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The alpha carbon of all amino acids is attached to 4 groups:
- The R group is the part that is variable in different amino acids & determines specific aspects of each amino acid.
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__ side chains act as acids or bases which tend to be __ under physiological conditions. Side chains form __ bonds and are often involved in chemical reactions.
- Hydrophilic;
- fully charged (+ or -);
- ionic
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neutral (uncharged) polar amino acids
- Hydrophilic side chains allow them to participate in chemical reactions, form H-bonds, and associate with water.
- post-translational modifications: phosphorylation of OH- groups
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Nonpolar amino acids have __ side chains that consist almost entirely of __ atoms.
- These amino acids tend to form the inner core of soluble proteins, buried away from the aqueous medium. They play an important role in membranes by associating with the lipid bilayer.
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Except __, all amino acids have 4 different groups attached to carbon alpha. This gives them the chirality.
glycine (R group is H)
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Amino acids in regular proteins are __ amino acids.
- L
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The __ group of one amino acid is condensed with the __ group of another amino acid. A __ bond is formed and one __ is released.
- carboxyl;
- amino;
- peptide;
- H2O
- The process can be repeated & a polymer can be produced: polypeptide.
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bonds that can rotate
- bond between N & C alpha
- bond between C & C=O
- R chain bonds
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bond that has very little rotation
amide bond (N-C=O)
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side chain consists only of hydrogen atom & can fit into either a hydrophilic or hydrophobic environment. often resides at sites where 2 polypeptides come into close contact
 - Rotation at glycine residue is more free
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Though the side chain has polar, uncharged character, it has the unique property of forming a covalent bond with another __ to form a disulfide link
 - contains SH in the side chain
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Though the side chain has hydrophobic character, it has the unique property of creating kinks in polypeptide chains and disrupting ordered secondary structure
 - Proline's side chain is bound to the N (imino acid) → rotation at proline residue is very restricted and also no hydrogen bond is made on N of proline
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Protein aggregates
interaction of hydrophobic parts of several not correctly folded protein molecules with each other
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primary structure of proteins
sequence of amino acid residues in the polypeptide chain
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secondary structure of proteins
- regular local structures with repeated hydrogen bonds in the backbone
- alpha helix (collagen) & beta sheet (spider silk)
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alpha helix
- right handed helix
- hydrogen bonds between the backbone carbonyl (C=O) of one residue & backbone (N) of the amide
- 4 amino acid residues down the chain
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beta sheet
- C=O and N residues are projected laterally in an alternating way (left and right)
- R groups are projected alternatively up or down the plane of the sheet
- The C=O groups from one backbone make hydrogen bonds with the N atoms of the adjacent backbone.
- The backbone is not fully stretched (zigzag)
- The adjacent backbones can be parallel or anti-parallel with each other for making the beta sheet
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tertiary structure
- folded structure of an entire polypeptide
- side chain dependent packing of the secondary elements and some other elements between them such as a loop or a turn made of amino acid residues
- can fold into different shapes: fibrous: elongated, often structure roles. globular: compact, often enzymes
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Protein domains occur when __
- proteins are composed of 2 or more distinct regions
- Each domain is a functional region.
- example: Several alpha helices make a barrel shape structure.
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Protein domains are classified either by the __ or by __
- fold (typology): considers the folding within the structure of a polypeptide (secondary structures & their connections with each other)
- homology: enough similarities in the sequence of amino acids between 2 domains of 2 proteins and therefore both have similarities in shape and function
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3 types of folds
- all alpha helices
- 2 beta strand domains
- combination of both
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If the connection between the domains is a longer linker, __
- there is more possibility of movement by the domains
- There should not be long stretches of hydrophobic amino acids.
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Short connections between domains creates a __
tight and rigid interaction between domains
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quaternary structure
- interactions between 2 or more distinct polypeptide chains to make a full functional protein
- e.g. hemoglobin is made of 4 polypeptides (2 beta globins & 2 alpha globins)
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Often __ participate in making the quaternary structure by their secondary & tertiary structures, but in some cases __
- fully folded polypeptides
- interaction between the 2 polypeptides help form a secondary or tertiary structure within a peptide
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protein-protein interactions
- Results from large-scale studies can be presented in the form of a network
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