Chemistry of Life

CHAPTER 2: CHEMISTRY OF LIFE Atom  Organism Atom vs. Element Subatomic Particle Atomic Number Mass Number Isotopes Chemical Bonds Covalent vs. Ionic H2O Polar Covalent Bond Hydrogen Bond Cohesion vs. Adhesion Solution/Solvent/Solute Water as a Solvent pH Scale Dissociation Acid vs. Base Buffers Organic Chemistry Macromolecule Chart Monomer vs. Polymer Carbohydrates Lipids Proteins Nucleic Acids Chemical Reactions Chemical Equations Metabolism Activation Energy Enzymes

Atom Element = the smallest unit of matter that cannot be broken down = a pure substance made of only one kind of atom

Atoms are composed of even smaller parts, called subatomic particles. Protons = positive electric charge (1+) Neutrons = neutral charge (0) Electrons = negative charge (1-)

Each element has a unique number of protons = atomic number.

Atoms have equal numbers of P and e- The atomic number = tells the number of protons and the number of electrons

Mass number = the sum of the number of protons and neutrons in the nucleus of an atom. # Neutrons = Mass # - Atomic # # protons? # electrons? # neutrons? Carbon =

In nature, an element occurs as a mixture of isotopes. Atoms of a given element may differ in the number of neutrons = isotopes. In nature, an element occurs as a mixture of isotopes. For example, 99% of carbon atoms have 6 neutrons (12C). Most of the remaining 1% of carbon atoms have 7 neutrons (13C) while the rarest isotope, with 8 neutrons is 14C.

6 C Carbon 12.01

 P N e- Electron Shells Energy Levels 1st Shell = 2 electrons 2nd Shell = 8 electrons 3rd Shell = 8 electrons (stable)

Atoms are mostly “empty space” If Nucleus = golf ball 1km (10 football fields) ----------------------------------------------------- e-

 Valence Electrons = electrons in outer energy shell Electron Shells Energy Levels  Valence Electrons = electrons in outer energy shell Valence Electrons do the interaction during chemical reactions. The nuclei do not come close enough to interact.

Groups/Families (Reactivity/Valence e-)  Periods (+ Protons/electrons) 

Valence Electrons? 2/8 1 ? 2 3 4 5 6 7 ? ? ? ? ? ?

Atom Interaction? ~ 50 trillion cells Each cell 1,000’s atoms Valence Electrons

Atoms want to be “stable” = full valence shell. Chemical bonds Atoms want to be “stable” = full valence shell. Share or transfer electrons. To become stable, atoms will hold together by chemical bonds. The strongest chemical bonds are covalent bonds and ionic bonds.

Single Atoms Chemical Bond

A covalent bond is the sharing of a pair of electrons by two atoms. Hydrogen H2 Subscript (2 atoms)

“Hydrogen Molecule” (H2) Single Covalent “Hydrogen Molecule” (H2) Double Covalent “Oxygen Molecule” (O2) Two or more atoms held together by covalent bonds constitute a molecule

Ionic bond = one atom strips an electron completely from the other. Ions = charged atoms or molecule NaCl

Top 4 Atoms found in Organisms? C = 18.5% H = 9.5% N = 3.3%

Properties of Water

Cells 70-95% Water ~75% Earth Astronomers Life evolved in water

H2O

“Polar Molecule” Polar Covalent Bond = electrons not shared equally - +

Hydrogen bonds = a weak chemical attraction between polar molecules. H+  O-

Up to 4 per water molecule

Cohesion = water molecules bonding to each other. “Surface tension” prevents stretch or break the surface

Adhesion = clinging of one substance to another (polar  polar).

Water is the “solvent” of life Solution = homogenous mixture. Solute = Solvent = substance dissolved dissolving agent

Forms hydrogen bonds with charged and polar covalent molecules. Solvent? Solute? “Dissolve”

pH “Dissociation” H2O <=> H+ + OH- pH scale = Hydrogen Ion pH  H+ “Dissociation” H2O <=> H+ + OH- pH scale = concentration of H+ in a solution Acid = any compound that forms hydrogen ions (H+) ions in solution Buffers = weak acids or bases that prevent sudden changes in pH Base = any compound that forms hydroxide ions (OH-) in solution “Homeostasis”

pH

Hydrogen Ion  H+

Dissociation H2O <=> H+ + OH- In pure water only one water molecule in every 554 million is dissociated.

