Protein Structure
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Understanding Protein Structure: Amino Acids, pKa, and Protein Formation, Study notes of Biochemistry
An overview of protein structure, focusing on the role of amino acids and their properties, including pKa values. It covers the formation of peptide bonds, the organization of proteins into secondary, tertiary, and quaternary structures, and the importance of non-covalent bonds. The document also discusses methods for determining protein structures.
Typology: Study notes
2021/2022
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Protein Structure
Amino Acids
Amino acids are the building blocks of proteins. All AA’shave the same basic structure:
CarboxylGroup
AlphaCarbon AminoGroup
SideChain
Polar Residues
Nonpolar Residues
Basic Residues
Amino Acids
More depictions from Petsko and Ringe
Amino Acid Properties
pK
a
• You know that the pH is defined in termsof the proton concentration
pH = -log[H
+ ]
and that this is based on an equilibriumthat is reached between an acid (or base)and it constituent parts
HA
+ H
+ A
pK
a
• Taking the log of each side (with a minussign) gives us • This is the Henderson-Hasselbachequation
−
base acid
pK
pH
A HA
K
H
a
a log
]
[
]
[
log
log
]
log[
Val
Ile
Tyr
His
Trp
Gly
Thr
Gln
Ser
Glu
Pro
Cys
Phe
Asp
Met
Asn
Lys
Arg
Leu
Ala
R
NH
+ 3
COOH
AA
R
NH
+ 3
COOH
AA
pK
of amino acidsa^
The Peptide Bond
To make a protein, these amino acids are joined togetherin a polypeptide chain through the formation of a peptidebond.
Polypeptides
-^ Proteins are nothing more than long polypeptide chains.•^ Chains that are less than 40-50 amino acids or residuesare often referred to as polypeptide chains since they aretoo smal to form a functional domain.•^ Larger than this size, they are called proteins•^ The structure, function and general properties of aprotein are all determined by the sequence of aminoacids that make up its primary sequence.
Angles and Bonds
trans (
ω=180) is strongly favored over cis (
ω=0)