BIOCHEMISTRY IBIOCHEMISTRY I

General ChemistryGeneral ChemistryAugust 2014August 2014

CHEMISTRY OF LIFECHEMISTRY OF LIFE

• AtomAtom: the actual basic unit - : the actual basic unit - composed of protons, neutrons, composed of protons, neutrons, and electronsand electrons

THE ATOMTHE ATOM

• Just like cells are the basic unit of life, the Just like cells are the basic unit of life, the ATOMATOM is the basic unit of matter. is the basic unit of matter.

• They are very small. If placed side by side They are very small. If placed side by side one million would stretch a distance of one million would stretch a distance of 1cm1cm. .

• The atom is made up of The atom is made up of threethree particles. particles.ParticleParticle ChargeCharge PROTONPROTON ++

NEUTRONNEUTRON NEUTRAL (0)NEUTRAL (0)

ELECTRONELECTRON --

• Electrons are not present within the atom. Electrons are not present within the atom. Instead, they revolve around the nucleus of the Instead, they revolve around the nucleus of the atom and form the atom and form the ELECTRON CLOUDELECTRON CLOUD

• Below is a diagram Below is a diagram of a helium atom.of a helium atom.

+ +-

-

PROTONSNEUTRONS

ELECTRONS

ATOMIC # = 2 (PROTONS)

ATOMIC MASS = 4 (PROTONS & NEUTRONS)

The Element

• ElementsElements: : simplest form of a substance - cannot be simplest form of a substance - cannot be broken down any further without changing what it isbroken down any further without changing what it is

• It is a substance composed of one type of atomIt is a substance composed of one type of atom• There are There are 9292 living elements living elements

– 11 in living things11 in living things

Living Elements

• 99% of atoms in the body are:– Nitrogen (N)– Oxygen (O)– Carbon (C)– Hydrogen (H)– Sulfur (S)– Phosphorus (P)

Role in Biogeochemical Cycles

• These six elements play important roles in the biogeochemical cycles – Biogeochemical cycle: A pathway by which a chemical

element or molecule moves through the living and non-living parts of Earth

• The major cycles include: Carbon, Nitrogen, Oxygen, Phosphorus, Sulfur, and Water water (molecule)

COMPOUNDSCOMPOUNDS

• A substance formed by the chemical A substance formed by the chemical combination combination of 2 or more elements in of 2 or more elements in definite definite proportionsproportions– Ex: water, salt, glucose, carbon dioxide Ex: water, salt, glucose, carbon dioxide

• The The cell is a COMPLEX CHEMICAL cell is a COMPLEX CHEMICAL FACTORY containing some of the same FACTORY containing some of the same elements found ielements found in the nonliving n the nonliving environment. environment.

• carbon (C), hydrogen (H), oxygen (O), and carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) are present in the greatest nitrogen (N) are present in the greatest percentagespercentages

TWO TYPES OF COMPOUNDSTWO TYPES OF COMPOUNDS

• OrganicOrganic - Contain Carbon bonded to - Contain Carbon bonded to other Carbons, H and O in some ratio other Carbons, H and O in some ratio (usually referred to as chemicals of life) (usually referred to as chemicals of life)

– Carbohydrates, Proteins, Lipids, Nucleic AcidsCarbohydrates, Proteins, Lipids, Nucleic Acids

• InorganicInorganic - usually "support" life - no - usually "support" life - no specific ratio of C, H, and Ospecific ratio of C, H, and O

– Water (H2O), Carbon Dioxide (CO2)Water (H2O), Carbon Dioxide (CO2)

Molecule Vs. Compound

• A molecule is formed when two or more atoms join together chemically– Can be the same or different atoms– Ex: Hydrogen (H2), Oxygen (O2), and Water (H2O)

• A compound is a molecule that contains at least two different elements– Ex: Water (H2O), Carbon dioxide (CO2)

• *All compounds are molecules but not all molecules are compounds

CHEMICAL BONDSCHEMICAL BONDS

• Chemical bonds hold the atoms in a Chemical bonds hold the atoms in a molecule together. molecule together.

• There are 2 main types of chemical bonds: There are 2 main types of chemical bonds: IONICIONIC and and COVALENTCOVALENT

IONIC BONDSIONIC BONDS

• Occur when 1 or more electrons are Occur when 1 or more electrons are TRANSFERREDTRANSFERRED from one atom to another. from one atom to another.

• When an atom loses an electron it is a When an atom loses an electron it is a POSITIVEPOSITIVE charge. charge.

• When an atom gains an electron it is a When an atom gains an electron it is a NEGATIVENEGATIVE charge charge

• These newly charged atoms are now called These newly charged atoms are now called IONSIONS– Example: NaCl (SALT)Example: NaCl (SALT)

COVALENT BONDSCOVALENT BONDS

• Occur when electrons are SHARED by atoms. Occur when electrons are SHARED by atoms. • These new structures that result from covalent These new structures that result from covalent

bonds are called bonds are called MOLECULESMOLECULES• ** In general, the more chemical ** In general, the more chemical bonds a bonds a

molecule has the more energy it contains molecule has the more energy it contains

SHARING IS CARING!SHARING IS CARING!

MIXTURESMIXTURES

• Water is not always pure. It is often found as part of a Water is not always pure. It is often found as part of a mixture. mixture.

