Proteins and Amino Acids Overview

Study Notes

Amino acids are the fundamental units of proteins.
They have a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and an R group.
The R group varies among amino acids, giving them different properties.

Zwitterions are molecules with both a positive and a negative charge.
Amino acids exist as zwitterions at neutral pH.
The amino group gains a positive charge, and the carboxyl group loses a proton, gaining a negative charge.

Amino acids are classified based on the properties of their R groups.
Nonpolar amino acids contain mostly hydrocarbon chains in their R groups.
Polar amino acids contain polar functional groups like alcohols, thiols, and amides in their R groups.
Acidic amino acids have a carboxyl group in their R groups.
Basic amino acids have an amine group in their R groups.

Specific examples of amino acid structures are shown with their respective functional group classifications.

Amino acids link together via peptide bonds to form peptides (short chains) and proteins (long chains).
A peptide bond forms between the carboxyl group of one amino acid and the amino group of another amino acid.
Water is released in the process.
A dipeptide is formed from two amino acids.
A tripeptide is formed from three amino acids.
N-terminus is the end of the amino acid chain with the free amino group.
C-terminus is the end of the amino acid chain with a free carboxyl group.

Protein structure describes how amino acid sequences fold into complex three-dimensional shapes.
Primary structure: The linear sequence of amino acids with a unique sequence. Differences in sequence lead to different 3-D structures.
Secondary structure: Local folding of the polypeptide chain, often forming α-helices or β-sheets.
Tertiary structure: Three-dimensional arrangement of the entire polypeptide chain through various interactions between R groups. Specific interactions include hydrogen bonds, hydrophobic interactions, salt bridges, and disulfide bonds.
Quaternary structure: Structure formed from interactions between multiple polypeptide chains to form a functional protein complex

Enzymes are biological catalysts that speed up biochemical reactions millions to billions of times faster.
They do this without the need for extreme conditions like high temperatures or pressures.
Enzymes are highly specific to a particular reaction.
Each enzyme uniquely speeds up a specific reaction, and often use a "lock and key" mechanism (substrate binds to a specific region of the enzyme; the active site).
Enzymes are essential for sustaining life.

Substrates bind to the active site of an enzyme.
The enzyme's shape changes slightly to enhance substrate binding, and the enzyme/substrate complex is formed.
The reaction occurs, and the enzyme transforms substrates into products.
Products are released from the enzyme, and the enzyme returns to its original shape.