Amino acids, Proteins and DNA Flashcards
What 2 groups does an amino acid contain
Carboxyl group
Amino group
Which part of an amino acid reacts with a base
Carboxyl group
Which part of an amino acid reacts with an acid
Amino group
Write an equation for the reaction between 2-aminopropanoic acid and H+
Write an equation for the reaction between 2-aminobutanoic acid and NaOH, name the organic product formed
What is the name of the point at which amino acids are neutral
Isoelectric point
What determines how acidic or basic an amino acid is
The R group attached,
Alkyl groups are electron releasing
Acyl groups are electron withdrawing
How do amino acids exist in neutral solution
As zwitterions
How do amino acids exist in a solution of low pH
NH2 gains H+ to become NH3+
How do amino acids exist in a solution of high pH
COOH looses H+ to become COO-
Describe the structure and melting point of amino acids in the solid form
They have crystalline structures with high melting points due to the strong electrostatic forces of attraction than must be overcome between the zwitterions
What occurs when an amino acid reacts with an alcohol in the presence of conc H2SO4
- The carboxyl group undergoes esterification
- NH2 gains a proton from the sulfuric acid
Write an equation for the reaction between 2-aminopropanoic acid and methanol in the presence of H2SO4
Which part of an amino acid reacts with an acyl chloride
Amino group
Which part of an amino acid reacts with an acid anhydride
Amino group
What is the major product when we react an amino acid with excess halogenoalkane
Quaternary ammonium salt
Outline the stages in TLC chromatography for amino acids
Wear plastic gloves to hold onto the TLC plate to prevent contamination of hands to plate
Draw pencil line 1.5cm from bottom of plate
Use capillary tube to apply small drop of amino acid to mid point of pencil line
Allow spot to dry
Add solvent of depth 1cm (must be below pencil line or will dissolve mixture from plate)
Place TLC plate in developing tank
Allow developing solvent to rise up the plate (not reaching the very top)
Remove plate and quickly mark position of solvent front with pencil mallow to dry in fume cupboard (solvent may be toxic)
Spray with developing agent Ninhydrin
Measure distance from initial pencil line to spots (A)
Measure distance from initial pencil line to solvent front (B)
Calculate RF values (A/B)
What does an RF value indicate in amino acids TLC
The solubility of the amino acid within the solvent
If a TLC player is coated with a non polar substance, and the solvent is polar, what does a large RF value tell us
The greater the attraction for the mobile phase and the weaker the attraction for the stationary phase (ie, the more polar the amino acid)
What does a primary protein structure show us
The individual amino acids which make up a protein molecule
What are the 2 forms of secondary protein structure
Alpha helix chain
Beta pleated sheet
What causes a secondary protein structure to form
Hydrogen bonds between peptide links in the polymer chain which pulls a straight chain into a coiled or pleated structure
Describe the structure of a tertiary protein
Further folding folding of the secondary structure of the protein
What type of bonds are different protein shapes held together by
Hydrogen bonds and disulphide bonds
How do disulphide bonds arise
Thoil groups (-SH) can lose the H atom and the sulfur atoms can bond forming a disulphide (S-S) bond
How does temperature and pH change the shape of a protein
By affecting hydrogen bonds and the formation of disulphide bonds
What are enzymes
Proteins which are biological catalysts that speed up the rate of a reaction
Where do chemical reactions occur in enzymes and what reacts together
The 3D active site which is part of the tertiary protein structure.
This is where substrates can react with the enzyme
What is the condition which determines whether a substrate can react with an enzyme
The substrate must fit into the active site
How can the rate of a reaction be slowed down and how does this work
By using inhibitors which block an active site from a substrate
What does an active site being stereospecific mean
Enzymes have chiral centre and so only one enantiomer will fit into the active site of an enzyme, meaning they are stereospecific
What is an inhibitor
A substance that has a similar shape to the substrate that fits into the active site of an enzyme that blocks the active site from a substrate to enter
What effect does a higher concentration of an inhibitor have on rate of reaction
Higher concentration of an inhibitor means a slower rate of reaction
What two factors affect the effectiveness of an inhibitor
Concentration of inhibitor
How strongly the inhibitor binds to the active site of an enzyme
How do antibiotics act as inhibitors
They block the active site of the enzyme that is responsible for making the cell wall of a bacteria cell
If the cell wall cant be made then the cell will burst and die
How can we use computer modelling to design new drugs to act as inhibitors
Allows scientists to test how a drug will respond by enzymes without having to make the drug
This makes it faster and cheaper
What type of method is used when developing new drugs
Trial and error
Scientists will see which inhibitors work and refine the molecule to make it more efficient
What are the monomers of DNA
Nucleotides
What are the 3 components which make up a nucleotide
A phosphate
A sugar
A base
Circle which nitrogen on these bases bond to 2-deoxyribose in a nucleotide
Draw the simplified structure of a nucleotide
What is a sugar phosphate backbone
Where a phosphate on one nucleotide is covalently bonded to a sugar on another. When this occurs many times, we form the backbone
What is the process by which we form a sugar phosphate backbone. What type of bond is formed
Condensation polymerisation
Phosphodiester bond is formed and water is eliminated
How is DNA formed, and what holds the structure together
Formed from 2 polynucleotide strands that are twisted together to form a double helix which is held together by hydrogen bonds between base groups on opposite strands
Which bases form hydrogen bonds between each other in a strand of DNA
A-T
C-G
What atoms are hydrogen bonds formed between bases in a DNA strand
NH2 with double bond O
NH with double bonded N
Why can no other base pairings occur other than the specific pairs
Partially charged atoms would be too close to each other and repel
OR
Atoms would not get close enough to allow for H bonds to form
Why is DNA twisted into a double helix structure
To allow bases to align perfectly to form H bonds
How does Cis-Platin act as an anti cancer drug
Cis platin bonds to DNA in cancer cells
As it attaches to DNA it prevents the cell from reproducing through cell division
Thus, the cell dies as it is unable to repair itself
Explain the action of atoms in cis platin when it acts as an anti cancer drug
Chloride ions in the complex are easily displaced from the complex
Platinum can then bond to the nitrogen atoms on a GUANINE base within DNA
This creates a distortion in the DNA strand which means it cannot unwind and be copied
What is the issue with cisplatin
Also prevents healthy cells from reproducing
It affects cells in the blood which can supress the immune system and increase risk of infection and kidney damage
How can the side effects of cis-platin be reduced
By giving it in lower doses and in short bursts, using targeted delivery methods
Why is cis-platin still used in chemo even though it has short term side effects
Due to the long term benefits it can bring in eliminating cancer
Draw the structure of cis-platin
How do hydrogen bonds arise in secondary protein structure
Electron deficient H attracts lone pair/electron pair on O
What are the reagent and conditions for acid hydrolysis
Reagent: HCl
Conditions: Reflux
Draw how adenine forms hydrogen bonds with thymine
Draw how guanine and cytosine form hydrogen bonds together