• MixtureMixture: a material made of two or more elements or : a material made of two or more elements or compounds that are physically mixedcompounds that are physically mixed– Ex: salt & pepper mixed, sugar and sand – can be easily Ex: salt & pepper mixed, sugar and sand – can be easily

separated separated

SOLUTIONSOLUTIONCannot be separated once mixedCannot be separated once mixedTwo parts:Two parts:• SOLUTESOLUTE – substance that is being dissolved (sugar, – substance that is being dissolved (sugar,

salt) salt) • SOLVENT - tSOLVENT - the substance in which the solute he substance in which the solute

dissolvesdissolves• MaterialMaterials s that do not dissolve are known as that do not dissolve are known as

SUSPENSIONSSUSPENSIONS. . – Blood is the most common example of a suspension. Blood is the most common example of a suspension. – Cells & other particles remain in suspension.Cells & other particles remain in suspension.

FORMULAFORMULA

• The The chemical symbols and numbers that chemical symbols and numbers that compose a compound ("recipe")compose a compound ("recipe")

• StructuralStructural Formula – Line drawings of the Formula – Line drawings of the compound that shows the elements in compound that shows the elements in proportion and how they are bondedproportion and how they are bonded

• MolecularMolecular Formula – the Formula – the ACTUAL ACTUAL formula for a compoundformula for a compound

CC22HH66OO

Chemical Equations

• The beginning substances (reactants) are changed into other substances (products)

CH4(g) + 2 O2(g) CO2(g) + H2O (g)

Reactants Products

WATER (H2O)

• The most important inorganic compound for living organisms

• Most cellular activities take place in water solutions• Water is most often what substances dissolve in

Water is a Polar Molecule• Polar molecule: molecule in which the charges are

unevenly spread• Because of its positive and negative charge, water

molecules are attracted to each other• The atoms bind in such a way that

there are excess electrons on the Oxygen side and an excess of positive charges on the Hydrogen side

Non-Polar Molecules

• Non-polar molecules have electrons distributed more symmetrically and so do not have an abundance of charges at the opposite sides– All charges cancel each other out

• Examples: Methane, Gasoline

Hydrogen Bonds of Water

• Because of its partial positive and negative charges, water molecules can attract each other

• Hydrogen bond: the pull between a partially positive hydrogen atom on one molecule and a partially negative oxygen atom on another– Form between the H2 atoms and O2 atoms of different

water molecules

Hydrogen Bonds of Water

• Hydrogen bonds are not as strong as covalent or ionic bonds

– But, they give water 3 special properties…

Adhesion

• Water molecules stick to other substances

• This causes water to be higher on edges of a graduated cylinder than in the middle

Grab a graduated cylinder and add water. Draw your observation on

the diagram

Cohesion• Water molecules stick together

– Water is attracted to water

Surface Tension

• This is the measure of the difficulty to break or stretch the surface of a liquid

• Water has strong surface tension because of the hydrogen bonds between water molecules at the water’s surface– Causes a film that can support the weight

of some animals

Water: The Universal Solvent

• It is capable of dissolving a variety of substances• It dissolves more substances than any other liquid• This is important to every living thing on Earth• Wherever water goes (eg. the ground, our bodies),

it takes along valuable chemicals, minerals and nutrients

ACIDS & BASESACIDS & BASES• Acids: always (almost) begin with "H" because of Acids: always (almost) begin with "H" because of

the excess of H+ ions (hydrogen)the excess of H+ ions (hydrogen)– Ex: lemon juice (6), stomach acid (1.5), acid rain Ex: lemon juice (6), stomach acid (1.5), acid rain

(4.5), normal rain (6)(4.5), normal rain (6)– HCL, HHCL, H22SOSO44

Facts about AcidsFacts about Acids• Acids usually Acids usually taste taste SOURSOUR. . • You eat acids daily You eat acids daily

• Examples: coffee, vinegar, soda, spicy foods, etc…Examples: coffee, vinegar, soda, spicy foods, etc…

ACIDS & BASESACIDS & BASES• Bases: always (almost) end with -OH because Bases: always (almost) end with -OH because

of the excess of hydroxide ions (Oxygen & of the excess of hydroxide ions (Oxygen & Hydrogen)Hydrogen)– EX: oven cleaner, bleach, ammonia, sea water, EX: oven cleaner, bleach, ammonia, sea water,

blood, pure waterblood, pure water– NaOH, Ca(OH)NaOH, Ca(OH)22

Facts about BasesFacts about Bases• Bases uBases usually sually feel feel SLIPPERYSLIPPERY to touch and to touch and

taste taste BITTERBITTER. .

pH SCALEpH SCALE• measures degree of measures degree of

substance alkalinity or substance alkalinity or acidityacidity

• Ranges from Ranges from 0 to 14 0 to 14

• 0 – 5 strong acid0 – 5 strong acid• 6-7 neutral6-7 neutral• 8-14 strong base8-14 strong base

• The goal of the body is to maintain The goal of the body is to maintain HOMEOSTASISHOMEOSTASIS (neutrality) – to do this when (neutrality) – to do this when pH is concerned, we add weak acids & bases to pH is concerned, we add weak acids & bases to prevent sharp changes in pH. prevent sharp changes in pH.

• These are These are called called BUFFERSBUFFERS