1. Using full amino acid names (serylglycaltyrosylalanylleucine) 2. 3-letter code abbreviation (Ser-Gly-Tyr-Ala-Leu) 3. 1-letter code for longer peptides/proteins (SGYAL)

Amino Acids, Peptides, Proteins and Enzymes (Lec 2) Flashcards by Harley Waddell

AA Characteristics

All amino acids (except Proline) have:
−	acidic carboxyl group
−	basic amino group
−	α hydrogen
−	R substituent (side chain, makes AA unique)

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Chirality of AA’s

All amino acids are chiral (except glycine) meaning that they are non-superimposable on their mirror images (enantiomers).

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AA Classification

Nonpolar, aliphatic (7), Aromatic (3), Polar, uncharged (5), Positively charged (3), Negatively charged (2)

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Ionization of AA’s

At low pH, the amino acid exists in a positively charged form (cation)
− Carboxyl and amino groups are protonated

At high pH, the amino acid exists in a negatively charged form (anion)
− Carboxyl and amino groups are deprotonated

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Zwitterion Form

The condition in which an Amino Acid exists as both a positively and negative chargely charged molecule

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AA with Uncharged Sidechains

Amino Acids with uncarged side chains (E.g. Glycine)
• The pKa of the α-carboxyl group is 2.34.
• The pKa of the α-amino group is 9.6.
Glycine can therefore act as a buffer in 2 pH ranges

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Isoelectric Point

Specific pH point where AA carry a ‘net charge’ of 0

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Peptide Ends

Are NOT the same
1st side: Amino-terminal end (amino terminus = N-terminal)
2nd side: Carboxyl-terminal end

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Naming Peptides

Using full amino acid names (serylglycaltyrosylalanylleucine)
3-letter code abbreviation (Ser-Gly-Tyr-Ala-Leu)
1-letter code for longer peptides/proteins (SGYAL)

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Protein Composition

Polypetides and possibly; Cofactors, Coenzymes, Prosthetic groups, Covalently attached cofactors, etc.

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Protein Structure

Protein molecules adopt a specific 3D conformation (native fold) that is able to fullfil a specific biological function

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Native Fold

The 3-dimensional structure that proteins adopt when folding

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Four Levels of Protein Structure

Primary Structure (amino acid sequence joined by peptide bonds)
Secondary Structure (multiple primary structures arranged into units of secondary structure e.g. Helix or Sheets)
Tertiary Structure (built up of secondary structures)
Quaternary Structure (built up of tertiary structures)

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Primary Strucutre: Peptide Bonds

Sequence of amino acids bonded covalently in a line by peptide bonds. Each bond has some double-bond character due to resonance and CANNOT ROTATE

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Peptide Bond Resonance

Resonance causes the peptide bonds to:

be less reactive (very strong)
be rigid and nearly planar (not free to rotate)

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Secondary Structures

Refers to the local spatial arrangement of the polypeptide backbone. Produces 2 common arrangements:

Alpha Helixes
Beta Sheets

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Random Coil

Irregular arrangement of the polypeptide backbone

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The Alpha Helix

Stabilised by Hydrogen Bonds between nearby residues producing a helix structure. Right (clockwise) or Left (anti-clockwise) handed with 3.6 residues (5.4 Å) per turn.

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The Alpha Helix: Bonding

Stabilised by H Bonds between the backbone amides of n and n+4 amino acids (H bonds between every 4 amino acids)

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The Beta Sheet

The planarity of the peptide bond and tetrahedral geometry of the alpha carbon create a pleated sheet-like structure.

The Beta Sheet: Bonding

H Bonds between the backbone amides in different strands hold backbone together

Parallel Beta Sheet

H-Bonded strands run in the same direction

H bonds between strands are bent (weaker)
More resistant to temp.

Antiparallel Beta Sheet

H-Bonded strands run in opposite directions

H bonds between strands are linear (strong)
Less resistant to temp.

Tertiary Structures

Refers to the overall spatial arrangement of atoms (sheets or helixes) in a protein

Tertiary Structures: Bonding

Stabilized by numerous weak interactions between amino acid side chains. Largely hydrophobic and polar interactions, can be stabilized by disulfide bonds

Tertiary Structures: 2 Major Classes

1. Fibrous (water soluble) | 2. Globular (lipid soluble)

Quaternary Structures

Formed by the assembly of individual polypeptides into a larger functional cluster (Primary -> Secondary -> Tertiary -> Quaternary)

Protein Stability and Folding

A protein's function determined by its 3D structure

Protein Folding Speed

Proteins fold to lowest-energy fold in μsecs. Search for minimum is not random as direction to lowest energy native structure is thermodynamically favourable

Chaperones

Prevent misfolding and aggregation of onfolded peptides

Globular Protein Functions

Reverse binding of ligands, transport/storage of ions and molecules, defense against pathogens, muscular contraction, biological catalysis

Protein Interaction with other Molecules: Ligand

A molecule that binds to a protein is a Ligand. Ligands bind via same non-covalent interactions that dictate protein structure. Reversible, transient process of chemical equilibrium (A + B ↔AB).

Binding Specificity

1. Lock and Key Model | 2. Induced Fit Model

Specificity: Lock and Key Model

Assumes that proteins and ligands have complementary binding site which allows for high specificity. Complementary in: size, shape, charge, hydrophobic /hydrophilic properties

Specificity: Induced Fit

Assumes that both the protein and ligand exhibit conformational changes upon ligand binding. Allows for tighter binding of ligand and higher affinity for different ligand.

Enzymatic Catalysis

Enzymes increase reaction rate (k) by decreasing activation barriers (ΔG‡)

How to Lower ΔG‡

Enzymes use binding energy of substrates to organise reactants into a rigid ES complex. Allows reaction to become thermodynamically favourable

Catalytic Mechanisms

1. Acid-base catalysis: give or take protons 2. Covalent catalysis: change reaction paths 3. Metal Ion catalysis: use redox cofactors (pKa shifters)

Covalent Catalysis

A transient covalent bond between the enzyme and the substrate that changes the reaction pathway

Metal Ion Catalysis

Involves a metal ion bound to the enzyme that interacts with substrate to facilitate binding

Enzyme Inhibition

Compounds that decrease an enzyme's activity

Competitive Inhibition

Competes with substrate for binding - binds active site - does not affect catalysis

Competitive Inhibition: Lineweaver-Burk

* No change in Vmax; apparent increase in KM | * Lineweaver-Burk: lines intersect at the y-axis (1/Vmax).

Uncompetitive Inhibition

Only binds to ES complex - does not affect substrate binding - inhibits catalytic function

Uncompetitive Inhibition: Lineweaver-Burk

* Decrease in Vmax; apparent decrease in KM * No change in KM/Vmax * Lineweaver-Burk: lines are parallel.

Mixed Inhibition

Binds enzyme with or without substrate - binds to regulatory site - inhibits both substrate binding and catalysis

Mixed Inhibition: Lineweaver-Burk

* Decrease in Vmax; apparent change in KM * Lineweaver-Burk: lines intersect left from the y-axis. * Noncompetitive inhibitors are mixed inhibitors such that there is no change in KM.

Non-Covalent Modification (Allosteric)

Allosteric regulators are: - generally small chemicals - can be positive (improve enzymatic catalysis) - can be negative (reduce enzymatic catalysis)

Covalent Modification

Irreversible or reversible, positive or negative