good morning or afternoon!!. basic chemistry chapter 2

GOOD MORNING or AFTERNOON!!

Basic Chemistry

Chapter 2

The Basics-Matter & Energy• CHEMISTRY

– the science that explores changes in matter & energy

• matter– has mass (same as weight for our purposes)– occupies space– can exist in three “phases”

• solid• liquid• gas

The Basics-Matter & Energy…(cont’d)

• Thus we are matter!!!

• S-O-O-O-O-O

CHEMISTRY IS THE STUDY OF US!!!

STRUCTURE OF MATTER• 117 “basic kinds” of matter

• elements– 92 naturally occurring (25 created in nuclear reactors)

• each is “pure matter• basic building blocks from which everything is made

• atoms– smallest unit (pieces) of elements– interact during chemical reactions to form

compounds• matter formed from two or more elements• molecules smallest units of compounds

STRUCTURE OF AN ATOM• subatomic particles

– protons• in the nucleus

– center of the atom

• positively charged• mass of “1” (AMU)• ATOMIC NUMBER

ATOMIC STRUCTURE…(cont’d)

• neutrons– have no electrical charge– mass of “1” (AMU)

• AMU = “atomic mass unit”

– in the nucleus– number may vary

• isotopes– atoms of an element that differ in the number of

neutrons

ATOMIC STRUCTURE (cont’d)

• electrons– negatively charged– mass of “0”– in energy shells, or orbits” surrounding

the nucleus

ATOMIC MASS

• mass of all protons + mass of all neutrons + mass of all electrons

• (number of protons) (mass of 1 proton) + (number of neutrons) (mass of 1 neutron) + (number of electrons) (mass of 1 electron)

• ATOMIC NO. + NUMBER OF NEUTRONS = ATOMIC MASS

• NUMBER OF NEUTRONS = ATOMIC MASS - ATOMIC NUMBER

ELECTRON DISTRIBUTION

• modern theory recognizes e- in “clouds” or energy levels– The further from the nucleus, the more energy

e-’s have

• Bohr model has e-’s in 2-D orbits– # varies with shell

• 2 in the first• 8 in the second• 8 in the third (sometimes 18)

– generally 8 is the most stable configuration

ELECTRON DISTRIBUTION…cont’d

All atoms “want” 8 electrons in their outermost shells and will interact with other atoms to the end that all reach 8.

Basis for formation of molecules (compounds)

FORMATION OF MOLECULES

• atoms interact such that both (all) have 8 electrons in outermost orbit

• thus, molecules are the most stable energy states for atoms and their electrons

• attractions between atoms in a molecule are chemical bonds– attractions result from distributing electrons so that each

atom in the molecule has 8 in its outermost shell, at least part of the time

TYPES OF CHEMICAL BONDS

• IONIC-one atom loses electrons, other gains electrons– atom that loses electrons has a net positive charge

• cation

– atom that gains electrons has a net negative charge• anion

– unlike charges attract• molecules form

• many elements in the body occur as ions– called electrolytes

TYPES OF CHEMICAL BONDS…cont’d)

• COVALENT-two atoms share one or more pairs of electrons

• each has 8 electrons in its outermost orbit at least part of the time– non-polar covalent bond

• atoms share electrons equally– carbon tetrachloride– methane

– polar covalent bond• unequal sharing of electrons between atoms

– water

WATER• 70% of human body

– some tissues higher

• functions in the body1. coolant

• high specific heat– can absorb heat w/o large increase in temperature

1. solvent• solute-molecule that dissolves

– lubricant– enters reactions

TYPES OF CHEMICAL BONDS…cont’d)

• HYDROGEN bonds– form between molecules not within molecules– each weak

• many hydrogen bonds form very strong structures• water as an example

CHEMICAL REACTIONS• Necessary for cells to remain alive• Atoms in reacting substances

(reactants) are rearranged to form different substances (products)

• Each cell is a chemical factory– growth, maintenance, repair,

secretion, contraction•metabolism

Types of Chemical ReactionsDECOMPOSITION- AB -> A + B

– molecules broken into smaller molecules• occurs in cells as well as outside them, e.g.

