MOL100H23 lecture 3 protein structure and folding

Protein

Protein

A large biomolecule made up of amino acids that performs various functions in the body.

Folding

The process by which a protein adopts its three-dimensional structure.

Amino acids

The monomeric subunits of proteins that are connected to each other via peptide bonds.

Peptide bond

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

Polypeptide

A single chain of amino acids, which can be >30 amino acids long.

Protein conformation

The three-dimensional shape of a protein, determined by its amino acid sequence and interactions with other molecules.

Primary structure

The specific sequence of amino acids in a polypeptide chain.

Secondary structure

The local spatial arrangement of segments within a polypeptide chain, such as alpha helices and beta sheets.

Tertiary structure

The overall three-dimensional conformation of a single polypeptide chain.

Quaternary structure

The arrangement of multiple polypeptide chains in a protein complex.

Hydrogen bond

A weak non-covalent interaction between a hydrogen atom and an electronegative atom, such as oxygen or nitrogen.

Covalent bond

A strong chemical bond formed by the sharing of electron pairs between atoms.

Polymerization

The process of joining small subunits (monomers) together to form a larger molecule (polymer).

Macromolecules

Large molecules, such as proteins, nucleic acids, and polysaccharides, formed by the polymerization of smaller subunits.

Non-covalent interactions

Weak interactions between molecules, such as hydrogen bonds, van der Waals forces, and hydrophobic interactions.

Backbone

The repeating sequence of atoms in a polypeptide chain, consisting of the N-C-C backbone.

Side chain

The part of an amino acid that extends from the backbone and gives each amino acid its unique properties.

Alpha helix

A common secondary structure in proteins, characterized by a spiral-like shape stabilized by hydrogen bonds.

Beta sheet

Another common secondary structure in proteins, characterized by a sheet-like arrangement of beta strands stabilized by hydrogen bonds.

Beta turn

A type of secondary structure that connects two adjacent segments of a polypeptide chain, often forming a sharp bend.

Disulfide bond

A covalent bond formed between two cysteine residues, contributing to the stability of protein structure.

Domain

A distinct structural and functional unit within a protein, often folding autonomously and performing specific activities.

Structural motif

A recurring pattern of secondary structures that forms a specific three-dimensional shape within a protein.

Zinc finger

A structural motif in proteins that binds to zinc ions, often involved in DNA binding.

Functional domain

A domain within a protein that is responsible for a specific activity or function, such as kinase activity or DNA binding.

Quaternary structure

The number and position of polypeptides (subunits) in a multimeric protein.

Multimeric protein

Proteins consisting of more than one polypeptide chain.

Hydrophobic interactions

Interactions between nonpolar molecules in a hydrophilic environment.

Hydrogen bonds

Weak chemical bonds formed between hydrogen atoms and electronegative atoms.

Structural motifs

Repeating patterns of secondary structure elements in proteins.

Domains

Distinct functional and structural units within a protein.

Primary structure

The sequence of amino acids in a protein.

Biomolecular condensates

High-density protein aggregates without a defined quaternary structure.

Intrinsically disordered proteins

Proteins that lack a fixed conformation and can adopt different shapes when bound to other proteins.

AlphaFold

A software that predicts protein conformation with high accuracy.

Globular proteins

Compact, roundish proteins that are often water-soluble.

Fibrous proteins

Elongated proteins that are often stiff and not easily water-soluble.

Integral membrane proteins

Proteins with a domain embedded in cell or organelle membranes.

Functional classes of proteins

Categories based on the role and function of proteins.

Regulatory proteins

Proteins that control the activity of other proteins.

Structural proteins

Proteins that organize the cell and stabilize its shape.

Motor proteins

Proteins that move other proteins, vesicles, and organelles along the cytoskeleton.

Enzymes

Proteins that catalyze chemical reactions.

Transporter proteins

Proteins that move molecules across membranes.

Signaling molecules

Proteins that transmit information within or between cells.

Protein folding

The process by which a polypeptide chain adopts its native, functional conformation.

Denaturation

The disruption of a protein's secondary and tertiary structure, often caused by heat or chemical agents.

Peptide bonds

Covalent bonds that connect amino acids in a polypeptide chain.

Protein folding

The process of a protein molecule adopting its functional three-dimensional structure.

Chaperones

Proteins that assist in the folding of other proteins, ensuring they fold correctly and preventing them from interacting with other molecules prematurely.

Cytoplasm

The gel-like substance within a cell, where protein synthesis occurs.

Native state

The properly folded and functional conformation of a protein.

Ribosomes

Cellular structures responsible for protein synthesis.

Endoplasmic reticulum (ER)

A network of membranes involved in protein synthesis and folding.

Hsp70

Heat shock protein 70kDa, a type of molecular chaperone that binds to unfolded proteins and aids in their correct folding.

ATP

Adenosine triphosphate, a molecule that provides energy for cellular processes.

Chaperonins

Large protein "chambers" that provide a protected environment for proteins to fold correctly.

GroEL/GroES

Examples of chaperonins that consume ATP for their function.

Primary structure

The linear sequence of amino acids in a protein.

Peptide bonds

Chemical bonds that link amino acids together in a protein chain.

Proline

An amino acid with a unique structure that restricts rotation around peptide bonds.

Alpha carbon

The central carbon atom in an amino acid.

Side chains

The variable groups attached to the alpha carbon in an amino acid, which can influence protein folding.