Polymers And Life - Video Flashcards
Amino acids?
Have groups NH2 and COOH.
They are amphoteric, meaning they have acidic and basic properties.
They have an organic side chain, shown with R, expect for glycine, where R is hydrogen.
Amino acids, except for glycine, are chiral molecules, because they have 4 different groups around a central carbon. We know they are chiral because they rotate plane polarised light.
What are zwitterions?
A zwitterion is a molecule with both positive and negative ions.
Zwitterions only exist at the amino acids isoelectrical point - the ph of which the overall charge is zero. This is dependant on the R group.
If the ph is at the isoelectrical point (overall charge is 0), a zwitterion will form. This means on an amino acid, both the carbonyl group and the amino acid groups are ionised.
Different ph’s on a zwitterion?
If the ph is lower than the isoelectrical point, the COO- group is likely to accept the H+
If the ph is higher than the isoelectrical point, the NH3+ is likely to loose the H+
TLC?
Thin layer chromatogram allows us to separate and identify amino acids because amino acids all have different solubility’s.
Uses a stationary phase of silica or alumina mounted on a glass/metal plate.
Pencil line is drawn and the amino acids are added on the line.
Place the plate in mobile phase - liquid solvent. Solvent must be below the pencil line.
Leave until the solvent has reached near the top of the plate. Mark the solvent front and allow to dry.
The amino acid mixture spots dissolve in the solvent. Some chemicals don’t dissolve as much and stick to the stationary phase. We are left with a chromatograph.
We identify the amino acids by finding the positions on the chromatogram.
Name the ways amino acids can be identified using TLC chromatogram?
Amino acids are colourless. They can be seen using ninhydrin solution, iodine solution, or fluorescent dyes and UV.
Identifying amino acids using fluorescent dyes?
Add a fluorescent dye to the silica/alumina plate and then shine UV light onto it.
The plate will turn the colour of the dye, but the colourless spots will be visible under the UV.
Draw around the spots and mark where they are.
Identifying amino acids using iodine and ninhydrin?
Place the chromatogram in a sealed jar with a few iodine crystals.
The iodine vapour sticks to the chemicals dying them purple.
The iodine vapour is a locating agent, ninhydrin can also be used in this way.
Calculating Rf values?
Amino acids can be identified by calculating the Rf values from a chromatogram.
The number of spots on the plate tells you how many amino acids there are that make up the mixture.
Rf = distance travelled by the spot / distance travelled by the solvent
Find the value and compare it to the library of known Rf values for amino acids. They are fixed for each amino acid.
You must make sure the conditions you have used in your experiment match the conditions in the library. This includes: temperature, solvent and make up of plate. All of these change the value you will get.
Proteins?
Proteins are polymers made up of amino acids monomer units. They are condensation polymers.
The link that joins the amino acids monomers is a peptide link. This forms a dipeptide polymer.
A dipeptide has a -COOH at one end and a -NH2 at the other so further reactions can take place to make a polymer chain.
To determine the amino acids that make the polymer, we break the bond in the peptide link via hydrolysis. This requires severe conditions of 6 mol dm-3 HCL (very strong) 110 degrees and reflux for 24 hours.
Then we add water (OH and H) to each of the amino acid units.
Primary structure?
E.g. HOOC- glycine - valine - lysine - NH2
Polypeptide chain
Sequence of amino acids
Secondary structure?
Hydrogen bonds exist between the peptide links in the polymer chain and this pulls the chain into a coiled (alpha helix) or pleated (beta pleated sheet).
Tertiary structure?
The protein shape coils itself up to create a unique shape.
Additional bonds hold the long coiled shape together.
Additional bonds in tertiary structure?
Specific shapes are held together by hydrogen bonds,
Disulfide bonds,
Ionic interactions,
Instantaneous dipole-induced dipole forces.
The shape of the protein determines its functions. Intermolecular forces hold this shape together.
Disulfide bonds?
Cysteine is an amino acid that has the thiol group -S-H-
They can loose the H atom and the sulfur atoms can bond, forming a disulphide S-S bond in between the amino acid chain.
Temperature and Ph change the shape of proteins by affecting the hydrogen bonding and the formation on disulphide bonds.
Hydrogen bonds?
Hydrogen bonds exist between highly electronegative elements such as O and N with H.
