chapter 3: amino acids, peptides, proteins
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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:. - PowerPoint PPT PresentationTRANSCRIPT
Chapter 3: Amino Acids, Peptides, ProteinsHLY-JU-JS-CD
Amino Acids (AA) are the building blocks of peptides and proteinsPeptides generally contain 2-10
AAPolypeptides contain 10-100 AAProteins contain >100 AAGeneral structure of AA:
at pH ~7.4:
L-Amino Acids are the biologically relevant enantiomer
Of the 20 common AA, 10 of them are considered essentialsee page 67 of your book
Of the 20 common AA, 10 of them are considered essentialsee page 67 of your bookMnemonics: MILK FTW RHV“ESSENTIAL” = cannot be
produced de novo by the bodySome AA are conditionally
essentialNote though that there are now
more than 20 AA! (but we will only focus on the 20)
Selenocysteine is a derivative of Cys used to derive protein structures
The 20 AA can be grouped according to functional classesAliphatic (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.
There are 7 AA With Aliphatic Side Chains
Pro is an aliphatic AA with the amino and the acid group in one 5-membered ring
There are 3 AA with Aromatic Side Chains
Of the 6 polar uncharged AA, 2 have Hydroxyl Side Chains (except Tyr)
One AA has a Sulfhydryl (-SH) Side Chain
There are 3 AA With Basic Side Chains, 2 of them ccharged (RK)
Two AA have acidic side chains (DE). Their amide counterparts (NQ) are polar, uncharged
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
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+
Isoelectric point (pI) of an AA (or peptide/protein) is equal to the pH when net charge = 0
AA net charge is (-) if pH > pI, and (+) if pH < pIpI is estimated to be the
AVERAGE of the two pK values representing neutral species.
AA net charge is (-) if pH > pI, and (+) if pH < pICASE I: ONLY TWO IONIZABLE
GROUPS:Ex. Alanine:
AA net charge is (-) if pH > pI, and (+) if pH < pICase II: MORE THAN TWO
IONIZABLE GROUPS.Ex. Aspartic Acid
Activity, open book/notes BUT no talking (20 points)1. Determine the pI of Lysine.
Show ALL conformations and the net charges at different pH’s.
2. Draw the titration curve for Lysine.
3. 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
• Two ends are form: amino or N terminus and carboxyl or C terminus
• Peptide formation is a condensation reaction (loss of H2O)
AA can link together via AMIDE BOND to form peptidesVIDEO!
Peptides are cleaved via hydrolysisAcids, bases or enzymes can be
used to facilitate the hydrolysisIn 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 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 proteins1. Catalysts (Enzymes)
2. Transport & Storage
• The largest class of proteins, accelerate rates of reactions
DNA Polymerase
Hemoglobin
Catalase CK2 Kinase
OvalbuminSerum albumin Ion channels
There are six major classes of functions of proteins3. Structural
4. Generate MovementCollagen Keratin Silk Fibroin
Actin Myosin
There are six major classes of functions of proteins5. Regulation of Metabolism and Gene
Expression
6. Protection
Insulin Lac repressor
Immunoglobulin Thrombin and Fibrinogen
Venom Proteins
Proteins have four levels of structure