

AA with acidic side chains have a pI point ______ 6, while AA with a basic side chain has a pI point ______ 6.

Answer 18

1. Below
2. Above

Question 19

How are peptide bonds formed? broken?

Answer 19

1. Dehydration/Condensation (loss of H2O)
   
   1. Nucleophilic attach of amine Nitrogen on carboxyl alpha carbon (where OH leaves thens comes back to steal a H+ from amine group)
2. Hydrolysis (addition of H2O)
   
   1. Catalyzed by hydrolytic enzymes (Trypsin or Chymotrypsin)

Question 20

Describe the Primary Structure of AA.

Answer 20

Linear sequence of AA, held stabilized by covalent peptide bonds between adjacent AA.

Also important to note that the primary structure alone encodes for all info needed for folding at higher structural levels.

Question 21

Describe te seconday structure of AA. List the two types.

Answer 21

1. Hydrogen bonding between backbone structures of AA
2. Types
   
   1. Alpha Helices
   2. Beta sheets

Question 22

Describe the structure of alpha helices.

Answer 22

1. Right handed spiral conformation
2. Hydrogen bonds between amine hydrogen and carboxyl oxygen located 4 residues away

(alpha helices are important component of keratin)

Question 23

Describe the Structure of Beta Pleated Sheets.

Answer 23

1. Rippled Strands that lie alongside one another
   
   1. Antiparallel
   2. Parallel
2. Connected via H-Bonds
   
   1. carboxyl oxygen on one strand with joins with amine hydrogen on on adjacent strand

^{<em>(Think Fibrinin)</em>}

Question 24

Describe tertiary structure of an AA.

Answer 24

Three dimensional shape of a single polypeptide chain

Question 25

What are the five ways in which tertiary structures are stabilized?

Answer 25

1. H-bonds
2. Salt-Bridges
3. Disulfide Bridges
4. Acid-Base interactions
5. Hydrophobic/Hydrophillic Interactions of side chains (Most tertiary structures are determined by these types of interactions with hydrophobic residues on the interior and hydrophillic residues on the exterior)

Question 26

Bonds that form when two cysteine moleclues become oxidized to form cystine.

Answer 26

Disulfide bridges

Question 27

Associated with a protein losing its tertiary structure, and therefore its function.

Answer 27

Denaturation

Question 28

Descriibe the Quaternary structure of an AA.

Answer 28

1. Creation of multiple subunits based on polypeptide chain interactions with the protein (ONLY exists in proteins with more than one polypeptide chain)

Question 29

Proteins with covalently attached molecules. What is the name of the molecule?

Answer 29

1. Conjugate Proteins
2. Prosthetic Group
   
   1. Non-polypeptide (contains no AAA) required for biological functioning of some proteins

Question 30

Increasing what two things can lead to denaturation of a protein? Is denaturation reversible?

Answer 30

1. Heat and Solutes
2. It can be reversible, but is usually irrerversible

Question 31

What are the reasons for conjugating a protein?

Answer 31

1. Necessary for proper functioning of the protein
2. Direct their delivery to cell membrane
3. Direct delivery to a particular organelle

Question 32

What is a buffer?

Answer 32

solution that resists changes to pH (buffering capacity comes from the presence of a weak acid and its conjugate base (or weak base and its conjugate acid) in roughly equal amounts)

Question 33

Hydrolysis ocf a protein by another protein.

Answer 33

proteolytic cleavage (protease/proteolytic enzyme does the cleaving)

Question 34

Enzyme that transfers a phosphate fron a high energy carrier (i.e. ATP) to another molecule.

Answer 34

Kinase

Question 35

Enzyme that removes a phosphate group from a molecule.

Answer 35

phosphatase

Question 36

Transfers a phosphate to an iorganic molecule.

Answer 36

Phosphorylase

Question 37

How are thermodynamically unfavorable reactions able to be carried out?

Answer 37

Reaction Coupling

Definition: when one thermodynamically reaction is used to drive another thermodynamically unfavorable reaction.

(an example can be the hydrolysis of ATP to drive another unfavorable reaction)

Question 38

What is another way in which enzyme activity can be regulation (other than inhibition)?

Answer 38

1. covalent modifcation (i.e. addition/removal of a phosphate group)
2. proteolytic cleavage
3. Association with other polypeptides
   
   1. i.e.: constitutive activity
      
      1. continuous rapid catalysis if a regulatory subunit is not bound
   2. Some enzymes need to bind to a specific polypeptide in order to function