Lecture 1 - Amino acids Flashcards
What is the Primary structure of a Protein
The sequence of Amino Acids
What is the secondary structure of a protein
Alpha Helix and Beta pleated sheet
What is tertiary protein structure
Overall 3D shape and arrangement of a polypeptide
What is Quaternary protein structure
Association of several protein chains or subunits into a closely packed arrangement
What is an Alpha amino acid
A carbon is connected to both Amine and Carboxylic acid groups
How many amino acids are there
20
What are the groups for Amino Acid structure
Aliphatic
Aromatic
Basic
Acidic
Polar
Other
Which amino acids are found in the aliphatic group
Alanine, Ala, A
Valine, Val, V
Leucine, Leu, L
Isoleucine, Ile, I
Methionine, Met, M
Which amino acids are in the aromatic group?
Phenylalanine, Phe, F
Tyrosine, Tyr, Y
Tryptophan, Trp, W
Which amino acids are in the basic group?
Histidine, His, H
Lysine, Lys, K
Arginine, Arg, R
Which Amino acids are in the acidic group
Aspartic Acid. Asp, D
Glutamic Acid, Glucose, E
Which Amino acids are in the polar group
Cystine, Cys, C
Serine, Ser, S
Threonine, T
Asparagine, Asn, N
Glutamine, Gln, Q
Which amino acids are in the others group?
Glycine, Gly, G
Proline, Pro, P
What is the amino acid structure and grouping based off
Chemical Properties, Shapes, function
What are some traits of aliphatic amino acids
Hydrophobic, Non-polar
What are some traits of Aromatic Amino Acids
Non-polar
Pi- Stacking
What is Pi Stacking
The stacking of aromatic rings on top of one another causing interactions and orbital overlap between the rings involved
What charge does Aspartic acid and Glutamic acid have on them?
Negative (-)
What charge do Lysine and Arginine have on them?
Positive (+)
What are some traits of Polar Amino acids
Very Hydrophilic
What are the traits of the unique group of amino acids
No real R groups
Flexible - can allow a protein to change function
What are the main properties that are studied in Amino acids
Light absorption
Ionisation states
Chirality
What is the Beer-Lambert Law used to measure
Concentration of Solutions based on how they absorb light
What is the Beer-Lambert Equation
A = Ɛ c l
A - Absorbance
Ɛ - Extinction Coefficient
c - Concentration
l - Path Length
How do you calculate Protein Concentration (Using Beer-Lambert Law)
Slide 18 Slovell lecture
What is pKa described as in relation to a molecule or functional group
Inherent property
What is a zwitterion
A molecule with functional groups, of which at least one has a positive and one has a negative charge, and an overall net charge of 0
What is the Isoelectric point (pl)
The pH at which a particular molecule carries no net charge (zwitterion formed)
(each amino acid is different)
What are chiral stereoisomers
Same bonds between the same atoms but different spatial arrangement
What are D and L amino acids
Non-superimposable mirror images (chiral stereoisomers)
Why is chirality important
(D and L amino acids have) different shapes and enzymes partly recognise substrate my shape
If the substrate is wrong, it won’t be processed by enzyme
(nature tends to use L amino acids for some random reason)
What is an example of the importance of the correct stereoisomer
Thalidomide D= Sedative L = Teratogenic
What is an amino acid called if it a rotates plane of polarised light in the clockwise direction
Dextrorotatory or (+)
(not related to D and L)
What is an amino acid called if it rotates a plane of polarised light in the counterclockwise direction
Levorotatory or (-)
How is amino acid configuration obtained
(A light source and) a polarimeter (slide 32)
How is specific rotation calculated
slide 32
What is the reference molecule for the L and D system of amino acid configuration
Glyceraldehyde
What is the CORN rule (slide 34)
CORN = L amino acid (anticlockwise)
CONR = D amino acid (clockwise)
(YouTube video if not understood https://www.youtube.com/watch?v=Nw6kIrcpWEU)
What does the RS amino acid configuration involve
Absolute nomenclature - uses relative ranking of various functional groups
(https://www.youtube.com/watch?v=lwowv5bobt8)
R= Right arc
S+ left Arc
