The Chemistry of Life Chapter 2 Section 2-3 and 2-4.

The Chemistry of LifeThe Chemistry of LifeChapter 2Chapter 2

Section 2-3 and 2-4Section 2-3 and 2-4

Carbon CompoundsCarbon Compounds

Section 2-3

Learning ObjectivesLearning Objectives

1.1. List characteristics of carbohydrates, List characteristics of carbohydrates, lipids, nucleic acids and proteinslipids, nucleic acids and proteins

2.2. Describe basic nucleotide structureDescribe basic nucleotide structure

3.3. Explain the special role of nucleic acids Explain the special role of nucleic acids in heredity and cellular controlin heredity and cellular control

4.4. Explain why molecular structure and Explain why molecular structure and shape is crucial to life – it determines shape is crucial to life – it determines how most molecules recognize and how most molecules recognize and respond to each otherrespond to each other

AssignmentsAssignments

Read Section 2-3 Complete Chapter 2 Chapter Notes

through Section 2-3 Read Section 2-4

Protein – Green atoms are carbonProtein – Green atoms are carbon

The Chemistry of CarbonThe Chemistry of Carbon

Cells are 70-95% water, the rest consists Cells are 70-95% water, the rest consists mostly of carbon-based compoundsmostly of carbon-based compounds Proteins, DNA, carbohydrates, and othersProteins, DNA, carbohydrates, and others All composed of carbon atoms bonded to All composed of carbon atoms bonded to

each other and to atoms of other elementseach other and to atoms of other elements These other elements commonly include These other elements commonly include

hydrogen (H), oxygen (O), nitrogen (N), hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), and phosphorus (P)sulfur (S), and phosphorus (P)


““Carbon is a girls best friend”Carbon is a girls best friend”

http://www.youtube.com/watch?v=JH96P4Lpobchttp://www.youtube.com/watch?v=JH96P4Lpobc

Depression is a mental illness that is sometimes treated with lithium.

Carbon is recycled naturally on Earth in a cycle called the carbon cycle.

A substrate is something that forms a base for something else to be put on.

Allotrope is any of the forms that an element may come in.

Organic chemistryOrganic chemistry The study of carbon compoundsThe study of carbon compounds,,

focuses on any compound with carbon focuses on any compound with carbon (organic compounds).(organic compounds).

The term organic is archaicThe term organic is archaic Though Though organic compoundsorganic compounds implies implies

that these compounds can only come that these compounds can only come from biological processes, they can be from biological processes, they can be synthesized by non-living reactionssynthesized by non-living reactions


Organic compoundsOrganic compounds Any compound with carbon is said to be Any compound with carbon is said to be

organicorganic COCO22 to CH to CH44 to proteins and nucleic to proteins and nucleic

acidsacids


History of Organic ChemistryHistory of Organic Chemistry Began with attempts to purify and improve Began with attempts to purify and improve

the yield of products from other the yield of products from other organisms.organisms. First learned to synthesize simple First learned to synthesize simple

compounds in the laboratory, butcompounds in the laboratory, but they had no success with more complex they had no success with more complex

compounds.compounds.


Swedish chemist Berzelius made a Swedish chemist Berzelius made a distinction between organic compounds distinction between organic compounds that seemed to arise only in living that seemed to arise only in living organisms and inorganic compounds from organisms and inorganic compounds from the nonliving world.the nonliving world.

This led early organic chemists to propose This led early organic chemists to propose vitalismvitalism,, the belief in a life outside the limits of the belief in a life outside the limits of

physical and chemical laws.physical and chemical laws.


Support for vitalism began Support for vitalism began to sink as chemists to sink as chemists synthesized more complex synthesized more complex organic compounds in the organic compounds in the laboratory.laboratory. Early 1800s, German Early 1800s, German

chemist Friedrich Wöhler chemist Friedrich Wöhler synthesized urea in lab synthesized urea in lab from totally inorganic from totally inorganic starting materials.starting materials.


Herr Doktor Frederich Wöhler


Milestones in organic chemistryMilestones in organic chemistry 1856 – an attempt to manufacture anti-1856 – an attempt to manufacture anti-

malarial drug quinine led to accidental malarial drug quinine led to accidental discovery of a carbon-based dye, Perkin’s discovery of a carbon-based dye, Perkin’s mauvemauve

1874 – DDT 1874 – DDT DDichloro-ichloro-DDiphenyl-iphenyl-TTrichloroethane (insecticide properties not richloroethane (insecticide properties not discovered until later)discovered until later)

1890’s – Aspirin (acetylsalicylic acid) by 1890’s – Aspirin (acetylsalicylic acid) by Bayer AG of GermanyBayer AG of Germany


1953, Stanley Miller 1953, Stanley Miller at the University of at the University of Chicago was able to Chicago was able to simulate chemical simulate chemical conditions conditions on the primitive on the primitive Earth to demonstrate Earth to demonstrate the spontaneous the spontaneous synthesis of organic synthesis of organic compounds.compounds.



Organic chemists finally rejected vitalism Organic chemists finally rejected vitalism and embraced and embraced mechanismmechanism.. all natural phenomena, including the all natural phenomena, including the

processes of life, are governed by the processes of life, are governed by the same physical and chemical laws.same physical and chemical laws.


