Transcript Chapter 2 Small Molecules… - Tri

Chapter 2 Small Molecules…
Biology 101
Tri-County Technical College
Pendleton, SC
I Love Chaos Theory
 Quirks, smurks, gluons, nutrinos, and on
and on
 Let’s keep it short and sweet
 ATOM is smallest unit of a chemical
element
 Consists of a nucleus and one or more electrons
 ELEMENT is pure substance that contains
only one type of atom
Beam me up Scotty….
• Atom consists of dense, positively charged
nucleus around which one or more negatively
charged electrons move
• Nucleus contains proton(s) [+ charge]; neutron(s)
[no charge]
• Atoms and their components have MASS
• Mass measures the quantity of matter present
• Proton and neutron have value of 1 each; electrons
such small mass, they are ignored
Scan for carbon units…oh yeah!
• C, H, N, O, P, and S make up 98% of all living
matter
• An element is distinguished from all other
elements by number of protons in its nucleus
• This number, its atomic number, does NOT
change
• Every element except hydrogen has one or more
neutrons in its nucleus
• Mass number of atom = total number of protons
and neutrons in its nucleus
More Atomic Theory
• Atomic mass (atomic weight) is average of mass
numbers of representative sample of element (with
all isotopes in their normally occurring
proportions)
• Valence = bonding capacity of atom and is
generally equal to number of unpaired electrons in
atom’s outermost shell
• Valence shell = outermost energy shell containing
valence electrons involved in chemical reactions
of the atom
Isotopes
• Isotopes of same element have same number of
protons but differ in the number of neutrons in
nucleus
• 12C; 13C; 14C
• Radioisotopes are unstable and give off energy
(alpha, beta, gamma) as radiation
• Such decay transforms the nucleus into another
atom
• Used in medicine (radiation therapy) and in
science in radioactive dating and other
experiments
Isotope Visual
Electron Shells
• Given orbital can only be occupied by at
most 2 electrons
• Orbitals constitute series of electron shells
(energy levels)
• First (innermost) shell consists of only ONE
orbital (can only hold 2 electrons)
• Second shell = 4 orbitals= 8 electrons
– 1 s and 3 p orbitals
Shells, cont.
• For our course ONLY: 1st shell = 2; 2nd shell
= 8; and 3rd shell = 8 electrons
– 3rd will hold more so you have been informed!!
• KEY: atoms are most stable (happy) when
their outer shell is filled
• Can be obtained by sharing electrons with
other atoms or by gaining or losing one or
more electrons from outermost shell
Key terms and concepts
• Molecule defined as two or more atoms
linked by chemical bonds
• Tendency of atoms in stable molecules to
have eight electrons in outermost orbit is
called the octet rule
• Useful concept but limited…
• For our course, an atom would like to have
its outermost shell FULL
Care to bond?
• Covalent bond occurs when two atoms share
electrons
• Chalk talk time on covalent bonds with examples
• Strongest bond we study; quite stable
• Represent with single, unbroken line
• Electronegativity is attractive force atom exerts
on electrons
• Closer two atoms are in electronegativity, more EQUAL their
sharing of electrons will be
Bonding II
• When electrons shared equally , bond is called
nonpolar covalent bond
• Atoms with differing electronegativities share
electrons unequally (just like kids)
• Results in a polar covalent bond (delta + and -)
• Produces polar molecules or polar regions of
larger molecules
• Polar bonds very important to chemistry of life
Charge…
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Ion is atom that has lost or gained an electron(s)
Chalk talk time on sodium and chlorine
Ions may have multiple charges (Ca2+; Fe3+)
Groups of covalently bonded atoms that carry
charge are called complex ions
– NH4+ SO2/4- PO3/4-
• Ionic bonds formed by electrical attraction
between ions bearing opposite charge
• Ions can interact with polar molecules as well as
other ions
More on ions…
• In solids, ionic bonds are strong because
ions are close together
• In solvents, ionic bond much weaker
• Water is main biological solvent
• Hydrophilic versus hydrophobic and chalk
talk time
Ion Visual
Hydrogen Bonding
• Bonding that occurs between hydrogen atom of
one polar molecule and the highly electronegative
atom of another polar molecule
• Water is a polar molecule
– Many properties of water dependent on hydrogen
bonding
• Are very weak bonds but tend to be SO many of
them, they influence structure and properties of
substances
Water Visual
Chemical Reactions
• Occur when atoms combine or change bonding
partners
• Chalk-talk time on reactants/products
• Matter/energy cannot be created nor destroyed
• Energy is capacity to do work (work is movement
of mass through space)
• CRs do not create/destroy energy; but changes in
energy usually accompany them
Water as Polar Molecule
• Shape of water molecule (tetrahedron), its
polar nature, and its capacity to form
hydrogen bonds give it unique properties
• Ice floats; excellent solvent , cohesive,
adhesive, and energy changes that
accompany its transitions from iceliquid
gas are important in living systems
Five Unique Properties of Water
• Ice floats
• Melting and freezing
– Excellent moderator of temperature change
• Heating and cooling
– has a high heat capacity
– specific heat of substance is amount of heat
energy required to raise 1 g by 1oC
– Takes large amount of energy to just break
hydrogen bonds that hold liquid water together
Properties, cont.
