Amino Acids, Proteins and DNA Flashcards
What are the two functional
groups of amino acids?
NH2 and COOH (amine and carboxylic acid)
How many naturally occurring amino acids are there in the body?
20
What type of amino acids are found in the body?
What does this mean about their structure?
⍺-amino acids (alpha) It means that NH2 is always on the carbon next to COOH
Are α-amino acids chiral? Why?
Yes, one carbon has 4 different substituents.
Except glycine, where R = H.
Which enantiomer do α-amino acids exist as in nature?
(-) enantiomer
How can amino acids be synthesised industrially?
RCHO + NH4CN → RCH(NH2)CN via nucleophilic addition.
RCH(NH2)CN + HCl + 2H2O→ RCH(NH2)COOH + NH4Cl
(hydrolysis, HCl is dilute) Need to reflux the reaction mixture
Is the product from amino acids being synthesised
naturally optically active? Why?
No, a racemic mixture is formed as the CN- ion can attack from above or below the planar C=O bond with equal likelihood.
An equal amount of each enantiomer is formed, so
no net effect on plane polarised light.
In what form do amino acids exist as solids? What consequences does this have?
Zwitterions (ionic lattice) - high melting and boiling points
What colour solids are most zwitterions at room
temperature?
White solids
Do zwitterions dissolve in water? Non-polar solvents? Why?
Yes, but not in non-polar solvents. Due to ionic nature/polar bonds.
Define a zwitterion
Ions which have both a permanent positive and negative charge, but are neutral overall.
How do zwitterions occur in amino acids?
COOH is deprotonated → COO-
NH2 is protonated → NH3+
What happens to amino acids in acidic conditions?
Gains a proton on NH2 group
What happens to amino acids in alkaline conditions?
Loses a proton from COOH group
What is the peptide linkage?
-CONH-
What is a dipeptide?
Two amino acids bonded together (a dimer)
What name is given to chains of amino acids up to
50 amino acids?
Polypeptides
What name is given to chains of amino acids with
more than 50?
Proteins
What are polypeptides and proteins found in?
Enzymes, Wool, Hair, Muscles
What is the process called by which polypeptides or proteins can be broken down into their constituent
amino acids?
hydrolysis
What conditions are needed for hydrolysis to occur?
6 mol dm-3 HCl, reflux for 24 hours
What is the primary structure of a protein? How is it
bonded?
The sequence of amino acids along the protein chain. Bonded by covalent bonds
How is the primary structure represented?
Sequence of 3 letter abbreviations of the amino
acids
How can the primary structure of a protein be broken up?
Hydrolysis, 6M HCl, 24 hour reflux
What is the secondary structure of a protein?
The shape of the protein chain
What are the two options for the secondary structure?
Alpha-helix shape or beta-pleated sheets
How is the secondary structure held together?
Hydrogen bonding, e.g. between C=O and N-H groups
What is the tertiary shape of a protein?
Alpha-helix or beta-pleated sheet is folded into a complex 3D shape; this is the tertiary structure
How is the tertiary structure held together?
- Hydrogen bonding
- ionic interactions between R groups
- sulfur bonding (disulfide bridges)
- van der Waals forces of attraction
Why is the tertiary structure important?
The shape of protein molecules is vital in their function - e.g. for enzymes
How can amino acids bond/be attracted to each
other? (3 main ways)
- Hydrogen bonding
- Ionic interactions between groups on side chains
- disulfide bridges;2 S atoms oxidised to form an S-S bond
What is wool? How is it held together?
Protein fibre with secondary alpha-helix structure; held together by hydrogen bonds
What does wool’s structure and bonding mean for wool’s properties?
- Can be stretched, H bonds extend.
- Release it and it returns to its original shape
- Wash too hot and H bonds permanently break so garment loses its shape.
What is a TLC plate made of?
Plastic sheet coated with silica, SiO2. This is the
stationary phase. (The solvent is the mobile phase)
Describe how you would carry out Thin Layer
Chromatography
- Spot the samples onto a pencil line 1 cm above the base of the plate.
- Place this in a beaker or tank, with solvent level below the pencil line.
- Ensure there is a lid on the beaker to keep the inside saturated with solvent vapour.
- Wait until the solvent front is almost at the top of the TLC plate; then remove from the beaker and analyse.
Why does TLC separate amino acids (or other molecules)?
- Solvent carries amino acids up the TLC plate. The rate of movement depends on the balance between that amino acid’s affinity for the solvent and affinity for the stationary phase (attraction to the silicon with hydrogen bonding).
What do you often have to do to enable the amino acids to be seen on the chromatogram?
Spray with ninhydrin (amino acids are colourless,
ninhydrin turns their spots purple)
Or shine UV light on them
How do you calculate an Rf value?
Distance moved by substance/ distance moved by the solvent front
How can Rf values verify which amino acid is which?
Compare the experimental Rf values to known/accepted values in the same solvent.
Or run pure amino acids in the same solvent and compare results to identify amino acids
What is 2D TLC?
