CHEMISTRY Composition of Matter n Matter Everything in

CHEMISTRY

Composition of Matter n Matter - Everything in universe is composed of matter n Matter is anything that occupies space or has mass n Mass – quantity of matter an object has n Weight – pull of gravity on an object

Elements n n Pure substances that cannot be broken down chemically into simpler kinds of matter More than 100 elements (92 naturally occurring)

n n 90% of the mass of an organism is composed of 4 elements (oxygen, carbon, hydrogen and nitrogen) Each element unique chemical symbol n Consists of 1 -2 letters n First letter is always capitalized

Atoms n n n The simplest particle of an element that retains all the properties of that element Properties of atoms determine the structure and properties of the matter they compose Our understanding of the structure of atoms based on scientific models, not observation

The Nucleus n n Central core Consists of positive charged protons and neutral neutrons Positively charged Contains most of the mass of the atom

The Protons n n n All atoms of a given element have the same number of protons Number of protons called the atomic number Number of protons balanced by an equal number of negatively charged electrons

The Neutrons n n The number varies slightly among atoms of the same element Different number of neutrons produces isotopes of the same element

Atomic Mass n n n Protons & neutrons are found in the nucleus of an atom Protons and neutrons each have a mass of 1 amu (atomic mass unit) The atomic mass of an atom is found by adding the number of protons & neutrons in an atom

The Electrons n n Negatively charged high energy particles with little or no mass Travel at very high speeds at various distances (energy levels) from the nucleus

n n n Electrons in the same energy level are approximately the same distance from the nucleus Outer energy levels have more energy than inner levels Each level holds only a certain number of electrons

Energy Levels n n Atoms have 7 energy levels The levels are K (closest to the nucleus), L, M, N, O, P, Q (furthest from the nucleus) The K level can only hold 2 electrons Levels L – Q can hold 8 electrons (octet rule)

Periodic Table n n n Elements are arranged by their atomic number on the Periodic Table The horizontal rows are called Periods & tell the number of energy levels Vertical groups are called Families & tell the outermost number of electrons

Compounds n n Most elements do not exist by themselves Readily combine with other elements in a predictable fashion

n n A compound is a pure substance made up of atoms of two or more elements n The proportion of atoms are always fixed Chemical formula shows the kind and proportion of atoms of each element that occurs in a particular compound

n n Molecules are the simplest part of a substance that retains all of the properties of the substance and exists in a free state Some molecules are large and complex

Chemical Formulas n n Subscript after a symbol tell the number of atoms of each element H 20 has 2 atoms of hydrogen & 1 atom of oxygen Coefficients before a formula tell the number of molecules 3 O 2 represents 3 molecules of oxygen or (3 x 2) or 6 atoms of oxygen

n The physical and chemical properties of a compound differ from the physical and chemical properties of the individual elements that compose it

n n The tendency of elements to combine and form compounds depends on the number and arrangement of electrons in their outermost energy level Atoms are most stable when their outer most energy level is filled

n n n Most atoms are not stable in their natural state Tend to react (combine) with other atoms in order to become more stable (undergo chemical reactions) In chemical reactions bonds are broken; atoms rearranged and new chemical bonds are formed that store energy

Covalent Bonds n Formed when two atoms share one or more pairs of electrons

Ionic Bonds n n Some atoms become stable by losing or gaining electrons Atoms that lose electrons are called positive ions

n n Atoms that gain electrons are called negative ions Because positive and negative electrical charges attract each other ionic bonds form

Energy and Matter n Energy n The ability to do work or cause change n Occurs in various forms n Can be converted to another form n Forms important to biological systems are chemical, thermal, electrical and mechanical energy n Free energy is the energy in a system that is available for work

