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ChemistryChapter 2

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Learning Objectives

• Describe what atoms are, their structure, and how they bond.

• Understand water’s features that help it support all life.

• Describe carbohydrates—their structure and function.

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• Describe lipids—their structure and function.

• Describe proteins—their structure and function.

• Describe nucleic acids—their structure and function.

Learning Objectives

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2.1: Everything is made of atoms

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• element - substance that cannot be broken down chemically into any other substances

• atom - matter that cannot be subdivided any further without losing its essential properties

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“CHONPS”

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2.2: An atom’s electrons determine

how (and whether) the atom will bond with

other atoms.

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What characteristic of an atom gives it its chemical properties?

1. the number of protons2. the number of neutrons3. the number of electrons4. the number of electrons in its outer

orbital

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2.3 Atoms can bond together to form molecules or

compounds.

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CHEMICAL BONDS• Covalent• Ionic• Polar Covalent• Hydrogen• Metallic

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Covalent Bonds

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Ionic Bonds

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Ionic Bonds

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A sodium ion is positively charged (+1). How many electrons did it originally have in its outer orbital as a sodium atom?1. 12. 23. 34. 75. 6

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A chloride ion is negatively charged (1). How many electrons did it originally have in its outer orbital as a chlorine atom?

1. 12. 23. 34. 75. 6

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Potassium chloride (KCl) is formed using ionic bonding. Potassium ions have a net positive charge (+1). Chloride ions have a net negative charge (1). How many electrons were in the outer orbital of the potassium (K) and chloride (Cl) atoms?1. K=7; Cl=72. K=1; Cl=63. K=7; Cl=64. K=1; Cl=7

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Polar Covalent Bonds

• electrons shared by the atoms spend a greater amount of time, on average, closer to one nucleus than the other

• due to geometry of molecule and electronegativity differences

• result is a charge separation in the molecule, where one part of the molecule has a partial negative charge and one part has a partial positive charge

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Polar Covalent Bonds• molecule is not an ion (no excess of

protons or electrons)• water is the most common but not the only

molecule that can have polar covalent bonds

• other molecules that have polar covalent bonds are peptide bonds and amines

• the biological consequence of polar covalent bonds is that these kinds of bonds can lead to the formation of a weak bond called a hydrogen bond

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Polar Covalent Bonds

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Hydrogen Bonds• formed when a charged part of a molecule

having polar covalent bonds forms an electrostatic interaction with a substance of opposite charge

• molecules that have nonpolar covalent bonds do not form hydrogen bondsclassified as weak bonds because they are easily and rapidly formed and broken under normal biological conditions

• under the right environmental conditions, any compound that has polar covalent bonds can form hydrogen bonds

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Hydrogen Bonds

• important in biological systems• explains many of the properties of

water• used to stabilize and determine

the structure of large macromolecules like proteins and nucleic acids

• involved in the mechanism of enzyme catalysis

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BUT WAIT, THERE’S MORE…

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Metallic Bonds

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2.4 A molecule’s shape gives it unique characteristics.

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•often determines the molecule’s function•enables physical properties such as taste and smell

Molecular Shape

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Discovering C*A*S*T

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2.5 Hydrogen bonds make water cohesive2.6 Water has unusual properties that make it

critical to life

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• All life on earth depends on water; organisms are made up mostly from water and require it more than any other molecule.

• Hydrogen bonding among water molecules gives water several important properties that contribute to its important role in the biology of all organisms.

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States of Water

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Cohesion & Adhesion•Cohesion – water is attracted to other water •Adhesion – water is attracted to other materials

•oxygen end of water has a negative charge •hydrogen end has a positive charge•hydrogens of one water molecule are attracted to oxygen of another water molecule • this attractive force is what gives water

its cohesive and adhesive properties

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Surface Tension•cohesion of water molecules at the surface of a body of water•all the water molecules on the surface of a quantity of water (a bead, cup, pond, etc.) are 'holding' each other together, creating surface tension

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Surface Tension•Surface tension allows water striders to 'skate' across the top of a pond. •Many objects are heavier than water, but because of surface tension, the water is able to hold up the metal.•Surface tension is not the force that keeps boats floating.

