Chemistry, Water, and Biochemsitry The Organic Molecules “You are what you eat!”

Chemistry, Water, and Chemistry, Water, and BiochemsitryBiochemsitry

The Organic MoleculesThe Organic Molecules

““You are what you eat!”You are what you eat!”

Biochemistry Biochemistry Preview/ReviewPreview/Review

90 naturally occurring elements on Earth’s crust90 naturally occurring elements on Earth’s crust 11 are common to living organisms11 are common to living organisms 20 found in trace amounts20 found in trace amounts 4 elements make up approximately 96.3% of 4 elements make up approximately 96.3% of

the total weight of the human body:the total weight of the human body: nitrogennitrogen carboncarbon oxygenoxygen hydrogenhydrogen

In varying combinations and amounts, these In varying combinations and amounts, these four elements make up mostly all of the four elements make up mostly all of the compounds found in living thingscompounds found in living things

Elements by Mass in the Elements by Mass in the Human BodyHuman Body

Oxygen: 65%Oxygen: 65% Carbon: 18.5%Carbon: 18.5% Hydrogen 9.5%Hydrogen 9.5% Nitrogen: 3.3%Nitrogen: 3.3% Phosphorus: 1.0%Phosphorus: 1.0% Sulfur 0.3%Sulfur 0.3% Sodium: 0.2%Sodium: 0.2% Magnesium: 0.1%Magnesium: 0.1% Silicon: traceSilicon: trace Fluorine: traceFluorine: trace

C.H.N.O.P.

Chemical Bonds: Hydrogen Chemical Bonds: Hydrogen BondsBonds

Hydrogen bonds are a type of weak chemical bond formed when the partially positive hydrogen atom participating in a polar covalent bond in one molecule is attracted to the partially negative atom participating in a polar covalent bond in another molecule or in another part of the same macromolecule

Properties of WaterProperties of Water

Water is unique in that Water is unique in that it is the only natural it is the only natural substance that is found substance that is found in all three states — in all three states — liquid, solid (ice), and liquid, solid (ice), and gas (steam) — at the gas (steam) — at the temperatures normally temperatures normally found on Earth. found on Earth.


Water is a polar molecule. A polar covalent bond is an

attraction between atoms

that share electrons unequally

because the atoms differ in

electronegativity. The shared

electrons are pulled closer to

the more electronegative atom,

making it partially positive.


Water freezes at 0oC (32o F) and boils at 100o C (212o F) at sea level, (but 186.4° at 14,000 feet). In fact, water's freezing and boiling points are the baseline with which temperature is measured.

Water is unusual in that the solid form, ice, is less dense than the liquid form, which is why ice floats.

Water expands upon freezing. Water molecules is an ice crystal are spaced relatively far apart because of hydrogen bonding. Floating ice insulates the water below and prevents seas and lakes from freezing solid.


• Water has a high specific heat Water has a high specific heat index.index. Hydrogen bonds absorb heat Hydrogen bonds absorb heat when they break, and release heat when they break, and release heat when they form, minimizing when they form, minimizing temperature changes. temperature changes. • This means that water can absorb a This means that water can absorb a

lot of heat before it begins to get hot. lot of heat before it begins to get hot. This is why water is valuable to This is why water is valuable to industries and in your car's radiator as industries and in your car's radiator as a coolant. a coolant.

• The high specific heat index of water The high specific heat index of water also helps regulate the rate at which also helps regulate the rate at which air changes temperature, which is why air changes temperature, which is why the temperature change between the temperature change between seasons is gradual rather than seasons is gradual rather than sudden, especially near the oceans. sudden, especially near the oceans.


Water has a very high surface tensionWater has a very high surface tension. Hydrogen bonds hold . Hydrogen bonds hold molecules together. molecules together. Water is sticky and elastic, and tends to clump together in drops Water is sticky and elastic, and tends to clump together in drops

rather than spread out in a thin film. rather than spread out in a thin film. Surface tension is responsible for capillary action, which allows Surface tension is responsible for capillary action, which allows

water (and its dissolved substances) to move through the roots water (and its dissolved substances) to move through the roots of plants and through the tiny blood vessels in our bodies. of plants and through the tiny blood vessels in our bodies.

Adhesion:Adhesion: The attraction between different kinds of The attraction between different kinds of molecules.molecules.

Cohesion:Cohesion: The attraction between molecules of the same The attraction between molecules of the same kind. kind.

