1A: Structure & function of proteins and their constituent amino acids Flashcards Preview

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1

Amino Acids

Contain a carboxylic group, alpha carbon, alpha amino group and alpha hydrogen

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Absolute Configuration at the α position (Optical Activity)

D (+) = clockwise rotation of polarized light
L (-) = counterclockwise rotation of polarized light

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Naturally occurring amino acids

L-Amino Acids

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Absolute Configuration at the α position (Stereochemistry)

R (right) vs S (left)

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Amino Acids as Dipolar Ions

Low pH = cationic
High pH = anionic
Isoelectric Point = Neutral Zwitterion

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Acidic Amino Acids [2] (-)

Aspartic Acid (Aspartate)
Glutamic Acid (Glutamate)

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Basic Amino Acids [3] (+)

Arginine
Lysine
Histidine

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Hydrophobic/Lipophilic Amino Acids [8]

Alanine (A)
Valine (V)
Leucine (L)
Isoleucine (I)
Proline (P)
Methionine (M)
Phenylalanine (F)
Tryptophan (W)

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Hydrophilic/Lipophobic Amino Acids [12]

Glycine (G)
Serine (S)
Threonine (T)
Arginine (R)
Asparagine (N)
Aspartate (D)
Glutamate (E)
Glutamine (Q)
Cysteine (C)
Lysine (K)
Histidine (H)
Tyrosine (Y)

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Sulfur Linkage Reaction

Cysteine-SH + HS-Cysteine -> Cystine-S-S-Cystine

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Importance of cystine

Important for tertiary structure

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How are peptide bonds formed?

The carboxyl group of one amino acid reacts with the amino group of a second amino acid; releases water a product

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How are peptide bonds broken?

A water molecule is introduced into the peptide bond releasing a free amino acid from the peptide chain

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Primary Structure of Proteins

Linear sequence of amino acids, linked by peptide bonds

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Secondary Structures of Proteins

Consists of alpha helices and beta sheets; linked by hydrogen bonds

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Tertiary Structure of Proteins

Chains of peptides folded onto themselves, linked by disulfide bonds, ionic interactions, van der waals, hydrogen bonds

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Importance of Proline

Introduces kinks that cause turns

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Importance of Cysteine/Cystine

Forms disulfide bonds

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Hydrophobic Bonding

Occurs within the core of proteins between the non-polar/hydrophobic R-groups creating stability (hydrophobic collapse)

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Quaternary Structure of Proteins

3D structure with multiple subunits of proteins interacting; linked by non-covalent interactions between subunits

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Conformational Stability

The dG difference between the native state (folded) and unfolded state of a protein

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Denaturation

Occurs due to temperature, chemicals, enzymes and pH

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How does temperature denature?

It disrupts all bonding expect peptide bonds; this increases hydrophobic interactions since active globular proteins will fold

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How do chemicals denature?

They break hydrogen bonds, disrupts all except peptide bonds

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How do enzymes denature?

They break down directly to peptide bonds

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How does pH denature?

Ionic bonds are broken down so tertiary and quaternary structures are disrupted

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How does a solvation layer affect stability?

It decreases the amount of ionic interactions between proteins

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Isoelectric Point (Separation)

Proteins move until they reach the pH equal to their isoelectric point in electrophoresis

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Electrophoresis (Separation)

Separates charged particles using an electric field

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Agarose Gel Electrophoresis

Separates nucleic acids; their negatively charged structures move toward the cathode and help with identification of sizes of particles