Biological molecules

• Carbohydrates - Carbon, Hydrogen, Oxygen

  Lipids - Carbon, Hydrogen, Oxygen

  Proteins - Carbon, Hydrogen, Oxygen, Nitrogen, Sulphur

  Nucleic acids - Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus
• Water - polar molecules (regions of slight negativity and slight positivity). Characteristics;

  • high boiling point
  • ice is less dense than water (floats)
  • water is cohesive (moves as one because molecules are attracted to each other).
  • water is adhesive (molecules are attracted to other materials
  • maintains surface tension
• Water for life -

  • Solvent where solutes in an organism can be dissolved
  • Transport medium through cohesion and adhesion
  • acts as a coolant, maintaining temperature balance
  • stable, not changing temperature easily provides a constant environment. Ice floats, forming an insulating layer
  • surface tension can support small insects such as pond skaters
• Carbohydrates -

  • Monosaccharide - single sugar unit - glucose, fructose, ribose, galactose
  • two monosaccharides link to create a disaccharide - lactose, sucrose, maltose
  • Many monosaccharides link to create a polysaccharide - glycogen, cellulose, starch
• Alpha glucose - H, H, OH, H

  Beta glucose - OH, H, OH, H
• When two glucose molecules join, it is a condensation reaction and called a glycosidic bond.
• Amylose is a polysaccharide composed of long chains of glucose molecules joined by 1,4 glycosidic bonds and twisting into a helix.
• Amylose is compact and not very soluble.
• Amylopectin contains both 1,4 and 1,6 glycosidic bonds, giving it a branched structure and making it insoluble.
• Glycogen forms more branches than amylopectin, making it more compact and requiring less space for storage.
• Glycogen has many free ends where glucose molecules can be added or removed, speeding up storing and releasing of glucose and making it insoluble.
• Cellulose is composed of beta glucose molecules that cannot bond normally, every other one must flip so they can bond.
• Cellulose forms a straight chain.
• testing for carbohydrates - Benedict's test

  Reducing sugars - all monosaccharides and some disaccharides.

  Reducing sugars will react and the solution will turn from blue to brick-red.

  1. place sample into boiling tube
  2. add equal volume of Benedict's reagent
  3. Heat gently in a water bath for 5 minutes
• Benedict's testing for non-reducing sugars

  Non-reducing sugars do not react with Benedict's solution and will remain blue after warming, indicating a negative result.

  Sucrose is the most common non-reducing sugar.

  If sucrose is fist boiled with dilute hydrochloric acid, it will give a positive result when warmed with benedicts solution. This is because sucrose will have been hydrolysed to glucose and fructose, both reducing sugars.
• Iodine test for starch -

  • a few drops of iodine dissolved in potassium iodide solution are mixed with a sample.
  • If the solution changes from yellow/brown to blue/black, then starch is present in the sample.
• Lipids -

  Triglycerides - combining one glycerol molecule with three fatty acids.

  Both molecules contain hydroxyl groups. They interact leading to the formation of three water molecules and bonds between the glycerol and fatty acids. These are called ester bonds and is a condensation reaction known as esterification.
• Saturated and unsaturated -

  Fatty acid chains that have no double bonds present between the carbon atoms are called saturated.

  Fatty acids with double bonds are unsaturated. One double bond = monounsaturated and more than one = polyunsaturated.
• Phospholipids - modified triglycerides which contain phosphorus, carbon, hydrogen and oxygen.

  They have non-polar (hydrophobic) tails that are repelled by water. They have charged (hydrophilic) heads. Because of this, they form a layer on the surface of water with the phosphate heads in the water and the fatty acid tails sticking out of the water. They can also form a bilayer with all of their hydrophobic tails pointing towards the centre of the sheet, protected by the hydrophilic heads.
• Roles of lipids -

  • membrane formation and the creation of hydrophobic barriers
  • hormone production
  • electrical insulation necessary for impulse transmission
  • waterproofing (bird feathers and plant leaves)
  • thermal insulation to reduce heat loss
  • cushioning to protect vital organs such as the heart and kidneys
  • buoyancy for aquatic animals
• Identification of Lipids - Emulsion test

  • Sample is first mixed with ethanol
  • resulting solution is mixed with water and shaken
  • if a white emulsion forms - lipids are present
  • if the solution remains clear, the test is negative
• Proteins - Different 'R' groups result in different amino acids.

  The synthesis of peptides - The hydroxyl in the carboxylic acid group of one amino acid reacts with a hydrogen in the amine group of another amino acid. A peptide bond is formed between the amino acids and water is produced - resulting compound is a dipeptide.

  when many amino acids are joined by peptide bonds, they form a polypeptide.
• Primary structure - sequence of amino acids in a protein chain. Determines the final shape of the protein.
• Secondary structure - folding of the primary structure into alpha helices or beta pleated sheets. This gives proteins their unique shapes.
• Tertiary structure - Folding of a protein into its final shape. Following interactions occur between the 'R' groups:

  • Hydrophobic/ hydrophilic interactions between polar and non- polar 'R' groups.
  • hydrogen bonds - weakest bonds formed.
  • ionic bonds - form between oppositely charged 'R' groups.
  • disulfide bridges - covalent and form between 'R' groups that contain sulfur.
• Quaternary structure - Association of two or more subunits. The interactions are the same as in the tertiary structure except they are between different protein molecules instead of being within the same one. The subunits can be identical or different. Enzymes contain two identical subunits whilst insulin contains two different ones. Haemoglobin has four subunits.
• Types of proteins -

  Globular proteins - compact, water soluble and roughly spherical in shape - formed when proteins fold into tertiary structures so that their hydrophobic 'R' groups are away from the aqueous environment.

  insulin is an example of a globular protein. Insulin is a hormone, so it is important that it is soluble so that it can be transported in the bloodstream.
• Types of proteins -

  Conjugated proteins - Globular proteins that contain a prosthetic group. Lipids or carbohydrates can combine with proteins forming: lipoproteins or glycoproteins. Haem groups are prosthetic groups containing iron and they are found in catalase and haemoglobin.

