Carbon-based molecules. Organic chemistry is the study of carbon-based molecules. Nearly all of the...

Organic chemistry is the study of carbon-based carbon-based molecules.molecules.Nearly all of the compounds that a cell makes are composed of carbon bonded to other carbon atoms and to atoms of other elements.

Organic ChemistryOrganic Chemistry

Images : Copyright © The McGraw-Hill Companies, Inc.


Carbon is unparalleled in its ability to form large, diverse molecules.Recall that carbon has six electrons:

– 2 in its innermost shell and 4 in its outermost shell

C

Carbon completes its outer shell by sharing electrons with other atoms in 4 covalent bonds.


The diversity of carbon molecules is the driving force behind the myriad of molecules and chemical processes required for life, and explains the great diversity of life on Earth!



Carbon can share its electrons with four hydrogen atoms, creating CH4 or methane.

CH

H

H

HMethane is an example of an organic compound and is the simplest of all organic compounds.

Organic Compunds

• When Carbon shares electrons with Hydrogen atoms, a hydrocarbon results

• Hydrocarbons are the major components of petroleum

• Petroleum (crude oil) consists of the partially decomposed remains or organisms that lived millions of years ago

• This is why the burning of fossil fuels increases carbon dioxide into our atmosphereCH4 + 2 O2 → 2 H2O + CO2 + Energy

Organic Chemistry

The unique properties of an organic compound depend upon the size and shape of its carbon skeleton and the groups of atoms that are attached to that skeleton.Of the six groups of atoms that are essential to life, five serve as functional groupsfunctional groups. Functional groups affect a molecule’s function by participating in chemical reactions in characteristic and predictable ways.

carbon skeleton: the chain of carbon atoms in an organic molecule

Hydroxyl group – polar, consists of a Hydrogen bonded to an Oxygen

Carbonyl group – polar, Carbon linked by a double bond to an Oxygen

Carboxyl group – polar, a Carbon double-bonded to both an Oxygen and a Hydroxyl group

Amino group – polar, composed of a Nitrogen bonded to 2 Hydrogen atoms and the Carbon skeleton

Phosphate group – polar, consists of a Phosphorus atom bonded to 4 Oxygen atoms

Methyl group – nonpolar and not reactive,Carbon bonded to 3 Hydrogen

Same structure, but different functional groups

Estradiol – female sex hormone

Testosterone – male sex hormone

Hydroxyl group

Carbonyl group

Methyl group Female Lion

Male Lion

Besides water, all biological molecules are organic, or carbon-based.There are many organic molecules, but most of the human body is made up of just four types: carbohydrates, lipids, proteins and carbohydrates, lipids, proteins and nucleic acids.nucleic acids.

Carbohydrates, lipids, proteins and nucleic acids are called macromoleculesmacromolecules, and are the building blocks of cells and their chemical machinery.Cells make most of these large molecules by joining together smaller molecules, or monomersmonomers, into chains called polymers.

Cellular structure Polymer Monomer

Chromosome DNA strand Nucleotide

Nuc

leic

Aci

d

The key to the great diversity of macromolecules is in the arrangement of its monomers.DNA is built up of only four monomers (nucleotides), and proteins are made with only twenty monomers (amino acids), but both macromolecules are incredible diverse.The proteins in you and a fungus are made with the same twenty amino acids!

A cell links monomers together to form polymers by way of a dehydration reaction.dehydration reaction.A dehydration reaction is so named because it results in the removalremoval of a water molecule.An unlinked monomer has a hydroxyl group (--OH) at one end, and a hydrogen atom (--H) at the other end.

Hydrogen Hydrogen atomatom

Hydroxyl Hydroxyl groupgroup

polymerpolymer monomermonomer

Hydrogen Hydrogen atomatom

Hydroxyl Hydroxyl groupgroup

Dehydration Reaction Dehydration Reaction

By removing the hydroxyl group of the polymer, and the hydrogen atom of the monomer that is being added, a water molecule is released.

Water Water moleculemolecule

Dehydration ReactionDehydration Reaction

Images : Copyright © Pearson Education, Inc.

