Download The Chemistry of Life

The Chemistry of Life
Chapters 2 and 3
Atoms
Smallest unit of matter that retains
physical properties
 3 Basic Parts

Proton
 Neutron
 Electron

Nucleus gives an atom its mass
 Electrons give an atom is behavior

Elements

Made up of only 1 type of atom


Isotopes have same number of p+, but
different numbers of n0, so atomic mass
varies
Form compounds
Chemical Bonds
 Formula tells the ratio of atoms in a
compound


98% of living things are made of CHNOPS
Chemical Bonds

The valence electrons are involved in the
bond

Atoms are stable when their valence shell is
filled

Covalent Bonds- atoms share valence
electrons and are held together
Non-metal to non-metal
 Molecule is the smallest part of a compound
that retains the properties

Polarity
Covalent bonds share electrons between
atoms
 Electrons shared equally result in a nonpolar bond
 Electrons shared unequally between the
atoms create regions of positive charge
and negative charge, though the molecule
is neutral, results in a polar bond

Polar molecules can interact with each other
and with ions
 Whole molecules can be polar or select bonds
in a molecule can be polar


Ionic Bonds are a result of the transfer of
valence electrons
Atoms that lose electrons have more p+ than
e- and are called positive ions (cations)
 Atoms that gain electrons have more e- than
p+ and are called negative ions (anions)
 Metals form cations and non-metals form
anions
 The positive ion is attracted to the negative
ion and they stick together

Energy

Comes in many forms

Kinetic, Potential, Chemical, Thermal, Radiant
The ability to do work
 Can be converted from one form to
another
 When atoms for chemical bonds energy
can either be absorbed or released

Living Things and Energy



All living things require energy
1000s of chemical reactions occur in living
organisms a day
Energy is either stored in bonds formed during a
reaction or it is released by the reaction


Living organisms use this energy to carry out life
processes
Metabolism is all of the chemical reactions that occur
in an organism
Activation Energy

Energy required for a chemical reaction to
occur


Can be a large amount
Catalysts lower the activation energy for a
reaction
They are not used up and can be used
repeatedly
 Enzymes are proteins or RNA that act as
catalysts in living organisms- there are 1000s


Enzyme has a specific shape that will interact
with a specific substrate
 Substrate
is reactant being catalyzed fits in active
site on enzyme
Enzyme’s shape is changed when substrate
bonds at active site
 Change
in shape causes bonds in substrate to
weaken and break
 Products are released by enzyme
 Enzyme is unchanged and reacts anew with another
substrate

Enzymes require very specific temperature and
pH ranges
 Changes
can cause the enzyme to denature
Enzyme Catalyzed Reaction
Oxidation Reduction Reactions
AKA- Redox reactions
 Reactions that involve the transfer of
electrons
 LEO says GER

Lose electrons oxidize
 Gain electrons reduce


Oxidation and Reduction are coupled
together- something is oxidized because
something else is reduced
Water and Solutions
Cells are mainly water and the water is an
arena for the chemical reactions of life to
occur
 Water is polar

H is slightly +, O is slightly –
 Allows water molecules to interact with each
other, ions, and other polar molecules
 Water is universal solvent because of its
polarity- it dissolves a lot of stuff

 Hydrogen
bonds form between water
molecules allowing them to stick together
 Hydrogen
bonds form between H with a slight +
charge and areas of – charge or with anions
 Can be formed or broken easily and repeatedlyweak independently, strong in great numbers
 Many occur at one time in water
 H bonds allow water to experience
 Cohesion-
water molecules stick together
 Adhesion- water molecules stick to other things

When ionic compounds are dissolved in water
they ionize- break apart into cations and
anions

Water is less dense as a solid than as a
liquid


Ice floats- pond ecosystems are conserved
even in winter
Water has a high specific heat capacity

Water absorbs large amounts of heat with
little temperature change
Solutions

Solutions are homogeneous mixtures


All substances are evenly distributed
throughout
Composed of solute and solvent
Solute is what is dissolved (less of this)
 Solvent does the dissolving (more of this)


Can have different concentrations
How much solute is dissolved in the solvent
 Saturated- the max amount of solute is
dissolved


Aqueous solutions have water as the
solvent

Essential for life
 Aqueous
solutions are essential for cells
 Blood is an aqueous solution
 Many organisms live in aqueous solutions- The
ocean! Ponds! Lakes! Rivers! Your gut!
Acids and Bases

Water can ionize (split into ions)

H2O
H+ + OH -
OH - is the hydroxide ion
 H+ is a proton
 Water can also accept a proton (H+),
forming hydronium ion (H30+)
 H+ + H2O
H30+
 This occurs all of the time in water

Acids and bases are determined by the
ratio of hydronium ions to hydroxide ions
 Acids H30+ > OH Bases H30+ < OH Compounds that are acids donate a H+
and it will react with H20 to form H3O+
 Bases produce OH- which will increase
their concentration


pH scale is a way to measure the
concentration of H3O+

It is a logarithmic scale- so each number is a
ten-fold difference in concentration of H3O+

Buffers are chemical substances that can
absorb excess acids or bases to maintain
pH


