amino acids, proteins, and DNA [O2] PAPER 2 Flashcards
A student uses thin-layer chromatography (TLC) to identify these amino acids.
The amino acids cannot be seen as they move during the experiment.
State how the amino acids can be made visible at the end of the experiment.
UV lamp
state why different amino acids have different Rf values.
each amino acid has different relative affinity to stationary and mobile phases
components of a DNA molecule?
• 2-deoxyribose
• phosphate group
• nitrogenous base [adenine / thymine/guanine / cytosine]
complementary base pairs in DNA?
• adenine with thymine
• cytosine with guanine
how do complementary bases in DNA join?
• hydrogen bonding
• 3 hydrogen bonds between C and G
• 2 hydrogen bonds between A and T
hydrogen bonding between adenine and thymine?
hydrogen bonding between cytosine and guanine?
State the meaning of the term complementary when it is used to refer to DNA strands.
(Complementary means the two strands must have base sequences) that match (all) adenine to thymine and cytosine to guanine
DNA strand structure?
X = base
Y = phosphate group
the NH2 groups in urea are able to substitute for the hydrogen bonds in the double helix
explain the bonding between cytosine and guanine
• top N–H of cytosine forms hydrogen bonds to lone pair of electrons on O of guanine
• lone pair of electrons on N of cytosine bonds to H–N of guanine
• a lone pair of electrons on O bonds to lower H–N of guanine
Cisplatin works because one of the atoms on guanine can form a co-ordinate bond with platinum, replacing one of the ammonia or chloride ligands. Another atom on another guanine can also form a co-ordinate bond with the same platinum by replacing another ligand.
On Figure 1, draw a ring round an atom in guanine that is likely to bond to platinum.
An adverse effect of cisplatin is that it also prevents normal healthy cells from replicating.
Suggest one way in which cisplatin can be administered so that this side effect is minimised.
use in very small amounts
how does cisplatin prevent DNA replication in cancer cells?
• ligand substitution reaction with DNA
• a coordinate bond is formed between platinum and a nitrogen atom on guanine
• prevents DNA replication continuing
why can cancer drugs have adverse effects?
cisplatin could occasionally bond to healthy DNA strands, causing adverse side effects, e.g. hair loss
DNA replication
After cisplatin enters a cell, one of the chloride ligands is replaced by a water molecule to form a complex ion, B. Give the equation for this reaction.
general structure of an amino acid?
When the overall pH of an amino acid is zero, a zwitterion forms. What is the zwitterion of an amino acid?
amino acid in acidic conditions?
amino acid in alkaline conditions?
what is the primary structure of a protein?
single polypeptide chain of amino acids
what is the secondary structure of a protein?
alpha helix / beta pleated sheet, held by hydrogen bonds between C=O of one amino acid and NH of another
what is the tertiary structure of a protein?
3D folding of a polypeptide, held by hydrogen, ionic and disulfide bonds
Name the type of protein structure in the figure.
secondary
Explain the origin of the interaction represented by the dotted lines in the figure above.
• nitrogen and oxygen are very electronegative
• so, C=O and N–H bonds are polar
• results in the formation of a hydrogen bond between O and H in which a lone pair of electrons on a oxygen atom is strongly attracted to the δ+ H
by what process is a protein split into its constituent amino acids?
hydrolysis
In terms of the intermolecular forces between the polymer chains, explain why polyamides can be made into fibres suitable for use in sewing and weaving, whereas polyalkenes usually produce fibres that are too weak for this purpose.
• hydrogen bonding in polyamides
• van der Waals forces in polyalkenes
• hydrogen bonding is stronger
Protein chains are often arranged in the shape of a helix. Name the type of interaction that is responsible for holding the protein chain in this shape.
hydrogen bonding
how to calculate Rf value?
distance travelled by spot / distance travelled by solvent
what is an enzyme?
• biological catalyst
• type of protein with a tertiary structure that determines the active site of the enzyme, which binds to the substrate
Enzymes are stereospecific. What is meant by this?
they can only break down one enantiomer of a substrate, and has no effect on the other
What does an enzyme inhibitor do?
block the active site of an enzyme, so the substrate is unable to bind
• enzyme has an active site
• G-Enantiomer has the correct stereochemistry / is the complementary shape to the active site of the enzyme
Suggest why it was necessary to use two different solvents.
some of the amino acids didn’t separate with the first solvent
OR
some amino acids have the same affinity/Rf value with the first solvent
Outline the steps needed to locate the positions of the amino acids on the
TLC plate and to determine their Rf values.
• use UV (to locate the positions of the amino acids on the TLC plate)
• measure distances from the initial pencil line to the spots (x)
• measure distance from initial pencil line to the solvent front line (y)
• Rf value = x / y
Explain why different amino acids have different Rf values.
amino acids have different polarities, so have different retention on the stationary phase or different solubility in the developing solvent
suitable reagent for the hydrolysis of a protein?
CONCENTRATED HCl