Just as removing a water molecule linkslinks monomers together (to form polymers), the addition of a water molecule breaksbreaks a polymer chain apart (releasing a monomer).The process of breaking up polymers is called hydrolysis.hydrolysis.Hydrolysis is essentially the reverse of a dehydration reaction.Hydrolysis is necessary to break down polymers that are too large to enter a cell otherwise.

HydrolysisHydrolysisWater Water

moleculemolecule

Hydrogen Hydrogen atomatom Hydroxyl Hydroxyl

groupgroup

shorter polymer

monomerImages : Copyright © Pearson Education, Inc.

HydrolysisHydrolysis

Note that the addition of a water molecule results in the reinstatement of a hydroxyl group at the detached end of the polymer, and the hydrogen atom at the detached end of the newly formed monomer.

Hydrogen atom

Hydroxyl group

shorter polymer

monomerImages : Copyright © Pearson Education, Inc.

Enzymes

• Both dehydration reactions and hydrolysis require the help of enzymes to make and break bonds

• Enzymes are specialized proteins that speed up the chemical reactions in cells

• Enzymes are extremely important – without them, many reactions cannot take place. If you lack lactase, you cannot hydrolyze the bond in lactose

CarbohydratesCarbohydrates are polymers made up of carbon, hydrogen, and oxygen atoms.Carbohydrates play important roles in the energy storage and structural support of organisms, and are themselves an excellent source of energy.

Carbcarbon

ooxygen

hydrhydrogen

The monomers that make up carbohydrates are called monosaccharides.monosaccharides.

A monosaccharide is a small sugar, that can link together to form larger, more complex sugars.

Monosaccharides generally contain carbon, hydrogen and oxygen in a ratio of 1:2:1.

Glucose, the sugar that carries energy to the cells of your body, is a monosaccharide with the chemical formula of C6H12O6. Images : Copyright © Pearson Education, Inc.

When two monosaccharides are linked together by dehydration synthesis, they form a disaccharide.disaccharide.Examples of disaccharides include the table sugar sucrose, the milk sugar lactose, and maltose which is formed by linking two glucose molecules together.


Recall that all polymers are built by a dehydration reaction.dehydration reaction.


Monosaccharides can also be linked together to form polysaccharides.polysaccharides.A polysaccharide is a large polymer consisting of hundreds or thousands of monosaccharides linked by dehydration reactions.

Polysaccharides function as storage molecules or structural compounds.The most common types of polysaccharides are starch, glycogen, cellulose, and chitin.

Polysaccharide: StarchPolysaccharide: Starch

StarchStarch is an energy storage polysaccharide used by plants.Starch consists entirely of repeating glucose monomers.

glucoseglucose

glucoseglucoseglucoseglucose

glucoseglucoseglucoseglucose

glucoseglucose

glucoseglucose

glucoseglucose

glucoseglucose

glucoseglucose

glucoseglucose

glucoseglucose

glucoseglucose

glucoseglucose

glucoseglucose

glucoseglucose

glucoseglucose

glucoseglucose

glucoseglucose

glucoseglucose


Through the process of photosynthesis, plants produce glucose as an energy source.Often, a plant produces more glucose than is readily needed, so the plant stores this energy as long chains of glucose molecules, or starch!Starch is found in potatoes and grains, such as wheat, corn and barley.

Polysaccharide: GlycogenPolysaccharide: Glycogen

GlycogenGlycogen is an energy storage polysaccharide used by animals.Glycogen also consists entirely of repeating glucose monomers, but is much longer and more branched than starch.Glycogen is broken down into glucose as energy is needed.

Polysaccharide: CellulosePolysaccharide: Cellulose

CelluloseCellulose is a structural polysaccharide used by plants.Cellulose is the most abundant organic compound on Earth, forming the cell walls of all plant cells.

Polysaccharide: CellulosePolysaccharide: Cellulose

Cellulose consists of long chains of glucose molecules linked in such a way that they can not be broken down easily.Humans are unable to digest cellulose and it makes up the fiber in our diets.Certain microbes can digest cellulose, and reside in the guts of herbivores, such as cows, sheep, and even termites!

CelluloseCellulose

22

33

44

11

Polysaccharide: ChitinPolysaccharide: Chitin

ChitinChitin is a structural polysaccharide used by animals.Animals that use chitin for external skeletons include insects and crustaceans.Fungi also have chitin in their cell walls for structural support.Chitin attaches to proteins forming a tough and resistant protective material.