0 - 14 7 = neutral (H+ = OH-) 0-6 = acidic (H+) 8-14 = basic (OH-) pH scale = concentration of H+ in a solution 0 - 14 7 = neutral (H+ = OH-) 0-6 = acidic (H+) 8-14 = basic (OH-)

Acid = any compound that forms hydrogen ions (H+) ions in solution Base = any compound that forms hydroxide ions (OH-) in solution Factor of 10

Buffers = weak acids or Cell pH = 6.5 – 7.5 “Homeostasis” bases that prevent sudden changes in pH

CARBON COMPOUNDS “ORGANIC CHEMISTRY”

96% 4% Life depends on 25 elements ------------------- “Trace elements” 4% -------------------

“CARBON COMPOUNDS” Although cells are 70-95% water, the rest consists mostly of carbon-based compounds. Proteins, DNA, carbohydrates, and other molecules are all composed of carbon atoms bonded to each other and to atoms of other elements.

Organic chemistry = the study of carbon compounds (organic compounds). C bonds with: H O N S P

3-D

Hydrocarbons “Petroleum”

Functional groups unique properties

Macromolecules   Form MONOMERS POLYMERS Large Carbon Based Molecules “Single” Form   Bond POLYMERS “Multiple”

MACROMOLECULES Elements Monomers Example Carbohy-drates Lipids C,H,O 1:2:1 Monosac- carhides Starch Glucose Sucrose Lipids Glycerol Fatty Acids Fats Oils Cholesterol Proteins C,H,O,N Amino Acids Insulin Hemoglobin Nucleic C,H,O, N, P Nucleotides DNA RNA

1. CARBOHYDRATES “Sugar” Main source of energy

Monomer = “Monosaccharide” Glucose C6H1206 1:2:1

Polymer = “Polysaccharide” Starch Glucose Glucose

2. LIPIDS (fats, oils, waxes) Monomers: Fatty Acid Glycerol

Polymer Monomer

Store energy Solid at room Temp (Bad) Straight Kinked Liquid at Room Temp (Good) Double bond prevents “packing”

Steroids Cholesterol

3. PROTEINS Monomer = Polymer = Amino Acids “Polypeptide” “Peptide” Bond AA—AA—AA—AA Polymer = “Polypeptide”

20 different Amino Acids “R Group”

Proteins: Control rate of reactions Regulate cell processes Form bone and muscle Transport substances into and out of the cell Fight disease

4. NUCLEIC ACIDS Monomers = Nucleotides

Polymer = Nucleic Acids (DNA/RNA) Monomer  Monomer  

Section 4: Energy and Chemical Reactions Energy = the ability to move or change mater Chemical reactions = chemical bonds between atoms are broken and new ones formed Chemical equations: Reactants  Products NaCl  Na+ + Cl- Metabolism = all the chemical reactions that occur in an organism Activation energy = the energy needed to start a chemical reaction Enzyme = a substance that increases the speed of chemical reactions Speeds-up reaction by reducing activation energy

Section 4: Energy and Chemical Reactions Energy = the ability to move or change mater

CHAPTER 2: CHEMISTRY OF LIFE Atom  Organism Atom vs. Element Subatomic Particle Atomic Number Mass Number Isotopes Chemical Bonds Covalent vs. Ionic H2O Polar Covalent Bond Hydrogen Bond Cohesion vs. Adhesion Solution/Solvent/Solute Water as a Solvent pH Scale Dissociation Acid vs. Base Buffers Organic Chemistry Macromolecule Chart Monomer vs. Polymer Carbohydrates Lipids Proteins Nucleic Acids Chemical Reactions Chemical Equations Metabolism Activation Energy Enzymes McMush Lab Gelatin/Enzyme Lab

Na + Cl  Na+Cl- NaCl  Na+ + Cl- Chemical reactions = chemical bonds between atoms are broken and new ones formed Energy is released or stored Chemical equations: Reactants  Products Na + Cl  Na+Cl- NaCl  Na+ + Cl-

Energy Releasing Reaction NaCl  Na+ + Cl- “Bonds Broken”

Energy Absorbing Reaction Na + Cl  Na+Cl- “Bonds Formed”

Metabolism = all the chemical reactions that occur in an organism

Activation energy = the energy needed to start a chemical reaction “Push” needed

“catalyst” Cells require activation energy Enzyme = a substance that increases the speed of chemical reactions “catalyst”

Speeds-up reaction by reducing activation energy

Amylase Catalase End in “-ase”

substrate 1. Substrate binds to enzyme active site induced fit Reaction rate is substrate concentration dependant denature 4. Active site is available for another substrate 2. Substrate is converted to products Enzymes are unaffected by the reaction and are reusable 3. Products are released

6 C Carbon 12.01