Transcript The Chemistry of Life

The Chemistry of
Life
Chapter 2 (M)
Matter
 Organisms
are composed of
matter
Matter is anything that takes
up space and has mass.
Matter consists of chemical
elements in pure form and in
combinations called compounds
Life depends on chemistry
All living things
share the same
chemical building
blocks and depend
on the same
chemical processes
Life Requires 25 Elements
 Element
Pure
substance made up of one kind
of atom
Cannot be broken down into other
substances by chemical means
More than 100 known , about
25 found in living organisms

Element
 Shown
by a short hand symbol
 Either a capital letter only  C,
N, H, O
 Or a capital and lower case
letter  Ca, Na, Mg
Life Requires 25 Elements
4 make up 96%
C carbon
N nitrogen
O  oxygen
H hydrogen
 Most of the remaining 4%  Calcium,
Phosphorus, Potassium, Sulfur (CHNOPS)
 Trace elements  <0.01% but are
essential
Ex: 0.15mg Iodine/day Thyroid function

The Nature of
Matter
Section 2.1
Atom
Atom is the smallest unit of matter that
still retains the properties of an element.
Atoms  composed subatomic particles.
 Neutrons and Protons, are packed
together to form a dense core, the
atomic nucleus, at the center of an
atom.
 Electrons form a cloud around the
nucleus.
Atoms
Protons
positively charged
 Neutrons  no
charge
 Electron  (-),
are in constant
motion
 Atomic Number
 # of Protons

Chemical Compound

A compound is a substance consisting of two
or more elements in a fixed ratio.
Physical and chemical properties usually
very different from those of the
elements from which they are formed
Table salt (sodium chloride or NaCl) is a
compound with equal numbers of chlorine
and sodium atoms.
Attraction between (+) Proton
&
(-) Electron keep the electrons
in the vicinity of the nucleus.
Isotopes
Two atoms of the same number
of protons but different
number of neutrons
Radioactive Isotopes.
The
nuclei are unstable and decay
spontaneously, giving off particles
and energy.
Pure sodium metal, chlorine gas,
combination forms an edible
compound.
Chemical Bonds
Chemical Bonds Join Atoms
 Ionic
Bonds when an atom
transfers an electron to
another atom
 Covalent Bonds when two
atoms share electrons
Ionic Bond
An atom that loses electrons has a
positive charge
 An atom that gains electrons has a
negative charge

Covalent Bonds
 Two
atoms share electrons
 Can be
Single
bond  2 electrons are shared
Double bond 4 electrons are shared
Number of bonds
 Number
of bonds = # of electrons
available to fill outer shell
 Hydrogen 1 bond
Number of bonds
 Oxygen
 2 bonds
Number of bonds
 Methane
 Carbon & Hydrogen
Molecule
2
or more atoms held together by
covalent bonds
Modeling of Molecules
 Structural
Formula which is the
number and types of atoms linked
together by bonds
 Chemical Formula Number and
types of atoms in a molecule
 Space Filling Model drawing that
depicts a 3-dimensional model
Modeling of Molecules
Van der Waals Forces
Molecules can attract and repel each
other
 The attractive forces are collectively
called "van der Waals forces".
 Van der Waals forces are much
weaker than chemical bonds

Chemical Reactions
 Chemical
reactions  bonds are
broken and reformed, leading to new
arrangements of atoms.
 The starting molecules Reactants
 The end molecules  Products
 The reactions must be “balanced”
# of atoms in the reactants = # of
atoms in the products.
Chemical Reactions
Properties of Water
Section 2.2
Water
 Life
depends on water
 Human body and cells  70-95%
water
 Abundance of water  Earth can
support life
 Water exists in three possible
states: ice, liquid, and vapor
Properties of Water
 Polar
Molecule
 Cohesion- Adhesion
 High Surface Tension
 High Specific Heat
 Low Density of ice
 Excellent solvent
Structure of Water
 Water
is a polar molecule 
uneven distribution of charge
between the hydrogen and
oxygen atoms  regions of
partial + and – charges
 Each water molecule can form
H- bonds with up to 4
neighbors.
Structure of Water
Cohesion - Adhesion
 Cohesion
 tendency of
molecules of the same kind
to stick together. Strongest
in water.
 Adhesion  attraction
between unlike molecules
Cohesion - Adhesion
Surface Tension
Water behaves as if
covered by an invisible
film.
 High surface tension
because hydrogen
bonds among surface
water molecules
resist stretching or
breaking the surface

High Specific Heat
 Water’s
high specific heat is
due to hydrogen bonding
 Water resists changes in
temperature because it takes a
lot of energy to speed up its
molecules.
Low Density of Ice
Water is unusual because it is less dense
as a solid than as a liquid.
 Ice floats on the cool water below.
 This has important consequences for
life.

