LIPPINCOTT’S BIOCHEMISTRY:
NOTES
Unit 1: chapters 1-5
, Unit 1 Amino Acids chapter 1 Basic amino acids at physiological pH are
positively charged
Amino acids are mirror images of each
Each amino acid has 3 components other, the l-enantiomer occurs in proteins,
1. Carboxyl group the d-enantiomer occurs in antibiotics
2. Primary amino group (except proline) Amino acids can act as buffers whose pH is
3. Distinctive side chain bonded to a- determined by the Henderson-Hasselbach
carbon equation
[𝐴− ]
At physiological pH (7.4), o 𝑝𝐻 = 𝑝𝐾𝑎 + log [𝐻𝐴]
o Carboxyl group is dissociated o A buffer is a solution that can resist
o Amino group is protonated changed in pH on addition of an
In proteins, peptide linkages between acid/base between +/- 1pH of the pKa;
carboxyl and amino groups exist max buffering when pH=pKa
o Generally, not available for chemical o Amino acids at normal physiological pH
reactions except for hydrogen bonding. are generally neutral and are called
Side chains will determine the nature of the ampholytes
protein
Amino acids are: Unit 1 Structure of proteins chapter 2
o Non-Polar (uneven distribution of
electrons)
o Polar (acidic/basic) Primary structure of proteins
o Uncharged polar Amino acid sequence formed by covalent
Non-polar side chains promote peptide bonds
hydrophobic interactions o Peptide bond named from N-terminus to
o Nonpolar AA’s cluster together at the C-terminus and each residue is given
core of the protein in an aqueous solution “yl” suffix except C-terminal
(hydrophobic effect) o Peptide bond formation is a dehydration
o Nonpolar side chains are found on the reaction
outside in a hydrophobic medium
o Proline contains 5-membered ring Secondary structure
“imino acid” which contributes to Alpha helix is a common structure found in
fibrous structures in collagen, however it a diverse set of proteins
interrupts alpha helices o Stabilised by extensive h-bonding
Uncharged polar side chains participate in which are parallel to the spiral and link
hydrogen bonding to the –NH group 4 residues up
o Can from a disulfide bond between 2 o This ensure the first and last peptide
cysteines (cystine) components are not linked by intrachain
o Side chains can be used as attachment h-bonding
sites for other molecules to the protein o H-bonding is collectively strong
Amino acids which are acidic are fully o Each turn of a-helix contains
ionized at physiological pH approximately 3.6 amino acids
o Proline’s structure disrupts the a-helix by
forming kinks; charged amino acids also
2
NOTES
Unit 1: chapters 1-5
, Unit 1 Amino Acids chapter 1 Basic amino acids at physiological pH are
positively charged
Amino acids are mirror images of each
Each amino acid has 3 components other, the l-enantiomer occurs in proteins,
1. Carboxyl group the d-enantiomer occurs in antibiotics
2. Primary amino group (except proline) Amino acids can act as buffers whose pH is
3. Distinctive side chain bonded to a- determined by the Henderson-Hasselbach
carbon equation
[𝐴− ]
At physiological pH (7.4), o 𝑝𝐻 = 𝑝𝐾𝑎 + log [𝐻𝐴]
o Carboxyl group is dissociated o A buffer is a solution that can resist
o Amino group is protonated changed in pH on addition of an
In proteins, peptide linkages between acid/base between +/- 1pH of the pKa;
carboxyl and amino groups exist max buffering when pH=pKa
o Generally, not available for chemical o Amino acids at normal physiological pH
reactions except for hydrogen bonding. are generally neutral and are called
Side chains will determine the nature of the ampholytes
protein
Amino acids are: Unit 1 Structure of proteins chapter 2
o Non-Polar (uneven distribution of
electrons)
o Polar (acidic/basic) Primary structure of proteins
o Uncharged polar Amino acid sequence formed by covalent
Non-polar side chains promote peptide bonds
hydrophobic interactions o Peptide bond named from N-terminus to
o Nonpolar AA’s cluster together at the C-terminus and each residue is given
core of the protein in an aqueous solution “yl” suffix except C-terminal
(hydrophobic effect) o Peptide bond formation is a dehydration
o Nonpolar side chains are found on the reaction
outside in a hydrophobic medium
o Proline contains 5-membered ring Secondary structure
“imino acid” which contributes to Alpha helix is a common structure found in
fibrous structures in collagen, however it a diverse set of proteins
interrupts alpha helices o Stabilised by extensive h-bonding
Uncharged polar side chains participate in which are parallel to the spiral and link
hydrogen bonding to the –NH group 4 residues up
o Can from a disulfide bond between 2 o This ensure the first and last peptide
cysteines (cystine) components are not linked by intrachain
o Side chains can be used as attachment h-bonding
sites for other molecules to the protein o H-bonding is collectively strong
Amino acids which are acidic are fully o Each turn of a-helix contains
ionized at physiological pH approximately 3.6 amino acids
o Proline’s structure disrupts the a-helix by
forming kinks; charged amino acids also
2