Organic chemistry was redefined as the Organic chemistry was redefined as the study of carbon compounds regardless of study of carbon compounds regardless of origin.origin. Still, organisms produce most organic Still, organisms produce most organic

compounds in an amazing diversity and compounds in an amazing diversity and complexity.complexity.

However, the same rules apply to However, the same rules apply to inorganic and organic compounds alike.inorganic and organic compounds alike.


Organic chemistryOrganic chemistry The term “organic” is an archaic or obsolete term The term “organic” is an archaic or obsolete term

held over from the old days when all chemical held over from the old days when all chemical compounds were divided into two classes:compounds were divided into two classes: Inorganic – derived from the nonlivingInorganic – derived from the nonliving Organic – derived from livingOrganic – derived from living

For convenience sake, the terms are still used For convenience sake, the terms are still used today.today.


Organic chemistryOrganic chemistry ““Organic chemistry is the chemistry of Organic chemistry is the chemistry of

carbon compounds. Biochemistry is the carbon compounds. Biochemistry is the study of carbon compounds that crawl.”study of carbon compounds that crawl.” Mike AdamsMike Adams


What is the structure of the carbon atom?What is the structure of the carbon atom? With a total of 6 electrons, a carbon atom With a total of 6 electrons, a carbon atom

has 2 in the first shell and 4 in the second has 2 in the first shell and 4 in the second shell.shell.


How does carbon’ s structure relate to its How does carbon’ s structure relate to its chemical behavior?chemical behavior? Like any atom, carbon will tend to form Like any atom, carbon will tend to form

chemical bonds with other atoms to fill up chemical bonds with other atoms to fill up its valence shellits valence shell

Like any atom, carbon valence shell has a Like any atom, carbon valence shell has a maximum capacity of eight electronsmaximum capacity of eight electrons

Therefore, carbon will tend to form Therefore, carbon will tend to form chemical bonds with other atoms to chemical bonds with other atoms to “share” their electrons to fill up its valence “share” their electrons to fill up its valence shell.shell.


How does carbon’ s structure relate to its How does carbon’ s structure relate to its chemical behavior?chemical behavior? Carbon usually completes its valence shell Carbon usually completes its valence shell

by sharing electrons with other atoms in by sharing electrons with other atoms in four covalent bondsfour covalent bonds..

This This tetravalencetetravalence by carbon makes large, by carbon makes large, complex molecules possible.complex molecules possible. Carbon has little tendency to form ionic Carbon has little tendency to form ionic

bonds by loosing or gaining 4 electrons.bonds by loosing or gaining 4 electrons.


Carbon’ s structure makes it themost Carbon’ s structure makes it themost versatile building blocks of molecules.versatile building blocks of molecules.

C


The electron configuration of carbonThe electron configuration of carbon Gives it covalent compatibility with many Gives it covalent compatibility with many

different elementsdifferent elements

H O N C

Hydrogen

(valence = 1)

Oxygen

(valence = 2)

Nitrogen

(valence = 3)

Carbon

(valence = 4)


Inorganic compounds Inorganic compounds are not based on are not based on carbon:carbon: A “C” will not be part of their molecular A “C” will not be part of their molecular

formulaformula Salts, water, phosphates, sulfates, etc.Salts, water, phosphates, sulfates, etc. NaCl, HNaCl, H22SOSO44, HCl, etc, HCl, etc

Yet organic living things get needed Yet organic living things get needed elements in the form of inorganic elements in the form of inorganic compounds.compounds.


From one organism to the nextFrom one organism to the next No real difference in the overall No real difference in the overall

percentages of the major elements of percentages of the major elements of life (C, H, O, N, P, and S).life (C, H, O, N, P, and S).

Yet because of carbon, the diversity of Yet because of carbon, the diversity of molecules is not limitedmolecules is not limited



Key part of carbon compound diversity is the Key part of carbon compound diversity is the formation of formation of carbon chainscarbon chains Carbon atom covalently bonding to carbon Carbon atom covalently bonding to carbon

atom covalently bonding to carbon atom…atom covalently bonding to carbon atom… Carbon chains form the carbon skeletons of Carbon chains form the carbon skeletons of

most organic molecules.most organic molecules. Vary in length and may be straight, Vary in length and may be straight,

branched, or arranged in closed rings.branched, or arranged in closed rings. May also include double bonds.May also include double bonds.


Carbon skeletons

Double bond

Ring Structure



Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings


Naming carbon ring structures (just Naming carbon ring structures (just kidding!)kidding!)


Cells join smaller organic molecules Cells join smaller organic molecules together to form larger molecules, known astogether to form larger molecules, known as MacromoleculesMacromolecules, may be composed of , may be composed of

thousands of atoms and weigh over thousands of atoms and weigh over 100,000 100,000 daltonsdaltons

MacromoleculesMacromolecules

DaltonsDaltons Dalton is unit of measurement equivalent Dalton is unit of measurement equivalent

to atomic mass unitsto atomic mass units One dalton = one atomic mass unit (amu)One dalton = one atomic mass unit (amu) Periodic table displays the atomic mass of Periodic table displays the atomic mass of

the atoms of the elements in amuthe atoms of the elements in amu


Three of the four classes of macromolecules Three of the four classes of macromolecules form chainlike molecules called form chainlike molecules called polymerspolymers.. Polymers consist of many similar or Polymers consist of many similar or

identical building blocks linked by identical building blocks linked by covalent bonds.covalent bonds.

