BiochemistryBiochemistry

Background information Background information relevant to your study of relevant to your study of

biochemistry (you learned it biochemistry (you learned it in your previous science in your previous science

classes)classes)

Properties of MatterProperties of Matter

Matter Matter – any substance that has mass – any substance that has mass and volume.and volume.– MassMass - the quantity of matter in an object. - the quantity of matter in an object.– VolumeVolume - the amount of space that the - the amount of space that the

matter takes up.matter takes up.

The more properties we can identify for a The more properties we can identify for a substance, the better we can understand substance, the better we can understand its nature!its nature!

Properties of MatterProperties of Matter

Physical propertiesPhysical properties of matter can be of matter can be observed and measured without observed and measured without changing the identity of the matter.changing the identity of the matter.

Physical changePhysical change - can affect size, - can affect size, shape, or color of a substance but shape, or color of a substance but does NOT affect the composition of does NOT affect the composition of the matter.the matter.

Physical Properties of MatterPhysical Properties of Matter

MassMass ColorColor VolumeVolume OdorOdor TextureTexture TasteTaste

LusterLuster HardnessHardness Melting PointMelting Point Boiling PointBoiling Point PhasePhase DensityDensity

Chemical Properties of MatterChemical Properties of Matter Chemical propertiesChemical properties of matter of matter

describe a substancedescribe a substance’’s ability to s ability to change into a NEW substance as a change into a NEW substance as a result of a result of a chemical changechemical change..

Chemical changeChemical change - bonds are broken - bonds are broken and new bonds form between atoms. and new bonds form between atoms. – Substances display different physical and

chemical properties after the change. – A chemical change is irreversible!

Signs a chemical change Signs a chemical change occurred include…occurred include…

Production of light Production of heat Color change Gas production (bubbles) Odor Sound A substance was created that wasnA substance was created that wasn’’t there before!t there before!

Examples: burning coal, ripening banana, baking a cake.Examples: burning coal, ripening banana, baking a cake. Examples: food is metabolized in body, photosynthesis.Examples: food is metabolized in body, photosynthesis.

Physical vs. Chemical Changes

Physical Change: Reversible

– You can “un-freeze water”

No new substance is formed– Water and ice are

both H2O molecules

Chemical Change: Not reversible

– You can’t “un-burn” wood

A new substance is formed– Burning wood

results in CO2, ash, etc.

Phases/States of Matter

Phase of matter - physical property of matter that describes one of a number of different states of the same substance.

Phases/States of MatterPhases/States of Matter

SolidSolid - definite shape, definite volume - definite shape, definite volume LiquidLiquid - no definite shape, definite - no definite shape, definite

volumevolume GasGas - no definite shape, no definite - no definite shape, no definite

volumevolume PlasmaPlasma - no definite shape, no definite - no definite shape, no definite

volumevolume– highly ionized gas that occurs at high highly ionized gas that occurs at high

tempstemps

Chapter 2 - Chapter 2 - BiochemistryBiochemistry

AtomsAtoms

AtomAtom - basic unit of matter. - basic unit of matter.– Greek word Greek word ““atomosatomos”” – unable to cut. – unable to cut.– Atoms are the smallest component of a Atoms are the smallest component of a

cell.cell.

AtomsAtoms

Atoms compose all living and non Atoms compose all living and non living things.living things.– Atoms contain subatomic particles: Atoms contain subatomic particles:

protons protons (+), (+), neutronsneutrons (neutral), and (neutral), and electrons electrons (-).(-).

– Protons and neutrons are found in the Protons and neutrons are found in the center of the atom in the center of the atom in the atomic nucleusatomic nucleus..

– Electrons float around the nucleus in Electrons float around the nucleus in energy levelsenergy levels and are attracted to the and are attracted to the nucleus by the protons (+nucleus by the protons (+’’s attract –s attract –’’s).s).

AtomsAtoms

Atoms are Atoms are electrically neutralelectrically neutral because their because their protonproton number and number and electronelectron number balance out their number balance out their charges.charges.

