Biological Molecules

Molecules

Made of two or more atoms

Compound

If atoms in a molecule are different.

Element

If atoms in a molecule are the same.

Types of compounds (think bonding)

Ionic- metal and non-metal

molecular (covalent)- just non-metals

Ions

Charged particles through loss or gain of electrons from an atom.

Polar vs non-polar molecules

Polar- slight charge across molecule

Non-polar- no charge across molecule

Properties of ions and polar compounds

Attract oppositely charged particles.

Important structurally.

Properties of non-polar compounds

Lipid-soluble rather than dissolving in water.

Four most common elements making up human body mass.

Carbon, Hydrogen, Oxygen, Nitrogen

C, H, O: These are the main components of all organic molecules

C, H, O, N: Found in amino and nucleic acids

Calcium in human body + plants

• ion

• role in humans + plants

Ca2+

2%

Strengthens teeth, bones and cell walls in plants.

Phosphorus in the human body

PO4 3-

Present in cell membranes/ ATP/ Nucleic acids

Magnesium in human body

Mg2+

0.05%

Used for enzyme function (and chlorophyll function in plants)

Iron in human body

Fe2+

0.004%

Oxygen transport

Potassium in human body

K+

0.35%

Nervous impulse transmission

Sulfur in human body

SO4 2-

Some amino acids (for disulphide bonds in tertiary protein structure)

Organic compounds

• components

• origin

Always contain C, H. May contain O and/or N.

Usually produced by living organisms or from decay of dead organisms. E.g. crude oil

Inorganic compounds

Can also contain C, H, O, N.

Can be made without involvement of living organisms. E.g. CO2, H2O.

Biochemicals

Compounds made by and found in living organisms

3 types of biochemicals

Carbohydrates

Lipids

Proteins

Structure of water molecule

Solid lines drawn showing bonds between H and O atoms.

Water is polar so hydrogen atoms have a partial positive charge and oxygen atoms hv a partial negative charge. These are shown by δ+, delta positive and δ− delta negative.

Due to their polarity, water molecules attract each other forming hydrogen bonds. This can be shown by a series of vertical lines.

Water as a universal solvent

Required in all biochemical reactions as they all take place in aqueous solutions, dissolved in water.

Because of waters polarity, water molecules are attracted to other water molecules and charged particles. (see properties of polar molecules). This helps charged particles dissolve in water.

Water as a metabolite in chemical reactions (condensation and hydrolysis reactions, photosynthesis and respiration)

Water as a reactant:

• Large molecules are often broken down by the addition of a water molecule- hydrolysis

• Photosynthesis

Water as a product:

• Many small organic molecules can be combined with the loss of a water molecule- condensation reaction.

• Aerobic respiration

Significance of ice being less dense than water.

This forms an insulating layer over the surface of aquatic habitats, so e.g. ponds don’t freeze solid and animals can still swim beneath in a comfortable temperature.

Significance of water as a liquid

Water is liquid at most temperatures; lots of heat energy is required to change state.

Can be used as a transport medium. E.g. in blood in mammals, in xylem in plants.

Significance of transparency of water

Light can pass through for aquatic plants to photosynthesise.

Significance of water’s high surface tension

Surface of water can support and become a habitat for organisms like pond skaters.

Significance of water’s high specific heat capacity

Lots of energy required to increase its temp by 1 degrees c.

The temperature of aquatic environments remains constant and thermally stable. Cells at optimum temp- don’t denature.

Significance of waters high specific latent heat of vapourisation.

Lots of energy needed to evaporate water.

Useful for organisms to cool down- frog panting and sweating, leaf transpiration.

Aquatic environments dont diminish easily.

Significance of water’s hydrogen bonds for strong cohesive and adhesive properties

Due to hydrogen bonds, water molecules stick together (cohesion) and stick to other charge substances. This means they can be placed under high tensile (pulling) forces and pulled through plants in transpiration.

Water support in plant cells

Water can act as a structural support by filling vacuoles in plant cells and upholding the plant

Water and buoyancy

Water has a high density as a liquid so can provide buoyancy to aquatic organisms allowing them to float.

Carbohydrates

All contain C,H & O

General formula: CnH2nOn E.g. C6H12O6​

Monosaccharides

General types of monosaccharide

General formula

simple sugar carbohydrate monomers named by number of carbons.

E.g. triose, pentose and hexose.

C_n(H₂O)_n

Glyceraldehyde

• type of monosaccharide

• structure

Triose

Structural isomers monosaccharides

Molecules with the same molecular formula but different structural formula. E.g. glucose, galactose, fructose.

