Unit #1Biochemistry

The Chemistry of Life

Organic Chemistry

Organic Compounds

• Organic compounds are compounds that contain carbon (with the exception of CO2 and a few others).

Organic Compounds

• Carbon based molecules• Carbon based molecules

• Make up most of living organisms

• Carbon can easily bond with up to 4 other elements

4 valence electrons = 4 covalent bonds

Organic Compounds

Can bond to 4 H

Carbon can form various bonds

• Single bond (ethane)

• C-C

• Double bond (ethene)

• C=C

• Triple bond (ethyne)

• Carbon atoms form the “backbone” of long chains or rings

• Organic molecules can be extremely large and complex; these are called macromolecules (or polymers)

Organic Compounds

Ring structured

Functional Groups

• Various elements attach to the hydrocarbon backbone to form different types of compounds.

• These reactive clusters of atoms are called functional groups.

• Elements include: H, O, S, N & P

Functional Groups

Hydroxyl group

• -OH• Found in alcohols

• E.g. Ethanol

• Polar

Functional Groups

Carboxyl group

• -COOH• Found in acids

• Polar

E.g. Vinegar- acetic acid CH3COOH

Functional Groups

Amino group

• -NH2

• Found in bases

• E.g. Ammonia

Functional Groups

Sulfhydryl group

• -SH• Often referred to as a thiol group

• Found in Rubber

- Thiols smell like garlic and are often added to natural gas to provide a detectable smell.

Functional Groups

Phosphate group

• -PO4

• Found in ATP

Carbonyl group

• If this group is at the end, the compound is called an aldehyde

• If it is found in the middle, it is called a ketone

Functional Groups

Functional Groups

Carbonyl group #1

The Aldehydes

• -COH• E.g. Formaldehyde

Functional Groups

Carbonyl group #2

The Ketones

• -CO-• E.g. acetone

Functional Groups

TEST YOUR KNOWLEDGE• What functional groups are in this molecule?

Test Your Knowledge…

• Name the functional groups

Test Your Knowledge…

• Name the functional groups

Amino group

Sulfhydryl group

Carboxyl group

Carbonyl group(Ketone)

Organic CompoundsThe 4 main types of organic macromolecules:

Carbohydrates Lipids

Proteins Nucleic Acids

Making & Breaking Organic Compounds

Anabolic ReactionsCondensation Reactions (Dehydration synthesis Reaction)

• The removal of a –H from the functional group of one unit and a –OH from another unit to form a water molecule (H2O).

• Energy absorbed

Making & Breaking Organic Compounds

Catabolic ReactionsHydrolysis Reactions

• A water molecule (H2O) is used to break a covalent bond holding subunits together.

• A –H from is given to one unit and a –OH to the another• Energy released

Enzymes

• Enzymes are biological catalysts.

• They speed up reactions without actually being consumed in the reaction.

• They are needed for condensation & hydrolysis reactions.

Enzyme Action Example:

Isomers• Isomers are molecules that have the same

formula, but a different physical structure.

• Glucose (C6H12O6) and galactose (C6H12O6) and fructose (C6H12O6) are examples of isomers.

Isomers

• Because of their differing arrangement of the atoms, they have different physical and chemical properties.

• E.g. Carvone is a flavour compound that. There are 2 isomers of carvone. One makes things taste like spearmint the other like caraway.

End Part IGet ready for Carbohydrates!

Carbohydrates• Main energy source for living things

• Breakdown of sugars supplies immediate energy for cell activities

• Plants store extra sugar as complex carbohydrates called starches

• The most common organic material on Earth.

• The general formula is C : H : O

•Count the # of each atom in the molecule shown here:

• In a ratio of 1 : 2 : 1

Carbohydrates

•

What are the functional groups on carbohydrates?

What are the functional groups on carbohydrates?

Their functional groups include:

1.Carbonyl group (an aldehyde or ketone)

2.Hydroxyl groups

• There are 3 major classes:

- Monosaccharide,

- Oligosaccharide and

- Polysaccharide

Saccharide (means “Sugar” in Greek) The names of carbohydrates end in “ose”.

Carbohydrates

Carbohydrates• Single sugar molecules are called

monosaccharides

• Monosaccharides with 5 or more carbons are linear in the dry state but form rings when dissolved in water.

Monomer of Carbohydrates:Monosaccharides

• Simple sugar• It is the main source of energy in the body• Eg. glucose – most common galactose – milk sugar fructose – fruit sugar

Carbohydrates• Oligosaccharides are sugars containing 2

or 3 simple sugars attached to one another by covalent bonds called glycosidic linkages.

• Recognize the dehydration reaction?

Examples of Disaccharides

Examples of Disaccharides

• Sucrose = glucose + fructose

Table sugar

• Maltose = glucose + glucose

Sugar in beer

• Lactose = glucose + galactose

Sugar in milk

Carbohydrates• Large molecules of many monosaccharide

are called polysaccharides• Also known as complex carbohydrates.