Cohesion theory of water transport.Cohesion theory of water transport. Theory that the Theory that the collective cohesive strength of their hydrogen bonds allows collective cohesive strength of their hydrogen bonds allows water molecules to be pulled up through a plant’s xylem in water molecules to be pulled up through a plant’s xylem in response to transpiration (evaporation of water) from leaves. response to transpiration (evaporation of water) from leaves.


Water has a high heat of vaporization.Water has a high heat of vaporization. Hydrogen bonds must be broken for water to Hydrogen bonds must be broken for water to

evaporate. evaporate. Evaporation of water cools the surfaces of Evaporation of water cools the surfaces of

plants and animals. plants and animals. The The heat of vaporizationheat of vaporization is the amount of is the amount of

heat energy needed to convert one gram of a heat energy needed to convert one gram of a liquid into a gas.liquid into a gas.


Water has versatility as a solvent: Water has versatility as a solvent: Charged regions of polar water molecules are Charged regions of polar water molecules are

attracted to ions and polar compounds.attracted to ions and polar compounds. Water is an effective medium for complex chemical Water is an effective medium for complex chemical

reactions in organismsreactions in organisms

A A solutionsolution is a liquid consisting of a homogeneous is a liquid consisting of a homogeneous mixture of two or more substances.mixture of two or more substances.

A A solventsolvent is the dissolving agent. is the dissolving agent. A A solutesolute is the substance that is dissolved is the substance that is dissolved

pHpH

Water tends to disassociate into HWater tends to disassociate into H++ and OH and OH-- ions. In ions. In this disassociation, the oxygen retains the this disassociation, the oxygen retains the electrons and only one of the hydrogens, becoming electrons and only one of the hydrogens, becoming a negatively charged ion known as hydroxide. a negatively charged ion known as hydroxide.

Pure water has the same number (or Pure water has the same number (or concentration) of Hconcentration) of H++ as OH as OH-- ions, therefore the pH ions, therefore the pH is 7 is 7

Acidic solutionsAcidic solutions have more H have more H++ ions than OH ions than OH-- ions. ions. Basic solutionsBasic solutions have less H have less H+ + ions than OHions than OH-- ions. ions. An acid causes an increase in the numbers of HAn acid causes an increase in the numbers of H++

ions and a base causes an increase in the numbers ions and a base causes an increase in the numbers of OHof OH-- ions. ions.

pHpH

The pH scale is a The pH scale is a logarithmic scalelogarithmic scale representing the representing the concentration of Hconcentration of H+ + ions in a solution. ions in a solution.

If we have a solution with one in every ten molecules If we have a solution with one in every ten molecules being H+, we refer to the concentration of Hbeing H+, we refer to the concentration of H++ ions as ions as 1/10. Remember from algebra that we can write a 1/10. Remember from algebra that we can write a fraction as a negative exponent, thus 1/10 becomes fraction as a negative exponent, thus 1/10 becomes 1010-1-1. Conversely 1/100 becomes 10. Conversely 1/100 becomes 10-2-2 , 1/1000 , 1/1000 becomes 10becomes 10-3-3, etc. , etc.

Logarithms are exponents to which a number (usually Logarithms are exponents to which a number (usually 10) has been raised. The log 1/10 (or 1010) has been raised. The log 1/10 (or 10-1-1) )

pH, a measure of the concentration of H+ ions, is the pH, a measure of the concentration of H+ ions, is the negative log of the Hnegative log of the H++ ion concentration. ion concentration.

If the pH of water is 7, then the concentration of H+ If the pH of water is 7, then the concentration of H+ ions is 10ions is 10-7-7, or 1/10,000,000. , or 1/10,000,000.

pHpH

What is polymerization?What is polymerization?

The formation of The formation of larger compounds larger compounds from smaller from smaller compoundscompounds

The bonding processThe bonding process

Polymers formed from monomers via Polymers formed from monomers via dehydration synthesisdehydration synthesis Where water is removed from the two Where water is removed from the two

joined moleculesjoined molecules

Separated via Separated via hydrolysishydrolysis Where water is put back in placeWhere water is put back in place

Dehydration SynthesisDehydration Synthesis

A + B + C = ABC + 2 molecules of H2O

H2O H2O

HydrolysisHydrolysis

ABC + 2 molecules of H2O = A + B + C

In order to reverse the previous reaction (dehydration synthesis), we need to add water to the product ‘ABC’.

So:

Example of a Modular Home

(i.e., Macromolecule)

Living RoomBed

Room

Kitchen Bathroom

MonomersMonomers

All of the individual monomers form the single polymer

So What’s In The Foods So What’s In The Foods You Eat?You Eat?

