1. Chapter 2 The Chemical Context of Life

2. Overview: A Chemical Connection to Biology
Living organisms follow basic laws of physics and chemistry
use of formic acid by ants to maintain “devil’s gardens,” stands of Duroia trees
2 Hypotheses: 1 Ants kill nearby trees of other species; 2 trees kill trees of other species
Experiment: Cedrela trees plants inside and outside Devil’s Garden, half inside have sticky insect barrier, half outside have insect barrier…which survives?
Ants observed injecting formic acid into leaves that died within 24 hrs. Formidable habitat for trees= formidable habitat for ant colony.
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

3. Organisms composed of matter
Concept 2.1: Matter consists of chemical elements in pure form and in combinations called compounds
Organisms composed of matter
Matter: anything that takes up space and has mass
Made up of elements
Element: substance that cannot be broken down to other substances by chemical reactions
Compound: substance consisting of two or more elements in a fixed ratio
Compound may not have same characteristics as elements it’s made of
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

4. Essential Elements of Life
Only 25 of 92 elements essential to life
96% of living matter:
Carbon, hydrogen, oxygen, and nitrogen
Remaining 4%:
Calcium, phosphorus, potassium, and sulfur
Trace elements: those required by an organism in minute quantities
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

5. (a) Nitrogen deficiency (b) Iodine deficiency
Fig. 2-4
Figure 2.4 The effects of essential-element deficiencies
(a) Nitrogen deficiency
(b) Iodine deficiency

6. Concept 2.2: An element’s properties depend on the structure of its atoms
Neutron mass & proton mass are almost identical
measured in daltons
Subatomic Particles
Neutrons (no electrical charge)
Location: Atomic Nucleus
Protons (positive charge)
Electrons (negative charge)
Location: In cloud around nucleus
Each element consists of unique atoms
Atom: smallest unit of matter that still retains the properties of an element
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

7. Atomic Number and Atomic Mass
Atomic number: number of protons in nucleus
Mass number: sum of protons plus neutrons in nucleus
Atomic mass: atom’s total mass AKA mass number
Same element = same number of protons but may differ in number of neutrons
Isotopes: two atoms of an element that differ in number of neutrons
Radioactive isotopes: decay spontaneously, giving off particles and energy
GREAT for labeling proteins and cells
Applications:
Dating fossils
Tracing atoms through metabolic processes
Diagnosing medical disorders
Measure effect of temperature on cells making DNA
Labeled with 3H(radioactive H isotope) cells making more DNA incorporate 3H into new cells measure amount of 3H=amount of new DNA made
PET Scan: Positron-emission tomography; detects locations of intense chemical activity in body
First patient injected with radioactive nutrient, usually glucose these particles collide with electrons made available via chemical reactions in body cancer = very active = lots of energy( the light ) detected
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

8. The Energy Levels of Electrons
Energy: capacity to cause change
Potential energy: that matter has because of its location or structure
Electrons of atom differ in amounts of potential energy
Electron’s state of potential energy is called its energy level, or electron shell
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

9. Electron Distribution and Chemical Properties
Valence electrons: in the outermost shell, or valence shell
Elements with full valence shell are chemically inert
Chemical behavior of atom determined by distribution of electrons in electron shells, MOSTLY by valence electrons
Periodic table of the elements shows electron distribution for each element
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

10. Electron Orbitals
An orbital is the three-dimensional space where an electron is found 90% of the time
Each electron shell consists of a specific number of orbitals
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

11. Concept 2.3: The formation and function of molecules depend on chemical bonding between atoms
Covalent bond: sharing of a pair of valence electrons by two atoms
Incomplete valence shells can share/transfer valence electrons with other atoms
usually result in chemical bonds
atoms staying close together, held by attraction
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

12. Structural formula: notation used to represent atoms and bonding
Molecule: consists of two or more atoms held together by covalent bonds
A single covalent bond, or single bond, is the sharing of one pair of valence electrons
A double covalent bond, or double bond, is the sharing of two pairs of valence electrons
Structural formula: notation used to represent atoms and bonding
Ex: H–H
Molecular formula: indicates the amount and type of atoms in a molecule
Ex: H2
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

13. Covalent bonds can form between same OR different elements
Compound: combination of two or more different elements
Valence: Bonding capacity of atom
Electronegativity: atom’s attraction for electrons in covalent bond
More electronegative an atom = the more strongly it pulls electrons
Nonpolar covalent bond: electrons equally shared
Polar covalent bond: one atom is more electronegative  electrons unequally shared
Unequal sharing  partial positive or negative charge
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

14. Sodium chloride (NaCl)
Fig Na Cl Na Cl Na Cl
Na+
Cl–
Sodium atom
Chlorine atom
Sodium ion
(a cation)
Chloride ion
(an anion)
Figure 2.14 Electron transfer and ionic bonding
Sodium chloride (NaCl)

15. Animation: Ionic Bonds
Ion: charged atom or molecule
After the transfer of an electron  both atoms have charges
Cation: positively charged ion
Anion: negatively charged ion
Ionic bond: attraction between anion and cation
Ionic compounds, or salts: compounds formed by ionic bonds
Salts like NaCl often found in nature as crystals
Animation: Ionic Bonds
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

16. Weak Chemical Bonds
Most of the strongest bonds in organisms are covalent bonds
form a cell’s molecules
Weak chemical bonds:
reinforce shapes of large molecules
help molecules adhere to each other
Hydrogen bond: forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom
In living cells electronegative partners usually oxygen or nitrogen atom
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

17. Van der Waals Interactions
Electrons are distributed asymmetrically“hot spots” of positive or negative charge
Van der Waals interactions: attractions between molecules that are close together as a result of these charges
Together can be strong, as
Ex: between molecules of a gecko’s toe hairs and a wall surface
100’s of 1000’s toe hairs increase surface area and forces between gecko and wall
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

18. Molecular Shape and Function
Shape = Function
Shape determined by positions of atoms’ valence orbitals
In covalent bond s and p orbitals may hybridize  specific molecular shapes
Biological molecules recognize and interact based on molecular shape
Similar shapes = similar biological effects
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

19. Concept 2.4: Chemical reactions make and break chemical bonds
Chemical reactions: making and breaking of chemical bonds
Reactants: starting molecules of chemical reaction
Products: final molecules of a chemical reaction
Photosynthesis IMPORTANT chemical reaction
Sunlight powers the conversion of carbon dioxide + water  glucose + oxygen
6 CO2 + 6 H20 → C6H12O6 + 6 O2
All chemical reactions reversible
products of the forward reaction become reactants for the reverse reaction
Chemical equilibrium reached when the forward and reverse reaction rates are equal
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

20. You should now be able to:
Identify the four major elements
Distinguish between the following pairs of terms:
neutron and proton,
atomic number and mass number,
atomic weight and mass number
Distinguish between and discuss the biological importance of the following:
nonpolar covalent bonds,
polar covalent bonds,
ionic bonds,
hydrogen bonds, and
van der Waals interactions
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

21. Electrons (– charge) form negative cloud and determine
Fig. 2-UN3
Nucleus
Protons (+ charge)
determine element
Electrons (– charge) form negative cloud
and determine
chemical behavior
Neutrons (no charge)
determine isotope
Atom

22. Single covalent bond Double covalent bond
Fig. 2-UN5
Single
covalent bond
Double
covalent bond

23. Fig. 2-UN9

24. Fig. 2-UN10

25. Fig. 2-UN11