Proteins and Amino Acids Lecture

Flashcards covering the foundational concepts of protein chemistry, including amino acid structure, structural hierarchies, enzyme function, and the physical properties of proteins as discussed in the lecture notes.

Alpha carbon

The central carbon in an amino acid that is attached to four things: an amino group ($-NH_2$), a carboxyl group ($COOH$), a hydrogen atom, and an R group (side chain).

R-group

The side chain that differs between amino acids and determines polarity, charge, and special properties such as whether it is acidic, basic, or hydrophobic.

Zwitterion

A form of amino acid that has both a positive and negative charge but is overall neutral; at physilogical pH (~$7.4$), the amino group is protenated ($+$-charge) and the carboxyl group is deprotenated ($+$-charge).

Peptide bond

A covalent bond formed by a dehydration (condensation) reaction between the carboxyl carbon of one amino acid and the amino nitrogen of another, resulting in the release of water.

N-terminus

The end of a polypeptide sequence that finishes with a free amino group ($-NH_3^+$).

C-terminus

The end of a polypeptide sequence that finishes with a free carboxyl group ($-COO^-$).

Primary Structure

The linear sequence of amino acids in a polypeptide chain, held together by peptide bonds.

Secondary Structure

Local folding patterns of a polypeptide backbone (short range order) stabilized by hydrogen bonds between backbone $C=O$ and $N-H$ groups.

Alpha helix ($\alpha$-helix)

A type of local folding pattern found in the secondary structure of a protein.

Beta pleated sheets ($\beta$-sheets)

A type of secondary structure folding pattern, also noted as p-sheets.

Tertiary structure

The overall $3D$ shape of a single polypeptide chain created by interactions between R groups (side chains) and the environment.

Hydrophobic interactions

A stabilizing force for tertiary structure where non polar side chains cluster inside.

Disulfide bonds

Covalent $S-S$ bonds formed between cyestine residues that help stabilize the protein's tertiary structure.

Quaternary Structure

The arrangement of two or more polypeptide chains (subunits) into a functional protein complex, such as hemoglobin which has $4$ subunits.

Protein denaturation

The loss of $3D$ structure (secondary, tertiary, and quaternary) often leading to loss of function, caused by factors like high temperature, high salt concentration, extreme pH, detergents, or organic solvents.

Fibrous proteins

Long, strand like, structural proteins such as collagen and keritin.

Globular proteins

Compact, spherical, functional proteins such as enzymes, hormones, and antibodies.

Enzymes

Biological catalysts that speed up reactions by lowering the activation energy; most are proteins, though some are RNA-ribozymes.

Active site

The region of an enzyme where a substrate binds and a reaction occurs, with specificity determined by its chemistry and shape.

Substrate

The specific molecules that enzymes act on.

Essential amino acids

Amino acids that cannot be synthesized by the human body and must be obtained through the diet.

Isoelectric point ($pI$)

The pH at which a protein or amino acid has no net charge (the zwitterion form dominates), making the molecule least soluable and unable to move in an electric field.

Acidic amino acids

Amino acids like aspartate and glutamate whose side chain (R group) is negativley charged at physiological pH.

Basic amino acids

Amino acids like lysine, arginine, and histidine whose side chain (R group) is positivley charged at physiological pH.