The Chemistry of Life Chapter 2 (M). Matter Organisms are composed of matter Matter is anything...

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