States of Matter n n Atoms are in constant motion The rate at which atoms or molecules in a substance move determines its state

n Solid n Molecules tightly linked together in a definite shape n Vibrate in place n Fixed volume and shape

n Liquids n Molecules not as tightly linked as a solid n Maintain fixed volume n Able to flow and conform to shape of container

n. Gas Molecules have little or no attraction to each other n Fill the volume of the occupied container n Move most rapidly n To cause a substance to change state, thermal energy (heat) must be added to or removed from a substance n

Energy and Chemical Reactions n Living things undergo thousands of chemical reactions as part of the life process

n n Many are very complex involving multistep sequences called biochemical pathways Chemical equations represent chemical reactions Reactants are shown on the left side of the equation Products are shown on the right side

n n The number of each kind of atom must be the same on either side of the arrow (equation must be balanced) Bonds may be broken or made forming new compounds

Energy Transfer n n n Much of the energy organisms need is provided by sugar (food) Undergoes a series of chemical reactions in which energy is released (cell respiration) The net release of free energy is called an exergonic (exothermic) reaction

n n n Reactions that involve a net absorption of free energy are called endergonic (endothermic) reactions Photosynthesis is an example Most reactions in living organisms are endergonic; therefore living organisms require a constant source of energy

n n Most chemical reactions require energy to begin The amount of energy needed to start the reaction is called activation energy

n n Certain chemical substances (catalysts) reduce the amount of activation energy required Biological catalysts are called enzymes

n Enzymes are an important class of catalysts in living organisms n Mostly protein n Thousands of different kinds n Each specific for a different chemical reaction

Enzyme Structure n n n Enzymes work on substances called substrates Substrates must fit into a place on an enzyme called the active site Enzymes are reusable!

Reduction-Oxidation Reactions n Many of the chemical reactions that help transfer energy in living organisms involve the transfer of electrons (reduction-oxidation = redox reactions)

n Oxidation reaction – reactant loses electron(s) becoming more positive

n Reduction reaction – reactant gains electron(s) becoming more negative

Solutions

Solutions n A solution is a mixture in which 2 or more substances are uniformly distributed in another substance

n n n Solute is the substance dissolved in the solution n Particles may be ions, atoms, or molecules Solvent is the substance in which the solute is dissolved Water is the universal solvent

n n n Solutions can be composed of varying proportions of a given solute in a given solvent --- vary in concentration (measurement of the amount of solute) A saturated solution is one in which no more solute can be dissolved Aqueous solution (water) are universally important to living things

n Dissociation of water n Breaking apart of the water molecule into two ions of opposite charge (due to strong attraction of oxygen atom of one molecule for H atom of another water molecule) n H 2 O H+ (hydrogen ion) + OH- (hydroxide ion) n H + + H 2 O H 3 O (hydronium ion)

Acids and Bases n One of the most important aspects of a living system is the degree of acidity or alkalinity

Acids n Number of hydronium ions in solutions is greater than the number of hydroxide ions n HCl H+ + Cl-

Bases n Number of hydroxide ions in solution is greater than the number of hydronium ions n Na. OH Na+ + OH-

p. H Scale n n logarithmic scale for comparing the relative concentrations of hydronium ions and hydroxide ions in a solution ranges from 0 to 14 § Each p. H is 10 X stronger than next § e. g. ph 1 is 10 times stronger than ph 2

n n n the lower the p. H the stronger the acid the higher the p. H the stronger the base p. H 7. 0 is neutral

Buffers n n Control of p. H is very important Most enzymes function only within a very narrow p. H Control is accomplished with buffers made by the body Buffers keep a neutral p. H (p. H 7)

n n Buffers neutralize small amounts of either an acid or base added to a solution Complex buffering systems maintain the p. H values of your body’s many fluids at normal and safe levels

Water n A water molecule (H 2 O), is made up of three atoms: one oxygen and two hydrogen. H O H

Hydrogen Bonds -formed between a highly electronegative atom of a polar molecule and a Hydrogen -one hydrogen bond is weak , but many hydrogen bonds are strong

Properties of Water • At sea level, pure water boils at 100 °C and freezes at 0 °C. • The boiling temperature of water decreases at higher elevations (lower atmospheric pressure). • For this reason, an egg will take longer to boil at higher altitudes

Properties of Water n What are they?

