Introduction to Chemistry I thought we were in biology this year……

Bio and chem perfect together The chemical basis of life leads us to an understanding of how things work in biology So we need to know some basic chemistry first Really this might be a review for everyone

Atoms and Compounds Element is a substance that cannot be broken down any further Periodic Law (you know the Table) Smallest unit of an element is an atom Atom comprised of nucleus and electrons Nucleus comprised of protons and neutrons

Atoms and Compounds (2) What makes one element different from another is the number of protons and electrons in each 92 elements occur in nature, 20 more made in a lab Only 6 make up 99% of all living organisms (C, H, N, O, P, S)

Atoms and Compounds (3) All the CHNOPS elements are small, light, form covalent bonds, electrons close to the nucleus, form bonds with two or more atoms (except H) The links between atoms are called bonds A substance formed by bonding of atoms is called a compound

Atoms and Compounds (4) IMPORTANT: an atom is the smallest part of an element, a molecule is the smallest part of a compound Two types of bonds important in biochemistry: Ionic and Covalent

Bonds (1) Ions –An atom that has gained or lost an electron and thus acquires a negative or positive chargIons Ionic bond –The strong attraction beteween oppositely charged ions –Usually link atoms in small compound together –Stabilize macromolecules

Bonds (2) Covalent bonds; electrons are shared between two atoms A group of atoms linked by covalent bonds behaves as one unit. This is called a molecule Polar vs. non-polar covalent bonds (important for water later on) IMPORTANT: an atom is the smallest part of an element, a molecule is the smallest part of a compound

Chemical Formulae Shorthand used by scientists to write the names of elements and compounds Some examples on periodic table

Water (1) H2O Electrically neutral but does not behave that way Has a slight negative charge at one end, slight positive charge at the other end; this is called polarity Water dissolves substances, the resulting liquid is called a solution; biochemistry is solution chemistry, everything happens in solution

Water (2) Water can dissociate (come apart) into ions H + and OH – H + and OH – are two of the most reactive ions in nature A compound that produces H ions is called an acid A compound that produces OH ions is called a base

Water (3) The acidity and basicity of a solution is important in biochemistry We measure the acidity/basicity of a solution by measuring the concentration of H ions in it. The concentration scale is called the pH scale. Values of pH 1-7 are acids, 7-14 are bases

More on Water (1) On earth water is a common liquid ¾ of earths surface is covered in water 50-90% of the weight of a living system is water Common is not the same as ordinary Water is an extraordinary liquid for many reasons

More on Water (2) Water and the Hydrogen Bond Polar molecule Electrically asymmetrical Opposite charges lead to hydrogen bonding Every water molecule can form a hydrogen bond with four other water molecules A single H bond is very weak, all together however H bonds are very strong

More on Water (3) Water and the Hydrogen Bond H bonding gives water surface tension The only liquid with a greater surface tension that water is mercury Water has cohesive and adhesive properties (cohesion holding together like substances, adhesion holding together unlike substances) Mercury is only cohesive

More on Water (4) Water and the Hydrogen Bond Cohesive and adhesive properties lead to water having capillary action and imbibition Capillary action is the ability of water to move upwards or downwards in small spaces, imbibition is ability of water to move inside unlike substance like wood

More on Water (5) Water and Temperature Water has a high specific heat (heat capacity) –Due to H-bonding –Energy of movement (kinetic energy) is first used to break H bonds, then temperature can increase –Heat and temperature are not the same!! –TEMP: measured in degrees, represents average kinetic energy –HEAT: measured in calories, represents number and mass of molecules present

Yep More on Water (6) Water has a high heat of vaporization (evaporation) –Due to H bonding again –Takes 540 calories to change 1 g water to vapor –Consequence is that evaporation of a water molecule carries a lot of heat with it –Evaporation has a cooling effect; organisms can unload excess heat by evaporation of water

Water (7) The freezing point of water is also the melting point (at 0 degrees C) (heat of fusion) Ice and snow are temperature syabilizers Water maximum density is at 4 degrees Solid water takes up more volume than liquid –Solid water forms on the top of a pond –Insulates the water underneath at close to 0 degrees (but not frozen)

Water (8) The solvent Hydrophilic compounds dissolve in water to make solutions Hydrophobic compounds do not dissolve in water H bonding forces hydrophobic compounds to self associate –Very important for biological structures

Macromolecules Most are polymers (called macromolecules in biology) –Base unit is a monomer –Composed of C, H, N, O, P, S –Monomers: simple sugars, amino acids, nucleotides, fatty acids and glycerol –Polymers: carbohydrate, proteins, nucleic acid, lipids

Macromolecules Carbohydrate –Monomer is simple sugar Protein –Monomer is amino acid Lipid –Monomer is glycerol and fatty acid Nucleic acid –Monomer is nucleotide

ENZYMES The way things work

Enzymes Chemical reactions –A process that changes one set of substances into another set of substances –Some happen naturally (rusting) –Some happen without control (explosions) –Some happen under control Control pressure, temperature, concentrations, catalyst (metals like Pd, Pt, Al, Mo, Mn, V, Cr, Rh, Fe, Zn, Ni, Co)

Enzymes are biological catalysts Biological chemical reactions happen at ambient temperature, within a narrow pH range, at atmospheric pressure, in very narrow ranges of chemical concentrations Biochemical reactions are made possible by catalysts that are called enzymes Mostly these are proteins, some are RNA

Enzyme Kinetics The compounds that bind to the enzyme are called substrates The place where substrates bind to the enzyme is called the enzyme active site After binding, enzyme causes the reaction to occur then releases the products (lowers activation energy) The enzyme is unchanged

Mechanisms Enzyme substrate binding is called the lock and key model. Enzymes and substrates fit together like a key fits into a lock

Enzymes All energy transformations and utilization in an organism is controlled by enzymes Energy of movement is kinetic energy Energy of position is potential energy Forms of energy in organisms: chemical, mechanical, electrical, heat, magnetic,