Atomic StructureAtomic Structure

Protons

Neutrons

Electrons

Atomic StructureAtomic Structure

The Nature of AtomsThe Nature of Atoms

ProtonsProtons determine the identity of an determine the identity of an atom!atom!– Atomic numberAtomic number – number of protons in the – number of protons in the

nucleus of an atom. Each atom has a nucleus of an atom. Each atom has a different proton number (identity).different proton number (identity).

ElectronsElectrons determine how an atom determine how an atom behaves!behaves!– Electrons float around the nucleus in Electrons float around the nucleus in

energy levels; most of an atom is empty energy levels; most of an atom is empty space.space.

The Nature of AtomsThe Nature of Atoms

Mass numberMass number is the total number of is the total number of protons and neutrons in the nucleus.protons and neutrons in the nucleus.– Most of the mass of an atom is in the Most of the mass of an atom is in the

nucleus!nucleus!

Atomic number equals the number of protons in nucleus.

Atomic mass or mass number equals the number of protons + neutrons.

Atomic NumberSymbolNameAtomic Mass (Mass #)

Atoms have EnergyAtoms have Energy

ElectronsElectrons in an atom have energy. in an atom have energy. Energy is needed to keep electrons Energy is needed to keep electrons

in the clouds so that they are not in the clouds so that they are not pulled into the nucleus.pulled into the nucleus.

Atoms have EnergyAtoms have Energy

•Each energy level can hold a certain number of electrons.

•First level: 2 electrons

•Second level: 8 electrons

•Third level: 8 electrons

•Fourth level: 10 electrons

ElementsElements

Elements Elements - substances that are - substances that are composed of only one type of atom.composed of only one type of atom.– Cannot be chemically broken down to any Cannot be chemically broken down to any

other substances.other substances.– Are represented by Are represented by chemical symbolschemical symbols on on

periodic table.periodic table.– More than 100 elements are known, about More than 100 elements are known, about

25 are found in living organisms.25 are found in living organisms. 6 most abundant include: O, C, H, N, P, S6 most abundant include: O, C, H, N, P, S

IsotopesIsotopes

IsotopesIsotopes - atoms of the same element - atoms of the same element that differ in the number of neutrons.that differ in the number of neutrons.– Still have the same number of protons - Still have the same number of protons -

(proton number identifies the substance).(proton number identifies the substance).

Isotopes of an element have the Isotopes of an element have the samesame chemical properties. They differ by the chemical properties. They differ by the number of number of neutronsneutrons (a physical property). (a physical property).

Radioactive IsotopesRadioactive Isotopes Radioactive isotopesRadioactive isotopes - are unstable and - are unstable and

from time to time breakdown releasing from time to time breakdown releasing radiation from their nucleus.radiation from their nucleus.– Used to study organisms, diagnose disease Used to study organisms, diagnose disease

(as tracers), treat disease (kill cancer cells), (as tracers), treat disease (kill cancer cells), sterilize food, measure the ages of rocks.sterilize food, measure the ages of rocks.

– Radiation is dangerous! It can kill or damage Radiation is dangerous! It can kill or damage living things (i.e. Chernobylliving things (i.e. Chernobyl’’s radioactive s radioactive fallout).fallout).

Chemical CompoundsChemical Compounds A A chemical compoundchemical compound is a group of atoms is a group of atoms

held together by chemical bonds.held together by chemical bonds. Compounds are represented by Compounds are represented by chemical chemical

formulasformulas.- show the proportion of atoms .- show the proportion of atoms in a compoundin a compound

Examples of chemical formulas:Examples of chemical formulas:– NaCl – table saltNaCl – table salt

– HH22O – waterO – water

– NHNH3 3 – ammonia– ammonia

– CC66HH1212OO66 - glucose - glucose

Interactions of MatterInteractions of Matter Atoms want to achieve stability – full Atoms want to achieve stability – full

outermost energy level (valence shell).outermost energy level (valence shell). In order to achieve stability, atoms will In order to achieve stability, atoms will

either gain, lose, or share electrons with either gain, lose, or share electrons with other atoms in a process called other atoms in a process called chemical chemical bonding.bonding.– Atoms will bond with other atoms if the bonding Atoms will bond with other atoms if the bonding

will give both atoms complete outermost energy will give both atoms complete outermost energy levels.levels.

