Proteins and Amino Acids - 1

Question 1

what are proteins ?

Answer 1

linear unbranched chains of amino acids that are joined by peptide bonds ( CONH)

Question 2

what occurs to the N and C termini at physiological pH (7.4)

Answer 2

They carry charges - the C terminus is negative and the N terminus is +

Question 3

how many different kinds of amino acid residues is there and what determines this ?

Answer 3

the genetic code determines only 20 different amino acid residues.

Question 4

how is a protein produced ?

Answer 4

By translation that occurs in the at the ribosme

Question 5

how will the other residues be found ?

Answer 5

By post translational modification , i.e addition of hydroxyl group

Question 6

what is the most common form of configuration D or L and how are they designated ?

Answer 6

chiral alpha carbon descides if D or L . L configuration is most common in natural proteins. D does occur must is rare and found in bacteria mostly.

Question 7

single letter code G

Answer 7

glycine

Question 8

v

Answer 8

valine

Question 9

i

Answer 9

isoleucine

Question 10

s

Answer 10

serine

Question 11

c

Answer 11

cysteine

Question 12

N

Answer 12

asparagine

Question 13

w

Answer 13

tryptophan

Question 14

m

Answer 14

methionine

Question 15

a

Answer 15

alanine

Question 16

l

Answer 16

leucine

Question 17

p

Answer 17

proline

Question 18

t

Answer 18

threonine

Question 19

F

Answer 19

phenylalanine

Question 20

Q

Answer 20

glutamine

Question 21

Y

Answer 21

tyrosine

Question 22

where they charged or uncharged ?

Answer 22

uncharged

Question 23

d

Answer 23

aspartic acid co2-

Question 24

k

Answer 24

lysine NH3+

Question 25

R

Answer 25

arginine NH3+

Question 26

E

Answer 26

glutamic acid C02-

Question 27

H

Answer 27

histidine NH+ ring

Question 28

are they charged or uncharged ?

Answer 28

charged

Question 29

what is a pKa value ?

Answer 29

it indicates the strength of an acid and how much it dissociates in water

Question 30

what does a low pKa value indicate

Answer 30

a strong acid as it will dissociate more fully in water.

Question 31

whats the 2 unusual amino acids and why ?

Answer 31

glycine - no side chain

proline - bends round on itself and is an imino as contains amine and carboxyl group

Question 32

if an OH is present in an amino acid what can form?

Answer 32

hydrogen bonds , stabilises

Question 33

if an SH present what can form ?

Answer 33

disulphide bridge , covalent and stabilises

Question 34

what is the primary structure of a protein ?

Answer 34

this is the linear chain of amino acids

Question 35

how come the amino acid sequence is subject to change ?

Answer 35

due to genetic mutations

Question 36

how come proteins evolve over time ?

Answer 36

due to the mutations that occur

Question 37

where is the information held to define the 3D structure of a protein?

Answer 37

in the primary sequence

Question 38

whats the stages of a secondary structure forming ?

Answer 38

The polypeptide chain will fold at certain points which then pack together to form a domain. These domains then dock.

Question 39

what do secondary structures originate from ?

Answer 39

stereochemical restrictions on the chain conformations

Question 40

what geometry does the peptide bond have and why?

Answer 40

planar due to the delocalisation of electrons across the C-N bond , therefore cannnot rotate

Question 41

What bonds can rotate in the peptide bond?

Answer 41

those either side of the alpha carbon

Question 42

are all combinations of phi and psi bonds energetically favourable ?

Answer 42

no as some have steric overlap of neighbouring atom especially if a side chain is present

Question 43

what’s the most energetically favourable angle ?

Answer 43

when the amide groups can form hydrogen bonds between them

Question 44

where is the hydrogen bonds in an alpha helix ?

Answer 44

in the amide backbone

Question 45

whats the orientation of the side chains in an alpha helix ?

Answer 45

they stick outwards

Question 46

what is a dipole and why is it present on the helix ?

Answer 46

this is a seperation in charge and due to the positive carbon and negative oxygen

Question 47

what protein is nearly all alpha helix ?

Answer 47

keratin

Question 48

what occurs to an alpha helix as it gets longer ?

Answer 48

it bends