1

The ChemicalLevel of

Organization2.4-2.5

August 13, 2012

AgendaGeneral

HousekeepingReview

TerminologyQuiz

2.4 2.5

Chapter 2 Assignments Stations

Reading BuildingMolecules

Review• What is a free radical?

• What is the significance of the valence shell ofan atom?

• Compare the properties of ionic, covalent, andhydrogen bonds

• Compare potential energy and kinetic energy

• How do catalysts affect activation energy?

2.4 Inorganic Compounds & Solutions• Objectives

– Describe the properties of water and thoseof inorganic acids, bases, and salts

– Distinguish among solutions, colloids, andsuspensions

– Define pH and explain the role of buffersystems in homeostasis

Inorganic Compounds• Inorganic compounds are structurally simple

molecules that usually lack carbon - like thesalt potassium chloride (KCl)

Water• Water is the most important

and abundant inorganiccompound in all living systems

• Water’s most importantproperty is polarity, theuneven sharing of valenceelectrons that enablesreactants to collide to formproducts

• Sodium and Chloride ions dissolve in thepolar water molecules

Water as a Solvent• In a solution, the solvent dissolves the solute

• Substances which contain polar covalent bondsand dissolve in water are hydrophilic, whilesubstances which contain non-polar covalentbonds are hydrophobic

• The polarity of water and its bent shape allow it tointeract with several neighboring ions or molecules

• Water’s role as a solvent makes it essential forhealth and survival

Properties of Water• Water has a high heat capacity, meaning it can

absorb or release a relatively large amount of heatwith only a modest change in its own temperature

– This property is due to the large number ofhydrogen ions in water

– Heat of vaporization (amount of heat needed tochange from a liquid to a gas) is also high

– Evaporation of water from the skin removeslarge amounts of heat

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• Water serves as the medium for most chemicalreactions in the body

– May participate as a reactant or product in somereactions

– Hydrolysis involves the addition of water tobreak large molecules down into smallermolecules

– In Dehydration Synthesis, water is produced assmaller molecules join to form a larger molecule

• Water is a major component of mucus and otherlubricating fluids

Mixtures• A mixture is a combination of elements or

compounds that are physically blended together butare not bound by chemical bonds

• In a solution, a substance called the solvent dissolvesanother substance called the solute. Usually there ismore solvent than solute in a solution

– In our bodies, the most common solvent is water:

•We are 65-80% water

Colloids• A colloid differs from a solution mainly on the

basis of the size of its particles, with the particlesin the colloid being large enough to scatter light

• In a suspension, the suspended material may mixwith the liquid or suspending medium for sometime, but it will eventually settle out

Methods of Measurement• The concentration of a molecule is a way of

stating the amount of that molecule in solution• Percent gives the relative mass of a solute found

in 100 ml of solution (usually water)• A mole is just a convenient way of counting large

numbers of small things (like atoms or molecules)– 1 mole is 6.02 x 1023 representative particles

Inorganic Acids, Bases, & Salts• An acid is a substance that dissociates into H+ and

is considered a proton donor• A base is a substance that dissociates into OH-

and removes H+ from a solution (protonacceptor)

• Salts, when dissolved in water, dissociates intocations and anions, neither of which is H+ or OH-

• Acids and bases react with one another to formsalts

pH• pH = –log[H+]

– Concentration of H+ in moles/L

• It is a scale that runs from 0 to 14

• The pH scale is a logarithmic scale, not a linearscale– Because of the “negative” in the formula, the

lower the number, the higher the H+

concentration ([H+])• Because it is logarithmic, a change of two or three

pH units represents a change in the [H+] of 100 or1000– A solution with pH=1 is 100 times more

concentrated in H+ ions than a solution with apH=3

– A solution with pH=11 contains 1000 times lessH+ ions than a solution with a pH=8

• pH < 7 is acidic ([H+] > [OH-])

