AP Bio Chapter 2- Basic Chemistry

9/22/2011

Basic Chemistry

Why are we studying chemistry? • Biology has chemistry at its foundation

Elements
• All matter composed of basic substances called elements
• Living organisms require about twenty of the known elements

Together, carbon, hydrogen, nitrogen and oxygen make up 95% of the elements found in the body.

Atoms
• All elements made of tiny particles called atoms • Made up of:
– Nucleus
• contains protons (+ charge) and neutrons
(no charge)

– Outside the nucleus
• Contains electrons (extremely small, - charge)

– In an atom, # of protons = # of electrons
– SO…Atoms are electrically neutral!

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What makes elements different from one another?
• Atomic number – the number of

• Different elements contain different numbers of PROTONS!

protons in the atoms of a particular element – Ex: Hydrogen has one proton and an atomic number of 1

• Atomic weight –
# of protons + # of neutrons = atomic weight
(approx.)

Atomic symbols – the periodic table
ATOMIC NUMBER

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C

SYMBOL OF ELEMENT

Carbon

NAME OF ELEMENT
ATOMIC WEIGHT

12.01

Isotopes
• Atoms of the SAME element with a
DIFFERENT number of neutrons
– Unstable isotopes can be radioactive causing radiation. – In anatomy:
• a radioactive isotope can be introduced to trace a metabolic pathway.
• Radioactive isotopes can change chemical structures used to treat cancers

CARBON

Atomic bonding
• The goal of bonding is to produce a full & stable outer electron shell. – 1st shell (closest to nucleus) – 2 electrons to be full
– 2nd shell – 8 electrons to be full
– 3rd shell – 8 electrons to be full

Bonding properties
• Effect of electrons
– chemical behavior of an atom depends on its electron arrangement
• the number of electrons in its outermost shell, the valence shell

How does this atom behave?

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Bonding properties
• Effect of electrons
– 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

How does this atom behave?

Elements & their valence shells
• Elements in the same column have the same valence & similar chemical properties

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

How do they achieve stable structure? • Gain or lose electrons

form ionic bonds

– Ex: Sodium has 1 electron in its outer shell to LOSE
(Na+)
• Positive ion = cation

– Chlorine has 7 electrons in its outer shell – wants to
GAIN one (Cl-)
• Negative ion = anion

• Opposite charges attract an ionic bond is formed. (NaCl)
• Relatively weak bond (in aqueous solution)
– Note: in biology, we are pretty much only concerned with behavior in solution, because that’s where all our chemical reactions take place – living things are 70% water!!! 3

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How do they achieve stable structure? • Sharing electrons – covalent bond
• Ex: Each Hydrogen atom has one electron in the outer shell.
– Two hydrogen atoms can get together and share these electrons.
– Covalent bonds can be single (one electron pair), double (2 electron pairs) or triple (3 electron pairs).
– Strong bonds

Polar covalent bonds
• Pair of electrons not shared equally by 2 atoms • Ex: Water
– oxygen has stronger “attraction” for the shared electrons than hydrogen
– oxygen has higher electronegativity
• What’s electronegativity?

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
• Intermolecular force

Polar covalent bonds
• 2 hydrogens in the water molecule form an angle • Water molecule is polar
– oxygen end is –
– hydrogen end is +

• Leads to many interesting properties of water….(hold that thought…we’ll come back to it)

Water
• Hydrogen bonding: http://programs.northlandcollege.edu/biolo gy/Biology1111/animations/hydrogenbond
s.html

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What is a molecule?
• When two or more atoms bond, they form a molecule.
• Atoms of the same element can combine to form a molecule of that element.
– Ex: H2, N2, O2

• Atoms of different elements can combine to form a molecule of a COMPOUND.
– Ex: H2O

Formulas

Formulas
• Molecular formula – indicates the number and types of atoms in a molecule
– Ex: H2O contains two atoms of hydrogen and one of oxygen.

• Typically –
– H can form 1 bond
– O can form 2 bonds
– N can form 3 bonds
– C can form 4 bonds

Chemical reactions
• 2 major types (that we’re going to worry about – right now)
• Sum of all chemical reactions = metabolism
• Metabolism = catabolism + anabolism
• Both involve water

• Structural formulas
– illustrates how atoms are joined and arranged – Water’s important – we’ll get to it later

Synthesis
• Making a large molecule
(polymer) from two smaller ones.
• AKA dehydration synthesis because water is removed to form bonds. • These new bonds contain energy (that must be put into the system), so the reaction is
ENDERGONIC

Decomposition
Energy

A+B

A-B + H2O

• Opposite of synthesis – take a polymer and break it down into smaller molecules (monomers)
• Water is used to break the bonds, so it is hydrolysis (hydro = water, lysis = split)
• Breaking the bonds releases energy
(EXERGONIC)

A-B + H2O

A+B+ energy 5

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Factors affecting rate of rxn
•
•
•
•
•

Particle size
Temperature
Concentration
Catalysts
For each of the above – explain how/why they effect the rate of a reaction

Salts in water
• Salts will dissociate (split) into ions in H2O
– these are electrolytes.

Inorganic compounds
Water, salts, and pH

Water forms ions
• Hydrogen ion (H+) splits off from water to leave a hydroxide ion (-OH)
H2O ----> H+ + -OH
•
•
•
•

If concentration of 2 ions is equal, neutral
If [H+] > [-OH], acidic
If [-OH] > [H+], basic pH scale = how acidic or basic a solution is

– Ie: NaCl in H2O splits into Na+ and Cl– Needed in precise amounts for many processes, like muscle contraction and nerve impulses. pH Scale
• In pure water only 1 water molecule in every 554 million is dissociated.
– very small amount of ions
– [H+] or [OH-] is 10-7M

[H+] [OH-] = 10-14
• pH scale is based on this equation

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pH Scale
• In neutral solution
[H+] = 10-7 → pH = 7
• Values for pH decline as [H+] increases
• Acids
– adding acid increases
[H+]

• Bases
– adding base increases
[OH-]

pH & Biology
• pH of a neutral solution = 7
• Acidic solutions = pH < 7
Basic solutions = pH > 7
• Most biological fluids have pH 6 – 8
– pH values in human stomach can reach 2

• Each pH unit represents a 10-fold difference in H+ & OH- concentrations.

Acids and bases
• Acids – release H+ ions in water
• Bases -- release OH- ions in water
• pH is a measure of hydrogen ion (H+) concentration – Lower pH – acidic
– Higher pH basic
– pH is logarithmic – a difference of 1 (from pH 4 to 5) is actually a ten-fold increase in H+ conc.
• From 3 to 7?

Water
• Why are each of the following properties of water important to life?
– Polar molecule
– Hydrogen bonding
– Participation in chemical reactions
– High heat of vaporization
– Anything else that we need water for?

– small change in pH actually indicates a substantial change in [H+] & [OH-]

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

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