The repeated units are small molecules The repeated units are small molecules called called monomersmonomers.. Some monomers have other functions of Some monomers have other functions of

their own.their own.


How are links in a chain like monomers?

Figure 2-13

When small molecules called monomers join together, they form polymers, or large molecules.


We shall explore the structure and function We shall explore the structure and function of the four major classes of macromolecules of the four major classes of macromolecules which are:which are: CarbohydratesCarbohydrates LipidsLipids ProteinsProteins Nucleic acidsNucleic acids


CarbohydratesCarbohydrates

Carbon, hydrogen and oxygen atoms in a 1:2:1 Carbon, hydrogen and oxygen atoms in a 1:2:1 ratioratio

Food molecule – source of energyFood molecule – source of energy Energy is stored when chemical bonds are Energy is stored when chemical bonds are

formed – some bonds store more than formed – some bonds store more than othersothers

Energy released when chemical bonds breakEnergy released when chemical bonds break Digestion of carbohydrates, such as pasta Digestion of carbohydrates, such as pasta

and bread, break these bonds are release and bread, break these bonds are release the energythe energy

Also used as a structural moleculeAlso used as a structural molecule

Each six sided Each six sided shape is a shape is a glucose glucose molecule.molecule.

Glucose is the Glucose is the monomer - monomer - monosaccharidmonosaccharidee in a starch in a starch polymer - polymer - polysaccharidepolysaccharide


Hydrogen bonds between OH groups of carbons 3 and 6


Cellulose is difficult to digestCellulose is difficult to digest Cows have microbes in their stomachs to Cows have microbes in their stomachs to

facilitate this processfacilitate this process


ChitinChitin – important – important structuralstructural polysaccharide polysaccharide used in the exoskeletons of arthropods used in the exoskeletons of arthropods

(including insects, spiders, and crustaceans).(including insects, spiders, and crustaceans). similar to similar to cellulosecellulose, except that it contains a , except that it contains a

nitrogen-containing appendage on each nitrogen-containing appendage on each glucose.glucose.

Pure chitin is leathery, but the addition of Pure chitin is leathery, but the addition of calcium carbonate hardens the chitin.calcium carbonate hardens the chitin.

Used to make strong, flexible surgical thread Used to make strong, flexible surgical thread that decomposes after the wound heals.that decomposes after the wound heals.

Chitin also forms Chitin also forms the structural the structural support for the support for the cell walls of cell walls of many fungi.many fungi.

LipidsLipids

Not generally soluble in waterNot generally soluble in water Mostly carbon and hydrogen atoms; also oxygenMostly carbon and hydrogen atoms; also oxygen Fats, oils and waxes, plus some steroids Fats, oils and waxes, plus some steroids

(hormones)(hormones) The job of a lipid is to:The job of a lipid is to:

Store energyStore energy Give structure to cell membranesGive structure to cell membranes As steroids, function as a chemical messengerAs steroids, function as a chemical messenger

Glycerol

Fatty Acid

LipidsLipids

The three fatty acids in a fat can be the The three fatty acids in a fat can be the same or different.same or different.

Fatty acids may vary in length (number of Fatty acids may vary in length (number of carbons) and in the number and locations of carbons) and in the number and locations of double bonds.double bonds. If there are no If there are no

carbon-carbon carbon-carbon double bonds, double bonds, then the molecule then the molecule is a is a saturated fatty saturated fatty acidacid - a hydrogen - a hydrogen at every possible at every possible position.position.

If there are one or more carbon-carbon If there are one or more carbon-carbon double bonds, then the molecule is an double bonds, then the molecule is an unsaturated fatty acidunsaturated fatty acid - formed by the - formed by the removal of hydrogen atoms from the removal of hydrogen atoms from the carbon skeleton.carbon skeleton.

Saturated fatty acids Saturated fatty acids are straight chains, are straight chains, but unsaturated fatty but unsaturated fatty acids have a kink acids have a kink wherever there is wherever there is a double bond.a double bond.

Fig. 5.11b

Fats with Fats with saturatedsaturated fatty acids are fatty acids are saturated fats.saturated fats. Most animal fats are saturated.Most animal fats are saturated. Saturated fats are solid at room Saturated fats are solid at room

temperature.temperature. A diet rich in saturated fats may A diet rich in saturated fats may

contribute to cardiovascular disease contribute to cardiovascular disease (atherosclerosis) through plaque deposits.(atherosclerosis) through plaque deposits.

LipidsLipids

Fats with Fats with unsaturatedunsaturated fatty acids are fatty acids are unsaturated fats.unsaturated fats. Plant and fish fats, known as oils, are Plant and fish fats, known as oils, are

liquid are room temperature.liquid are room temperature. The kinks provided by the double bonds The kinks provided by the double bonds

prevent the molecules from packing prevent the molecules from packing tightly together.tightly together.

LipidsLipids

Major function of fats is Major function of fats is energy storageenergy storage.. One gram of fat stores more than twice as One gram of fat stores more than twice as

much energy as a gram of a much energy as a gram of a polysaccharide.polysaccharide.

Humans and other mammals store fats as Humans and other mammals store fats as long-term energy reserves in adipose cells.long-term energy reserves in adipose cells.

Plants use starch for energy storage when Plants use starch for energy storage when mobility is not a concern but use oils when mobility is not a concern but use oils when dispersal and packing is important, as in dispersal and packing is important, as in seeds.seeds.