Alpha vs Beta glucose

Ring isomerism with differing position of OH group on carbon 1.

Fructose

Has central ring of 4 carbons with one oxygen atom, and CH2OH at carbons 1 and 6.

Structural isomer of glucose

Galactose

Central ring of five carbons (like glucose) and one oxygen atom with a CH2OH group at carbon 6.

Disaccharides

• components

• type of reaction

• bond formed

• naming of bond

• 3 examples

Sugars made of two monosaccharides joined by condensation reaction, forming a glycosidic bond. These bonds can be broken by hydrolysis reaction. The bond is named by the number of each carbon connecting the bond. E.g. Maltose, sucrose, lactose

Maltose

Disaccharide

two alpha glucose molecules with a 1,4 glycosidic bond.

Lactose

Disaccharide:

Galactose + alpha glucose by 1,4 glycosidic bond.

Sucrose

What type of molecule? Nature

Disaccharide:

Fructose + alpha glucose by 1,2 glycosidic bond.

Examples of polysaccharides- storage or structure?

Structure:

Cellulose (in plant cell wall)

Chitin (in fungi cell wall)

Storage:

Starch (in plants like potatoes)

Glycogen (in animals)

Storage polysaccharides similiarities

Can store and release glucose as necessary.

Made of chains of alpha glucose.

Starch structure

Made of two different polysaccharides: amylose and amylopectin

Amylose is a straight chain molecule made of alpha glucose with 1,4 glycosidic bonds. It forms coils into a helix through its hydrogen bonds between molecules.

Amylopectin is a branched molecule made of alpha glucose with 1,4 glycosidic bonds, and 1,6 glycosidic bonds at branching points.

How is starch structure relative to function?

Due to coils from H bonds, starch is a compact molecule thats less soluble in water, so ideal to store glucose. It also means starch is osmotically stable.

Branches allow more ‘ends’ for hydrolysis to occur releasing glucose monomers, which can be used in respiration to produce ATP.

Glycogen structure

Branched chain of alpha glucose with both 1,4 and 1,6 glycosidic bonds. Similiar to amylopectin but more branched.

How is glycogen structure relative to its function?

Glycogen can form granules in cells and act as carbohydrate/energy store.

Branches allow more ‘ends’ for hydrolysis to occur releasing glucose monomers, which can be used in respiration to produce ATP.

Cellulose structure

Made of beta glucose molecule with 1,4 glycosidic linkage between adjacent molecules. This means each adjacent molecules are rotated 180 degrees so OH groups are aligned and a water molecule can be removed.

The rotating of alternate molecules causes H bonds to not form between glucose molecules in the same chain but between glucose molecules in separate chains. This is formation of cross linkages which hold chains together forming long threads called microfibrils.

How does cellulose structure relate to its function?

Makes cellulose completely insoluble so increases stability.

Microfibrils are layed in overlapping layers in plant cell walls, making it difficult to digest and giving cellulose high tensile strength so is difficult to break when stretched (less likely to burst due to excess water intake).

Chitin structure

Not a true polysaccharide, as it has side groups containing N- instead its a heteropolysaccharide.

Has similar structure to cellulose; made of beta glucose with alternating rotated glucose molecules and hydrogen bonds between glucose molecules of different chains.

Due to presence of N, more hydrogen bonds can form.

How does chitin structure relate to its function?

More hydrogen bonds means greater tensile strength.

What are Reducing sugars? 3 examples

Carbohydrate that act as reducing agents by donating electrons or hydrogen atoms. E.g. glucose, lactose and maltose

Food test experiment: Reducing sugars

1) Put 2cm cubed glucose solution into boiling tube

2) Add an equal volume of Bendicts reagent

3) Heat in a water bath for 5 mins

Positive result turns mixture from blue to brick red.

Non-reducing sugars

Do not have the ability to reduce other substances by donating electrons or hydrogen atoms. E.g. sucrose.

Food test experiment: Non-reducing sugars

1) Put 2cm cubed sucrose into boiling tube

2) Add 2 drops dilute HCl

3) Place in water bath for 2 mins

4) Add 2 drops of dilute NaOH

5) And 2cm cubed Benedicts reagent

6) Place in water bath for 5 mins

Positive result- blue to brick red.

Lipids

Organic molecule with C,H & O. They have a high proportion of CH2 groups.

They also have a low solubility in water but high solubility in organic solvents like ethanol.

Triglycerides

• what molecules does it form? what determines this?

• what is it made up of? what bonds are formed?

Molecules that form fats or oils.

