Proteins and Enzymes Flashcards

Proteins and Enzymes

Lecture Overview

• Fundamentals of proteins and their importance.

• How proteins are assembled (some chemistry involved).

• Chemical bonds in biology and their significance.

• Amino acids as protein building blocks.

• Nomenclature around protein structure.

• Enzymes and their function.

• This serves as a foundation for second-year biochemistry (medical and biological science students).

Chemical Background

Atomic Structure

• Atoms with unfilled outer electron shells (not filled with eight electrons) are reactive.

• They form bonds with other atoms/molecules by sharing, losing, or gaining electrons.

• These bonds create molecules, which can form larger structures like proteins.

• The octet rule: atoms form stable molecules to achieve eight electrons in their outer shell.

• Chemical bonds: attractions linking atoms together (not always physical covalent links).

Types of Chemical Bonds

• Range from strongest to weakest:

  1. Covalent bond: sharing electrons between atoms (strongest).

  2. Ionic bond: attraction between positive and negative charges (can be nearly as strong as covalent).

  3. Hydrogen bond: weak attraction between hydrogen and oxygen due to partial charges.

  4. Hydrophobic interactions: proteins bits come together because of their hydrophobicity in aqueous environment.

  5. Van der Waals interactions: weak interactions between non-polar molecules.

• These bonds are critical for protein folding and function.

• Form and function go hand in hand at a molecular level. Protein shape dictates function.

Covalent Bonds

• Sharing of electron pairs between atoms.

• Important for metabolism, where electrons captured between atoms are released to produce ATP (energy-rich molecule).

• ATP drives many cellular reactions.

• Electrons are extracted from food molecules (carbohydrates, fats, proteins) to make energy for building other molecules.

Polar Covalent Bonds

• Example: water (H2O), where covalent bonds between hydrogen and oxygen create partial negative and positive sides.

• Polarity affects protein folding in an aqueous environment.

Ionic Bonds

• Electrons move from one atom to another (e.g., sodium and chloride).

• Results in ions (positive or negative).

• Similar ionic interactions occur between amino acids in proteins.

Isomerism

• Amino acids can form isomers.

  • Structural isomers: same components rearranged differently (important metabolically).

  • Optical isomers: mirror images of a molecule with a central carbon atom and four different groups attached.

  • Left and right-handed versions exist.

  • Even though made of the same constituent parts, a left or a right handed version of the same molecule can be picked up or detected by other molecules and proteins within the cell.

  • One fits, one doesn't to proteins within the cell.

• These are central carbon has four different groups around it, and they are left and right hand versions.

• The only way to get from one version to the other is to disassemble some bonds and rearrange them. You cannot rotate the molecule to turn it from one form to another.

Macromolecules in Living Things

• Four major types in all living organisms:

  1. Water: 60-70% of body mass (fluctuates).

  2. Ions and small molecules: small proportion.

  3. Macromolecules: ~25% (proteins, nucleic acids, carbohydrates, lipids).

     • Proteins: over half of macromolecules, determine cell functionality; proteins expressed differ between organs/tissues.

     • Nucleic acids: ~25% (DNA and RNA).

     • Carbohydrates: smaller chunk (polysaccharides, sugars).

     • Lipids: small chunk; primarily in membranes (cell and organelle membranes) and can be lipid-based hormones; depends on the cell type (e.g. adipocytes).

Protein Functions

• Proteins give cells their functionality (phenotype).

• Enzymes: biological catalysts that drive cellular reactions. Each reaction typically has a specific enzyme.

• Defensive proteins: antibodies.

• Hormonal/regulatory proteins: control reactions based on changing conditions.

• Receptors: cell surface and intracellular, respond to signals (hormonal).

• Storage proteins: store amino acids.

• Structural proteins: provide cell shape (e.g., neurons, liver cells).

• Transport proteins: carry molecules (e.g., hemoglobin).

• Gene regulatory proteins: control gene expression.

Amino Acids: Building Blocks of Proteins

• Proteins are polymers of 20 different amino acids.

• Formed from polypeptide chains (many amino acids linked together).

• Unbranched chain of amino acids that folds in on itself to define its structure and therefore its function.

• The sequence of amino acids determines its structure.

• Some proteins consist of multiple polypeptide chains working together.

Amino Acid Structure

• Each amino acid has:

  • Central carbon atom.

  • Hydrogen atom.

  • Amino group ($\NH_2$).