LipidsLipids

Fat also functions to:Fat also functions to: Cushion vital organs.Cushion vital organs. Insulate the organism against the Insulate the organism against the

environment.environment. This subcutaneous layer is especially This subcutaneous layer is especially

thick in whales, seals, and most other thick in whales, seals, and most other marine mammalsmarine mammals

LipidsLipids

Nucleic AcidsNucleic Acids

Contain carbon (C), hydrogen (H), oxygen Contain carbon (C), hydrogen (H), oxygen (O), nitrogen (N) and phosphorus (P)(O), nitrogen (N) and phosphorus (P)

Function as the Function as the hereditary moleculehereditary molecule Two formsTwo forms

RNA – ribonucleic acidRNA – ribonucleic acid DNA – deoxyribonucleic acidDNA – deoxyribonucleic acid

Individual monomers are called Individual monomers are called nucleotidesnucleotides

Five carbon sugar Five carbon sugar molecule (gray)molecule (gray)

Nitrogenous base Nitrogenous base (green)(green)

Phosphate group Phosphate group (blue)(blue)

Thousands of these Thousands of these monomers may be monomers may be linked by covalent linked by covalent bonds to create DNA bonds to create DNA or RNA or RNA


RNA vs DNARNA vs DNA

Key difference in structureKey difference in structure RNA contains the sugar riboseRNA contains the sugar ribose DNA contains the sugar deoxyriboseDNA contains the sugar deoxyribose

Do you see the difference?

How nucleic How nucleic acids function to acids function to store and store and transmit transmit heredity heredity information will information will be covered later be covered later in the year.in the year.


ActivityActivityBuilding Model of Building Model of DNA Double HelixDNA Double Helix

Students will build a model of the DNA Students will build a model of the DNA double helix using the Kinex model systemdouble helix using the Kinex model system

STUDENT

Proteins mayProteins may Control the rate of chemical reactionsControl the rate of chemical reactions Form muscles and boneForm muscles and bone Others transport materials in and out of Others transport materials in and out of

cellscells Still others fight diseaseStill others fight disease

ProteinsProteins

StructuralStructural proteins – support proteins – support StorageStorage proteins – storage of amino acids proteins – storage of amino acids TransportTransport proteins – transport of other proteins – transport of other

substancessubstances HormonalHormonal proteins – coordination of proteins – coordination of

activitiesactivities ReceptorReceptor proteins – response of cell to proteins – response of cell to

chemical stimulichemical stimuli

ProteinsProteins

ContractileContractile proteins – movement proteins – movement DefensiveDefensive proteins – immune response proteins – immune response

(antibodies)(antibodies) EnzymaticEnzymatic proteins – selective acceleration proteins – selective acceleration

of chemical reactionsof chemical reactions

ProteinsProteins

ProteinsProteins

PolypeptidesPolypeptides Are polymers of Are polymers of amino acidsamino acids

A proteinA protein Consists of one or more polypeptidesConsists of one or more polypeptides

An amino acidAn amino acid Is only a monomer; a single moleculeIs only a monomer; a single molecule It is not proteinIt is not protein

ProteinsProteins

Amino acidsAmino acids Are organic molecules possessing both Are organic molecules possessing both

carboxyl and amino groupscarboxyl and amino groups Differ in their chemical properties due to Differ in their chemical properties due to

differing side chains, called differing side chains, called RR groups groups

ProteinsProteins

ProteinsProteins

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• 20 different amino acids make up proteins

O

O–

H

H3N+ C C

O

O–

H

CH3

H3N+ C

H

C

O

O–

CH3 CH3

CH3

C C

O

O–

H

H3N+

CH

CH3

CH2

C

H

H3N+

CH3

CH3

CH2

CH

C

H

H3N+ C

CH3

CH2

CH2

CH3N+

H

C

O

O–

CH2

CH3N+

H

C

O

O–

CH2

NH

H

C

O

O–

H3N+ C

CH2

H2C

H2N C

CH2

H

C

NonpolarGlycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)

Methionine (Met) Phenylalanine (Phe)

C

O

O–

Tryptophan (Trp) Proline (Pro)

H3C

S

O

O–

Amino Acid Monomers

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

O–

OH

CH2

C C

H

H3N+

O

O–

H3N+

OH CH3

CH

C C

HO–

O

SH

CH2

C

H

H3N+ C

O

O–

H3N+ C C

CH2

OH

H H H

H3N+

NH2

CH2

OC

C C

O

O–

NH2 O

C

CH2

CH2

C CH3N+

O

O–

O

Polar

Electricallycharged

–O O

C

CH2

C CH3N+

H

O

O–

O– O

C

CH2

C CH3N+

H

O

O–

CH2

CH2

CH2

CH2

NH3+

CH2

C CH3N+

H

O

O–

NH2

C NH2+

CH2

CH2

CH2

C CH3N+

H

O

O–

CH2

NH+

NHCH2

C CH3N+

H

O

O–

Serine (Ser) Threonine (Thr)Cysteine

(Cys)Tyrosine

(Tyr)Asparagine

(Asn)Glutamine

(Gln)

Acidic Basic

Aspartic acid (Asp)

Glutamic acid (Glu)

Lysine (Lys) Arginine (Arg) Histidine (His)

Amino Acid Monomers

There are 20 amino acid monomers that put There are 20 amino acid monomers that put together together polypeptidespolypeptides..

