Download Chemical Basis of Life

Chapter 2
Matter
 Any substance that has mass and takes up space
 Composed of 1 or more elements
 Found in 1 of 3 states
 Gas – no definite shape or volume
 Liquid – shape conforms to container
 Solid – definite shape
Human
Elements
 Substances that can’t be broken down
by ordinary chemical processes
 92 occur naturally on Earth
Oxygen
Carbon
Hydrogen
Nitrogen
Calcium
Phosphorus
Potassium
Sulfur
61.0%
23.0
10.0
2.6
1.4
1.1
0.2
0.2
 About 25 are essential to life
 96% of human body, as well as other living organisms, from 4
elements (CHON)
 Composed of atoms
 2+ of same atoms is a molecule (O2)
 2+ of different atoms is a compound (NaCl, H2O)

Metal + poisonous gas = edible product

Gas + gas = liquid
96%
Atoms
 Smallest particles that retain the properties of an
element
 Made up of subatomic particles:
 Protons (+) in nucleus
 Electrons (-) orbits nucleus
 Neutrons (no charge) in nucleus
 Protons and neutrons
 Mass of about 1 dalton (atomic mass unit, amu)
 Electrons
 Mass is negligible (1/2000 amu)
Reading A Periodic Table
 Elements differ depending on the number of
subatomic particles
 Atomic symbol
 1st letter or 2 (usually)
 Atomic number
 Determined by number of protons

Neutral atoms contain equal # of electrons
 Element specific
 Mass number
 Determined by number of protons + neutrons
 Atomic weight: average of relative weights of all
isotopes, versions of the element
The Periodic Table
Most Common Elements in
Living Organisms
Chemical Bonds
 Energy relationship between electrons
 Energy is the capacity to do work, cause change, or move
matter


Kinetic: energy of motion
Potential: energy due to location or structure; capability
 Electrons repel one another (magnets), but attracted to
protons (opposites attract)
 Determine chemical properties, reactivity, of atoms
 Orbitals are key
 Closer to the nucleus = lower energy and filled first
 Octet rule: hold up to 8 electrons (not 1st = 2)
 Outermost is valence shell
 Chemical reactions are making and breaking bonds
Electron Shell Models
 Inert versus reactive elements
 Valence electrons
Ionic Bonds
 One atom loses electron(s) to become _____ charge?
 Another atom gains these electrons to become _____ charge?
 Charge difference attracts the two ions to each other
 Clinically called electrolytes
 Very weak bond
 E.g. Salts
cation
anion
Covalent Bonds
 Atoms share a pair(s) of electrons to fill valence shell
 Form single, double, or triple covalent bond, based on
number of electrons shared
 Strong bonds
What’s Mine is Yours or Just Mine
Nonpolar molecules
 Electrons shared equally
 Example: carbon dioxide(CO2)
Polar Molecules
 Electrons spend more time
near the nucleus with the most
protons (electronegativity)
 Example: water (H20)
Hydrogen Bonds
 Special case of covalent bonds
 Attractions between molecules
 Polar hydrogen (slightly ‘+’ charge) attracted to another
polar molecule (slightly ‘-’ charge)
 Hold large molecules in a specific 3D shape
Chemical Reactions
 Chemical equation: reactant(s) + reactant(s) = product(s)
 May be reversible
 Move to equilibrium
 Types
 Synthesis: (A + B  AB) usually anabolic and endergonic
 Decomposition: (AB  A + B) usually catabolic and exergonic
 Exchange: (AB + CD  AD + BC) may or may not be
endergonic/exergonic
 Redox: may gain or lose electrons


Oxidized – loses electrons (LEO)
Reduced – gains electrons (GER)
 Affected by temperature, concentration, catalysts, etc.
Biologically Important Compounds
 Inorganics lack carbon (generally)
 E.g. salts, water, acids, and bases
 Organics contain carbon, are covalently bonded, and
generally large
 E.g. carbohydrates, lipids, proteins, and nucleic acids
Properties of Water
 Temperature-stabilizing effects
 Absorbs and releases large amounts of heat w/o significant
change
 Sun, wind, muscle activity
 High heat of evaporation
 Absorption of heat breaks bonds; liquid  gas
 Sweating
 Polar molecule
 Hydrophobic and hydrophilic


