lecture 2🅱️ Flashcards
what happens during induced fit
the target changes shape in order to bond more tightly,, this shortens bond,, making it stronger
stronger binding interaction due to induced fit
what are the building blocks of protein
amino acids
what do amino acids possess on the same c atom
they have an
amine
carboxylic acid
on the same carbon
charge of amine on aa
NH3
+
charge of carboxylic acid on aa
COO -
amine + carboxylic acid form which bond
amide bonds
peptide bonds
are the NH3+ or COO- ever seen
only on terminal amino acids.
theyre normally present as peptide bonds
most important group of an amino acid
the R group.
its unique
what elements are present in amino acids
C,O,S,H,N
what does amino acid classification depend on
depends on the R group or the side chain.
same thing different name
classification of amino acids
- non polar,, aliphatic
- aromatic
- polar,, uncharged
- positively charged
- negatively charged
non polar + aliphatic can give what bonds
VDW
hydrophobic
polar // uncharged aa can give what bonds
DD, hydrophilic,, H bonding
positively and negatively charged aa can give what bond
ionic bonds
hydrogen bond donor
NH2
OH
FH
electronegative atom covalently bonded to a H
hydrogen bond acceptor
electronegative + lone pair
not covalently bonded to a H.
C=O
name 3 structural biology techniques
- NMR
- x ray crystallography
- neutron diffraction
what is xray crystallography
using crystals to diffract an xray in order for the diffraction pattern to be detected (xray detector) to give an electron density map (using computers + graphics) and therefore a secondary protein structure.
what is a limitation of xray crystallography
the object must be crystallised.
in order for the bonds to be a certain distance
so they can defract X-rays.
protons cannot be seen - no h bonds
static picture: crystal packing forces may affect the structure observed
positives about xray crystallography
atomic scale picture is very accurate
must important structural biology technique
crysal structure data gives coordinates and there can be used as a starting point for computer modelling/ simulations
why does the crystal have to be 3d + crystallised
the diffraction pattern must be collected for the whole crystal structure:: the crystal must be turned 360* to allow a complete diffraction pattern
what does nmr stand for
nuclear magnetic resonance
are all nmrs 1d
nope!!
1d
2d
3d
negatives for nmr
smaller proteins only!!
size limitation
positives for nmr
- doesnt need to be a crystal
- atomic scale picture is very accurate
-u can see protons - dynamic picture given (can be in solution - not crystalline)
- can be used as a starting point for computer modelling / simulations
5 key features of amino acids
- alpha amino acids: all possess amine and carboxylic acid on the same carbon atom
- possess a side chain on each carbon (except glycine)
- linked to form polymers (proteins) using the alpha amino and carboxylic acid
- possess 5 elements: N O C H S
4 key features of amino acids
- alpha amino acids: all possess amine and carboxylic acid on the same carbon atom
- possess a side chain on each carbon (except glycine)
- linked to form polymers (proteins) using the alpha amino and carboxylic acid
- possess 5 elements: N O C H S
NMR steps
- labelled proteins
- data acquisition
- spectroscopy processing
- computer simulations
