Biological Molecules

Hydrogen bonds

Form between positive (+) and negative (-) molecules

Individually Weak

Continually breaking and reforming

Water is a dipolar molecule

Specific Heat Capacity

The heat energy that is needed to raise the temperature of 1kg of substance by 1^OC

Water has a lot of hydrogen bonds so lots of energy required to break those bonds so high specific heat capacity so can buffer temperature change

Aquatic Environment

Fairly constant temperature allowing aquatic organisms to survive

Ice is less dense than water

When water freezes the water molecules are pushed out

Importance of Ice floating on water

Animals can float on water

A body of water freezing over means the ice acts as an insulator during colder seasons for aquatic life such as fish

Latent Heat of Vaporisation

Energy required to turn water to gas

Importance:

Animals that sweat cool down as they use the heat energy of their body to evaporate the water off their surface

Plants are also cooled when water evaporates from their leaves

Water is cohesive

Means that water molecules tend to stick to each other due to hydrogen bonding between their polar molecules

Used for transpiration, allows small animals to live on the surface water of bodies

The many hydrogen bonds help hold water molecules together so they can flow in a continuous stream

Leads to surface tension making water behave as there is a skin

Water Adhesion

Water molecules stick to other surfaces or materials that are not water, due to intermolecular forces such as hydrogen bonding and electrostatic interactions

Water is a solvent

Things can dissolve in it

Important for reactions and dissolving positive and negative charges of water attracted to other molecules causing them to separate from each other and dissolve

Dissolved substances are free to move around and react with other molecules

Metabolite

Something involved in a metabolic reaction

Water molecules can also be involved in chemical reactions directly condensation and hydrolysis reactions

Hydrophillic

Can dissolve in water, substances attracted to water

Always polar molecules and ions

Hydrophobic

Insoluble in water

Non-polar

Inorganic Ions

Ion that doesn't contain Carbon or Hydrogen molecules

There are lots in the body that have a specific role

e.g. calcium, phosphate, potassium, hydrogen, iron, sodium ions

Hydrogen Ions

Protons

Concentration of H⁺ ions in a solution determines pH

More H⁺= Lower pH

Less H⁺= Higher pH

Iron Ions

2 types: Ferrous ions (Fe²⁺) and Ferric ions (Fe³⁺)

Bind oxygen

Haemoglobin is made up of 4 polypeptide chains that contain Fe²⁺

Sodium Ions

Required for the transport of glucose and amino acids across cell-surface membranes e.g. small intestine

Required for transmission of nerve impulses

Phosphate Ions

Attach to other molecules to form phosphate groups which are an essential component of DNA, RNA and ATP

Phosphates are also found in phospholipids, which are key components of the phospholipid bilayer of cell membranes

Calcium Ion

Activate ATP hydrolase, releasing energy that powers muscle contraction

4 main types of large biological molecules

Are called macromolecules which include:

Carbohydrates

Lipids

Proteins

Nucleic Acids

They are all made by joining smaller molecules together

Monomers

Small molecules that can join with another molecule to form larger molecules.

e.g. amino acids, glucose, fructose, galactose, ethane, nucleic acid

Monomer = 1 amino acid

Dipeptide = 2 amino acids

Monomers are formed by

Hydrolysis reaction

Polymers are formed by

Condensation reaction

Condensation

Release of water molecules in order to build up large molecules

Hydrolysis

Addition of a water molecule in order to break down large molecules

Polymer

A repeating chain of monomers bound together

Isomer

Same chemical formula but different arrangement of atom

Carbohydrate

CARBO HYDR ATE

carbon hydrogen oxygen

Monosaccharide

Monomers that make up carbohydrates e.g. glucose, galactose, fructose

No. of carbon atoms

Diose 2

Triose 3

Tetrose 4

Pentose 5

Hexose 6

Heptose 7

All monosaccharides

Can reduce Benedict's Reagent (which is reducing sugars)

