Polymers and Life Flashcards
What are Zwitterions?
An overall neutral molecule that has both positive and negative parts within the molecule.
Amino Acids need to be near their Isoelectric point to become Zwitterions.
If the pH is too high -COOH loses a proton.
If pH is too low -NH₂ will become -NH₃
What are Proteins?
Proteins are condensation polymers made by joining amino acid monomers with peptide links (dipeptide bonds).
Protein Structure
· Primary Structure - The sequence of amino acids.
· Secondary Structure - ⍺-helix chains and β-pleated sheets.
· Tertiary Structure - Folds and coils in the chain, 3D shape.
Bonds in the Tertiary Structure
· Instantaneous dipole-induced dipole bonds.
· Ionic interactions.
· Hydrogen Bonding.
· Disulphide bridges.
DNA and RNA
Deoxyribonucleic Acid and Ribonucleic Acid.
DNA and RNA are polymers of nucleotides.
Different Pentose Sugars: DNA is Deoxyribose, RNA is Ribose.
DNA has base Thymine, RNA has Uracil instead.
Nucleotides
Nucleotides are made up of a Phosphate Group, a Pentose Sugar (Deoxyribose or Ribose), and a Base (Thymine, Cytosine, Adenine, Guanine, Uracil).
Structure of DNA
DNA is made of two polynucleotide strands, in a double helix.
The two strands are held together by the hydrogen bonds between the bases.
The bases only join to a specific complementary base, A-T and G-C. This is due to the pair being able to make the same number of hydrogen bonds.
DNA - Self Replication
· Hydrogen bonds break and the DNA double helix splits into two stands.
· Bases on free-floating nucleotides in the cytoplasm pair up with the complementary bases on the nucleotides in the DNA.
· Enzyme (DNA polymerase) joins the new nucleotides together to form a polynucleotide chain.
· Producing two identical DNA helixes.
What are Codons?
Codons are a sequence of three nucleotides which together form a unit of genetic code in a DNA or RNA molecule.
Types of RNA
· mRNA - Messenger RNA - Single polynucleotide strand, reverse copy of a DNA section (complimentary codon).
· tRNA - Transfer RNA - Single polynucleotide strand in the shape of a clover, anticodon on bottom and binding site for amino acid on top.
· rRNA - Ribosomal RNA - Polynucleotide strands that are attached to proteins to make ribosomes.
Protein Synthesis - Transcription
· The DNA double helix unwinds to reveal a single strand portion.
· The DNA bases attract free RNA nucleotides with complimentary bases.
· The RNA nucleotides are joined together by the enzyme RNA polymerase. Forming mRNA.
· DNA coils up again.
Protein Synthesis - Translation
· A Ribosome attaches to the mRNA, and moves along it till it finds the start codon (AUG).
· The ribosome pauses at the start codon until a tRNA with the correct anticodon bases pairs with the start codon.
· The ribosome then moves three bases forward, and waits for a tRNA with the correct anticodon to pair.
· The two amino acids brought by the two tRNAs are now in the ribosome, where they are joined by a peptide link.
· The ribosome then moves another three bases forward and repeat the process.
· This continues until a stop codon is reached, causing the ribosome to release the peptide chain.
What are Enzymes?
Enzymes are biological catalysts for essential reactions in living organisms.
They are proteins.
Enzymes have an active site specific to that enzyme which forms from the tertiary structure.
How do enzymes work?
Enzymes have active sites that only fit specific substrates, this is called the lock and key model.
The substrate is held in the active site by hydrogen bonds and dipole bonds. This is the enzyme-substrate complex.
How does Temperature and pH effect enzyme function?
Enzymes only work well in a narrow range of temperature and pH.
At low temperature the reaction is slow because the molecules have a low kinetic energy.
Too high temperatures and too high or low pH cause the enzyme to denature, as they break the tertiary structure.
What are Competitive Inhibitors?
Competitive inhibitors are molecules with a similar shape to the substrate, they bond to the active site so it can no longer break down the substrate.
Order of enzyme catalysed reactions
· Uncatalysed reactions are first order.
