3. Protein Structure and F(x)

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21 Terms

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Prions

Altered folded forms of normal proteins that can induce misfolding in other proteins, associated with diseases.

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Molecular Chaperones

Proteins that facilitate folding and prevent inappropriate interactions between unfolded proteins

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Condensation Reaction

A chemical reaction where two molecules combine, resulting in the loss of a small molecule (usually water), forming a larger molecule.

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R Group (Side Chain)

The variable group attached to the central carbon of an amino acid that determines its specific characteristics and properties.

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Ionization

The process by which an atom or molecule gains or loses an electron, forming charged ions, in this context involving amino and carboxyl groups in amino acids.

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Denaturation

Denatured (unfolded) proteins don’t function normally

  • denatured = loss of 3D structure (unfolded) due to breakage of chemical bonds

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Kuru

A prion disease that affects the brain, characterized by neurodegeneration, associated with the consumption of infected human tissue.

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Attributes necessary for the origin of life

  1. Molecules must be able to store genetic information,

  2. They must catalyze chemical reactions

  3. They should have the ability to self-replicate.

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Structure of Amino Acids

Amino acids consist of a central carbon atom, an amino group (NH3+), a carboxyl group (COO-), a hydrogen atom, and a variable R group (side chain).

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Solubility of Amino Acids

  • polar & charged R-groups are hydrophilic - dissolve

  • non-polar R-groups are hydrophobic - insolluble

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Determine is an Amino Acid is Acidic, basic, or polar/nonpolar

Determined by R-group

  • Acidic - negative charge

  • Basic - positive charge

  • Polar - no charge, has Oxygen

  • Nonpolar - no charge, usually has C-H bond

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Explain how Peptide Bonds are formed

Through a condensation reaction where the carboxyl group of one amino acid reacts with the amino group of another, releasing water.

<p>Through a condensation reaction where the carboxyl group of one amino acid reacts with the amino group of another, releasing water.</p>
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Primary Structure of Proteins

The unique sequence of amino acids in a polypeptide chain, determining the protein's identity and function.

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Secondary Structure of Proteins

The localized folding of the polypeptide chain into alpha helices or beta-pleated sheets bc of hydrogen bonds

<p>The localized folding of the polypeptide chain into <strong>alpha helices</strong> or <strong>beta-pleated</strong> <strong>sheets</strong> bc of hydrogen bonds</p>
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Tertiary Structure of Proteins

The overall 3D shape of a SINGLE polypeptides.

  • cause chain of peptide bonds to bend & fold

  • caused by the 5 types of side chain interactions

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Quaternary Structure of Proteins

The overall 3D shape formed from 2 or more polypeptide chains into a single functional protein.

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Types of Interactions Affecting Protein Folding

Five types of interactions:

  1. Hydrophobic interactions - force hydrophic side chains together

  2. Hydrogen bonds,

  3. Ionic bonds

  4. Covalent -

  5. Van der Waals forces - weak electrical interactions between hydrophobic side chains

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Prion Diseases

Diseases caused by misfolded proteins that induce misfolding in normal proteins; Kuru is an example linked to consuming infected tissues.

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Key Points About Peptide Bonds

  1. R-group orientation

  2. Directionality

    • on 1 end of backbone (chain of peptide bonds) there is a N-terminus (amino group) and on the other a C-terminus (carboxyl group)

  3. Flexibility - the single bonds can rotate

<ol><li><p>R-group orientation</p></li><li><p>Directionality</p><ul><li><p>on 1 end of backbone (chain of peptide bonds) there is a <strong>N-terminus </strong>(amino group) and on the other a <strong>C-terminus </strong>(carboxyl group)</p></li></ul></li><li><p>Flexibility - the single bonds can rotate</p></li></ol><p></p>
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Define poly- , oligo-, peptides and protein

peptide = amino acids linked by peptide bonds

oligopeptide = chain of <50 amino acids

polypeptide = chain of >50 amino acids

protein = may be composed of multiple polypeptides, complete & functional

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Protein Folding & Function

normal protein folding is crucial & often spontaneous

  • folded proteins are more stable than unfolded ones, & energetically favorable