Chemistry of Life Chapter 2. AN INTRO TO CHEMISTRY.
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Transcript of Chemistry of Life Chapter 2. AN INTRO TO CHEMISTRY.
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Chemistry of Life
Chapter 2
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AN INTRO TO CHEMISTRY
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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
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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
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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)
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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
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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
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HYDROGEN1p+ , 1e-
HELIUM2p+ , 2e-
CARBON6p+ , 6e-
OXYGEN8p+ , 8e-
SODIUM11p+ , 11e-
CHLORINE17p+ , 17e-
NEON10p+ , 10e-
electron
proton
neutron
Electron Shell Models
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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)
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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
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Covalent Bonds
• Atoms share outer pair or pairs of valence electrons– Single, double, or triple covalent bond
• Strong bonds
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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)
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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
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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.
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AN INTRO TO BIOCHEMISTRY
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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
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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
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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+
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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
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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
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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
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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
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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)
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Protein Types
• Fibrous (structural proteins)– Building materials of the body• Keratin, elastin, and collagen
– Movement• Actin and myosin
• Globular (functional proteins)– Enzymes – Transport– Immunity
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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
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Nucleic Acids
• DNA and RNA • Composed of nucleotides
with 3 components– Pentose sugar– Phosphate group (PO4)
– Nitrogenous base form complementary pairs
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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
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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