Lecture 17&18- proteins and amino acids Flashcards
The biological world stages
Biosphere -> domains of life + viruses -> phylum, genus, species, strain -> cells -> molecular biology
It is suggested that …. evolved through ….
Eukaryotes
Archea
Alanine
ALA
A
Arginine
Arg
R
Asparagine
Asn
N
Aspartic acid
Asp
D
Cysteine
Cis
C
Glutamic acid
Glu
E
Glycine
Gly
G
Histidine
His
H
Isoleucine
Ile
I
Leucine
Leu
L
Lysine
Lys
K
Methionine
Met
M
Phenylalanine
Phe
F
Proline
Pro
P
Serine
Ser
S
Threonine
Thr
T
Tryptophan
Trp
W
Tyrosine
Tyr
Y
Valine
Val
V
In vertebrates, … of the 20 amino acids can be made in cells and … cannot be synthesised in human cells
11
9
All amino acids except … have the same structure:
-….. carbon atom (chiral in all amino acids except glycine
-…… group
-….. group
-…… group
Alpha
Carboxyl
Amine
R
Chirality/ handedness
The object or molecule can’t be superimposed on it’s mirror image by any translations or rotations
Amino acids are always ….-isomers
L
Aliphatic
R-group chain isn’t branched
Aromatic
R-group os based on a benzene ring (hydrophobic)
Polar
The R-group carries a small charge, both positive and negative
Charged
The R-group is ionisable creating positive or negative charge depending on pH and type of R group
In ….. amino acids have two ionisable groups: ….. and …..
Solution
Carboxyl
Amine
Amphoteric
An acid can both donate and accept protons
pKa
Acid dissociation constant
measure of how easily the proton is lost
How well something mops up protons
As dissociation increases, pKA decreases
Low pKa = strongly acidic
….. & … have delocalised charge
Arg
His
…. & …. are polar- form H-bonds
Ser
Thr
Zwitterion
An ion that contains 2 functional groups, 1 +ve and 1 -ve
Hydropathy values
How well a protein mixes with water
High value= hydrophobic
AA with aromatic R groups
Phe, Tyr, Trp
AA with small R-groups
Gly, Ala
AA with kinks
Pro
AA with thiol group
Cys
Electrostatic/ ionic interactions
Occur between oppositely charged atoms
Strongest as ionic bonds formed between fully/ formally charged atoms
Proteins with R-groups with charged atoms for ionic bonds
Asp, Glu, Lys, Arg, His
Example of essential ionic bond in enzyme activity
ATPase
ATP -> ADP
ATPase hydrolyses ATP and a phosphate group is lost
lysine amino acid R-group bonds ionically to ATP
Polar bonds: hydrogen bonding
Specialised type of polar interaction
Involves slightly electropositive H atom and an electronegative acceptor atom
Mostly form between H, O & N
Salvation shell
Formed by water around proteins
Formed by a network of hydrogen bonds
Van der Waals interactions
Temporary dipole formed
Can induce a dipole on adjacent atoms
Hydrophobic forces
Not bonds
Hydrophobic molecules crowd together in water
Allows hydrophobic packing
AA that are hydrophobic
Val, Leu, Ile, Met
hydrophobic AA stick together in….
Cores
Hydrophobic forces Increase with increasing …. and …..
Temperature
Salt