  • Carboxyl group ($\COOH$).

  • R group (residue or side chain): this is the part that differs between amino acids.

• The amino and carboxyl groups link amino acids.

• The carbon in the middle is sometimes called an alpha carbon, and it's an asymmetric carbon, so it has two forms.

• Only L-amino acids are incorporated into proteins expressed from genes, because ribosome recognizes L form amino acids.

R Groups and Chemical Properties

• R groups impact chemical and functional properties.

• Amino acids classified by side chains:

  • Electrically charged & hydrophilic: can hydrogen bond with water (positive or negative).

  • Polar & uncharged: interact with water molecules (hydrophilic).

  • Non-polar: hydrophobic.

• In an aqueous environment, polypeptides fold with hydrophilic amino acids on the outside and hydrophobic ones buried inside.

Special Cases

• Cysteine: See below.

• Glycine: smallest amino acid, increases flexibility of polypeptide chain.

• Proline: causes kinks or sharp bends.

• Methionine: initiates amino acid chains (start codon), always that start codon coded amino acid.

• Cysteine:

  • Forms disulfide bridges (covalent links between R groups).

  • Important in protein folding.

  • Far more common in extracellular proteins.

  • Disulfide bonds stabilize proteins (like insulin) in harsh environments like the bloodstream and help to keep the two smaller chains of A and B chains together, because if they're not together, then the insulin can't function properly.

  • Insulin is a good example, it's expressed as a single peptide that folds up into proinsulin. A whole chunk of its structure is chopped off to give the active insulin protein , which is recognized then by insulin receptors on cells in your body.

Peptide Bonds

• Link amino acids together.

• Formed between the carboxyl group of one amino acid and the amino group of another.

• Condensation reaction (creates water).

• Opposite reaction: hydrolysis (breaking apart with water).

• Hydrolyzed protein: protein broken down because covalent links between amino acids have been cleaved.

• The bond is planar (flat), which is important structurally.

• No rotation around the central carbon-nitrogen bond, meaning oxygen and hydrogen stick out in opposite directions.

• Electrons flip flop between the oxygen and nitrogen, maintaining structure. Act as a double bond which can't rotate around each other.

Protein Structure

Primary Structure

• The sequence of amino acids.

• Dictates all other structures of the protein and how they occur.

• Number of possible proteins from 20 amino acids is huge.

• Peptide linkage is the peptide bond between each one, and they can't rotate around each other, so you always have oxygen sticking up and always a hydrogen sticking down.

Secondary Structure

• Alpha helices and beta sheets (or beta-pleated sheets).

• Formed by hydrogen bonding between oxygen and hydrogen atoms in the peptide bonds.

• Oxygen interacts with hydrogen somewhere up the chain and vice versa.

• Planar structures are crucial for this.

• Alpha helices the hydrogen bonds line up with each other.

• Beta pleated sheets are pleated like a concertina; here's one example of the oxygens sticking down and one sticking up.

• Alpha helices and beta sheets often form the functional parts of proteins.

Tertiary Structure

• How the protein folds in 3D space with alpha helices, beta sheets, and unstructured regions.

• Surface is critical for interactions within the cell.

• The hydrogen bonds align in rows in the alpha helix and lineup in a line on the beta sheet.

• The final tertiary structure is determined by the interaction of the R groups from the individual amino acids.

• It is determined by R groups from amino acids (charges, hydrophobic/hydrophilic properties, disulfide bonds).

Protein Visualization

• Be aware of what proteins actually look like.

• Ribbon structures highlight functional parts (alpha helices, beta sheets).

• Proteins aren't empty ribbons; they're solid.

Protein Folding

• Central dogma: information flows from DNA to RNA to protein.

• Information for protein folding is encoded in the amino acid sequence (chemical signatures).

• Denaturing a protein (unfolding it) removes its function.

• Removing denaturing agents (heat/chemicals) allows refolding into its functional form.

Quaternary Structure

• Not all proteins have this.

• Involves multiple subunits (polypeptides) coming together.

• Example: hemoglobin (four subunits) with heme groups that bind oxygen; two beta peptides and two alpha peptides.

• Without all subunits, hemoglobin doesn't function.

• Shape important for subunits to fit together.

• Interactions: ionic bonding, hydrogen bonding, van der Waals forces, hydrophobic interactions.

Factors Affecting Protein Structure

• High temperature.

• pH changes.

• High polar molecule concentrations.

• Non-polar substances.