BCM9

Question 1

What is the Pka of the amino group?

Answer 1

9.6

Question 2

What is the Pka of the carboxyl group?

Answer 2

2.2

Question 3

What are AA referred to as?

Answer 3

amphoteric

Question 4

What is the isoelectric point?

Answer 4

pH at which protein has no over all charge

Question 5

What does a high pKa mean?

Answer 5

it is less likley to dissociate

Question 6

What is the rule for determining if an AA is charged?

Answer 6

if Narg + Nlys > Nasp + Nglu

= charged at neutral pH and pka > 7

Question 7

What is the corn law?

Answer 7

• put h behind carbon
  CO - R - N
  if clockwise it is the l form

Question 8

Where are D amino acids found?

Answer 8

peptidoglycan

Question 9

What are the amino acids with a postively charged side chain at neutral ph?

Answer 9

arginine
lysine
- histinde = partially positive

Question 10

what are the amino acids with a negatively charged side chain at neutral ph?

Answer 10

aspartic acid

glumatic acid

Question 11

pka of aspartic acid?

Answer 11

4.1

Question 12

pka of glutamic acid?

Answer 12

4.1

Question 13

pka of histine

Answer 13

6.1

Question 14

pka of argine

Answer 14

12.5

Question 15

pka of lysine

Answer 15

10.8

Question 16

why is histine only partially charged at ph7?

Answer 16

as imidazole ring loses proton above ph6..1

Question 17

what is the guanidium group?

Answer 17

NHC(NH2)2

Question 18

where is a guanidium group found?

Answer 18

arigine

Question 19

What is found on the side chain of glutamic acid?

Answer 19

carboxylate group

which is stabilised by resonance

Question 20

how is guanidium group stabilised?

Answer 20

resonance

Question 21

What are the 5 amino acids with polar uncharged side chains

Answer 21

asparagine
threonine
serine
glutamine

Question 22

what ate the 8 amino acids with hydrophobic side chains?

Answer 22

alanine
phenyl alanine
leucine
isoleucine 
valine
methionine
tyrosine
tryptophan

Question 23

what are the 3 amino acids containing aromatic rings?

Answer 23

phenylalanine
tyrosine
tryptophan

Question 24

what do not form in the cytosol?

Answer 24

disulfide bonds

Question 25

what are disulfide bonds used for?

Answer 25

help rigidity where proteins would become unorganised | eg. outside of cell in changing pH or temp

Question 26

what do disulfide bonds form between?

Answer 26

two cysteine residues

Question 27

what is a peptide bond?

Answer 27

-CONH

Question 28

where does the equilbrium lie to in peptide bond formation?

Answer 28

the left

Question 29

what catalyses peptide bond formation?

Answer 29

ribosome

Question 30

what cataylses peptide bond hydrolysis?

Answer 30

proteases or proteinases | eg. trypsin, chymotrypsin, collagenase

Question 31

draw and name the mechanism that occurs in peptide bond formation?

Answer 31

addition elimination - nucleophillic attach of carbony by lone pair of electrion from amino group - results in h20 elimination

Question 32

what is the reality of peptide bond formation mechanism?

Answer 32

both carboylate ion and amino group will be charged extra proton on amino group transfered to carboxylate during the reaction the o- acts as a nucelophile on one of the hydrogens

Question 33

what defines a condensation reaction?

Answer 33

water eliminated | - protein residues = lack water

Question 34

what is the peptide bond? | - draw structures

Answer 34

a resonance hybrid structure between two competeting structures = double bond character delocalisation of pi electron over entire peptide boind rather than simply over the c=o bond -

Question 35

why is NHCO bond planar?

Answer 35

restricted rotation around around NH-CO bond | due to double bond characteristic of NH CO

Question 36

which conformation frorm is favoured in peptide bonds and by what amount? why? draw

Answer 36

trans 1000:1 | or there could be steric clashes or r groups

Question 37

what conformation from is favoured in prolines? | and by what amount

Answer 37

trans 15:1

Question 38

what are 4 other AA acids found in the cell and where?

Answer 38

ornithine - urea cycle citrulline - urea selenocysteine - rare, few proteins homocysteine - cysteine + extra ch2

Question 39

give examples of amino acid neurotransmitters

Answer 39

glutamate | GABA

Question 40

what does neurotransmitter gaba do?

Answer 40

inhibitory neurotransmitter | release opens cl- channels

Question 41

what does glutamate do?

Answer 41

release leads of opening of cation channels and depolarisation of the membrane

Question 42

What amino acids can be post translationally modified by phosphorylation?

Answer 42

serine threonine tyrosine residues

Question 43

which amino acids can be glycosylated and where?

Answer 43

``` serine threonine asparagine side chains in endoplasmic reticulum and golgi body ```

Question 44

what is the most common post translational modification?

Answer 44

acetylation of amino group and N terminal resudies

Question 45

give examples of 4 post translational modifications

Answer 45

1. myristoylation - add lipid for membrane proteins 2. ubiquinination and sumoylation and acetylation of lysine 3. thrombin cleaves fibrogen to fibrin 4. transglutaminase cross link lysine and glutamine