Because the amino acids have different Because the amino acids have different RR groups, groups, they can have different chemical properties.they can have different chemical properties. Polar vs. nonpolarPolar vs. nonpolar

ProteinsProteins

RR groups, assembled in a polypeptide, will interact with groups, assembled in a polypeptide, will interact with each other – attracted or repelled.each other – attracted or repelled.

R group interactions determine the polypeptide 3D R group interactions determine the polypeptide 3D shape.shape.

Protein shape makes protein function possibleProtein shape makes protein function possible Shape follows function!Shape follows function!

ProteinsProteins

Just 20 amino acid building blocks? Even that few Just 20 amino acid building blocks? Even that few can create incredible diversity. Just do the math.can create incredible diversity. Just do the math. How many polypeptides 4 amino acids long can How many polypeptides 4 amino acids long can

be made from 20 amino acids?be made from 20 amino acids? 20204 4 or 20 x 20 x 20 x 20 = 160,000or 20 x 20 x 20 x 20 = 160,000

ProteinsProteins

ProteinsProteins

Amino acidsAmino acids Are linked by Are linked by

covalent covalent peptide peptide bonds bonds

OH

DESMOSOMES

OH

CH2

CN

H

C

H O

H OH OH

Peptidebond

OH

OH

OH

H H

HH

H

H

H

H

H

H H

H

N

N N

N N

SHSide

chains

SH

OO

O O O

H2O

CH2 CH2

CH2 CH2CH2

C C C C C C

C CC C

Peptidebond

Amino end(N-terminus)

Backbone

(a)

(b) Carboxyl end(C-terminus)

Animation – Protein SynthesisAnimation – Protein Synthesis

http://highered.mcgraw-hill.com/olc/dl/120077/micro06.swf

Proteins have four levels of organizationProteins have four levels of organization PrimaryPrimary – the linear sequence of amino – the linear sequence of amino

acidsacids SecondarySecondary – the amino acid chain twists and – the amino acid chain twists and

folds upon itselffolds upon itself TertiaryTertiary – two or more protein chains link to – two or more protein chains link to

each other by van der Waals weak bondseach other by van der Waals weak bonds QuaternaryQuaternary – highest level; two or more – highest level; two or more

tertiary units form weak bonds with each tertiary units form weak bonds with each otherother

ProteinsProteins

Four Levels of Protein Four Levels of Protein StructureStructure

PrimaryPrimary structure structure Is the unique Is the unique

sequence of sequence of amino acids in a amino acids in a polypeptidepolypeptide

–

Amino acid subunits

+H3NAmino

end

oCarboxyl end

oc

GlyProThrGlyThr

Gly

GluSeuLysCysProLeu

MetVal

Lys

ValLeu

AspAlaVal ArgGly

SerPro

Ala

Gly

lle

SerProPheHisGluHis

Ala

GluVal

ValPheThrAlaAsn

AspSer

GlyProArg

ArgTyrThr

lleAla

Ala

Leu

LeuSer

ProTyrSerTyrSerThr

Thr

Ala

ValVal

ThrAsnProLysGlu

ThrLys

SerTyrTrpLysAlaLeu

GluLle Asp


SecondarySecondary structurestructure Is the folding or Is the folding or

coiling of the coiling of the polypeptide into a polypeptide into a repeating repeating configurationconfiguration

Relies on Relies on hydrogen bondshydrogen bonds


TertiaryTertiary structure structure Overall 3-D shape of a polypeptideOverall 3-D shape of a polypeptide Results from interactions between amino Results from interactions between amino

acids and R groupsacids and R groupsCH2

CH

OH

O

CHO

CH2

CH2 NH3+ C-O CH2

O

CH2SSCH2

CH

CH3

CH3

H3C

H3C

Hydrophobic interactions and van der Waalsinteractions

Polypeptidebackbone

Hyrdogenbond

Ionic bond

CH2

Disulfide bridge


QuaternaryQuaternary structure structure Is the overall protein Is the overall protein

structure that results structure that results from the aggregation from the aggregation of of two or more two or more polypeptide subunitspolypeptide subunits

Polypeptidechain

Collagen Chains

ChainsHemoglobin

IronHeme

Summation of Summation of the four levels of the four levels of protein protein structure.structure.

Why is understanding these four Why is understanding these four levels of organization important?levels of organization important? Shape is critical to protein Shape is critical to protein

functions!functions! Lose the quaternary level means losing Lose the quaternary level means losing

their shape – conformation – which their shape – conformation – which means losing functionmeans losing function

Now think of bee sting venom and Now think of bee sting venom and powered meat tenderizer…powered meat tenderizer…

ProteinsProteins

You will now work together to learn what You will now work together to learn what they are, what they do and how they are they are, what they do and how they are built.built.


InstructionInstructionss

1. Divide class into 4 person teams with one person for each macromolecule.

2. Position teams in room corners.3. Each “macromolecule” will

complete the worksheet column for their macromolecule.