• Evaporation and Cooling
– Has high heat of vaporization requiring lots of energy
to change from liquid to gas
– Evaporation has cooling effect on environment
– Our sweating
• Cohesion and surface tension
– Columns of water can “stretch”
– Evaporates from leaves (transpiration/MSG)
• Has high surface tension meaning surface exposed
to air is difficult to break
Solving the Solution
• Solution is produced when substance is
dissolved in water (aqueous) or another
liquid
• Solution = solvent + solute(s)
• Qualitative analysis deals with substances
dissolved in solvent and chemical reactions
that occur there
• Concentrations [ ]s = amount of substance
in given amount of solution
Mighty Mole..and more
• Mole is amount of ion or compound in grams
whose weight is equal to its molecular weight (1
mole sugar=342g)
• Avogadro’s number = 6.02 x 1023 molecules per
mole
• 1 mole of substance dissolved in water to make 1
liter is called a 1 molar (1M) solution
• a 1um (micromolar) solution has 6.02 x 1017
molecules of solute per mole
• Many molecules present in living systems exist in
micromolar (um) to millimolar (mM) [ ]s
Who’s on first…?
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Acid releases H+ ions (protons) in solution
Base will accept H+ ions
Terms “acidic” and “basic” refer only to solutions
Acidity/alkalinity of solution depends on relative [
]s of H+ and OH- ions in it
• Acid and base refer to compounds and ions
• If donates a proton = acid
• Accept a proton(s) = base
Disassociation of Water
• Water will ionize into a hydrogen ion (H+)
and a hydroxide ion (OH-)
• Two actually participate—one becomes a
hydroxide ion and the other a hydronium
ion (H3O+)
• For simplicity: H2OH+ + OH• Ionization of water very important for all
living creatures
pH Scale
• Stands for “potential of hydrogen”
• pH value defined as negative logarithm of the
hydrogen ion [ ] in moles per liter (molar
concentration)
• pH = -log10[H+]
• In practical terms, lower pH means higher H+ [ ]
or greater acidity
• Water is neutral at pH 7; less than 7 = acidic; more
than 7 = basic
• **Scale is logarithmic
pH Scale Visual
Buffers and Bicarbonate System
• Buffer is chemical system that maintain relative
constant pH even when substantial amounts of
acid or base are added
• Buffer is mixture of weak acid and its
corresponding base
– Carbonic acid (HcCO3) and bicarbonate ion (HCO3-)
• Buffers minimize effect of added acid/base
• Law of mass action states addition of component
one one side of reversible reaction drives reaction
in direction that uses up that component
Scan for carbon units…
• Organic (text) defined as containing carbon
atoms
– What does one do with CO2?
• We shall define an organic molecule as one
containing both carbon and hydrogen
• H2O; CO2; CH4; C6H12O6
• You have been cautioned…enough said
Functional Groups
• Functional groups are groups of atoms that
make up part of larger molecule and have
particular chemical properties
– Shape, polarity, reactivity, and solubility
• Chalk-talk time on hydroxyl, carbonyl
(aldehyde/ketone), carboxyl, amino,
phosphate, sulfhydryl
• Will see next test and on the final
exam…enough said
Isomers
• C6H12O6 is glucose unless I tell you differently…
• Can also be fructose and galactose
• Structural isomers have same chemical formula
but different structural arrangements
• Optical isomers are mirror images of each other
– Amino acids and many sugars
– D-amino acids(dextro) and L-amino acids (levo)
– Only L-amino acids commonly found in most
organisms