Amino Acids Flashcards
What are the two functional groups of amino acids?
NH2 and COOH
How many naturally occurring amino acids are there in a human body
20
What type of amino acids are found in the body?
What does this mean about their structure?
Alpha-Amino aicids
NH2 functional group is on the adjacent carbon to COOH
Draw a general formula for alpha amino acids
Are alpha amino acids Chiral?
Yes , one carbon has four different subsistent
Exception = Glycine where R = H
Write the equation for the first step of industrial amino acid synthesis
Aldehyde + Nitrile to produce an amino nitrile
Write an equation for the second step of industrial amino acid synthesis
And any conditions
Amino nitrile (in step 1) + Hydrochloric acid + Water —> Amino acids + Ammonium Chloride
Hydrolysis, use dilute HCl and under reflux
In what form do amino acids exist as solids?
Alpha amino acids as zwitterions in an ionic lattice - High melting and boiling point
What colours are zwitterions at room temperature
White solids
Do Zwitterions disolve in water
Yes, zwitterions have permanent +Ve and -Ve charges which causes electrostatic attraction between the +Ve charge and the lone pair within water molecules
Define a zwitterion
Ions which both have a permanent positive and negative charge, but are neutral overall
How do zwitterions occur in amino acids
COOH is deprontonated
NH2 is protonated
When the acid has reached its isoelectric point in ph
What happens to amino acids when the ph is lower then its isoelectric point
NH2 group is protonated
What happens to amino acids when it’s ph is higher then the isoelectric point
COOH is depotonated
Draw a peptide linkage
What is a dipeptide
Draw a general one for amino acids
Two amino acids bonded together
Under a peptide link
What name is given to amino acid chains up to 50 monomers
polypeptides
What name is given to chains of amino acids with more then 50
proteins
What is the process in which polypeptides are broken down into their constituent amino acids
Hydolysis
What conditions are needed for the hydrolysis oof amino acid chains
6moldm^-3 HCl
Reflux for 24h
110 Degrees
Draw the formation of a peptide link using trio generalised amino acids
hydrolysis
What is the primary structure of a protein?
The sequence of amino acid monomers along the peptide chain bonded by covalent bonds.
How is the primary structure of an amino acids represented
Sequence of 3 letter add revisions of amino acids
What is the secondary structure of a protein
The shape of the protein chain
Alpha Helix or Beta pleated sheet
What are the two options for the secondary structure of a protein
Alpha-helix shape or beta-pleated sheet
How is the secondary structure held together
Hydrogen bonding Between C=O and N-H on the polypeptide backbone
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
a combination between
Hydrogen bonding
Ionic interactions between R groups
Sulphur-Sulphur bonding (disulphide bridges)
Van Der Waals
Why is tertiary structure important
The shape of the protein molecules is vital in their function
Eg active sites in enzymes
How can amino acids. be attracted to each other
Hydrogen bonding
Ionic interactions between groups or side chains
Sulphur-Sulphur/ Disulphide bridges
2 S atoms are oxidised to form an S-S bond
What is wool
How is it held together
Protein fibre with a secondary alpha helix structure held together by hydrogen bonds
What does the structure and bonding in wool mean for its properties
wool= Protein fibre with a secondary alpha helix structure held together by hydrogen bonds
Can be stretched and elastic —> Hydrogen bonds extend and when the force is removed they return to their original shape
Wash too hot and the H bonds permanently break so the garment looses its shape
What is a Thin layer Chromatography plate made of
Plastic sheet coated with silica ( SiO2) This is the stationary phase
The solvent is the mobile phase
Amino acids have basic and acidic properties what is this quality called?
Amphoteric
How would you cary out thin Layer Chromotography
Spot the samples onto a pencil line a few cm above the talc plate
Place this in as breaker 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 sol;vent is almost a that the top of the TLC plate
Remove from beaker and analyse
How do you name an amino acid using IUPAC
1) Find longest carbon chain - carboxylic acid
2) Number carbons - 1 is the carboxyl group carbon
3) Note the carbon number where the amide groups lie
4) Use prefix amino over amide
5) Name other groups that aren’t COOH or NH2 first
Why does TLC separate amino acids
Solvent carries amino acids up the TLC plate.
