Lecture 3 - Intro to Proteins

BIOLOGY 173, EXAM 1, LECTURE 3

Proteins Function

• Do the work of the cell

  • Numerous different functions (e.g. enzymes, structural components. transport, etc.)

Macromolecules

• Large molecule made of smaller molecules linked together w/ covalent bonds

Monomers vs. Polymers Definition

• Monomer: smaller basic molecules (chemical building blocks)

• Polymer: Large molecule (macromolecule) made of multiple repeating monomer units

Protein’s Monomer and Polymer

• Monomer: AMINO ACIDS

  • Building blocks of protein

• Polymer: POLYPEPTIDES

  • ARE PROTEINS

Proteins Definition

• Chains of amino acids linked together via covalent bonds

  • 20 different types of amino acids

• Each protein has CARBOXYL and AMINO Group:

  • Carboxyl: COOH or –CO2H

  • Amino: -NH₂

R Group Side Chain Properties

• Non-polar side chains

  • No charged/electronegative atoms to form H bonds

  • Insoluble in H2O

• Polar side chains

  • Partial charges can form H bonds

  • Soluble in H2O

• Electrically charged side chains

  • Charged side chain forms H bonds

  • Highly soluble in H2O

R Group Differences

• Size

• Shape

• Reactivity

• Interactions w/ H2O

Polar v. Nonpolar R-groups

• Polar R-groups

  • Hydrophillic

  • Form H bonds

  • Readily dissolve in H2O

• Nonpolar R-groups

  • Hydrophobic

  • Don’t form H bonds

  • Pooly dissolve in H2O

Special Amino Acid

• Side chains potentially forming H or ionic bonds w/ other molecules

  • Hydroxyl functional group

  • Amino functional group (polar)

  • Carboxyl functional group (polar)

  • Sulfhydryl functional group (polar)

• Side chains w/ potential hydrophobic interactions b/w other molecules

  • Carbon atoms

  • Hydrogen atoms (polar)

Polypeptide Definition

• Long, continuous chain of amino acids linked together by peptide bonds

• Have an AMINO and CARBOXYL terminal

Peptide Bond Definition and Properties

• Proteins(made of many amino acids) linked with covalent bond

  • Links CARBOXYL and AMINO GROUPS b/w amino acids

Forming/Breaking Peptide Bonds

• Making Peptide Bond

  • Condensation reaction

  • Loses H2O

  • Requires energy

• Breaking Peptide Bond

  • Hydrolysis reaction

  • Adds H2O

  • Releases energy

Four Levels of Protein Structure Overview

• Primary Structure

• Secondary Structure

• Tertiary Structure

• Quarternary Structure

Primary Structure

• Linear sequence of amino acids

• Held together in chain via peptide bonds (covalent bonds) b/w amino acids

Protein Structure Overview

• Polypeptides (proteins) must fold into 3D structure to be functional

• Four levels of protein structure

  • Primary Structure: Sequence of amino acids

  • Secondary Structure: Interactions of nearby amino acids

  • Tertiary Structure: 3D Shape of a protein

  • Quaternary Structure: Interactions of polypeptide subunits

Secondary Structure

• Interactions b/w atoms in backbone

• Hydrogen bonds b/w CARBONYL (C=O) group and AMIDE (C=O AND -NH2) group of different amino acids

• Bending of protein allows H bonds to form:

  • Alpha-helices

  • Beta-strands OR Beta-sheets

• Depends on Primary Structure

  • Some more likely involved in alpha helices

  • Some more likely involved in beta sheets

Alpha Helices

• Secondary structure

• Held together via hydrogen bonds b/w AMIDE (C=O AND -NH2) and CARBONYL (C=O) groups

• Carbonyl group in backbone forms hydrogen bond w/ amide group 4 residues (4 amino acids) away

Beta Strands

• Secondary structure

• Held together via H bonds b/w AMIDE (C=O AND -NH2) and CARBONYL (C=O) groups

• Adjacent [next to] strands can run in:

  • same direction (parallel)

  • opposite directions [antiparallel]

Tertiary Structure

• Overall 3-D shape of polypeptide

• Held together by interactions b/w R groups

  • Hydrophobic interactions

  • Hydrogen bonds

  • Ionic bonds

  • Covalent (disulfide [S-S]) bonds

• Structures are diverse

Quaternary Structure

• Multiple polypeptide chains (SUBUNITS) come together in single complex

• Held together via:

  • Covalent Bonds

  • Ionic Bonds

  • Hydrogen Bonds

  • Hydrophobic Interactons

Subunits

• Multiple polypeptide chains

Denaturing Protein Causes

• By changing conditions in cell environment

  • Temperature

  • Salts (ions)

  • pH

Denaturation

• Loss of protein conformation

• Promoted by:

  • heat

  • pH change

  • chemicals

• inhibited by chaperones

Chaperone Proteins

• Folding aids

• Assists in folding other proteins

• Creates sheltered environment to allow protein to adopt specific configuration

• Helps w/ partially unfolded or unfolded proteins

• PREVENTS premature/inappropriate association of hydrophobic regions b/w denatured polypeptides

Protein Differences

• Proteins differ in

  • Charge

  • Polarity

  • Size

  • R Group