Biological molecules

Structure of an amino acid

Central carbon atom, amine group, carboxyl group, hydrogen atom, R group

How does a peptide bond form

A condensation reaction occurs between the amine group in one amino acid and the carboxyl group in the next, removing a molecule of water. An -OH is removed from the carboxyl group, and an H from the amine group.

Primary structure in a protein

The sequence of amino acids in a polypeptide (coded for by DNA)

Secondary structure of a protein

Either an alpha helix or a beta pleated sheet, due to hydrogen bonds, formed between the oxygen atoms in the C=O group and the H of the NH group in the next turn of the helix or sheet.

Tertiary structure of a protein

Bonds between the R groups of amino acids. These can be hydrogen bonds, ionic bonds (between positive and negative R groups or between carboxyl and amine groups not used in forming peptide bonds), or disulfide bridges (covalent S—S bonds between two cysteine amino acids)

Quaternary structure

Only applies to some proteins - this is when a protein is made up of more than one polypeptide chain. They are synthesised and folded separately, but come together to function.

Two types of protein

Fibrous and globular

Properties of globular proteins

• Soluble (due to hydrophilic side chains projecting out from the side of molecules)

• Polypeptide chain folded into a compact spherical shape

• Precise shapes as they are used in metabolic reactions

• Not very stable - tertiary structure can be easily disrupted

Properties of fibrous proteins

• Insoluble

• Long chain structure, often several parallel, cross-linked, chains

• Structural roles

• Very stable and strong

How does a structure of a protein depend on the amino acids it contains

• The structure of a protein is determined by the relative positions of the amino acids

• The primary structure is the sequence of amino acids

• The secondary structure can be an alpha helix or a beta pleated sheet, and is formed by hydrogen bonds between the amino acids

• The tertiary structure is determined by ionic bonds/hydrogen bonds/disulfide bridges between R groups of amino acids

• The quaternary structure is formed by bonds between the polypeptide chains

• The unique shape of a protein is important, e.g. as the active site of an enzyme

Difference between different amino acids

They have different R groups

How are all dipeptides similar

• All contain C, H, O, N

• They have an amine group at one end

• They have a carboxyl group at the other end

• They have 2 R groups as they have 2 amino acids

Properties of lipids

• Contain C, H, O

• Proportion of oxygen to carbon and hydrogen is smaller than in carbohydrates

• Insoluble in water

• Soluble in organic solvents, e.g. alcohols and acetone

• Lower density than water

• Fats are solid at room temperature whereas oils are liquid

How do triglycerides form

Condensation reactions occur between the -OH group in glycerol and the -COOH group at the head of a fatty acid, removing a molecule of water to form an ester bond. In total, three ester bonds are formed and three water molecules are removed.

Roles of lipids

• Source of energy (release more energy per mass than carbohydrates)

• Waterproofing (as they are insoluble in water), e.g. waxy cuticle

• Insulation (to retain body heat, and also electrical insulation in the myelin sheath around nerve cells)

• Protection (around delicate organs, e.g. the kidney)

Types of hydrocarbon chains in lipids

Saturated, monounsaturated, polyunsaturated

Why do unsaturated fats have lower melting points

The C=C double bond(s) produce kinks in the hydrocarbon tails, so that they cannot pack together as closely, meaning that the intermolecular forces of attraction between lipid molecules are weaker, so less heat energy is needed to overcome these.

Properties and usefulness of triglycerides

• High ratio of energy-storing C-H bonds to C atoms - excellent source of energy

• Low mass to energy ratio - good storage molecules

• Insoluble in water

• High ratio of hydrogen to oxygen atoms - produce water when oxidised - important source of water, esp for desert dwellers

Difference between a triglyceride and phospholipid

Triglycerides have 3 fatty acids bonded to a glycerol molecule; phospholipids have 2 fatty acids and one phosphate group bonded to a glycerol molecule

Which is polar: phospholipid or triglyceride

Phospholipids, as they have a negatively charged, hydrophilic head and a hydrophobic tail

Bond between two monosaccharides

Glycosidic bond

Test for non-reducing sugars

Boil the solution in hydrochloric acid for a minute, then neutralise with a base. Then add an equal volume of Benedict’s reagent, and heat in a water bath above 90*C. A positive result will be a colour change from blue to brick red (or yellow, green or orange).

Starch structure

• Alpha glucose monomers

• Amylopectin joined together by 1,4 and 1,6 glycosidic bonds, so is highly branched

• Amylose joined together by 1,4 glycosidic bonds, forms an alpha helix

• All alpha glucose molecules have the same orientation

Why are glycogen and starch good storage molecules

• Insoluble so don’t affect water potential

• Large and insoluble so won’t diffuse out of cells

• Compact (starch is coiled) so a lot can be stored in a small space

• Forms alpha glucose when hydrolysed, which is easily transported and readily used in respiration

• Branched, (glycogen more) so has many ends, which enzymes can act on simultaneously, so that alpha glucose monomers can be released rapidly

Structure of glycogen

• Alpha glucose monomers

• Joined by 1,4 and 1,6 glycosidic bonds

• Highly branched

• All alpha glucose monomers have the same orientation

Cellulose structure

• Beta glucose monomers

• Joined by 1,4 glycosidic bonds

• Beta glucose molecules are alternately orientated

• Straight, unbranched chains

What makes cellulose good for cell walls

• Long and straight chains

• Become linked together by many hydrogen bonds to form fibrils

• Provide strength to cell wall

What are maltose, sucrose and fructose made up of

• Maltose: glucose + glucose

• Sucrose: glucose + fructose

• Lactose: glucose + galactose