Biological Molecules

Water

Water makes up 70-80% of a cell.
FUNCTIONS

• It's a reactant in important chemical reactions, including Hydrolysis.
• It's a Solvent - which means substances can dissolve in it. Most biological reactions take place in a solution.
• It Transports substances. it is good at this because it is a Liquid and is a Solvent.
• It helps with Temperature Control because it has a High Specific Heat Capacity and a High Latent Heat of Evaporation.
• Water is a Habitat. many organisms can survive and reproduce in it.

STRUCTURE

• H₂O is the chemical formula for water. This means that in every molecule of water, there are 2 Hydrogen atoms, and 1 Oxygen atom. The hydrogen atoms are joined to the oxygen atom by a Covalent Bond, which simply means it Shares Electrons.

• Because the Shared Negative Hydrogen Electrons are pulled Towards the Oxygen atom, each hydrogen atoms are left with a Slight Positive Charge.
• The Unshared Electrons on the Oxygen atom give it Slight Negative Charge.
• This makes water a Polar Molecule. its slightly negatively charged on one side, and slightly positively charged on the other.

• The δ sign is called 'Delta' and just means 'Slight', so δ- is delta negative, so it has a slightly negative charge. δ+ is delta positive, so it has a slightly positive charge.
• The slightly negatively charged Oxygen atoms Attract the slightly positively charged Hydrogen atoms of Other Water Molecules. this is called Hydrogen Bonding and gives Water some of its useful properties.

PROPERTIES

• High Specific Heat Capacity
• specific heat capacity is the energy needed to increase the temperature of 1 gram of a substance by 1°C.
• Hydrogen Bonds between water molecules can Absorb a lot of Energy
• Basic terms - it takes a Lot of Energy to Heat It Up.
• Water doesn't have rapid temperature changes, meaning it is a Good Habitat - the temperature underwater is likely to be more stable than it is on land.
• High Latent Heat of Evaporation
• It takes a Lot of Energy to Break the Hydrogen Bonds between water molecules.
• Therefore, lots of energy is used up when it evaporates.
• this is great for organisms because water is Good at Cooling things down. This is why some mammals sweat when they're too hot. when sweat evaporates, it cools the surface of the skin.
• Very Cohesive
• Cohesion is the Attraction Between Molecules of the Same Type. Water molecules are very cohesive because they are polar.
• This helps water to Flow, making it good for Transporting Substances.
• It also helps water to be Transported Up Plant Stems in the transpiration stream.
• Good Solvent
• Lots of important substances are Ionic (e.g. salt) which means they consist of one positively charged atom or molecule, or one negatively charged atom or molecule
• Because water is polar, the delta positive end of a water molecule will be attracted to the negative ions and vice-versa. (Opposites Attract!)
• This means the Ions will get Completely Surrounded by Water Molecules, i.e. they dissolve.
• Less Dense When Solid
• At low temperature, water freezes - it turns from liquid to solid.
• In ice, Water Molecules are Held Further Apart than they are in a liquid state, because each molecule forms four hydrogen bonds to other water molecules, making a Lattice Shape. because of this, ice is less dense than water and this explains why ice floats.
• This is useful for organisms because, in cold temperatures, Ice Forms an Insulating Layer on top of the water, which is why the Water Below Doesn't Freeze. So organisms that live in water don't freeze and can still move around when it's cold.

Carbohydrates

Carbohydrates are Polymers. This simply means it is a molecule made up of many similar, smaller molecules (Monomers) bonded together.
The monomers that make up carbohydrates are called Monosaccharides.
Glucose is a monosaccharide with Six Carbon Atoms. This means it is a HEXose monosaccharide.
There are two forms of glucose, Alpha (α) and Beta (β). They both have a Ring Structure.

In this diagram, each line represents a bond between atoms or molecules. As you can see, the H and OH, highlighted in blue and pink, are opposite in the Alpha and Beta Glucose Molecules.
The structure of Glucose is related to its function as the Main Energy Source in animals and plants. the ring structure makes it Soluble so it can be Easily Transported. the bonds contain a lot of energy.
Ribose is a structure with 5 Carbon Atoms - so it is a Pentose Monosaccharide. Unfortunately, this is another silly diagram we need to know how to draw. (NOTE: WE DO NOT NEED O LEARN ABOUT DEOXYRIBOSE! ... I couldn't crop the picture...Also, we can ignore the numbers, that's chemistry stuff!)