Uses a square TLC plate. 1. Spot the amino acids in one corner, then run TLC in first solvent.
2. Flip the plate through 90o and repeat TLC in a second, different solvent.
What are the benefits of 2D TLC (2 main ones)?
Separates the spots more - it is extremely unlikely that 2
amino acids will have identical Rf values in 2 solvents.
Gives you 2 Rf values for each amino acids; you can be more confident in verifying the identity of the amino acids when
comparing to known values, as 2 Rf values can be verified
How do you find the primary structure of a protein?
Reflux with 6M HCl and reflux for 24 hours
Carry out TLC to find the number and type of amino acids present.
How do you find the secondary and/or tertiary
structure of a protein?
Various techniques, e.g. X-Ray
Diffraction
What is an enzyme?
Protein based catalysts that speed up reactions in the body by factors of up to 10^10.
How many reactions is each enzyme designed to catalyse?
One reaction - they are very specialised
What is the structure of an enzyme?
Globular protein with a creft/ crevice in it, known
as an “active site”. Very particular shape
How does its structure help the function of the enzyme? What is this hypothesis known as?
The reacting molecules fit precisely into the active site and are held at exactly the right orientation to react. This is the lock and key
hypothesis
How else do enzymes increase the rate of reaction?
Reacting molecules form temporary bonds to the enzyme. This weakens the bonds in the molecules, promotes electron movement and lowers EA
What does the stereospecificity of enzymes mean?
Active sites are so selective of the shape of
substrates that only reactions involving one
enantiomer are catalysed.
What does stereospecificity mean for most naturally
occurring molecules?
Most naturally occurring molecules only occur as 1 enantiomer due to stereospecific enzymes
How are enzymes denatured?
Change in temperature or pH outside the optimum
How does enzyme inhibition work?
A molecule with a very similar shape and structure to the substrate is devised. Binds to the enzyme’s active site.
Blocks the active site (does not desorb easily). Substrate cannot adsorb to the active site, so reaction cannot be catalysed
An example of a drug that works through enzyme
inhibition?
Penicillin
What are the benefits of modelling new molecules on
computers?
Now we understand factors that affect the shapes of
extremely complex proteins, we can model drugs that haven’t even been synthesised, predict their properties and design drugs that will treat a range of medical conditions
What does DNA stand for?
Deoxyribonucleic acid
What does DNA do?
It is present in all cells and is a blueprint from which all organisms are made
What structure does DNA take?
A polymer with 4 monomers; they can be
combined differently
What constitutes a nucleotide?
A phosphate ion, a sugar a base (A (adenine), C (cytosine), G (guanine), T (thymine))
What forms between bases of adjacent nucleotides?
Hydrogen bonding
Which bases pair up between nucleotides?
Adenine with Thymine (A and T)
Guanine with Cytosine (C and G)
How does DNA polymerise?
OH on phosphate group and OH on number 3
carbon of 2-deoxyribose react to eliminate a molecule of H2O
What kind of polymer does the polymerisation of DNA lead to?
Condensation polymer chain → backbone of
phosphate and sugar molecules, with bases
attached
What defines the properties of the DNA molecule?
The order of the bases
Why does DNA have a double helix shape?
Exists as 2 strands; these 2 strands are held together by hydrogen bonding (C and G and A and T). The complementary DNA molecule has bases that hydrogen bond in the same order to those on another molecule → double helix shape is formed
Why is it important that DNA is exactly copied when cells divide?
Because it codes for proteins and makes all cells
How is DNA is exactly copied when cells divide?
Hydrogen bonds between base pairs break.
Covalent bonds in polymer chains remain intact.
The sequence of bases is
maintained.
Separate nucleotide molecules that have been
created move to hydrogen bond to their relevant bases. They polymerise, thus, DNA is replicated exactly.
How does the body use information that is stored in
DNA?
Template for arranging amino acids into protein
chains → codes for proteins. “Recipe” for proteins that make up all living things; enzymes, flesh etc
What is cisplatin’s function? How does it do this?
Anti-cancer drug
Bonds to strands of DNA to distort shape and prevent cell replication.
It bonds to the N (nitrogen) atoms on 2 adjacent G bases.
The N atoms replace the Cl- ligands in a ligand
substitution reaction.
Why are Cl- ions able to be replaced by N on the base?
N atoms on the G base have lone pairs of electrons that can co-ordinately bond to the Pt ion; N atoms are better ligands than Cl-, so
replace them
What are the drawbacks of using cisplatin?
Affects healthy cells that are replicating quickly,
e.g. hair follicles → lose hair during chemotherapy
Thought to damage kidneys
What happens when excess bromomethane is added to an amino acid?
CH3Br is in excess, so every H on the N atom and the lone pair on the N atom is replaced by a CH3 group → quaternary ammonium ion. (makes a salt with Br-)
What happens if an amino acid is added to an excess of methanol in the presence of concentration sulfuric acid?
Methyl ester forms with COOH group → COOCH3
NH2 is protonated by the acid → NH3+
