Biochemistry Ch.

1 Intro: 1
1. 5 Components of Life
a. Cellular
b. Self-sustaining
c. Complex & dynamic
d. Information-based
e. Adapts and evolves
2. 3 domains of living organisms
a. Bacteria
b. Eukarya
c. Archaea
3. Protein found in all organisms
a. TATA-box binding protein, binds to DNA
4. Metabolites
a. Low-molecular-weight molecules
i. Glucose and glycerol
b. Chemically transformed in biological processes
5. 4 Major Classes of Biomolecules (Structure of molecule affects function)
a. Proteins
b. Carbohydrates
c. Lipids
d. Nucleic Acids
6. Review of Functional groups (9)
a. Alcohol, aldehyde, ketone, acids, amine, amide, thiol, ester, alkene
7. DNA illustrates the basic principle the intimate relation between structure and function
a. Linear polymer made up of four different types of monomers
i. Fixed backbone
1. Built of repeating sugar-phosphate units
b. Double helix structure published by Watson and Crick in 1953
i. Intertwined strands
c. Specific base pairs (bp) held by H-bonds, not covalent bonds, envision with dotted
lines
d. Watson and Crick has two properties of central importance to the role of DNA
i. Base pairs have essentially the same shape
ii. One strand completely determines the sequence along the other strand
e. It is not just the H-bonds that holds them together
i. Electrostatic repulsion
ii. Base stacking Van der Waals
iii. H-bonds between base pairs
iv. Hydrophobic effect
1. Seems like entropy is reduced because there is more order, but what
we are not measuring is that there is heat given up
8. Forces between atoms
a. Non-covalent bonds
i. Ionic/Electrostatic Interactions
1. A charged group on molecule can attract an opposite charged group on
another molecule
2. Salt bridges, electrostatic, charge-charge interactions
3. Sensitive to: pH and salt concentration
ii. Hydrogen Bonds
1. Also electrostatic interaction with partial positive and negative charges
2. The H is partially shared by two electronegative atoms such as N or O
3. The HBD includes the atom boned to the H and is more tightly linked
4. The HBA is less tightly linked to the H

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5. Responsible for specific base-pair formation
iii. Hydrophobic Effect
1. The re-ordering (releasing of water) thus increasing the entropy so that
the reaction is favorable
2. The interactions of nonpolar molecules with water molecules are not
are favorable as are interactions between the water molecules
themselves
a. Water forms cages in contact in nonpolar molecules so are more
ordered
b. When nonpolar molecules come together, water is released
allowing them to act freely with bulk water
3. Drives most interactions
a. Membrane formation is powered by the hydrophobic effect
b. Protein folding
iv. Van der Waals Forces
1. Dipole-dipole
2. Dipole-induced
3. Induced dipole-induced dipole (London dispersion forces)
4. Van der Waals radius ideal distance between atoms
5. Transient symmetry
b. Covalent
i. Strongest
ii. H-bonds are longer than covalent bonds
iii. The stronger the bond, the straighter the bond
9. Thermodynamics
a. 1st Law Energy content of the Universe is constant
i. Energy can take different forms
b. 2nd Law Total entropy of a system (plus that of surroundings) always increases
i. Heat is released in the formation of the double helix
ii. Local vs surrounding
c. Equations
i. Ssurr = -Hsys/T
ii. Stot = Ssys + Ssurr
iii. G = Hsys - TStot
iv. G = Hsys TSsys < 0
10.Acid-Base Reactions
a. Hydrogen ions are added to molecules or removed from them
b. Can disrupt the double helix
i. As the pH increases, the double helix begins to dissociate
ii. The OH- can react with bases in DNA base pairs to removed certain protons
c. pKa is the susceptibility of proton removal by reaction with base
i. Ka = [H+][A-]/[HA]
ii. pKa = -log(Ka)
iii. The lower the pKa, the stronger the acid
d. Isoelectric point
i. Point where is no net charge and pH is equal to pK a
ii. pH = pKa
e. Buffer
i. Changes in pH can protonate or deprotonate key groups, potentially
disrupting structure and initiating harmful reactions.
ii. Buffers resist changes in pH
iii. An acid-base conjugate pair resists changes in the pH of a solution
iv. A buffer is most effective at a pH near its pK a

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v. Capacity
1. Ability of given buffer to resist changes in pH on addition of acid or
base, best near its pKa, the flat zone
2. The higher the concentration (molarity), the more buffering capacity
3. Ratio of their concentrations of acid and conj. Base
vi. Titration
1. Monoprotic or polyprotic
2. pH decreases gradually in the middle of the titration because when
hydrogen ions are added to this solution, they react with acetate ions
to form acetic acid
vii. Cells and Tissues
1. Bicarbonate
a. Carbonic acid is formed from dissolved CO2 and water in a
reversible manner = BLOOD
2. Phosphate
a. An important buffer in biological systems is based on phosphoric
acid (H3PO4)
i. The acid can be deprotonated in three steps to form a
phosphate ion
ii. Phosphate solutions function as effective buffers near pH
7.4
b. Phosphate concentration of intracellular fluids where
concentration is ~ 75 milliequivalents per liter (4 mEq outside
the cells)
3. Proteins
a. Zwitterionic contains several types of ionizable groups that can
donate or accept protons
b. Hemoglobin (Hb) significant concentration due to abundance