Chapter 3: Protein Structure and Function
1. Most cell functions depend on proteins.
2. Amino acids are the building blocks of proteins. Amino acids vary in structure and
function because their side chains vary in composition.
3. Proteins vary widely in structure. The structure of a protein can be analyzed at four levels
that form a hierarchy, the amino acid sequence, substructures called: Alpha helices,
Betapleated sheets, interactions between amino acids that dictate a protein’s overall
shape, and combinations of individual proteins that make up larger, multiunit molecules.
4. In cells, most proteins are enzymes that function as catalysts. Chemical reactions occur
much faster when they are catalyzed by enzymes. During enzyme catalysis, the
reactants bind to an enzyme’s active site in a way that allows the reaction to proceed
3.1 Early Originoflife Experiments
Miller’s Experiment: Can simple molecules and kinetic energy lead to chemical evolution?
1. Attempted to produce microcosm of ancient Earth
2. Large flask represented atmosphere with methane gas, ammonia and hydrogen with high
3. Large flask was connected to small flask by glass tubing
4. Small flask had 200mL of water (Tiny ocean)
5. To connect mini atmosphere with mini ocean, Miller boiled the water constantly.
6. This added water vapour to the mix of gases in the large flask.
7. Water vapour circulated through the system
8. Formed simulated version of the prebiotic soup.
9. Miller sent electrical discharges across the electrodes he’d inserted into the atmosphere,
mini lightning bolts occurred.
10. After a day of boiling and sparking the solution began to turn pink
11. After a week it was deep red and cloudy.
12. Miller found large quantities of hydrogen cynaide and formaldehyde in the mini ocean
THEREFORE: Chemical evolution occurs readily if simple molecules with high free energy are
exposed to a source of kinetic energy.
3.2 Amino Acids and Polymerization
Structure: Carbon atoms forms bonds between:
1. NH2 The amino functional group
2. COOH The carboxyl functional group
3. H A hydrogen atom
4. an “Rgroup” an atom or group of atoms called a side chain. → In water at pH7, amino groups act as a base by attracting protons to form NH3+.
→ The carboxyl group is acidic because of the two highly electronegative oxygens. They pull
electrons away from the hydrogen atom. (COO)
Charges on these functional groups are important because:
1. They help amino acids stay in solution, where they can interact with one another and with
2. They alter amino acid chemical reactivity
Nonpolar Side Chains: No charged or electronegative atoms to form hydrogen bonds
Not soluble in water.
Polar Side Chains: Partial charges can form hydrogen bonds
Soluble in water
Electrically Charged Side Chains: Charged side chains form hydrogen bonds
Highly soluble in water.
How Do Amino Acids Link to Form Proteins?
● A molecular subunit like an amino acid, nucleotide, or sugar is called a monomer (“one
● Monomers bond together to form a polymer (“many parts”)
● Polymerization: linking monomers together to form polymers.
● Amino acids polymerize to form proteins.
● Macromolecule: made up of smaller molecules joined together.
● Protein= Macromolecule
● Amino acids (monomers) DO NOT selfassemble into macromolecules such as
● Polymerization decreases the disorder (entropy) of the molecules involved.
● Polymers are energetically much less stable than their component monomers.
● Polymerization reactions are ENDERGONIC and NONSPONTANEOUS
→ Monomers polymerize through condensation reactions, (AKA dehydration reactions).
Bond form results in the loss of a water molecule.
Hydrolysis: Breaks polymers apart by adding a water molecule.
→ In the prebiotic soup: hydrolysis dominates because it is exergonic, it increases entropy and
is favourable energetically.
→ Growing macromolecules are protected from hydrolysis if they cling or absorb to a mineral
→ In conditions that simulate hot, metalrich environments of undersea volcanoes, amino acid
formation and polymerization occurred.
→ Amino acids formed into polymers in cooler water if carbour and sulphur containing gas is present. (Commonly ejected from undersea volcanoes)
The Peptide Bond
→ When a bond forms between the carboxyl group of one amino acid and the amino group of
another. The CN bond that results from this condensation reaction is a peptide bond.
→ Because water is lost in the condensation reaction, the carboxyl group of the amino acid is
converted to a carbonyl functional group in the polymer.
→ Peptide bonds are usually stable because the electrons involved are partially shared between
the peptide bond and the neighbouring carbonyl functional group. The degree of electron sharing
is great enough that peptide bonds actually have some of the characteristics of a double bond.
Peptide bond is planar.
Polypeptide: When amino acids are linked by peptide bonds into a chain, the amino acids are
referred to as residues.
3 Points about the peptidebonded backbone of a polypeptide:
1. Rgroup orientation: The side chains present in each residue extend out from the
backbone, making it possible for them to interact with each other and with water.
2. Directionality: there is an amino group (NH3+) on one end of every polypeptide chain and
a carboxyl group (COO ) on the other.
→ Write amino acid sequences in the same direction:
→ End of the sequence with free amino group= Nterminus (aminoterminus)
→ End with free carboxyl group appears on the right hand side is the CTerminus
→ Amino acids are numbered starting from the Nterminus because that is where
proteins are synthesized in cells.
3. Flexibility: Peptide bonds itself cannot rotate because of the double bonds, but the single
bonds on either side of the peptide bond can rotate. Therefore structure as a whole is flexible.
● When the carboxyl group of one amino acid reacts with the amino group of another
amino acid, a strong covalent bond called a peptide bond forms.
● Polypeptides are polymers made up of amino acids.
3.3 Proteins are the most versatile large molecules in cells
Hemoglobin: carries oxygen from your lungs to cells throughout the body.
Carbonic anhydrase: on every RBC, is a protein that is important for moving carbon dioxide
from cells back to the lungs where it can be breathed out. (These are catalysts)
Proteins are crucial to most tasks required for cells to exist such as:
1. Catalysis: Many proteins are specialized to “catalyze” or speed up chemical
reactions. Enzyme: A protein that functions as a catalyst.
2. Defence: Proteins called antibodies and complement proteins attack and destroy
viruses and bacteria that cause disease.
3. Movement: motor proteins and contractile proteins are responsible for moving the
cell itself or for moving large molecules and other types of cargo inside the cell.
4. Signalling: Proteins are involved in carrying and receiving signals from cell to cell