Amino Acids, Proteins and DNA Flashcards
Functional groups of amino acids
Amino acids contain 2 functional groups, a -COOH (carboxyl) group and a -NH2 (amine) group
General formula of an alpha amino acid
R-CH(NH2)-COOH
What are the physical properties of amino acids
Crystalline solids
Relatively high melting points
Dissolve in water but do not form organic solvents
What do amino acids exist as in neutral solutions
Zwitterions
What is the general structure of a zwitterion and why
R-CH(N+H3)COO-
The COOH group is acidic and loses a H+ ion
The NH2 group is basic and gains the H+ ion
Why do amino acids like alanine have high melting points
They exist as zwitterions.
A large amount of energy is needed to break the strong ionic attractions between different zwitterions
Predict the pH of the solution when alanine is dissolved in water and why
The pH of the solution will be 7 because alanine exists as zwitterions so is neither acidic or alkaline
Why are amino acids amphoteric
They can react with both acids and bases
Why can amino acids act as buffer solutions
They will react with and remove small amounts of acid or alkali that are added to it
What is formed if a zwitterion is in alkaline solution/ high pH
R-CH(NH2)COO-
What is formed if a zwitterion is in acidic solution/ low pH
R-CH(N+H3)-COOH
Isoelectric point
The pH at which the zwitterion is formed and each amino acid has its own unique isoelectric point.
How do amino acids react with alkalis
They form salt and water
How do amino acids react with alcohols
They form an ester and water
How do amino acids react with acids
They form ammonium salts
Why do most amino acids show optical isomerism
They are a chiral molecule as they have a carbon atom bonded/attached to 4 different groups
Why would an amino acid obtained from a living organism be only one stereoisomer
The receptors in the body are stereospecific
The two isomers have different three-dimensional shapes
Only one of the optical isomers has the correct stereochemistry to bind to the receptor molecule
If alanine was made from propanoic acid the product does not show optical activity. Explain why
It is a racemic mixture.
A racemic mixture does not show optical activity because the rotations of the two isomers cancel each other out.
Why is it possible to separate and analyse a mixture of amino acids using TLC
TLC is used because different amino acids have different Rf values
Explain why different amino acids have different Rf values
Different amino acids have different polarities therefore they have different solubility in the solvent/ different adsorption on the stationary phase
Describe how to use TLC to identify and separate amino acids
- Put a small spot of the mixture on the base line of a chromatography paper and allow it to dry.
- Place the paper in a beaker containing a suitable solvent, making sure the solvent is below the base line.
- Put a lid on the beaker to prevent the solvent from evaporating, and leave until the solvent front is near the top of the paper.
- Remove the paper from the solvent and mark the position of the solvent front with a pencil line.
- Dry the paper.
- Spray the chromatogram with ninhydrin to detect the amino acids.
- Find Rf value of each amino acid by doing Rf = distance moved by spot / distance moved by solvent front
- Compare Rf values obtained with Rf values of known reference amino acids
Explain why different amino acids have different retention times
Different amino acids have different polarities. Therefore they have different adsorption on the stationary phase/ different solubility in the solvent
Why is the solvent added in TLC not added to a depth of more than 1cm
If solvent line is higher than pencil line, it will dissolve the mixture from the plate
Why is the TLC plate dried in a fume cupboard
The solvent is toxic
What are dipeptides
The simple combination molecules of two amino acids with one amide link
Describe hydrolysis of dipeptides/proteins
If heated with conc HCl or conc strong alkalis they can be hydrolysed and split into their constituent amino acids
What are proteins
Polymers made from combination of amino acids. The amino acids are linked by peptide links
What is the primary structure of proteins
The sequence of the 20 different naturally occurring amino acids joined together by condensation reactions with peptide links
What are the 2 different secondary structures of a protein
Alpha helix
Beta pleated sheet
Describe the secondary structure of a alpha helix protein
3D arrangement of amino acids with the polypeptide chain in a corkscrew shape.
The R groups on the amino acids are all pointed to the outside of the helix
How is a secondary structure alpha helix protein held together
It is held in place by the hydrogen bonds between the H of the N-H group and the O of the C=O of the fourth amino acid along the chain
Describe the secondary structure of the beta pleated sheet for proteins
The protein chain folds into parallel strands side by side
How is the protein chain held together in Beta pleated sheets
By the hydrogen bonds between the H of the -NH group and the O of the C=O of the amino acid much further along the chain in the parallel region
What is the tertiary structure of proteins
The folding of the secondary structure into more complex shapes.
