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Chapter 3: Amino Acids, Peptides, Proteins. HLY-JU-JS-CD. Amino Acids (AA) are the building blocks of peptides and proteins. Peptides generally contain 2-10 AA Polypeptides contain 10-100 AA Proteins contain >100 AA General structure of AA: at pH ~7.4:.

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amino acids aa are the building blocks of peptides and proteins
Amino Acids (AA) are the building blocks of peptides and proteins
  • Peptides generally contain 2-10 AA
  • Polypeptides contain 10-100 AA
  • Proteins contain >100 AA

General structure of AA:

at pH ~7.4:

of the 20 common aa 10 of them are considered essential1
Of the 20 common AA, 10 of them are considered essential
  • see page 67 of your book
  • Mnemonics: MILK FTW RHV
  • “ESSENTIAL” = cannot be produced de novo by the body
  • Some AA are conditionally essential
  • Note though that there are now more than 20 AA! (but we will only focus on the 20)
the 20 aa can be grouped according to functional classes
The 20 AA can be grouped according to functional classes
  • Aliphatic (GAVLIMP)
  • Aromatic (WYF)
  • Polar, uncharged (CHNQST)
  • Polar, charged – acidic (DE)
  • Polar, charged – basic (RK)

*Histidine is basic but uncharged

See structures on page 70 of your book.

two aa have acidic side chains de their amide counterparts nq are polar uncharged
Two AA have acidic side chains (DE). Their amide counterparts (NQ) are polar, uncharged
chemical reactivity of aa are dependent on their r group
Chemical reactivity of AA are dependent on their “R group”
  • AA structures and reactivity will be important in understanding protein structures and functions
  • AA electric charges also affects protein structure and function
slide20

Isoelectric point (pI) of an AA (or peptide/protein) is equal to the pH when net charge = 0

pK1: -COOH  -COO- + H+

pK2: -NH3+ -NH2 + H+

pKR: -RH  -R- + H+

aa net charge is if ph pi and if ph pi
AA net charge is (-) if pH > pI, and (+) if pH < pI
  • pI is estimated to be the AVERAGE of the two pK values representing neutral species.
aa net charge is if ph pi and if ph pi1
AA net charge is (-) if pH > pI, and (+) if pH < pI
  • CASE I: ONLY TWO IONIZABLE GROUPS:

Ex. Alanine:

aa net charge is if ph pi and if ph pi2
AA net charge is (-) if pH > pI, and (+) if pH < pI

Case II: MORE THAN TWO IONIZABLE GROUPS.

Ex. Aspartic Acid

activity open book notes but no talking 20 points
Activity, open book/notes BUT no talking (20 points)
  • Determine the pI of Lysine. Show ALL conformations and the net charges at different pH’s.
  • Draw the titration curve for Lysine.
  • Determine the inflection points, and draw the structure/s of Lysine at each interval (i.e., before pK1, at pK1, after pK1 but before pK2, etc.)
aa can link together via amide bond to form peptides
AA can link together via AMIDE BOND to form peptides
  • Two ends are form: amino or N terminus and carboxyl or C terminus
  • Peptide formation is a condensation reaction (loss of H2O)
peptides are cleaved via hydrolysis
Peptides are cleaved via hydrolysis
  • Acids, bases or enzymes can be used to facilitate the hydrolysis
  • In our stomach or intestine, peptidases or proteases are present
  • Enzymes specific to some AA are used for protein analysis (more of this later )
proteins in our body play different important roles
Proteins in our body play different important roles
  • Biological functions of proteins depend on the AA sequence (central dogma!)
  • Six major classes of protein functions:
    • Enzyme
    • Transport and Storage Proteins
    • Structural Proteins
    • Muscle Contraction and Mobility Proteins
    • Regulatory and Receptor Proteins
    • Immune or Defense Proteins
there are six major classes of functions of proteins
There are six major classes of functions of proteins
  • Catalysts (Enzymes)
  • Transport & Storage
  • The largest class of proteins, accelerate rates of reactions

DNA Polymerase

CK2 Kinase

Catalase

Ovalbumin

Ion channels

Hemoglobin

Serum albumin

there are six major classes of functions of proteins1
There are six major classes of functions of proteins
  • Structural
  • Generate Movement

Collagen

Keratin

Silk Fibroin

Actin

Myosin

there are six major classes of functions of proteins2
There are six major classes of functions of proteins
  • Regulation of Metabolism and Gene Expression
  • Protection

Lac repressor

Insulin

Thrombin and Fibrinogen

Venom Proteins

Immunoglobulin