CHAPTER 2CHAPTER 2

Basics of Life Chemistry

INTRODUCTIONINTRODUCTIONAll living things are composed of matter

– Any substance that has mass and occupies space

All matter made up of chemicals

– O, C, H, N, C, etcChemicals used for

– communication, defense, reproduction etc.

Features of matterFeatures of matterEnergy: all matter has energy: Life uses energy–Potential energy:

–Kinetic energy:

Composition of MatterComposition of MatterAtoms (e.g. H, O)

–Smallest unit of matter/building blocks

Form elements–Pure substances: one kind of atoms

Structure of an atom:Structure of an atom:Bohr ModelBohr Model

ProtonsNeutrons Electrons: form chemical bonds

– Orbits/energy levels

– insignificant weight

– form chemical bonds

Elements vary in Neutrons but not Elements vary in Neutrons but not protonsprotonsatomic number -> # of protons ( = # electrons)

– Constant (unique for an element)Atomic mass unit = mass of one protonNeutrons may vary for one element

– Isotope-Atoms of same element containing a different number of neutrons

Mass number = # protons + # neutronsAtomic weight: average weight of all isotopes

Compound Compound --

A substance formed by chemical union of atoms of 2 or more different elements in a specific ratio–E.g water: H2O

moleculemolecule --

smallest unit of a compound–water - H2O

–sucrose – C12H22O11

some are diatomic molecules–H2, O2, N2

Periodic Table of the ElementsPeriodic Table of the Elements - - Periodic Table of the ElementsPeriodic Table of the Elements - -

Provides information about elements– arrangement of elements by properties

– Name & chemical symbol for each element

– atomic number - # of protons (= # electrons)

– Atomic weight

What is a chemical bond?What is a chemical bond?

Attractive force that holds atoms of molecules together

ELECTRON DISTRIBUTION & chemical ELECTRON DISTRIBUTION & chemical bondsbonds

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

e-’s have Bohr model

– # 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…ELECTRON DISTRIBUTION…cont’dcont’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 MOLECULESFORMATION 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 BONDSTYPES 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 (charged atom)– called electrolytes

Sodium ChlorideSodium Chloride

–chlorine - 7 electrons in the outer orbit

–sodium - 1 electron in the outer orbit

–Na+ + Cl- -> sodium chloride NaCl

TYPES OF CHEMICAL BONDS…TYPES OF CHEMICAL BONDS…cont’d)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– methane

– polar covalent bond• unequal sharing of electrons between atoms

– water

Covalent bonds (cont)-Covalent bonds (cont)-

form proteins, carbohydrate, lipids (fats) and nucleic acids

hydrogen -hydrogen -atomic number is 1

– has 1 proton & 1 electronenergy level 1 – needs 2 electrons

– forms 1 covalent bond

– only H2 exists naturally

• H-H -> structural formula

• H2 -> empirical

helium –helium –atomic number is 2

–2 electronsenergy level 1 – fillednoble gas

carbon –carbon –atomic number is 6

– 6 electronsenergy level 1 – filledenergy level 2 – has 4: Forms

• 4 covalent single bonds (formed by sharing a pair of electrons)

hydrogen bondshydrogen bonds (not really) (not really)

Form mostly between molecules, do not bond atoms

Always between H & O; or H & NEach weakMany hydrogen bonds form very strong

structureswater as an example

strength of bonds –strength of bonds –

covalent > ionic > hydrogen

IONIC COMPOUNDSIONIC COMPOUNDS

AcidsBases Salts

pH Scale -pH Scale -

Measures acidity /alkalinity or– H ion conc.

pH Scale - ranges from 0 to 14pH 7 = neutral

pH Scale -pH Scale -high [H+] = low pH / acid

–< 7low [H+] = high pH / base

–>7

Summary: Define these termsSummary: Define these terms– Atom– Element– Molecule– Compound– Atomic mass unit– Atomic number– Chemical symbol– Atomic nucleus– Atomic weight– Acids– Bases– Salt

pH Proton Electron Neutron Ion Cation Anion Kinetic energy Chemical reaction Ionic Bond Covalent Bond Hydrogen Bond

