Unit 2: Section 1

Water makes up 80% of a cell's contents. Its functions include:

• It's a reactant in important chemical reactions, e.g. photosynthesis and hydrolysis.
• It's a solvent, so substances dissolve in it. Most biological reactions take place in solution, so water is important.
• It transports substances such as glucose and oxygen around plants and animals.
• It helps with temperature control. It carries away heat energy when it evaporates from a surface, which cools the surface and helps to lower temperature.

Structure:

• One atom of oxygen joined to two hydrogen atoms by shared electrons.
• The shared negative electrons are pulled towards the oxygen atom, leaving the other side of each hydrogen atom with a slight positive charge.
• The unshared negative electrons on the oxygen atom give it a slight negative charge.
• Water is a polar molecule - it has a negative charge on one side and a positive charge on the other.
• The negatively charged oxygen atoms of water attract the positively charged hydrogen atoms of other water molecules - hydrogen bonding.

How water's structure is related to its properties and functions:

• Hydrogen bonds give water a high specific heat capacity (the energy needed to raise the temperature of 1g of a substance by 1.C) - Hydrogen bonds between water molecules can absorb a lot of energy; it takes a lot of energy to heat it up. This is useful as it stops rapid temperature changes in living organisms, allowing them to keep a fairly stable temperature.
• Hydrogen bonds give water a high latent heat of evaporation - it takes a lot of energy/heat to break the hydrogen bonds between water molecules. This is useful for living organisms because it means water's great for cooling things.
• Water's polarity makes it very cohesive (attraction between molecules of the same type) - This helps water to flow, making it great for transporting substances.
• Water's polarity makes it a good solvent - A lot of important substances in biological reactions are ionic, so they're made from one positively charged atom and one negatively charged atom. The positive end/negative end of a water molecule will be attracted to the negative/positive ion, meaning the ions will get totally surrounded in water molecules, allowing them to dissolve. Therefore, water's polarity makes it a good solvent for other polar molecules.

• A dipeptide is formed when two amino acids join together.
• A polypeptide is formed when more than two amino acids join together.
• Proteins are made up of one or more polypeptides.

Structure:

• All amino acids have the same general structure - a carboxyl group (-COOH) and an amino group (-NH2) attached to a carbon atom.
• The difference between different amino acids is the variable (R) group they contain.
• Amino acids are linked together by peptide bonds to form dipeptides and polypeptides.
• A molecule of water is released during the reaction. This is a condensation reaction.
• The reverse of this reaction adds a molecule of water to break the peptide bond. This is called a hydrolysis reaction.

• Primary structure - the sequence of amino acids in the polypeptide chain. Held together by the peptide bonds between amino acids.
• Secondary structure - Hydrogen bonds form between the amino acids in the chain, making it coil into an alpha helix or a beta pleated sheet.
• Tertiary structure - The coiled or folded chain of amino acids is coiled and folded further. For proteins made from a single polypeptide chain, the tertiary structure forms their final 3D structure. Bonds used:
  > Ionic interactions - weak attractions between negative and positive charges on different parts of the molecule.
  > Disulfide bonds - whenever two molecules of the amino acid cysteine come close together, the sulfur atom in one cysteine bonds to the sulfur in the other cysteine.
  > Hydrophobic and hydrophillic interactions - when hydrophobic groups are close together in the protein, they clump together, meaning the hydrophillic groups are pushed to the outside, affecting how the protein folds up into its final structure.
  > Hydrogen bonds.
• Quaternary structure - some proteins are made of several different polypeptide chains held together by bonds. The quaternary structure is the way they're assembled together. Determined by tertiary structure, so same bonds. 

Protein shape relating to its function:

Collagen

• A fibrous protein (tough and rope shaped, usually found in connective tissue) that forms supportive tissues in animals, so it needs to be strong.
• Made of three polypeptide chains tightly coiled into a strong triple helix.
• The chains are interlinked by strong covalent bonds.
• Minerals can bind to the triple helix to increase its rigidity.

Haemoglobin

• A globular protein (round and compact, soluble and easily transported in fluids) with an iron-containing haem group that binds to oxygen, carrying it around the body.
• Its structure is curled up so that hydrophillic side chains are on the outside of the molecule and hydrophobic side chains face inwards.
• This makes haemoglobin soluble in water, making it good for transport in the blood.

