Lecture 3: Biological (Organic) Molecules

Covers Chapter 3

Organic Molecules Contain CARBON*

• Organic molecules have a carbon skeleton bonded to hydrogen atoms.

• The term “organic: is derived from the ability of living organisms to synthesize and use these types of molecules.

• Life is created, sustained, and propagated due to the fact that organic molecules can interact in complex ways.

Carbon

• Carbon (6) has 6 electrons and 6 protons

• 2 electrons in inner shell, 4 in outer shell

• Room for 4 more electrons in outer shell to become stable.

• Carbon can form single bonds with 4 other molecules, double bonds with 2 other molecules, and even triple bonds.

Carbon bonds

•

Functional Groups*

• Once carbon has formed these molecules, the atoms that attach to the carbon become functional groups of the molecule. Since carbon is so stable, it is the functional groups which are most likely to react chemically with other substances.

Example of Organic Molecule with blue functional groups

Table 3-1

Common Functional Groups and how they interact with other molecules

Organic molecules react with other organic & non-organic molecules

• The structure of a molecule as well as the chemical properties of that molecule (which are a result of its structure) determine how it will react with other molecules

• Result of this is organic molecules with complex shapes: branched chains, rings, sheets, etc

Example of organic reaction

Molecules can do work!*

• In addition, molecules can change structure and chemical properties as a result of interactions with other molecules.

• These changes in structure and properties give cells the ability to:– Eliminate waste– Move– Grow– Reproduce– EVOLVE?

Living organisms prefer small molecules

• Living organisms prefer to assemble small molecules and hook them together to make large intricate molecules

• Ex: trains are made up of individual cars…

• Individual subunits of organic molecules are called monomers.

• Chains of monomers are called polymers

Monomers join together via DS

• Subunits are joined together via a chemical reaction called dehydration synthesis (DS)

• A hydrogen atom is removed from one subunit and a hydroxyl ion is removed from the second subunit, and a molecule of water is created, as a by product, while the two monomers become bonded together.

Dehydration Synthesis

Fig. 3-1

dehydrationsynthesis

Reverse of DS is hydrolysis

• Long subunits sometimes need to break down into small units (ex: the food we eat)

• Our bodies like to break down long subunits and use the small pieces

• Hydrolysis is the donation of a water molecule to a polymer. H and OH break apart, and are added to the ends of each monomer that is created.

• Digestive enzymes use hydrolysis to digest food.

Hydrolysis

Fig. 3-2

hydrolysis

What types of organic molecules exist in living organisms?*

• There are 4 types of molecules (monomers)that living organisms use:– Carbohydrates– Lipids– Proteins– Nucleic Acids

Carbohydrates (Sugars)

• A molecule with C, H, and O in approximately a 1:2:1 ratio.

• Major functions of carbs: – Store energy in cells– Strengthen cell walls in bacteria, fungi and

plants– Form protective armor for insects, crabs and

other animals.

Monosaccharides: monomers of carbohydrates

• Monosaccharides are single units of carbs. They have the ability to join with other monosaccharides to form polysaccharides

• Monosaccharides have between 3 and 7 carbon atoms arranged in a “backbone.”

• Glucose is the most common monosaccharide. Structure is C6 H12 O6

Monosaccharides

Fig. 3-5

galactosefructose

6

5

4

32

12

34

5

1

6

Non-humans make different monosaccharides

– Fructose: monosaccharide made by fruit– Galactose: monosaccharide found in milk

Disaccharides

• 2 monosaccharides joined together by dehydration synthesis.

• Often used for short term energy storage in plants.• When energy is needed, disaccharide is broken

into 2 monosaccharides (via hydrolysis) and each monosaccharide can be broken down to release energy that is stored in chemical bonds

• Sucrose, Lactose, maltose are examples

Synthesis of a Disaccharide

Fig. 3-7

glucose fructose sucrose

dehydration synthesis

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Polysaccharides*

• Long chain of monosaccharides, used for energy storage– Starch: made by plants– Glycogen: made by animals (stored in muscle

and liver)– Cellulose: made by plants but used as a

STRUCTURAL molecule (tree bark)– Chitin:made by bugs and crabs, used as a

STRUCTURAL molecule (crunchy body)

Starch is an Energy-Storing Plant Polysaccharide

(b) A starch molecule

(a) Potato cells

(c) Detail of a starch molecule

starch grains

Fig. 3-8

Fig. 3-9

Lipids*

• Diverse group of molecules that contain regions composed almost entirely of carbon and hydrogen

• Functions:– Store energy

– Waterproof coverings on plant or animal bodies

– Primary component of cell membranes

– Hormones

Fatty Acids: monomers of Lipids

• Molecules containing long chains of C & H with carboxylic functional groups (-COOH)

• If chain contains carbon-carbon double bond, the FA is said to be unsaturated.

• If no double bonds, it is considered saturated.

Fatty Acid

Lipid Classification*

• 3 major groups– 1.) Oils, fats, and waxes– 2.) Phospholipids– 3.) Steroids

1.) Oils, Fats, Waxes

• Also known as triglycerides• Oils and fats are primarily for energy storage• Formed by dehydration synthesis by linking 3

fatty acids to a molecule of glycerol (a three carbon molecule.)