– Valence electrons- electrons in outermost Valence electrons- electrons in outermost energy levelenergy level

Chemical ReactionsChemical Reactions

Chemical reactionChemical reaction – a process that – a process that changes one set of chemicals into changes one set of chemicals into another set of chemicals; involves the another set of chemicals; involves the breaking and reforming of chemical breaking and reforming of chemical bonds.bonds.– ReactantsReactants - chemicals that undergo a - chemicals that undergo a

change (left side of equation).change (left side of equation).– ProductsProducts - chemicals that are the result of a - chemicals that are the result of a

change (right side of equation).change (right side of equation).

AA ++ BB ---------> ---------> C C ++ D D

Energy in Chemical Energy in Chemical ReactionsReactions

Energy is stored within chemical bonds. Energy is stored within chemical bonds. – When bonds are broken, energy is released.When bonds are broken, energy is released.– All living organisms must have a source of All living organisms must have a source of

energy to carry out chemical reactions!energy to carry out chemical reactions! Two types or reactions deal with the Two types or reactions deal with the

energy stored in chemical bonds:energy stored in chemical bonds: Endergonic reactionsEndergonic reactions Exergonic reactionsExergonic reactions

Endergonic ReactionsEndergonic Reactions

Endergonic reactionsEndergonic reactions – reactions that – reactions that absorbabsorb energy. energy.– Need a source of energy to trigger the Need a source of energy to trigger the

reaction (donreaction (don’’t occur spontaneously).t occur spontaneously).– Reactions tend to feel cold.Reactions tend to feel cold.

Exergonic ReactionsExergonic Reactions

Exergonic reactionsExergonic reactions – reactions that – reactions that releaserelease energy. energy.– Energy is released as heat, light, or gas.Energy is released as heat, light, or gas.– Can occur spontaneously.Can occur spontaneously.– Often feel warm.Often feel warm.

Ionic bondsIonic bonds

Ionic bonds Ionic bonds – chemical bonds that – chemical bonds that transfer electrons from one atom to transfer electrons from one atom to another forming charged particles another forming charged particles called called ionsions..

Example: NaCl is a Example: NaCl is a compound formed by ionic compound formed by ionic

bonds.bonds.– Na has 1 electron in its outermost energy Na has 1 electron in its outermost energy

level. level. When Na looses an electron, it becomes positively When Na looses an electron, it becomes positively

charged (Nacharged (Na++, or a sodium ion)., or a sodium ion).

– Cl needs 1 electron to fill its outermost Cl needs 1 electron to fill its outermost energy level.energy level. When Cl gains an electron from Na, it produces a When Cl gains an electron from Na, it produces a

negatively charged ion, Clnegatively charged ion, Cl--..

– The two oppositely charged ions are attracted The two oppositely charged ions are attracted to one another and form NaCl through to one another and form NaCl through transferring electrons in transferring electrons in ionic bondingionic bonding..

Covalent bondsCovalent bonds

Covalent bonds Covalent bonds – chemical bond – chemical bond formed by the sharing of electrons so formed by the sharing of electrons so that each atom fills its outermost that each atom fills its outermost energy level.energy level.– Most bonds in living organisms are Most bonds in living organisms are

covalent.covalent.

– Examples: HExamples: H22O, COO, CO22, NH, NH33, C, C66HH1212OO66..

MoleculeMolecule – smallest particle of a – smallest particle of a covalently bonded compound.covalently bonded compound.

Dogs Teaching Bonding: http://www.youtube.com/watch?v=_M9khs87xQ8&sns=em

Intermolecular Forces

Intermolecular forces - also called molecular attraction.

Are forces of attraction between stable molecules.– Example: hydrogen bonds (see

section 3-3).

Two types of IM forces:

Cohesion - intermolecular force of attraction between LIKE molecules.

Adhesion - intermolecular force of attraction between DIFFERENT molecules.

Intermolecular Forces

Why do they occur?– Due to differences in charge densities

or uneven distribution of electrons!