• pH > 7 is alkaline ([H+] < [OH-])

• A salt (like KCl) is neutral

Buffers• The pH values of different parts of the body are

maintained fairly constant by buffer systems,which usually consist of a weak acid and a weakbase

• Buffers convert strong acids and strong bases intoweak acids and weak bases– They do this by “hiding” excess H+ ions or

excess OH– ions as other molecules (likeHCO3

– )• The major buffer system in the body is carbonic

acid-bicarbonate buffer system

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2.5 Organic Compounds• Objectives

– Describe the functional groups of organicmolecules

– Identify the building blocks and functions ofcarbohydrates, lipids, and proteins

– Describe the structure and functions ofdeoxyribunucleic acid (DNA), ribonucleic acid(RNA), and adenosine triphosphate (ATP)

Organic Compounds• Organic compounds always contain

carbon and are usually large, complexmolecules

– Usually contain hydrogen

– Always have covalent bonds

• The chain of carbon atoms in an organicmolecule is called a carbon skeleton

• Hydrocarbons are carbons bonding tohydrogen

• Functional groups attach to the carbonskeleton

Functional Groups• Functional groups are certain molecular

configurations which are easy to recognize• They are found attached to the carbon

skeleton and impart certain properties tothe organic molecule

Macromolecules• Very large molecules are called macromolecules

– “Polymers” if all the monomer subunits aresimilar)

• Isomers have the same molecular formulas butdifferent structures

– Glucose & galactose are both C6H12O6

Carbohydrates• Carbohydrates provide most of the energy needed

for life and include sugars, starches, glycogen, andcellulose

• Some carbohydrates are converted to othersubstances which are used to build structures and togenerate ATP

• Other carbohydrates function as food reserves• Carbohydrates are divided into three major groups

based on their size: monosaccharides, disaccharides,and polysaccharides

• Monosaccharides are thesimplest sugars

– 5 carbon sugars areused in nucleic acids

– 6 carbon sugars are themost easily recognizablein our diet

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• Disaccharides are made by combining 2monosaccharides by removing a watermolecule (dehydration synthesis):- Glucose + Fructose = Sucrose- Glucose + Galactose = Lactose

• Polysaccharides are the largestcarbohydrates and may contain hundredsof monosaccharides

• The principal polysaccharide in the humanbody is glycogen, which is stored in theliver or skeletal muscles– When blood sugar level drops, the liver

hydrolyzes glycogen to yield glucosewhich is released from the liver into theblood

• Starches are polysaccharides formed fromglucose by plants

• Cellulose is a polysaccharide formed fromglucose by plants that cannot be digestedby humans

Lipids• Like carbohydrates, they contain carbon, hydrogen,

and oxygen

• Unlike carbohydrates, they do not have a 2:1 ratioof hydrogen to oxygen

• They have few polar covalent bonds, which makesthem hydrophobic and mostly insoluble in water

• They combine with proteins (lipoproteins) fortransport in blood

• The simplest lipids are the fatty acids

– Used to synthesize triglycerides and phospholipids, andcan be catabolized to generate ATP

– Consists of a carboxyl group and a hydrocarbon chain– Saturated fatty acids contain only single covalent bonds

(saturated with H atoms)– Unsaturated fatty acids contain one or more double

covalent bonds and has a kink/bend at the site of thedouble bond

• Triglycerides are the most plentiful lipids in thebody and provide protection, insulation, andenergy (both immediate and stored)

• At room temperature, triglycerides may be eithersolid (fats) or liquid (oils)

• Triglyceride storage is virtually unlimited

• Excess dietary carbohydrates, proteins, fats, andoils are deposited in adipose tissue as triglycerides

• Triglycerides provide more than twice as muchenergy per gram as either carbohydrates orproteins

• Consists of a glycerol molecule and threefatty acid molecules

• Fat is a triglyceride that is a solid at roomtemperature

– Mostly saturated because the fatty acids lackdouble bonds in their hydrocarbon chains

