Exam 1, Topic 7: Proteins

Protein

A functional unit composed of one or more polypeptides. Each polypeptide is composed of a linear sequence of amino acids.

Functions of proteins

Gene expression & regulation, movement, defense, metabolim, cell signaling, structural support, transport

Membrane proteins

Transmemvbrane, membrane-associated, lipid linked, peripheral

Amino acid

Monomer of proteins

Amino acid structure

Central carbon + Hydrogen + amino group (N-terminus) + carboxyl group (C-terminus) + R-group

Peptide bond

Covalent bond formed between C and N-terminus of 2 amino acids via dehydration synthesis

Polypeptide

A chain of amino acids

Direction of polypeptide synthesis

N-terminus to C-terminus (new amino acids always added to -COOH)

What happens when amino acids are dissolved in water?

At neutral pH (7), the amino acid ionizes so that the amino group has a partial positive due to the H+ ion and the carboxyl group has a partial negative

What form of amino acids are found in proteins?

L-amino acids

Where are D-amino acids found?

The cell walls of certain bacteria

Which amino acid does not have more than one isomeric form?

Glycerine

How are the 20 amino acids differentiated?

By their R-groups

Uncharged, polar R-groups

Contain C-O, C-N, or -OH

Uncharged, nonpolar R-groups

Contains lots of C and N (some S)

Positively charged (basic)

Contain H+ (have already accepted a proton)

Negatively charged (acidic)

Contain O- (have already donated a proton)

Primary structure

Linear amino acid sequence

Secondary structure

First level of folding; hydrogen bonding occurs between peptide bonds

Elements of secondary structure

α-helix, β-pleated sheet

How are α-helices formed?

Hydrogen bonding between the C=O in the top coil and the N-H in the bottom coil

How are β-pleated sheets formed?

Hydrogen bonding between the C=O and N-H when two segments of a polypeptide overlap in either a parallel (same directionality) or an antiparallel (opposite directionality) orientation

Prion

Misfolded protein that somehow induces normal versions of the protein to fold the same incorrect way

What structure is impacted in prions?

Secondary

How are prions harmful?

They impact the function of the protein and create plaques that lead to spongiform encephalopathies (sponge-like brain disease)

Examples of pongiform encephalopathies

Mad Cow, Scrapies, Creutzfeldt-Jakob

Tertiary structure

The unique 3D folded structure; the final, most complex structure of a single polypeptide (also the final conformation of some proteins)

What causes tertiary structure?

Interactions between R-groups and stabilizing forces

Stabilizing forces

Hydrogen bonding between polar/charged side chains, hydrogen bonding between hydrophilic side chains and the backbone, ionic bonding between acidic & basic amino acids, hydrophobic clustering of nonpolar side chains, Van der Waals forces, and disulfide linkages

Hydrophobic clustering

Water molecules surround a protein which causes it to contort so that hydrophobic side chains are on the inside and hydrophilic ones are on the outside

Random coiled regions

Secondary structure elements that can act as hinges when tertiary structure is being formed

Why is "random coiled regions" a terrible name?

NOT random, NOT coiled

Van der Waals forces

Attractions between atoms that are at an optimal distance from each other

Disulfide linkage

Covalent bond between 2 cysteine side chains

Quaternary structure

The 3D structure of a protein with multiple subunits

Subunit

A polypeptide in a protein with quaternary structure

Homodimer

A protein with 2 identical subunits

Heterodimer

A protein with 2 different subunits

Hemoglobin

A heterotetramer with 2 alpha and 2 beta subunits; distributes oxygen to the bloodstream

What is meant by the "stability" of a biomolecular force?

Whether or not the interaction is intentional; does it happen because it can happen or does it happen because the conditions are met?

Most stable biomolecular force

Disulfide linkage (Covalent bonding)

Second most stable biomolecular force

Ionic bonds

Third most stable biomolecular force

Hydrogen bonding + hydrophobic clusters

Least stable biomolecular force

Van der Waals forces (literally just happen for any atom)

Denaturation

Removal/inactivation of stabilizing forces; reverts protein to primary structure

Is the information for protein folding in its primary structure?

Yes; when a protein is renatured with the necessary stabilizing forces, it can refold properly

Chaperone proteins

Proteins that help other proteins fold appropriately

Sickle cell disease cause

A substitution mutation in the beta-globin gene