Are sweet tasting

Are soluble

Are easily transported

Are the main respiratory substances

Alpha Glucose

C₆H₁₂O₆
Hexose
Energy source.
Component of starch and glycogen

Beta Glucose

C₆H₁₂O₆
Hexose

Disaccharides

2 monosaccharides joined together to make a disaccharide

Glycosidic bonds

Between 2 monosaccharides

Maltose

Glucose and glucose

Sucrose

Glucose and fructose

Lactose

Glucose and galactose

Polysaccharides

Joining 2 or more monosaccharides

e.g. starch, cellulose, glucose

Starch

Long chain of alpha glucose molecules together

2 Types of starch

Amylose

Amylopectin

Amylose

Alpha 1-4 bonds

Amylopectin

Alpha 1-4 + Alpha 1-6 bonds

Branched

Structure of Starch

• Insoluble - won’t affect water potential (water won’t move in or out by osmosis)

• Large - doesn’t diffuse out of cells

• Coiled - compact - a lot of it can be stored in a small place

• When hydrolysed forms Alpha glucose - easily transported and readily used in respiration

• The branched form has many ends - can be acted on by enzymes simultaneously meaning that glucose monomers are released very rapidly

• Made up of alpha glucose

Glycogen

A form of energy store in animals. It is mainly stored in the muscles and liver. It is very similar to starch except it has more alpha 1-6 bonds glycosidic bonds.

More branches are important to animals because animals need more energy

Cellulose

Polysaccharides found in plants in cell wall. It is made up of a long chain of beta glucose

In cellulose, beta glucose overcomes this problem by flipping every other molecule by 180 degrees.

Several cellulose molecules run in parallel to one another and H bonds form between these chains

Starch v glucose

• Both insoluble

• Orientation difference

• Both contain 1-4 glycosidic bonds

• Cellulose has H bonds, starch doesn’t

Lipids

• Test: ethanol = emulsion test

• Found in cell membrane

• Broken down by lipase

• Made up of 1 glycerol and 3 fatty acids (triglyceride)

• Energy storage

• Provide insulation, protection

Lipids

• A diverse group of chemicals that dissolve in organic solvents such as alcohol but not in water

• Made up 5% of organic matter

• The main group of lipids are called triglycerides

If lipids are at room temp then they are

Solid and we call it fat

If lipids are liquid

They are oil

Lipids are mainly composed of

Carbon, hydrogen, oxygen

3 main types of liids

• Triglyceride

• Phospholipids

• Steroids

Functions of lipids

• Protection of vital organs

• Insulate the body

• Source of energy

• Component of cell membranes

• Form myelin sheath around neurones (electrical impulses)

• Prevent evaporation in plants and animals e.g. wax

What’s a major component lipids

Fatty Acids

Each fatty acid has

• A carboxylic group (-COOH)

• A long hydrocarbon chain

• A methyl group (-CH₃)

Stearic acid

Saturated fatty acid

Oleic acid

Monounsaturated fatty acid

Linoleic acid

Polyunsaturated fatty acid

Unsaturated fatty acids can be:

Cis - hydrogen atoms are on the same side of a double bond

Trans - hydrogen atoms are on opposite sides of a double bond

What are the most common lipids in living organisms

Triglycerides

Ester bonds

Between any lipids joined together

Differences

• Different lipids have different properties and this is due to the fatty acids which are bound to the glycerol

• Saturated fats have no double bonds so chains are straight which increases melting point due to more IMF

• Unsaturated fats have double bonds so kinks in chain which lowers melting point due to less IMF. Polyunsaturated fatty acids tend to be liquid at room temperature

Phospholipids

Very similar in structure to triglycerides, except instead of a fatty acid, a phosphate group is covalently bonded to the third OH group of the glycerol

A bilayer is formed when

Phospholipids are exposed to water

The cell membrane is made up of

Phospholipid bilayer

The cell membrane is fluid, the fluidity can change

The higher % of unsaturated fatty acid tails in the phospholipids, then the more fluid membrane there will be

Phosphate head is

Hydrophillic

Phosphate tails are

Hydrophobic

Cholesterol

A small molecule made from carbon-based rings. It is used to form steroid hormones (testosterone, oestrogen) and to increase cell membrane stability

Proteins

• Made up of amino acids (monomers)

