Lecture 3: Cell Chemistry 2 (Amino Acids)

1° (Primary Protein Structure)

-Linear amino acid sequence
-Peptide bonds

2° (Secondary Protein Structure)

-α-helix
-β-sheet

3° (Tertiary Protein Structure)

-Spatial arrangement of single polypeptide
-Arranges 2° structures and AAs that are not a part of a 2° structure.

4° (Quaternary Protein Structure)

-Spatial arrangement of multiple polypeptides
-Multiple proteins fitting together

Polypeptide

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Generic Amino Acid

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Generic Amino Acid at pH7

Uncharged Polar Amino Acids

asparagine (Asn, or N)
glutamine (Gln, or Q)
serine (Sec, or S)
threonine (The, or T)
tyrosine (Tyr, or Y)

Charged Amino Acids: Basic

lysine (Lys, or K)
arginine (Arg, or R)
histidine (His, or H)

Charged Amino Acids: Acidic

aspartic acid (Asp, or D)
glutamic acid (Glu, or E)

Nonpolar Amino Acids

glycine (Gly, or G)
alanine (Ala, or A)
leucine (Leu, or L)
isoleucine (Ile, or I)
valine (Val, or V)
cysteine (Cys, or C)
methionine (Met, or M)
tryptophan (Trp, or W)
phenylalanine (Phe, or F)
proline (Pro, or P)

N-Terminus

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C-Terminus

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Polypeptide Backbone

-Uncharged
-Polar
-Directional

Protein Stereochemistry

-All twenty amino acids used in protein formation are L-Stereoisomers
-Some D-stereoisomers exist in bacteria

Which amino acid is rarely found in α-helices? Why?

Proline.
Because it has a ring structure on the αCarbon making it difficult for free rotation to occur.

β-Sheet Properties

-Stabilized by Hydrogen bonds
-Have a parallel and a anti-parallel form
-Sidechains stick out above and below the sheet

What type of bonds shape proteins?

Non-covalent bonds (electrostatic attractions, hydrogen bonds, van der Waals attractions)

Why do proteins fold?

The different polar and non-polar side chains (hydrophilic and hydrophobic) automatically assemble in such a way that the hydrophobic non-polar side chains are separated from the water.