Amino Acids, Peptides & Proteins
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Amino Acids, Peptides & Proteins. a -amino acid:. Amino Acids. Are >500 naturally occurring amino acids identified in living organisms Humans synthesize 10 of the 20 they use. The other 10 are called essential amino acids. Amino Acids, Peptides & Proteins. Peptides & proteins:

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Amino Acids

  • Are >500 naturally occurring amino acids identified in living organisms

  • Humans synthesize 10 of the 20 they use. The other 10 are called essential amino acids.

Amino Acids, Peptides & Proteins

  • Peptides & proteins:

  • Derived from amino acids through peptide or amide bonds.

  • The amine and acid ends of amino acids couple to form amide (peptide) bonds

  • in peptides/proteins/enzymes.

  • Proteins fold into well-defined structures. The hydrophobic residues

  • segregate to the water-free interior, while the polar/charged residues favor

  • the exterior.

Peptides: Coupling AAs Together

  • Peptides & Proteins: Linear oligomers of the 20 amino acids

  • Peptides ≤ 20 amino acids; Proteins > 20 amino acids

  • Functions:

  • Catalysis - enzymes

  • Membrane channels

  • Structural support (boundaries)

  • Regulate metabolites (storage & transport)

  • Antibodies; cellular signaling (recognition & binding)


  • Discovery story:

  • In 1965 by Jim Schlatter

  • working on discovering new

  • treatments for gastric

  • ulcers.

  • Made a dipeptide intermediate,

  • which he spilled on his hand

  • Tested the dipeptide in coffee


  • 4 calories per gram

  • 180 times sweeter than sugar

Aspartame: A Dipeptide

Two main constituents:


Aspartic acid


Make the methyl

ester of phenylalanine

2. Make a peptide (amide)

bond between phenylalanine

and aspartic acid

Overall - two main steps to this synthesis

Dipeptides: Coupling of 2 AAs

Consider the synthesis of the dipeptide val-ala (valine-alanine):

  • Coupling of amino acids is an application of nucleophilic acyl substitution

  • Issue of selectivity arises:

  • val + ala  val-ala + ala-val +

  • val-val + ala-ala

  • A mixture of 4 possible amide

  • products

Merrifield’s Solid-Phase Synthesis

In order to get the desired peptide (val-ala), the appropriate NH2 and CO2

units must be joined.

The selectivity is accomplished through the use of protecting groups.

Merrifield’s approach:

Protect N-terminus of valine

Protect C-terminus of alanine

Couple valine and alanine

Deprotect to get dipeptide

Merrifield’s Solid-Phase Synthesis

1. Protection of valine’s N-terminus:

Merrifield’s Solid-Phase Synthesis

2. Protection of alanine’s C-terminus:

Attach the C-terminus to a plastic bead (solid-phase synthesis!)

  • Benefits of solid-phase:

  • Ease of attachment

  • Ease of removal; just filter away from product solution

Merrifield’s Solid-Phase Synthesis

3. Couple valine and alanine:

Merrifield’s Solid-Phase Synthesis

3. Deprotection of Fmoc & bead:


  • Amino acid polymers; when long enough, they fold back on themselves to

  • create intricate, well-defined 3D structures

  • The structure of a protein specifies its function.

  • The AA sequence specifies its structure.

  • The AA chain typically adopts regional sub-structures which sum together

  • to deliver the overall structure of the protein.

  • Forces/Factors that dictate protein folding:

  • Planarity of amide bonds

  • H-bonding

  • Hydrophobic interactions

  • Electrostatic Attraction

  • Disulfide linkages


1. Planarity of amide bonds:


2. H-bonding:

H-bond worth ~ 5 kcal/mol

H-bonds orient the chain


3. Hydrophobic Interactions:

Lots of hydrophobic interactions

between Rs and H2O -


Protein folds to “clump” R

groups together in the

interior of protein to avoid

H2O - very energetically



4. Electrostatic Attraction:


5. Disulfide Linkages:

  • Covalent S-S

  • Drastically alters shape

  • Worth ~ 50 kcal/mol


  • Overall, these 5 structural/energetic features leads to the final 3D protein

  • structure. However, predicting the structure from the amino acid sequence

  • is still a challenge.

  • Hierarchy of Structural Elements of Proteins

  • Primary structure: AA sequence

  • Secondary structure: discrete sub-structural elements (modules)

    a-helix & b-sheet

a-helix: see board for depiction


Internal H-bonding

The way the side chains line up

3.6 AAs per turn

b-sheet: see board for depiction


Chain-to-chain H-bonding

Alternating (up-down, up-down)

Pattern of R groups


  • Hierarchy of Structural Elements of Proteins

    3. Teritary Structure: the individual secondary structural elements organized

    in 3D.

    See board for depiction.

    4. Quaternary Structure: non-covalent complexation of different proteins.


  • Structurally diverse, derived from living organisms

  • Functional theme is hydrophobicity - water avoiding due to long alkyl chains

  • Often found at the interface of aqueous compartments

  • 3 Major Classes of Lipids:

  • Fats and oils

  • Phospholipids

  • Cholesterol & derivatives (steroids)


Fats & Oils

Derived from glycerol and fatty acids:

Weak intra-


attractive forces

between chains


  • Fats & Oils

  • In order for a fat to melt, these weak dispersive forces must be broken.

  • More contacts, the better the packing and the higher the m.p. of the fat

  • Less contacts, worse packing of chains, the lower the m.p.

    Unsaturated Fats:

Oils are polyunsaturated - lots of

alkenes & have low mp due to less packing

Butter has very little unsaturated & has

higher mp


Soaps & Detergents

  • Hydrolyzed fats

  • A long chain carboxylate molecule:


Soaps & Detergents

In H2O, forms

a micelle.

Grease & dirt get

trapped in the interior.

Micelle is H2O soluble

so can wash out dirt.


2. Phospholipids:

  • Have hydrophobic and hydrophilic regions

  • Forms membranes

  • Precursors to prostaglandins


2. Phospholipids:

  • Forms membranes: self-organize at certain concentrations to form bilayers

  • Membranes are largely impermeable to charged species that exist in

    biological environments.

Cell membrane


3. Cholesterol & Steroids


27 carbons

4 rings

8 stereocenters

Derived from terpenes

Cholesterol is a precursor to several steroidal hormones:

Testosterone (male hormone)

Estrone (female hormone)


Cholesterol is a precursor to several steroidal hormones:

Testosterone (male hormone)

Estrone (female hormone)

These hormones operate at the genetic level (turn genes on and off) to

control biochemistry. They are recognized by specific protein receptors.

Antioxidants & Chocolate

  • Antioxidants:

  • Protect against cardiovascular disease, cancer and cataracts

  • Thought to slow the effects of aging

  • Chocolate:

  • High levels of antioxidants - complex mixtures of phenolic comounds

  • By weight, has higher concentration of antioxidants than red wine or

  • Green tea

  • 20x higher concentration of antioxidants than tomatoes

Dark chocolate has more than 2x the level of antioxidants as milk chocolate.

Side note: The main fatty acid in chocolate, stearic acid, does not appear to raise blood cholesterol levels the way other saturated fatty acids do.