4. Macromolecules will then meet together; proteins with proteins, nucleic acids with nucleic acids, …

5. These macromolecule groups share information to improve their work.

6. Macromolecule groups will break up and return to original groups.

7. Now all four will share their facts so that everyone completes the worksheet.

8. Completed worksheets are collected (or completed at home).

SummationSummation

1.1. List characteristics of carbohydrates, List characteristics of carbohydrates, lipids, nucleic acids and proteinslipids, nucleic acids and proteins

2.2. Describe basic nucleotide structureDescribe basic nucleotide structure

3.3. Explain the special role of nucleic acids Explain the special role of nucleic acids in heredity and cellular controlin heredity and cellular control

4.4. Explain why molecular structure and Explain why molecular structure and shape is crucial to life – it determines shape is crucial to life – it determines how most molecules recognize and how most molecules recognize and respond to each otherrespond to each other


Read Section 2-3 Complete Chapter 2 Chapter Notes

through Section 2-3. Complete the Worksheet Section 2-3 / Due

next class Read Section 2-4

Cornell Notes

• Using your Cornell Notes, you will now:– compare notes with a partner for one minute.– write reflection in bottom space.– possible open-notes quiz.

• Cornell Notes must be turned in on day of chapter test; they will be graded.

Cornell Notes

• Tonight– Reread your Cornell Notes in the right

column.– Review the ideas in the left column.– Study your summary/reflection.

Chemical Reactions and Chemical Reactions and EnzymesEnzymes

Section 2-4Section 2-4


1.1. Given a chemical reaction, identify the Given a chemical reaction, identify the reactants and products, and the reactants and products, and the coefficients.coefficients.

2.2. Distinguish between energy absorbing Distinguish between energy absorbing and energy releasing chemical reactions.and energy releasing chemical reactions.

3.3. Explain the concept of activation energy.Explain the concept of activation energy.


4.4. Explain why molecular structure and shape is Explain why molecular structure and shape is crucial to life – it determines how most crucial to life – it determines how most molecules recognize and respond to each molecules recognize and respond to each other.other.

5.5. Explain why chemical reactions do not create Explain why chemical reactions do not create new matter.new matter.

6.6. Explain the relationship between Explain the relationship between concentration and the rate of reaction.concentration and the rate of reaction.

7.7. Explain the importance of enzymes to Explain the importance of enzymes to biochemical reactions.biochemical reactions.


Complete Chapter 2 Chapter Notes through Section 2-4.

Complete the Worksheet Section 2-4 / Due next class

Chemical propertyChemical property – – abilityability of a of a substance to undergo a specific chemical substance to undergo a specific chemical changechange Example – rust is a chemical reaction Example – rust is a chemical reaction

between iron and oxygen to create iron between iron and oxygen to create iron oxideoxide

Composition of matter always changesComposition of matter always changes

Chemical ReactionsChemical Reactions

No new matter is created or No new matter is created or destroyed during a chemical reactiondestroyed during a chemical reaction If you weighed all the matter of the If you weighed all the matter of the

reactants, and did the same for the reactants, and did the same for the products, their masses would be the products, their masses would be the samesame

The number of atoms on both sides The number of atoms on both sides would be exactly the samewould be exactly the same

The reactions must be “balanced.”The reactions must be “balanced.”



Some chemical reactions go to Some chemical reactions go to completion; that is, all the reactants are completion; that is, all the reactants are converted to productsconverted to products

Most chemical reactions are Most chemical reactions are reversiblereversible,, the the products products in the forward reaction in the forward reaction

becoming the becoming the reactantsreactants for the reverse for the reverse reactionreaction


Example: 3HExample: 3H22 + N + N22 <=> 2NH <=> 2NH33

Hydrogen and nitrogen molecules combine to Hydrogen and nitrogen molecules combine to form ammonia, but ammonia can decompose form ammonia, but ammonia can decompose to hydrogen and nitrogen moleculesto hydrogen and nitrogen molecules Initially, when reactant concentrations are Initially, when reactant concentrations are

high, they frequently collide to create high, they frequently collide to create productsproducts

As products accumulate, they collide to As products accumulate, they collide to reform reactantsreform reactants


How do we know a chemical reaction How do we know a chemical reaction happened?happened? Clues one can senseClues one can sense Change in colorChange in color Change in temperature / heat energyChange in temperature / heat energy Gas productionGas production Formation of a precipitateFormation of a precipitate


Demonstration:Demonstration:Chemical ReactionsChemical Reactions

Polyurethane FoamPolyurethane Foam Rainbow colorsRainbow colors Mystery nylon polymerMystery nylon polymer

TEACHER

Chemical reactions always require the breaking and forming of chemical bonds.

Break bonds of reactants.

Form new bonds in products.


Rust is a chemical reaction – Iron and oxygen reactants combine to form iron oxide product.

Photosynthesis: a solar-powered rearrangement of Photosynthesis: a solar-powered rearrangement of matter – Light energymatter – Light energy

6CO2 + 6H2O -> C6H12O6 + 6O2

Energy in ReactionsEnergy in Reactions

Energy involved in any chemical reactions.Energy involved in any chemical reactions. Break bonds, release energy.Break bonds, release energy. Form bonds, absorb energy.Form bonds, absorb energy.

EnergyEnergyCapacity of a physical system to do work.Capacity of a physical system to do work.A system can have energy in a variety of A system can have energy in a variety of forms, for example:forms, for example:

kinetic energy due to its motion,kinetic energy due to its motion, potential energy due to the positions of potential energy due to the positions of

the components,the components, chemical energy stored in chemicals that chemical energy stored in chemicals that

can undergo a reaction. can undergo a reaction.


Energy in biochemistry is:Energy in biochemistry is: stored when chemical bonds are formed.stored when chemical bonds are formed. Released when chemical bonds are Released when chemical bonds are

broken.broken. Though biochemical systems always lost Though biochemical systems always lost

some energy as heat.some energy as heat. The trick in biology is to set up systems The trick in biology is to set up systems

that recapture, store and release energy that recapture, store and release energy in controlled circumstances.in controlled circumstances.


