3.3.13 Amino acids, proteins and DNA Flashcards
Draw structure of amino acid
AMINO ACIDS ARE AMPHOTERIC SO THEY HAVE ACIIC AND BASIC PROPERTIES.
AMINO ACIDS ARE CHIRAL MOLECULES EXCEPT GLYCINE (as it has H instead of side chain). SO THEY ROTATE PLANE POLARISED LIGHT
How do you name amino acids
- find longest carbon chain
- number carbons starting from carboxyl group
- note which carbon the NH2 is attached to (named amino)
- name any other groups in standard way
so it is an …amino….oic acid
define zwitterion, explain this with the structure of amino acid as a zwitter ion
a molecule with both positive and negative ions
An amino acid only exists as a zwitterion at its isoelectric point, define isoelectric point
- the pH at which the average overall charge is 0.
What is th isoelectric point of an amino acid dependant on
its R group
Explain the change that occurs if pH gets altered above or below the isoelectric point of the amino acid
- if pH is lower than isoelectric point then COO- is likely to accept a H+
-if pH is above isoelectric point then NH3 is likely to lose a H+
How can we identify different amino acids and why is this possible
via Thin layer chromatography
- TLC allows us to separate and identify amino acids as they have different solubilities
Explain the process of TLC and the equipment/reagents
- TLC uses stationary phase of silica or alumina mounted on a glass/metal plate
- pencil base line drawn on plate
-drops of different amino acid mixture along base line - solvent in beaker must be below base line level
- cover beaker with lid to prevent solvent evaporating
- leave solvent to move near top of plate
-remove, mark solvent front and let dry
How do you spot amino acid front on the chromatogram if amino acids are colourless?
1: VIA FLUORESCENT DYES AND UV LIGHT
- add fluorescent dye to silica/alumina
-shine UV light to see
-colourless spots block glow from fluorescent dye
-circle round these spots to mark
2: VIA IDOINE/NINHYDRIN
- place chromatogram in sealed jar with few iodine crystals
-iodine vapour sticks to chemicals on plate dying it purple
How do you spot amino acid front on the chromatogram if amino acids are colourless?
1: VIA FLUORESCENT DYES AND UV LIGHT
- add fluorescent dye to silica/alumina
-shine UV light to see
-colourless spots block glow from fluorescent dye
-circle round these spots to mark
2: VIA IDOINE/NINHYDRIN
- place chromatogram in sealed jar with few iodine crystals
-iodine vapour sticks to chemicals on plate dying it purple
How to calculate Rf values and find what compound it is
Rf = distance travelled by spot / distance travelled by solvent front
compare your experimental Rf value to library of know Rf values to find the amino acid / compounds
(CONDITIONS FOR YOUR EXPERIMENT MUST BE THE SAME AS IN LIBARY OF VALUES IN ORDER TO CORRECTLY COMPARE Rf VALUES)
What links amino acid monomers to form a polypeptide?
peptide bond/link
Draw the structure of a dipeptide or repeating unit of polypeptides
In order to hydrolyse polypeptides, what conditions does it require
- 6 moldm-3 HCL
- 110 degrees celcius
- under REFLUX FOR 24 HRS
describe a primary protein structure
the sequence of amino acids in the polypeptide chain
describe secondary protein structure
hydrogen bonds exist between the peptide links in polymer chain and this results in alpha helix coiling or beta pleased sheet folding
describe tertiary protein structure
due to the interactions (hydrogen bond, ionic bond, disulphide bond) between the R groups of adjacent amino acids , the polypeptide chain further twists and folds into its unique tertiary structure
in proteins what causes the chain to hold a protein shape and what does this shape allow for
- disulphide bonds, CYSTEINE amino acid has -SH group, it lose H and form S-S bond
-hydrogen bonds, between highly electronegative elements e.g O AND N in -NH2 and -OH in amino acids
This specific 3d tertiary shape determines the proteins function
How does temp and pH affect tertiary structure
it affects hydrogen bonding and the formation of disulphide bonds
How does temp and pH affect tertiary structure
it affects hydrogen bonding and the formation of disulphide bonds
Why can enzymes have chiral centres?
as they are made up of amino acids
define stereospecific in terms of enzymes
enzymes have a specific active site which is only complementary to one enantiomer
How can an inhibitor affect rate of reaction and what is an inhibitor
- an inhibitor is a substance that has a similar shape to substrate that fits into active site of enzyme
- it blocks active site from substrate binding
- higher the conc of inhibitor, the more active site blocked so ROR decreases
- also the strength of the inhibitor binding affects the ROR, if poorly bonded then ROR won’t be reduced by much
