Biological molecules

• A fibrous protein
• Forms supportive tissues in animals
• Strong and flexible
• Made of three polypeptide chains-tightly coiled into strong triple helix
• Chains interlinked by strong covalent bonds
• Minerals can bind to triple helix to increase rigidity

• Globular protein
• Carries oxygen around body
• Curled up structure-hydrophilic side chains on outside, hydrophobic chains inside
• Soluble in water-makes it good for transport in blood

• Weak acids found in nuclei of cells
• Polymers composed of monomers called nucleotides
• Deoxyribonuleic acid (DNA)
• Ribonucleic acid (RNA)
• Contain instructions that make every living organism on the planet

Nucleotides are the monomers that make up nucleic acids (DNA, RNA). They have three parts to them:

• A phosphric acid
• A deoxyribose-a 5 carbon pentose sugar
• A nitrogenous base
  • 5 organic bases
  • All contain elements carbon, hydrogen, oxygen, and nitrogen
  • Two groups-purines (2 rings of carbon and nitrogen atoms) and pyrimidines (1 ring of carbon and nitrogens)
  • The bases are: Adenine, Cytosine, Guanine, Thymine, Uracil
  • Thymine only found in DNA, Uracil only found in RNA

Structure

• One molecule of glycerol with 3 fatty acids attached to it
• Fatty acids joined by an ester bond
• Fatty acid molecules have long 'tails' made of hydrocarbons which are hydrophobic.
• Tails make lipids insoluble in water

Function

• Mainly used as energy storage for molecules
  • long hydrocarbon chains contain lots of energy-released when broken
• Lipids contain twice as much energy per gram than carbohydrates 
• Insoluble (water entering the cell by osmosis would make them swell)
• Triglycerides bundle together as insoluble droplets
  • hydrophobic tails face inwards and are shielded by their glycerol heads

Structure

• Hydrophilic heads and hydrophobic tails-form a double layer with heads facing out towards water
• Similar to triglycerides except one fatty acid molecule is replaced by a phosphate group (which is ionised and attracts water)

Function

• Make up the bilayer of cell membranes
• Centre of bilayer is hydrophobic
  • water soluble substances can't easily pass through, so the membrane acts as a barrier to those substances

A group of substances used as both energy sources and structural materials in organisms.

• All carbohydrates contain carbon, hydrogen, and oxygen with the general formula: Cx(H2O)y
• There are three mains groups:
  • Monosaccharides-simple sugars with the general formula (CH2O)n, where can can be 3-7
  • Disaccharides-'double sugars', formed from 2 monosaccharides
  • Polysaccharides-large molecules formed from many monosaccharides

• An abundant and very important monosaccharide
• Contains six carbon atoms-therefore a hexose sugar
• General formula-C6H12O6
• Major energy source for most cells
• Highly soluble
• Main form in which carbohydrates are transported around the bodies of animals
• Glucose exists in different forms called structural isomers
  • alpha glucose and beta glucose are two common structural isomers
  • only difference is the position of the -OH group
  • has a major effect of the roles of both

Other hexose monosaccharides:

• Fructose-sweeter than glucose
• Galactose-not as souble as glucose

Pentose monosaccharides:

• Ribose
• Deoxyribose
  • both important constituents of RNA and DNA

• Join together with a glycosidic bond
• This forms between a hydroxyl group on one and a hydroxyl group on another monosaccharide
• When naming the bond, you must say which carbons are involved
  • in maltose, sucrose, and lactose the bond is a 1-4 glycosidic bond
• A condensation reaction

• Polymers containing many monosaccharides linked by glycosidic bonds
• Formed by condensation reactions
• Mainly used as energy stores and as structural components of cells
• The major polysaccharides are starch and cellulose in plants, and glycogen in animals

Made of many alpha glucose molecules arranged into two structural units: amylose and amylopectin.

• Amylose contains glucose molecules joined mainly by alpha 1-4 glycosidic bonds
• Amylose is an unbranched molecule and forms a helical structure (compact)
• Amylopectin mainly contains 1-4 glycosidic bonds, but also contains many more alpha 1-6 glycosidic bonds
• Most starch is amylose but does contain some amylopectin
• Amylopectin has a highly branched structure

• Starch usually stored as intracellular starch grains in organelles called plastids
  • plastids include green chloroplasts and colourless amyloplasts
• Starch is produced from glucose and is broken down during respiration

Another polysaccharide and is the main part of plant cell walls. It is the most abundant organic polymer.

• Very strong (unlike starch) and prevents cells from bursting when they take in excess water
• Consists of long chains of beta glucose molecules joined by beta 1-4 glycosisdic bonds
• Chains of glucose form rope-like microfibrils which are layered to form a network
• Every other glucose molecule rotates through 180 degrees so that hydroxyl groups on each molecule are adjacent to each other in the structure of cellulose
• Results in long unbranched chains
• Hydrogen bonding between chains gives cellulose molecules great tensile strength-there are thousands of chains and thousands of bonds

• Has a similar structure to amylopectin, containing more aplha 1-6 glycosidic bonds that produce an even more branched structure
• Stored as small granules
• Less dense and more soluble than starch and is broken down more rapidly-this indicates the higher metabolic requirements of animals compared with plants
• A very energy dense molecule
• Branches in the molecule are for enzymes to attach more glucose to the glycogen molecule or for glucose to be broken off from it
• Because glycogen is not soluble it does not affect the water potential of the cell-if it was stored as glucose the cell would burst as it draws in more water