How is the tertiary structure of proteins held together
By interactions between the R side groups in more distant amino acids.
These can be a variety of interactions including hydrogen bonding, sulfur-sulfur bonds and ionic interactions.
How are hydrogen bonds formed in tertiary structure of proteins
Hydrogen bonds could form between two serine (or other amino acids) side chains in different parts of the folded chain
How are ionic interactions formed in tertiary structure of proteins
Ionic interactions could form between acidic and basic amino acids as zwitterions are formed.
What are enzymes
Proteins
How can a substrate molecule bind to the amino acid side chains
Hydrogen bonding
Van der Waals forces
Permanent dipole-dipole forces
Ionic interactions
How strong do the interactions between a substrate and amino acid side chains need to be
Strong enough to hold the substrate for long enough for the enzyme catalysed reaction to occur but weak enough for the product to be released
What is an enzyme-substrate complex
When the substrate bonds to the active site of the enzyme
Describe how drugs can act as enzyme inhibitors
By blocking the active site.
The inhibitor will often bind to the active site strongly so stopping the substrate attaching to the enzyme.
What are computers used for in drugs
Making drugs which act as enzyme inhibitors
What is a nucleotide made up of
A phosphate ion bonded to 2-deoxyribose which is bonded to one of the 4 bases
How does the sugar attach to the phosphate group
It attaches to the carbon to the left of the oxygen 2-deoxyribose which is the 5th carbon (COUNT)
It attaches to the-CH2 with the O- specifically attaching to the-CH2 and the -OH previously attached to the -CH2 leaves
How does the base join to the sugar
It attaches to the carbon to the right of the O on the 2-deoxyribose which is the first carbon
The nitrogen on the -NH bond of the base attaches to the carbon, removing the -OH previously there and the H on the -NH from the base .
What is a single strand of DNA
A polymer of nucleotides linked by covalent bonds between the phosphate group of one nucleotide and the 2-deoxyribose of another nucleotide.
What does DNA stand for
deoxyribonucleic acid
How do sugar-phosphate-sugar-phosphate chains form/join together
First phosphate group attaches to the 5th carbon of the first sugar
-OH on the 3rd carbon of the sugar attaches to the -OH of the second phosphate group on the 5th carbon of the second sugar.
H2O is lost.
How does DNA exist
As 2 complementary strands of the sugar phosphate polymer chain arranged in the form of a double helix
What does complementary mean in DNA
The two strands must have base sequences that match all A’s to T’ and all C’s to G’s
How many hydrogen bonds are formed in the C-G pair
3
How many hydrogen bonds are formed in the A-T pair
2
What is formed between two Cys -R groups
disulfide bridge
Explain why the strength of the interaction between two cysteine R groups differs from the strength of the interaction between a serine R group and an aspartic acid R group.
Two Cys R groups form a disulfide bridge
Ser and Asp R groups form Hydrogen bonds
Disulfide bridges are stronger than H bonds
Because disulfide bridges are covalent bonds (while H bonds aren’t) / Because covalent bonds are stronger (than H bonds)
Explain why different amino acids have different Rf values
Amino acids have different polarities
Therefore, have different retention on the stationary phase or different solubility in the developing solvent
What is used as an anticancer drug
The Pt(II) complex cisplatin
What does cisplatin do
Prevents DNA replication in cancer cells
How does cisplatin prevent DNA replication in cancer cells
By a ligand replacement reaction with DNA in which a dative covalent bond is formed between platinum and nitrogen atom on guanine
How does the cisplatin join to guanine
Two chloride ions are displaced and replaced by 2 -NH3 atoms
Why can’t some oxygen and nitrogen molecules on the bases bond to cisplatin
They are involved in the bonding within the DNA molecule
What are the adverse side effects of cisplatin
Prevents replication of healthy cells by bonding onto healthy DNA which leads to unwanted side effects such as hair loss.
How to minimise unwanted side effects on cisplatin
By giving it in small doses
Why are plastic gloves worn in TlC
To prevent contamination from the hands to the plate
Describe the structure of cisplatin
Square planar complex with a platinum metal ion, 2 ammonia ligands and 2 chloride ion ligands
