lecture 2🅱️

Question 1

what happens during induced fit

Answer 1

the target changes shape in order to bond more tightly,, this shortens bond,, making it stronger

stronger binding interaction due to induced fit

Question 2

what are the building blocks of protein

Answer 2

amino acids

Question 3

what do amino acids possess on the same c atom

Answer 3

they have an
amine
carboxylic acid

on the same carbon

Question 4

charge of amine on aa

Answer 4

NH3
+

Question 5

charge of carboxylic acid on aa

Answer 5

COO -

Question 6

amine + carboxylic acid form which bond

Answer 6

amide bonds

peptide bonds

Question 7

are the NH3+ or COO- ever seen

Answer 7

only on terminal amino acids.

theyre normally present as peptide bonds

Question 8

most important group of an amino acid

Answer 8

the R group.
its unique

Question 9

what elements are present in amino acids

Answer 9

C,O,S,H,N

Question 10

what does amino acid classification depend on

Answer 10

depends on the R group or the side chain.

same thing different name

Question 11

classification of amino acids

Answer 11

• non polar,, aliphatic
• aromatic
• polar,, uncharged
• positively charged
• negatively charged

Question 12

non polar + aliphatic can give what bonds

Answer 12

VDW
hydrophobic

Question 13

polar // uncharged aa can give what bonds

Answer 13

DD, hydrophilic,, H bonding

Question 14

positively and negatively charged aa can give what bond

Answer 14

ionic bonds

Question 15

hydrogen bond donor

Answer 15

NH2
OH
FH

electronegative atom covalently bonded to a H

Question 16

hydrogen bond acceptor

Answer 16

electronegative + lone pair
not covalently bonded to a H.

C=O

Question 17

name 3 structural biology techniques

Answer 17

• NMR
• x ray crystallography
• neutron diffraction

Question 18

what is xray crystallography

Answer 18

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.

Question 19

what is a limitation of xray crystallography

Answer 19

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

Question 20

positives about xray crystallography

Answer 20

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

Question 21

why does the crystal have to be 3d + crystallised

Answer 21

the diffraction pattern must be collected for the whole crystal structure:: the crystal must be turned 360* to allow a complete diffraction pattern

Question 22

what does nmr stand for

Answer 22

nuclear magnetic resonance

Question 23

are all nmrs 1d

Answer 23

nope!!
1d
2d
3d

Question 24

negatives for nmr

Answer 24

smaller proteins only!!

size limitation

Question 25

positives for nmr

Answer 25

• 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

Question 26

5 key features of amino acids

Answer 26

• 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

Question 27

4 key features of amino acids

Answer 27

• 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

Question 28

NMR steps

Answer 28

• labelled proteins
• data acquisition
• spectroscopy processing
• computer simulations