Chitin forms the Chitin forms the exoskeleton of exoskeleton of crustaceans crustaceans such as crabs such as crabs and lobsters, as and lobsters, as well as insects well as insects and spiders!and spiders!


StoragStoragee

StructureStructure

AnimalAnimalss

PlantsPlants

GlycogenGlycogen

ChitinChitin

StarchStarch

CelluloseCelluloseImages : Copyright © The McGraw-Hill Companies, Inc.

LipidsLipids

• For short-term energy storage, animals convert glucose into glycogen.

• For long-term storage, however, organisms usually convert sugars into fats, or lipids.lipids.

• Lipids are a diverse group of molecules that includes oils, fats, waxes, phospholipids, and steroids.

• All lipids are insoluble insoluble in water because they are non-polar.


LipidsLipids• Lipids are important for energy storage

because they contain many more energy-rich C-H bonds than carbohydrates.

• A gram of lipids contains twice as much energy as a gram of polysaccharides, such as starch.


Lipids: FatsLipids: Fats• Fats are made up of 2 smaller molecules:

glycerolglycerol and fatty acids.fatty acids.• A fat molecule contains 1 glycerol 1 glycerol and 3 fatty 3 fatty

acids.acids.• For this reason, fats are called triglyceridestriglycerides.


Lipids: FatsLipids: Fats

• A fatty acid consists of a long chain of carbon and hydrogen atoms.

• The arrangement of these atoms can vary, affecting the fat molecule’s physical properties.

• Fats whose fatty acids contain the maximum number of hydrogen atoms that can fit are called saturated fatssaturated fats.

Lipids: FatsLipids: Fats• Fats whose fatty acids contain double bonds

between some of the carbon atoms are called unsaturated fatsunsaturated fats because they contain fewer than the maximum amount of hydrogen atoms.


Lipids: FatsLipids: Fats• The double bonds (C=C) in unsaturatedunsaturated fats

cause kinks, or bends, in the carbon chains of the fatty acids.

• These kinks prevent the molecules from packing tightly together so unsaturated fats (like corn oil) remain liquid at room temperature.


Lipids: FatsLipids: Fats• In contrast, saturatedsaturated fats have no double

bonds (or kinks).• The molecules can then pack more tightly

together, so saturated fats (like butter) are solid at room temperature.


Who You Calling Fat?!• Triglycerides (fats and oils):

– Store energy– Insulate (blubber, etc)– Provide cushioning– Prevent dehydration– Help to maintain internal temperature

Lipids: PhospholipidsLipids: Phospholipids

• PhospholipidsPhospholipids are structurally similar to fats, but contain only 2 fatty acids 2 fatty acids attached to a glycerol molecule.

• Each phospholipid molecule has a polar, or hydrophilichydrophilic end, and a non-polar, or hydrophobichydrophobic end.

• Phospholipids are the main component of cellular membranes.

Lipids: PhospholipidsLipids: Phospholipids• The polar, or hydrophilic end of

a phospholipid is “water-loving” and water soluble.water soluble.

• The non-polar, or hydrophobic end of a phospholipid is “water-fearing” and water insolublewater insoluble.



• The membranes of all cells are composed of two layers of phospholipids, called a bi-layerbi-layer.

• The polar, hydrophilic ‘heads’ face outward and are in contact with the aqueous environment on either side of the membrane.

• The non-polar, hydrophobic ‘tails’ cluster together in the middle of the membrane.


Water (outside of cell)Water (outside of cell)

Water (inside of cell)Water (inside of cell)


Hydrophilic headHydrophilic head

Hydrophobic Hydrophobic tailstails

Lipids: SteroidsLipids: Steroids• A steroidsteroid is a type of lipid that does not

contain fatty acids.• Instead, steroids are composed of 4 carbon

rings fused together.


4 Carbon 4 Carbon ringsrings

11 22

33 44

Lipids: SteroidsLipids: Steroids• Cholesterol is a common steroid found in

animal cell membranes.• Cholesterol is also part of some sex hormones

like testosterone, estrogen and progesterone.

Cholesterol

Testosterone

Estrogen

• Proteins are a very diverse group of organic molecules. The many shapes of protein molecules allow them to perform a variety of functions.