Solvent/solute relationship
Blood circulation, waste disposal, and cleaning
 Reactivity
 Hydrolysis and dehydration reactions
Electrolytes
 Ions able to conduct electrical current
 Kidneys regulate
 Salts contain ions other than H+ or
OH-
 E.g. NaCl, CaCO3, and calcium
phosphates
 Acids are hydrogen ion (H+) donors
 Concentration determines acidity of a
solution
 E.g. pH < 7; HCl, H2CO3
 Bases are hydrogen acceptors
 Form water upon disassociation
 E.g. pH > 7; Mg(OH) 2, HCO3-, and NH3
 Buffers release H + with increasing pH
and accept H + when decreasing
 H2CO3
HCO3- + H+
Building Organic Molecules
 Monomers: small repeating units
 Universal, similar in all forms of life
 Polymers: chains of monomers, functional components of
cells (macromolecules)
 DNA is composed of 4 monomers (nucleotides)
 Variation based on arrangement
 Proteins from 20 different amino acids (AA’s)
 Variation distinguishes within and between species
Making and Breaking Polymers
Dehydration reaction
Hydrolysis reaction
 Links monomers
 Breaks polymers
 Loss of water for each
 Addition of water for each
monomer added
 Forms a covalent bond
1
2
broken bond
4
3
1
1
2
3
2
3
4
4
1
2
3
4
Carbohydrates
 General (CH2O)n ratio, end in ‘ose’
 Fuel source for cells
 Glycosidic bonds
 Dehydration vs. hydrolysis
 Monosaccharides (simple)
 Pentoses: ribose and deoxyribose
 Hexoses: glucose, fructose, & lactose (energy
production)
 Disaccharides (simple)
 Maltose, lactose (glu + gal), & sucrose (glu + fru)
 Polysaccharides (complex)
 Glycogen (animal storage)
 Starch (plant storage)
Lipids
 Composed of fatty acids (long carbon chains) and a glycerol (3 carbons)
 Triglycerides
 3 FA’s
 Most usable form of energy
 Fats (animal) and oils (plants)
 Saturated or unsaturated (mono- or poly-)
 Phospholipids
 2 FA’s and a phosphate group
 Amphipathic molecule

Cell membranes
 Steroids
 Hydrocarbon rings
 Cholesterol and sex hormones
 Eicosanoids
 In all cell membranes
 Prostaglandins role in blood clotting,
inflammation, and labor contractions
Proteins
 Chains of amino acids joined by peptide bonds
 20 different types (alphabet)
 Peptide, polypeptides, and proteins (words) are all slightly different
 Structural levels
 Primary (1°) – sequence of amino acids
 Secondary (2°) – primary level folds to form alpha (α) – helixes and
beta (β) - pleated sheets
 Tertiary (3°) – folding of secondary structures on each other
 Quaternary (4°) – 2+ polypeptides interact to form a protein
 Denaturation destroys structure which alters or inhibits
function
 Changes in pH and temperature
 Reversible or permanent depending on extend of change (fevers)
Protein Types
 Fibrous (structural proteins)
 Building materials of the body

Keratin, elastin, and collagen
 Movement
 Globular (functional proteins)
 Enzymes
 Transport
 Immunity
Enzymes
 Globular proteins acting as catalysts to speed a reaction
 Lower energy of activation (EA)
 End in ‘ase’ and named for substrate
 Mechanism of enzyme action:
 Enzyme binds substrate at its active site on the enzyme.
 Enzyme-substrate complex undergoes an internal
rearrangement that forms a product.
 Product released and now catalyzes another reaction
Nucleic Acids
 DNA and RNA
 Composed of nucleotides with 3
components
 Pentose sugar
 Phosphate group (PO4)
 Nitrogenous base form
complementray pairs


Purines (2 rings): adenine (A) and
guanine (G)
Pyrimidines (1 ring): thymine (T),
cytosine (C), and uracil (U)
How DNA and RNA Differ
DNA
(deoxyribonucleic acid)
RNA
(ribonucleic acid)
 Directs protein synthesis;
 Carries out protein synthesis
replicates self; genetic material
 Sugar is deoxyribose
 Sugar is ribose
 Has -OH
 Bases are A, C, G, and U
 Has –H
 Bases are A,C, G, and T
 Single-stranded
 Double-stranded helix
 Not confined to nucleus
 Only in nucleus
 3 major types
 1 type
Adenosine Triphosphate (ATP)
 RNA nucleotide with 3
phosphate groups
 Stores energy from break
down of glucose
 Transfers phosphate groups
to release energy,
phosphorylation
 Controls energy release