Biochemistry

• Study of chemical reactions that take place in our body everyday

• Chemical reactions allow us to remain alive– Rearrangement of chemical bonds to form products

from reactants

Chemical Fundamentals Review • Living things are composed of

matter. • Matter has mass, occupies space.• Atoms composed of: – Small nucleus• Proton (positive charge)• Neutron (no charge)

– Surrounded by• Electrons (negative charge)

Isotopes• Atoms of an element with the same atomic number but a different

mass number– Number of protons ALWAYS stays the same– Number of neutrons changes which distinguishes isotopes from

one another– All isotopes of an element have the same chemical properties

(electrons)

Nonradioactive carbon-12 Nonradioactive carbon-13 Radioactive carbon-14

6 electrons6 protons6 neutrons

6 electrons6 protons8 neutrons

6 electrons6 protons7 neutrons

Radioisotopes (Carbon 14) • Isotope with

radioactivity• Not stable• Spontaneously

decay into other forms

• Half life– The time it takes

for one half of the nuclei sample to decay

Radioactive Tracers• Used to identify

abnormal bodily processes

• Designed to mimic naturally occurring substances (glucose) – Thyroid – iodine– Bones –

phosphorous– Muscles –

potassium • PET

– Positron emission tomography

Why Are Electrons so Important?

Chemical behaviour of an atom: -Electron configuration

- distribution of electrons in the atom’s electron shells - valence electrons – outermost electrons in an atom’s

electron shell - incomplete valence shells are chemically reactive

(bond formation)

Octet Rule = atoms tend to gain, lose or share electrons so as to have 8 electronsC would like

to N would like toO would like toH would like to

Gain 4 electronsGain 3 electronsGain 2 electronsGain 1 electron

Lewis Dot Diagrams- Diagrams of the elements only showing valence

electrons.

Atoms bond to form compounds

• Compounds are made up of at least 2 different kinds of atoms (e.g., H2O)

• Bonds are formed by the sharing or transfer of electrons

2 Types of Chemical Bonds

Ionic Bonds

Covalent bonds

Ionic Bonds - occur when one atom donates or gives up one or more electrons (metal + non-metal)

Ionic Compound ( Na+Cl-) Salt crystals

Opposite charges

attract to form ionic

bonds

Covalent Bonds – involve a sharing of a pair of valence electrons between atoms (non-metal + non-metal)

Single covalent bond

Double covalent bond

Four single covalent bonds

Two single covalent bonds

2 Types of Covalent Bonds

Polar Covalent Non-polar covalent

Equal sharing of electrons

Unequal sharing of electrons

Determined by the atoms

ELECTRONEGATIVITY

E.g. H2O2

E.g. H2O

ElectronegativityThe measure of an atom’s attraction for additional electrons

Polar Covalent Bond-unequal sharing of electrons between two atoms with different electronegativity results.

Non-Polar Covalent Bond -equal sharing of electrons between two atoms.

Electronegativity = Stronger pull of shared electrons

The electronegativity difference (∆En) is the difference in electronegativity number between two atoms participating in a covalent bond.

Electronegativity Differences

Molecular Polarity• Depends on

– Distribution of charges – Symmetry

• Polar Molecules – One side, or end of molecule

has a slight positive charge, and the other side, or end, has a slight negative charge

– Occurs when the molecule is not completely symmetric

• Non-polar Molecules – Molecule is completely

symmetric – All atoms attached to central

atom are the same– Hydrocarbon

Polar or Non-Polar?

VSEPR• Valence shell

electron pair repulsion

• Electrons repel one another forming the shape of the molecule

• Includes both bonded electron pairs and non-bonding electron pairs (lone pairs)

Polar Molecules• Align themselves to other polar molecules to create

stability– Hydrogen bonding (DNA)

• Soluble in water (polar) and non-polar organic solvents (turpentine)

Importance of Polar and Non-Polar Molecules• Hydrophobic properties of

fatty acids in phospholipids (cell membrane)

• Consumption of antioxidants in our diet (vitamin C)

• ATP – energy currency of cell

• DNA – double helix structure

• Enzyme catalyzed reactions• Water – universal solvent

Intermolecular Forces• intermolecular forces of attraction exist between

molecules• Influence physical properties of a molecule– (Solubility, Melting point, Brittleness etc)

• Intermolecular forces are known as van der Waals forces.

Example of van der Waals Forces• Hydrogen Bonds– Strongest and most biologically

significant – Crucial to function of cells and

cellular processes (DNA replication)

– Weaker when compared with ionic and covalent bonds

– Example WATER– Properties are high heat capacity,

high melting point and boiling points, cohesion, adhesion, surface tension

Other van der Waals forces• London forces

and dipole-dipole – Weak forces– Prominent in

non-polar molecules

– Size and shape of molecule influence strength of attraction (gas, liquid at room temperature)

Chemical Reaction• Breaking and formation of chemical bonds

rearranging atoms and ions

• 4 Types– Dehydration – Hydrolysis– Neutralization – Redox reactions

Dehydration• Also called condensation reactions • Removal of a –OH (hydroxyl group) and a -H

(hydrogen) from reactants to form a water molecule• Most common reaction used by cells• Assemble complex carbohydrates and proteins

Hydrolysis• Reverse of dehydration reactions• A water molecule is used to split a larger molecule• A hydroxyl group and a hydrogen attach to small sub

units• Two products are formed

Neutralization• Acid reacts with a base to form water and a salt

Acid + Base Salt + Water

Redox • Electrons are lost from one atom and gained by

another• Oxidation is loss of electrons (OIL)• Reduction is gain of electrons (RIG)• Responsible for most energy transfers in cells

Carbon• Makes up the base of

every organic molecule

• Form 4 covalent bonds (single, double, triple)

• Hydrocarbons– Long chains, rings, or

branched structure of carbon

• Chains can be linear or branched

Carbon• In Biological Molecules

Carbon mostly bonds with– Hydrogen– Nitrogen– Sulfur– Oxygen

• These elements provide biological molecules with different functional properties

• Four categories– Carbohydrates– Proteins– Nucleic Acids– Lipids

Functional Groups• Found on all 4 major

classifications of biologically important molecules

• Small reactive groups that participate in chemical reactions

• Usually ionic or strongly polar (helps to initiate chemical reactions)

• Form different types of bonding