Chemistry/Water Biology Ch 2. Matter Anything that has mass and takes up space Matter has Two Major Types of Properties: – Physical Properties – Chemical.

Chemistry/Water

Biology Ch 2

Matter

• Anything that has mass and takes up space• Matter has Two Major Types of Properties:– Physical Properties– Chemical Properties

Physical Properties of Matter

• Properties that can be observed and measured without permanently changing the identity of the matter.

• Examples:– Mass– Volume– Color– Texture– State/phase– Boiling and melting points

Types of changes in matter• Physical change– a change in which a

substance is NOT permanently altered

– ex. Ice to water example

Types of changes in matter

• chemical change in matter– a process in which a

substance is permanently altered. When a chemical change is complete, it is difficult (and perhaps impossible) to get the original substance back.

– Example: frying and egg; burning wood

element

• a pure substance that cannot be broken down into any simpler substances.

• An element is matter that consists entirely of one type of atom.

periodic table of elements

• 109 different elements - 90 of these are found in nature

atom

• the smallest piece of an element that still has all the characteristics of the element

atomic structure

• nucleus of an atom - the center of the atom; composed of protons and neutrons– proton - subatomic particle that has mass and a

positive charge– neutron - subatomic particle that has mass and

has no charge

atomic structure

• electron cloud - the region outside the nucleus where electrons may be found.– electron – • almost no mass • negative charge• Constant motion• outside nucleus

Related Terms

• atomic number - the number of protons an atom has.

• atomic mass - the total number of neutrons and protons in an atom– Electrons are not considered because they have

so little mass.

ion

• when an atom loses or gains electrons it becomes an ion.

• Ions are atoms that have either a positive or negative charge.

Combinations of Elements

• Mixtures, solutions, compounds, molecules…

mixture

• two or more substances that are physically combined– they still retain their

own properties and can be separated using simple physical means.

solution

• solution - a mixture in a liquid form.– Atoms/molecules are very evenly dispersed.

• solute – the substance that gets dissolved in making a solution

• solvent – the substance that does the dissolving in a solution. – Water is said to be the "universal solvent" because it

dissolves lots of different things.

compound• a substance that consists of two

or more different types of atoms that are chemically combined– that is, they cannot be easily

separated, – the individual characteristics as

elements no longer exist - they change completely.

– The elements in a compound are combined in very definite proportions - unlike the substances in a mixture. THINK WATER!!!

molecule

• the smallest part of a compound that still has the characteristics of the compound.

chemical bonds

• the means by which different atoms are combined to make compounds.

• bonds occur due to interactions between the electrons of different atoms.

• Chemical bonds form as atoms "try" to achieve stability - this means having complete outer energy levels.

ionic bonds

• a bond resulting from the total transfer of an electron from one atom to another.

• Their resulting opposite electrical charges will hold them together. – This is a strong bond, but

can be easily broken.– Animation link

covalent bond• a chemical bond formed

by the sharing of electrons. – By sharing electrons, each

atom fills up its outer electron shell.

• very strong bond • This is a and is found in

most of the chemicals in living organisms.

• Covalent bonds may be single, double or triple.

chemical reaction

• any process in which a chemical change occurs.

• reactants - substances that enter into a chemical reaction

• products - substances that result from a chemical reaction

WATER

• Water = H20 = 2 hydrogen atoms covalently bound to an oxygen atom.

Water is unique and very important for life on Earth

• Water has unique properties that make it essential for life. Life as we understand it could not exist without water.

• 75% of Earth's surface is covered with water.

• Water is the most abundant compound in nearly all living things.

What is so unique about water??

• It begins with Oxygen – Oxygen is electronegative. – This means that oxygen LOVES electrons and will NOT share them

EQUALLY in a covalent bond.• In a water molecule, oxygen pulls the electrons of the two

hydrogen atoms closer to itself. • As a result, the two ends of a water molecule are DIFFERENT.

– One end (the oxygen end) has a slight negative charge – the other end (the hydrogen end) has a slight positive charge. – Because of this, water is said to be POLAR.

• Polarity - when molecule has one end that is different from another.