• In living organisms, they are used for transport, structure, metabolism, communication, and even to detect stimuli such as light.

ProteinsProteins


• The protein hemoglobin carries oxygen in your blood, and the protein keratin helps support your skin, hair and nails.

Amino AcidsAmino Acids• Like other organic polymers, proteins are made of

many monomers bonded together.• These monomers are called amino acidsamino acids, and

there are 20 different kinds found in protein molecules.

• Every amino acid molecule contains an amino group (--NH2) and a carboxyl group (--COOH).


Amino acids are linked together via dehydration synthesis.

The bonds between amino acid monomers are called peptide peptide bonds.bonds.

Peptide bond


• A polypeptide contains hundreds or thousands of amino acids linked together by peptide bonds.

• The unique combination of amino acids in a protein molecule determines its specific shape, or structure.

ProteinsProteins


• The shape of a protein The shape of a protein determines its specific determines its specific function.function.

Primary StructurePrimary Structure• The primary structure primary structure of a protein describes

its unique sequence of amino acids.sequence of amino acids.• The primary structure is determined by the

cell’s genetic information (DNA).


Secondary StructureSecondary Structure• The secondary structure secondary structure of a protein describes

its folding pattern.folding pattern.• Chains of polypeptides may fold into shapes

like a pleated sheet or an alpha helix


Secondary Structure• The many hydrogen

bonds within the polypeptide chain of silk fibers make spider fiber as strong as steel; uses of silk proteins include fishing line, surgical thread and bulletproof vests!

Tertiary StructureTertiary Structure• The tertiary structure tertiary structure of a protein describes its

overall 3-dimensional shape.3-dimensional shape.• This includes all of the pleated sheets and alpha

helixes and is the active form of the protein.


Quaternary StructureQuaternary Structure

• The quaternary structure quaternary structure of a protein describes the complex association of multiple multiple polypeptide chains.polypeptide chains.

• Not all proteins consist of 2 or more polypeptide chains, but those that do have a quaternary structure.

• Each polypeptide chain in the association has its own primary, secondary, and tertiary structures.

Quaternary StructureQuaternary Structure

Quaternary structure

Tertiary

structu

re

Secondary structure

Primary structure


Quarternary Structure

• Collagen is formed by several polypeptide chains in a rope-like arrangement

• Gives connective tissue, bone, tendons, and ligaments its strength!

• Hemoglobin is another example of a quarternary structure protein (transports oxygen in blood)

Polypeptidechain

Collagen

• When exposed to excessive heat, or changes in salinity or pH, a protein can denature.denature.

• Denaturation causes the polypeptide chains in a protein to unravel, and lose their specific shape.

Protein shape determines functionProtein shape determines function

Denaturation

Denatured protein

Properly-folded protein


• When this happens, a protein will no longer function normally.

EnzymesEnzymes• EnzymesEnzymes are proteins that increase the rate of

chemical reactions and so are called catalystscatalysts.• Like other proteins, the structure of enzymes

determines what they do.


• Since each enzyme has a specific shape, it can only catalyze a specific chemical reaction.

• The digestive enzyme pepsin, for example, breaks down proteins in your food, but can’t break down lipids or carbohydrates.

Proteins gone bad

• So what happens is a protein folds incorrectly?• Many diseases, such as Alzheimer’s and

Parkinson’s involve an accumulation of misfolded proteins

• Prions are infectious agents composed of proteins

• Prion diseases are currently untreatable and always fatal

Prions

• Prions infect and propogate by refolding abnormally into a structure that is able to convert normally-folded molecules into abnormally-structured form

• This altered form accumulates in infected tissue, causing tissue damage and cell death

• Prions are resistant to denaturation due to their extremely stable, tightly packed structure

Prions

• Prions are implicated in a number of diseases in a variety of mammals:– Bovine Spongiform Encephalopathy (“Mad Cows

Disease”) – spread by feed containing ground-up infected cattle

– Creutzfeldt-Jakob Disease – degenerative neurological disorder spread by skin grafts or human growth hormone products; Kuru is a similar disease spread by cannibalism among the Fore tribe of Papua New Guinea