Very important job
Enzymes (biological catalysts) can only
function in specific pH ranges

Cells must regulate their pH
Biochemistry
The study of the chemistry that allows life
to exist and flourish
 Biochemistry is centered around the
element Carbon

Organic compounds are those that contain
carbon
 Inorganic compounds do not generally contain
carbon

Carbon

Carbon has 4 valence electrons and
needs 8


Forms covalent bonds to complete its valence
shell
Carbon is special because is will bond with
up to 4 other carbon atoms

Can form rings, straight chains, and branched
chains

A covalent bond is formed when two
atoms share 2 electrons

Represented with a straight line
Carbon can form single, double, and triple
bonds
 Carbon can form almost endless
compounds as a result

Functional Groups
Organic molecules all contain Carbon- so
what makes one compound different from
another- Functional Groups
 Functional Groups are specific clusters of
atoms attached to a carbon compound
 Each functional group has specific
properties that it gives the compound

Large Carbon Molecules
Monomers are small, simple molecules
that can be bonded together to form
polymers
 Macromolecules are made from polymers

Condensation and Hydrolysis
Reactions

Monomers are bonded together through
condensation reactions

With the addition of each monomer a water
molecule is lost

Polymers can be broken down into
polymers through hydrolysis reactions

A water molecule must be added in order to
split one monomer away from the polymer
Energy Currency

Remember chemical bonds contain
energy


Breaking or making a bond can either absorb
or release energy
Some compounds have a lot of energy
stored in their bonds

This energy can be used to power cell
functions

Adenosine Triphosphate (ATP) is a high
energy compound
Bond between the second and third
phosphate is hydrolyzed to release energy for
cellular functions, leaving ADP and P
 ATP + H2O  ADP + P + Energy
 ADP + P + energy  ATP + H2O

Molecules of Life

Carbohydrates, Lipids, Proteins, Nucleic
Acids


Each type has different properties and
responsibilities
All have C, H, O; some also have N, P, S

Put together in different ratios
Carbohydrates
Roles include energy source and structural
components
 Made of C, H, O in a 1:2:1 ratio (CH2O)n
 Monomer- monosaccharide



Glucose (simple sugar), galactose (milk),
fructose (fruits)
Disaccharides are made by a
condensation rxn joining 2
monosaccharide

Glucose + Fructose  Sucrose

Polymers are polysaccharides- large
molecules made by joining many
monosaccharides
Animals store excess sugar as Glycogen
 Plants store excess sugar as Starch


Cellulose is a polysaccharide made by
plants that gives cell walls strength and
rigidity

Can be broken down by hydrolysis reactions
Proteins

Have a diversity of structures, resulting in
a wide range of functions
Account for ~50% dry mass of cells
 Act as enzymes, play roles in defense,
storage, transport, cell communication,
movement, structural support
 Each protein has a unique 3-D shape


Composed of mainly C, H, O, N

Monomer is amino acid


Amino Acids have same basic structure


There are 20 amino acids used to build
thousands of proteins
Amino group, central C, Carboxyl group, and
R group (variable- distinguishes 1 aa from
another)
Polymer is polypeptide
Long chain of amino acids
 Held together by peptide bonds

 Covalent
bonds formed via condensation rxn

1 or more polypeptide chain(s) fold into
complex shapes
Shape is essential to function
 Chains held together via interactions like
hydrogen bonds


Enzymes are important group of proteins
Act as biological catalysts
 Enzyme has a specific shape that will interact
with a specific substrate

 Substrate
is reactant being catalyzed fits in active
site on enzyme
Lipids
Function as long term energy storage, in
membranes, water proof coverings,
steroids (hormones) as chemical
messengers
 Have C, H, O- higher ratio of C and H to O


Long chains of C and H store more energy

Fatty Acids

Carboxyl Group connected to a long carbon
chain
 Carboxyl
group is polar and therefore hydrophilic
 Hydrocarbon chain is non-polar and hydrophobic
Fatty acids that have each C bonded to 4
things are called saturated
 Fatty acids that have double bonds between
some C atoms are called unsaturated


Triglycerides have 3 fatty acids joined to a
glycerol head
Saturated triglycerides have a high melting
point and are solid at room temp- butter, fats,
red meat
 Unsaturated triglycerides are usually liquid at
room temp- Plant oils (olive, sunflower, etc)


Phospholipids- 2 fatty acids
bonded to a glycerol head
and a phosphate group


Form water-tight barriers, such
as cell membrane (lipid bilayer)
Waxes are long chains of
fatty acids bonded to large
alcohol groups

Help plants retain water and
earwax protects ear from
invaders

Steroids are made of 4 carbon rings and
functional groups attached

Hormones are steroids that have important
roles transmitting chemical messages and
roles in the cell membrane (cholesterol)
Nucleic Acids
Function to store and transfer information
in cells, including hereditary material
 Composed of C, H, O, N, P
 Monomer- Nucleotide


Three parts: 5-C sugar, Nitrogenous base,
Phosphate group
 ATP

Polymer- Nucleic Acid

DNA, RNA