Water’s Polarity

how polar substances interact

• Polarity causes a water molecule to act like a "little magnet".– The negative end will be attracted to positive

particles – The positive end will be attractive to negative

particles.• The Polarity of water is the quality of water

that causes all of its other important properties to exist.

hydrogen bonds

– Water molecules are attracted to each other due to their polarity

– Weak bonds are created between the oppositely charged regions of different water molecules.• These bond are called Hydrogen Bonds. • They are weak compared to covalent bonds, BUT• They are stronger than having no bonds at all. • It is because of these bonds between water molecules that water

acts so uniquely and is so important to life.

hydrogen bonds

Properties of Water

• All of waters unique properties are derived from its polarity.

Water is Cohesive

• Water tends to stick to itself

• Example:– Surface tension– Water striders– Helps in pulling water

up plants from the roots

Water is adhesive

• Water tends to stick to other substances– As long as they are also

polar or charged• Examples

– Capillary action• Water rises up very

narrow tubes b/c it clings to the walls of the tube.

– Also aids in pulling water up plants from roots

Water has a high specific heat

• Means it takes a lot of energy to raise the temperature of water by 1 degree C.

• Water can store lots of heat without changing it's temperature very much.

• Why?– It takes lots of energy to break the hydrogen bonds and

allow water molecules to move rapidly.• Causes our body temperature and temperature of

earth to be more stable.

Water has a high heat of vaporization

• Means it takes a lot of energy to change a gram of water from the liquid to the vapor (gas) state. Water is not easily evaporated.

• Allows us to retain our oceans, etc – they don't evaporate away into space;

• Good for evaporative cooling – when you sweat, water evaporates and takes lots of heat energy with it and thus cools you down.

Ice FLOATS• Water is less dense as

a solid than as a liquid • Ponds do not freeze

solid – ice forms a layer that insulates/protects the water underneath from getting too cold.

Water is a GREAT solvent

• As long as the solute is charged or polar.

• “the universal solvent”

• Think salt water

Water tends to "organize" non polar substances.

• Water would rather cling to itself than any nonpolar substance – so it separates from nonpolar substances.

• Cell membranes are able to form because of this property!

pH

• a measure of the acidity or basicity of a solution.– Acid - a solution with excess hydrogen ions– Base - a solution with excess hydroxide ions

pH

• Water = H2O = HOH • HOH sometimes separates (dissociates) into

H+ and OH- ions.– More H+ ions gives an acid. – More OH- ions gives a base. – Pure water always has the same number of H+

and OH-, hence its pH is NEUTRAL

pH scale

• Neutral pH = 7 • Acid pH = 0 to 7• Base pH = 7 to 14

What makes water become acidic or basic?

• ADDING acid or base• What is an acid?– A substance that readily gives up H+ ions to water

• What is a base?– A substance that gives up OH- ions to water

Remember, water is a great solvent…

• It readily pulls apart ionic substances• Example:– HCl (hydrogen chloride) is readily pulled apart by

water into H+ and Cl-– Thus there are excess H+ in solution – You get an acid

pH in living things

• Organisms seek to maintain a NEUTRAL pH (example - human blood - pH around 7.5).

• HOMEOSTASIS!– Living things attempt to keep internal conditions

CONSTANT

• Buffers are substances in living things that will absorb excess H+ ions or OH- ions as needed to maintain a neutral pH.

Biology Ch 2

Organic Compounds

Elements and Compounds in Living Things

• 90 elements NATURALLY occurring• Only 11 are common in living things– MOST Common are:

• Carbon• Nitrogen• Oxygen• Hydrogen

– These 4 elements make up 96.3% of the human body• 20 elements are found in small (TRACE) amounts in

living things

2 Main Groups of Chemical Compounds

• Organic• Inorganic

Organic Compounds• Contain carbon• Also tend to be

– Large molecules (made up of lots of atoms)

– Complex – Lots of carbon and hydrogen atoms

bound covalently • These are the primary compounds

that make up the working structures of living things!

Inorganic Compounds• Generally do NOT contain carbon

– CO2 is an exception• Also tend to be

– Small– Simple

• While NOT the major building blocks of life, they are absolutely necessary for life– Think WATER and Carbon Dioxide!

What’s so special about CARBON?

• It’s a great Tinker Toy! – 4 outer

(valence) electrons

– Can bind with 4 different atoms

What’s so special about CARBON?

• Readily forms COVALENT bonds with other atoms that are strong and stable

What’s so special about CARBON?• Can form chains of

almost unlimited length by bonding with other carbon atoms

• These long chains can then FOLD to make many complex shapes

THE BOTTOM LINE about CARBON

• It has HUGE potential for making a WIDE VARIETY of different types of molecules!

