Chapter 3: Organic Chapter 3: Organic MoleculesMolecules

Biology 100Spring 2009

Carbon: The Central AtomCarbon: The Central AtomOrganic Molecules contain

Carbon, and are usually complex. ◦Carbon atoms can be arranged in

rings or chains

Carbon: The Central AtomCarbon: The Central AtomCarbon is the central atom in all

organic molecules.Can bond to one another, creating

long chains or rings.Carbon likes to have ______

covalent bonds.When several carbon are present,

they form the backbone to which other elements or molecules attach.

Carbon: The Central AtomCarbon: The Central AtomC-C and C-H bonds are rich

in______. The simplest hydrocarbon is methane (CH4), which is dominant in natural gas.

A major component of gasoline is the 8-carbon molecule called octane.

Carbon: The Central AtomCarbon: The Central AtomIn addition, carbon can also form

double and triple bonds.A double bond is indicated by two

lines between atoms.◦C=O or C=C

Triple bonds are denoted by three lines between atoms.

Carbon: The Central AtomCarbon: The Central AtomEmpirical Formula of a chemical

formula is a simple expression of the relative number of atoms in it.◦C2H6O

Structural Formula is the graphic arrangement and bonding of atoms.

IsomersIsomersAn isomer has the same

empirical formula, but different structural formulas.◦Example is the empirical formula

C3H8O, but can be structurally different.

Propan-1-ol Propan-2-ol Methoxyethane

IsomersIsomersStructural isomers may also

involve differences in the carbon backbone itself.

IsomersIsomersGeometric isomers have the same carbon

backbone and even the same elements or functional groups attached to the same carbons.

But they differ from each other in ______________ these elements or groups are located around a C=C bond.

IsomersIsomersWhile we draw biological molecules as if they

were two-dimensional, they are actually three-dimensional.

Enantiomers are ________ images of one another, like a right hand and left hand.

Functional GroupsFunctional GroupsAs mentioned earlier, carbon is the

backbone of organic molecules. However, attached to these carbon atoms are combinations of other elements, including carbon. These are known as functional groups.

MacromoleculesMacromoleculesMacromolecules are very large,

organic molecules.Macromolecules are organized

into four major classes because of similarities in structure and form

Carbohydrates Proteins

Nucleic Acids Lipids

MacromoleculesMacromoleculesMonomer is a small molecule

◦ Monomers may have their own specific functions and/or can be linked by covalent bonds to form larger molecules.

Polymers are composed of identical or similar monomers linked together by covalent bonds.

Glucose is a monomer, but when many glucose molecules chemically bond to one another, it can become the polymer, starch.

CarbohydratesCarbohydratesCarbohydrates are also known as

sugars and their names often end in –ose (fructose, sucrose, cellulose).

Carbohydrates are composed of carbon, hydrogen, and oxygen.◦ They have a typical chemical formula:

CnH2nOn, with twice as many hydrogen atoms as carbon and equal numbers of carbon and oxygen atoms.

• Is it a carbohydrate?• C6H1206

• C2H6O

MonosaccharideMonosaccharideGlucose, C6H12O6, is a

very common monosaccharide

It has a terminal carbonyl group

And 5 hydroxyl groups

Glucose and many other monosaccharides are an important sources of fast energy.

MonosaccharideMonosaccharide Important 5C

monosaccharides are ribose (C5H10O5) and deoxyribose (C5H10O4).

Glucose is the most common 6C monosaccharide, but its structural isomer, fructose, is common as well.

An enzyme, isomerase (ase = enzymes), converts one isomer to the other.

DisaccharideDisaccharideA disaccharide is formed by a

dehydration reaction between two monosaccharides.

Disaccharides function in extracellular transport of sugars (e.g., sucrose in plant sap, lactose in mammalian milk).

The monosaccharides glucose and fructose combine to form the disaccharide, sucrose (plant sugar).

Disaccharides function in extracellular transport of sugars (e.g., sucrose in plant sap, lactose in mammalian milk).

DisaccharideDisaccharide

While most babies are able to digest lactose into glucose and fructose, many people have a hard time digesting lactose as they age.◦ Unfortunately, intestinal bacteria will take

advantage of this food source, producing gas, and inducing diarrhea, bloating, and nausea.

One major reason for this problem is that levels of the key enzyme for this hydrolysis, lactase, decline as we age, starting as early as age 2.

There are also geographic differences in lactose intolerance.

web.lemoyne.edu/~hevern/psy340/graphics/lactose.intolerance.jpg

PolysaccharidePolysaccharidePolysaccharides are long chains with

hundreds or thousands of monosaccharides.Polysaccharides have two functions:

◦ Energy Storage (e.g. glycogen, starch)

◦ Extracellular Structural Materials (cellulose)

ProteinsProteinsProteins are polymers composed of

amino acids.Amino acids have C, N, O, and H in

their structure. Made of four different parts.