• Most carbohydrates are large, complex molecules composed of long chains of monosaccharides.
• Single monosaccharides are also called carbohydrates.
• Glucose is a monosaccharide with six carbon atoms in each molecule.
• There are two forms of glucose - alpha and beta.
• Glucose's structure is related to its function as the main energy source in animals and plants. Its structure makes it soluble so it can be easily transported. Its chemical bonds contain lots energy.

Monosaccharides

• Monosaccharides are joined together by glycosidic bonds.
• During synthesis, a hydrogen atom on one monosaccharide bonds to a hydroxyl group on the other, releasing a molecule of water - a condensation reaction.
• The reverse of this synthesis is hydrolysis. A molecule of water reacts with the glycosidic bond, breaking it apart.
• A disaccharide is formed when two monosaccharides join together. For example, two alpha glucose molecules are joined together by a glycosidic bond to form maltose.
• A polysaccharide is formed when more than two monosaccharides join together. For example, lots of alpha glucose molecules are joined together by glycosidic bonds to form amylose.

Polysaccharides

Starch - the main energy storage material in plants:

• Cells get energy from glucose. Plants store excess glucose as starch. When a plant needs more glucose for energy, it breaks down starch to release the glucose.
• Starch is a mixture of two polysaccharides of alpha glucose - amylose and amylopectin:
  - Amylose: A long, unbranched chain of alpha glucose. The angles of the glycosidic bonds give it a coiled structure, almost like a cylinder. This makes it compact, so it's good for storage, as you can fit more into a small space.
  - Amylopectin: A long, branced chain of alpha glucose. Its side branches allow the enzymes that break down the molecule to get at the glycosidic bonds easily. This means that the glucose can be released quickly.
• Starch is insoluble in water, so doesn't cause the water to enter cells by osmosis. This makes it good for storage. 

Glycogen - the main energy storage material in animals:

• Animal cells get energy from glucose too. But animals store excess glucose as glycogen, another polysaccharise of alpha glucose.
• Its structure is very similar to amylopectin, except it has loads more side branches coming off it. Loads of branches means that stored glucose can be released quickly, which is important for energy release in animals.
• It's a very compact molecule, so good for storage.

Cellulose - the major component of cell walls in plants:

• Cellulose is made of long, unbranched chains of beta glucose.
• The bonds (hydrogen) between the sugars are straight, so the cellulose chains are also straight.
• The cellulose chains are linked together by hydrogen bonds to form strong fibres called microfibrils. The strong fibres mean cellulose provides structural support for cells.

Triglycerides

• A triglyceride is made up of one molecule of glycerol with three fatty acids attached to it.
• Fatty acid molecules have long tails made of hydrocarbons.
• The tails are hydrophobic.
• These tails make lipids insoluble in water.
• All fatty acids consist of the same basic structure, but the hydrocarbon tail varies.
• Mainly used as an energy storage molecule.
• The long hydrocarbon tails of the fatty acids contain lots of chemical energy - a load of energy is released when they're broken down. Because of these tails, lipids contain about twice as much energy per gram as carbohydrates.
• They're insoluble, so they don't cause water to enter the cells by osmosis. The triglycerides bundle together as insoluble droplets in cells, because the fatty acid tails are hydrophobic - the tails face inwards, shielding themselves from water with their glycerol heads.

Phospholipids

• The lipids found in cell membranes are phospholipids.
• Phospholipids are similar to triglycerides except one of the fatty acid molecules is replaced by a phoshate group.
• The phosphate group is ionised (electrically charged), which makes it attract water molecules.
• The phosphate part of the phospholipid is hydrophillic, while the rest is hydrophobic.
• Phospholipids make up the bilaye of cell membranes. Cell membranes control what enters and leaves a cell.
• Their heads are hydrophillic and their tails are hydrophobic, so they form a double layer with their heads facing out towards the water on each side.
• The centre of the bilayer is hydrophobic, so water-soluble substances can't easily pass through it - the membrane acts as a barrier to those substances.

Cholesterol

• Cholesterol is a type of lipid often found in cell membranes. It's also used to make other things such as steroids.
• It has a hydrocarbon ring structure attached to a hydrocarbon tail.
• The hydrocarbon ring has a polar hydroxyl group attached to it, which makes cholesterol soluble in water. However, it's insoluble in blood, so is carried around the body by proteins called lipoproteins.
• Cholesterol molecules help strengthen the cell membrane by interacting with the phospholipid bilayer.
• The small size and flattened shape allows it to fit in between the phospholipid molecules in the membrane.
• They bind to the hydrophobic tails of the phospholipids, causing them to pack more closely together.
• This helps to make the membrane less fluid and more rigid.