Chapter 1-6 Notes: Introduction to Proteins, Amino Acids, and Enzyme Structure

Vocabulary flashcards covering key terms from the lecture notes on proteins, amino acids, and enzyme structure.

Hydroxyl group

A functional group consisting of an oxygen bonded to hydrogen (–OH); participates in condensation reactions to link monomers into polymers.

Condensation reaction (dehydration synthesis)

A reaction where two monomers join with the loss of a water molecule, forming a covalent bond between them.

Monomer

A small molecule that can join with others to form a polymer.

Polymerization

The process of linking monomers to form a polymer.

Information (biological)

The concept that life requires a system to store, transmit, and copy information (e.g., genetic information from DNA/RNA).

Replication

The process by which genetic information is copied to produce identical molecules or copies.

Amino acid

An organic molecule with an amino group, a carboxyl group, a central alpha carbon, and a variable R side chain; the building blocks of proteins.

Zwitterion

An amino acid at physiological pH with both a positive amino group and a negative carboxylate, giving a net neutral charge.

R group

The side chain attached to the alpha carbon of an amino acid; determines the amino acid’s properties.

Glycine

The simplest amino acid, with a hydrogen as its side chain.

20 amino acids

The set of amino acids commonly found in humans and many species.

Charged amino acids

Amino acids that carry a net charge at physiological pH; divided into acidic (negative) and basic (positive).

Acidic amino acids

Amino acids with negatively charged side chains.

Basic amino acids

Amino acids with positively charged side chains.

Polar amino acids

Amino acids with polar side chains capable of hydrogen bonding.

Nonpolar (hydrophobic) amino acids

Amino acids with nonpolar side chains that tend to be buried inside proteins away from water.

Amino group

The –NH2 group on an amino acid; participates in peptide bond formation.

Carboxyl group

The –COOH group on an amino acid; part of the backbone and forms peptide bonds.

Backbone

The repeating N–C–C units in a polypeptide chain that link amino acids together.

N-terminus

The end of a protein with a free amino group.

C-terminus

The end of a protein with a free carboxyl group.

Primary structure

The linear sequence of amino acids from N-terminus to C-terminus.

Three-letter abbreviations

Amino acid abbreviations using three letters (e.g., Asp for aspartate).

One-letter codes

Amino acid abbreviations using a single letter (e.g., D for aspartate).

Peptide bond

The covalent bond formed between the carboxyl of one amino acid and the amino group of the next.

Collagen

A structural protein with a triple-helix arrangement of three polypeptide chains.

TATA box binding protein

A DNA-binding protein rich in positively charged residues that interacts with the negatively charged DNA.

DNA

Deoxyribonucleic acid; carries genetic information and has a negatively charged backbone.

Pore (membrane protein)

A membrane protein that forms a channel allowing substances to pass through the cell membrane.

Globular protein

A compact, roughly spherical protein with diverse functions.

Protease

An enzyme that cleaves peptide bonds in proteins, aiding digestion.

Alpha helix

A common right-handed secondary structure stabilized by backbone hydrogen bonds.

Beta pleated sheet

A secondary structure where beta strands are connected by hydrogen bonds forming a sheet-like arrangement.

Beta sheet

Another term for the beta-pleated sheet secondary structure.

Random coil

An unstructured segment of a polypeptide lacking defined secondary structure.

Secondary structure

Local folding patterns such as alpha helices and beta sheets stabilized by backbone hydrogen bonds.

Tertiary structure

The overall three-dimensional shape of a single polypeptide, including side-chain interactions.

Quaternary structure

The arrangement of two or more polypeptide chains into a functional protein.

Chaperone

Proteins that assist in correct protein folding and prevent misfolding.

Heat shock protein 90 (HSP90)

A chaperone protein that helps proteins fold and respond to stress.

Hydrogen bond

A bond formed between a slightly positive hydrogen and a slightly negative atom (often O or N) that stabilizes structure.

Hydrophobic interactions

Attraction among nonpolar side chains that drives folding away from water.

Van der Waals interactions

Weak intermolecular forces that help pack atoms in close contact within a protein.

Hydrophobic core

The interior region of a folded protein rich in nonpolar amino acids, shielded from water.

Misfolding

Incorrect folding of a protein, potentially leading to loss of function or disease.

Active site

The region of an enzyme where the substrate binds and the reaction occurs.

Substrate

The molecule upon which an enzyme acts.

Enzyme

A protein (or RNA) that accelerates a chemical reaction by lowering activation energy, typically with a specific active site.

Catalysis

The acceleration of a chemical reaction by an enzyme or other catalyst.

Protein folding

The process by which a polypeptide chains folds into its functional three-dimensional shape.