The Chemistry of Life
Chapter 2 (M)
Matter
Organisms are composed of matterMatter is anything that takes up space and has mass.
Matter consists of chemical elements in pure form and in combinations called compounds
All living things share the same chemical building blocks and depend on the same chemical processes
Life depends on chemistry
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 essentialEx: 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 AtomsIonic 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 waterHuman body and cells 70-
95% waterAbundance of water Earth
can support lifeWater exists in three possible
states: ice, liquid, and vapor
Properties of Water
Polar MoleculeCohesion- AdhesionHigh Surface TensionHigh Specific HeatLow Density of iceExcellent solvent
Structure of WaterWater 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
BuffersSubstances that can prevent or
resist sharp changes in pHImportant – because molecules in cells are very sensitive to concentrations of H+ or OH- ions. Even the slightest maybe harmful to living things
Section 2.3
The Chemistry of Carbon
BiomoleculesMost molecules of a cell are
carbon basedThese “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 moleculesEx: H2O, O2 NH3
Hydrocarbons Molecules of only Carbon & HydrogenEx: 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 lipidsproteins nucleic acids Protein that makes up a spider’s webProtein 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 numberPolymers 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)Water (hydro) is used to break down break down (lysis(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 celluloseAnimals glycogen
CarbohydratesMonosaccharides 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 Two monosaccharides
can join with a can join with a disaccharidedisaccharide via via dehydration.dehydration.Sucrose, table sugar Sucrose, table sugar formed by joining formed by joining glucose and fructose glucose and fructose and is the major and is the major transport form of transport form of sugars in plantssugars in plants..
Polysaccharides Polymers of hundreds to thousands of
monosaccharides Function of polysaccharidesFunction 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 PolysaccharidesStarch found in plants
consists of glucose monomers.
Glycogen found in animals, consists of glucose monomers, stored in the liver & muscle.
Cellulose.
CelluloseMajor 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 LipidsAn exception not made of polymers.
Have little or no affinity for water Hydrophobic
Are highly diverse in form and function.
FatsAssembled 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 FatsUnsaturated 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.
SteroidsLipids with a carbon skeleton
consisting of four fused carbon rings.
Different steroids are created by varying functional groups attached to the rings.
SteroidsSteroids include cholesterol and certain hormones
Circulate in blood as chemical signals
Steroids are hormones sex hormonesTestosteroneEstrogen
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 PolymersStore and transmit hereditary
informationA polymer of nucleotides
Types of Nucleic Acid DNA (Deoxyribonucleic
Acid) - transmits genetic information that is passed from one generation to the next-double helix
RNA (Ribonucleic Acid)
Nucleotide
Composed ofa nitrogen
base a pentose
sugara 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 bondsCovalent bondsH bondsVan der Waals forces
Is its unique sequence of amino acids.
Slight change in primary structure can affect a protein’s shape & ability to function.
Primary Structure
Secondary StructureAre coils (an
alpha helix) or folds (beta pleated sheets)
The structural properties of silk are due to beta pleated sheets.
Tertiary Structure
Quarternary Structure- aggregation 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