• Proteins are unbranched molecules made of amino acids joined together by peptide bonds
• There are 20 different amino acids
• Singles chains of amino acids are polypeptides
  • they can be folded in 3d shapes to form globular proteins
  • or formed into simpler shapes such as helicer to form fibrous proteins

Uses of proteins

• 50% of the living matter of a cell
• Large molecules made of C, H, O, and N. Some also contain S.
• Functions:
  • structural
  • membrane carriers and pores
  • enzymes
  • many hormones
  • antibodies

• R-groups are what create the differences in amino acids
• Some R-groups are larger than the C-N-N part of the molecule
• Some R-groups are +, some -, or they can be hydrophobic or hydrophilic

Plants and animals

• Plants can manufacture AAs, using nitrogen from the soil converted into amino groups
• Animals must ingest proteins in their diet
• Some (8-10 of the 20) AAs are called essential amino acids
  • most essential AAs are found in meat or soya.
• AAs that are surplus to the body's requirements cannot be stored
• Urea is toxic due to the amine group in AAs.
• They are processed in the liver, where urea is formed.

• Condensation reaction
  • between the acid group of one amino acid and the amine group of another
• Forms a covalent bond
• A water molecule is produced
• New bond is called a peptide bond
• New molecule is called a dipeptide
• A peptide bond can be broken in a hydrolysis reaction

• Proteins may consist of hundreds of amino acids, or even more than one polypeptide chain bonded to form a larger molecule
• Synthesised in the cell on ribosomes
• Uses mRNA to put the amino acids in the right order
• The mRNA passes through the ribosome joining the AAs together one at a time
• The formation of different polypeptides uses different mRNA molecules.

'm' in mRNA stands for messanger

• The primary structure is the structure first determined by the specific amino acid sequence
• All proteins have an amine group at one end, and an acid group at the other, no matter the length
• Function is determined by structure 
• There are around 10,000 different proteins that we know of, each with its own function

Protein

• Add Biuret Reagent to sample
• If positive, change from pale blue to lilac

Reducing sugar

• Heat with Benedict's solution
• If positive, change from blue to orange-red precipitate

Non-reducing sugar

• Boil with hydrochloric acid, cool solution and add sodium hydrogencarbonate or sodium carbonate solution and repeat Benedict's test
• If positive (once Benedict's test repeated) change from blue to orange-red precipitate

Lipid

• Mix sample with ethanol and then pour the liquid into water contained in a clean test tube
• If positive, cloudy white emulsion will form near top of water

Starch

• Add iodine to sample
• If positive, change from yellow-brown to blue-black

• All globular proteins
• 3D shape usually has hydrophobic AA R-groups in the centre of the ball, and hydrophilic AA R-groups outside the ball.
• Soluble in water
• Catalyst
• Specific

Active site

• Only a tiny proportion of the AAs make up the active site (often fewer than 10 AAs)
• Very specific shape
• The job of the rest of the amino acids is to keep the enzymes this specific shape

Biological catalysts

• Speed up chemical reactions
• Usually work much faster than inorganic catalysts
• Specific to one catalytic reaction
• Do not produce a range of unwanted by-products
• Area of industrial research

Enzymes in cells

• Metabolism is enzyme driven
• Bond formation and breakage is usually enzyme driven
• Protein synthesis, digestion, respiration, and photosynthesis all require a number of enzymes
• Estimated that each cell contains over 100 different enzymes
• Substrate and products (substrate=molecule that binds with enzyme)
• Named after substrate with suffix -ase 

• Bond breaking happens in digestion
• Internal digestion
  • enzymes are extracellular or intracellular
  • extracellular enzymes are released outside cells to perform catalysis
  • intracellular enzymes are found in the cytoplasm or attached to cell membranes
• Enzymes are also used as protection - white blood cells and bacteria

• Substrate fits into active site
• Substrate=key
• Active site=lock
• Substrate held in place so reaction can go ahead

• Substrate collides with enzyme's active site, the enzyme molecule changes shape slightly
• Active site fits more closely around substrate
• Substrate held more closely by oppositely charged groups on substrate and active site
• Forms enzyme-substrate complex (ESC)
• Change in the enzyme places strain on substrate molecule
• This destabilises the substrate molecule so the reaction occurs more easily
• This produces a product, and is now the enzyme-product complex
• Products formed are a different shape from the substrate
• Products no longer fit active site-move away
• Active site reverts to original shape
• Enzyme is now able to catalyse the same reaction with another substrate molecule

pH

• Too high-lots of OH- ions, hydrogen bonds break, ionic bonds break, tertiary structure unfolds. Denatures.
• Too low-lots of H+ ions (same happens again). Denatures.

Temperature

• Increases-rate of reaction increases.
• Too high-bonds in enzyme molecule break, active site changes shape. Denatures.
• Too low-not enough kinetic energy, fewer collisions-rate of reaction decreases.

Concentration

• Increased substrate concentration-increased rate of reaction, to a point (working at optimum level).
• Increased enzyme concentration has the same effect.