Proteins

DNA Codes for Proteins

• It is estimated that there are about 20 –25 000 genes in the human genome.
  • A gene is simply a recipe for making a protein—genes code for proteins.
• It is estimated there are anywhere from 500 000 to a million proteins in humans.
• Proteins can be thought of as the “molecule of life.”
  • They are responsible for just about anything you can think of.
  • The diversity we see in humankind is due to proteins.

Diverse Functions of Proteins

• Structural support: spider silk, collagen in tendons and ligaments
• Storage of amino acids: egg white for embryos, casein in milk
• Transport of other substances: hemoglobin in blood
• Hormones: insulin
• Receptors of chemical signaling: nerve cell receptor proteins
• Contraction: actin and myosin in muscles
• Enzymes: speed up chemical reactions

Amino Acids

• Basic building blocks of proteins.
• All amino acids have a central carbon surrounded by four things:
  • Amino group
  • Carboxyl group
  • Hydrogen
  • R group
• All proteins are made from a combination of twenty different amino acids—the “alphabet” of proteins.
  • Each of the 20 amino acids has a different R group.
  • The R group is what makes each amino acid unique.

Unlabeled figure, page 68, Campbell's Biology, 5th Edition

The Importance of R Groups

• An R group can be as simple as a hydrogen or as complicated as a multiple ringed structure.
• The R group is the only thing that distinguishes amino acids from one another.
  • Since there are 20 different amino acids, there are 20 different R groups.
• The R groups dictate the chemistry of proteins.
  • They can be nonpolar and therefore hydrophobic.
  • They can be polar and therefore hydrophilic.
  • They can be electrically charged and therefore influenced by pH.

Amino Acids with Nonpolar R Groups

Part of figure 5.15, page 69, Campbell's Biology, 5th Edition

Amino Acids with Polar R Groups

Part of figure 5.15, page 69, Campbell's Biology, 5th Edition

Amino Acids with Electrically Charged R Groups

Part of figure 5.15, page 69, Campbell's Biology, 5th Edition

Making a Protein: a Polymer of Amino Acids

• Dehydration synthesis (condensation reaction)
  • The reaction between the carboxylic acid and amino functional groups produces water.
  • A peptide bond is formed.
• The resulting polymer of amino acids has several names which are all basically synonymous:
  • Protein
  • Peptide
  • Polypeptide

Figure 5.16(a), page 70, Campbell's Biology, 5th Edition

The Resulting Protein

• Note the peptide bonds between each amino acid.
• Note that the protein has one amino end and one carboxyl end.
• Note the different R groups; they are responsible for the unique chemistry of each polypeptide.

Figure 5.16(a), page 70, Campbell's Biology, 5th Edition

Review of Making a Protein

Unknown source

Structure Leads to Function

• Proteins have four levels of structural complexity.
• The structure of the protein is often responsible for its function.
• The structure of proteins is due to the way the R groups interact with one another.

Primary Structure

• The unique sequence of amino acids.
• The average length of a protein is around 300 amino acids long.

Figure 5.18, page 71, Campbell's Biology, 5th Edition

Secondary Structure

• Simple folding of the protein due to hydrogen bonding between what were the amino and carboxyl groups (not the R groups)
  • A hydrogen bond occurs when a hydrogen atom covalently bonded to an electronegative atom is attracted to another electronegative atom.
  • The hydrogen bond is a weak bond.
  • In living systems the electronegative partners are usually oxygen or nitrogen atoms.
• In proteins, the hydrogen bonding is between the double-bonded oxygen (electronegative atom) and the hydrogen attached to the nitrogen (electronegative atom).

Unknown source

• This hydrogen bonding results in two types of folding:
  • α-helix: a coil due to hydrogen bonding between every fourth amino acid
    • Discovered by Linus Pauling, the only person to win two unshared Nobel prizes (1954: chemistry; 1962: peace).
  • β-pleated sheet: a pleated structure that is due to hydrogen bonding between parallel strands of the polypeptide chain

Unknown source; Unknown source; Figure 5.20, Campbell's Biology, 5th Edition

Tertiary Structure

• Three-dimensional folding due to R-group interactions.
• Kinds of interactions:

  Hydrophobic

  Nonpolar R groups cluster together to avoid the watery environment they are in.

  Van der Waals

  Temporarily induced dipoles help bond nonpolar R groups.

  Hydrogen bonds

  Certain R groups form these bonds in the part of the molecule exposed to water; also occurs between R groups and peptide bonds or between peptide bonds.

  Ionic bonds

  Other R groups will form these bonds in the part of the molecule exposed to water

  Disulfide bridges

  The amino acid cysteine has a sulfhydryl group: if two cysteine R groups come together, they form this very strong covalent bond.
  
  Protein Folding Animation
  
  Protein Folding Animation #2

Unknown source

Quaternary Structure

• Two or more polypeptides linked together
• These polypeptides are held together by R-group interactions
  • These R-group interactions that hold the polypeptides together are the same as the ones seen in tertiary structure, except that the interactions hold the different polypeptides together.
• Collagen
  • Three polypeptides (each having an α-helix structure) are wound together into a quaternary structure.
  • Composes 40 % of the protein in the human body.
  • Strengthens connective tissue in the skin, bones, ligaments, and tendons.
• Hemoglobin
  • Four polypeptide subunits are linked together into a quaternary structure.
  • Each subunit can bind to an oxygen molecule.
  • Found in red blood cells, and used to help transport oxygen to all the cells in the body.
    
    Four levels of protein structure animation. Click on red arrow to see the four levels of protein structure.
    
    Animation of the protein folding process. Select button on the right that says, "Folding Illustration" and click through the lesson.

Figure 5.23, page 75, Campbell's Biology, 5th Edition

How to “Mess Up” a Protein

• Since the structure of a protein dictates its function, if the structure is somehow messed up then it will not longer function properly.
• Changing the structure of a protein is called denaturation.
• How to denature a protein:
  • Heat it: bonds break and it unravels.
  • Drastically change the pH: disrupts bonds that depend on the acidity of the solution in which the protein resides.
    • This is why living systems have buffers—chemicals that resist pH change.
    • Living systems can't afford to have their pH change very much or their proteins will begin to denature.
    • As soon as proteins denature, they no longer function properly, and since proteins control just about everything in living systems the organism dies.

Figure 3.11, Purves's Life: The Science of Biology, 7th Edition