· If the substrate concentration is low the reaction is first order.
· If the substrate concentration is high the reaction tends to zero order.
What is a Pharmacophore?
The Pharmacophore is the part of the drug molecule that fits into the receptor site and makes it medicinally active.
What allows a Pharmacophore to fit to the Receptor Site?
· Size and Shape
· Bond Formation:
* Dipole-Dipole interactions
* Hydrogen Bonding
* Ionic Interactions
·Orientation
Optical Isomers
Have a chiral carbon (a carbon atom with has four different groups attached to it). These groups can be arranged in two different ways, these arrangements are called enantiomers or optical isomers.
They are mirror images of each other which cannot be superimposed.
Naming Acid Anhydrides
R-CO₂COR’
R-oic R’-oic anhydride
What is an Amine and Amide?
Amine: R-NH₂
Amide: R-CONH₂ or R-CONHR’
Naming Amines
Propan-1-amine
Hexane-2,4-diamine
Naming Primary and Secondary Amides
Primary: Propanamide
Secondary: N-ethylpropanamide
Why are Amines Basic?
Amines have a Lone Pair of Electrons, meaning they can accept protons to form a cation, by making a dative covalent bond with a H⁺ ion.
Neutralised by adding Acid:
RNH₂ + HX → RNH₃⁺X⁻
Hydrolysing Amides
Basic Conditions:
Amide + Water → Carboxylic Acid + Ammonium Salt
Acid Conditions:
Amide + Water → Carboxylate Ion + Ammonia
Carboxylic Acids with Metals, Carbonates, and Alkalis
Carboxylic Acid + Metal → Salt + Hydrogen
Carboxylic Acid + Carbonate → Salt + Carbon Dioxide + Water
Carboxylic Acid + Alkali → Salt + Water
Esters
Functional Group: -COO-
Alcohol + Carboxylic Acid → Ester + Water
Propyl Ethanoate
Propyl from alcohol
Ethan from carboxylic acid
Hydrolysing Esters
Acidic:
Ester + Water → Carboxylic Acid + Alcohol
Base:
Ester + NaOH → Carboxylate Salt + Alcohol
Acyl Chlorides
Functional Group: -COCl-
General Formula: CₙH₂ₙ₋₁OCl
Carboxylic Acid with -Cl instead of -OH
Naming: -oyl chloride
Acyl Chloride with Alcohols
Acyl Chloride + Alcohol → Ester + HCl
Acyl Chlorides with Amines
Acyl Chloride + Amine → Secondary Amide + HCl
Addition Polymerisation
Made from Alkene Monomers.
Double bond opens up and bond together to form addition polymers.
Condensation Polymerisation
Each monomer has 2 functional groups, each functional group reacts with a functional group on the other monomer.
A small molecule is formed, usually water or HCl.
Polyamides and Polyesters
Polyamide - Monomers: Dicarboxylic Acid and Diamine
Polyester - Monomers: Dicarboxylic Acid and Diol
Nylon-X,Y and Nylon-X
Nylon-X,Y is made from 2 monomers, diamine and dicarboxylic acid, X is the number of Carbons in the Diamine, Y is the number of Carbons in the Dicarboxylic Acid.
Nylon-X is made from 1 monomer with a carboxylic acid group and an amine group. X is the number of Carbons in this monomer.
Mass Spectroscopy
Ionisation → Acceleration → Deflection → Detection
Peak with highest M/Z ratio is tells you the Mr of the original molecule, M peak.
If a fragment is radical or not charged it will not appear on the mass spectrum.
Process of NMR Spectroscopy
· Sample is placed in a strong magnetic field and exposed to many different frequencies of radio waves.
· The nuclei of certain atoms absorb energy from the radio waves.
· The amount of energy absorbs depends on the environment of that atom.
Types of NMR Spectroscopy
· Carbon-13 NMR - gives information about the number and types of different carbon environments that are in a molecule.
· High Resolution proton NMR - gives information about the number of hydrogen atoms that are present and the environments they are in. Area under the peak shows the ratio of atoms in different environments.
