OCR AS Biology- Biological Molecules

Water

Hydrogen bond- A weak interaction that can occur wherever molecules contain a slightly negatively charged atom bonded to a slightly positively charged hydrogen.

Small molecule with two hydrogen atoms covalently bonded to an oxygen atom.

Covalent bond= Bond formed by a shared pair of electrons

Water is a polar molecule, and is slightly negatively charged at the oxygen end and slightly positively charged at the hydrogen ends. This is because the shared electrons aren't shared evenly and the oxygen atom is capable of pulling the shared electrons towards it and away from the hydrogen atoms.

In water's liquid state the molecules form hydrogen bonds, creating a network that lets the molecules move around and make/break hydrogen bonds whilst moving. Making it difficult for water molecules to escape the liquid and become gaseous.

So water has a relatively high boiling point of one hundred degrees celsius. Whereas hydrogen sulphide (similar size to water) is a gas at room temperature.

When temperature is decreased the water molecules move less as they have less kinetic energy

although more hydrogen bonds are made they do not break as easily. When water becomes solid the hydrogen bonds formed hold the structure in a semi-crystaline form which is LESS DENSE THAN LIQUID so ice can form on the surface of water.

Hydrogen bonds in liquid water restrict movement of molecules so a relative amount of energy is needed to increase the temperature of water, so this keeps the temperature of lakes and oceans stable even in large temperaute changes.

Water evaporation uses quite a lot of energy so the water evaporating from a surface removes heat from the surface <-- using heat energy in evaporation

Ice is less dense than water, As water cools it's density increases until the temp. drops to 4 degrees celsius, then the density starts to decrease. So ice can float on water and insulate the water underneath so organisms can live and survive the winter.

Water molecules stick to each other- COHESION

Results in surface tension on the surface of water.

The solubility of a substance depends on whether water molecules can interact with it.

A polar molecule can dissolve in water because:

- The solute has slightly negative and slightly positive areas that can interact with water molecules

- Water molecules move around the charged parts of the solute molecules

- Keeping the solute molecules apart so they can dissolve

- In solution molecules can move and react with other molecules

Water stays liquid over a large temp. range and is a solvent for many chemicals. Making water a very good transport medium.

Properties of Water:

Solvent- 70-95% cytoplasm is water and dissolved chemicals are involved in processes such as respiration and photosynthesis

Liquid- Blood in animals uses water as a liquid transport medium

Cohesion- Transporting water in the xylem relies on cohesion

Freezing- Lakes don't usually totally freeze, so organisms living in them survive

Thermal Stability- Oceans have a stable temp.

Metabolic- used in hydrolysis reactions and in photosynthesis

Amino acids are the monomers of all proteins. They all have the same basic structure and there are twenty different amino acids involved in protein synthesis. Only the R group bonded to the central carbon differs.

Proteins make up around 50% of organic matter of a cell. Large molecules made up of carbon, hydrogen, oxygen and nitrogen. Sometimes contain sulphur.

Functions:

Structural components (Muscle & bone)

Membrane carriers & pores (Active transport & facilitated diffusion)

Enzymes are proteins

Hormones can be proteins and antibodies are proteins too.

Proteins are polymers made by joining lots of monomers- amino acids.

Proteins are long chains of amino acids.

The simplest amino acid is glycine.

Same basic structure but differing R groups. R groups are large, some are positive and some are negative, some are hydrophobic [water hating] and some are hydrophillic [water loving].

Amino acids joined together give a repeating backbone, e.g. N-C-C-N-C-C-N-C-C-N-C-C

Essential amino acids are the amino acids that animals can't build from materials consumed, so they have to be part of their diet. There are 8-10 essentials. Found in meat

Animals can't store excess amino acids because they can be toxic, so the amino group is removed by deamination which in mammals happens in the liver. The amino groups are converted to urea and removed in the urine.

Condensation reactions between the acid group of an amino acid and the amino group of another forms a covalent bond between the two amino acids. This forms a water molecule also.

There is a new peptide bond. The new molecule made is a dipeptide and the peptide bond can be broken by hydrolysis <-- which adds a water molecule to break the bond.

Making and breaking peptide bonds is needed in the building and rebuilding of all of the protein molecules in organisms. Breaking proteins down to amino acids is used in digestion.

As more amino acids are joined by peptide bonds a polypeptide is formed.

Part of the amino acid molecule is los tin the condensation reaction that makes the peptide bond.

Protein synthesis takes place in the ribosome cells.

Using info from mRNA to put amino acids in the right order to make specific polypeptide chains.