Certain biochemical processesCertain biochemical processes unleash the energy stored in sugar molecules,unleash the energy stored in sugar molecules, recapture it with other molecules, and then use recapture it with other molecules, and then use

it to (re)build yet more molecules needed by it to (re)build yet more molecules needed by the cell.the cell.

Organisms take in energy from their surrounding Organisms take in energy from their surrounding – light energy or chemical energy from food – light energy or chemical energy from food molecules – and then release energy as heat or in molecules – and then release energy as heat or in waste molecules, such as carbon dioxide. waste molecules, such as carbon dioxide.


Energy ChangesEnergy ChangesChemical reactions either release energy or Chemical reactions either release energy or absorb energyabsorb energyReactions releasing energy often occur Reactions releasing energy often occur spontaneously.spontaneously.Reactions absorbing energy do not go until Reactions absorbing energy do not go until provided with source of energy.provided with source of energy.

Energy ChangesEnergy Changes

The relationship of energy to stability, work capacity, and spontaneous changeThe relationship of energy to stability, work capacity, and spontaneous change

There is a tendency of all things to seek their lowest state of energy.

The molecule at far right has high-energy chemical bonds that are not stable, so it has a tendency to split apart and release that energy.

Energy-releasing chemical reaction between hydrogen Energy-releasing chemical reaction between hydrogen and oxygenand oxygen

The amount of energy on the reactant side will equal the amount of energy on the products side (remember some energy always lost as heat energy

Ignite with a flame or spark, inputting energy.

Energy changes in energy-releasing and energy-Energy changes in energy-releasing and energy-absorbing reactionsabsorbing reactions

Energy ChangesEnergy Changes

Energy is stored in chemical bonds of Energy is stored in chemical bonds of molecules.molecules.

Energy SourcesEnergy Sources

Activation energyActivation energy – – The peak in the curve The peak in the curve is the amount of is the amount of energy required to get energy required to get the reaction going.the reaction going.

Strike at match and Strike at match and you’ll see an example you’ll see an example of activation energy.of activation energy.

The match starts The match starts burning only because burning only because another chemical another chemical reaction provided the reaction provided the activation energy.activation energy.

Activation EnergyActivation Energy

Essential controlling feature of biochemical Essential controlling feature of biochemical systems.systems.

Life could not exist by relying on Life could not exist by relying on spontaneous reactions.spontaneous reactions.

Activation energy functions as a control or Activation energy functions as a control or brake on reactions.brake on reactions.

Biology links energy-releasing Biology links energy-releasing reactions to get the activation energy reactions to get the activation energy for energy-absorbing reactions.for energy-absorbing reactions.

Activation EnergyActivation Energy

Demonstration: Demonstration: Decomposition of Decomposition of

SugarSugar

Students will observe the decomposition of Students will observe the decomposition of sugar by a strong acid – a sugar by a strong acid – a chemical chemical reactionreaction

Dehydration of water – removal of water Dehydration of water – removal of water from sucrose which is also an exothermic from sucrose which is also an exothermic reaction.reaction.

http://www.youtube.com/watch?http://www.youtube.com/watch?v=pqi50sjJVc0&feature=relatedv=pqi50sjJVc0&feature=related

TEACHER

Demonstration:Demonstration:Energy Held in Energy Held in

Bonds of a Bonds of a CarbohydrateCarbohydrate

Students will observe the decomposition of Students will observe the decomposition of sugar by a strong oxidizer – potassium chlorate sugar by a strong oxidizer – potassium chlorate – a – a chemical reactionchemical reaction

Highly exothermic requiring we go Highly exothermic requiring we go outside.outside.

Chemical bond energy turned into heat energy Chemical bond energy turned into heat energy and light energy.and light energy.

http://www.youtube.com/watch?v=dVRBDRAsP6U&feature=related

TEACHER

Some biochemical reactions just will not Some biochemical reactions just will not work well, or at all, work well, or at all, without helpwithout help..

Perhaps their activation energy is too high.Perhaps their activation energy is too high. Perhaps the reactant concentration is Perhaps the reactant concentration is

always too low.always too low.

EnzymesEnzymes

The help comes in the form of a The help comes in the form of a catalystcatalyst:: Substance that speeds up the rate of a Substance that speeds up the rate of a

chemical reaction.chemical reaction. Are not changed due to the chemical Are not changed due to the chemical

reaction.reaction. Catalysts lower a reaction’s activation Catalysts lower a reaction’s activation

energy.energy.

EnzymesEnzymes

Enzymes lower a reaction’s Enzymes lower a reaction’s activation energyactivation energy

Easier to get the red line reaction going, isn’t it?

So what is an enzyme exactly?So what is an enzyme exactly? Protein molecules of a very specific shape Protein molecules of a very specific shape

(conformation).(conformation). Shape is specific for the reactant(s).Shape is specific for the reactant(s). Reactant is now called a Reactant is now called a substrate.

EnzymesEnzymes

Enzymes may put two reactants together Enzymes may put two reactants together to form a new molecule, orto form a new molecule, or

Enzymes may take a large molecule and Enzymes may take a large molecule and break it into smaller molecules. Enzymes break it into smaller molecules. Enzymes capture the reactants, thereby bringing capture the reactants, thereby bringing them close together.them close together.