Lipids with long hydrocarbon chains are likely to be fats (solid at room temp). Lipids with short hydrocarbon chains are likely to be oils (liquid at room temp).

They are made from glycerol, combined with three fatty acids through a condensation reaction with the release of 3 water molecules, forming ester bonds.

Functions of trigylcerides (4)

1) Efficient energy storage molecules. Store 38kJ of energy.

2) Good thermal insulators- protection for organs.

3) Fats provide buoyancy for aquatic animals as they are less dense than water.

4) Some animals spread oil for waterproofing because fats are hydrophobic and repel water.

Saturated fatty acids

What substance if often formed?

Only single carbon to carbon bonds with maximum hydrogen atoms.

Generally form fats as straight chains can pack close together forming forces of attraction between molecules so more energy is required to break the bonds so higher melting point.

Unsaturated fatty acids

Contains one or more carbon to carbon double bonds between carbon atoms, so fewer hydrogen atoms.

Usually oils at room temperature as double bonds form kinks so chains cannot pack as close together. Therefore weaker forces of attraction between molecules so lower melting point.

Phospholipids

Essential component in cell membranes.

Made of glycerol, a hydrophillic charged phosphate head and two hydrophobic fatty acid tails.

Functions of phospholipids

Form phospholipid bilayer in cell membranes.

Affect the fluidity of the cell membranes. Saturated fatty acids make membrane least fluid, unsaturated fatty acids make membrane most fluid.

LDL

Low-density lipoprotein cholesterol levels.

Bad cholesterol leading to blockages and eventually heart disease.

HDL

High density lipoprotein (good cholesterol)

Effect of saturated fat on body health

Where are they found?

Increases total cholesterol (waxy substance found in blood) and LDL. Best to consume in moderation.

Found in: red meat, whole milk, cheese, coconut butter, processed meat, many baked goods and deep fried foods.

Effect of polyunsaturated fats on body health

Where are they found?

Essential for the body as it is not produced by our bodies. It lowers LDL.

Found in: most cooking oils, pumpkin seeds, pine nuts, sesame seeds, fatty fish.

AKA: omega-3, omega-6

Monounsaturated fat

Considered as healthy fat: Lowers LDL and maintains HDL.

Found in: olive oil, avacado, avacado oil, most nuts and nut butters

Practical food test for lipids

1) Mix fat/oil with 5cm cubed of ethanol in a boiling tube.

2) Shake the tube and pour the mixture into another boiling tube with equal volume of water.

Positive result goes from clear to milky.

What is the bond between fatty acids and glycerol called?

Ester bonds

Amino acid

Building blocks for proteins.

There are 20 different amino acids.

It has 4 functional groups: Amine group (NH2), Carboxylic acids -(COOH), a hydrogen atom (H) and a variable group (R).

What is the bond formed between amino acids called

Peptide bonds formed from condensation reactions.

Primary protein structure

Specific sequence of amino acids in a polypeptide chain.

Secondary protein structure

Hydrogen bonds form between amine and carboxylic polar groups on amino acids. These make the polypeptide chain and fold into a new shape which is commonly an alpha helix or a beta pleated sheet.

Structural role of alpha helices

Used for fibrous proteins where several alpha helices coil together to form an insoluble rope like arrangement. E.g. collagen in skin

Tertiary structure of proteins

Forms the basic 3D shape of the protein.

Dependent on the properties of the R groups, 3 types of bonds can form, twisting the polypeptide chain further to form its 3D protein shape:

• Hydrogen bonds forming between polar variable groups

• Ionic bonds between charged variable groups. Can interact with water helping protein dissolve.

• Disulphide bridges formed from two variable groups containing sulfur atoms. These covalent bonds are strong and more difficult to break.

Globular proteins

Formed from additional folding to a protein in its tertiary structure, with charged groups on the outside and hydrophobic parts on the inside of the protein.

Examples include:

• Enzymes- active sites to bind to substrate.

• Antibodies- sites binding to antigens.

• Hormones- sites binding to specific receptors.

Quaternary protein structure

Proteins made of 2 or more polypetide chains combined, each chain having its own primary, secondary and tertiary structure.

Globular proteins with quaternary structure and metabolic functions.

Formed by disulphide bridges between polypeptides

• insulin

• haemoglobin

What are two fibrous proteins with quaternary structure and structural functions?

Formed by hydrogen bonds between polypeptides.

• collagen

• keratin

Protein food test practical

1) Add 2cm cubed albumen for protein solution to a test tube

2) Add biurets reagent to the boiling tube.

3) Invert the tube once, covering the mouth of the tube.

Positive result shows colour change from blue to purple.