Properties of Water n Cohesion

Properties of Water n Cohesion n Adhesion

Properties of Water n Cohesion n Adhesion n High Specific Heat

Properties of Water n Cohesion n Adhesion n High Specific Heat n High Heat of Vaporization

Properties of Water n n n Cohesion Adhesion High Specific Heat High Heat of Vaporization Less Dense as a Solid

Cohesion • Attraction between particles of the same substance - why water is attracted to itself Results in: Surface tension (a measure of the strength of water’s surface) • surface film on water -allows insects to walk on the surface of water

Adhesion • Attraction between two different substances. - water will make hydrogen bonds with other surfaces such as glass, soil, plant tissues, and cotton. • Capillary action-water molecules will “tow” each other along when in a thin glass tube. - i. e. transpiration process which plants and trees remove water from the soil, and paper towels soak up water.

High Specific Heat Amount of heat needed to raise or lower 1 g of a substance 1° C. • Water resists temperature change, both for heating and cooling. • Water can absorb or release large amounts of heat energy with little change in actual temperature.

High Heat of Vaporization Amount of energy to convert 1 g or a substance from a liquid to a gas • In order for water to evaporate, hydrogen bonds must be broken. As water evaporates, it removes a lot of heat with it.

“Water vapor forms a kind of global ‘blanket’ which helps to keep the earth warm. Heat radiated from the sun-warmed surface of the earth is absorbed and held by the vapor. ” n

Water is Less Dense as a Solid • Ice is less dense as a solid than as a liquid (ice floats) Liquid water has hydrogen bonds that are constantly being broken and reformed. Frozen water forms a crystal-like lattice whereby molecules are set at fixed distances.

Water is Less Dense as a Solid • Which is ice and which is water?

Water is Less Dense as a Solid Water Ice

Homeostasis Ability to maintain a steady state despite changing conditions n Water is important to this process because: a. Makes a good insulator b. Resists temperature change c. Universal solvent d. Coolant e. Ice protects against temperature extremes n

CARBOHYDRATES

Characteristics of Carbohydrates n n n Consist of carbon, hydrogen, & oxygen Energy containing molecules Some provide structure Basic building block is a monosaccharide (CH 2 O)n ; n = 3, 5, 6 Two monosaccharides form a disaccharide

Different Forms of Glucose

Three Monosaccharides C 6 H 12 O 6

Dehydration Synthesis of a Disaccharide

Formation of Disaccharides

Hydrolysis of a Disaccharide

Important Polysaccharides: Starch n n Consists of glucose subunits Plant energy storage molecule Glycogen is a very similar molecule in animals. Starch and glycogen can be digested by animals.

Important Polysaccharides: Cellulose n n Composed of glucose subunits Different bond formed than starch Structural component in plants Cannot be digested by animals

BIOENERGETICS

What is Bioenergetics? The study of energy in living systems (environments) and the organisms (plants and animals) that utilize them

Energy n n Required by all organisms May be Kinetic or Potential energy

Kinetic Energy n n Energy of Motion Heat and light energy are examples

Potential Energy n n Energy of position Includes energy stored in chemical bonds

Two Types of Energy Reactions

Endergonic Reactions n n Chemical reaction that requires a net input of energy Photosynthesis SUN Light Energy photons 6 CO 2 + 6 O 2 6 H 2 O C 6 H 12 O 6 + (glucose)

Exergonic Reactions n Chemical reactions that releases energy n Cellular Respiration Energy C 6 H 12 O 6 + 6 O 2 6 CO 2 + 6 H 2 O+ (glucose) ATP

