B1 protein structure and function

Question 1

amino acids are chiral, what does this mean

Answer 1

4 different groups are bonded to a tetrahedral a-carbon

Question 2

what are the two mirror image forms of amino acid
what is the only isomer found in proteins

Answer 2

L and D isomer
only L isomer exist in proteins

Question 3

what do free amino acids in a sol at neutral H exist as

Answer 3

dipolar ion

Question 4

in dipolar ion aa what are the groups that are charged

Answer 4

amino group (NH3+)
carboxyl group (COO)

Question 5

what 3 ionisation states exist and how do they vary

Answer 5

protonated
zwitterionic form
deprotonated

Question 6

the 20 aa found in proteins have unique side chains that vary in what

Answer 6

size
shape
charge
hydrogen bonding capacity
hydrophobic character
chemical reactivity

Question 7

what aa have nonpolar R groups

Answer 7

proline
leucine
methionine
isoleucine
glycine
alanine
valine
-phenylalanine
-tryptophan

Question 8

what aa have polar R groups

Answer 8

serine
threonine
cysteine
asparagine
glutamine
-tyrosine
-histadine
-lysine
-arginine
-aspartate
-glutamate

Question 9

what aa have aromatic R groups that are nonpolar

Answer 9

phenylalanine
tryptophan

Question 10

what aa have aromatic R groups that are polar

Answer 10

histidine
tryosine

Question 11

what aa have +ve charged R groups
aromatic R groups
polar R groups

Answer 11

histidine

Question 12

what aa have -ve charged R groups that are polar

Answer 12

aspartate
glutamate

Question 13

peptide bond formation is carried out by what reaction

Answer 13

condensation
releases water

Question 14

primary protein structure

Answer 14

aa sequence

Question 15

what can be said about the polypeptide chain in terms of its formation

Answer 15

has directionality
amino terminal end is taken as the beginning of the pp chain

Question 16

what is the backbone and variable part of the polypeptide

Answer 16

backbone- repeating part
variable part- distinctive aa side chain

Question 17

what bonding potential does the backbone have and why

Answer 17

hydrogen bonding
carbonyl groups and H atoms that are bonded to the nitrogen of the amine group

Question 18

how many aa do most proteins consist of

Answer 18

50-2000

Question 19

what is protein mass referred to as

Answer 19

daltons
1 dalton= 1g mol -1

Question 20

in some proteins what can the pp chain be cross linked by and how

Answer 20

disulphide bonds
form by the oxidation of two cysteines

Question 21

what are the cross linked cysteines called

Answer 21

cystine

Question 22

what can be said about the peptide bonds shape

Answer 22

planar
6 atoms (Cα,C, O, N, H, Cα) lie in a plane

Question 23

the peptide bond has partial double bond character, why and what does this result in

Answer 23

resonance
thus rotation about the bond is prohibited

Question 24

what form of peptide bond is strongly favoured and why

Answer 24

trans form
because of steric clashes that arise in the cis form

Question 25

where in the amino acid chain is rotation permitted

Answer 25

about the N-Cα bone (the phi Φ bond) about the Cα- carbonyl bond (the psi ψ bond)

Question 26

rotation in the aa chain allows proteins to do what

Answer 26

to fold in many different ways

Question 27

what 2 things make protein folding possible

Answer 27

restrictions by the rigidity of the peptide bond restricted set of allowed Φ and ψ angles (steric hindrance)

Question 28

what is the secondary structure

Answer 28

the 3D structure formed by hydrogen bonds between peptide NH and CO groups of aa that are near each other in primary structure

Question 29

what are 3 examples of secondary structure

Answer 29

alpha a-helix beta b-strand turns

Question 30

appearance of a-helix

Answer 30

tightly coiled rod like structure R groups sticking from axis of the helix

Question 31

what parts of the a helix backbone do not form hydrogen bonds

Answer 31

those at the end of the helix

Question 32

what is the a helix stabilised by

Answer 32

intrachain hydrogen bonds

Question 33

are a helices left or right handed

Answer 33

right

Question 34

what are b-sheets formed by

Answer 34

adjacent b-strands

Question 35

what can be said about b-strands in contrast to a-helix

Answer 35

b-strand is fully extended

Question 36

what are b sheets stabilised by

Answer 36

hydrogen bonds between the polypeptide strands

Question 37

what positions could b-sheets be in

Answer 37

parallel antiparallel mixed and may be flat or twisted

Question 38

polypeptide chains can change directions with b-turns what are they

Answer 38

hairpin turns- reverse turns omega loops bigger, irregular

Question 39

what does the tertiary structure refer to

Answer 39

the spatial arrangement of aa that are far apart in the primary structure and it refers to the pattern of disulfide bond formation

Question 40

size and space of globular proteins

Answer 40

very compact little/no empty space in interior of globular proteins

Question 41

what does the interior of globular proteins consist of

Answer 41

mainly hydrophobic aa

Question 42

what does the exterior of globular proteins consist of

Answer 42

charged and polar aa

Question 43

what is to be said about the distribution of hydrophobic/philic aa in membrane proteins

Answer 43

reverse distribution hydrophobic exterior water filled hydrophilic channel (porin (PDB 1PRN))

Question 44

what are motifs

Answer 44

supersecondary structures combinations of secondary structure

Question 45

what are domains

Answer 45

an independent folding unit of the 3D protein structure

Question 46

what is the role of b-mercaptoethanol in regards to disulphide bonds

Answer 46

reducing reduced disulphides and is itself oxidised forming dimers

Question 47

what is the quaternary structure

Answer 47

proteins composed of multiple polypeptide chains (subunits)

Question 48

what does the aa sequence determines

Answer 48

the folding of a protein into its 3D structure

Question 49

what occurs after translation which determines many proteins fate in the cell

Answer 49

post translational modifications

Question 50

examples of post translational modifications

Answer 50

-converting a proprotein by proteolytic cleavage to a mature protein -addition of various chemical groups -small proteins like ubiquitin -fatty acids like myristoyl or prenyl groups -branched glycosylations -glycosyl phosphatidyl inositol (GPI) anchors

Question 51

what 3 groups can undergo post translational modification by the addition of a chem group

Answer 51

-N terminal amino group -C terminal carboxyl group -side chains of amino acids throughout the length of the protein

Question 52

lack of appropriate protein modification can result in

Answer 52

pathological conditions

Question 53

alack of hydroxylation of proline in collagen results in

Answer 53

scurvy (vit C deficiency)

Question 54

lack of carboxylation of clotting proteins results in

Answer 54

haemorrhaging (vit K deficiency)