Enzymes work only when they are at their Enzymes work only when they are at their highest level of organization – quanternary highest level of organization – quanternary structure.structure.

EnzymesEnzymes

Breaking up isn’t hard to do…

Enzyme hexokinase converts the reactants (substates) glucose and ATP into glucose-6-phosphate and ADP

Enzyme sucrase breaks down sucrose into two smaller sugars, fructose and glucose

Generally speaking…Generally speaking…

One enzyme for one chemical reaction.One enzyme for one chemical reaction. So enzyme names come from the So enzyme names come from the

reaction is catalyzes.reaction is catalyzes. Look for the –Look for the –asease suffix to recognize an suffix to recognize an

enzyme’s name.enzyme’s name. Carbonic anhydrCarbonic anhydrasease catalyzes reaction catalyzes reaction

that removes water from carbonic acid.that removes water from carbonic acid.

It’s all about breaking existing bonds and It’s all about breaking existing bonds and forming new bonds.forming new bonds.

Enzymes provide a site where reactants Enzymes provide a site where reactants can be brought together, thereby reducing can be brought together, thereby reducing activation energy.activation energy.

EnzymesEnzymes

Enzymes are built for specific substratesEnzymes are built for specific substrates SpecificitySpecificity comes from ability to form comes from ability to form

weak bonds between active site and weak bonds between active site and substratesubstrate Wrong substrate may not be able to Wrong substrate may not be able to

form these bondsform these bonds Weak bonds hold the substrate to the Weak bonds hold the substrate to the

active siteactive site

EnzymesEnzymes

The reactant binds to the The reactant binds to the enzymes active siteenzymes active site

Metaphor for the enzyme-Metaphor for the enzyme-substrate complexsubstrate complex

Enzymes are very specific for substrates, much like a lock is very specific for a key.

Enzymes work if the conditions are right.Enzymes work if the conditions are right. Enzymes will not work if temperature, pH Enzymes will not work if temperature, pH

or other factors disrupt the shape of the or other factors disrupt the shape of the enzyme molecule.enzyme molecule. DenaturationDenaturation – weak bonds that hold – weak bonds that hold

an enzyme together break; loss of shape an enzyme together break; loss of shape and function.and function.

Regulation of Enzyme ActivityRegulation of Enzyme Activity

Cells also regulate enzymes by using Cells also regulate enzymes by using protein messengers that bind to enzymes protein messengers that bind to enzymes to turn them off or turn them on.to turn them off or turn them on.

Regulation of Enzyme ActivityRegulation of Enzyme Activity

Demonstration:Demonstration:DenaturationDenaturation

Fry an egg in class.Fry an egg in class.

TEACHER

Analyzing DataAnalyzing Data

Read the chart.

What do you see?

SummationSummation

1.1. Given a chemical reaction, identify the Given a chemical reaction, identify the reactants and products, and the reactants and products, and the coefficients.coefficients.

2.2. Distinguish between energy absorbing Distinguish between energy absorbing and energy releasing chemical reactions.and energy releasing chemical reactions.

3.3. Explain the concept of activation energy.Explain the concept of activation energy.

SummationSummation

4.4. Explain why molecular structure and shape is Explain why molecular structure and shape is crucial to life – it determines how most crucial to life – it determines how most molecules recognize and respond to each molecules recognize and respond to each other.other.

5.5. Explain why chemical reactions do not create Explain why chemical reactions do not create new matter.new matter.

6.6. Explain the relationship between Explain the relationship between concentration and the rate of reaction.concentration and the rate of reaction.

7.7. Explain the importance of enzymes to Explain the importance of enzymes to biochemical reactions.biochemical reactions.


Complete Chapter 2 Chapter Notes through Section 2-4.

Complete Chapter 2 Chapter Review Problems (graded)

Complete the Chapter 2 Chapter Notes to end

Check FirstClass for test dates

Cornell Notes

• Using your Cornell Notes, you will now:– compare notes with a partner for one minute.– write reflection in bottom space.– possible open-notes quiz.

• Cornell Notes must be turned in on day of chapter test; they will be graded.

Cornell Notes

• Tonight– Reread your Cornell Notes in the right

column.– Review the ideas in the left column.– Study your summary/reflection.

LabLabEffect of Effect of

Temperature on Temperature on Enzyme ActivityEnzyme Activity

Distribute lab instructions, Tootpick-ase: An Introduction to Enzymes

Simulation of how substrate concentration and temperature affect enzyme function.

STUDENT

LabLabEffect of Effect of

Temperature on Temperature on Enzyme ActivityEnzyme Activity

Distribute lab instructions, Effect of Temperature on Enzyme (Catalase) Activity

Conduct lab, Effect of Temperature on Enzyme (Catalase) Activity

Students must read and complete the Pre-Lab activity

STUDENT

LabLab

Conduct lab, Effect of Temperature on Enzyme (Catalase) Activity Students must have read and

completed the Pre-Lab activity

Test, Chapter 2Test, Chapter 2

Following the acid/base lab.Following the acid/base lab. Tentative date:Tentative date:

The Chemistry of Life Chapter 2 Section 2-3 and 2-4.

Documents

carbon organic compounds

chemistry of carbon

carbon compounds section

complex organic compounds

study of carbon compounds

inorganic compounds

complex compounds

organic chemists