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BDS year 1 - biochemistry > Amino acids + proteins > Flashcards

Amino acids + proteins Flashcards

1
Q

what makes up most of cell’s dry mass

A

amino acids

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2
Q

how many amino acids are in plants, animals + microbial + how many are encoded by genetic code

A

300

20

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3
Q

what does a alpha carbon mean

A

central Carbon - hydrogen + amine + carboxyl group + variable side chain attached to

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4
Q

what do optical isomers mean

A

same structural formula but different spatial arrangement of atoms
2 enantiomers - mirror images

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5
Q

which amino acid doesn’t have a optical isomer and why

A

glycine

doesn’t have asymmetric carbon - doesn’t have 4 diff gaps attached

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6
Q

what way can most amino acids rotate the polarised light

A

L - rotates light to the left

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7
Q

what does it mean if optical isomers are optically active

A

can rotate the plane of polarised light
L - light to the left
D - light to the right

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8
Q

what are the charges on amino acids

A

dipolar ions = positive + negative charged

but are zwitterions - net charge = 0

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9
Q

what is pK values for carboxylic acid groups

A

2.2 - strong acid

readily donate protons

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10
Q

what is pK value for alpha amino group

A

9.4

readily ionise

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11
Q

what happens to amino groups + carboxylic acid groups on AA at pH 7.4

A

amino acid group protonated - POSITIVE (NH3+)

carboxylic acid grp –> carboxylate (conjugate base)(COO-)

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12
Q

what happens to the amino acid in very acidic conditions

A

net charge is positive

excess number of free protons present from acid

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13
Q

what happens to the amino acid at neutral pH

A

net charge is neutral

it is a zwitterion

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14
Q

what happens if the amino acid net charge is negative

A

it is in Anionic form

its in basic condition

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15
Q

why are amino acids amtopheric

A

they have basic + acidic groups

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16
Q

what happens to the groups on the amino acid at a high pH

A

carboxylic group will lose proton first –> bound more loosely than amino group
COO- + NH2

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17
Q

what happens to the groups on amino acid as the pH decreases

A

NH3+ AND COOH

amino group is protonated

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18
Q

describe the beginning of graph of titration of amino acid

A
    • curve is steep up to pH 2 –> there’s no buffer - so can’t resist pH change
  2. pH 2.34 carboxyl group acts as buffer + loses proton (COO-) –> Ph doesn’t change much = BUFFERING REGION
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19
Q

what is the isoelectric pH of amino acid

A

pH 6.1

net charge of molecule = 0

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20
Q

what is the pKa of carboxylate ion

A

pKa 2.34

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21
Q

what happens to the amino group of the AA at around pH 10 and what is the pKb of the amino group

A

amino group acts as a buffer now

pKb = 9.87

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22
Q

what does it mean if the AA is negatively charged

A

all groups have been ionised

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23
Q

what is the overall trend of the AA graph

A

as the pH increases, AA net charge goes from positive –> negative

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24
Q

how many inflection point are there on the AA titration graph + what do they mean

