3. Protein Structure and F(x)

Based on Vocab and Learning Objectives

Prions

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

Molecular Chaperones

Proteins that facilitate folding and prevent inappropriate interactions between unfolded proteins

Condensation Reaction

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

R Group (Side Chain)

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

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.

Denaturation

Denatured (unfolded) proteins don’t function normally

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

Kuru

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

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.

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).

Solubility of Amino Acids

• polar & charged R-groups are hydrophilic - dissolve

• non-polar R-groups are hydrophobic - insolluble

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

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.

Primary Structure of Proteins

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

Secondary Structure of Proteins

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

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

Quaternary Structure of Proteins

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

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

Prion Diseases

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

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

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

Protein Folding & Function

normal protein folding is crucial & often spontaneous

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