Amino Acids, Proteins and DNA Flashcards
What functional groups make up an amino acid?
An amino acid is made up of the amine and carboxyl functional group
What kind of isomerism do amino acids have?
They are chiral molecules, except glycerol, because the carbon has four different groups attached. So a solution of a single amino acid enantiomer will rotate plane polarised light.
What is the difference between systematic and common names for amino acids?
Systematic names are the IUPAC names for the compounds while common names are the general name for the amino acid e.g. glycine, serine
What is a zwitterion?
A zwitterion is a dipolar ion—it has both a positive and a negative charge in different parts of the molecule. Zwitterons only exist near an amino acid’s isoelectric point.
What is the isoelectric point?
This is where the pH where the average overall charge on the amino acids is zero. It is due for different amino acids, it depends on their R group.
What happens to the amino acid molecule at low pH?
In conditions more acidic than the isoelectric point, the COO- group is likely to gain a H
What happens to the amino acid molecule at the isoelectric point?
At the isoelectric point, both the carboxyl group and the amino group are likely to be ionised, forming an ion called a zwitterion.
What happens to the amino acid molecule at high pH?
In conditions more alkaline than the isoelectric point, the NH3+ group is likely to lose an H
Why do amino acids have varying solubilities in the same solvent?
They have different R groups
How do you carry out thin layer chromatography to separate and identify unknown amino acids?
1) Draw a pencil line near the bottom of a thin layer chromatography plat and put a concentrated spot on the mixture of amino acids on it.
2) Dip the bottom of the plate into a solvent
3) As the solvent spreads up the plate, the different amino acids move with it, but at different rates, so they separate.
4) When the solvent’s nearly reached the top, take the plate out and mark the solvent front with pencil. Then leave the plate to dry
5) Amino acids are not visible so you need to make the spots visible.
6) You can work out the R value of each amino acid
7) Then you can use a table of known amino acid R values to identify the amino acids in the mixture.
How are proteins formed?
Proteins are made up of lots of amino acids joined together by peptide links. The chain is put together by condensation reactions and broken apart by hydrolysis reactions.
How can you make amino acids visible?
- spray ninhydrin solution on the plate which will turn the spots purple
- alternatively, you can use a special plate that has a fluorescent dyr added to it. The dye glows when UV light shines on it. Where there are spots of chemical on the plate, they cover the fluorescent dye- so the spots appear dark. You can put the plate under a UV lamp and draw around the dark patches to show where the spots are.
How do you work out the Rf value?
distance travelled by spot/distance travelled by solvent
What is the primary structure of proteins?
The primary structure of proteins is the amino acid sequence in the polypeptide chain
What conditions do you need to hydrolyse a protein?
Hot aqueous 6M hydrochloric acid and heat the mixture under reflux for 24 hours
What is the secondary structure?
The peptide link can form hydrogen bonds with each other, meaning the chain isn’t a straight line. The shape of the chain is called its secondary structure. The most common secondary structure is a spiral called an alpha helix. Another common type of secondary structure is a beta pleated sheet. This is a layer of protein folded like a concertina.
What are two important bonds that hold proteins in shape?
- Hydrogen bonding is one type of force that holds proteins in shape. Hydrogen bonds exist between polar groups. They stabilise both the secondary and the tertiary structure of the protein.
- The amino acid cysteine contains a thio group. Thiol groups on different cysteine residues can lose their H atoms and join together by forming a disulphide bond. These disulphide bonds link together different parts of the protein chain, and help to stabilise the tertiary structure.
What factors can affect protein structure?
- temperature
- pH
As they can affect hydrogen bonding and the formation of disulphide bonds and so can change the shape of proteins.
How do enzymes work?
They catalyse every metabolic reaction in the bodies of living organisms. They are proteins that can sometimes contain nonprotein components. Every enzyme has an area called the active site. This is the part that the substrate fits into so that it can interact with the enzyme. The active site is three-dimensional, it is part of the tertiary structure of the enzyme protein.
How do enzymes have high specificity?
Enzymes are specific to certain substrates as only certain substrates can fit in the active site.
Why can enzymes be described as stereospecific?
Enzymes are made up of amino acids, so they contain chiral centres. This makes their active sites stereospecific, they’ll only work on one enantiomer of a substrate. The other enantiomer won’t properly fit in the active site, so the enzyme can’t work on it, it’s a bit like how your left shoe doesn’t fit on your right foot properly.
How do competitive inhibitors work?
Molecules that have a similar shape to the substrate act as enzyme inhibitors. They compete with the substrate to bond to the active site, but no reaction follows. Instead they block the active site, so no substrate can fit in it.
What factors affect the amount of enzyme inhibition?
- How strongly the inhibitor bonds to the active site
- the relative concentrations of substrates and enzymes
How do some drugs work as inhibitors?
They block the active site of an enzyme and stop it from working. For example some antibiotics work by blocking the active site of an enzyme in bacteria that helps to make their cell walls. THis causes their cell walls to weaken over time, so the bacteria burst.
