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Lecture 2 (06) Website
Lecture 2 (06) Website
• Learning Objectives
1. Understand how amino acids are joined together via
peptide bonds to form a polypeptide. Be able to write out
the structure of the reactants and the product.
Nonpolar groups-energetically
unfavorable for them to contact water
Amino acids are linked together by covalent
peptide bonds (Fig. 4-1)
Proteins are made up of a polypeptide backbone with
attached side chains
(Fig. 4-2)
Characteristics of Polypeptide synthesis
(Pitch)
Secondary structure of proteins – β sheet
Polypeptide chains are held together by H bonds between N-H group
of one polypeptide chain and C=O group of the other chain
(e.g. in the protein fibroin - abundant in silk) [Fig. 4-10, p. 128]
helices can wrap around one another by interactions
between their hydrophobic side chains to form a stable
coiled-coil. [Fig. 4-16]
e.g. keratin in the skin and myosin in muscles
Tertiary structure of proteins
• 3D conformation or shape
• Depends on the properties of the R groups
of amino acid residues
• Fold spontaneously or with the help of
molecular chaperones
• Stabilized by covalent and non-covalent
bonds
Many proteins are composed of separate
functional domains e.g. bacterial catabolite protein (CAP).
Protein domain: a segment (100 – 250 aa) of a polypeptide chain that
fold independently into a stable structure [Fig. 4-19]
Noncovalent bonds help protein folding (Fig. 4-4)
Also review Panel 2-7 (pp. 78,79) on noncovalent bonds
Covalent disulfide bonds between adjacent
cysteine side chains help stabilize a favored
protein conformation [Fig. 4-29]
Molecular chaperone proteins assist folding
of other proteins
[Horton et al. Principles of Biochemistry, 2nd ed.]
How is the tertiary structure of a
polypeptide chain stabilized?
• Ionic bonds (usually between charged amino acid side
chains at cellular pH 7.0) (Fig. 4-4) (eg. Lys-NH3
+ and Asp-COO-)
• Hydrogen bonds between R groups (remember
uncharged polar amino acids can H-bond!!! –Ser-OH,
Thr-OH and Tyr-OH with for example Glu=O or Gln=O)
• Covalent bonds (disulfide bonds between cysteines, see
Fig. 4-29)
• Hydrophobic interactions-non-polar side chains
associate in the interior of the molecule and exclude
water) (Fig. 4-5)
• van der Waals interactions
Quaternary structure of proteins: hemoglobin, a
protein in red blood cells, has four sub units (two
copies each of - and β-globins containing a heme
molecule [Fig. 4-23].
Gel electrophoresis method is used to separate proteins
[Lehninger et al. Principles of Biochemistry]
Problem Solving: Shown in the table below are the
sequences of selected amino acids from different types of
human hemoglobin (abbreviated Hb). Some forms of
hemoglobin are defective, while others are not. From what you
know about protein structure, explain why Sickle Cell and
Hammersmith Hbs are defective while delta Hb is not.