1 The Atoms of Life H, O, C, N constitute 99% of the atoms in the human body. Why? ( S and P are also important in biomolecules) Ability to form covalent bonds by sharing electrons - covalent bonds are stronger Lightest atoms capable of forming such bonds strength of covalent bonds is inversely proportional to atomic weights of atoms so they form the strongest covalent bonds. C, N, O can form double bonds, C and N can form triple bonds 1s1s 2s2s 2p2p H 1s1s 2s2s 2p2p C 1s1s 2s2s 2p2p N 1s1s 2s2s 2p2p O 1 bond no lone pairs 4 bonds no lone pairs 3 bonds 3 pairs 2 bonds 2 lone pairs

2 Biomolecules are Carbon Compounds All biomolecules contain carbon very versatile in forming covalent bonds - can form the most - 4 four covalent bonds arranged tetrahedrally - adds to versatility can bond to N, O, and H can form single bonds to itself stably - unlike N and O - N-N and O-O single bonds are very unstable Atoms other than carbon are called heteroatoms in organic and biochemistry. 1s1s 2s2s 2p2p C CH 4 CH 3 OH CH 3 NH 2

3 Functional Groups Determine Physical and Chemical Properties Over 18 million organic molecules can be classified into 14 families. Classification depends on the functional groups present in the molecule. Below are the most important functional groups in biochemistry. The reactive part of the molecule (the part that has a functional).

4 Biological macromolecules have a Sense or Directionality They have Structural Polarity - they are not symmetrical Monomers have a head and a tail - joining occurs in a head-to-tail fashion My favorite class is Biochemistry not P. E. P.E. not Biochemistry is class favorite my Properties of Biomolecules Amino terminus Carboxy terminus Ala-Glu and Glu-Ala will have different reactive properties Ala-Glu Glu-Ala

5 More Properties of Biomolecules Biological macromolecules are informational Reading some biological macromolecules in the proper direction can specify information - like reading words in the proper direction gives information DNA read in the proper direction codes for genes Must have some mechanism for recognizing and deciphering the information, though. Biomolecules have unique and characteristic 3D shapes HIV-1 Protease with Inhibitor PDB code 1A30 What gives biomolecules their unique and characteristic shapes? Deoxygenated Human Hemoglobin PDB code 2HHB

6 Biomolecules interact through structural complementarity Life is dependent on the ability of millions of biomolecules to recognize and interact with one another in very specific ways. HIV-1 Protease with inhibitor Enzyme-substrate, DNA strands, receptor-ligand, antibody-antigen, sperm-egg, protein subunits, enzyme-inhibitors What determines structural complementarity?

7 May the Weak Forces Be with You Weak forces direct and maintain b iological structure covalent bonds hold atoms together to form molecules Intramolecular - occur between different parts of same molecule non-covalent forces determine the 3D shape of molecules (e.g. they determine the characteristic shape of proteins) Weak forces determine structural complementarity Intermolecular - occur between different molecules non-covalent forces direct enzyme-substrate interactions, hold 2 strands of DNA together and subunits of proteins, help ligands find the correct receptor (also partly responsible for physical properties) Weak forces permit transient interactions biomolecular interactions should be transient - ligands must come off receptors, DNA strands must separate for replication Weak forces demand certain environmental conditions weak forces are destroyed if a narrow range of conditions are not present pH, ionic strength, and temperature must be kept semi-constant or biological structure is destroyed (called denaturation) If structure is destroyed, so is function

8 There are 4 Major Types of Weak Forces in Biochemistry Van der Waals Interactions occurs between nuclei of one atom and electron cloud of another operates only over a limited inter-atomic distance very weak - many must add to be significant Atoms of Gln 121 from lysozyme fit neatly into a pocket on an antibody against lysozyme. The atoms of Gln 121 and those of the antibody are of the correct distance apart to have favorable van der Waals interactions. These interactions stabilize the binding of lysozyme to its antibody.

9 Hydrogen bonds occur between a hydrogen covalently bound to an electronegative atom (O or N) and the lone pair of a second electronegative atom (O or N) hydrogen bond donor - the hydrogen bound to the electronegative atom hydrogen bond acceptor - the second electronegative atom stronger than van der Waals hydrogen bonds are highly directional - form straight bonds between donor, hydrogen, and acceptor atoms. Very important in nucleic acid and protein structure GC base pair AT base pair The base pairs of nucleic acids such as DNA interact through hydrogen bonds and other weak chemical forces. It is largely the hydrogen bonds that direct DNA replication and transcription. linear H-bondnon-linear H-bond donor acceptor

10 Ionic Interactions (Salt Bridges) occur between a positively charged atom (like NH 4 + ) and a negatively charged atom (like COO - ) like nonmetal cations and metal anions to form salts can also have repulsive electrostatic interactions Protein strand Intramolecular ionic bonds between oppositely charged groups on amino acid residues in a protein

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12 Hydrophobic Interactions Warning: Many textbook descriptions of the hydrophobic effect are incorrect or incomplete driving force for DNA strand association, for protein folding, and for membrane formation hydrophobic - water hating - nonpolar hydrophilic - water loving - polar nonpolar molecules dont prefer to interact - it is the water that prefers non-ordered interaction with itself and excludes nonpolar molecules in the process. Water molecules would have to be ordered around a non-polar molecule (entropically disfavored). The aggregation of nonpolar requires less water to be ordered than if each nonpolar molecule were surrounded by water by itself. Non-polar amino acids are buried inside a protein and DNA bases are buried inside the helix. Related Application: The Power of Soap Hydrophobic interactions allow dirt and grease (nonpolar substances) to be washed away in water. Through the formation of micelles, the long, nonpolar, and hydrophobic tails of soap surround the particles of grease and dirt. The polar head groups of soap interact favorably with water. water Sodium oleate - amphiphilic Na + Polar head group Nonpolar hydrocarbon tail