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Cell and its organelles

Supramolecular - Macromolecules - Monomeric
Chromosome - DNA - Nucleotide
Plasma Membrane - Protein - Amino Acid
Cell Wall - Cellulose - Sugars

Protein found in Human and E.coli

- human: 30,000
- E.coli: 3000

Bulk & Trace Elements

Bulk Elements
- CHNO, large amount (99% mass of cell)
- mostly heavy metals

Trace elements
- required in trace amount
- still essential to sustain life

Functional group (memorise drawing) + determine properties

- hydroxyl
- carbonyl
- carboxyl
- amino
- sulfhydryl
- phosphate
- methyl
Note un-ionized form, replace charge with H


1. Powerful solvent
- Electrostatically interact with charged solutes
- forms hydrogen bonds easily in aq solution
2. Participant in many biochemical reaction
3. Required in Buffering
4. Drives hydrophobic interaction

2 types
1. Hydrophilic
2. Hydrophobic

Hydrogen bonds (in water)

- Solid ice: up to 4 H bonds
- liquid: up to 3.3~3.5 H bonds
- transient (milliseconds)
- accounts for high boiling point for water

- Individually weaker than covalent bond

Hydrogen bonds (bond formation)

1. Occur betw Hydrogen atom & Electronegative atom
2. Hydrogen: High positive partial charge
Acceptro: High negative partial charge
3. H bond is slightly stronger than simple electrostatic interaction
- due to add. covalent contribution from overlap of hydrogen orbital with acceptor

Hydrophobic effect

1. When nonpolar molecules exposed to water, water molecules form highly ordered shells around non-polar molecules, ↓ entropy, unfav free energy change

2. Hydrophobic effect drives formation of micelles of amphipatic compounds in water, group nonpolar regions of biomolecules tgt, ↓ordered shells of water, ↑ entropy, fav free energy change

Contributes to:
A) membrane structure
B) three-dimensional folding of a polypeptide chain
C) binding of a hormone to its receptor protein
D) enzyme-substrate interactions

Delta G= Delta H - TDelta S

Thermodynamically favourable free energy change
- G <0
- screening effect, ↑ entropy, molecule is soluble

Thermodynamically unfavourable free energy change
- G >0
- molecule not soluble

Weak, noncovalent Interactions

- Crucial to thermodynamics of protein folding, macromolecular structure & function

1. hydrogen bonds
2. ionic interactions (longest range, non-directional)
3. hydrophobic interactions (nonpolar molecules)
4. van der waals interactions

Ionic Interactions

- Betw a pair of charged molecules
1. Attraction between oppositely charged molecules
2. Repulsion between same charged molecules

- long ranged
- non-directional

Ionization of Water:
Define pH

- negative logarithm of [H+] in an aqueous solution
- provides indication of [H+] in an aqueous solution

Ionization of Water:
Define pOH

- negative logarithm of [OH-] in an aqueous solution
- provides indication of [OH-] in an aqueous solution

Define pKa
Ans to Qn: pH = 4.4

- negative logarithm of an equilibrium constant
- equal to the pH value where one-half of a weak acid is dissociated; equal concentrations of a weak acid and its conjugate base
- pKa occurs at the midpoint of the titration curve of weak acid, center of the titration curve providing maximum buffering capacity of the conjugate acid-base pair
- pKa are unchanging properties of ionizable groups in biomolecules


- aqueous system that tend to resist changes in pH when small amounts of acid (H+) or base (OH-) are added
- *important in maintaining cellular homeostasis

*Memorise Henderson-Hasselbalch Eqn

Bicarbonate buffer system
Acid [HA] : [H+]
Conjugate Base [A-]: [HCO3-]


1. Diff betw DNA & RNA
- Carbon 2, H in DNA, OH in RNA (2 cinemas, watch HD movie)
2. All nucleotide bases absorb UV light due to ring resonance
3. Linked by phosphodiester bonds in nucleic acids
4. Free purines & pyrimidines are weakly basic compounds

Amino Acids

1. linked by peptide bonds
2. unique chemical properties determined by nature of side chain
3. absorb UV light by aromatic amino acids (FWY) [peak at 280nm]
4. forms zwitterion when dissolved in water (acts as acid & base)
5. sequence (order) determine 3D structure of protein

Biological role for amino acids

A) components of proteins
B) components of peptide hormones
C) function as neurotransmitters
D) components of enzymes


- Apoptosis: translocation of phosphatidylserine (PS) from the inner side to outside side of plasma membrane

Normal condition
- Flippase keeps PS on inner side of PM
- Scramblase externalizes PS to mark for cell death

1. Alcohol + FA
2. Ester bond

Increasing size
1. Amino acid
2. Protein
3. Ribosome
4. ER

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