The Chemical Context of Life AP Biology Why

The Chemical Context of Life AP Biology

Why are we studying chemistry? § Biology has chemistry at its foundation AP Biology

The Basics § Everything is made of matter § Matter is made of atoms § Atoms are made of: protons u neutrons u electrons u + 0 - mass of 1 mass <<1 nucleus orbits § Different kinds of atoms = elements AP Biology

The World of Elements AP Biology

Models of atoms AP Biology (c)

Atomic structure determines behavior § The number of protons in an atom determines the element # of protons = atomic number u this also tells you # of electrons u § All atoms of an element have same chemical properties all behave the same u properties don’t change u AP Biology

Life requires ~25 chemical elements § About 25 elements are essential for life u Four elements make up 96% of living matter: • carbon (C) • oxygen (O) u • hydrogen (H) • nitrogen (N) Four elements make up most of remaining 4%: • phosphorus (P) • calcium (Ca) • sulfur (S) • potassium (K) AP Biology

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Isotopes § Different number of neutrons (heavier) § Some are unstable u nuclear reactions / decay § Split off neutrons &/or protons u radioactivity § Biological tool § Biological hazard AP Biology

Bonding properties § Effect of electrons chemical behavior of an atom depends on its electron arrangement u depends on the number of electrons in its outermost shell, the valence shell u How does this atom behave? AP Biology

Bonding properties § Effect of electrons u AP Biology chemical behavior of an atom depends on number of electrons in its outermost shell How does this atom behave?

Elements & their valence shells § Elements in the same row have the same number of shells AP Biology

Elements & their valence shells § Elements in the same column have the same valence & similar chemical properties AP Biology

Elements & their valence shells § Moving from left to right, each element has a sequential addition of electrons (and protons) AP Biology

Chemical reactivity § Atoms tend to Complete a partially filled outer (valence) electron shell or u Empty a partially filled outer (valence) electron shell u u AP Biology This tendency drives chemical reactions

Ionic bonds AP Biology

Ionic bonds § Transfer of an electron § Forms + & - ions + = cation u – = anion u § Weak bond AP Biology § example: u salt = dissolves easily in water

Covalent bonds § Two atoms need an electron § Share a pair of electrons § Strong bond u both atoms holding onto the electrons § Forms molecules § example: u AP Biology water = takes energy to separate

Double covalent bonds § Two atoms can share more than one pair of electrons double bonds (2 pairs of electrons) u triple bonds (3 pairs of electrons) u § Very strong bonds AP Biology

Multiple covalent bonds § 1 atom can form covalent bonds with two or more other atoms forms larger molecules u ex. carbon u AP Biology

Polar covalent bonds § Pair of electrons not shared equally by § 2 atoms Water = O + H oxygen has stronger “attraction” for the shared electrons than hydrogen u oxygen has higher electronegativity u AP Biology

Polar covalent bonds § 2 hydrogens in the water molecule form § an angle Water molecule is polar oxygen end is – u hydrogen end is + u § Leads to many interesting properties of water…. AP Biology

Hydrogen bonds § Positive H atom in § § 1 water molecule is attracted to negative O in another Can occur wherever an -OH exists in a larger molecule Weak bonds AP Biology

Reductionist view of biology § § § § Matter is made of atoms Life requires ~25 chemical elements Atomic structure determines behavior of an element Atoms combine by chemical bonding to form molecules Weak chemical bonds play important roles in chemistry of life A molecule’s biological function is related to its shape Chemical reactions make & break chemical bonds AP Biology

Water— The Elixir of Life! AP Biology

Why are we studying water? § All life occurs in water u AP Biology inside & outside the cell

Chemistry of water § Water is polar molecule remember polar covalent bonds u + & – poles u AP Biology

Chemistry of water § H 2 O molecules form H bonds with each other + attracted to – u creates a sticky molecule u AP Biology

Cohesion § H bonding between H 2 O creates cohesion water is “sticky” u surface tension u drinking straw u § can you suck sugar up a straw? AP Biology

How does H 2 O get to top of tree? § Transpiration AP Biology

Adhesion § H 2 O molecules form H bonds with other substances capillary action u meniscus u water climbs up fiber u § ex. paper towel AP Biology

Water is the solvent of life § H 2 O is a good solvent due to its polarity polar H 2 O molecules surround + & – ions u solvents dissolve solutes creating aqueous solutions u AP Biology

Hydrophilic § Hydrophilic substances have affinity for H 2 O u polar or non-polar? u ionic u AP Biology

Hydrophobic § Hydrophobic substances do not have affinity for H 2 O u polar or non-polar? u non-ionic u AP Biology fat (triglycerol)

The special case of ice § Most (all? ) substances are more § § dense when they are solid But not water… Ice floats! u AP Biology H bonds form a crystal with loose structure

Ice floats AP Biology

Why is this important? § Oceans & lakes don’t freeze solid u if ice sank… § eventually all ponds, lakes & even ocean would freeze solid § during summer, only upper few inches would thaw u surface insulates water below § allowing life to survive the winter u seasonal turnover of lakes § cycling nutrients AP Biology

Specific heat § H 2 O has high specific heat u due to H bonding § H 2 O resists changes in temperature takes a lot to heat it up u takes a lot to cool it down u § H 2 O moderates temperatures on Earth AP Biology

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Evaporative cooling § Organisms rely on heat of vaporization to remove heat AP Biology

Water forms ions § Hydrogen ion (H+) splits off from water to leave a hydroxide ion (-OH) H 20 ----> H+ + -OH § If concentration of 2 ions is equal, § § § water is neutral If [H+] > [-OH], water is acidic If [-OH] > [H+], water is basic p. H scale = how acidic or basic a solution is AP Biology

p. H Scale § In pure water only 1 water molecule in every 554 million is dissociated. very small amount of ions u [H+] or [OH-] is 10 -7 M u [H+] [OH-] = 10 -14 § p. H scale is based on this equation AP Biology

p. H Scale § In neutral solution § § [H+] = 10 -7 p. H = 7 Values for p. H decline as [H+] increase Acids u adding acid increases [H+] § Bases u AP Biology adding base increases [OH-]

p. H & Biology § p. H of a neutral solution = 7 § Acidic solutions = p. H < 7 § Basic solutions = p. H > 7 Most biological fluids have p. H 6 – 8 u p. H values in human stomach can reach 2 § Each p. H unit represents a 10 -fold difference in H+ & OH- concentrations. u AP Biology small change in p. H actually indicates a substantial change in [H+] & [OH-]

Overview § Water is a polar molecule § The special properties of water make § life on Earth possible The chemical behavior of water governs how organisms function AP Biology