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Archimedes’ Principle•an object is immersed in a fluid is buoyed up by a force equal to the weight of the fluid displaced by the object•applies to object of all densities• density of object > density of fluid object will

sink• density of object = density of fluid object will

neither sink nor float• density of object < density of fluid object will

float•note: buoyant force does not depend on weight or shape of submerged object, only on weight of displaced fluid

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Capillary Attraction

•related to adhesive properties of water•click here for demonstration• water 'climbs' up the straw as the water

molecules are attracted to the straw molecules• when one water molecule moves closer to the

straw molecules the other water molecules (which are cohesively attracted to that water molecule) also move up into the straw.

•limited by gravity and size of straw; thinner straw/tube the higher up capillary action will pull the water means water will travel higher

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Low Density as a Solid

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Coastal vs. Inland Climate•Large bodies of water, especially oceans, can absorb huge amounts of heat from the sun during warm times of the year, reducing temperature increases on the land. •Similarly, during cold times of year the ocean slowly cools, giving off heat that reduces the temperature drop on shore.

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Why don’t oceans freeze as easily as fresh water lakes?

•Because there is so much salt dissolved in oceans, many of the water molecules have their positively charged sides all facing the Cl ions. •Simultaneously, many molecules of water are turned the other way: with their negatively charged sides facing the Na+ ions. •Consequently, the orderly lattices of hydrogen bonds cannot form in salt water, and it does not freeze well.

Fish live in water. What property of water is important for the survival of fish during the winter?

1. Cohesion2. Heat capacity3. Ice floats4. Water is a good solvent

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Summary – Properties of Water

CohesionAdhesion

Surface tensionCapillary Attraction

Archimedes’ PrincipleHigh heat capacity

Low density as a solid

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2.7 Living systems are highly sensitive to acidic and basic conditions

Hydrogen Ions and Hydroxide Ions

Ionized Hydroxide Molecule

OH -

Non-Ionized Water Molecule

O O

H H H

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H2O

In pure water, the amount of H+ and OH must be exactly the same; each time a water molecule splits, one of each is produced. But in some fluids containing other dissolved materials, the fluid can have more H+ or more OH.

pH Scale

The amount of H+ in a solution is a measure of its acidity and is called pH.

Acids – pH < 7.0

Bases – pH > 7.0

Neutral – pH = 7.0

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H+ Ions and Acids

• H+ very reactive• Example: H+ can bind with atoms in metals,

causing them to corrode• Acids can donate H+ to other chemicals• Stomach acid• helps to kill most bacteria that you ingest• enhances breakdown of chemicals in food • enhances efficiency of digestion and absorption

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Bases

• Low H+; High OH

• Baking soda, Alka-seltzer, milk of magnesia

• Antacids• OH ions bind with excess H+ ions, neutralizing the acid

• Household cleaners

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Which statement is true when comparing lemon juice (acidic) to baking soda (basic)?

1. Lemon juice has more OH compared to baking soda.

2. Lemon juice has more H+ compared to baking soda.

3. Lemon juice and baking soda both have an equal amount of OH and H+.

4. Baking soda has more H+ when compared to lemon juice.

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Buffers

• quickly absorb excess H+ ions to keep a solution from becoming too acidic, OR

• quickly release H+ ions to counteract any increases in OH concentration

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Blood pH

•usually 7.4•Since most cellular reactions produce or consume H+ molecules, there ought to be great swings in the pH of our blood • our bodies can’t tolerate such swings• Most chemicals that aid in chemical

reactions in blood/cells stop functioning well if pH swings by less than .5

•buffers quickly absorb/release excess H+ ions to keep blood pH at proper levels

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Test 2a

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Macromolecules•Life on earth is carbon based• large molecules found in cells all contain

carbon.•Why is carbon so important?• it can form 4 covalent bonds with other

atoms•Carbon can be thought of as the wheel in a tinkertoy set to which other components are attached • they can be joined by single or double bonds

and connect in chains or rings, making carbon extremely versatile

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Macromolecules1. Carbohydrates

• composed mainly of carbon, hydrogen and oxygen in a CH2O proportion

• polymers of simple sugars• important as:

• short term energy storage molecules (simple sugars such as glucose and fructose

• long term energy storage molecules (starches and glycogen)

• structural molecules (e.g. cellulose, which is found in all plant cell walls)

• important components of DNA and RNA

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Macromolecules2. Lipids• defined by their solubility

• insoluble in polar solvents (such as water), but will dissolve in non-polar solvents

• composed of fatty acids and glycerol• non-polar• fats, oils, waxes, steroids• function as:

• energy storage molecules• insulation and protection for internal organs• lubricants • hormones

• phospholipids are the major structural elements of membranes

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Macromolecules3. Proteins• polymers of amino acids•important biological functions include:• support• hormones• blood proteins• receptor sites on membranes•movement• defense• enzymes

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Macromolecules4. Nucleic Acids• DNA and RNA, the two nucleic acids, are

polymers of nucleotides• nucleotide• phosphate• 5 carbon sugar (deoxyribose )• nitrogenous base – adenine (A),

cytosine (C), guanine (G), and thymine (T)

• RNA: sugar is ribose, bases are A, C, G, and uracil (U) instead of T

If you were going to build a large macromolecule or polymer it needs to be strong.  What type of chemical bond do you think would work best for building macromolecules?