The primary structure of a protein is given by the specific sequence of amino acids that make up the protein

DIFFERENT AMINO ACIDS HAVE DIFFERENT PROPERTIES. E.g. if a protein has lots of amino acids with hydrophobic R groups then the final protein will be a certain shape and could be found embedded in a membrane.

Breaking down peptide bonds in organisms is catalysed by enzymes. Covalent bonds are very strong so don't simply appear or break in cells.

Enzymes that catalyse the breaking of peptide bonds are known as protease enzymes.

Not only found in parts of the organism where digestion occurs but also:

hormone regulation hormones must be broken down so their effects are temporary and controlled.

Ageing Skin loses it's elasticity and wrinkles because older skin is less able to rebuild the collagen protein to give smooth and elastic skin.

Secondary Structure- Refers to coiling and pleating of parts of the polypeptide molecule

Tertiary Structure- The overall 3D structure of the final polypeptide/protein molecule

To make a specific protein the amino acids have to be bonded in a specific sequence determined by the DNA. To prevent tangling/breaking of the amino chain as more amino acid bonds, parts of the chain are stabilised by coils/pleats and held together by hydrogen bonds. The amount of pleats/coiling depends on the type of amino acids added to the chain and primary structure.

The secondary structure of a protein is formed when the chain of amino acid coils/folds to make an alpha helix/beta pleated sheet. Hydrogen bonds hold the coils and although these bonds are weak as multiple bonds are made the overall strength is large on the molecule.

Final 3D shape of the protein is made when the coils/pleats coil/fold with straight runs of amino acids between.

The 3D shape is held in place by many bonds. The tertiary structure of a protein is crucical to it's function.

E.g. a hormone has to be a certain shape to fit into it's hormone receptor of a target cell. Or an enzyme must have an active site that is complementary to that of it's substrate.

Heating a protein increases kinetic energy of the molecule. Causing it to vibrate and break some bonds that hold the tertiary structure in place. As the bonds are quite weak they can be easily broken, if enough heat is applied the entire tertiary structure can unravel so the protein won't function. This is called denaturation. Even with cooling, the protein can't reform it's original structure.

The 3D shape of proteins have two main categories

Globular- roll up into a ball shaped structure and are usually soluble in water. They usually have metabolic roles. E.g. Enzymes found in all organisms. Plasma proteins and antibodies in mammalian blood. Hydrophobic R groups are turned inwards towards the centre of the structure and hydrophillic R groups are usually on the outside so they're soluble.

Fibrous- Form fibres, usually have regular repetitive sequences of amino acids. Usually insoluble in water and have structural roles. E.g. collagen in bone and cartilage, keratin in hair and fingernails.

Quaternary structure refers to the fact that some proteins are made up of more than one polypeptide subunit joined together or a polypeptide and an inorganic component. These proteins only function if all subunits are present. E.g. Haemoglobin

The haem group of haemoglobin is not made from amino acids but is an essential part of the molecule, it is called a prosthetic group. These can be found in lots of proteins.

Haemoglobin

• Globular
• Soluble in water
• Range of amino acid parts in primary structure
• Has a haem prosthetic group
• Lots of the molecule is wound into alpha helix structures

Collagen

• Fibrous
• Insoluble in water
• Around 35% of it's primary structure is glycine (1 amino acid)
• Doesn't have a prosthetic group
• Most of the molecule is made of left handed helix structures

Lipids are a diverse group of chemicals that dissolve in organic solvents such as alcohol but not in water. They include fatty acids, triglycerides and cholesterol.

Make up around 5% of organic matter of a cell. at RTP a solid lipod is fat and at liquid the lipid is called oil.

Functions

• Energy (Lipids can be respired to release energy to make ATP)
• Energy Storage (Stored in apidose cells)
• Biological membranes (Lipids make them)
• Insulation
• Protection
• Hormones

Contain the elements- Carbon, Hydrogen and Oxygen

Glycerol and fatty acids are found in all fats and oils that have a role in energy storage, supply and membranes.

Glycerol molecules are always the same in fats but the fatty acid molecule in lipids can differ.

Animals can't make some fatty acids needed from the material taken in to their bodies so they are called ESSENTIAL FATTY ACIDS and must be taken in complete as part of their diet.

All fatty acids have an acid group at one end which is the same as the acid group found in an amino acid and the rest of the molecule is a hydrocarbon chain which can be two to twenty carbons long. Typically, the fatty acids have around eighteen carbons in the hydrocarbon chain.

Unsaturated fatty acids have C=C bonds so fewer hydrogen atoms can be bonded to the molecule.

A single C=C double bond gives a mono-unsaturated fatty acid. Multiple C=C double bonds give polyunsaturated fatty acids.