Low Density of Ice
If ice sank  all ponds,
lakes, and oceans would
freeze solid.
 The surface layer
of ice insulates liquid water
below, preventing it from
freezing and allowing life
to exist under the frozen
surface.

Water is the Solvent of Life
A
liquid that is a completely
homogeneous mixture of two or
more substances is called a solution
 The dissolving agent is the solvent
and the substance that is dissolved
is the solute.
 In an aqueous solution, water is the
solvent.
Water
surrounds and
separates the
positive and
negative ions
Acids, Bases and pH
A hydrogen atom shared by two water
molecules shifts from one molecule to the
other.
 leaves
its electron behind and is transferred
as a single proton - a hydrogen ion (H+).
 molecule that lost a proton is now a hydroxide
ion (OH-).
pH Scale
 The
scale that
describes how acid
or basic a solution
is.
 Ranges from 0-14
 pH 2 is 10X more
acidic than pH 3
 pH 7 is neutral
Acids and Bases
Acid  compound that donates H+ ions
 Base compound that donate OH- ions
or removes H+ ions

Buffers
 Substances
that can prevent or
resist sharp changes in pH
Important – because molecules
in cells are very sensitive to
concentrations of H+ or OHions. Even the slightest maybe
harmful to living things
Section 2.3
The Chemistry of Carbon
Biomolecules
 Most
molecules of a cell are
carbon based
 These “biomolecules”backbones of carbon atoms
bonded to one another – called
“organic molecules”, can be
gigantic in size
Organic & Inorganic
Molecules
 Organic
Most Carbon based
molecules
 Inorganic Non carbon based
molecules
Ex: H2O, O2 NH3
 Hydrocarbons Molecules of only
Carbon & Hydrogen
Ex: Methane-CH4
Carbon Skeletons &
Functional Groups
 Functional
group – group of atoms
within a molecule that interacts in
a predictable way
 Carbon skeleton + attached
functional group determines the
properties of an organic molecule
Functional Groups
Functional Groups
Functional Groups
Macromolecules
 Cells
join smaller organic molecules
together to form larger molecules.
 Four major classes of macromolecules
carbohydrates
lipids
proteins

nucleic acids
Protein that makes up a spider’s web
Monomers & Polymers
Monomer - Small building block of a
larger molecule
 Polymer – straight chain of monomers,
about a total of 50 in number

 Polymers
consist of many similar or identical
building blocks linked by covalent bonds.

The repeated units are small molecules
called monomers
Building Polymer Dehydration

Each time a monomer is added water is
removed
Breaking Polymers  Hydrolysis
Water (hydro) is used to break down (lysis)
a molecule
Carbohydrates
Made of C, H, & O ratio 1:2:1
 Main source of energy breakdown
gives immediate energy
 Also used for structural purposes

 Plants
cellulose
 Animals glycogen
Carbohydrates
 Monosaccharides
the simplest
carbohydrates or simple sugars.
 Disaccharides two
monosaccharides joined by a are
condensation reaction.
 Polysaccharides polymers of
monosaccharides
Monosaccharides
 Generally
have
molecular formulas that
are some multiple of
CH2O.
For
example, glucose has
the formula C6H12O6.
Most names for sugars
end in -ose.
Disaccharides
 Two
monosaccharides
can join with a
disaccharide via
dehydration.
Sucrose, table sugar
formed by joining
glucose and fructose
and is the major
transport form of
sugars in plants.
Polysaccharides


Polymers of hundreds to thousands of
monosaccharides
Function of polysaccharides
 an
energy storage macromolecule that is
hydrolyzed as needed.
 serve as building materials for the cell or
whole organism.

Starch is a storage polysaccharide
composed entirely of glucose monomers.
Types of Polysaccharides
 Starch
found in plants
consists of glucose monomers.
 Glycogen found in animals,
consists of glucose monomers,
stored in the liver & muscle.
 Cellulose.
Cellulose
 Major
component of the tough
wall of plant cells
 Humans can’t digest, but
needed to keep digestive
system healthy
 Carbohydrates  Hydrophilic,
BUT cellulose does not dissolve
in water
Lipids include fats
and steroids
Characteristics of Lipids
 An
exception  not made of
polymers.
 Have little or no affinity for
water Hydrophobic
 Are highly diverse in form and
function.
 Assembled
Fats
from smaller molecules
by dehydration reactions.
 Is constructed from two kinds of
smaller molecules, glycerol and
fatty acids
Saturated Fats
The three fatty acids contain a hydrogen
at every possible position
 All carbons form a single bond
 Animal fats
 Solid at room temp

