Chemistry of Life

Chapter 2

AN INTRO TO CHEMISTRY

Matter

• Substance that has mass and takes up space– Compose all living things

• Generally found in 1 of 3 states

• Composed of 1 or more elements

Elements• Can’t be broken down by ordinary chemical processes

• 92 occur naturally on Earth– 96% of the human body is (CHON)

– 25 are essential to life

• Composed of atoms

Atoms

• Smallest particles that retains 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

• Electrons– Mass is negligible (1/2000)

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 – Element specific

• Mass number– Determined by number of protons + neutrons

Chemical Properties of Atoms

• Electrons are key– Move in orbitals called shells– Repel one another, but attracted to protons

• Electron shells– Outermost (valence) determines chemical properties

• Closer to the nucleus = lower energy and are filled first– Holds up to 2 or 8 electrons (Octet Rule)

• Filled are unreactive• Unfilled are reactive

– Number differs between atoms• Chemical reactions are making and

breaking bonds

HYDROGEN1p+ , 1e-

HELIUM2p+ , 2e-

CARBON6p+ , 6e-

OXYGEN8p+ , 8e-

SODIUM11p+ , 11e-

CHLORINE17p+ , 17e-

NEON10p+ , 10e-

electron

proton

neutron

Electron Shell Models

Chemical Bonds

• Hold 2 or more atoms together– Complete outer shells

– By sharing, donating, or receiving electrons

• Form molecules (H2, I2, and O2) or compounds

(H20, NaCl, C6H12O6)

– Demonstrates emergent properties

• 2 H+ (gas) + O- (gas) = H2O (water)

• Na+ (metal) + Cl- (poisonous gas) = NaCl (table salt)

Ionic Bond• One atom loses electrons cation (charge?)• Another atom gains these electrons anion

(charge?)• Charge difference attracts the two– Very weak bond– Table salt (NaCl)

cation anion

Covalent Bonds

• Atoms share outer pair or pairs of valence electrons– Single, double, or triple covalent bond

• Strong bonds

What’s Mine is Yours or Just MineNonpolar Covalent Bonds

• Electrons shared equally• Example: carbon dioxide(CO2),

hydrogen gas (H2)

Polar Covalent Bonds• Electrons spend more time

near the nucleus with the most protons (electronegativity)

• Example: water (H20)

Hydrogen Bond

• Positive charge on H attracts negative charge on another atom

• Individually weak, but often numerous = strong

• Important to many biological compounds– E.g. water

• Makes up 70 – 90% of all living things• Bonds create unique properties

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.

AN INTRO TO BIOCHEMISTRY

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. carbs, lipids, proteins, and nucleic acids

Properties of Water• High heat capacity

– Absorb and release water with little temp. change– Environmental changes (internal and external)

• High heat of vaporization– Lots of heat required to transform water to steam– Sweating

• Polarity– Slightly negative AND slightly positive ends– Dissociation of salts, hydration layers, and transport

• Reactant– Solubility– Dehydration and hydrolysis

• Cushion/shock absorber– Acts as a barrier/buffer– CSF and joints

Electrolytes• Ions able to conduct electrical current

– Kidneys regulate• Salts contain ions other than H+ or OH-

– E.g. NaCl, KCl, and calcium phosphates• Acids are hydrogen ion (H+) donors

– Concentration determines acidity of a solution– E.g. pH < 7; HCl, H2CO3

• Bases are hydrogen ion (H+) 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 are composed of 20 different amino acids (AA’s)

• Variation distinguishes within and between species

Making and Breaking Polymers

Dehydration reaction• Links monomers• Loss of water for each

monomer added• Forms a covalent bond

Hydrolysis reaction• Breaks polymers• Addition of water for each

broken bond

1 42

21

3

3 4

1

2

2 3

3

4

41

Carbohydrates• General (CH2O)n ratio, ends in ‘ose’• Fuel source for cells• Glycosidic bonds

– Dehydration vs. hydrolysis• Monosaccharides

– Pentoses– Glucose, fructose, & galactose

• Disaccharides– Maltose, lactose, & sucrose

• Polysaccharides– Glycogen – Starch

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

• Steroids– Hydrocarbon rings– Cholesterol and sex hormones

Proteins• Chains of amino acids joined by peptide bonds

– 20 different types (alphabet)– Peptides, 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• Actin and myosin

• Globular (functional proteins)– Enzymes – Transport– Immunity

Enzymes

• Globular proteins acting as catalysts to speed a reaction– Lowers 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 complementary pairs

How DNA and RNA DifferDNA

(deoxyribonucleic acid)

• Directs protein synthesis; replicates self; genetic material

• Sugar is deoxyribose– Has –H

• Bases are adenine (A), cytosine (C), guanine (G), and thymine (T)

• Double-stranded helix• Only in nucleus• 1 type

RNA(ribonucleic acid)

• Carries out protein synthesis

• Sugar is ribose– Has -OH

• Bases are adenine (A), cytosine (C), guanine (G), and uracil (U)

• Single-stranded• Not confined to nucleus• 3 major types

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