Prions

• Chronic Wasting Disease – found in deer, moose, elk in U.S. and Canada

• Fatal Familial Insomnia – very rare, inherited prion disease (50 families worldwide have the responsible gene mutation); insoluble protein causes plaques to develop in the thalamus, the region of brain responsible for the regulation of sleep; fatal within several months

Proteins gone bad (or maybe not…)• Sickle cell anemia is caused by a genetic

mutation of hemoglobin (not a prion); causes a sickling of the red blood cell

• Those with 2 copies of the mutated gene have a reduced life expectancy; those with only 1 copy have “Sickle trait” – cells only sickle under reduced oxygen load

• Sickle cell disease common in tropical and subtropical regions where malaria is common; provides a selective advantage against malaria!

Sickle Cell Anemia

• Remember natural selection is a pessimistic process

• Those with the sickle cell mutation survive malaria infestation better than those without

• “Heterozygous advantage”

Normal red blood cell

Sickle blood cells

Nucleic AcidsNucleic Acids

• Nucleic acids Nucleic acids are molecules, like DNA, that store genetic information - the instructions cells need to build proteins.

• A nucleic acid contains information on what type of amino acids are needed to make a protein and in what order they should be linked to give the protein its structure, and function.


NucleotidesNucleotides• The monomers that are linked together to

form a nucleic acid polymer are called nucleotides.nucleotides.

Every chromosome in our cells contains

nucleic acids

Chromosome Polymer = nucleic acid

Nucleic acids are polymers

Monomer = nucleotide

Many nucleotide monomers make up

each nucleic acidImages : Copyright © The McGraw-Hill Companies, Inc.

NucleotidesNucleotides

• Every nucleotide has three parts:– 5-carbon sugar– Phosphate group– Nitrogenous base



• Nucleotides can encode information because they contain more than one type of nitrogenous base.

• There are 5 different nitrogenous bases:



PyrimidinesPyrimidines

CytosineCytosine ThymineThymine UracilUracil

PurinesPurines

AdenineAdenine GuanineGuanine



• There are two types of nucleic acids:–RNARNA–DNADNA


• There are two types of nucleic acids:– RNA = ribonucleic acidRNA = ribonucleic acid– DNA = deoxyribonucleic acid DNA = deoxyribonucleic acid

• Both are nucleotide polymers but they differ in both their structures and their functions.

RNARNA

• Ribonucleic acid Ribonucleic acid contains the sugar ribose.ribose.• RNA contains the nucleotide uracil (U) instead

of the nucleotide thymine (T).

RNA contains:RNA contains:• adenine (A)adenine (A)• uracil (U)uracil (U)• cytosine (C)cytosine (C)• guanine (G)guanine (G)


RNARNA


RNARNA

• RNA exists as a long, single strand single strand of nucleotides.


DNADNA• In deoxyribonucleic aciddeoxyribonucleic acid, a hydroxyl group on

the sugar is replaced with a hydrogen atom.• DNA contains the nucleotide thymine (T)

instead of the nucleotide uracil (U).

DNA contains:DNA contains:• adenine (A)adenine (A)• thymine (T)thymine (T)• cytosine (C)cytosine (C)• guanine (G)guanine (G)


DNADNA


DNADNA

• DNA exists as a two two strands strands of nucleotides wound around each other to form a double helix.double helix.


The Double HelixThe Double Helix

• DNA’s double helix results from hydrogen hydrogen bondsbonds formed between its nitrogenous bases.

• Large nitrogenous bases (adenine and guanine) pair with smaller bases (thymine and cytosine).

• Adenine bonds with thymine (A-T) Adenine bonds with thymine (A-T) and guanine bonds with cytosine (G-C).guanine bonds with cytosine (G-C).

The Double HelixThe Double Helix

• Because of its A-T, G-C pairing, each DNA strand is complimentarycomplimentary to the other.

• If the sequence of one strand is ATCGATATCGAT, the sequence of the other strand must be TAGCTATAGCTA because A always bonds to T, and C always bonds to G.


DNA Double HelixDNA Double Helix


DNA double helix

• The 2 DNA chains are held in a double helix by hydrogen bonds between their paired bases

• Most DNA molecules have thousands or millions of base pairs– (A and T would be considered a base pair; as

would C and G)

Hydrogen bonds (dotted lines)

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