C=C double bonds change the shape of the hydrocarbon chain, making the molecules in a lipid push apart making more fluid. Lipids containing lots of unsaturated fatty acids are usually oils but those with mainly saturated fatty acids are usually fats.

Lots of animal lipid contains saturated fatty acids. Whereas, plant lipids usually contain lots of unsaturated fatty acid and are liquid at rtp.

Saturated fatty acids are single bonded C-C with all bonds are made with hydrogen.

A triglyceride is made up of one glycerol molecule bonded to three fatty acid molecules. All fatty acid molecules are joined to glycerol molecules identically. Condensation reaction with the acid group of a fatty acid molecule and on the the OH groups of a glycerol molecule makes a covalent bond and a water molecule is made.

The bond is called an ester bond. The molecule produced is a monoglyceride. If there were condensation reactions with the remaining OH groups on the glycerol molecule would make a triglyceridemolecule.

Triglyceride's are insoluble in water and so hydrophobic. Because charges on the molecule are evenly distributed around the molecule so the hydrogen bonds can't form with water molecules so the two molecule types don't mix easily.

Phospholipid molecules are almost identical to triglyceride molecules. Phospholipids consist of a glycerol molecule with fatty acid molecules bonded by condensation reactions to form ester bonds.

In phospholipids the third fatty acid is not added to the glycerol molecule, the phosphate group is covalently bonded to the third OH group on the glycerol and the bonding of the phosphate group occurs by condensation reaction, therefore a water molecule is released.

Phosphate head= hydrophillic

Hydrocarbon chain fatty acid tail= hydrophobic

Fatty acids making up a phospholipid can be saturated/unsaturated. Organisms control the fluidity of their membranes with this. E.g. Organisms living in cold climates have increased amounts of unsaturated fatty acids in their phospholipid molecules, so their membranes remain fluid even in low temps,

Respiration of lipids requires hydrolysis of ester bonds holding the fatty acids and glycerol together. (The reverse of the condensation reaction joining them) Glycerol and fatty acids can be totally broken down to make carbon dioxide and water, releasing energy needed to make ATP.

Specifically the respiration of just 1g of lipid gives 2x the energy of respiration of 1g of carbohydrate. Lipids are insoluble in water so they can be stored in a compact way and do not affect water potential of cell contents. So triglyceride is a very good energy storage molecule. Also, the respiration of a lipid gives out more water than carbohydrate, this metabolic water is crucial to some organisms.

Cholesterol= lipid

Steroid hormones like testosterone, oestrogen and vitamin D are made from cholesterol. The lipid nature of these hormones mean they can pass through the phospholipid bilayer of membranes easily to meet there target receptor. Usually inside the nucleus. [Bilayer of nuclear envelope]

Cholesterol is vital to living organisms so many cells, like the liver, can make it though it can be a problem to humans in excess as:

bile. Cholesterol can stick together to form lumps called gallstones

blood. Cholesterol can be deposited in inner linings of blood causing circulatory problems and atherosclerosis

High blood cholesterol that runs in the family (FHC) is a genetic disorder whereby cells make and secrete cholesterol despite there being enough in the blood for the organisms needs, this happens because cells don't obey signals to stop cholesterol production because they don't have a specific cell surface receptor.

Trigyceride-

glycerol + 3 fatty acids

Compact energy store

Insoluble in water <-- so doesn't affect cell water potential

stored as fat for thermal insulation and protection

Phospholipid

Glycerol + 2 fatty acids + phosphate group

part hydrophobic & part hydrophillic ideal for cell surface membranes

Phosphate group can join carbohydrates to make glycolipids for cell signalling

Cholesterol

four carbon based ring structures joined

small/thin fits in lipid bilayer for mechanical strength and stability

Used to form steroid hormones

Carbohydrates

Make up a group of molecules containing carbon, hydrogen, and oxygen in the ratio Cn(H20)n

Make up about 10% of organic matter of a cell, they are an:

• Energy source i.e. released from glucose during respiration
• Energy store i.e. starch
• Structural i.e. cellulose

Some even form part of larger molecules like nucleic acids and glycolipids.

Simple Sugars

The simplest carbohydrates are called monosaccharides, they are monomers of carbohydrates. Larger carbohydrates are joined monosaccharides.

They contain between three and six carbon atoms and are:

• Soluble in water
• Sweet tasting
• Able to form crystals

Monosaccharides are grouped according to the number of carbon atoms in the molecule, so:

3 carbon monosaccharides (Each molecule) are triose sugars

5 carbon monosaccharides are pentose sugars & 6 Carbon are hexose sugars.

Glucose has two forms- chain and ring.

There is also alpha glucose and beta glucose.

The only difference with alpha and beta glucose are the positions of the OH group and the H on Carbon 1.