How to BUILD (and take apart) Organic Molecules

• Polymer – a large molecule made up of many smaller subunits

• Monomer – a small subunit (building block) that can be joined with other subunits to make a polymer

How to BUILD (and take apart) Organic Molecules

• Polymerization – the process of building LARGE molecules by joining together many smaller subunits– Provides a way for really large complex molecules

to form from smaller ones

• Macromolecule – term for VERY large polymers

How to BUILD (and take apart) Organic Molecules

• Dehydration Synthesis– Process that MAKES

polymers– Two monomers are

joined together by removing a molecule of water from between them• Dehydration – lose water• Synthesis – making or

putting together

How to BUILD (and take apart) Organic Molecules

• Hydrolysis– Process in which

polymers are broken apart

– Add back the water that was taken out

– Breaks polymer into monomer subunits

– Example: digestion

Bottom Line about Making Polymers

• Small subunits link together to make large polymers– Dehydration reactions link them• Removal of water

– Creates covalent bonds between subunits• To break apart polymers into subunits, you just add

the water back– Hydrolysis reaction– Breaks covalent bonds between subunits

Bottom Line about Making Polymers

• Really LONG complex molecules can be made and broken down by these methods.

• Like linking and unlinking cars in a train.

FOUR MAJOR GROUPS of Organic Compounds

• Carbohydrates• Lipids• Proteins• Nucleic Acids

Carbohydrates

• Functions– Quick ENERGY– Energy STORAGE in PLANTS– Energy STORAGE in ANIMALS– Structural compounds for SUPPORT

GENERAL CARB STRUCTURE: Monomers and Polymers

• Monomers– Monosaccharides– Individual car in the train

• Polymers– Polysaccharides– The whole train

Monosaccharides

• Monomers of carbs are monosaccharides

• Simple/single sugars• Basic formula CH2O• Example:

– GLUCOSE; C6H12O6– Sugar made by plants in

photosynthesis– Others: galactose (milk

sugar); fructose (fruit)

Why monosaccharides are important

• Energy in them can be made QUICKLY available to living things– Energy is stored in the chemical bonds of the

sugar molecules• In particular, bonds between CARBON and HYDROGEN

atoms store lots of energy– When these bonds are broken, energy is released– This energy is then available to use• Cellular respiration converts this energy to a usable

form!

Monosaccharide - Glucose

• Note that there are lots of these C-H bonds in a sugar molecule

• Each has lots of potential energy stored in it

Disaccharides

• DOUBLE sugars• Two monosaccharides

joined• Examples:– Sucrose (table

sugar)• Glucose + fructose

– Lactose (milk)• Galactose + glucose

Why are Disaccharides useful?• Not quite so easily broken

down as monosaccharides• Can by used by plants /

animals for safe temporary storage of sugars– Used in transport in

plants• Sugar not consumed on its

way from leaves to roots– Makes milk harder to

digest in animals• MOST adult animals

cannot digest milk• Keeps it for YOUNG ONLY

Polysaccharides

• Made by joining MANY monosaccharides• Sugar (thus energy) is STORED in this form

TYPES of Polysaccharides

• STARCH– PLANTS store energy in this form– LOTS of GLUCOSE molecules linked in LONG

CHAINS– Animals CANNOT store energy in this form, but

they CAN digest and USE it!

Starch

TYPES of Polysaccharides

• GLYCOGEN– Energy storage carbohydrate in ANIMALS– Found in the liver, mostly.– ALSO made of lots of glucose linked together– As you consume sugar, your liver converts it to

glycogen and stores it.• Through the day as you need energy, the liver breaks

off sugars from the glycogen molecules for you to us

Glycogen

Cellulose

• STRUCTURAL carbohydrate in PLANTS

• ALSO lots of glucose linked together

• CELL WALLS in plant cells• SUPPORT and

PROTECTION• UNDIGESTABLE BY

ANIMALS• WOOD

Chitin

• STRUCTURAL carbohydrate

• Cell walls of fungi• Exoskeleton of

arthropods

Lipids

• Waxes • Oils• Fats• Steroids

Functions of Lipids

• Energy Storage - animals and plants

• Insulation– Keeps animals

warm– blubber

Functions of Lipids• Waterproofing

– Duck feathers are kept dry by a layer of oil

– Mammal fur (beaver, otter, etc.), too.