Fats (a.k.a.- Lipids)

Proteins

Carbohydrates

Organic v. Inorganic Organic v. Inorganic Compounds?Compounds?

Contain carbon to hydrogen (C-H) Contain carbon to hydrogen (C-H) bondsbonds

Inorganic compounds = Inorganic compounds = NONO (C-H) (C-H) bondsbonds

“Bucky Ball”

Compounds of Life: The Compounds of Life: The MacromoleculesMacromolecules

There are four groups of organic There are four groups of organic macromolecules:macromolecules:

CarbohydratesCarbohydrates Sugars, StarchesSugars, Starches

LipidsLipids Fats, Waxes, OilsFats, Waxes, Oils

ProteinsProteins Amino acidsAmino acids

Nucleic acidsNucleic acids RNA, DNARNA, DNA

CarbohydratesCarbohydrates

Commonly referred to as Commonly referred to as sugarssugars and and starchesstarches

Energy stored in the bonds of the Energy stored in the bonds of the carbohydrate moleculecarbohydrate molecule 1 grams = 4 calories (Kilocalorie)1 grams = 4 calories (Kilocalorie)

Bonds easily broken down (water) by Bonds easily broken down (water) by the body so “Carbs” are the body’s the body so “Carbs” are the body’s First Choice of Energy!First Choice of Energy!

CarbohydratesCarbohydrates

They consist of Carbon, Hydrogen They consist of Carbon, Hydrogen and Oxygen atoms in a consistent and Oxygen atoms in a consistent ratio of 1:2:1 or Cratio of 1:2:1 or C11HH22OO11

The simplest unit/monomer: The simplest unit/monomer: monosaccharidesmonosaccharides

MonosaccharidesMonosaccharides

Simple SugarsSimple Sugars Some examples are glucose, galactose Some examples are glucose, galactose

and fructoseand fructose

They all have the same chemical They all have the same chemical formula, Cformula, C66HH1212OO66, but they have , but they have different molecular structuresdifferent molecular structures

Called Called IsomersIsomers

Monosaccharide IsomersMonosaccharide Isomers

Glucose- Plant Sugars

O OH H OH OH OH

H C C C C C C H

H OH H H H

Galactose- Milk Sugars

O OH H H OH OH

H C C C C C C H

H OH OH H H

Fructose- Fruit Sugars

OH O H OH OH OH

H C C C C C C H

H OH H H H

Monosaccharide IsomersMonosaccharide Isomers

Forming Carbohydrate Forming Carbohydrate PolymersPolymers

Two Two monosaccharides:monosaccharides: glucose & glucose & fructosefructose Form a Form a disaccharide:disaccharide: Sucrose (Table Sucrose (Table

Sugar)Sugar) Put table sugar in a pan and turn on Put table sugar in a pan and turn on

the heat…what happens?the heat…what happens?

Disaccharide formationDisaccharide formation

Glucose Fructose

C6H12O6 C6H12O6

+OH OH O

+ H2O

Sucrose

C12H22O11

Water formed from bond between two -OH structures with an ‘O’, remaining at bond

DisaccharidesDisaccharides

Other disaccharides are:Other disaccharides are: Maltose (malt sugars) Maltose (malt sugars) Lactose (milk sugars)Lactose (milk sugars)

““Di-” & “Poly-” are “Di-” & “Poly-” are “complex carbscomplex carbs” ” ““Mono-” are “Mono-” are “simple sugarssimple sugars””

Reversing Disaccharide Reversing Disaccharide formation with Hydrolysisformation with Hydrolysis

O

Sucrose

C12H22O11

+ H2O

OH OH

Glucose Fructose

C6H12O6 C6H12O6

Add Water to Reaction

Function of PolysaccharidesFunction of Polysaccharides

Polysaccharides are many (3 or Polysaccharides are many (3 or more) monosaccharides joined more) monosaccharides joined togethertogether

This is the form of sugar that is This is the form of sugar that is stored in living thingsstored in living things

Storage forms of Storage forms of PolysaccharidesPolysaccharides

•Glycogen is the animal form of stored sugar

•It can be hundreds to thousands of glucose molecules long

•It also shows a distinctive “branching” pattern

•Starch is the plant form of stored sugar

•It can be hundreds to thousands of glucose molecules long

•It does not “branch” like glycogen

Starches continuedStarches continued

CelluloseCellulose is a type of starch that plants synthesize is a type of starch that plants synthesize

It is the principal component of wood, or the cell It is the principal component of wood, or the cell walls of plantswalls of plants

The human appendix is believed to have been used The human appendix is believed to have been used to break down cellulose tens of thousands of years to break down cellulose tens of thousands of years agoago

