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Y1 Genes, Molecules and Cells > Proteins and Amino acids > Flashcards

Proteins and Amino acids Flashcards

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Organic Chemistry 101 flashcards
1
Q

Proteins are made up of which monomers

A

Amino acids

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2
Q

How is it suggested that eukayotes and Archaea are linked
Why wasnt always believed

A

It is believed that eukaryotes came from archaea
This wasn’t always believed due to the similarities in appears from bacteria and archaea, where archaea was believed to be a form of bacteria
Now in research we can use the molecular biology of archaea to make informed decisions about human cells

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3
Q

Why is it belived that viruses could be living

A

The mimivirus, which was discovered was thought to be a bacterium but was actually a virus which is alive

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4
Q

Protein take up what % of of macromolecules in a cell

A

15%
This is the vast marority compared to other macromolecules

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5
Q

You can describe cells as

A

Highly organised
Even prokaryotes without a nucleus

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6
Q

All naturally occuring proteins are based upon which type of amino acids

A

L-amino acids

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7
Q

What type of reaction is it which forms a peptide bond between the two amino acids
What is the name of the reverse of this reaction

A

Condensation
Hydrolysis

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8
Q

How many common, naturally occuring amino acids

A

20

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9
Q

Which amino acid is Ala
What is its one letter abbrebiation

A

Alanine
A

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10
Q

Which amino acid is Arg
What is its one letter abbrebiation

A

Arginine
R

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11
Q

Which amino acid is Asn
What is its one letter abbrebiation

A

Asparagine
N

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12
Q

Which amino acid is Asp
What is its one letter abbrebiation

A

Aspartic acid
D

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13
Q

Which amino acid is Cys
What is its one letter abbrebiation

A

Cysteine
C

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14
Q

Which amino acid is Glu
What is its one letter abbrebiation

A

Glycine
G

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15
Q

Which amino acid is His
What is its one letter abbrebiation

A

Histidine
H

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16
Q

Which amino acid is ile
What is its one letter abbrebiation

A

Isoleucine
i

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17
Q

Which amino acid is Leu
What is its one letter abbrebiation

A

Leucine
L

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18
Q

Which amino acid is Lys
What is its one letter abbrebiation

A

Lysine
K

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19
Q

Which amino acid is Met
What is its one letter abbrebiation

A

Methionine
M

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20
Q

Which amino acid is Phe
What is its one letter abbrebiation

A

Phenylalanine
F

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21
Q

Which amino acid is Pro
What is its one letter abbrebiation

A

Proline
P

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22
Q

Which amino acid is Ser
What is its one letter abbrebiation

A

Serine
S

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23
Q

Which amino acid is Thr
What is its one letter abbrebiation

A

Threonine
T

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24
Q

Which amino acid is Trp
What is its one letter abbrebiation

A

Tryptophan
W

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25
Q

Which amino acid is Tyr
What is its one letter abbrebiation

A

Tyrosine
Y

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26
Q

Which amino acid is Val
What is its one letter abbrebiation

A

Valine
V

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27
Q

What group on the amino acids affects its chemical properties

A

The R group

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28
Q

Which amino acid R group is this?

A

Alanine

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29
Q

Which amino acid R group is this?

A

Arginine

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30
Q

Which amino acid R group is this?

A

Asparagine

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31
Q

Which amino acid R group is this?

A

Aspartic acid

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32
Q

Which amino acid R group is this?

A

Cysteine

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33
Q

Which amino acid R group is this?

A

Glutamic acid

34
Q

Which amino acid R group is this?

A

Glutamine

35
Q

Which amino acid R group is this?

A

Glycine

36
Q

Which amino acid R group is this?

A

histidine

37
Q

Which amino acid R group is this?

A

Isoleucine

38
Q

Which amino acid R group is this?

A

Leucine

39
Q

Which amino acid R group is this?

A

Lysine

40
Q

Which amino acid R group is this?