A

4 inflection points

  1. half zwitterions + half cations (NH3+ , COOH)
  2. all AA are zwitterions
  3. half zwitterions + half anions (NH2 , COO-)
  4. all AA are anions
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25
what does anion mean
negative charged NH2 and COO-)
26
what does cation mean
positive charged NH3+ AND COOH
27
what amino acids are non-polar, neutral + aliphatic inside + outside protein
``` glycine alanine valine leucine isoleucine ```
28
what amino acid are non - polar, neutral + imino acid (bent chain)
proline
29
what amino acids are non polar, neutral + aromatic
phenylalanine | tryptophan
30
what amino acids are non- polar, neutral + contain sulphur
cysteine | methionine
31
what amino acids are polar, neutral + aromatic --> what is it used for
tyrosine | aromatic = site for phosphorylation
32
what amino acids are polar, neutral + contain OH group --> what is used for
threonine serine OH group --> site for glycosylation
33
what amino acids are polar, neutral + contain NH2 groups + what reason
asparagine glutamine site for glycosylation
34
what amino acids are polar, acidic + carry negative OH carboxyl group
aspartic acid | glutamic acid
35
what amino acids are polar, basic + carry positive NH3 amino group
arginine lysine histidine
36
what is the isoelectric point
point at which AA doesn't carry net charge
37
what is the formula to work out pI (isoelectric point) + when can you use this formula
pI = (pKa + pKb) / 2 | when there are more than 2 ionisable groups
38
what to do if you want to find pI but have 3 or more ionisable groups on AA
take pK values closest to neutral + use those vlues
39
how to find pI of glutamic acid
acidic, take lowest pK charges
40
how to find pI of arginine
basic | take pK charges of 2 highest values
41
which AA are precursors of nucleotides
aspartate, glycine, glutamine
42
what is serotonin and which AA is its precursor
it is a neurotransmitter | tryptophan is precursor
43
In a polypeptide, what is the N terminal and the C terminal
N terminal = free amino group at the first AA in polypeptide | C terminal = free carboxyl group in polypeptide
44
which terminal is always synthesised first in protein synthesis
N terminal | left to right
45
what is post translational modification
AA contained in proteins are altered after translation in protein synthesis
46
what can post translational modifications include
phosphorylation | glycosylation are essential for protein function
47
what are most common function + uses of protein
growth + repair | enzymes, hormones, DNA, RNA
48
what is protein folding
protein has more than 1 stable folded conformation, each has its own conformation + function but only 1 is active its reversible
49
what is a prosthetic group
proteins tightly associated with other chemical/non-protein species helps to perform function
50
what is the primary structure of a protein
AA sequence peptide bonds between each AA determined by our DNA
51
what is secondary structure of protein
folding/ coiling of polypeptide chain into alpha helix or beta pleated sheet weak H bonds between H atom + electronegative atoms (N or O)
52
how many turns in secondary structure for polypeptide chain in alpha helix + how do the bonds form
3.6 amino acids | H atom in peptide bond is shared with 4th AA instead
53
what is the tertiary structure of protein
3D shape of polypeptide chain | fibrous or globular
54
what type of bonds are there in terry structure of protein
electrostatic attraction/ salt bridge van der Waals forces disulphide bon hydrophobic interaction
55
how does electrostatic attraction / salt bridge occur in tertiary structure
between oppositely charged ions or groups
56
how do van Der Waals forces occur in tertiary structure
weak but needed in close packed interior of proteins + specific shape of enzyme active site
57
how do disulphide bonds occur in tertiary structure
strong bond between specific cysteine AA | locks protein in configuration
58
how does hydrophobic interaction occur in tertiary structure
between non-polar hydrophobic AA
59
what is quaternary structure of protein
combo of more than 1 proteins + involves non-covalent bonds between proteins
60
give example if 1 protein with 4 polypeptide chains + 1 protein with 3
haemoglobin - 4 polypeptide chains + 4 haem groups | collagen - 3 helical polypeptide chain supercoiled with each other
61
what are the 3 protein classes
globular fibrous membrane associated
62
what are the characteristics of globular proteins
soluble enzymes/ antibodies Tertiary structure when non - polar hydrophobic AA move in + polar hydrophilic AA bound outwards
63
give 2 examples of globular proteins + give their uses
carbonic anhydrase - large beta pleated sheet in centre + active site has Zn ion ---> catalyses hydration of CO2 --> HCO3- + H+ Hb - 4 globular proteins bound together - electrostatic attraction + H bonds + hydrophobic interaction each protein associated with haem grp contains iron that binds to O2
64
what are the characteristics of fibrous proteins
``` wire like structural/storage function used to construct connective tissues + bones repeated AA sequences contains cross links between chains ```
65
what is use + nature of keratin
keratin - tough + insoluble high proportion of small AA (glycine + alanine) lots of cysteine --> lots disulphide bridge -- thermal stable + permanent --> rigid can assemble into intermediate filaments for cell cytoskeleton
66
what are 2 examples of fibrous proteins
keratin | collagen
67
what is use + nature of collagen
secreted by connective tissue cells | most abundant protein in mammals (25%)
68
what do membrane associated proteins include (where found)
transmembrane proteins integrated in phospholipid bilayer lipid associated proteins -- inner + outer of membrane + proteins transporters, linkers, receptors, enzymes on cell membrane

BDS year 1 - biochemistry (14 decks)

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