Eukaryotic Exam 1

most abundant elements in organisms vs earth’s crust

• organisms: hydrogen, carbon, and oxygen

• crust: oxygen, silicon, and then other elements

valence electrons

• carbon: 4 valence electrons; can form 4 bonds

• oxygen: 6 valence electrons; can form 6 bonds

• silicon: 4 valence electrons; can for 4 bonds

why is carbon the backbone of biological molecules vs silicon?

• most bc of likely electronegativity

• bonds with silicon are more easily broken

electronegatives of elements

F > O > Cl > N > S > C > H > P > Si

two factors determining electronegativity

• the number of positive charges in its nucleus

• the distance of the outer electrons from the nucleus

covalent bonds

• two atoms sharing electrons

• atoms joined by a single bond are able to rotate relative to one another

  • ex. H2O, H:O:H

• double bonds can function as energy capturing centers

  • ex. O2, O=O

• triple bonds

  • ex. N2, N=-N

• quadruple bonds are unknown

polar and nonpolar covalent bonds

• polar: unequal sharing of electrons between two different non-metals; partial ionic charges

• nonpolar: equal sharing of electrons between two identical non-metals

noncovalent bonds

• ionic bonds

• hydrogen bonds

• hydrophobic interactions

• van der waals forces

ionic bonds

• bonding of oppositely charged ions; metal and non-metal

• transfer of electrons

• electron will only move around the ion with the stronger electronegativity

why don’t strong ionic bonds exist in cells

• because they contain water

• water is highly polarized so it will break an ionic bond between two ions

• strong water shields will form around ions

weak ionic bonds in cells

• when two big biological molecules (like a protein and DNA) come together and interact, water will be expelled at the interface (hydrophobic interactions)

• atoms with partial charges will attract forming weak ionic bonds

  • ex. O- from DNA double helix and N+ from protein

hydrogen bonds

• similar to weak ionic bond

• usually between hydrogen and oxygen or nitrogen

  • bc they are usually electrically charged and will form a bond with positively charged hydrogen when they get close

hydrophobic interactions

• in a water environment in the cell, hydrophobic molecules tend to aggregate to reduce the the surface exposed to water

• hydrophobic interactions are not due to an interaction between hydrophobic molecules, it is bc the water comes together to form hydrogen bonds

• when hydrophobic molecules come together, their surface that interacts with water becomes smaller and the water molecules can react with each other

hydrophobic vs hydrophilic

• hydrophobic: nonpolar molecules

• hydrophilic: polar molecules

van der waals forces

• very small

• attraction between molecules at a certain distance

  • optimal van der waals interaction

• occurs bc of unequal charges

• ex. antigen and antibody fit together, and the formation of one van der waals force between the two will trigger the unequal distribution at the labor site to form a charge again at an adjacent position, and so on

  • one interaction forms and induces other places to form more van der waals forces

• helps form the structure of molecules as well as helps interactions between molecules

i’m sorry ava I tried

water

• most important molecule for life

• each molecule can form 4 hydrogen bonds

• molecules hold on to each other tightly and require lots of energy to break their bonds

• highly polarized; very good solvent and reacts well with many other molecules

• the product of many reactions

dissociation of water molecules

• can dissociate into a proton and a hydroxy ion

• in pure water at room temp., the concentration of protons and hydroxy ions are equal

• can change the concentration of protons and ions, but 10^-14 is constant

acids and bases

• acids are capable of releasing a proton

• bases are capable of accepting a proton

• an amphoteric molecule is capable of acting as an acid or a base

• acids and bases exist in pairs

• the ability of an acid or base to interaction with a proton is dependent on their strength

pH

• pH is used to express the acidity of a solution

  • pH = -log [H+]

buffers

• a mixture of a week acid and its conjugate base or a weak base and its conjugate acid

• organisms use buffers to protect cells from pH fluctuation

• the blood is buffered by carbonic acid and bicarbonate ions to keep pH about 7.4

• the cell fluid is buffered by H₂PO₄- and HPO₄^2- to keep pH about 7