• Oil is a triglyceride that is a liquid at roomtemperature

– Mostly unsaturated and can be eithermonounsaturated or polyunsaturated

• Phospholipids are important membranecomponents

• Both polar and nonpolar regions make themsoluble in both water and fats– This is called amphipathic, they are both

hydrophilic and lipophilic– They have a polar head formed from a

phosphate group (PO4-3) and a glycerol

molecule (forms H-bonds with water), and 2nonpolar fatty acid tails that interact only withlipids

• Phospholipids have a polar head and 2non-polar tails

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• Steroids are lipids molecules that have fourrings of carbon atoms– Sex hormones

– Bile salts

– Some vitamins

– Cholesterol, which serves as an importantcomponent of cell membranes and asstarting material for synthesizing othersteroids

• Steroids are based onthe lipid cholesterolmolecule

– They include themolecules used assex hormones, aswell as otherhormones used incoping with stress(cortisol)

• Eicosanoids are lipids derived from a 20-carbonfatty acid called arachidonic acid

– Prostaglandins modify responses to hormones,contribute to inflammatory response, preventstomach ulcers, dilate airways to the lungs

– Leukotrines participate in allergic andinflammatory responses

• Fat-soluble vitamins such as beta-carotene,vitamins D, E, and K, and lipoproteins

Proteins• Proteins are large

molecules that containcarbon, hydrogen, oxygen,and nitrogen

• The normal adult body is12-18% protein

• Proteins areconstructed fromcombinations ofdifferent amino acids

• 20 human amino acids

– All amino acids (a.a.)have the same basicstructure - only the“R” group changes

• Dipeptides are formed from 2 amino acidsjoined by a covalent bond called a peptidebond

– This process involves dehydration synthesis

• Polypeptide chains contain 10 to 2000 aminoacids

• There are 4 levels at whichproteins are structurallyorganized :– Primary (10)– Secondary (20)– Tertiary (30)– Quaternary (40)

• The resulting shape of theprotein greatly influences itsability to recognize and bindto other molecules

• Primary Structure is the unique sequence of a.a.that are linked by covalent peptide binds to forma polypeptide chain

• Secondary Structure is the repeated twisting orfolding of neighboring a.a. in the polypeptide chain

• Tertiary Structure is the 3-D shape of apolypeptide chain and determines how it willfunction

• Quarternary Structure is the arrangement ofindividual polypeptide chains relative to oneanother

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• Fibrous proteins are insoluble in water and theirpolypeptide strands form long strands that areparallel to each other

– Structural function

• Globular proteins are more or less soluble inwater and their polypeptide chains are spherical inshape

– Metabolic functions

• Denaturation (loss of protein structure) by ahostile environment causes loss of itscharacteristic shape and function– An egg white turning solid white when

exposed to high temperatures is an exampleof protein denaturation

Enzymes• Enzymes are special proteins that catalyze (speed

up) metabolic reaction in all living cells

• Some enzymes consist of two parts

– An apoenzyme protein portion

– A non-protein portion called a cofactor

•Metal ions or coenzymes

• The substrate is the substance upon which anenzyme has its effect

– In this regard, enzymes are highly specific

• Enzymes are subject to a variety of cellularcontrols

• Enzymes speed up chemical reactions byincreasing frequency of collisions, loweringactivation energy, and properly orienting collidingmolecules

Nucleic Acids• Nucleic acids are huge organic molecules composed

of monomeric nucleotides

– They contain carbon, hydrogen, oxygen, nitrogen,and phosphorus, and form the principlemolecules that contain our genetic code

•DNA and RNA

• Nucleic acids are universal inliving things

– These molecules carry geneticinformation asdeoxyribonucleic acid (DNA)and ribonucleic acid (RNA)

• By controlling the formation ofproteins, the genetic coderegulates most of the activitiesthat take place in our cellsthroughout a lifetime

