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Chemical Foundations for Cells
Chapter 6
Chemical Benefits and Costs
• Understanding of chemistry provides fertilizers, medicines, etc.
• Chemical pollutants damage ecosystems
Elements• Fundamental forms
of matter
• Can’t be broken
apart by normal
means
• 92 occur naturally
on Earth
Most Common Elements in Living Organisms
Oxygen = 65%
Hydrogen = 9.5%
Carbon = 18.5%
Nitrogen = 3.3%
What Are Atoms?
• Smallest particles that retain properties
of an element
• Made up of subatomic particles:
– Protons (+)
– Electrons (-)
– Neutrons (no charge)
HYDROGEN HELIUM
electron
proton
neutron
Hydrogen and Helium Atoms
Atomic Number
• Number of protons
• All atoms of an element have the same atomic number
• Atomic number of hydrogen = 1
• Atomic number of carbon = 6
Mass Number
Number of protons
+Number of neutrons
Isotopes vary in mass number
Isotopes
• Atoms of an element with different numbers of neutrons (different mass numbers)
• Carbon 12 has 6 protons, 6 neutrons
• Carbon 14 has 6 protons, 8 neutrons
What Determines Whether Atoms Will Interact?
The number and arrangement of their electrons
Atoms seek to be more stable – complete orbitals
Electrons
• Carry a negative charge
• Repel one another
• Are attracted to protons in the nucleus
• Move in orbitals - volumes of space that surround the nucleus
Z
X
When all p orbitals are full
y
Electron Orbitals
• Orbitals can hold up to two electrons
• Atoms differ in the number of occupied orbitals
• Orbitals closest to nucleus are lower energy and are filled first
Shell Model
• First shell
– Lowest energy
– Holds 1 orbital with up
to 2 electrons
• Second shell
– 4 orbitals hold up to 8
electrons
CALCIUM20p+ , 20e-
Electron Vacancies
• Unfilled shells make atoms likely to react
• Hydrogen, carbon, oxygen, and nitrogen all have vacancies in their outer shells
CARBON6p+ , 6e-
NITROGEN7p+ , 7e-
HYDROGEN1p+ , 1e-
Chemical Bonds, Molecules, & Compounds
• Bond is union between electron structures of atoms
• Atoms bond to form molecules
• Molecules may contain atoms of only one element - O2
• Molecules of compounds contain more than one element - H2O
Chemical Bookkeeping
• Use symbols for elements when writing formulas
• Formula for glucose is C6H12O6
– 6 carbon atoms
– 12 hydrogen atoms
– 6 oxygen atoms
Chemical Bookkeeping
• Chemical equation shows reaction
Reactants ---> Products
• Equation for photosynthesis:
6CO2 + 6H2O ---> + C6H12O12 + 6H2O
Important Bonds in Biological Molecules
Ionic Bonds
Covalent Bonds
Hydrogen Bonds
Covalent Bonding
Atoms share a pair or pairs of electrons to fill outermost shell
•Single covalent bond
•Double covalent bond
•Triple covalent bond
Nonpolar Covalent Bonds
• Atoms share electrons equally
• Nuclei of atoms have same number of protons
• Example: Hydrogen gas (H-H)
Polar Covalent Bonds
• Number of protons in nuclei of participating atoms is NOT equal
• Electrons spend more time near nucleus with most protons
• Water - Electrons more attracted to O nucleus than to H nuclei
Ion Formation
• Atom has equal number of electrons and protons - no net charge
• Atom loses electron(s), becomes positively charged ion
• Atom gains electron(s), becomes negatively charged ion
Ionic Bonding
• One atom loses electrons, becomes positively charged ion
• Another atom gains these electrons, becomes negatively charged ion
• Charge difference attracts the two ions to each other
Formation of NaCl
• Sodium atom (Na) – Outer shell has one electron
• Chlorine atom (Cl) – Outer shell has seven electrons
• Na transfers electron to Cl forming Na+ and Cl-
• Ions remain together as NaCl
7mm
SODIUMATOM11 p+
11 e-
SODIUMION
11 p+
10 e-
electron transfer
CHLORINEATOM17 p+
17 e-
CHLORINEION
17 p+
18 e-
Fig. 2.10a, p. 26
Formation of NaCl
Hydrogen Bonding
• Molecule held together by polar covalent bonds has no NET charge
• However, atoms of the molecule carry different charges
• Atom in one polar covalent molecule can be attracted to oppositely charged atom in another such molecule
onelargemolecule
anotherlargemolecule
a largemoleculetwistedbackonitself Fig. 2.12, p. 27
Examples of Hydrogen Bonds
Hydrogen Ions: H+
• Unbound protons
• Have important biological effects
• Form when water ionizes
The pH Scale
• Measures H+ concentration of fluid• Change of 1 on scale means 10X
change in H+ concentration
Highest H+ Lowest H+
0---------------------7-------------------14Acidic Neutral Basic
Acids & Bases
• Acids
– Donate H+ when dissolved in water
– Acidic solutions have pH < 7
• Bases
– Accept H+ when dissolved in water
– Acidic solutions have pH > 7
Properties of Water
Polarity
Temperature-Stabilizing
Cohesive
Solvent
Water Is a Polar Covalent Molecule
• Molecule has no net charge
• Oxygen end has a slight negative charge
• Hydrogen end has a slight positive charge
O
H H
O
H
HO
H
H
+ _
++
+
_
+
+
Liquid Water
Water Cohesion• Hydrogen bonding holds
molecules in liquid water together
• Creates surface tension
• Allows water to move as continuous column upward through stems of plants
Temperature-Stabilizing Effects
• Liquid water can absorb much heat before its temperature rises
• Why?