Examples:• glycogen – animals use it to store excess sugar• starch – plants use to it store excess sugar• cellulose – fibers that give plants their rigidity &

strength• Chitin – exoskeleton & fungi

Polysaccharide: many sugars

• Some polysaccharides are straight, others are branched.

Starch

• A storage molecule for plants.

• It is made of 2 polysaccharides:– Amylose– Amylopectin

The chains form tight coils which make them insoluble in water.

Cellulose• Cellulose molecules are not coiled or

branched.

• The chains form cross-linkages between each other.

• The fibers intertwine to form microfibrils.

• Used to build cell walls.

Chitin• Exoskeleton of insects & crabs

• The cell wall of fungi

• Chitin has uses in medicine:– Contact lenses– Biodegradable suture thread

Which is a monosaccharide?A disaccharide? A polysaccharide?

• cellulose• chitin• glucose• glycogen• sucrose• starch

Which is a monosaccharide?A disaccharide? A polysaccharide?

• Cellulose P• Chitin P• Glucose M• Glycogen P• Sucrose D• Starch P

End Part IIGet ready for Lipids!

Lipids:• Store energy

• Build cell membranes (& other cell parts)

• Act as chemical signals

Lipids:Fall into 4 families of fats:

1.Fats

2.Phospholipids

3.Steroids

4.Waxes

Lipids:• Contain carbon, hydrogen and oxygen• Have fewer polar –OH bonds &• More non-polar H-C bonds than

carbohydrates.

• Therefore, they are non-polar• They are NOT soluble in water but they are

soluble in other non-polar substances.

Lipids:• Fats store more energy than

carbohydrates or proteins.

• 1g fat = 38 kJ (9 Kilocalories)

• 1g carb = 17 kJ (4 Kilocalories)

• Calories are non-SI units of energy

• 1 cal = 4.18 kJ of energy

Lipids:• Animals convert excess

carbohydrates into fats and store the fat molecules as droplets in cells of adipose (fat) tissue.

Lipids:• Triacylglycerols (triglycerides) are the

most common fat in plants and animals.

They are made from a glycerol backbone with 3 fatty acid chains attached.

Lipids:• Glycerol is a 3-carbon alcohol

containing a hydroxyl group attached to each carbon.

Lipids:• Fatty acids are long hydrocarbon chains containing

a single carboxyl group at one end. • They are usually even numbered (16-18 carbons

long)

Lipids:• Fatty acids can be saturated (meaning that all

carbons contain the maximum number of hydrogen). These have no double bonds.

• Unsaturated fatty acids contain double or triple bonds so they are missing hydrogen-carbon bonds.

If they have many double/triple bonds they are called polyunsaturated fatty acids.

Lipids:Fatty acid shapes:

1.Saturated fatty acids have straight chains that fit tightly together allowing van der Waals attractions to form along their length.

2.These cross attractions make them solid at room temperature.

Lipids:Fatty acid shapes:

1.Unsaturated fatty acids have kinked chains that do not fit tightly so van der Waals attractions do not form.

2.Without the van der Waal attractions they are liquid at room temperature.

E.g. vegetable oils, fish oil, nut oils, etc.

Lipids:Hydrogenation:

is a process that adds hydrogen to the double bond areas “saturating” the fatty acid.

This converts oils, like canola and corn oil into semi-solid fats known as margarine or shortening.

How to make a lipid1. Link a glycerol unit and fatty acid chains…

2. A dehydration reaction takes place between the hydroxyl groups on the glycerol and the carboxyl group of the fatty acid. Three waters are removed.

3. The bond that results is called an ester linkage.

4. The process is known as esterification.

Phospholipids:1. Form the majority of cell membranes.

2. They contains:a) Glycerol molecule (backbone)

b) 2 fatty acids (non-polar tails)

c) Phosphate group (highly polar head region)

d) Choline (nitrogen compound, part of the head)

Phospholipids:1. Have a hydrophilic head (water-loving)

2. Have a hydrophobic tail (water-fearing)

Phospholipids:When added to water, the phospholipids will rearrange themselves into balls called a micelles so that the tails all face inward and the heads face outward.

Phospholipids: Cell Membrane1. The hydrophobic middle of the cell membranes do not

allow polar or charged molecules to pass through.

2. Membranes need channel pores to allow them through.

Sterols (Steroids)1. Made from 4 fused hydrocarbon rings + numerous

functional groups.

2. Examples:A. Cholesterol

B. Testosterone

C. Estrogen

D. Progesterone

3. Cholesterol in animal cell membranes helps to stabilize the structure.

4. Too much cholesterol in our diets causes deposits in our blood vessels

Sterols: Cholesterol1. Cholesterol in animal cell membranes helps to stabilize

the bilayer structure.

2. Too much cholesterol in our diets causes deposits of fatty acids (called plaques) to build up in in our blood vessels.