Acids, Bases, and pH

Acid – a substance that releases hydrogen ions (H+ ) when dissolved in water.– Example: HCl ---> H+ + Cl-

Base – a substance that releases hydroxide ions (OH-) when dissolved in water.– Example: NaOH ---> Na+ + OH-

Acids, Bases, and pH

Water is a neutral solution - water separates forming an equal number of hydrogen and hydroxide ions.

Neutralization reaction - Hydrogen ions and hydroxide ions react to form water.– Occurs when H+ ions from strong acids

are mixed in perfect ratios with OH- ions from strong bases.H+ + OH- -----> H2O

pH Scale

pH – measures the amount of hydrogen in a solution, each measurement of pH represents ten times.

pH Scale - ranges from 0 to 14.– Less than 7 is for acids (more H+ than OH-).– Greater than 7 is for bases (more OH- than H+).– 7 is neutral (equal amounts of H+ and OH- in

solution).– Most cells have a pH of 6.5-7.5.

Controlling pH is an example of homeostasis.

pH Scale

Acids - substances that forms hydrogen ions when dissolved in water.– The more hydrogen ions (less hydroxide)

the more acidic.

Bases - substances that forms hydroxide ions when dissolved in water.– The more hydroxide ions (less hydrogen)

the more basic or alkaline.

pH Scale

What happens when acid is added to a solution?– As more acid is added the pH will go down, but

the H+ concentration goes up.

What happens when base is added to a solution?– As more base is added the pH will go up, but

the H+ concentration goes down.

BuffersBuffers

BuffersBuffers – weak acids or bases that – weak acids or bases that can react with strong acids or bases can react with strong acids or bases to prevent sharp, sudden changes in to prevent sharp, sudden changes in pH.pH.– Are important for maintaining Are important for maintaining

homeostasis in living organisms.homeostasis in living organisms. Ex. Carbonic acid and sodium bicarbonate Ex. Carbonic acid and sodium bicarbonate

buffer your blood’s pH.buffer your blood’s pH.

Properties of Water

All cells contain water.– About two thirds of the molecules in our

body are water. Water provides a medium in which

other molecules can interact. Water exists as all three

states/phases of matter. Water expands when it freezes!!!!

Water is Polar

Water is a polar molecule - molecule has slight charge (+ or -) on each end due to uneven distribution of electrons.– Oxygen pulls hydrogen’s electrons closer to

it therefore the oxygen atom is slightly negative and the hydrogen becomes slightly positive.

– This is the most important property of water! Allows a strong attraction between water

molecules or between water and other polar molecules!

Polar vs. Non-Polar Molecules Polar - unequal distribution of charge means a

great amount of attraction between molecules.

Non-Polar - equal distribution of charge means a weak attraction between molecules.

Do Polar and Non-Polar Solutions Mix?

•Polar solutions mix with other polar solutions!•Example: Milk and water.

•Non-polar solutions mix with other non-polar solutions!

•Example: Oil and grease.

•Polar solutions will NEVER mix with non-polar solutions!

•Example: Italian salad dressing.

Water clings to itself & other molecules

-Cohesion – Intermolecular force of attraction between like molecules.

Water molecules cling to other WATER molecules (hydrogen bonding) – Beading of water on a smooth surface.

– Adhesion – Intermolecular force of attraction between different molecules. Water molecules cling to other molecules –

Meniscus in a graduated cylinder.

Water is good at forming mixtures

•Due to slight charge of water molecules.

•Mixture - substance composed of two or more elements or compounds that are mixed together but not chemically combined (are not linked by chemical bonds).

•Examples: salt and pepper stirred together; atmosphere.

•Two types of mixtures: Solutions & Suspensions

Water’s role in suspensions

Suspension – a mixture where the solute does not fully dissolve.

Solute will settle out. Example blood (plasma and blood cells).

Water’s role in solutions

Solution – small particles are dispersed in mixture, all components are evenly distributed.

Solute the substance that is dissolved. Solvent the substance that does the

dissolving. Water acts as a solvent to dissolve solutes

(ex. sugar) forming solutions.