(alpha has the OH above and the H below, beta has the H above and the OH below)

Two monosaccharides can be joined in a condensation reaction making a disaccharide. A new covalent bond is formed called a glycosidic bond. Water is removed. Hydrolysis reverses this, using a water molecule to break the glycosidic bond.

Building polysaccharides like starch, glycogen and cellulose and breaking down large molecules (E.g. digestion) involves the making/breaking of glycosidic bonds.

Breaking glucose into simpler carbon dioxide and water molecules during respiration releases energy which can be used to make ATP.

Glucose + Oxygen --> Carbon dioxide + water + energy

Specific enzymes break down glucose in living organisms.

Animals and plants have enzymes that can only break alpha glucose down. These ezymes can't break beta glucose down because of the arrangement of the OH group and H on Carbon 1. The enzyme function is based on shape.

Alpha glucose can be respired but beta glucose can't.

Alpha glucose + Alpha glucose = Maltose (Disaccharide)

The same condensation can be repeated many times to form a molecule called amylose.

Amylose is thousands of glucose molecules bonded together, the glycosidic bond between the glucose subunits occurs between carbon number of one molecule 1 and carbon 4 of the next molecule so is often called a 1,4 glycosidic bond. Amylose is compact because the bonds and shape of glucose molecules form it into a coil/spring.

Iodine molecules can become traped in the coils (in potassium iodide solution) so the colour changes from yellow/brown to blue/black (test for starch)

Starch- energy storage for plants. Branched amylopectin and straight chain amylose molecules. Stored in chlorplasts and in starch grains. Starch can be broken down to glucose molecules that can be respired to release energy for ATP.

Glycogen- energy storage for animals. (Animal starch) Large molecule and made up of alpha glucose. The 1-4 glucose chains in glycogen are shorter than starch ones and glycogen has more branches extending from the chain. Glycogen is more compact than starch and makes glycogen granules in animal cells, e.g. liver and muscle cells.

They are insoluble so they don't affect water potential of cells.

They also hold glucose molecules in chains so they can be broken off from ends to provide glucose for energy when needed.

Beta glucose molecules can be bonded together to form polymers through condensation reactions, resulting in a long, straight chain. Cellulose is made from 10000 beta glucose molecules, it is a structural polysaccharide and found only in plants.

Cellulose molecules are arranged specifically to make plant cell walls. The glucose monomers contain many OH groups so hydrogen bonds are formed between them.

60-70 cellulose molecules are cross linked by hydrogen bonds to form bundles called microfibrils, these microfibrils are held by more hydrogen bonds to form even larger bundles called macrofibrils which have great mechanical strength. Close to that of steel. They are embedded in a polysaccharide glue of substances called pectins to make cell walls.

• Cell walls around plant cells give huge strength to each cell and support the entire plant
• Arrangement of macrofibrils allow water to move through/along cell walls and water can pass in/out easily
• Water movement in/out doesn't cause cells to burst like in animal cells. The wall avoids bursting and instead creates turgidity which is actually beneficial to support the plant
• Cell walls can even be reinforced with cholesterol and other substances to give even more support, strength and waterproof walls.
• Arrangement of macrofibrils in cell walls controls how cells grow/ change shape.

Monosaccharides- monomers- glucose, deoxyribose- small, soluble, sweet, crystaline, glucose provides energy via respiration and deoxyribose is part of DNA

Disaccharides- dimers- maltose (glucose+glucose)- small, soluble, sweet, crystaline, sugar made when starch is split by hydrolysis, maltose can be split further to make two glucose molecules for respiration.

Polysaccharides- polymers.

Starch and glycogen- large alpha glucose molecules joined by condesnation. Insoluble in water and form grains/granules. Energy storage carbohydrates, starch in plants and glycogen in animals and fungi.

Cellulose- large beta glucose molecules joined by condensation. Insoluble and very strong. Structural. Found in plants only to form cell walls.

Starch --> iodine in potassium iodide, starch is present a colour change from yellow/brown to blue/black

Reducing sugars--> Heated with benedicts solution colour change from blue to orange/red. Precipitate. (blue--green--yellow--orange--red)

Non reducing sugars--> Don't react with benedicts solution. Negative. No colour change. So make sure there are no reducing sugars, then boil with HCl <-- hydrolysing sucrose present, splitting sucrose molecules to make glucose + fructose. Cool and neutralise the solution. Do the reducing sugars test again and the test should be positive because monosaccharides glucose and fructose are present.

Proteins--> Biuret test. [Biuret re. is pale blue] The chemicals react with peptide bonds in protein resulting in a colour change to lilac.

Lipids--> Ethanol emulsion test. Positive test results in a cloudly white emulsion near the top of water. There is a band.