In amino acids, this is NH2 and OH
Temperature and Ph change the shape of proteins by affecting the hydrogen bonding and the formation on disulphide bonds.
If amino acid’s with polar side chains are situated on the outside of proteins, then hydrogen bonds can also form to water molecules surrounding the protein, so allowing the proteins to dissolve.
Instantaneous dipole-induced dipole forces?
Weak attractions exist between non-polar groups on the amino acid chain.
Ionic interactions?
Interactions between ionic groups such as CO2- and NH3+ on the amino acid chain.
Covalent bonds form, for example, where the -SH groups on neighbouring cysteine residues are oxidised to form -S—S- links.
DNA?
Deoxyribonucleic acid is a polymer made up of monomers called nucleotides.
Nucleotides are made up of a phosphate, sugar and a base.
Useful to look at the structures of these saved in favourites.
Sugar is 2-deoxyribose and the base is Thymine, guanine, cytosine or adenine. They all connect to the deoxyribose via the bottom, left nitrogen on their molecule.
RNA?
Ribonucleic acid is also a polymer made up of monomers called nucleotides.
It has a ribose sugar instead of a deoxyribose sugar. Look at the diagram saved to favourites to observe the different between moleucles.
Deoxyribose has a -OH and a -H at the bottom whereas ribose has 2x -OH at bottom.
RNA also has uracil to replace thymine. Thymine has an extra carbon.
Polynucleotide chains?
Polynucleotides are nucleotides joined together.
The drawing of the circle, pentagon and rectangle.
Forms a sugar-phosphate backbone by covalently bonding the sugar and phosphate via condensation polymerisation.
A phosphodiester bond is formed and water is elminiated.
OH groups on the phosphate can react further to extend chain.
How is DNA formed?
By 2 polynucleotide strands that are twisted together to form a double helix.
The polynucleotide strands are held together by the hydrogen bonds between the bases, pulling the strands into a structure.
A bonds with T, C bonds with G
Strands in DNA are complementary.
How are bases joined together?
Need to know how to draw. On notes.
Bases are joined together by hydrogen bonding.
A and T have 2 hydrogen bonds between them. They fit neetly together, to the point where you can easily guess where they are going to bond.
Hydrogen bonds can only form when a delta + hydrogen interacts with an electronegative elements with a lone pair such as O or N. It must be the correct distance apart to be able to bond.
A and T form hydrogen bonds as there are 2 atoms to form a hydrogen bond (with a lone pair bonding on a electronegative element).
No other base pairings can happen because the partially charged atoms would be too close to repel or not close enough for a hydrogen bond to form.
Guanine and cytosine have 3 atoms with a lone pair that can bond to an electronegative element. They have 3 hydrogen bonds.
DNA replication?
Use biology flashcards on transcription, translation, mRNA, tRNA to prepare for your exam on this.
Pharmaceuticals?
Medicines act on receptors on the surface of our cells to change a biochemical reaction.
Drugs with the right size and shape can bind to these receptors temporarily to either inhibit a biochemical reaction or commence one in the cell.
The drug must have the right molecular recognition. This means in order for the drug to be medicinally active (for it to work), the drug must have the right intermolecular recognition with the receptor.
What is a pharamcophore?
The part of the drug molecule that fits into the receptor.
The pharamcophore will only fit if it meets the correct criteria:
- Right size and shape to fit the receptor site.
- Right orientation (optical isomerism). Only one of these isomers will fit.
- They must be able to form temporary bonds with the receptors.
Examples of temporary bonds that form in pharamocophores?
- Ionic interactions - exist when a substrate receives or donates protons to form a charged group that can be attracted to the receptor.
- Hydrogen bonding - groups such as alcohols, carboxylic acids and amines can form hydrogen bonds with the receptors.
- Dipole-dipole interactions - if there are polar functional groups in the pharamcophore, then we can dipole-dipole with the receptor.
What does it mean if the pharamcophore is adapted?
The drug can be adapted around the pharmacophore to reduce side effects or to treat different conditions.
Lots of drugs have the same pharamcophore but treat different conditions.
Enzymes?
Enzymes complementary fit with substrates.
The 3D active site of an enzyme must be very specific to fit the substrate.
Enzymes have chiral centres because they are made of amino acids. This means that only one enantiomer in the substrate will fit into the active site.
We say active sites are sterospecific.
Enzymes always remain unchanged.