• Made by protein synthesis in the ribosomes

• Needed for growth, repair and maintenance

• Hormones

• Test using Biuret’s, Blue to Lilac

• Roles in structure

Proteins

Large molecules. They are a polymer made up of amino acids

All amino acids have

• An amine group

• Carboxylic group

• Hydrogen bonded to a central atom

Amino acids chemically bonded together to form proteins by

Condensation reaction

Bond between proteins is called

Peptide bond

Polypeptides are

Long chains of amino acids joined together by condensation reactions

Primary structure of proteins

Sequence of amino acids forming a protein or polypeptide chain, considered as the most basic element of its structure

Secondary structure of proteins

Local, repetitive folding pattern of the polypeptide backbone

primarily α‑helixes and β‑sheets

stabilized by hydrogen bonds between backbone amide hydrogens and carbonyl oxygens.

Tertiary structure of proteins

Unique three‑dimensional fold formed by interactions among amino acid side chains, including hydrogen bonds, ionic bonds, disulfide bonds

Hydrophilic out

Hydrophobic in

Quaternary structure of proteins

Between 2 or more polypeptide chains called subunits

Each subunit has has already folded into its own tertiary structure

e.g. haemoglobin

Globular Proteins

• Tend to form a ball like structure because they contain a lot of hydrophobic side chains. These move towards the middle which makes them water soluble

• They usually have metabolic roles e.g. enzymes, plasma proteins, antibodies

Haemoglobin

Main role is to transport oxygen

• Quaternary structure with 4 polypeptide chains (2 alpha polypeptide chains, 2 beta polypeptide chains) and an inorganic haem group

Soluble

Found in red blood cells

Binds to oxygen in the lungs and transporting the oxygen to tissue to be used in aerobic metabolic pathways

4 Polypeptide chains

Fibrous proteins

Form long chains which run parallel to each other. The chains are linked by cross bridges to form strong molecules and are interlinked

e.g. keratin and collagen

Insoluble

Found in cartilage, tendons, skin, teeth

Flexible structural protein forming connective tissues

3 Polypeptide chains

Enzymes

• Biological catalysts

• Increase ROR

• Decrease activation energy

• Denature by temp and pH

All enzymes are

proteins.

NOT all proteins are enzymes

Enzymes are globular proteins which

catalyse chemical reactions in the body

Catalysts

Alter chemical reactions without being used up

Activation energy

Energy required for chemical reactions to happen

Active site

A specific region of the enzyme.

It is functional and will bind with the substrate. The active site is unique to the enzyme and will bind with only one substrate

When the substrate binds to the active site it forms an

Enzyme substrate complex

Explain why a change in primary structure could impact enzyme functions (4 marks)

• Change in amino acid sequence

• Changes the ‘R’ groups which are present in the polypeptide

• This will change which ‘R’ groups interact with each other and therefore how the protein folds in the tertiary structure

• This may change the shape of the active site meaning the substrate no longer fits

Induced Fit

The active site has a general shape.

When the substrate binds it induces a change of shape to form the enzyme-substrate complex

Lock and Key model

The substrate fits perfectly into the active site

Limiting factor

What is in shortest supply

The rate of an enzyme catalysed reaction is determined by the rate of the slowest or limiting factor

How Substrate Concentration affects enzyme

Increasing substrate concentration [S] increases the rate of reaction. This is because more enzymes can be used to catalyse the reaction. However, at a certain point, all the enzymes are being used (saturated). After this point, increasing substrate concentration will have no effect on the rate of reaction. At this point, substrate concentration is no longer the limiting factor

How Enzyme Concentration affects enzyme

At the high substrate concentration, the enzyme concentration may be limiting. Increasing the number of active sites by increasing [E] increases the rate

How Temperature affects enzyme

As temp increases, the rate of reaction will also increases. This is because of increasing KINETIC ENERGY causing the number of COLLISIONS between substrate and enzyme to increase. For every 10^o temp increase the ROR doubles. However beyond the optimum temp the enzymes become denatured at the active site so the ROR declines rapidly

pH

The measure of OH^- and H⁺ ions concentration

How pH affects enzymes

Strongly acidic and alkaline conditions result in the ionization of groups at the active site, changing its shape and therefore resulting in denaturation