Topic 4 - Biological Organic Molecules

What is organic chemistry?

The study of carbon-containing compounds.

Why is organic chemistry important?

• It is pervasive in nature

• It is the chemical foundation of biology

• It helps improve standard of living

How is organic chemistry studied?

By examining the chemical structure of molecules and analysing how structure governs reactivity.

What are biological macromolecules?

Large, complex molecules found in living organisms that are essential for life.

What are biological macromolecules built from?

Smaller organic units called monomers.

What are the four classes of biological macromolecules?

• Proteins

• Carbohydrates

• Lipids

• Nucleic acids

Proteins – building blocks, function, and examples?

• Building blocks: Amino acids

• Functions: Provide cell structure, send chemical signals, catalyse reactions

• Examples: Keratin, hormones, enzymes, antibodies

Carbohydrates – building blocks, function, and examples?

• Building blocks: Monosaccharides

• Functions: Provide short-term energy, immune recognition, protein folding

• Examples: Glucose, fructose, sucrose, cellulose

Lipids – building blocks, function, and examples?

• Building blocks: Fatty acids and glycerol

• Functions: Provide long-term energy, form biological membranes

• Examples: Fats, phospholipids, steroids

Nucleic acids – building blocks, function, and examples?

• Building blocks: Nucleotides

• Functions: Store and pass on genetic information, catalyse reactions

• Examples: DNA, RNA

Where are proteins found?

Proteins are present in all living cells.

Approximately how much of your body’s dry mass is protein?

About 50%.

List major roles of proteins.

• Structural components

• Catalyse reactions

• Transport signals

Despite different functions, what do all proteins have in common chemically?

They are all composed of amino acids.

Why are amino acids amphoteric?

Because they contain both an acidic group and a basic group, so they can behave as either an acid or a base.

What does amphoteric mean?

A substance that can behave as either an acid or a base.

In aqueous solution, what form do amino acids mainly exist in?

As zwitterions.

What is a zwitterion?

A molecule with a net neutral charge that has both positively and negatively charged functional groups.

What are non-polar amino acid R groups like?

Hydrophobic—they tend to avoid water.

What are polar amino acid R groups like?

Hydrophilic—they interact well with water.

What are acidic amino acid R groups like?

They can carry a negative charge in water.

What are basic amino acid R groups like?

They can carry a positive charge in water.

What are the building blocks of proteins?

Amino acids.

How do amino acids form proteins?

Individual amino acids form bonds to create a chain of amino acids (a peptide), which folds into a protein.

What is a peptide bond?

The bond linking amino acids together.

What is another name for a peptide bond?

An amide bond.

What is the primary structure of a protein?

The order of amino acids in the chain.

Why is primary structure important?

Changing the order (e.g. mutation) changes the chemistry of the chain and often changes how it folds.

What is secondary structure of proteins?

Local, repeated folding patterns in the chain.

What are the two main types of secondary structure?

• Alpha helices (α-helices)

• Beta sheets (β-sheets)

What mainly stabilises secondary structure?

Hydrogen bonding along the backbone of the chain, not the side chains.

What is tertiary structure of proteins?

The overall 3D shape of a single polypeptide chain formed as helices and sheets fold and pack together.

What stabilises tertiary structure?

• Hydrophobic clustering

• Hydrogen bonds

• Ionic interactions (salt bridges)

• Van der Waals forces

• Covalent disulphide bonds

What is quaternary structure of proteins?

How two or more polypeptide subunits assemble into one functional protein.

Give the quaternary structure example from haemoglobin.

Haemoglobin consists of two α and two β chains, each carrying a haem group with an Fe²⁺ ion.

Why does structure determine protein function?

Because function depends on precise shape and chemical environment.

Why is enzyme folding especially important?

The active site must have the precise shape and chemical environment to bind its substrate; changes in folding disrupt function.

Are biological macromolecules static or dynamic?

Dynamic.

What are carbohydrates?

An important class of naturally occurring substances found in both plant and animal matter.

What are carbohydrates built from?

Monomeric building blocks called monosaccharides.

Chemically, what are carbohydrates?

Polyhydroxy aldehydes or ketones.

