Lecture 01

Question 1

Name examples of protein functions

Answer 1

Catalysis
Transport
Structure
Motion
Communication

Question 2

What is the one unifying concept about proteins regardless of their function?

Answer 2

Prior to any action taken by the protein a ligand must bind to it to signal a change

Question 3

What is the pH range of blood?

Answer 3

7.35 - 7.45

Question 4

What is a buffer?

Answer 4

Mixture of weak acid and conjugate base that provides a reservoir of proton-accepting and proton-donating species.

Question 5

Why are buffers important?

Answer 5

Maintains pH of body systems at the appropriate range

Question 6

When are buffer solutions most effective?

Answer 6

When the pH is equal to the pKa of the acid, but it can remain 1 unit above or below the pKa

Question 7

How do you find the buffering range?

Answer 7

Add and subtract 1 to the pKa; this is also the region where the titration curve is less steep

Question 8

pH < pKa

Answer 8

Protonated/acidic form dominates

Question 9

pH > pKa

Answer 9

Deprotonated/basic form predominates

Question 10

Name the major buffer systems of the human body

Answer 10

Proteins, phosphate, and carbon dioxide/bicarbonate

Question 11

Phosphate pKa2 is within the effective range of physiological pH (7.2)

Answer 11

6.8

Question 12

Bicarbonate buffer pKa

Answer 12

6.1

Question 13

Which buffer system is the only one regulated by physiological processes?

Answer 13

Bicarbonate

Question 14

What organ regulates carbon dioxide (CO2) levels?

Answer 14

Lungs

Question 15

What organ regulates bicarbonate (HCO3-) levels?

Answer 15

Kidneys

Question 16

Why does dissolved CO2 represent acid concentration?

Answer 16

Carbon dioxide forms carbonic acid but carbonic acid is not stable in aqueous solution

Question 17

Define dissolved CO2

Answer 17

Partial pressure of CO2 x solubility coefficient (alpha)

Question 18

Which amino acid is not chiral?

Answer 18

Glycine

Question 19

Which stereoisomer is physiologically relevant for the chiral amino acids?

Answer 19

L

Question 20

Why are the hydroxy groups of Ser, Thr, and Try significant?

Answer 20

They are potential sites of protein phosphorylation

Question 21

What is significant about the hydroxy groups of Ser and Thr, not Tyr?

Answer 21

They are targets of O-linked glycosylation

Question 22

What is significant about the amide nitrogen of Asn?

Answer 22

It is the target of N-linked glycosylation

Question 23

What is significant about the R groups of Tyr and Cys?

Answer 23

They are ionizable; Tyr is also aromatic

Question 24

Which amino acids are acidic and carry a full negative charge at pH 7.2?

Answer 24

Asp and Glu

Question 25

Which amino acids are basic and carry a full positive charge at pH 7.2?

Answer 25

Arg and Lys

Question 26

Which amino acid is basic but carries a partial positive charge?

Answer 26

His

Question 27

pKa ranges of alpha-carboxyl groups

Answer 27

2.2 - 2.8

Question 28

pKa ranges of alpha-amino groups

Answer 28

8.5 - 9.5

Question 29

Why is the pKa value of an amino acid R group in water not accurate when that amino acid is part of a protein?

Answer 29

Electrostatic interactions with other atoms in the proteins can increase or decrease its affinity for protons

Question 30

What amino acid is commonly found in the ligans binding sites of proteins?

Answer 30

His

Question 31

What is the pKa range of histidine side-chains in different proteins?

Answer 31

4 - 9; 5.0 - 8.0 frequently seen

Question 32

Define isoelectric point (pI)

Answer 32

pH at which an amino acid has a net charge of zero.

Question 33

What is true of an amino acid at its pI?

Answer 33

It is least solule in water and does not migrate in an electric field.

Question 34

How to calculate pI

Answer 34

If there is no ionizable side chain, take the average of the two pKas. If there is an ionizable side chain, locate the species with no net charge and use the pKa values on either side of it.

Question 35

What are the two torsional angles that define secondary structure of proteins?

Answer 35

Phi: alpha-carbon and alpha-amino Psi: alpha-carbon and alpha-carboxyl

Question 36

Why is a Ramachandran Plot important?

Answer 36

It reports on the compatibility of all possible combinations of the two torsion angles with respect to protein structure.

Question 37

What did the Ramachandran Plot demonstrate?

Answer 37

Steric hindrance caused by R groups limits the tolerated combinations of phi and psi angles.