Amino Acids:

Peptide Bond

1.Considering only 26 symbols in the English alphabet, how come we can make so many words? 2.How is it possible to make thousands of different proteins from just 20 amino acids?

Properties of Water H2OH2OH2OH2O Water Molecules are Polar:

Electrons spend more time around the O than the H. The “O” side is more negative and “H” side more positive. The + and – sides attract one another  Water is Sticky! Water Molecules are Polar:Notes Animation of water behavior Animation: Closeups on WATER

- + Polar Solute Non- Polar

Polar substances – Mix well with water (Sugar, Salt, Water colors…) Notes Non-polar substances – Do not mix well with water (Oils, waxes, Fats) The same can be said In other terms..

WATER: Observations 1. Capillary climbing 2. Glass versus Wax 3. Paper chromatography 4. Drops on Penny 5. Pepper on water and… soap! 6. Phooo on wet towel! 7. Oil and water?! For each – describe what you see..

1.What is in the surrounding of a protein within the living organism? xxxxxxxx 2.Accordingly – where do you expect to find POLAR amino acid, and a NON-POLAR amino acids? Think about points A and B. A B x x x x x x x x x

* Elimination of water upon formation. * Peptide bond is flat.

Non-polar Aromatic + Charged - Charged Groups of Amino acids: Residues (R’s): Polar, uncharged

* Water-loving (polar): - Charged: Has an NH3+, or COO- - not charged: Typically, contain an oxygen. * Water-’hating’ (non-polar): -Typically, R’s do not contain any oxygen, or Aromatic. * Small – Flexible (Glycine) Amino Acid Types:

Diversity of Amino Acid Sequences generated diversity at least as large of 3D structures. Lamin

..but how does the amino acid sequences (primary structure) determine the 3D structure? The side chains interact:

Types of interactions: Hydrogen Bond Disulfide Bond VanDerWaals (hydrophobic) Electrostatic

Hydrogen Bond Occurs between a hydrogen ‘donor’ and ‘acceptor’: Donor = Has a partially charged H. Acceptor = Has a partially negatively charged.

Electrostatic Interactions: Opposite charge – attraction Same charge = repultion

Disulfide Bonds An actual covalent bond. Is relatively strong, but not very common.

Van der Waals Interactions * Between atoms that are close enough: Attraction between electrons of one atom to the nucleus of another. * The weakest of all, but numerous. * Associated with hydrophobic exclusion.

Hydrophobic Exclusion: Rejection by the surrounding water forces R groups to come together, minimizing the contact with water. A MAJOR force in protein folding into domains. Hydrophobic folding

Protein folding - simplified PPi hydrolase Collagen InsulinAntibody

Modeling with the tubers: 1)Place the push pins in any order that you would like, about 2-inches apart. 2)Write down a possible order of amino acids that correspond to the colors of the pins 3)Fold the protein “by the rules.” PHOTO!

Reflect on your experience trying to fold the proteins ‘by the rules’: 1.Which guidelines did you try to apply? 2.Why do you think it is so hard to predict the actual shape of a protein from its amino acid sequence?

CC O ON HH H H Amino acid:

Let’s build a peptide (short protein): A. Receive a page of an amino acid. Draw in the atoms of the “R” group. B. Color the R group by category: Charged positively – Blue Charged negatively – Red Polar uncharged – Black Non-polar, Aromatic – Yellow Step One: Prepare amino acid

Step Two: Connecting by peptide bond 3. Find the –OH group for the COOH and the –H from the NH2 side. Circle them. 4. With your neighbor: One cuts out the OH, and the other the –H. 5. Bring the C=O and N-H together with a bond. Use Clip to connect.

We just made a class – size peptide. It has two edges: COOH and a NH2. The 3-dimentional structure will be determined by the categories of the amino acids (coloring)..

Enzymes, as proteins, are sensitive to both temperature and pH. But what IS pH?

pH: Power of Hydrogen pH is the measurement of the concentration of H + ions in the solution. Acids are high in H + bases are low in H + (high in OH - ). pH ranges from 1 to 14: 7114 High H+ Low H+ AcidsBases Neutral

The pH Scale Measures the Concentration of H + ions. AcidicBasic (Colors of an indicator) Low pHHigh pH

Hydrogen Bonds are interrupted by acids and sometimes by bases. Many of the forces that hold a protein fold together are hydrogen bonds: O-H ···· O H+H+

To summarize: Enzymes, as all proteins, can loose their shape under conditions of high temperatures and low pH and high pH.