In aqueous solution, what form of glucose exists in the vast majority?

The closed ring structure.

What are the two ring forms of glucose shown?

• α-glucose

• β-glucose

What is angle strain?

Strain due to deviation from one or more ideal bond angles.

What is torsional/eclipsing strain?

Strain due to repulsion between electrons in bonds that do not share an atom.

Why do monosaccharides undergo puckering?

To relieve angle strain and torsional strain.

What conformation do most monosaccharides adopt?

Chair conformation.

How are monosaccharides joined together?

By a glycosidic bond.

How is a glycosidic bond formed?

Via a condensation reaction where water is released as a by-product.

How are large carbohydrate chains formed?

Repeated condensation reactions link monosaccharides together.

What links amino acids into proteins vs monosaccharides into carbohydrates?

• Peptide bonds link amino acids

• Glycosidic bonds link monosaccharides

What is a disaccharide?

Two monosaccharide units joined by a glycosidic bond.

Why is a disaccharide considered distinct from its monosaccharides?

Because it has different properties from the original monosaccharide units.

What are the two broad biological roles of polysaccharides?

• Energy storage

• Structure

How do polysaccharides store energy?

As a compact way to store many glucose units.

Structural role of polysaccharides?

Strong fibres/frameworks, especially in plants.

What is the statement about glycans and proteins?

Studying a protein without glycans is like studying a bird without feathers.

What are lipids?

A diverse class of nonpolar biological molecules.

What are the major uses of lipids?

• Long-term energy storage

• Elements of biological structures

Which lipid is associated with long-term energy storage?

Fats

Which lipid is associated with biological structures?

Phospholipids

What are fats derived from?

Glycerol and fatty acids.

What is glycerol?

An alcohol with three hydroxyl groups

What is the IUPAC name of glycerol?

Propan-1,2,3-triol

What are fatty acids?

Carboxylic acids (RCOOH) where R is a hydrocarbon chain.

Typical fatty acid chain length?

Usually 15–19 carbon atoms.

Examples of saturated fatty acids given?

• Palmitic acid = Hexadecenoic acid (C16:0)

• Stearic acid = Octadecanoic acid (C18:0)

Example of unsaturated fatty acid given?

Oleic acid = Octadec-9-enoic acid (C18:1 Δ9) (C18:1 ω-9)

Are trans fats nutritionally required for humans?

No.

What is another name for a fat?

Triglyceride

How is a triglyceride formed?

One glycerol molecule linked to three fatty acids.

Describe the structure of a triglyceride.

Glycerol forms the backbone and fatty acids form the long tails.

What bond links glycerol and fatty acids?

Ester bond

How does the ester bond form?

By condensation between an –OH group on glycerol and the –COOH group of a fatty acid.

What is the difference between a triglyceride and a phospholipid?

Triglyceride: Glycerol + 3 fatty acids
Phospholipid: Glycerol + 2 fatty acids + phosphate

Why do phospholipids form bilayers?

Because hydrophilic heads face the aqueous environment while hydrophobic tails cluster inward away from water.

What are cellular membranes besides physical barriers?

They regulate movement of molecules into and out of cells and allow formation of specialised compartments.

What are nucleic acids?

Biopolymers that are the chemical carriers of an organism’s genetic information.

What are the monomers of nucleic acids called?

Nucleotides

What are nucleotides made of?

• A five-carbon sugar

• A nitrogen-containing organic base

• A phosphoric acid group

How do nucleotides differ?

Different nucleotides have different bases.

How do RNA and DNA differ in sugars?

RNA → Ribose
DNA → Deoxyribose

What is the sugar-phosphate backbone?

The regular structural framework formed when nucleotides repeatedly join through phosphate and five-carbon sugar bonds.

What is the bond linking nucleotides called?

Phosphodiester bond

How many hydrogen bonds are between Adenine and Thymine?

2 hydrogen bonds

How many hydrogen bonds are between Cytosine and Guanine?

3 hydrogen bonds

What is the overall structure of DNA called?

The double helix

Final review of the four biological macromolecules?

• Proteins → amino acids

• Carbohydrates → monosaccharides

• Lipids → fatty acids + glycerol

• Nucleic acids → nucleotides