know the parts of an amino acid 1. amino group 2. carboxylic acid (carboxylate) 3. r-group
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Know the parts of an amino acid◦ 1. Amino group◦ 2. Carboxylic Acid (Carboxylate)◦ 3. R-Group
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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
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R-groups composed of only Hydrogen and Carbons
One exception- Methionine contains sulfur, bound only to Carbon
Phenylalanine Methionine
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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
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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
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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
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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.
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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
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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
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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
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Bohr Effect
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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
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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-).
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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?