  Haemoglobin is a conjugated protein and is a red, oxygen carrying pigment that contains two alpha and two beta subunits which further each contain a prosthetic haem group.

  Catalase is an enzyme that contains four haem prosthetic groups which further contain iron II ions.
• Types of proteins -

  Fibrous proteins - formed due to the presence of a high proportion of amino acids with hydrophobic R groups in their primary structures. Amino acid sequence is usually repetitive so they are highly organised.

  Keratin - Hair, skin, nails. strong, inflexible and insoluble.

  Elastin - Elastic fibres in the blood vessel walls and alveoli. They are flexible and allow them to both expand and return to their original size.

  Collagen - skin, tendons, ligaments and the nervous system. Flexible.
• Nucleic acids - made up of: a pentose monosaccharide (sugar), a phosphate group and a nitrogenous base. Linked together by phosphodiester bonds to form a polymer called a polynucleotide. The phosphate at the fifth carbon of the pentose sugar (5') of one nucleotide forms a covalent bond with the OH group at the third carbon (3') of the pentose sugar of an adjacent nucleotide.
• DNA - Deoxyribonucleic Acid.

  Pyrimidines - single carbon ring structures - Thymine and Cytosine.

  Purines - double carbon ring structures - Adenine and Guanine.

  The double helix - the two strands are held together by hydrogen bonds between the bases, each strand has a phosphate group at one end (5') and an OH group at the other end (3'). They are antiparallel as they run in opposite directions.

  Base pairing rules - Adenine and Thymine bond to form two hydrogen bonds and Cytosine and Guanine bond to form three hydrogen bonds. This is known as complimentary base pairing.
• RNA - Ribonucleic acid.

  DNA is a very long molecule so is unable to leave the nucleus in order to supply the information directly to the site of protein synthesis. The short section of the DNA molecule that corresponds to a single gene is transcribed into mRNA. RNA is different to DNA as the pentose sugar is ribose rather than deoxyribose and the Thymine base is replaced with Uracil. RNA polymers are small enough to leave the nucleus and travel to the ribosomes. After protein synthesis, they are degraded in the cytoplasm and the RNA nucleotides are released and reused.
• DNA replication - When a cell prepares to divide, the two strands of the DNA double helix separate and each strand acts as a template for the creation of a new double stranded DNA molecule. Complimentary base pairing ensures that the new strand is exactly the same as the original.

  Semi-conservative replication - For DNA to replicate, the strands must unwind and separate, the hydrogen bonds between the bases are broken.
• DNA replication -

  1. The enzyme DNA helicase, causes the two strands to separate.
  2. Free nucleotides are attracted to their complimentary bases on the unzipped strands.
  3. The free nucleotides are matched and joined together by DNA polymerase.
  4. Finally, all of the nucleotides are joined and two new identical strands of DNA have been formed. Each double strand of DNA is composed of one new strand and one old strand. (semi-conservative replication)
• Genetic codes - the sequence of bases in a gene that codes for a specific amino acid.

  Triplet code - A sequence of three bases is called a codon and each codon codes for an amino acid. A section of DNA that contains the complete sequence of codons to code for an entire protein is called a gene.

  Degenerate code - many amino acids can be coded for by more than one codon. There are 64 different codons possible.
• Protein synthesis - occurs in the cytoplasm at ribosomes but chromosomal DNA is too large to leave the nucleus so must be transcribed into RNA and translated into a specific amino acid sequence.
• Transcription -

  1. the section of DNA containing the gene unzips and the hydrogen bonds between bases are broken.
  2. only the sense strand contains the code for the protein. (5'-3') So the antisense strand acts as a template for the new strand to be the same as the sense strand.
  3. Free RNA nucleotides are attracted towards the antisense strand, uracil binds to adenine and cytosine binds to guanine.
  4. Phosphodiester bonds are created by RNA polymerase. Transcription stops at the end of the gene and the new strand of RNA is called mRNA. It then detaches and leaves to attach to a ribosome.
• Translation - subunits on proteins contain rRNA. (catalyst).

  1. mRNA binds to small subunit on the ribosome.
  2. tRNA with the complimentary anticodon binds to the mRNA start codon.
  3. Another tRNA with a different anticodon and amino acid binds to the next codon on mRNA.
  4. The first amino acid is transferred to the second by the formation of a peptide bond. Catalysed by peptidyl transferase
  5. ribosome then moves along the mRNA, releasing the first tRNA. The second tRNA becomes the first.
• ATP - Cells require energy for synthesis of proteins, transport of molecules or ions across membranes and movement of muscles.

  ATP is composed of a nitrogenous base (only adenine), a (ribose) pentose sugar and three phosphate groups.

  ATP + H2O --> ADP + Pi + energy.

  ATP is small, water soluble, contains bonds large enough for cellular respiration energy that means energy is not lost as heat, releases energy in small quantities and easily regenerated.