• DNA molecules remain inside the nucleus ofcells and are the “master” template of ourgenetic code

• RNA is a slightly different nucleic acidmacromolecule that relays instructions fromthe nucleus to guide assembly of amino acidsinto proteins in the cytoplasm

• The basic units of nucleic acids arenucleotides, composed of a nitrogenousbase, a pentose sugar, and a phosphate

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• The nucleotides ofDNA and RNA arejoined to a “sugar-phosphate” backboneto make a long chain

• There are 2 sugar-phosphate strands ofDNA, joined in themiddle by hydrogenbonds from onenucleotide to another

• RNA structure differs from DNAin that it is single stranded (insteadof double stranded), ribosereplaces the sugar deoxyribose,and uracil is the nitrogenous basethat replaces thymine

• There are 3 types of RNA withinthe cell, each with a specificfunction:

– Messenger RNA

– Ribosomal RNA

– Transfer RNA

• Nucleic acids are also used in making a veryimportant energy-carrying molecule in the bodycalled adenosine triphosphate (ATP)

• ATP is used as a temporary storage of energythat is being transferred from exergoniccatabolic reactions to cellular activities

Adenosine Triphosphate• ATP is often called the “molecular unit of

currency” of intracellular energy transfer• Synthesis of ATP is catalyzed by the ATP

synthase enzyme which adds the terminal highenergy phosphate bond (often depicted as ~Pas opposed to a regular –P bond) to ADP– Energy from 1 glucose molecule is used

during both anaerobic and aerobic respirationto create 36 to 38 molecules of ATP

• When needed, the high energy phosphate ishydrolyzed by the enzyme ATPase to release thestored energy, leaving ADP (adenosine diphosphate)

• A human will use up his/her body weight of ATP overthe course of the day

– This means that each ATP molecule is recycled 1500times during a single day

• Cellular Respiration consists of two phases

– The Anaerobic Phase does not require oxygenand glucose is partially broken down by a seriesof catabolic reactions into pyruvic acid

•Each glucose molecule that is converted intoa pyruvic acic molecule yields two ATP

– The Aerobic Phase completely breaks down aglucose molecule into carbon dioxide andwater, in the presence of oxygen

•Generates heat and 36 or 38 ATP molecules

Clinical Connections• Fatty Acids in Health and Disease

– Essential Fatty Acis (EFAs) cannot be made by the humanbody and must be obtained from foods or supplements

– Omega-3 fatty acids, omega-6 fatty acids, and cis-fatty acids

– Omega-3 and omega-6 are polyunsaturated fatty acids thatare believed to work together to promote health

• Lowers total cholesterol, raises HDL, lowers LDL,decreases bone loss by increasing calcium utilization,promotes wound healing, improves mental function

• Omega-3: flaxseed, fish oils, walnuts

• Omega-6: cereal, bread, white rice, eggs, liver

– Cis-fatty acids are used by the body to produce hormone-like regulators and cell membranes• However, when hydrogenated, they are changed to

unhealthy trans-fatty acids• The H atoms are on opposite sides of the double bond

in an unsaturated fat• Hydrogenation is used to make vegetable oils solid at

room temperature and less likely to turn rancid• Found in commercially baked goods, some margarines,

and fried foods• Increases total cholesterol, decreases HDL, increases

LDL, increases triglycerides, increases the risk of heartdisease and other cardiovascular diseases

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• Artificial Sweeteners

– Aspartame (NutraSweet and Equal)– Saccharin (Sweet ‘N Low)

– Sucralose (Splenda)

– 100’s of times sweeter than sucrose

– Zero calories because they pass through thebody without being metabolized

– Does not cause tooth decay

Assignments• Finish Chapter 2 Review WS (due next class)

• Read Sections 3.1 - 3.2• Rank your top five choices for your Research

Paper

• Mid-Term Assessment #1 in one week!– On Chapters 1 & 2