• Much of the added energy disrupts hydrogen bonding rather than increasing the movement of molecules
Why Ice Floats
• In ice, hydrogen bonds lock molecules in a lattice
• Water molecules in lattice are spaced farther apart then those in liquid water
• Ice is less dense than water
Water Is a Good Solvent
• Ions and polar molecules dissolve easily in water
• When solute dissolves, water molecules cluster around its ions or molecules and keep them separated
Spheres of Hydration
Diffusion
• Brownian motion – molecules are in constant motion
• Diffusion – movement from area of high concentration to area of low concentration– Affected by
• Concentration• Temperature or agitation• Pressure
Dynamic Equilibrium
• Molecules are still in motion
• No net gain or loss of molecules
• Living systems seek to achieve
Organic Compounds
Hydrogen and other elements covalently bonded to carbon
Carbohydrates
Lipids
Proteins
Nucleic Acids
Carbon’s Bonding Behavior
• Outer shell of carbon has 4 electrons; can hold 8
• Each carbon atom can form covalent bonds with up to four atoms
Bonding Arrangements
• Carbon atoms can form chains or rings
• Other atoms project from the carbon backbone
Condensation Reactions
• Form polymers from subunits
• Enzymes remove -OH from one molecule, H from another, form bond between two molecules
• Discarded atoms can join to form water
Fig. 3.4a, p. 37
enzyme action at functional groups
CONDENSATION
Hydrolysis
• A type of cleavage reaction
• Breaks polymers into smaller units
• Enzymes split molecules into two or more parts
• An -OH group and an H atom derived from water are attached at exposed sites
enzyme action at functional groups
HYDROLYSIS
Fig. 3.4b, p. 37
Carbohydrates – energy source
Monosaccharides
(simple sugars)
Disaccharides
(two simple sugars)
Polysaccharides
(complex carbohydrates)
Monosaccharides
• Simplest carbohydrates
• Most are sweet tasting, water soluble
• Most have 5- or 6-carbon backbone
Glucose (6 C) Fructose (6 C)
Ribose (5 C) Deoxyribose (5 C)
Two Monosaccharides
glucose fructose
Disaccharides
• Two monosaccharides covalently bonded
• Formed by condensation reaction
+ H2O
glucose fructose
sucrose
Polysaccharides
• Straight or branched chains of many saccharides
• Most common are composed entirely of glucose– Cellulose
• tough, indigestible
• structural material in plants
– Starch• easily digested
• storage form in plants
– Glycogen• sugar storage form in animals
– Chitin• structural material for hard parts of invertebrates
• cell walls of many fungi
• Most include fatty acids– Fats– Phospholipids– Waxes
• Tend to be insoluble in water
• Energy source, insulation & protection
Lipids
Fatty Acids
• Carboxyl group (-COOH) at one end
• Carbon backbone (up to 36 C atoms)
– Saturated - Single bonds between carbons
– Unsaturated - One or more double bonds
Three Fatty AcidsWhat difference does the double bond make?
stearic acid oleic acid linolenic acid
Fats
• Fatty acid(s)
attached to
glycerol
• Triglycerides are
most common
Proteins
• Carbon, hydrogen, oxygen, nitrogen & sulfur
• Amino acid building blocks
• AA linked by peptide bonds
• Enzymes
• Build tissue
Enzymes
• Protein
• Act as catalyst– Helps reaction happen faster or at lower
temperatures
• Substrate specific shapes– Lock & key system– Recycled; not used up
Denaturation• Disruption of three-
dimensional shape
• Breakage of weak bonds
• Causes of denaturation:– pH
– Temperature
• Destroying protein shape disrupts function
Nucleic Acids
• Carbon, hydrogen, oxygen, nitrogen & phosphorus
• Nucleotides – building blocks
• DNA, RNA
• Genetic information