1. Covalent

2. Ionic

3. Hydrogen

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2.8 – 2.11 Carbohydrates

Energy is in the chemical bonds!

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•carbohydrates function well as fuels because their many carbon-hydrogen bonds store a great deal of energy•these C-H bonds are easily broken and organisms can capture the energy released when the bond is broken and put it to use

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Carbohydrates - Monosaccharides

•simple sugars• glucose, fructose, galactose

•glucose is extremely important • provides energy when broken down by the process

known as cellular respiration• crossroad of many chemical reactions• other molecules such as amino acids and fatty acids

can be synthesized from glucose • many molecules can be broken down to form

glucose• brain cannot store glucose, must be constantly

supplied with it by our blood• if supply stops for too long, brain cells will begin to

die

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Carbohydrates - Disaccharides•formed when two monosaccharides are joined together by a reaction known as a dehydration (condensation) synthesis

•water is removed, thus the name "dehydration”

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

•enzyme is required to make the reaction occur (more about enzymes later)

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Carbohydrates - DisaccharidesClick here to learn more about dehydration synthesis

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Carbohydrates - Disaccharides•reaction occurs in the reverse direction when you digest maltose, sucrose or other carbohydrates•water is added and the two monosaccharide molecules are split apart by an enzyme different from the one used in the dehydration synthesis•splitting apart reaction is called hydrolysis

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Carbohydrates - Polysaccharides•poly = many, saccharide = sugar•made of many sugar molecules joined together by dehydration synthesis reactions•many polysaccharides, including starch, glycogen, cellulose and chitin •all are made of many repeating units of glucose molecules•differ from each other:• amount of branching of the molecules• way in which molecules are connected to

each other • addition of amino groups to the glucose

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Starch•long term energy storage form of glucose in plants•found in abundance in the grains we eat, (rice, wheat, barley and rye) and in many vegetables, such as potatoes and corn•diagram shows part of a molecule of the starch amylose

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Glycogen•animal energy storage form of glucose•glucose molecules linked in the same way as in starch•molecules tend to be larger and much more branched than starch molecules •found in liver and muscles of animals•Humans - if supply of glucose in blood is sufficient, glucose will be polymerized into glycogen•excess glucose (not used for glycogen) is converted into fat

What is “carb-loading”?

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method by which athletes can, for a short time, double or triple the usual amount of glycogen that is stored in their muscles and liver, increasing the amount of fuel available for extended exertion and delaying the onset of fatigue during an endurance event

What is “carb-loading”?

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•two phases: depletion and loading•depletion begins 6-7 days before a competition• combination of a super-low carbohydrate

intake and exhaustive exercise • depletes glycogen in the muscles

•loading begins 2 days before the competition• super-high carbohydrate diet is combined with

reduced exercise • produces a higher blood glucose than is

necessary, so that much of the excess glucose is stored as glycogen

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Glycogen•plays a role in the initial rapid weight loss people experience when dieting•when caloric intake is reduced, body burns more calories it consumes• body must utilize stored forms of energy•most accessible molecules that can be broken down for energy in the absence of sufficient sugar in the bloodstream are glycogen molecules

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Glycogen•BUT, large amounts of water are bound to glycogen (every ounce of stored glycogen has as much as four ounces of water bound to it!•as glycogen is removed from the tissue, so too is water•this accounts for initial dramatic weight loss that occurs before your body resorts to utilizing stored fat, at which point the rate of weight loss slows considerably

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Cellulose•differs from starch and glycogen in the way in which glucose molecules are linked together•compare diagram below with that of starch

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Cellulose•position of hydrogen on 1st carbon atom differs•gives the two carbohydrates very different properties• amylose - water soluble, easily digested• cellulose - tough fibrous polymer of glucose, found in plant cell walls

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Cellulose•animals don’t have enzyme to break down cellulose• cannot be digested • instead, ingested cellulose is eliminated as fiber• termites (eat wood) depend upon microorganisms in their digestive tracts to break down cellulose

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Chitin

•differs from cellulose by having amino groups (NH2) attached to the glucose molecules•forms exoskeleton of all arthropods (e.g. insects, spiders, lobsters and crabs)

•made of glucose molecules linked in the same as in cellulose, making it equally indigestible.