Humans, as a whole, can no longer break down Humans, as a whole, can no longer break down cellulose and so it is now considered cellulose and so it is now considered fiberfiber in our in our dietsdiets

LipidsLipids Lipids includeLipids include

fats, fats, oilsoils waxeswaxes

**(Fats and waxes are solids at room temperature while oils are **(Fats and waxes are solids at room temperature while oils are not)not)

Lipids have three main functions:Lipids have three main functions:

Energy storageEnergy storage Forming biological membranes (cell membranes)Forming biological membranes (cell membranes) Chemical messengers in the bodyChemical messengers in the body

LipidsLipids

Energy StorageEnergy Storage: Potential Energy: Potential Energy

LipidsLipids

Biological Membranes:Biological Membranes: Cell Cell MembranesMembranes

LipidsLipids

Chemical Messengers:Chemical Messengers: i.e., Steroids i.e., Steroids

LipidsLipids

Cholesterol…Good or Bad?

Polymerization of a LipidPolymerization of a Lipid

H H H H H H

C C C C C C H

H H H H H H

O

OH C

H

H C OH

H C OH

H C OH

H

+ H2O

Glycerol

Fatty Acid Chain

Carboxyl

Saturated v. Unsaturated Saturated v. Unsaturated FatsFats

H H H H H H

C C C C C C H

H H H H H H

H H H H H

C C C C C C H

H H H H H

Saturated Fats: No openings; Hydrogen bonded to every Carbon.

Strong, hard to break bonds.

LARD or CRISCO!

Unsaturated Fats: Openings via Carbon to Carbon double bonds

Bonds now easier to metabolize.

CANOLA OIL, FISH OIL, ETC.

ProteinsProteins

Proteins contain N, O, H and CProteins contain N, O, H and C Proteins are made from long “chains” of Proteins are made from long “chains” of

amino acidsamino acids Bonds between amino acids called Bonds between amino acids called

peptidepeptide bondsbonds.. Proteins also called Proteins also called polypeptidespolypeptides..

Amino acids have the same basic structure Amino acids have the same basic structure with the exception of the “R” group: LEGO!with the exception of the “R” group: LEGO!

Amino Acid UsesAmino Acid Uses Proteins used for building and Proteins used for building and

maintenance of tissues: i.e., musclemaintenance of tissues: i.e., muscle

Not natural

Natural

Amino Acid UsesAmino Acid Uses

Proteins (amino acid chains) are your Proteins (amino acid chains) are your last resort as a food source because last resort as a food source because they are difficult to metabolizethey are difficult to metabolize

Amino Acid StructureAmino Acid Structure

H H O

N C C

H R OH

Carboxyl Group

Carbon Backbone w/”R” group

Amino Group

Forming a Polypeptide through Forming a Polypeptide through Dehydration SynthesisDehydration Synthesis

H H O

N C C

H R OH

H H O

N C C

H R OH

H2O

Forming a Polypeptide through Forming a Polypeptide through Dehydration SynthesisDehydration Synthesis

H H O

N C C

H R

H H O

N C C

R OH

The result of taking water from the two amino acids is a polymer, or protein, that has two

monomers connected at a Carbon and a Nitrogen

+ H2O

Nucleic AcidsNucleic Acids

2 different nucleic acids:2 different nucleic acids: RNA-Ribonucleic acidRNA-Ribonucleic acid DNA-Deoxyribonucleic acidDNA-Deoxyribonucleic acid

Both are composed of:Both are composed of: CarbonCarbon HydrogenHydrogen OxygenOxygen NitrogenNitrogen PhosphorusPhosphorus


Monomers of nucleic acids are called Monomers of nucleic acids are called nucleotidesnucleotides

Nucleotides have three basic parts:Nucleotides have three basic parts:

A special A special 5-carbon sugar5-carbon sugar

A A phosphate groupphosphate group

A A nitrogenous basenitrogenous base


The nitrogenous bases contain nitrogenThe nitrogenous bases contain nitrogen A nucleotide, depending upon DNA on A nucleotide, depending upon DNA on

RNA, will have one of the following RNA, will have one of the following nitrogenous bases:nitrogenous bases: Adenine (A)Adenine (A) Thymine (T)Thymine (T) Guanine (G)Guanine (G) Cytosine (C)Cytosine (C) Uracil (U)Uracil (U)

Diagram of a NucleotideDiagram of a Nucleotide

Phosphate Group

5-Carbon Sugar

Nitrogenous Base

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Chemistry, Water, and Biochemsitry The Organic Molecules “You are what you eat!”