The chemical context of life

Chemistry of Life Element - any substance that is comprised of one type of atom and cannot be broken down into another substance. Examples Hydrogen Oxygen Carbon Gold Silver

Atom - the smallest unit of matter that still retains the properties of the element. Atoms contain the same amount of protons and electrons (net charge = 0) Nucleus - center of the atom containing protons and neutrons. Proton - heavy positively charged particle. Neutron - heavy neutral particle. Orbitals - area around the nucleus containing electrons. Electron - light negatively charged particle.

Isotopes - atoms of the same element with differing numbers of neutrons

Chemical bonds Ionic bonds - formed through the transfer of electrons between two atoms. The bond is due to the attraction of oppositely charged ions (atoms with a negative or positive charge).

Chemical bonds Covalent bonds - formed through the sharing of atoms between atoms.

Mixture - a substance composed of two or more elements or compounds which are physically mixed together, but not chemically combined.

Solution - mixture of two or more substances in which the substances are evenly distributed. Solute - substance that is dissolved. Solvent - substance in which the solute is dissolved.

Water is the solvent of life

Chemical elements and water Elements of life (most common) –Carbon, hydrogen, oxygen Other necessary elements & function –Nitrogen (amino acids), –Calcium (bones, teeth), –Phosphorous (ATP, DNA), –Iron (hemoglobin), –Sodium (nerve transmision)

Like no other common substance, water exists in nature in all three physical states: –as a solid –as a liquid –as a gas

Properties of water Transparency: –Light can easily pass through –Reach inside cytoplasm (water) to chloroplast, retina –Reach organisms in water Cohesion: –Water molecules stick together (surface) Water can be pulled up trees Small animals can live on water surface (mosquito)

Properties of water Solvent Properties (universal solvent) –Allow substance carried in water blood, sap –Thermal properties (large heat capacity) requires lg. Amounts of energy to heat remains stable temperature –fish, blood (carry heat to cold parts)

Properties of water Thermal properties (cooling from evaporation) –evaporate at temperatures below boiling heat energy required to break hydrogen bonds, taken from liquid water cooling it down

Properties of Water Cohesion - attraction between molecules of the same substance. Adhesion - attraction between molecules of different substances.

Cohesion: Water molecules stick together surface tension

Cohesion: water molecules can move great distances

Water and Organisms plants and animals Coolant: sweat, blood Transport medium: blood, sap Habitat

Polar molecules are also soluble in water because they can also form hydrogen bonds with water. Even large molecules, like proteins, can dissolve in water if they have ionic and polar regions. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 3.8

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 3.7

Significance of water to living organisms Coolant: sweat Transport medium: blood, sap Habitat:

Biochemistry The chemistry of Life Bio-molecules –Proteins –Carbohydrates –Lipids (fats, membranes…) –Nucleic Acids (DNA…)

Trace elements May be needed in only small amounts but may cause harm if absent (iodine) goiter

Organic Compounds Contain carbon & found in living organisms –Inorganic Carbon compounds: CO 2, –Many inorganics found in living organisms Iron in blood

Macromolecules (polymers) are formed from smaller building blocks called monomers. Polymer (“chain”) Monomer (“links”) carbohydrate monosaccharides protein amino acid nucleic acid nucleotide

Macromolecules - large molecules formed through the joining of many monomers (small molecular units) into polymers (larger molecules). We will be studying 4 important macromolecules: Carbohydrates, lipids, proteins, nucleic acids. s/polymers/2973/images/Fig_9513.jpg

Carbohydrates - sugars which contain C, H and O and are the main energy source for all living things (some organisms also use carbohydrates for structural purposes). Monosaccharides - single sugar molecules (glucose, galactose). Disaccharides - carbohydrates composed of two sugar molecules (lactose). Polysaccharides - large carbohydrates composed of many monosaccharide monomers (starch, cellulose, glycogen). ca/courses/351/Carey5th/ Ch25/b-d-glucose06.gif com/town/park/gfm11/n omilkgif/LACTOSE.JPG ses/BIOL115/Wyatt/Bioche m/Carbos/Carb_poly.gif

Condensation Reaction: monomers form chains –Remove water to form bonds –Protein synthesis –Fatty acid synthesis 123 Unlinked monomer Removal of water molecule 1234 Longer polymer Figure 3.3A Short polymer

Hydrolysis - reverse process of condensation polymers are broken down to monomers –Using water 123 Addition of water molecule 123 4

Proteins are involved in –cellular structure –movement –defense –transport –communication –hair –Enzymes PROTEINS

Proteins have levels of organization. Proteins can be denatured.

amino acids link –dipeptides –polypeptide chains (Proteins) The bonds are called peptide bonds Protein Synthesis Dehydration synthesis Figure 3.13

Carbohydrate Polymers Monomer: glucose (energy) –Monosacccharide Polysaccharides: –Glycogen: energy storage Animal muscles –Starch: plant energy storage –Cellulose: plant structure

The structure of glucose

A disaccharide is made by linking two monosaccharides together. glucose + fructose = sucrose glucose + galactose = lactose

Examples Monosaccharides: –Glucose & Fructose Disaccharides: –Sucrose (glucose + fructose) –Maltose (glucose + glucose) Polysaccharides –Starch –Gycogen

Functions of Lipids (fats) Energy storage: Insulation: Protection: Membranes (phospholipids):

Glycerol & fatty acid

Enzymes Enzyme –Protein –Biological catalyst –Example: amylase Active Site –Location where substrate (reactant) binds

Proteins - macromolecules that contain N, H, O and C. Are comprised of amino acid (the order and combination of these amino acids determines the role of the protein) subunits. Types of proteins: Enzymes - carry out the chemical reactions in the organism (lactase, DNA helicase, catalase). Structural Proteins - aid in building muscles, bones and other components of the organism (keratin, collagen). Functional Proteins - assist in organism’s daily functioning such as messengers (hemoglobin, insulin), defense or transport. content/uploads/2007/11/0143.gif hemistry/chem227/structpr oteins/stash.jpg content/uploads/img182.imageshack.us/img182/8476/ t113722z01nootrrtridsp2oukoeukguinnessfe6.jpg

Lock and Key Model (enzyme-substrate specificity)

Factors influencing enzyme activity Optimum pH Optimum Temperature Please diagram

Effects of variables on enzymes Temperature pH

Denaturation Structural change in protein –Loss of functionality

I. Why Study DNA Replication? 1) To understand cancer 2) To understand aging 3) To understand diseases related to DNA repair Werner’s Syndrome Keith Richards (of the Rolling Stones) Example of premature aging NOT caused by a hereditary disease

Nucleic Acids - macromolecules that contain H, O, N, C and P. The 2 kinds of nucleic acids are DNA and RNA which store and transmit genetic information (the “blueprint” to make you). Comprised of nucleotide (5-C sugar, phosphate group and nitrogenous base) monomers.