Introduction to Biochemistry

What are the characteristics of water that make it such an important medium for life?

• Carbon, nitrogen, oxygen, and hydrogen make up more than 85% of atoms in  the human body

• They are so appropriate for life because of their ability to form covalent bonds by electron pair sharing

• Covalent bonds have the strongest bond energies, but Van der Waals  interactions, hydrogen bonds, ionic bonds, and hydrophobic interactions are  still all very important

Water & Biochemistry

• Water is very important for biochemical reactions because it serves as a  medium- it also actively participates in reactions that support life • Characteristics of water:

o High boiling point

o High melting point

Can water form hydrogen bonds with ionic substances?

If you want to learn more check out How do kings and queens get power?

o High heat of vaporization

o High surface tension

o Bent structure- makes it polar

o Good hydrogen bond donor/acceptor

o Capable of forming four hydrogen bonds per water

• Ions are always hydrated or solvated in water- water forms hydrogen bonds  with polar solvents

• Nonpolar solutes “organize” the hydrophobic parts so that they are not  touching water- decreases entropy (randomness)

Vocabulary Terms

• Amphiphilic/Amphipathic molecules- molecules that contain both polar and  nonpolar groups- they are attracted to both polar and nonpolar  environments

• pKa- used to express the relative strength of an acid or base

Does a phospholipid have both polar and nonpolar regions?

• Buffers- aqueous systems that tend to resist changes in pH when small  amounts of acid or base are added. Tends to happen in extreme  environments

Amino Acids, Peptides, & Proteins

• Proteins have many different functions:

o Catalysis

o Transport

o Structure

o Motion We also discuss several other topics like What are the seven themes of psychological science?

(Catalysis and structure will be talked about the most in this class)

• Proteins mediate most cellular processes, and they are the most abundant  macromolecule.

• Characteristics of amino acids:

o Capable of polymerization

o Useful for acid/base reactions

o Weak polyprotic acids

o Contain at least two dissociable hydrogens, aka ionizable groups ▪ Ionizable groups are not strongly dissociating

▪ Degree of dissociation depends on the pH

Basic Structure of an Amino Acid

COOH

                                                                              |

                                                                  H3N+-C-H

                                                                              |

                                                                             R

• COOH is a carboxyl group

• +NH3 is an amino group

• The R group varies from one amino acid to the next and gives them their  different properties- they function in chemical situations differently  

Zwitterions

                                                                             H Don't forget about the age old question of What do you call a measuring the quantity of the individual foods and beverages consumed during the course of one to several days or assessing the pattern of food use during the previous several months?

                                                                              | We also discuss several other topics like What are the two classes of challenges to efforts of a group to reach and implement agreements are important to discuss?

                                                                         R-C-COO- 

                                                                              |

                                                                                                                 +NH3 We also discuss several other topics like What is the cost of next best alternative forgone?

• Can act as an acid or a base

• Found mainly at neutral pHs

• The charge on the amino group and the charge on the carboxyl group balance  each other out

Titrations & Amino Acids

• Each amino acid has a characteristic titration curve that reflects their  tendency to ionize

• As you approach the pKa of an amino acid, the curve of the graph will start to  level out

o IMPORTANT!!! Once an amino acid goes one above its pKa value  (which will be given on exams), it is completely ionized and can never  get its proton back

Carboxyl groups always lose their proton before amino groups. If you want to learn more check out What is the main idea of rawls' theory of justice?

• The α carboxyl group pKa is relatively low (~2)- removing its proton results  in a negative charge on the carboxyl group (it starts off as neutral) • The α amino group pKa is relatively high (~10)- removing its proton results  in a neutral charge on the amino group (it starts off a positive)

Below is an example using the amino acid arginine (Arg, R). This helped me to  understand how amino acid titrations work. I hope it makes sense to you guys as  well!

Known:

α Carboxyl pKa= 2 (carboxyl group directly attached to center carbon) α Amino pKa= 10 (amino group directly attached to center carbon) “R-group amino” pKa= 12 (amino group that is found in the R-group)

• At a pH of 1, Arg is fully protonated (all hydrogens present)- the amino group  is positively charged and the carboxyl group is neutral

• When the pH rises to 4 (which is at least one above the α carboxyl pKa of 2),  the α carboxyl group loses its proton (hydrogen) and becomes COO- • When the pH rises to 11 (which is at least one above the α amino pKa of 10),  the α amino group loses its proton and becomes H2N

• When the pH rises to 14 (which is at least one above the R-group amino pKa  of 12), the R- amino loses its proton and becomes H2N

Keep in mind that once a group loses its proton, it cannot get it back!!

pH=1    pH=4   pH=11                                pH=14

           COOH             |

H3N+-C-H

            |

      (CH2)3

           |

          N-H

           |

          C=+NH2            |

          NH3+

           COO-             |

H3N+-C-H

            |

      (CH2)3

           |

          N-H

           |

          C=+NH2            |

          NH3+

           COO-             |

  H2N-C-H

            |

         (CH2)3            |

          N-H

          |

          C=+NH2            |

          NH3+

           COO-             |

  H2N-C-H

            |

         (CH2)3            |

          N-H

           |

          C=+NH2            |

          NH2

Net charge at each pH value:

pH=1: +3

pH=4: +2

pH=11: +1

pH=14: 0

Determining Charge of a Peptide

Below is an example that helped me learn how to determine the charge of a peptide.  • The “leading” amino group and the “lagging” carboxyl group need to be taken  into account

• All nonpolar, aromatic, and polar, uncharged amino acids (so, in this example,  Phe and Met), do not have charges that contribute to the final net charge of  the peptide, so they can be ignored in these types of problems

• NH3+ has the charges shown below because it starts out positive (pH 1), has a  relatively high pKa so it stays positive at neutral pH (pH 7), and once it  passes its pKa value by at least one (pH 14), it loses its proton and becomes  neutral  

• COOH has the charges shown below because it starts out neutral (pH 1), has a  relatively low pKa so it loses its proton at a lower pH and becomes negative  (pH 7), and since it cannot get its proton back it stays negative at all other  higher pHs (pH 14)

• It is important to memorize your amino acid properties/groups • Lysine is a positively charged amino acid- it will follow the same charges that  the positively charged carboxyl group has

• Glutamate is a negatively charged amino acid, it will follow the same charges  that the negatively charged amino group has

• Phenylalanine is an aromatic amino acid, so it does not contribute to the  overall net charge of this peptide.  

• Methionine is a nonpolar amino acid so it also does not contribute to the  overall net charge of this peptide.

pH

NH3+

Lys

Phe

Glu

Met

COOH

Net

1

+1

+1

0

0

+2

7

+1

+1

-1

-1

0

14

0

0

-1

-1

-2