Know the parts of an amino acid◦ 1. Amino group◦ 2. Carboxylic Acid (Carboxylate)◦ 3. R-Group

Amino acids are classified by their R-groups and the groups interaction with water◦ 1.Hydrophobic-The majority of R-groups◦ 2. Polar Uncharged◦ 3. Polar Charged

R-groups composed of only Hydrogen and Carbons

One exception- Methionine contains sulfur, bound only to Carbon

Phenylalanine Methionine

Look for Oxygens and Nitrogens Charged groups will be charged or have a

primary amine or carboxylic acid part.◦ Primary amines are written NH2 and Carboxylic

acids COOH

Amino acids can be proton donors The pH at which the Carboxylate group gives up

its proton is the pK1 and the Amino group is pK2 ◦ pK1 is the point where 50% of the carboxylate groups

are unprotonated, and pK2 is where 50% of the amino groups are unprotonated

Amino acids are good buffers at these points Add them together and divide by 2 to get the

isoelectric point (pI)◦ This is the point where all amino acids in a solution

have zero net charge◦ Amino acids are bad buffers at this point

Peptide Linkages: C-N bond◦ Different order equals different peptides

Ex: Gly-Ala-Pro isn’t the same as Pro-Ala-Gly◦ Number of possible combinations using each AA

once: (Number of Amino Acid)! Ex: tetrapeptide is 4! (4x3x2x1=24)

◦ Number of possible combinations using each AA as many times as we want:

(number of AA)number in polypeptide

Ex: 4 amino acids in a tetrapeptide =44

An amide plane forms around the peptide linkage

C,N,O,H are involved in the formation The double bonded O electrons resonate to

the C-N bond, giving the peptide linkage a partial double bonded characteristic.

Primary◦ Order of the amino acids◦ Ex: ala-gly-asp-leu-lys-phe◦ Main type of interaction: covalent between amino

acids, called peptide bond Secondary

◦ Alpha helix◦ Main type of interaction: hydrogen bonds between

amide planes

Tertiary◦ Main type of interactions: between R-groups◦ H-bonds, Electrostatic, Hydrophobic, Covalent

(disulfide bonds)◦ Specifically, covalent bond called disulfide

Between 2 cysteines’ sulfhydryl R-groups Quaternary

◦ Large molecular weights

Predominate AA: proline and glycine◦ Gly- small R-group for rope-like structure◦ Pro- Oxidizable R-group

Requires Vitamin C; deficiency=scurvy◦ Steps in formation

Immature collagen is hydroxylated (-OH groups added) becoming procollagen Need Vitamin C as reducing agent in this step. If

deficient, the person has scurvy Procollagen is glycolyslated (carbohydrate moeities

added) making tropocollagen Mature collagen formed by crosslinks between

hydroxylated prolines

Bohr Effect

HHb (protonated Hemoglobin) enters lungs◦ Lungs are more basic, so HHb more likely to give up

proton Oxygen (O2) binds to hemoglobin and it gives

up the H+ HHb+ O2+HCO3

- HbO2+H2O+CO2 The bicarbonate is the form that carbon dioxide

goes to the lungs as. It travels in the blood plasma.

All of the reactions occur inside the red blood cell

Oxygenated hemoglobin travels to the tissues where it encounters an acidic enviroment.◦ The acidity is the result of increase carbon dioxide,

which is a metabolic byproduct In an acidic environment, hemoglobin tends

to give up oxygen and bind the protons that are in the tissues◦ Extra protons are there as the result of the acid CO2

◦ Bicarbonate is moved out of the RBC, exchanged with Chloride (Cl-).

Know that pH and Gas Pressures drive respiration

Know which direction the equation is goingH2O + HbO2

- + CO2 HHb + O2 + HCO3-

Which one occurs in the lungs?

Which one occurs in the peripheral tissues?