digestion in the small intestine

– hydrolysis• decomposition involving water

– catabolism• all the decomposition reactions in a cell

Types of Chemical ReactionsSYNTHESIS – A + B -> AB

– opposite of decomposition– small molecules are “made” into large

molecules– dehydration synthesis (condensation) is

the formation of a bond by the removal of water• opposite of hydrolysis

– anabolism • all the synthesis reactions in a cell

Types of Chemical Reactions• REVERSIBLE

– if A + B -> AB, then AB -> A + B– two reactions occurring simultaneously

• one decomposition, one synthesis

– at equilibrium, the rates of the two reactions are balanced, i.e. as one molecule of AB is produced, one is broken down

ACIDS AND BASES

• acids– release H+ ions in solution– produce solutions of pH’s less than 7– minimum pH (most acidic solution) = 1

• bases (alkalis)– combine with hydrogen ions– release OH- ions in solution– produce solutions with pH’s greater than 7– maximum pH (most basic [alkaline] solution) =

14

pH SCALE

• measures degree of acidity or alkalinity of a solution

• measures amount of hydrogen ions in a solution• one in 10, 000,000 (107) water molecules ionizes to

produce a H+ and an OH - ion• thus, numbers of hydrogen ions = numbers of

hydroxyl ions– solution is neither acidic nor basic– solution is neutral– solution has a pH of 7

Some Bottom Line Considerations

1. Life is carbon-based.2. That is, to make the compounds of

life, we start with carbon atoms.3. The major compounds of life are-

1. carbohydrates2. lipids3. proteins4. nucleic acids

Some Bottom Line Considerations…cont’d

1. To make carbohydrates we start with carbon atoms and add hydrogen and oxygen atoms.

2. To make lipids we start with carbon atoms and add hydrogen, oxygen, nitrogen, phophorous and sulfur atoms

– albeit not all of them to carbon.

Some Bottom Line Considerations…cont’d

1. To make proteins we start with carbon atoms and add hydrogen, oxygen, nitrogen and sulfur atoms.

2. To make nucleic acids we start with carbon atoms and add hydrogen, oxygen, nitrogen and phosphorous atoms

– Albeit not all of them to carbon.

Carbon Skeletons & Functional Groups

• GENERAL REMARKS– since carbon has four electrons in its outer shell it can

bond with four other atoms– the bonds are covalent and hence quite strong– usually carbon bonds with hydrogen, oxygen, nitrogen

or another carbon– carbon atoms can share two electrons with another

carbon atom or with an oxygen atom• double bond

General Remarks..cont’d

• carbon-carbon bonding makes possible long chains containing as many as 50 or more carbon atoms– chains may contain one or more “internal” double

bonds• carbon chains can form “rings” (cyclic

compounds)– cyclic compounds may contain one or more “internal”

double bonds– cyclic compounds may contain one or more atoms

other than carbon, e.g. oxygen or nitrogen

General Remarks..cont’d

• carbon chains make up the skeleton or backbone of organic molecules

• functional groups can be attached to the carbon chain, or the cyclic compound– functional groups are clusters of certain atoms that

always behave in certain way (see Table 2.4 on page 44)

General Remarks..cont’d

• So, given these considerations about carbon• And with the knowledge of “functional groups” • We can look at ---

Carbon Skeletons & Functional Groups

• GENERAL REMARKS– since carbon has four electrons in its outer shell it

can bond with four other atoms– the bonds are covalent and hence quite strong– usually carbon bonds with hydrogen, oxygen,

nitrogen or another carbon– carbon atoms can share two electrons with another

carbon atom or with an oxygen atom• double bond

General Remarks..cont’d

• carbon-carbon bonding makes possible long chains containing as many as 50 or more carbon atoms– chains may contain one or more “internal” double

bonds• carbon chains can form “rings” (cyclic

compounds)– cyclic compounds may contain one or more “internal”

double bonds– cyclic compounds may contain one or more atoms other

than carbon, e.g. oxygen or nitrogen

General Remarks..cont’d

• carbon chains make up the skeleton or backbone of organic molecules

• functional groups can be attached to the carbon chain, or the cyclic compound– functional groups are clusters of certain atoms that

always behave in certain way (see Figure 3.2, page 35)• molecules composed of only carbon and hydrogen

are do NOT have a charged portion, hence do not attract other molecules– nonpolar– hydrophobic (since they do not attract water)

General Remarks..cont’d

• carbon molecules contain functional groups may have a charged portion– polar molecules– since they attract water they are said to be hydrophilic

(“water loving”)

MOLECULES OF LIFE

• organic molecules– molecules containing carbon– macromolecules (“large molecules)