Chemical Fuel

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•many disaccharides and polysaccharides are important sources of fuel•disaccharides and polysaccharides must energy can be released from their bonds. •sucrose is a disaccharide composed of two simple sugars, glucose and fructose, linked together but humans can’t directly utilize sucrose; they must first must break the bond linking glucose and fructose

Chemical Fuel

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•now the individual monosaccharides be broken down into component atoms and energy from broken bonds can be harvested and used

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2.12 – 2.14 Lipids

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Lipids•macromolecules with several functions, including energy storage•insoluble in water because they consist mostly of hydrocarbons, which are nonpolar•nonpolar molecules (or parts of molecules) tend to minimize contact with water and are considered hydrophobic•lipids cluster together when mixed with water, never fully dissolving•molecules that readily form hydrogen bonds with water, on the other hand, are considered hydrophilic

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Fats are tasty molecules too plentiful in our diets.

• Glycerol: “head” region

• Fatty acid “tails”

• Triglycerides – fat in most foods• If solid @ room temp:

FAT• If liquid @ room temp:

OIL

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Fat molecules contain much more stored energy than carbohydrate molecules

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•chemical breakdown of fat molecules releases significantly more energy than the same quantity of carbs•1 gram carbohydrates = 4 calories energy•1 gram fat = 9 calories energy

Fat molecules contain much more stored energy than carbohydrate molecules

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•Organisms evolving in an environment of uncertain food supply will build the largest surplus by consuming molecules that hold the most amount of energy in the smallest mass•This feature helped humans to survive millions of years ago, but today puts us in danger from the health risks of obesity now that fats are all too readily available

Saturated and Unsaturated Fats

• health considerations of saturated fats

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Things to think about…•Chocolate chip cookie recipes call for some lipids; how will the “chewy-ness” of the cookies differ depending on whether you use butter or vegetable oil as the lipid? •Which cookies will be healthier? •Many snack foods contain “partially hydrogenated” vegetable oils; why might it be desirable to add hydrogen atoms to a vegetable oil?•What are trans fats?•Olestra is a recently developed “fake fat” chemical that gives foods the taste of fat, without adding the calories of fats; what chemical structure might make this possible?

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Things to think about…•By attaining just the right degree of saturation, it is possible to create foods near the border of solid and liquid, like chocolate, that “melt in your mouth”. •Unfortunately, hydrogenation makes the food less healthful because the body is less likely to break them down, they are more likely to accumulate in the blood vessels, increasing risk of heart disease.

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Things to think about…•hydrogenation of unsaturated fats creates trans fats• trans fats cause your

body to produce more cholesterol• raises risk of heart

disease• reduces body’s

production of a type of cholesterol that protects against heart disease

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Steroid Hormones• estrogen influences

memory and mood (M/F)• testosterone stimulates

muscle growth• athletes often take

synthetic variants of testosterone to increase their muscularity

• usage often accompanied by dangerous side effects• extreme aggressiveness • high cholesterol• cancer

• nearly all athletic organizations have banned their use

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Phospholipids and Waxes• phospholipids : major component of cell

membrane• waxes• strongly hydrophobic• resemble fats but have only one long-chain

fatty acid, linked to glycerol head• fatty acid chain is highly nonpolar, waxes

strongly hydrophobic• natural coating on surface of many plants,

insects, birds

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2.15 – 2.18 Proteins

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Unique combinations of 20 amino acids are strung together, like beads on a string, and the resulting protein has a unique structure and chemical behavior.

