Lecture Notes on basic Chemistry and Biochemistry (Chapter 2)

Bohr’s Atom:

Nucleus – ___________ and proton

Electrons – Orbitals: shapes s,p,d,f
Energy Levels – ________ Numbers of 4
levels: Principle Q.N., Angular Q.N.,
Magnetic Q.N., Spin Q.N.
Atomic Number:_________: Elements
Atomic Mass: Neutrons + Protons; Isotopes with different
___________; Average Atomic Mass: due to _____________
of isotopes
Charges of Ions: ____________ electrons and protons
Shells: Clouds of layers (Orbials) designated K, L M,N..
Transition elements have colors due to electron from
penultimate orbitals jump to the ultimate orbital to
release light in different _____________ of energy.

Bonds:
• Ionic Bonds – one ______ an electron to form +ve charge,
_________; Another ______ an electron to form –ve
charge, _______.
• Covalent Bond – share electrons (paired, anti-parallel)
Polar (water-like) and non-polar bonds (C-C)
• H-bonding – nucleic acid in complimentary base pairing
 • Co-ordinate bond – around an metal ion e.g. Heme with
Fe+++

Water:
• Osmosis: semi-permeable membrane allows small
molecules to go through
Osmotic pressure and gradient
Active transport against gradient

• pH definition

• What is the [H+] at pH 7?

• Water molecules and Hydroxonium ions - angle of 104.5°

to form stable lattice and hydration sphere around ions;
what is hydration

• Functions of water:
1. Lubricant
2. Reactant
3. _________________ (Hydration)
4. Homeostasis (Temperature regulation and
electrolyte control in kidney)

Electrolyte: Na+ and Cl-

______________ electricity
Chemical Reactions
• Equilibrium:

• Law of Mass Action: rate of a chemical reaction is

proportional to the active __________of reacting
substances

Types of Chemical Reactions:

• Reversible
(Always in equilibrium with an Equilibrium Constant
to determine forward or backward reactions; to determine
concentrations of starting reactants and the product.)

• Non-reversible Reactions
(Initial stage: three species of reactants)
(Completed reaction: only one species)

• Synthesis:
 o Condensation
o Combination
• Decomposition: Hydrolysis
• Exchange:
o Single replacement
o Double Replacement

• Oxidation:
1. Gains oxygen
2. Removes hydrogen
3. Loses electron
4. Increase valence
• Reduction (Opposite to oxidation)

Cations moves towards Cathode (+ve ions to –ve pole)

Anions moves towards Anode (-ve ions to +ve pole)

Energy of Activation in chemical reaction:

Exergonic: produce heat

 Endergonic: absorbs heat

Catalyst and Enzyme (never be _________ in the reaction

only cleared from the system due to other enzymes reacting on
them, i.e. enzyme on enzyme)

Enzyme + Substrate ----- Complex -------- Product + Enzyme

Lock and Key Model

4 major Organic molecules in the Body

1. Proteins – amino acids

2. Lipids – fatty acids
3. Carbohydrates - monosaccharides
4. Phosphate compounds (ATP, DNA)

Amino Acid:

o Structure: amino group and carboxyl group, H and R

groups

Side-chain (R=variable group): acidic, basic and hydrophobic

o Linear polymer: Peptide Bond (Dehydration to form

peptide bond)
 o Elongation of amino acids to form Peptides and longer
ones are Proteins by process of _____________
(Synthetic)
o __________ water molecules between amino group
and the carboxyl group
o Digesting proteins to become peptides or amino acids by
process of ______________
o _______________ water molecules between amino
group and the carboxyl group
o Protein Structure:
1. Primary (linear chain)
2. Secondary (alpha helix or beta sheet)
3. Tertiary (hemoglobin, folding)
4. Quaternary (4 subunits to form an
aggregate)
Non essential amino acids: you need to take into the body
because the body needs them but cannot produce them.
Essential to our body: Isoleucine, Leucine, Valine,
Tryptophan, Phenylalanine, Methionine, Threonine,
serine, lysine
Semi-Essential (not critical): Arginine, Histidine

Carbohydrates

o Saccharides:
Structure: C6H12O6
Fisher Projection
Haworth Projection
o Reducible aldehyde group
 o Disscharide hydrolysed to monosaccharide, for further
energy processing
o General types
Monosaccharides: e.g. glucose, fructose, ribose
Disaccharides: e.g. sucrose
Polysaccharides: e.g. starch, glycogen

Lipids:

o Structure: Long carbon chain (fatty acids)

Saturated (single bond)
Unsaturated Bond (double bond)
o Functions:
1. Storage of food
2. Lubricant
3. Structure of membrane: bilayer
4. Protections

o Types:
1. Fatty Acid
2. Steroids
3. Phospholipids
4. Triglycerides: glycerol + 3 chains of fatty acids
(most abundant in the body)

Phospholipid bilayer:
Hydrophilic outside (on either side of the membrane)
 Hydrophobic inside

Nucleic Acids

o Stucture: Bases; two types

o Two-Ring Structure: Purines: Adenine and Guanine
o One-ring structure: Pyrimidines: Thymine (______)
and Cytosine

Nucleoside: Base + Ribose (Adenine becomes Adenosine)

Nucleotide: Base + Ribose + Phosphate

o H-Bonding between the ______________ base pairs:

3 bonds between G-C (Guanine-Cytosine)
2 bonds between A-T or A-U (Adenine-Thymine
or Uracil)

o Differences between DNA and RNA

1. Sugar: D=deoxyribose; R=ribose
2. Base in DNA is T and Base in RNA is U
 3. DNA is double helix, RNA is single chain

Summary & Review:

Smallest Unit of Matter

Atom, Molecule, proton, neutron, nucleus
Isotope
Atomic Number
Atomic Weight
Mixture
Compound
Ion (Cation +/Anion-)
Bonds: ionic, covalent, H-, metallic (co-ordinate)
Covalent bonds: sigma, pi, triple
Polar covalent bond
Electron shells: most stable (inert, like noble gas) with a pair
Reactions:
Acidity, pH, dissociation constant of H+
Buffer: Body fluid with sodium bicarbonates
Metabolites, inorganics (Fe, P…)
Electrolytes
Inorganic acids:
Carbohydrates (glycogen stored in muscles: animal storage)
1:2:1=C:H:O
Lipid functions
Fatty acids: saturated, unsaturated (polyunsaturated)
Most common lipid: triglycerides
Protein functions:
Peptide bonds, amino acids, R-groups
Nucleic acid: genetic information
Nucleotides and nucleosides
ATP: energy carrying molecules
Enzymes: active site, substrate, lock&key
Dehydration synthesis: carbohydrate, peptides
ATP – ADP
Structures of atom
Structures of Carbohydrates, lipids, amino acids