Unsaturated Fats
 Unsaturated
fatty acid one or
more carbon-carbon double bonds
 Fats with unsaturated fatty acids
are unsaturated fats.
 Plant and fish fats, known as oils,
are liquid are room temperature.
Steroids
 Lipids
with a carbon skeleton
consisting of four fused carbon
rings.
 Different steroids are created by
varying functional groups attached
to the rings.
Steroids
 Steroids
include cholesterol
and certain hormones
 Circulate in blood as chemical
signals
 Steroids are hormones sex
hormones
Testosterone
Estrogen
Cholesterol
 Cholesterol,
an important steroid, a
component in animal cell membranes.
 An essential molecule BUT, high levels
of cholesterol in the blood may
contribute to cardiovascular disease.
Nucleic Acids
 Informational
Polymers
 Store and transmit hereditary
information
 A polymer of nucleotides
Types of Nucleic Acid
 DNA
(Deoxyribonucleic
Acid) - transmits
genetic information
that is passed from one
generation to the nextdouble helix
 RNA (Ribonucleic Acid)
Nucleotide
 Composed
a
of
nitrogen base
 a pentose
sugar
a phosphate
group
Structure of DNA & RNA





DNA double
strands
(a) 5 carbon sugar deoxyribose
(b) phosphate group
(c) nitrogenous base
– adenine (A),
guanine (G), thymine
(T), cytosine (C)
A=T, G=C





RNA single strand
(a) 5 carbon sugar ribose
(b) phosphate
group
(c) nitrogenous
bases - adenine (A),
guanine (G), uracil
(U),cytosine (C)
A=U, G=C
Proteins
Proteins perform most
functions in cells
Proteins
 Polymers
constructed from a set of
20 monomers, called amino acids.
 Polymers are called polypeptides.
 A protein consists of one or more
polypeptides folded and coiled into a
specific conformation.
Amino Acid
A central carbon atom
bonded to amino group,
carboxyl group,
hydrogen atom
 4th group is a “side
group” or “R-group” is
responsible for the
particular chemical
properties of each
amino acid.

Building a Protein



Cells create proteins by linking amino acids
polypeptide”
Created by the dehydration reaction between
the amino group of one amino acid and the
carboxyl group of the next amino acid in the
chain.
Proteins are composed of one or more
polypeptide chains ,usually at least 100 amino
acids in length
Protein Shape
Functional protein consists of one or
more polypeptides precisely twisted,
folded,and coiled into a unique shape
 Influenced by the surrounding
environment
 Unfavorable change in the environment
(pH, temperature) can cause the protein
to unravel. This is called “denaturation”

Protein Shape
Four levels of structure
 Shape is maintained by

 Ionic
bonds
 Covalent bonds
 H bonds
 Van der Waals forces
Primary Structure
Is its unique
sequence of amino
acids.
 Slight change in
primary structure
can affect a
protein’s shape &
ability to function.

Secondary Structure
 Are
coils (an
alpha helix) or
folds (beta
pleated sheets)
 The structural
properties of
silk are due to
beta pleated
sheets.
Tertiary Structure
Quarternary Structureaggregation of 2 or more
polypeptides
Section 2.4
Chemical Reactions and
Enzymes
Chemical Reactions
 Chemical
reactions  bonds are
broken and reformed, leading to new
arrangements of atoms.
 The starting molecules Reactants
 The end molecules  Products
 The reactions must be “balanced”
# of atoms in the reactants = # of
atoms in the products.
Chemical Reactions
Enzyme- Biological Catalyst
Catalyst  a chemical agent that changes
the rate of a reaction without being
consumed by the reaction
 Enzyme is a catalytic protein.
 Enzymes provide a way for reactions to
occur by lowering the activation energy
 Activation Energy energy required to
get a reaction started

Enzyme Action
 Enzymes
are substrate specific
 A substrate is a reactant which binds
to an enzyme.
 A substrate to an enzyme 
catalyzes the conversion of the
substrate to the product
Lock and Key
 The
active site is on surface of the
protein
 Substrate molecule fits the active site
 Forms a temporary enzyme-substrate
complex - Lock and Key mechanism
Induced Fit
Enzyme, not with rigid shape, changes
slightly so that the it can fit snugly
around the substrate
 Hold reactants together so they can
react

Factors affecting the Rate of
Enzyme reaction
Small amount of enzyme for large amounts
of substrate
 Rate of reaction dependent on enzyme:
substrate concentration
 Coenzymes may be required sometimes
 Temperature
 pH -7

 Ex.
stomach enzymes: pH2; intestinal: pH8
Temperature
pH - enzyme has an optimal
pH