Chapter 2 Flashcards
Brownian motion
Movement of a molecule or ion along a random path. (h20 molecules)
Brownian mo-on is the movement of molecules powered by random fluctua-ons of environmental energy. •
Brownian mo-on of water ini-ates many biochemical interac-ons. •
Thermal motions powers biological rxns
Weak bonds permit dynamic interac-ons that form the basis of biochemistry. •
Water is the solvent of life in which most biochemical reac-ons occur. • Diffusion of biomolecules throughout cells, within organisms, and within the environment.
Brownian motion
Stabilizing Forces in Biological Molecules
- Chemical (Covalent) bonds – Biomolecules are mainly constructed by strong covalent bonds
But non-‐covalent interac-ons drama-cally influence biochemistry - Electrosta-c interac-ons
- Hydrogen bonds
- Van der Waal interac-ons
- Hydrophobic interac-ons
Strength in Numbers
Water molecule
Water is an asymmetric molecule. •
Water is a polar molecule, with the oxygen atom carrying a par-al nega-ve charge and the hydrogen atoms carrying par-al posi-ve charges. • The polarity of water also accounts for its ability to dissolve many important biochemical molecules.
Living organisms are largely composed of water (the average adult human body is composed of ~65% water by weight).
Weak Interac-ons are Important Biochemical Proper-es
The energy of an electrosta-c interac-on between two charges is give by Coulomb’s Law: E = kq 1 q 2 /Dr •
E is the energy of the interac-on •
q 1 and q 2 are the charges on the ions •
D is the dielectric constant •
r is the distance between the two ions (in Angstroms, Å) •
k is a propor-onality constant •
The dielectric constant is 1 in a vacuum, and 80 in water. •
Thus, water weakens electrosta-c interac-ons.
Hydrogen Bonds
Form between an electronega-ve atom and a hydrogen atom. • Hydrogen bonds are not unique to water molecules and can occur whenever H is covalently bonded to an electronega-ve atom. Examples: amino acids in proteins, nucleo-des in DNA or RNA • Hydrogen bonds are essen-ally a par-al electrosta-c interac-on.
Bond energies of 1 – 5 kcal/mol, depending on geometry at atoms involved (much weaker than covalent bonds). •
Lengths of hydrogen bonds are longer than covalent bonds.
Hydrogen bonding in water
Hydrogen bonds are weak and are con-nuously breaking and reforming. •
The polarity of water allows the forma-on of hydrogen bonds between water molecules and accounts for the cohesiveness of water. •
Each water molecule is capable of dona-ng 2 hydrogen bonds and accep-ng 2 hydrogen bonds (hydrogen bonds shown in green). (4 total bonds)
Water disrupts hydrogen bonds between two molecules by compe-ng for the hydrogen bonding capability.
van der Waals Interac-ons
Nonpolar, uncharged biomolecules can interact via van der Waals contacts. •
Result from the fluctua-ng asymmetry of electrons in the atom causing flee-ng dipoles. •
. • Typical van der Waals interac-ons have energies of 0.5 to 1.0 kcal/mole. •
This principle is relevant to chemical interac-ons in DNA, lipids, and proteins.
Van der waals contact distance
van der Waals contact distance = the distance that provides op-mal aVrac-on between two atoms. •
As the distance between atoms increases, aVrac-on decreases, consistent with Coulomb’s Law. •
At shorter distances, the electron clouds of the two atoms repel each other
Van der waals and assymetry
Assymetry forms in E clouds as clouds approach each other, leads to redistribution of electrons (not evenly distributed around nucleus)
Mul-ple Weak Bonds Contribute to the Stability of Biological Structures
Hydrogen bonds and van der Waals between nucleo-des contribute to the stability of the DNA double helix. •
However, these bonds are weak enough to be broken by the enzymes of DNA metabolism, thereby allowing access to the gene-c informa-on. • These weak bonds are essen-al for replica-on and transcrip-on of the DNA.
No covalent bonds
DNA strands are held together by hydrogen bonds and van der Waals interactions.
Nucleotides form base pairs via hydrogen bonds.
Hydrophobic Effect & Entropy
Spontaneous clustering of hydrophobic molecules in water is called the hydrophobic effect. •
Powered by the increase in the entropy of water that results when hydrophobic molecules come together. •
As water is a polar molecule, it does not effec-vely interact with or dissolve nonpolar molecules (e.g., they cannot form hydrogen bonds). • As a consequence, water forms a cage-‐like structure around nonpolar molecules.
Waters that par-cipate in this cage have reduced entropy (i.e., they lose their freedom to diffuse freely). This is energe-cally unfavorable. •
When nonpolar molecules coalesce, fewer waters are required to form this cage, leading to water molecules being released into solu-on. • This results in more disorder of water => increased entropy = energe-cally favorable.
Non polar coalesce because it leads to release of water, which is energe-cally favorable
Increased entropy of water as they are released because they are now free to move about
Membrane Forma-on is Powered by the Hydrophobic Effect
Phospholipids have both hydrophilic and hydrophobic proper-es = amphipathic. •
In an aqueous environment, phospholipids form membranes.
Hydrophilic head group forms hydrogen bonds with water, but hydrophobic tail cannot
Then reason for formation of lipid bilayer is due to hydrophobic effect
Hydrophilic head groups face outward in order to have contact with water
Hydrophobic Tails are found on inside where water is excluded
pH is an Important Parameter of Biochemical systems
• pH is the measure of H + concentra-on of a solu-on • It is defined as: pH = –log ([H + ]) with a scale of 1-‐14. •
Pure water has a pH value of 7 ([H + ] = [OH -‐ ]) •
Many biomolecules and organic compounds affect pH. • Controlling pH is a crucial func-on in biological systems. •
An acid is a proton donor, whereas a base is a proton acceptor.
Acids ionize to form a proton and a conjugate base. •
The acid formed when a base binds a proton is called its conjugate acid. •
The pH of blood is crucial for oxygen/CO 2 transport and is -ghtly regulated. •
Gastric Esophageal Reflux Disease (GERD) is a pathological condi-on that results when the esophagus is exposed to the acid of the stomach.
When ph=pka
Acid concentration = base concentration