Water’s role in solutions

Water dissociates - breaks down forming charged particles called ions (H+ and OH-) when its bonds are broken.H2O ----- H+ + OH-

Other compounds also dissociate (break down into their individual ions) when dissolved in water.Ex. NaCl ------> Na+ + Cl-

Water has a large heat capacity

Heat capacity – amount of heat required to change a substance’s temperature by a given amount.

Is a result of the multiple hydrogen bonds between water molecules.

A large amount of heat energy is required to cause the molecules to move faster (which is how the temperature of the water is raised).– Allows large bodies of water to absorb large

amounts of heat with only a small change in temperature.

– Alllows for regulation of cell temperature.

Water has properties of capillarity

Capillary action– the interplay of cohesion and adhesion to hold a solution in a thin tube against the force of gravity.– Draws water out of the roots of plants and up into the

stems and leaves.– Helps move blood through the body.

Biological MacromoleculesBiological Macromolecules

Inorganic vs. Organic Compounds

C, H, N, and O make up almost all chemical compounds in living organisms.

Organic compounds - contain carbon.– Carbon can form long carbon chains by

bonding to other carbon atoms. Unique because they are very strong/stable!

Inorganic compounds - do not contain carbon.– Exception: CO2

Carbon Compounds Polymerize

Polymerization - process by which large compounds are constructed by joining together smaller compounds (monomers). – Monomers are joined by chemical bonds to

form polymers.– Very large polymers are called

macromolecules.

Building macromolecules

Dehydration synthesisDehydration synthesis or or condensation reactions condensation reactions - reactions - reactions that joins two monomers into a that joins two monomers into a polymer and involves the loss of polymer and involves the loss of water.water.

HydrolysisHydrolysis - reaction that breaks a - reaction that breaks a polymer into monomers by using a polymer into monomers by using a water molecule.water molecule.

Carbon

Carbon is a key component of biological macromolecules for two reasons:

1. Carbon atoms have 4 valence electrons.– Allows them to form strong covalent bonds

with many other elements. 2. Carbon atoms can bond to other carbon

atoms.– Gives the ability to form chains, rings, multiple

bonds, and millions of different large, complex structures.

Carbohydrates

Carbohydrates - macromolecules that are composed of the atoms carbon, hydrogen, and oxygen in the proportion of 1:2:1.– 1 carbon : 2 hydrogen : 1 oxygen.– Examples: sugars and starches.

Carbohydrates - Carbohydrates - MonosaccharidesMonosaccharides Monosaccharide – simple, single sugar

molecule.– Examples: glucose (produced by green

plants), fructose (fruits), and galactose (milk).

– Sugars are important for living things because they contain a great deal of energy.

Carbohydrates - Disaccharides

DisaccharideDisaccharide – 2 sugar molecules – 2 sugar molecules bonded together by a covalent bond.bonded together by a covalent bond.– Examples: lactose or sucrose.Examples: lactose or sucrose.

Carbohydrates - reactions Dehydration synthesisDehydration synthesis - reaction that - reaction that

joins two monosaccharides into a joins two monosaccharides into a disaccharide and involves the loss of disaccharide and involves the loss of water.water.– HydrolysisHydrolysis - reaction that breaks a - reaction that breaks a

disachharide into monosaccharides by disachharide into monosaccharides by using a water molecules.using a water molecules.

Carbohydrates - Carbohydrates - PolysaccharidesPolysaccharides

PolysaccharidesPolysaccharides – macromolecules formed – macromolecules formed from linking many monosaccharides from linking many monosaccharides together.together.– Ex. Starch – a polysaccharide plants use to Ex. Starch – a polysaccharide plants use to

store energy; many glucose molecules bonded store energy; many glucose molecules bonded together.together.

– Ex. Glycogen - stored form of glucose from Ex. Glycogen - stored form of glucose from starch; stored for energy in liver of animals.starch; stored for energy in liver of animals.

– Ex. Cellulose – chains of glucose, structurally Ex. Cellulose – chains of glucose, structurally different from starch, tough flexible molecule different from starch, tough flexible molecule found in plants.found in plants.

