3.13 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
Alpha amino acids
It means that NH2 is always on the carbon next to COOH
Draw a general formula for alpha amino acid
Slide 10
Are alpha amino acids chiral? Why?
Yes, one carbon has 4 different substituents.
Except glycine, where R = H
Which enantiomer do alpha 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 + HCI + 2H2O —> RCH(NH2)COOH + NH4CI
(hydrolysis, HCI 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 consequence 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 zwitterion
Ions which have both a permanent positive and negative charge, but are neutral overall
How do zwitterions occur in amino acids? Draw a general structure of one
COOH is deported —> COO-
NH2 is protonated —> NH3+
slide 28
What happens to amino acids in acidic conditions? Draw this
Gains a proton on NH2 group
Slide 30
What happens to amino acids in alkaline conditions?
Draw this
Loses a proton from COOH group
Slide 32
What is the peptide linkage?
-CONH-
Slide 34
What is a dipeptide? Draw a general one for amino acids
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 acid 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 HCI, reflux for 24 hours
What is the primary structure of a protein? How is if 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 HCI, 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
Sulfer-sulfer bonding (disulfide bridges)
Van der waals forces of attraction
What 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
Sulfur - sulfur bonds/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 a few cm above the base of the TLC 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.
Waited until the solvent front is almost at the top of the TLC plate; then remove from the beaker and analyse
Why does TLC seperate amino acids (or other molecules)?
Solvent carries amino acids up the TLC plate. The rate of 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 are 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 acids 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. Spot the amino acids in one corner, then run TLC in first solvent. Flip the plate through 90degree and repeat TLC In a second, different solvent
What are the benefits of 2D TLC
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 24hrs
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 catalyst that speeds 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 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
How else do enzymes increase the rate of reaction?
Reacting molecules from temporary bonds (via intermolecular forces) 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 one enantiomer due to stereospecificic enzymes
How Enzymes denatured
Change in temp or pH
How does enzymes inhibition work?
A molecule with a very similar shape and structure to the substrate is devised. Binds to the enzymes active site. Blocks the active site (does not desire 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 (2-deoxyribose)
A base (A(adenine), C(cytosine), G(guanine), T(thymine))
Draw a nucleotide
Slide 122
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)
What does DNA polymerase?
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. Separated 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
Draw the structure of cisplatin
Slide 142
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 ligands 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 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?
Excess ester forms with COOH group —> COOCH3
NH2 is protonated by the acid —> NH3+