• made of long chains of carbon compounds• building blocks called monomers, I.e. “single

units”• monomers may be bonded together into

polymers, i.e.“many units”

CARBOHYDRATES• means “hydrated carbon”, i.e. carbon + water

– general formula = CH2O

– Made up of C,H and O

– simple carbohydrates are monomers• called monosaccharides, or sugars

– 6 carbon monosaccharides (C6H12O6)• called “hexoses”• glucose, fructose, galactose

– 5 carbon monosaccharides (C5H10O5)• ribose

• deoxyribose

Glucose

Fructose• May look 5-sided, but it has 6-Carbons, so

it is a hexose sugar

Galactose

• It may look a lot like glucose, but there are differences.

Glucose vs. Galactose

• Inquiring minds want to know ...

CARBOHYDRATES…cont’d

• complex carbohydrates– dimers

– two monomers (C12H22O11)

• glucose + glucose = maltose• glucose + fructose = sucrose• glucose + galactose = lactose

– polymers (polysaccharides)• starch

– polymer of glucose» straight chain

– plants– “amylose”

COMPLEX CARBOHYDRATES…cont’d

• glycogen – polymer of glucose– branched chain– animals

• stored in muscles and liver

COMPLEX CARBOHYDRATES…(cont’d)

• cellulose – plants– dietary fiber– straight chain

polymer of glucose– provides structural

support– Note the up/down

links at sharp angles between glucose molecules.

LIPIDS

• diverse in structure

• do not dissolve in water

• fats and oils – known as triglycerides

TRIGLYCERIDES

• composed of only three elements– C, H and O

• molecule of glycerol and three fatty acids– glycerol is a 3 carbon compound containing only

C, H and O– fatty acids

• long chains carbon and hydrogen with • saturated or unsaturated

FATTY ACIDS

• contain only C, H and O• saturated fats have saturated fatty acids• in animal fats• have hydrogen at every position along the

carbon chain• no double bonds

FATTY ACIDS (cont’d)

• unsaturated fats have unsaturated fatty acids

• in plant oils

• have one or more double bonds

SOAPS

• emulsifiers– emulsification = to break up into smaller

globules

• not lipids but help to emulsify lipids

• bile emulsifies fats in the digestive tract

PHOSPHOLIPIDS

• polar heads– negatively charged

• nonpolar tails • similar to triglycerides except that a

phosphate group replaces one of the fatty acids

• thus “elemental analysis” = C, H, O, P

STEROIDS

• made up of four fused carbon rings

• cholesterol is a precursor for many of them

• sex hormones are steroids– estrogen, progesterone, testosterone

PROTEINS• polymers of amino acids(monomers)• peptide bonds (covalent bonds) join amino

acids • 20 different amino acids used to make all

proteins• amino acids, hence proteins, contain only C,

H, O, N, • S

– P found in small numbers of very specialized nuclear proteins

PROTEINS (cont’d)

• serve a wide variety of functions in the body

• proteins have levels of organization – primary structure

• sequence of amino acids

PROTEIN STRUCTURE (cont’d)

• secondary structure – any twisting of the primary chain

• tertiary structure– any folding of the twisted chain

• quaternary structure – results when several polypeptides are

folded together

PROTEIN STRUCTURE (cont’d)

• shape of a protein is important to its function

• proteins can be denatured– unfolded and rendered nonfunctional

TYPES OF PROTEINS

• two types of proteins exist– globular proteins

• Enzymes and many non-enzyme molecules are globular

– fibrous proteins • have a rod-like shape• a structural function, like myosin in muscle

TYPES OF PROTEINS (cont’d)

• keratin – a fibrous protein found in skin, nails, and

hair

• collagen and elastin – fibrous proteins of tendons, ligaments,

bone, and cartilage

NUCLEIC ACIDS

• polymers of nucleotides– 3 parts

• 5 carbon sugar• N-containing base• phosphate group

• nucleotides contain C, H, O, N, P– hence the elemental analysis of nucleic acids is C,

H, O, N, & P

TYPES OF NUCLEIC ACIDS

• DNA– two “chains” of nucleotide polymers– genes– carry coded information for cell blueprint

• RNA– one “chain” of nucleotide polymers– “decodes” DNA– functions in protein synthesis

ATP

• adenosine triphosphate

• a carrier of energy

• our energy “currency”