C

R

H Hydrogen

“R” group or variable side chain

N

H

H________ group

COH

O_________ group

Amino AcidsAmino AcidsThere are

20 different R groups and these produce the 20 amino acids that are used for producing proteins.

Amino AcidsAmino Acids Humans cannot synthesize

8 of the 20 amino acids. While a diet with animal

products provides all these essential amino acids, a purely ______________ diet may lead to problems because some plants are deficient in these 8.

Since the body does not store amino acids, a single deficiency of an essential amino acid, can lead to a protein deficiency.

PolypeptidesPolypeptidesPeptide bond is a bond formed by two

molecules when a carboxyl group of one molecule reacts with an amine group in another molecule.

Polypeptides are polymers of amino acids linked by peptide bonds.

PolypeptidesPolypeptidesProteins are polypeptides that fold

into complex 3-D shapes.There are four different structures

of proteins.◦Primary◦Secondary◦Tertiary◦Quartenary

ProteinsProteinsPrimary structure of a protein, the order

of the amino acids will ultimately determine it’s shape.

Secondary structure of a protein are from amino acids forming weak bonds with other amino acids.

ProteinsProteinsTertiary structure of proteins is shaped

due interactions of side chains.

Quaternary structure is caused by interactions among separate polypeptides, each with their own tertiary structure.

Hemoglobin has 2 alpha and 2 betaglobin proteins

Small Changes Add UpSmall Changes Add UpThe genetic disease, sickle-cell anemia, is due

to a change of a single amino acid in the oxygen-carrying protein hemoglobin.

In individuals with sickle-cell anemia, valine (a non-polar AA) replaces the sixth amino acid, glutamine (a polar AA) of a normal globin.

Protein ShapeProtein ShapeProtein shape depends on the primary

structure of polypeptides and also on the physical environment and the presence of other proteins.◦ Smaller proteins “self-assemble” into their

functional shape.◦ Others require ________________ proteins to

assist in proper folding. Changes in the environment or binding (or

release) of other molecules cause proteins to change shape.

Protein ShapesProtein ShapesTwo proteins may have the same

amino acid sequence, but do not fold in the same way. This can cause them to function differently.

Prions are misfolded proteins, and when they enter the body, they can cause normal proteins to fold differently.

PrionsPrionsMad cow disease (BSE or bovine spongiform

encephalopathy) and related illnesses (scrapie in sheep, variant Creutzfeldt-Jakob disease in humans) are caused by an abnormal protein which can alter the shape of normal proteins.

In humans, the disease leads to neurological problems and death within a year of the onset of symptoms.

Mad-Cow DiseaseMad-Cow Diseasewww.cnn.com/interactive/world/europe/0010/cjd/bse.gif

Functions of ProteinsFunctions of ProteinsStructural proteins (e.g., collagen) are

intra- and extracellular supports.Storage proteins (e.g., ovalbumin) are a

source of amino acids to support the synthesis of new proteins during development.

Transport proteins either carry materials around the organism (e.g., hemoglobin) or carry molecules past biological membranes (e.g., Na+-K+ pump).

Hormonal proteins (e.g., insulin) are intercellular messengers.

Function of ProteinsFunction of ProteinsReceptor proteins detect chemical signals

(e.g., hormones) and alter the intracellular environment.

Contractile proteins (e.g., myosin) are responsible for organismal and cell movement.

Defensive proteins (e.g., antibodies) attack foreign molecules like viruses, bacteria, and other parasites.

Enzymatic proteins control specific chemical reactions.

NucleotidesNucleotidesNucleotides are molecules that

comprise the structural units of DNA and RNA

.

Fig. 3.15, pg. 57

Nitrogen Base

Phosphate Group

A 5C sugar

NucleotidesNucleotidesThe 5-carbon sugar in nucleotides

can be either ribose or deoxyribose.

Ribose (C5H10O5) is found in ribonucleotides.

Deoxyribose (C5H10O4) is found in deoxyribonucleotides.

NucleotidesNucleotidesThere are five possible

nitrogenous bases.

In DNA there is Adenine, Guanine, Cytosine, and Thymine.◦In RNA Thymine is replaced with

Uracil.

Classes of Nucleic AcidsClasses of Nucleic AcidsPolynucleotides (ribonucleic acid: RNA

and deoxyribonucleic acid: DNA) carry the information for and participate in protein synthesis.

ATP (adenosine triphosphate) and GTP (guanine triphosphate) store and release energy to support normal metabolic activities.

Nucleotides coenzymes transport high energy electrons from one site in the cell to another.