Metabolic Reactions of Cells

What is Metabolism? n The sum total of the chemical activities of all cells

Two Types of Metabolism n n Anabolic Pathways Catabolic Pathways

Anabolic Pathway n n Metabolic reactions, which consume energy (endergonic), to build complicated molecules from simpler compounds. light SUN energy Photosynthesis 6 CO 2 + 6 H 2 O C 6 H 12 O 6 + 6 O 2 (glucose)

Catabolic Pathway n Metabolic reactions which release energy (exergonic) by breaking down complex molecules in simpler compounds energy Cellular Respiration n C 6 H 12 O 6 + 6 O 2 6 CO 2 + 6 H 2 O + (glucose) ATP

Cellular Energy - ATP

ATP n Components: 1. adenine: nitrogenous base 2. ribose: five carbon sugar 3. phosphate group: chain of 3 adenine phosphate group P ribose P P

Adenosine Triphosphate n n Three phosphate groups-(two with high energy bonds Last phosphate group (PO 4) contains the MOST energy

Breaking the Bonds of ATP n n n Process is called phosphorylation Occurs continually in cells Enzyme ATP-ase can weaken & break last PO 4 bond releasing energy & free PO 4

How does ATP work ? n n Organisms use enzymes to break down energy-rich glucose to release its potential energy This energy is trapped and stored in the form of adenosine triphosphate(ATP)

How Much ATP Do Cells Use? n It is estimated that each cell will generate and consume approximately 10, 000 molecules of ATP per second

Coupled Reaction - ATP n The exergonic hydrolysis of ATP is coupled with the endergonic H 2 O dehydration process by transferring a phosphate group to another molecule. H 2 O

Hydrolysis of ATP + H 2 O ADP + P (exergonic) Adenosine triphosphate (ATP) P P P Hydrolysis (add water) P P + P Adenosine diphosphate (ADP)

Hydrolysis is Exergonic Energy Used by Cells

Dehydration of ATP ADP + P ATP + H 2 O (endergonic) Dehydration (Remove H 2 O P P + P Adenosine diphosphate (ADP) Adenosine triphosphate (ATP) P P P

Dehydration is Endergonic Energy is restored in Chemical Bonds

Enzymes

What Are Enzymes? n n n Most enzymes are Proteins (tertiary and quaternary structures) Act as Catalyst to accelerates a reaction Not permanently changed in the process

Enzymes Are specific for what they will catalyze n Are Reusable n End in –ase -Sucrase -Lactase -Maltase n

How do enzymes Work? Enzymes work by weakening bonds which lowers activation energy

Enzymes Without Enzyme With Enzyme Free Energy Free energy of activation Reactants Products Progress of the reaction

Enzyme-Substrate Complex The substance (reactant) an enzyme acts on is the substrate Substrate Joins Enzyme

Active Site n A restricted region of an enzyme molecule which binds to the substrate Active Site Substrate Enzyme

Induced Fit n n A change in the shape of an enzyme’s active site Induced by the substrate

Factors Affecting Enzyme Activity n n Temperature p. H Cofactors & Coenzymes Inhibitors

Temperature & p. H n n n High temperatures are the most dangerous reactions & denature enzymes (Most like normal Body temperatures) temperatures Most enzymes like near neutral p. H (6 to 8) Denatured (unfolded) by ionic salts

Cofactors and Coenzymes n n Inorganic substances (zinc, iron) and vitamins (respectively) are sometimes need for proper enzymatic activity Example: Iron must be present in the quaternary structure of hemoglobin in order for it to pick up oxygen

Two examples of Enzyme Inhibitors a. Competitive inhibitors: are chemicals that resemble an enzyme’s normal substrate and compete with it for the active site Substrate Competitive inhibitor Enzyme

Inhibitors b. Noncompetitive inhibitors: Inhibitors that do not enter the active site, site but bind to another part of the enzyme causing the enzyme to change its shape, shape which in turn alters the active site Substrate active site altered Enzyme Noncompetitive Inhibitor