Monosaccharides are joined together by Glycosidic Bonds.
During synthesis, (The combination of components to make a connected whole), Hydrogen atom on one monosaccharide bonds to a hydroxyl Group (OH) on the other Releasing a Molecule of Water. this is called a Condensation Reaction. The opposite of this is called Hydrolysis. This is where a Molecule of Water Reacts with the Glycosidic Bond, breaking it apart.
A Disaccharide is when Two Monosaccharides join together.
There are a few more disaccharides we need to know about:
Maltose - When Two Alpha Glucose molecules are joined together by a glycosidic bond.
Sucrose - Alpha Glucose and Fructose
Lactose - Beta Glucose and Galactose
Amylose - Lots of Alpha Glucose joined by glycosidic bonds, this is a Polysaccharide (when More Than Two Monosaccharides are joined together).

The three main Polysaccharides we need to know about are:

STARCH

1. Cells get energy from glucose. Plants Store Excess Glucose as Starch. So when a plant needs more energy, it Breaks Down Starch to Release the Glucose
2. Starch is a mixture of two polysaccharides, Amylose and Amylopectin:

Amylose	Amylopectin
A Long, Unbranched chain of Alpha Glucose.	A long, Branched chain of Alpha Glucose.
Angles of the glycosidic bonds make a Coiled Structure, almost cylindrical	The Side Branches allow the Enzymes that break down the molecule to get to the Glycosidic Bonds Easily.
This makes it Compact, so it's really Good for Storage because you can fit more in a small space.	This means the Glucose can be Released Quickly

  3.  Starch is Insoluble In Water, so it doesn't enter cells by osmosis, which would make them swell. This makes it good for storage.

GLYCOGEN

1. Animal cells get energy from glucose too. But Animals Store Excess Glucose as Glycogen, which is another polysaccharide of alpha glucose.
2. The structure of glycogen is very similar to amylopectin, except it has Lots more Side Branches, which allows stored glucose to be Released Quickly when it is needed.
3. It's also very Compact, making it Good for Storage.

CELLULOSE

1. Cellulose is made of long Unbranched Chains of Beta-Glucose.
2. When Beta-Glucose molecules bond, they Form Straight Cellulose Chains.
3. The chains are linked together by Hydrogen Bonds to form strong fibres called Microfibrils. The strong fibres mean cellulose provides Structural Support for cells, i.e. in Cell Walls.

Lipids

Simple terms: Fatty Oily Things. Some of them are just straight-forward fats, but others have additional parts. We need to know about 3 types of lipids:

• Triglycerides
• Phospholipids
• Cholesterol

All Lipids contain Carbon, Hydrogen and Oxygen atoms.

TRIGLYCERIDES

• Triglycerides are Macromolecules - they're complex, with a relatively large molecular mass.
• Triglycerides have one molecule of Glycerol, with 3 Fatty Acids attached to it.
• The Fatty Acids have a Long Tail made of Hydrocarbons (hydrogen and carbon only) which are Hydrophobic, so they repel water molecules. this makes them Insoluble in Water.

• All fatty acids have the same basic structure, but the hydrocarbon tail varies. 
• The picture below shows the chemical structure of a fatty acid: C is carbon, O is oxygen, H is hydrogen. As you can see, there is a double bond between the C and the O. The rest are single bonds. The R represents the Variable Hydrocarbon Tail.

• Triglycerides are Synthesised by the formation of an Ester Bond between each Fatty Acid and the Glycerol molecule.
• The Ester Bond is Formed by a Condensation Reaction (water molecule released) This process is called Esterification.
• Triglycerides Break Down when the Ester Bonds are Broken. Each Ester Bond is Broken by a Hydrolysis Reaction (when a water molecule is used up).

There are two types of fatty acids: Saturated, and Unsaturated.

SATURATED

• Saturated means it has No Double Bond between Two Carbon Atoms. 
• The General formula is something we just have to learn and know how to use it. 
• For Saturated fatty acids, the formula is C_nH_(2n+1)COOH

UNSATURATED

• Unsaturated means it has, At Least One Double Bond between Two Carbon Atoms.
• The General Formula is the same as saturated fatty acids, so the only real difference is the double bond.