Nucleic Acids Nucleic acids - Polymers made of building

blocks (monomers) called nucleotides.– Contain H, O, P, C, and N.– Made up of nitrogenous base, 5-C sugar, 1-3

phosphate groups Nitrogenous bases: Adenine, Thymine, Guanine,

Cytosine, Uracil (RNA only)

– Nucleic acids store and transmit hereditary information.

– Example – DNA and RNA. DNA has a deoxyribose sugar, RNA has a ribose sugar.

Lipids

Lipids - organic compounds that are oily or waxy.– Common examples: fats, oils, and waxes.– Lipids are made of C, H, and O (no ratio H to O).– Multiple rings of C– Lipids function in energy storage, form biological

membranes, and act as chemical messengers. Lipids have more energy than carbohydrates because

lipids have more hydrogens bonded to the carbon chain.

Lipids have a water loving portion, and a water hating portion.

Types of Lipids Lipids are polymers made of

monomers of fatty acids and glycerol.– Ex fatty acids: oleic acid, palmitic acid (produced by liver),

linolenic acid (essential)

– Saturated Lipids: contain the maximum number of carbon to

hydrogen bonds. Example – animal fats. Also called “bad fats”.

Types of Lipids

– Unsaturated Lipids: Contain carbon to carbon double bonds; less

hydrogen. Example – plant oils (corn oil, vegetable oil) Also called “good fats”.

Types of Lipids

Sterols - ringed structures that play roles in building cells and carrying messages.– Example – cholesterol; hormones.

Phospholipids - contain parts that dissolve well in water and parts that do not.– Spontaneously form bilayers to keep water

hating portions protected and water loving portions in contact with water.

Proteins Proteins - polymers made of building

blocks (monomers) called amino acids.– Amino acids have an amino group, carboxyl

group and an R group. Differences in R groups make each of the 20

amino acids different.

Peptides

Peptides - short polymers of amino acids linked by peptide bonds.

Peptide bonds are covalent bonds that join together amino acids.

Once a polypeptide (long chain of amino acids) is formed, it must be folded into a 3-D shape before it is called a protein.– The shape is important for recognition of the

protein by the cell and for the actions of the protein.

ProteinsProteins

Used to form skin, muscle, hair.Used to form skin, muscle, hair. Proteins play a role in metabolism, Proteins play a role in metabolism,

help fight disease, used to assist help fight disease, used to assist chemical reactions (enzymes), and chemical reactions (enzymes), and signaling other cellular functions.signaling other cellular functions.

EnzymesEnzymes are special proteins. are special proteins.

EnzymesEnzymes EnzymesEnzymes – proteins that act as biological – proteins that act as biological

catalyst and speed up the rate of a chemical catalyst and speed up the rate of a chemical reaction.reaction.– Enzymes are Enzymes are notnot changed by the reaction (so changed by the reaction (so

they can be re-used).they can be re-used).– Enzymes are very specific – they will only speed Enzymes are very specific – they will only speed

up up oneone chemical reaction. chemical reaction.– Enzymes speed up chemical reactions by Enzymes speed up chemical reactions by

lowering the lowering the ““start-upstart-up”” energy of a reaction. energy of a reaction.– The names of most enzymes will end in The names of most enzymes will end in ““asease””

such as ligase, amylase, polymerase.such as ligase, amylase, polymerase.

EnzymesEnzymes

Enzymes will bind to the reactants of the Enzymes will bind to the reactants of the chemical reaction that it will catalyze.chemical reaction that it will catalyze.– The reactants that enzymes bind to are The reactants that enzymes bind to are

called called substrates.substrates.– The site in which the substrates are brought The site in which the substrates are brought

to is called the to is called the active site.active site.– Substrates will fit into the active site like a Substrates will fit into the active site like a

lock and key.lock and key. If the substrates do not fit in the active site, it is If the substrates do not fit in the active site, it is

the wrong enzyme and it will not catalyze a the wrong enzyme and it will not catalyze a reaction!reaction!

EnzymesEnzymes

– Enzymes function in regulating chemical pathways, making materials that cells need, releasing energy, and transferring information.