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Biochemistry > Proteins > Flashcards

Proteins Flashcards

1
Q

what is the Henderson-Hasselbalch equation

A

pH= pKa +log10 ([A-]/[HA]

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2
Q

features of a peptide bond

A
  • planar bc of delocalised electron pair of the C=O

- resonance restricts the amount of conformations

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3
Q

what is a peptide bond

A

CO-HN

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4
Q

peptide bond and condensation vs hydrollysis

A

condensation:
build up from amino acid to protein
Hydrolysis:
break down protein to amino acid

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5
Q

what is cis

A

successive alpha C are on the same side of the peptide bond

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6
Q

what is trans

A

successive alpha C are on different side of peptide bond

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7
Q

cis or trans, which is more stable?

A

cis is less stable bc of steric interference- non-bonding interaction that affects conformation

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8
Q

how many amino acids

A

9 essential
11 non-essential
20 total

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9
Q

what is the structure of amino acids

A
  • amino group (NH2)
  • R group
  • Carboxyl group (COOH)
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10
Q

how many functional groups does an amino acid have

A

2: amino and carboxyl

- -> acts as a zwitterion

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11
Q

what is a zwitterion

A

a single species that contains both positively and negatively charged regions but has no overall charge

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12
Q

what determines the amino acid properties

A

R group bc it is variable

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13
Q

name the non-polar and no overall charge amino acids (hydrophobic)

A 
glycine
proline
leucine
alanine
phenyalanine
methionine
valine
tryptophan
isoleucine
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14
Q

name amino acids that are polar but uncharged side chains

hydrophilic

A 
serine
threonine
asparagine
cysteine
tyrosine
glutamine
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15
Q

name negatively charged amino acids (hydrophilic)

A

aspartate/ aspartic acid

glutamate/ glutamic acid

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16
Q

name positively charged amino acids

hydrophilic

A

lysine
arginine
histidine

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17
Q

what is the letter for glycine

A

g

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18
Q

letter for alanine

A

a

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19
Q

letter for valine

A

v

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20
Q

letter for leucine

A

l

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21
Q

letter for isoleucine

A

i

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22
Q

letter for phenylalanine

A

f

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23
Q

letter for methionine

A

m

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24
Q

letter for proline

A

p

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25
letter for tryptophan
W
26
letter for serine
S
27
letter for threonine
t
28
letter for tyrosine
Y
29
letter for cysteine
C
30
letter for asparagine
n
31
letter for glutamine
q
32
letter for aspartic acid
d
33
letter for glutamic acid
E
34
letter fr histidine
H
35
letter for lysine
L
36
letter for arginine
r
37
what is a chiral centre
molecule with 4 different groups attached
38
what are the properties of a chiral molecule
- lacks plane of symmetry - can't be superimposed on their mirror image - rotates planes of light
39
what is the only amino acid that isn't chiral
glycine
40
what are enantiomers
pairs of molecules that have the same Mr and the atoms are joined in the same way, but they occupy different spaces -optical isomers
41
difference between enantiomers
- rotates single plane of light in specific direction | - different properties
42
if only one enantiomer is present in a system, the system has
enantiometric specificity and is enantiomerically pure
43
what are diastereoisomers
pairs of stereoisomers that are not mirror images
44
how do you distinguish between enantiomers
-enantiomers cause optical rotation of light travelling in a single plane
45
what does +/- denote
the opposing effects that pain of enantiomers has of the behaviour of light
46
what does d/l refer to
the rotation of light direction
47
what is the primary structure of proteins
- basic sequence of amino acids - only covalent peptide bonds - determined by DNA and base sequence of mRNA - N terminus to C terminus
48
define the secondary structure of protein
- local fold in the sequence caused by interaction on the back bone - non-covalent bonding e.g hydrogen, Van der Waals and electrostatic forces of attraction
49
what are the 3 non-covalent bonding
- hydrogen - van der waal - electrostatic forces of attration
50
what structures does secondary have
- alpha helix - beta-pleated sheets - loop region
51
what are the alpha helices
- narrow bore tube | - 3.6 amino acids per turn and a pitch of 5.4 Å
52
how are alpha helices formed
H bonds form btw C=O of amino acid to N-H of another four amino acids
53
why do alpha helices form
- stability bc the side chains are well separated and each peptide link has 2 H bonds - dipole bc all H bonds point in the same direction
54
what are the two other types of alpha helix
pi: loose coil with H bond to the 5th residue 3(10): tight could with H bond to 3rd residue
55
structure of beta-pleated sheets
- /\/\/\/\ - regular, repeating H bonds - can be antiparallel or parallel - two residue repeats at a distance of 7Å
56
bonds in beta-pleated sheets
- polypeptide is fully stretched to allow N-H and C=O o point at right angles - H bonds form btw carboxyl O and amide ben strands are adjacent
57
describe parallel beta-pleated
- b strands run in the same direction | - less stable bc H bonds are on an angle - weaker
58
describe anti-parallel beta pleated
b strands run in same direction | more stable bc H bonds are small and straight
59
which is weaker, parallel or antiparallel
parallel
60
what is a loop region
connection btw beta-pleated sheets
61
describe structure of loop region
- rich in polat and charged residues - makes H bonds with water as they are on the surface - made from b-turns or hairpin loops - has glycne as second residue
62
where do proteases attack most
loop region
63
what are the top 3 amino acids in alpha helices
glutamic acid methionine alanine
64
what are the top 3 amino acids in b pleated sheets
valine isoleucine tyrosine
65
what are the top 3 amino acids in b turns
glycine asparagine proline
66
how are antiparallel sheets connected
small loop
67
how are parallel sheets connected
extensive crossover
68
what is supersecondary structure
compact 3d structure of several adjacent elements of secondary structure or motifs that are smaller than protein domains
69
describe tertiary structure
- 3D structure of the whole chain - affected by secondary structure and the atoms conformation - consists of two or more layers of 2nd to seal off the hydrophobic core from aqueous environment
70
why has teriary structure stayed the same in evolution
- form stable folding patterns - tolerates amino acid deletions, substitutions, and insertions - supports biological functions
71
how do the proteins fold
- hydrophobic interations (non-polar substances aggregate) - ionic interactions - H bonds - disulfide bridges
72
desribe ionic interaction
some amino acids have an extra COOH and others have extra NH2. fCOOH donated proton to amine
73
describe disulfide bridges
- covalent bond btw 2 thiol groups of 2 adjacent cysteine residues - created by the oxidation of sulfhydryl groups - formed in the ER - stabiliezes protein structure
74
describe Quaternary structure
made up of multiple polypeptie subunits
75
what are lots of subunits joined together called
supra molecular assemblies

Biochemistry (10 decks)

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