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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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slide2
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.
slide3
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.
slide4
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)
slide5
Aspartame
  • 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

Aspartame

  • 4 calories per gram
  • 180 times sweeter than sugar
slide6
Aspartame: A Dipeptide

Two main constituents:

Phenylalanine

Aspartic acid

Goal:

Make the methyl

ester of phenylalanine

2. Make a peptide (amide)

bond between phenylalanine

and aspartic acid

Overall - two main steps to this synthesis

slide7
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
slide8
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

slide9
Merrifield’s Solid-Phase Synthesis

1. Protection of valine’s N-terminus:

slide10
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
slide11
Merrifield’s Solid-Phase Synthesis

3. Couple valine and alanine:

slide12
Merrifield’s Solid-Phase Synthesis

3. Deprotection of Fmoc & bead:

slide13
Proteins
  • 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
slide14
Proteins

1. Planarity of amide bonds:

slide15
Proteins

2. H-bonding:

H-bond worth ~ 5 kcal/mol

H-bonds orient the chain

slide16
Proteins

3. Hydrophobic Interactions:

Lots of hydrophobic interactions

between Rs and H2O -

unstable

Protein folds to “clump” R

groups together in the

interior of protein to avoid

H2O - very energetically

favored

slide17
Proteins

4. Electrostatic Attraction:

slide18
Proteins

5. Disulfide Linkages:

  • Covalent S-S
  • Drastically alters shape
  • Worth ~ 50 kcal/mol
slide19
Proteins
  • 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

Note:

Internal H-bonding

The way the side chains line up

3.6 AAs per turn

b-sheet: see board for depiction

Note:

Chain-to-chain H-bonding

Alternating (up-down, up-down)

Pattern of R groups

slide20
Proteins
  • 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.

slide21
Lipids
  • 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)
slide22
Lipids

Fats & Oils

Derived from glycerol and fatty acids:

Weak intra-

molecular

attractive forces

between chains

slide23
Lipids
  • 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

slide24
Lipids

Soaps & Detergents

  • Hydrolyzed fats
  • A long chain carboxylate molecule:
slide25
Lipids

Soaps & Detergents

In H2O, forms

a micelle.

Grease & dirt get

trapped in the interior.

Micelle is H2O soluble

so can wash out dirt.

slide26
Lipids

2. Phospholipids:

  • Have hydrophobic and hydrophilic regions
  • Forms membranes
  • Precursors to prostaglandins
slide27
Lipids

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

slide28
Lipids

3. Cholesterol & Steroids

Cholesterol:

27 carbons

4 rings

8 stereocenters

Derived from terpenes

Cholesterol is a precursor to several steroidal hormones:

Testosterone (male hormone)

Estrone (female hormone)

slide29
Lipids

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.

slide30
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.

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