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Amino Acids• side chain is the unique part• simplest amino acid – glycine – side chain is

simply a hydrogen atom • other amino acids – side chain is 1-4 CH3 groups • most side chains include both hydrogen and

carbon; a few include nitrogen or sulfur atoms • side chain determines an amino acid’s chemical

properties, such as whether the amino acid molecule is polar or nonpolar

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Proteins• side chain is the unique part• simplest amino acid – glycine – side chain is

simply a hydrogen atom • other amino acids – side chain is 1-4 CH3 groups • most side chains include both hydrogen and

carbon; a few include nitrogen or sulfur atoms • side chain determines an amino acid’s chemical

properties, such as whether the amino acid molecule is polar or nonpolar

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Proteins are an essential dietary component

• elements of dietary proteins – especially nitrogen – are essential to constant growth, repair, and replacement in the body

• as protein is digested, the body collects amino acids needed for various building projects

• ALSO, proteins also store energy in their bonds and can be used to fuel living processes

• protein requirements vary• most individuals: need 40-80 g/day• bodybuilders: ≥ 150 g/day• pregnant or nursing women also need a

considerable amount of dietary protein

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Proteins are an essential dietary component

• each protein: different composition of amino acids• some are manufactured by the

body • others must come from diet• 8 of 20 amino acids are essential amino acids

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Proteins are an essential dietary component

• MDR’s on food labels do not take into account the amino acid composition of the protein in that food item

• For this reason, we shouldn’t just speak of needing “x grams of protein per day;” we need to consume all of the essential amino acids every day

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Proteins are an essential dietary component

• complete proteins – all 8 essential amino acids• animals products s/a milk, eggs, fish,

chicken• incomplete proteins – do not have

all essential amino acids • most vegetables, fruits, and grains

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Proteins are an essential dietary component

• varied diet is necessary so that all essential amino acids are consumed

• two incomplete but complementary proteins can provide all essential amino acids• traditional dishes in many

cultures• corn and beans

(Mexico)• rice and lentils (India)• rice and black-eyed

peas (southern U.S.)

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Protein functions are influenced by their three-dimensional shape

• proteins formed by linking individual amino acids together with a peptide bond• amino group of one amino acid is

bonded to the carboxyl group of another

• 2 amino acids = dipeptide• several amino acids = polypeptide

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Protein structure - summary112

Primary Structure• The sequence of amino acids

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Secondary Structure• Hydrogen bonding

between amino acids

• The two most common patterns:• twist in a corkscrew-

like shape• zig-zag folding

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Tertiary Structure

o Folding and bending of the secondary structure

o Due to bonds such as hydrogen bonds or covalent sulfur-sulfur bonds.

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Quaternary Structure• When two or more

polypeptide chains are held together by bonds between the amino acids on the different chains.

• Hemoglobin

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Denaturation• For proteins to function properly, they must

retain their three-dimensional shape. • When an egg is cooked, heat breaks the

hydrogen bonds giving the protein its shape. • The proteins in the clear egg white unfold,

losing their secondary and tertiary structure. • Disruption of protein folding is called

denaturation.• Almost any extreme environment

will denature a protein.

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hair texture depends on 1 - 3 structure; genetically controlled

Enzymes• proteins that initiate and speed up

chemical reactions• emerge in their original form when

the reaction is complete and thus can be used again and again

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“Misspelled” Proteins• Incorrect amino acid sequence

• Active site disruptions

• Phenylketonuria: inability to break down phenylalanine (amino acid)

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“Misspelled” Proteins123

Nucleic acids are macromolecules that store information

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Two Types of Nucleic Acids• Deoxyribonucleic

acid (DNA)

• Ribonucleic acid (RNA)

• Both play central roles in directing the production of proteins

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Information Storage

• information in a molecule of DNA is determined by sequence of bases

• each time sequence changes, so too does the protein for which the sequence codes

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DNA holds the genetic information to build an organism

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James Watson & Francis Crick, 1953

Base-Pairing (Chargaff)

• Erwin Chargaff, 1950• A pairs with T• G pairs with C

• What is the complimentary strand to this strand: CCCCTTAGGAACC?

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Base-Pairing

• sequence of base pairs that codes for a particular protein may be anywhere from a hundred bases long to several thousand

• human genome - three billion base pairs

• DNA - generally in nucleus

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DNA Game

• Click here to play the DNA game

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RNA is a universal translator, reading DNA and directing protein production

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RNA is a universal translator, reading DNA and directing protein production

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•process of building a protein from a DNA sequence is not direct •uses a “middle man” – RNA •segments of the DNA are read off, directing the production of short strips of RNA that contain the information from the DNA about the amino acid sequence in a protein•RNA moves to another part of cell, directs piecing together of amino acids into a three-dimensional protein•more detail in Chapter 5

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Two Types of Nucleic Acids134

thymine (T)deoxyribose

double strand

uracil (U)ribose

single strand

A, G, Cnucleotide – sugar, phosphate, base