3. This condition is known as atherosclerosis.

4. When blood vessels become blocked we can suffer from:

A. Stroke (blockage in the brain)

B. Heart attack (blockage to arteries in the heart)

Cholesterol & Sex Hormones1. Cholesterol gets converted into vitamin D (needed for

healthy bones and teeth) and bile salts (needed for the digestion of fats)

2. Sex hormones (testosterone, estrogen and progesterone) control the development of sex traits and sex cells (eggs & sperm)

Waxes• Waxes are long-chain fatty acids linked to alcohols or

carbon rings.• The hydrophobic molecules are firm and pliable.• Their structure makes them ideal for making waterproof

coatings on plant and animal parts.• Cutin is a wax produced by plant cells to coat the stem,

leaves and fruit.– This helps hold water in and keep infections out!

• Birds produce a waxy substance to waterproof their feathers.

• Bees produce a wax that they use to make their honey.combs

Waxes• Waxes are long-chain fatty acids linked to alcohols or

carbon rings.• The hydrophobic molecules are firm and pliable.• Their structure makes them ideal for making waterproof

coatings on plant and animal parts.

Waxes• Cutin is a wax produced by plant

cells to coat the stem, leaves and fruit.

– This helps hold water in and keep infections out!

• Birds produce a waxy substance to waterproof their feathers.

• Bees produce a wax that they use to make their honeycombs.

End Lipids!

BeginProteins!

Proteins• Most diverse functions of all macromolecules!

• They make up over 50% of the dry mass of cells.

• Genetic info in DNA codes for the specific proteins

• Cells contain 1000’s of different proteins, each performing a specific task.

Proteins: Some Functions• Biological catalysts

• Immunoglobulins protect animals for foreign invaders and cancers.

• Channel proteins help to transport materials across the cell membrane.

• Hemoglobin, on red blood cells, carries oxygen around the body

• Keratin, the most common protein in vertebrates, is a structural protein in hair and fingernails.

• Collagen forms protein component in bones, skin, ligaments and tendons.

Protein Structure• Amino Acids are the basic building blocks of

proteins

• An amino acid has a central carbon atom with an amino group attached to one end and a carboxyl group attached to the other end and a side chain in the middle:

Protein Structure• There are 20 amino acids (20 different R groups)

• Most of the 20 we can manufacture within our own bodies

• 9 amino acids must be obtained from our foods. These are called essential amino acids.

Proteins• Depending on the nature of the side

chain amino acids can be:

–Polar (hydrophilic)–Non-polar (hydrophobic)–Charged

• acidic = carboxyl group on side chain• basic = amino group on side chain

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Proteins• Individual amino acid units, called residues, link

together to form polymers, called polypeptides.

• The number and the sequence of specific amino acids code for all the different protein polymers.

• More than 20 amino acids can be joined in any order or number to make countless proteins (think of how many words can be made from 26 letters!)

• A protein made of 200 amino acids could be arranged in 20200 different sequences combinations.

Proteins Synthesis• Amino acids link together when the –OH bond of

the carboxyl group of one amino acid and an –H atom from the amino group of the other amino acid come together to form H2O. (Dehydration Rxn)

• The resulting bond is called a peptide bond (or an amide linkage).

Proteins Synthesis• The specific

sequence of the amino acids in a polypeptide is controlled by the DNA

• (more on this in a later chapter).

• Polypeptides have an amino group at one end, called the amino terminus (A-terminus)

• They have a carboxyl group at the other end called the carboxyl terminus (C-terminus)

Polypeptide Structure

A

Protein ConformationThe 3D shape of a

protein is determined by the sequence of amino acids it contains.

Globular protein are spherical and can be describe by their 4 levels of structure: Primary Secondary Tertiary Quaternary

Protein ConformationPrimary Structure = the amino acid sequence

Secondary Structure = either an α-helix (coil) or a β-pleated sheet

Strong H-bonds form between amino and carboxyl groups of distant amino acids in regular, repetitive ways.

Protein ConformationSecondary Structure

E.g. an α-helix (coil) Keratin in hair and

feathers

E.g. a β-pleated sheet Spider web proteins are

stronger than steel (they stretch 40% before breaking. Steel can only stretch 8%)

Protein ConformationTertiary Structure =

super-coiling of the polypeptide stabilized by side-chain interactions (covalent bonds & disulfide bridges).

Chaperone proteins help fold the growing polypeptide

Quaternary Structure = 2 or more polypeptide subunits forming a functional protein.

Protein DenaturationAny change in the structural shape of the protein

can prevent it from carrying out its biological function.

Proteins can be denatured by: Temperature pH Chemicals

Examples of denaturing enzymes: Curing meats with salt or sugar Pickling in vinegar Blanching fruits and vegetables Straightening hair with heat

End Proteins!

Nucleic Acids

• Contain C, H, O, N plus phosphorus

• Formed by bonding of individual units called nucleotides

nucleotideNucleic Acid

Nucleic Acids

• Store and transmit hereditary information–Ex: DNA (deoxyribonucleic acid)

RNA (ribonucleic acid)