3 Biochem: Amino Acids

Basic building blocks of proteins

Amino acids

Most L-amino acids have ___ configuration, except —- with _ configuration.

Most L-amino acids have S configuration, except Cysteine with R configuration.

Rank the biomolecules in terms of sources of energy

1. Carbohydrates

2. Lipids

3. Amino acids

4. Nucleotides (last resort)

Amino Acids: All 20 (acronyms)

1. alkyl Ala VaLue Iso

2. OH S Ser ThrCsty Me

3. Carbox AspGlu AspGlu

4. basicN His LysA

5. aromatic Phe Tier 3

6. glycosine ~H, proline ~cyclic penta 1N

Amino acids consist of 3 main structures:

1. Amino (-NH2)

2. Carboxyl group (-COOH)

3. R group/side chains (differs)

Amino acid with R=Alkyl (4)

1. Alanine (-CH3)

2. Valine (-1,ethane)

3. Leucine (-2,propane)

4. Isoleucine (-1,propane) “Ile I”

nonpolar, hydrophobic but can be soluble in water
“Ala ValLeu Iso”

Amino acids with R=OH or S (4)

1. Serine (-metOH)

2. Threonine (-etOH)

3. Cysteine (-CH2SH)

4. Methionine (-C2H2-S-CH2)

very polar. (3) cysteine can form disulfide, which makes it more stable.
“Ser, ThrCsty Me”

Amino acids with R=Carboxyl group (4)

1. Aspartic Acid (-CH2COOH) “Asp, D”

2. Glutamic Acid (-C2H4COOH) “Glu, E”

3. Asparagine (-CH2CONH2) “Asn, N”

4. Glutamine (-C2H4CONH2) “Gln, Q”

3 and 4 are polar, 1 and 2 are acidic
“AspGlu AspGlu”

Amino acids with R=basic

1. Histidine (-cyclopentane 1,4-ene 3,5-NH.N)

2. Lysine (-butaneNH2) “Lys, K”

3. Arginine (-C3H6C=NHNH2) “Arg, R”

lone pair N

“His LysA”

Amino acids with R=aromatic

1. Phenylalanine (-CH2Ar) “Phe, F”

2. Tyrosine (-CH2ArOH) “Tyr, Y”

3. Tryptophan (-cyclohexane-1N-pentane dikit) “Try, W”

conjugation, (1) phenylalanine can absorb light (minimal)

“Phe, Tyr Tryp”

Essential Amino Acids (9)

Try THe VIP MaLL | WTH VI FMKL What The Hell VI? Fck My Killer Life

1. Tryptophan Try W

2. Threonine Thr T

3. Histidine His H

4. Valine Val V

5. Isoleucine Ile I

6. Phenylalanine Phe F

7. Methionine Met M

8. Lysine Lys K

9. Leucine Leu L

(our bodies can synthesize these, but the metabolic pathways to produce them require EXPENSIVE energy, so just prefer to outsource them than synthesizing)

The only amino acid with an R configuration

Cysteine

The only achiral amino acid

Glycine

The only secondary amino acid

Proline

Amino acid that has indole side chain (cyclohexane-1N-pentane dikit) and largest molecular weight.

Tryptophan

Amino acid that act as buffer due to imidazole chain (cyclopentane 1,4-ene 3,5-NH.N)

Histidine

Amino acid with guanidinium group (NH-C(=NH)NH), and is highly basic

Arginine

Point where pH has net electric charge is 0:

(PI) Isoelectric point “Zwitterionic”

Steps to Establish Protonated, Zwitterionic, and Deprotonated Amino Acid

1. write fully protonated X+

2. remove proton from alpha C X0

3. remove proton from alpha NH3 X-

4. remove proton from R side chain X-2

Chain of amino acids linked by peptide bonds

Polypeptides

Covalent amide bonds formed between the amino group of 1 amino acid, and 1 carboxyl group of another (through dehydration -H2O) → Dipeptide

Peptide bonds

Biologically Important Peptide: regulates blood sugar levels

Insulin

Biologically Important Peptide: raises blood sugar levels

Glucagon

Biologically Important Peptide: “social bonding” hormone, reproduction, childbirth contractions

Oxitocin

Biologically Important Peptide: busog hormone, sends signals when body is full

Lepdin

Biologically Important Peptide: regulates water retention and blood pressure

Vasopressin

Types of Biologically Active Peptide

1. Peptide and Protein Hormones

2. Neuropeptides

3. Peptide Antibiotic

4. Peptide Toxins

Most abundant protein in humans. Provides strength and elasticity. Structure: extended triple helix

Collagen

Structures of Protein

1. Primary = peptide bond, polypeptide chain
   (cant participate: Gly-too small; Pro-too bulky)

2. Secondary = H bond, a-helices and B-pleated sheets

3. Tertiary = folding and bending

   1. H bond

   2. disulfide bond

   3. electrostatic interactions

   4. hydrophobic interactions

4. Quaternary = interchain interactions, not required

What facilitates O transfer, and O storage?

Hemoglobin = O transfer, quaternary, cooperative bonding, maximum O2 affinity

Myoglobin = O storage, tertiary, noncooperative bonding, minimal O2 affinity

This proceess yields the different functional structures. The process of rapid acquisition of the unique native conformation from linear amino acid sequence.

Protein Folding

_____ assist the protein folding process and preventing the protein from misfolding or aggregating, ensuring the final stable structure needed for biological activity is reliably achieved.

Molecular ChaperonesSi

Simple vs Conjugated Proteins

Simple = composed only of amino acids

Complex = has a non-protein component or prosthetic group

Fibrous vs Globular Proteins

Fibrous = long, narrow, structural, repetitive AA sequence, less sensitive to changes, (e.g. collagen keratin actin myosin elastin) generally insoluble in water

Globular = spherical (protects H-phobic AA inside), functional, irregular AA sequence, sensitive to changes, (e.g. enzymes, hemoglobin, insulin), generally soluble in water

Classification: Solubility of Protein

SPAGG

Solubility

1. Prolamin = soluble in 60-80 EtOH (plant seeds)

2. Albumin = soluble in water (transport, storage)

3. Globulins = soluble in dilute saline (transport, immune response)

4. Glutelins = soluble in dilute acids or bases (storage)

Classification of Proteins: Function

FET3S

Function

1. Enzymatic = DNA polymerase, trypsin

2. Transport = hemoglobin, Na-K pump

3. Structure = collagen, actin, tubulin

4. Storage = ferritin (Fe), casein

5. Signaling = insulin, growth factors