Organic Chemistry, The Chemistry Organic Chemistry, The Chemistry of Lifeof Life

Organic Chemistry, The Chemistry Organic Chemistry, The Chemistry of Lifeof Life

Chapter 3

Inorganic molecules -Inorganic molecules - Inorganic molecules -Inorganic molecules -

do not contain carbon linked to H

ex: water, salt, sodium hydroxide

Organic molecules-Organic molecules-Organic molecules-Organic molecules-contain carbon linked to H and oxygen (N,

S, P also, but not always)– proteins

– lipids (fats)

– carbohydrates

– nucleic acids

Carbon / central atom Carbon / central atom can form 4 covalent bondsbonds spaced evenly | -- C -- | Can form long chainsCan combine with many other atoms

All organic Molecules have a All organic Molecules have a Carbon skeleton / backbone Carbon skeleton / backbone All organic Molecules have a All organic Molecules have a Carbon skeleton / backbone Carbon skeleton / backbone Linear or a ring (fig 3.3)

_________

Length & shape confers uniqueness

Functional groups attached– determines the chemical

property of the molecules

–

Functional groups -Functional groups -Amino group -

– -NH2

– found in amino acids and proteinsPhosphate group

– PO4

– found in phospholipidsSee figure 3.7

Formation of organic Formation of organic molecules-molecules-

Formation of organic Formation of organic molecules-molecules-

Monomer = single unit – amino acid

– GlucosePolymer / macromolecules

–Starch:• glu-glu-glu-glu…glu

Dehydration / SynthesisDehydration / Synthesis - -Dehydration / SynthesisDehydration / Synthesis - -

the linking together of monomers with covalent bonds

molecule of water removed energy requiringSee figure 3.8

Hydrolysis-Hydrolysis-Hydrolysis-Hydrolysis-unlinking of monomerswater molecule added

energy releasingSee figure 3.8

Carbohydrates - sugars and Carbohydrates - sugars and starchesstarches --

Carbohydrates - sugars and Carbohydrates - sugars and starchesstarches --

function -

– provides energy

– support – cellulose

– component of other organic molecule -• DNA-> deoxyribose sugar• RNA -> ribose sugar• ATP -> ribose sugar

Simple sugars: MonosaccharidesSimple sugars: Monosaccharides

Form complex CHO–glucose – (dextrose)

–fructose –

–galactose-

Simple sugars: Disaccharides -Simple sugars: Disaccharides -Simple sugars: Disaccharides -Simple sugars: Disaccharides -

lactose (milk sugar) ->– glucose + galactose

sucrose (table sugar) -> – glucose + fructose

Maltose (malt sugar)– Glucose + glucose

Polysaccharides - complex Polysaccharides - complex carbohydrates - carbohydrates - Polysaccharides - complex Polysaccharides - complex carbohydrates - carbohydrates -

Long chains of monosaccharides joined together

Examples are:

Starch -Starch - Starch -Starch -

Polymer of glucoseCHO/energy storage in plants

–amylopectin (trees shaped)

– amylose (straight)

–Figure 3.10

Glycogen -Glycogen - Glycogen -Glycogen -

“tree” shaped polymer of glucose

energy storage in animals–found in muscle and liver cells

–provides rapid bursts of energy

Cellulose -Cellulose -PolysaccharideCell walls of plant celluloseCannot be digested by humans : no

caloriesDigested by ruminants

Lipids–Lipids– Lipids–Lipids–

3 classes–true fats –

–phospholipids –

–steroids –fat -> solid at room temperatureoil -> liquid at room temperature

Consist of C, H, & small amounts ofConsist of C, H, & small amounts of OO - -

large, non-polar molecules – can not dissolve in water

formed by dehydration / synthesis

True (neutral) fats – True (neutral) fats –

function -function - True (neutral) fats – True (neutral) fats –

function -function - insulation -

– prevents loss of body heatcushion internal organsenergy storage -

– fat -> 9 calories per gram – sugar -> 4 calories per gram

Structure of true fats -Structure of true fats -Structure of true fats -Structure of true fats -

1, 2, or 3 fatty acids attached to glycerol

Fatty acid-Fatty acid-long carbon chaincarboxyl (-COOH)

group attached to the end

FATTY ACID: Fig. FATTY ACID: Fig.