Functions of Lipids

• shock-absorption/protection of organs

• formation of membranes in cells and organelles

• make important compounds called steroids - cholesterol and hormones (estrogen and testosterone, for example)

Structure of Lipids

• Glycerol + 3 fatty acids– Glycerol is just a

“connector”– 3 fatty acids are the

most important part

Why are Fatty Acids the “important part”?

• fatty acids are LONG chains of carbon and hydrogen atoms

• remember: bonds between carbon and hydrogen atoms STORE ENERGY!

• So fats (with their 3 fatty acids) are PACKED with energy and are GREAT at energy storage

EFFICIENT energy storage

• Because there are SO MANY C-H bonds in fatty acids, lipids are VERY efficient ways of storing energy. – Fats produce more energy per gram than

carbohydrates do!

• more efficient means better for animals - lots of energy without much "baggage“ for animals that need to move.

Efficient energy storage

• Some plants do use oils for energy storage– Corn oil, peanut oil, etc.

• Efficiency is just not as important for plants since they don’t have to move around - so starch is still often the primary energy storage molecule for them

Saturated vs. Unsaturated Fats

• saturated fat - when each carbon in a fatty acid shares a single covalent bond with as many hydrogen atoms as possible

• causes the fatty acids to be very straight• fatty acids like this can pack very tightly together• because they can pack tightly, saturated fats tend to

be solid at room temperature• butter and lard

Saturated Fat

Saturated vs. Unsaturated Fats• unsaturated fat - a fatty acid that has at least two carbons

double bonded to each other instead of to hydrogen atoms - that is,

• the carbons are NOT bound to the maximum number of hydrogen atoms.

• causes the fatty acids to bend• fatty acids like this cannot pack very tightly together• because of this unsaturated fats tend to be liquid at room

temperature– oils

Saturated vs. Nonsaturated Fats

Protein

• Functions – MANY!– Structural – build structures in organisms– muscle contraction– communication between cells– movement of cell parts– MOST IMORTANT: ENZYMES!!!

Structure of Proteins• Monomers of Proteins are

AMINO ACIDS– ALWAYS a carbon in the

middle– ALWAYS an H at the “top”– ALWAYS an amino group on

one side– ALWAYS a carboxyl group on

the other side– R group is always there, but

TYPE of R-group VARIES• 20 different types• All have different

characteristics

Protein Structure

• A protein is a polymer of amino acids• Amino acid monomers link together by covalent

bonds called PEPTIDE BONDS. = Proteins are long chains of amino acids – sometimes called polypeptides in reference to

their peptide bonds.• Peptide bonds are formed the same way as all bonds

among the organic compounds we're discussing - DEHYDRATION reactions.

Making Proteins from Amino Acids

Enzymes

• Chemical reactions are what living things are all about.

• Most of the chemical reactions in your body, if left to themselves, would not happen quickly enough for you to survive.

• CATALYST - something that speeds up a chemical reaction

• Enzymes are proteins that act as catalysts for the chemical reactions in your body.

Enzymes• Enzymes have unique shapes

designed to fit the chemicals that they are to "speed up" (the SUBSTRATES of the REACTION)

• The region of the enzyme that FITS the substrate specifically is called the enzyme's ACTIVE SITE. – The substrate BINDS with the

enzyme at the enzyme's ACTIVE SITE.

Enzymes

• Enzymes can either:– bring two (or more) reactants together more

quickly and force them to react– stress bonds in a single substrate and cause it to

break apart more easily

Enzymes

• An enzyme itself is NOT CHANGED by the chemical reaction it catalyzes

• A single enzyme can repeat its catalytic activity with many, many substrate molecules - that is, it can be used over and over again.

Enzyme catalyzed reaction

Enzymes

• ENZYMES ARE VERY SPECIFIC! – If the shape of the enzyme's active site becomes

damaged, it will be unable to bind with its substrate

– Thus, it will be unable to function. – If an enzyme loses its shape it is said to be

DENATURED. • enzymes can be denatured by HEAT • or by extremes in pH.

Nucleic Acids

• Functions– tell the cell how to function– transmit genetic information to offspring

Nucleic Acids

• Structure– Monomers of nucleic

acids are nucleotides• Sugar• Phosphate• Base

– Many nucleotides linked together give a nucleic acid - RNA and DNA are the two main examples