3.13 - Amino Acids, Proteins and DNA Flashcards
What are the 2 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?
a-amino acids (alpha)
It means that the NH2 is always on the carbon next to the COOH
Draw a general formula for a-amino acids
search it up
or
pmt slide 9
Are a-amino acids chiral? Why?
Yes, one carbon has 4 different substituents. Except glycine, where R=H
Which enantiomer do a-amino acids exist as in nature?
(-) enantiomer
How can amino acids be synthesised industrially?
RCHO + NH4CN —> RCH(NH2)CN via nucleophillic addition.
RCH(NH2)CN + HCl + 2H20 —> 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 net effect on plane polarised light.
In what form do amino acids exist as solids? What consequences does this have?
Zwitterions (ionic lattice) - high MP and BP
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 can occur in amino acids?
COOH is deprotonated –> COO-
NH2 is protonated –> NH3+
What amains to amino acids in acidic conditions?
Gains a proton on the 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
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 moldm-3
- 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 between C=O and H-H groups
What is the tertiary shape of a protein?
Alpha-helix or beta-pleated sheet is folded into a complex 3D shape.
How is the tertiary structure held together?
- Hydrogen bonding
- Ionic interactions between R groups
- Sulfur-sulfure bonding (disulfide brideges)
- Van der Waals forces of attraction.
Why is the tertiary structure important?
The shape od 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 sie chains
- Sulfur-sulfur bonds; 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 in the mobile phase).
Describe how you would carry out Thin Layer Chromatography
- Spot the samples onto a pencil line a few cm above the base of the TLC plate.
- Place this in a beaker with solvent level below the pencil line. Ensure there is a lid on the beacker 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 the TLC separate amino acids or other molecules?
Solvent carries amino acids up the TLC plate. The rate of the movement depends on the balance between that amino acids affinity for the solvent (solubility in it) 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 colourless, ninhydrin turns their spots purple)
Or shine UV light on them
How do you calculate an Rf value?
Distance moved by that substance divided by the 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 the 2D TLC?
Uses a square TLC plate. Spot the amino acids in one corner, then run TLC in first solvent. Flip the plate through 90° 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 bases catalysts that speed up reactions in the body by factors of upto 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 an active site.
Has a very particular shape.
How does its structure help the function of the enzyme? What is the 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.