PHOSPHOLIPIDS

Phospholipids are also Macromolecules, so they look pretty similar to triglycerides, but instead of having one glycerol to 3 fatty acids, they have One Glycerol to Two Fatty Acids and One Phosphate Group

The Phosphate Group is Hydrophilic, so it attracts water molecules.

Structures & Functions of Triglyceride, Phospholipids and Cholesterol.

TRIGLYCERIDES	PHOSPHOLIPIDS	CHOLESTEROL
Energy Storing molecules	Found in the Cell Membranes of all Eukaryotes and Prokaryotes.	Hydrocarbon Ring  attached to  a Hydrocarbon Tail.
In Bacteria, it is used to Store Carbon too	They make up the Phospholipid Bilayer	Has a Polar Hydroxyl (OH) Group. (polar means it has a slightly negatively charged bit and a slightly positively charged bit).
They  are good for storage because: Long Hydrocarbon Tails  contain lots of Chemical Energy which is released when broken down Hydrophobic Tails  forces Triglycerides to bundle together as Insoluble Droplets with tails facing inwards, shielding themselves from water with their glycerol heads.	Phospholipid Heads are Hydrophilic, and their Tails are Hydrophobic, so they make a Double Bilayer with their heads facing outwards.	Small in size and Flattened shape - allowing Cholesterol to fit In Between the Phospholipid molecules in the Membrane
	The Centre of the Bilayer is Hydrophobic, so water soluble substances can't pass through easily.	They Bind to the Hydrophobic Tails of the Phospholipids, causing them to Pack more closely together - this makes the Membrane Less Fluid and More Rigid.

^^^Triglyceride - Insoluble droplets^^^

^^^Phospholipid Bilayer ^^^

^^^Cholesterol in the Bilayer^^^

Proteins
There are Millions of different proteins and they are essential to life.

• Proteins are Polymers.
• Amino Acid is the Monomer.
• A Dipeptide is when Two Amino Acids join together.
• A Polypeptide is when More Than Two Amino Acids join together.
• Proteins are made of one or more Polypeptides.

Amino Acids
All amino acids have the Same General Structure.

• 1 Carboxyl Group (-COOH)
• 1 Amino Group (-NH2)
• All attached to a Carbon Atom
• The only difference is the part labelled 'R' which is a Variable Atom

Peptide Bonds join Amino Acids together to form Dipeptides or Polypeptides. A Molecule of Water is Released during the reaction and the reverse of this reaction breaks the peptide bond (hydrolysis)

Primary Structure - The Sequence of amino acids:

Secondary Structure - The chain does not stay straight and flat. Hydrogen Bonds form Between the Amino Acids making it either coil into an α Helix or it folds into a β Pleated Sheet.

Tertiary Structure - The coiled and folded chain of amino acids is Coiled and Folded Further. For proteins made out of a single polypeptide chain, this phase forms their final 3D structure.

Quaternary Structure - Some proteins are made of more than one polypeptide chain. This phase is where the Different Polypeptide Chains are Assembled. i.e. haemoglobin is made of 4 polypeptides.

Different bonds hold together different structures of proteins:

1. Primary Structure - Peptide Bonds
2. Secondary Structure - Hydrogen Bonds between amino acids
3. Tertiary Structure - there's a few:
1. Ionic Interactions - Weak Attractions between the Positive and Negative parts of the molecule.
2. Disulphide Bonds - only when Two Molecules of an amino acid called Cysteine come Close Together, a Sulphur atom from Each Cysteine Join together.
3. Hydrophobic and Hydrophilic Interactions - when Hydrophobic Groups are Close together, they tend to Clump together, Pushing the Hydrophilic groups to the Outside
4. Hydrogen Bonds
4. Quaternary Structure - All of the above.

The shape of proteins relates to its function. There are two examples we need to know:

COLLAGEN

• A Fibrous protein
• Forms Supportive Tissues in animals, so it needs to be Strong.
• Made of 3 Polypeptide Chains Tightly Coiled into a Triple Helix.
• Chains are Interlinked by Strong Covalent Bonds
• Minerals can Bind to the Triple Helix to Increase its Rigidity.

HAEMOGLOBIN

• A Globular protein
• Contains a Haem Group with Iron in it that Binds to Oxygen, carrying it around the body.
• It has a Curled Up Structure.
• Hydrophilic Side Chains are on the Outside of the molecule, and Hydrophobic Side Chains face Inwards.
• This makes it Soluble in Water which makes it Good for Transport in the Blood.