The rate of moment depends on the balance between the amino acids affinity for the stationary and the affinity for mobile phase
What is the isoelectric point
Zwitterions only exist in an amino acid at its isoelectric point
Isoelectric point = The PH at which the average overall charge of a zwitterion is zero as there is a permanent positive charge at the amine group and a permanent negative charge at the carboxylate group
Name 2 ways to analyse a sample of TLC chromotography
Amino acids are colourless
Spray on ninhydrin - Amino acids are colourless, the vapours of this substance sticks to the chemicals turing the amino acids purple
Add fluorescent dye to the stationary phase, Shine UV light, Colourless amino acids block the flow from the fluorescent dye
How do you calculate an Rf Value
Distance moved by substance / Distance moved by solvent
How do you find the primary structure of a protein
Reflux with 6M HCl for 24h
to break down the peptide links, separating it into its monomers
Carry out TLC to find the number and types of amino acids present
How do you find the secondary/ tertiary structure of a protein
X-ray Crystallography
What is an enzyme
Biological catalyst
Specialised to increase the rate of reactions of a specific reaction.
Made of amino acids
Describe the structure of an enzyme
How does its structure helps its function
Globular protein with a creft in it know as the active site.
This active site is a unique shape that is designed to fit a very limited umber of substrate
Has a chiral centre
2)
active site is a unique shape that is designed to fit a very limited umber of substrate held at the perfect orientation for them to react/bind (stereospecificity) Locks and key hypothesis.
How else do enzymes increase the rate of reaction
binding molecules to the active site via forming temporary bonds with intermolecular forces
This weakens the bonds int the molecules, promotes electron movement and lowers the acitvation energy
What does the stereospecificity of an enzyme mean?
How does this effect naturally occurring molecules
Active sites are so selective of the shape of the substrates that can fit, it only catalyses reactions of a specific enantiomer but not the other one.
Most naturally occurring molecule have a much larger abundance of one enantiomer compared with he other due do an enzymes stereospecificity
How does enzyme inhibition work
A molecule with a a very similar shape and structure to the substrate is devised
Binds to the enzyme’s active site very strongly
Blocks the active site
As substrate cannot adsorb to the active site so reaction cannot be catalysed
What drug works via enzyme inhibition?
Penicillin
What causes enzymes to Denature
Change in Temperature or PH
What does DNA stand for
Deoxyribonucleic Acid
What consititutes as a nucleotide
A phosphate ion
A Sugar (2-deoxyribose)
A Base (Adenine cytosine guanine or thymine)
Draw the general structure for a nucleotide
What forms between bases of adjacent nucleotides
Hydrogen bonding
Which bases pair up between nucleotides
A & T
C & G
How does DNA Polymerise?
What type of polymer chain is this
OH on phosphate
OH on 3rd Carbon on 2 deoxyribose react to eliminate a molecule of water.
Condensation Polymer
What determines the properties of the DNA molecule
Unique order of bases
Explain the Structure of DNA
2 strands of amino acids held together by hydrogen bonding between complimentary base pairs wound together in a double helix
How is DNA Replicated exactly when Cells Divide
DNA Helixase unzips the chain by breaking the hydrogen bonds holding the base pairs together
Free nucleotides that are activated attach to their complimentary base pairs
The activated nucleotides bind to their complimentary bases with he aid of DNA Polymerase
Bases link together by forming the sugar phosphate backbone
How does the body use the information stored in DNA
Template for arranging amino acids into specific proteins, such as enzymes or flesh
Draw the Structure of CISplatin
What is Cisplatins Function?
How does it do this? (3)
Anti-Cancer Drug
Bonds to strands of DNA to distort shape and prevent cell replication.
It bonds to the Nitrogen atoms on 2 adjacent Guaneines.
Nitrogen atoms replace the Chlorine ligands in a ligand substitution reaction
What are the Cl- ligands are able to be replaced by Nitrogen on the base (Amino acids)
N atoms on the Guanine have lone pairs of electrons ions that can coordinately bond to the platinum
N atoms can donate electrons more readily so it replaces the chlorine ligands
What are the Disadvanatges to cisplatin
Affects Healthy cells that are replicating quickly as well as the cancer cells such as hair follicles
ph= 11.8
1.26 x 10^-24
Enzyme has a stereo-specific active site
G-enantiomer has the correct stereochemistry and the only accepted complimentary shape
State the meaning of the term complimentary in reference to DNA strands
complimentary means that the two strands must have base sequences that match
A to T and C to G
Secondary
N & O are very electronegative
therefore C=O and N-H are polar bonds
These polar bonds are sufficiently polarised to form hydrogen bonding between N & H and O&H on oppposing bases
In which a lone pair of electrons on an oxygen atom is strongly attracted to a delta positive hydrogen
series of nucleophilic substitution reactions
(amine + excess haloalkane = quaternary ammonium ion)
Base A
Top N-H forms hydrogen bonds with lone pair O of Guanine
The lone pair of electrons on N bonds to N-H of Guanine
A Lone pair of electrons on O bonds to lower H-N of guanine
Draw Hydrogen Bonds between each of the complimentary bases, include where the connection is to the sugar
Hydrogen Bonds form between urea and DNA strands
Urea has 2 amino groups, that goes in-between the strands to separate them
