Chapter 18

Proteins

Amino Acids

Compounds that contain both an amine and a carboxylic acid

Alpha carbon

The alpha of the carbon connecting everything. #spiderman keeping nyc together

Zwitterion

• When a compound contains both an amine and an acid, the hydrogen ion will move form the acid to the amine, resulting in a structure with one positive charge and one negative charge

means hybrid; mix of two different charges

Unique proteins

• most proteins are built from a combination of 20 different amino acids

• Unique because they have different side chains attached to the alpha carbon

• Side chain denoted as “R”

• Usually side chains only connect to alpha carbon except for proline

Proline

a ring that connects the alpha carbon to the amine nitrogen

• everyone connects to only alpha carbon but proline connects it to the nitrogen too

Hydrophobic (nonpolar) amino acids

side chains are nonpolar and thus NOT attracted to water

Hydrophilic (polar) amino acids

Side chains are polar and thus ARE attracted to water

Amino acids → side chain

• classified base on side chain

• Side chains with OH, SH, or an amide are considered polar neutral

• Side chains with a carboxylic acid are further classified as acidic

• Side chains with an amine are also classified as basic

Chirality of Amino acids

Same atoms different order. It looks the same but they aren’t the same if you flip them. Example: like your shoe is the same but if you flip it, you can’t fit the right shoe on left foot. But its the same thing, just a different order.

• Carbon atom is chiral if it is bonded to 4 completely different groups

• All of the amino acids contain a chiral alpha carbon EXCEPT GLYCINE

Enantiomers

It’s the atoms of the chirality. Like when it talkes about same atom different order the enantiomers is the atom. Example: the shoes are the enantiomer.

L-amino acids

Naturally occurring amino acids

D-amino acids

Enantiomer of L-amino acids (so it looks the same but where the molecule on the carbon is is not the same place) not found naturally

Peptide bond

Any chain of amino acids linked together by peptide bonds

• more amino acids can be added to create dipeptide → tripeptide → tetrapeptide, etc.

• Prefix indicates how. many are present. di=2 tri=3 tetra=4

Dipeptide bond

Peptide that consists of exactly two amino acids joined by one peptide bond

Polypeptide

Large number of amino acids linked together

• proteins are polypeptides typically with 100-500 amino acids

Primary Structure

Amino acids in protein are linked in a certain order

• Written from the N-terminus (free amino group) to the C-terminus (free carboxyl group).

Second Structure

Hydrogen bonds between peptide groups of the backbone commonly form two secondary structures, the alpha helix and the beta sheets

Tertiary Structure

Interactions between side chains of the amino acids in the proteins determine the final shape of a protein

Globular proteins (haha glob in glob shape)

• Hydrophobic amino acids tend to cluster together in the interior of a folded protein

• Hydrophilic amino acids tend to be on the surface of a folded protein

• Ionized acidic and basic amino acids are often found near each other

• A cysteine side chain can form a disulfide bond with another cysteine side chain

Other side chain interactions

• Some hydrophilic side chains can form side chain hydrogen bonding

• Ionized acidic and basic side chains can form a disulfide bridge

  • Disulfide bridge formation is an oxidation reaction that requires either O2 or a redox coenzyme like NAD+

Quaternary Structure

Formed when two or more polypeptides join to form an active protein like in hemoglobin

• Some proteins contain more than one polypeptide chains

• These chains are held together with a variety of the side chain interactions

Globular (hahaha glob)

Proteins are folded into a compact shape. Most water soluble proteins are globular

Fibrous

long narrow water insoluble protein

Membrane

proteins anchored in membrane

Enzymes

Proteins catalyst that speed up biological reactions

• highly specific and will only allow one of many possible products to form. (in a molecule, only happens in one spot)

• the substrate fits into the active sites of the enzyme much like a key fits into a lock (must be exact shape or won’t fit)

Substrate

the reactant in a biochemical reaction

Methods of Denaturation

• Changing the solvent

• Changing pH

• Raising the temperature

• Violent Agitation

• Adding ionic substances

Changing the solvent

• Organic solvents will shift the positions of hydrophobic and hydrophilic side chains

• Hydrophobic side chains will move to the exterior to interact with the nonpolar solvent

• Hydrophilic side chains will cluster in the interior

  • In water all of the nonpolar side chains are forced to the interior of the protein

  • In ethanol, mny of the nonpolar side chains move to the exterior of the protein

Changing pH

• if the pH of the solvent is changed, the ionization of the acidic and basic side chains will change and ion-ion attraction will be disrupted

• Lowering the pH will protonate (add a proton to) carboxylic acid side chains. Increasing the pH will deprotonate the amine side chain

  • At pH 7, aspartic acid and lysin have opposite charges and form an ion pair

  • At pH 2 (lowering pH), aspartic acid and lysins attract one another, but they cannot form an ion pair

Raising the temperature and Violent Agitation

• Increasing rate of temp or shaking violently will increase rate of denaturation

• raising temp and shaking violently speeds up the molecule movement

• vibrations will denature most proteins at 50-70 degrees F

• vigorous whipping of a protein solution will denature a protein

Adding ionic substances

• Addition of high concentrations of ionic compounds will interrupt ion-ion attraction

• Soaps will interrupt ion-ion attractions and hydrophilic and hydrophobic interactions

• Heavy metal ions such ads the ions of lead and mercury are strongly attracted to sulfur and will disrupt disulfide bridges (aka covalent bonds)

Essential amino acids

AMINO ACIDS BODY CAN’T MAKE SO HAS TO FIND IN DIET

Nonessential amino acid

AMINO ACIDSBODY MAKES IT SO YOU DONT HAVE TO FIND IN DIET

Animal products

COMPLETE proteins → CONTAINS ALL ESSENTIAL AMINO ACIDS

Most grains

INCOMPLETE proteins → LACK some essential amino acids