A Closer Look at A Closer Look at NucleotidesNucleotides

RNA (Ribonucleic Acid) is a __________ strand.

In single strands of RNA and DNA, the sugar group of one nucleotide bonds to the phosphate of the next.

RNA will only have Guanine, Adenine, Uracil,and Cytosine bases.

RNARNARNA molecules have multiple

roles◦rRNA (ribosomal RNA) combines with

proteins to form ribosomes which synthesize new proteins

◦mRNA (messenger RNA) sets the order with which amino acids should be bonded to synthesize a polypeptide

◦tRNA (transfer RNA) transfers or carries specific amino acids to the ribosome

A Closer Look at A Closer Look at NucleotidesNucleotidesDNA molecules are ___________ stranded.

The two strands are linked together by hydrogen bonds between nitrogen bases on the two strands.

Specific bases on one strand match up with specific bases on the other strand◦ ______ with C and

______ with T

The order of a section of nucleotides on DNA (a gene) contains the information for producing a __________________.

Each of the 100,000 different proteins synthesized by humans begins with a section of DNA.

This gene is transcribed from DNA to _______________.◦ The mRNA is

complementary to the nucleotides of DNA.

At the ribosome, the order of nucleotides on mRNA directs the addition of amino acids to form a protein during translation. Fig. 3.19, pg. 59

LipidsLipidsLipids are large, nonpolar organic

molecules that don’t dissolve in polar solvents well. ◦They are not polymers, and do not

have the same ratio of C, H, O as carbohydrates do. They usually have fewer oxygen in their empirical formula.

Classes of Lipids:◦Fats◦Phospholipids◦Steroids

Fatty AcidsFatty AcidsFatty Acids are the monomers of

fats.Fatty acids have lots of C & H

atoms and two O atoms.There is a long backbone of C &

H with a carboxyl (COOH) group at one end.

Fatty AcidsFatty AcidsSaturated Fatty Acids lack the C=C

in the backbone.

Most saturated fats are solid at room temperature. (animal fats)

It has as many Hydrogens attached to it as possible.

Fatty AcidsFatty AcidsUnsaturated Fatty Acids have one

(monounsaturated) or more (polyunsaturated) C=C bonds in the backbone.

Most unsaturated fatty acids are liquid at room temperature (plant oils).

Fatty acids are a major source of ________________ in cells.

Fatty AcidsFatty AcidsWhile your body can synthesize most of

the fatty acids that it requires, it cannot synthesize two essential fatty acids.

These fatty acids are used in the production of hormones that control cell growth and specialization. A lack of them can cause impaired growth, skin problems and neurological problems.

Omega-3 fatty acids are also linked with reduced risk of heart attack.

Fatty AcidsFatty AcidsNormally, polyunsaturated and

monounsaturated fats, from plant oils have positive effects on health.

However, in the many processed foods (cookies, fried foods, candies, crackers), some natural fats are converted to trans fats.

Trans fats elevate levels of cholesterol and LDL (low density lipoprotein) in the blood.

This can lead to elevated risk of heart attacks. Now manufacturers are required to list trans fat content.

TriacylglyceridesTriacylglyceridesTriacylglycerides are a fat that has one

glycerol molecule, attached to three fatty acids.

Account for 95% of fat stored in human tissue.

TriacylglyceridesTriacylglyceridesOne major function of

triacylglycerides is space-efficient (no water),high value, energy storage (e.g., seeds, fatty deposits).◦ Fats contain 9 calories per

gram, while carbohydrates or proteins have only 4 calories per gram.

◦ Benefits Creates layers of adipose cells (filled with

vacuoles of fat) under skin to insulate from cold

Pads of fat cells packed around joints or internal organs protect these structures by absorbing sudden forces.

PhospholipidsPhospholipidsPhospholipids have

C, H, O, P, and sometimes N.

In phospholipids, one fatty acid in a triacylglyceride is replaced by a phosphate group (-RPO4).

The phosphate group gives the phospholipid a net charge.

PhospholipidsPhospholipidsPhospholipids are a major component

of cell membranes. They separate the cell contents from the exterior environment.

In cell membranes, they form bilayers with the hydrophilic heads on the outside and the hydrophobic tails on the inside.

Hydrophilic Heads

Hydrophobic Tails

SteroidsSteroidsAll steroids consist of four rings of 6C,

6C, 6C, and 5 carbons. Cholesterol has a large hydrophobic

functional group off the 5 carbon ring. Cholesterol is an important component of cell membranes and the manufacturing of vitamin D.

Cholesterol issynthesized by thebody, as well as acquired by food.

SteroidsSteroidsSome steroids are

________________ messengers - hormones.

Modified steroids (bile salts) are secreted by the liver into the intestine to aid lipid _________________ and absorption.