Saturated Fatty AcidSaturated Fatty Acid

no double bonds / contains the maximum # of hydrogen atoms

from animal productsSolid at room temp

– examples: butter, lard

Unsaturated Fatty AcidUnsaturated Fatty Acidcontains C-C double bonds from plantsliquid at room temperature polyunsaturated fatty acids: many double bonds

– Ex: olive oil, soybean oilmonounsaturated fatty acids: one double bond

– Ex: sunflower oil, corn oil

Glycerol –Glycerol –3 C skeleton3 alcohol groups attached

–See page 56

Structure of lipidsStructure of lipids

Triglycerides–three fatty acids + one glycerol

–most abundant true fat in the body

Triglyceride: Triglyceride: Fig. 3.21Fig. 3.21

Omega –3 & 6 fatty acidsOmega –3 & 6 fatty acids

Essential fatty acidsUsed for growth & hormone prdndouble bond found after the 3rd

carbonAbundant in fish oil, soybeans

Hydrogenation -Hydrogenation - Hydrogenation -Hydrogenation -

Adding hydrogen to an unsaturated fat

solidifies the fatex: margarine

Phospholipids -Phospholipids - Phospholipids -Phospholipids -

1 Glycerol + 2 fatty acids + Phosphate cmpd

function - component of cell membranes

Steroids -Steroids - Steroids -Steroids - lipids without fatty acidsinterlocking rings

– cholesterol -• component of cell membranes• converted into bile salts (emulsify fat)• vitamin D

– hormones -• estrogen• testosterone

Proteins -Proteins - Proteins -Proteins -

function –structural -

•cell membranes

•muscle cells

•Hemoglobin

Protein function (cont) -Protein function (cont) -

regulation - –enzymes (organic catalysts)

–hormones- insulin, oxytocin

–antibodies - fight infection

Protein function (cont) -Protein function (cont) -Protein function (cont) -Protein function (cont) -

carriers - –lipoproteins - transport fats

• cholesterol

• triglycerides

• Phospholipids

Consist of –Consist of –Linked amino

acids (AA)Peptide bondsPolypeptide

chainOnly 20 AA

exist

Peptide bond: covalent bond Peptide bond: covalent bond between amino acidsbetween amino acids

Protein structure & Protein structure & OrganizationOrganization

Four levels of protein Four levels of protein organization -organization -

Four levels of protein Four levels of protein organization -organization -

primary - polypeptide chainsecondary - polypeptide chain

twists-– alpha helix (coil) - formed by

hydrogen bonds

– beta pleated sheet - formed by hydrogen bonds

Protein organization (cont) -Protein organization (cont) -

tertiary – 3 D– Folding of an

individual moleculequaternary – 4D

– interactions of individual 3D molecules

Changes in protein structure -Changes in protein structure -Changes in protein structure -Changes in protein structure -

sickle-cell anemia-–hemoglobin consist of 4

polypeptides–change in one amino acid causes

the hemoglobin to fold poorly –Forms a“sickle” shape under

increased oxygen demand

Denaturation-Denaturation-Denaturation-Denaturation-Change of a protein’s 3-D shapeBonds broken by

– heat, light, or pHnot reversible

–you can not unfry an egg!

Nucleic acids-Nucleic acids-Nucleic acids-Nucleic acids-function - component of DNA &

RNA–DNA - genetic code

–RNA - manufacturer of protein

Structure of nucleic acids -Structure of nucleic acids - Structure of nucleic acids -Structure of nucleic acids -

made up of nucleotides

Nucleotides -Nucleotides -

– 5- carbon simple suger• deoxyribose (DNA)• ribose (RNA)

– phosphate group– nitrogenous base

• Adenine• Guanine• Thymine • Cytosine• Uracil

NUCLEIC ACIDSNUCLEIC ACIDSDNA

–Genetic material–Nucleotides: building blocks

• 5-C sugar, deoxyribose• Phosphate• Nitrogenous Base• Adenine,Guanine,Thymine, Cytosine

NUCLEIC ACIDSNUCLEIC ACIDSDNA

– Double helix structure– Sugar-phosphate backbone– Bases complimentary paring

• A-T, C-G

– Coding strand• Protein synthesis

NUCLEIC ACIDSNUCLEIC ACIDSRNA

– Protein synthesis– Ribose sugar– Uracil base and no Thymine

3 forms of RNA– Messenger RNA : mRNA– Transfer RNA : tRNA– Ribosomal RNA : rRNA

SUMMARYSUMMARYChemistry of living things

– Based on Carbon

C atoms: all organic moleculesStructure of OM related to functionCommon OM

– CHO, Pns, Lipids, Nucleic acids