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bm210 biochemistry > B1 protein structure and function > Flashcards

B1 protein structure and function Flashcards

1
Q

amino acids are chiral, what does this mean

A

4 different groups are bonded to a tetrahedral a-carbon

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2
Q

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

A

L and D isomer
only L isomer exist in proteins

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3
Q

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

A

dipolar ion

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4
Q

in dipolar ion aa what are the groups that are charged

A

amino group (NH3+)
carboxyl group (COO)

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5
Q

what 3 ionisation states exist and how do they vary

A

protonated
zwitterionic form
deprotonated

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6
Q

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

A

size
shape
charge
hydrogen bonding capacity
hydrophobic character
chemical reactivity

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7
Q

what aa have nonpolar R groups

A

proline
leucine
methionine
isoleucine
glycine
alanine
valine
-phenylalanine
-tryptophan

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8
Q

what aa have polar R groups

A

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

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9
Q

what aa have aromatic R groups that are nonpolar

A

phenylalanine
tryptophan

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10
Q

what aa have aromatic R groups that are polar

A

histidine
tryosine

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11
Q

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

A

histidine

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12
Q

what aa have -ve charged R groups that are polar

A

aspartate
glutamate

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13
Q

peptide bond formation is carried out by what reaction

A

condensation
releases water

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14
Q

primary protein structure

A

aa sequence

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15
Q

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

A

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

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16
Q

what is the backbone and variable part of the polypeptide

A

backbone- repeating part
variable part- distinctive aa side chain

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17
Q

what bonding potential does the backbone have and why

A

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

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18
Q

how many aa do most proteins consist of

A

50-2000

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19
Q

what is protein mass referred to as

A

daltons
1 dalton= 1g mol -1

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20
Q

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

A

disulphide bonds
form by the oxidation of two cysteines

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21
Q

what are the cross linked cysteines called

A

cystine

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22
Q

what can be said about the peptide bonds shape

A

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

23
Q

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

A

resonance
thus rotation about the bond is prohibited

24
Q

what form of peptide bond is strongly favoured and why

A

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

25
Q

where in the amino acid chain is rotation permitted

A

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

26
Q

rotation in the aa chain allows proteins to do what

A

to fold in many different ways

27
Q

what 2 things make protein folding possible

A

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

28
Q

what is the secondary structure

A

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

29
Q

what are 3 examples of secondary structure

A

alpha a-helix
beta b-strand
turns

30
Q

appearance of a-helix

A

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

31
Q

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

A

those at the end of the helix

32
Q

what is the a helix stabilised by

A

intrachain hydrogen bonds

33
Q

are a helices left or right handed

A

right

34
Q

what are b-sheets formed by

A

adjacent b-strands

35
Q

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

A

b-strand is fully extended

36
Q

what are b sheets stabilised by

A

hydrogen bonds between the polypeptide strands

37
Q

what positions could b-sheets be in

A

parallel
antiparallel
mixed
and may be flat or twisted

38
Q

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

A

hairpin turns- reverse turns
omega loops
bigger, irregular

39
Q

what does the tertiary structure refer to

A

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

40
Q

size and space of globular proteins

A

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

41
Q

what does the interior of globular proteins consist of

A

mainly hydrophobic aa

42
Q

what does the exterior of globular proteins consist of

A

charged and polar aa

43
Q

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

A

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

44
Q

what are motifs

A

supersecondary structures
combinations of secondary structure

45
Q

what are domains

A

an independent folding unit of the 3D protein structure

46
Q

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

A

reducing
reduced disulphides and is itself oxidised forming dimers

47
Q

what is the quaternary structure

A

proteins composed of multiple polypeptide chains (subunits)

48
Q

what does the aa sequence determines

A

the folding of a protein into its 3D structure

49
Q

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

A

post translational modifications

50
Q

examples of post translational modifications

A

-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

51
Q

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

A

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

52
Q

lack of appropriate protein modification can result in

A

pathological conditions

53
Q

alack of hydroxylation of proline in collagen results in

A

scurvy (vit C deficiency)

54
Q

lack of carboxylation of clotting proteins results in

A

haemorrhaging (vit K deficiency)

bm210 biochemistry (19 decks)

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