• Fats produced by animals, oils produced by plants

glycerol fatty acids

triglyceride

Fig. 3-12

Oils are liquids, Fats are solids

• In oils, the carbons of the fatty acids are joined by single bonds, while in fats, the carbons in the fatty acids are joined by double bonds, making them solids at room temp.

An Oil

Fig. 3-13b

Fig. 3-13a

2.) Phospholipids*

• Component of cell membranes

• Similar to a fatty acid, except one of the three fatty acid tails is replaced by a functional group that contains nitrogen.

• Structure is fatty acid tails on one end (insoluble in water) and phosphate-nitrogen head (polar and water soluble)

Phospholipids

Fig. 3-14

polar head glycerolbackbone

phosphategroup

variablefunctional

group

(hydrophilic) (hydrophobic)

fatty acid tails

3.) Steroids*

• Composed of 4 rings of carbon atoms, fused together, with multiple functional groups protruding.

• Functions:– Regulate metabolism– Regulate immune response– Regulate reproduction

Steroids

Fig. 3-15

Proteins*

• Diverse group of molecules composed of one or more chains of amino acids. (AA’s)

Functions of Proteins*• Promote chemical reactions: these proteins are called

enzymes.• Provide structure to organisms: ex: keratin – principle

protein of hair, horns, nails, scales and feathers• Help organisms move: ex: actin/myosin in muscle• Provide defense for an organism: ex: antibodies in our

immune system• Provide food for developing animals ex: albumin in egg

white-feeds growing chick• Relay signals to other parts of the body: ex: insulin

released from pancreas, promotes glucose uptake

Amino Acids: monomers of proteins

• Amino acids are molecules that have a common structure: central carbon bonded to three different functional groups

– Nitrogen-containing amino group (NH2)

– Carboxylic acid group (COOH)

– An “R” group that varies among the different amino acids

• 20 common amino acids

• The “R” group gives the amino acid its distinctive properties:

– Some are hydrophobic

– Some are hydrophilic

Amino Acid Structure

Fig. 3-17

aminogroup

hydrogen

variablegroup

carboxylicacid group

glutamic acid (glu) aspartic acid (asp)

(a) Hydrophilic functional groups (b) Hydrophobic functional groups

(c) Sulfur-containingfunctional group

leucine (leu)phenylalanine (phe)

cysteine (cys)

Fig. 3-18

How are proteins made?

• Amino acids linked together via dehydration synthesis (the NH2 group of one AA is joined to the carbon in the carboxylic group of another AA)

• This is called a peptide bond

• Proteins can be three to thousands of AA’s long

Protein Synthesis

Fig. 3-19

amino acid

aminogroup

aminogroup

carboxylic acidgroup

amino acid peptide water

peptidebond

�

dehydrationsynthesis

Proteins exhibit up to 4 levels of structure

• Primary structure: the sequence of amino acids

• Secondary structure: shape of protein: helix, pleated sheet, etc (result of primary structure and caused by hydrogen bonding between the amino acids making up the protein)

Proteins exhibit up to 4 levels of structure

• Tertiary structure: folds in the protein caused by interaction of functional groups BETWEEN different AA’s AND the environment the protein is in (if protein normally exists in watery environment, hydrophilic functional groups will “point” outward and hydrophobic groups will “point” inward.)

Proteins exhibit up to 4 levels of structure

• Quaternary structure: only happens with some proteins where more than one AA chain exists

• Interaction between DIFFERENT AA chains (polypeptides)

Fig. 3-20

(a) Primary structure:The sequence of amino acids linked by peptide bonds

(c) Tertiary structure:Folding of the helix resultsfrom hydrogen bonds with surrounding water molecules and disulfide bridges between cysteine amino acids

(d) Quaternary structure:Individual polypeptides are linked to one another by hydrogen bonds or disulfide bridges

(b) Secondary structure:Usually maintained by hydrogen bonds, which shape this helix

helix

hydrogenbond

heme group

leu

val

lys

lys

gly

his

ala

lys

val

lys

pro

Structure confers function

• Ex: Hemoglobin• The type, position and number of AA’s with

specific functional groups determine its function• Specific R groups allow heme group to bind

oxygen• Polar amino acids on outside of molecule allow it

to remain dissolved in watery environment of RBC

Nucleic Acids*

• Large organic molecules that are responsible for encoding, transmitting and expressing genetic information

EX: DNA/RNA. The sequence of nucleotides in the DNA of living organisms carries hereditary information. DNA is a double-stranded molecule made up of 2 nucleotide strands. RNA is single stranded.

Nucleotides: monomers of nucleic acids*

• A nucleotide has a basic 3-part structure:– 5 carbon sugar– Phosphate functional group– Nitrogen-containing base (5 different bases exist)

• Nucleotides fall into 2 categories, depending on which sugar is present– Deoxyribose– Ribose

Nucleotide

•

The Energy-Carrier Molecule Adenosine Triphosphate (ATP) is also a nucleotide (3 phosphate groups instead of one)

Fig. 3-23