A

Methionine

41
Q

Which amino acid R group is this?

A

Phenylalanine

42
Q

Which amino acid R group is this?

A

Proline

43
Q

Which amino acid R group is this?

A

Serine

44
Q

Which amino acid R group is this?

A

Threonine

45
Q

Which amino acid R group is this?

A

Tryptophan

46
Q

Which amino acid R group is this?

A

Tryonsine

47
Q

Which amino acid R group is this?

A

Valine

48
Q

How many amino acids can be made in cells, and how many much come from the diet of the 20 nautrally occuring amino acids

A

11 of the core 20 are made in cells
9 amino acids cannot be synthesied in humans

49
Q

What is the general structure of an amino acids (except proline)

A

Alpha carbon: chrial in all amino acids (except glycine)
Carboxyl group
Amine group
R-group

50
Q

Amino acids (bar glycine) are chiral
What does this mean

A

They have 4 different groups bonded to the central carbon
This means they can form enantiomers in space

51
Q

What are the two enantiomers of Alanine

A

L-Alanine and D-Alanine

52
Q

Amino acids in proteins are always which isomer

A

L-isomers
They are homochiral

53
Q

What does Aliphatic mean

A

Means the R-group chain is not branched

54
Q

What does Aromatic mean

A

the R-group is based on a benzene ring (hydrophobic)

55
Q

What does polar mean

A

the R group carries a small charge, both positive and negative

56
Q

What does charged mean

A

the R-group is ionisable creating +ve or -ve charge depending on pH and type of R group (electrostatic/ionic interactions)

57
Q

Which amino acids are polar

A

Serine
Threonine
Cysteine
Asparagine
Glutamine
(These are likely to have C-O or C-N bonds)

58
Q

Which amino acids are positively charged

A

Lysine
Hisidine
Arginine
(arginine and hisdine have a delocalised charge)

59
Q

Which R groups are negatively charged

A

Aspartate
Gluatamate

60
Q

In solution, amino acids can ionise
Which two groups allow this

A

Carboxyl and amine
COOH will loose protons forming COO-
NH2 will gain protons forming NH3+

61
Q

Amino acids are amphoteric meaning

A

they can both donate and loose protons

62
Q

How is the pKa of an amino acid measured if it is amphoteric

A

is the pH at which a group has equal amount of protonated and unprotoned forms
So at pH below the pKa the group carries a positive charge

63
Q

Why are we more concerned about the ionisation of the R groups of the amino acids rather than the carboxyl and amine groups

A

Because the carboxyl and amine groups are used to form peptide bonds

64
Q

What is pKa in terms of amino acids

A

proton binding ability
a low pKa meaning it has a low affinity for protons

65
Q

Which amino acids are acidic at pH 7.4

A

Aspartic acid
Glutamic acid

66
Q

Give an example of two amino acids which are basic at 7.4
This means they will have a high affinity for protons

A

Arginine
Lysine

67
Q

What is a hydropathy value

A

It is the ability of an amino acid to dissolve within water
High value = hydrophobic
Low value = hyrdophillic

68
Q

Which amino acids have a high hydropathy value = hydrophobic

A

Valine
Leucine
Isoleucine
Methionine
These amino acids are more likely to exist within the protein
Bar tryosine, the aromatic R groups are also hydrophobic

69
Q

Which amino acids are good for structure and why

A

Glycine and Alanine because they have really small R groups

70
Q

Why is proline unique

A

It causes the back bone of the protein to kink

71
Q

Why is cysteine unique

A

cysteine forms covalent disulphide bonds

72
Q

What are the 4 fundamental forces of molecular biology

A

Electrostatic interactions (ionic)
Polar interactions (hydrogen bond)
Van der Waals interactions (dipole moment)
Hydrophobic interactions
(they are all non-covalent forces)

73
Q

The 4 forces that operate in proteins are generate by the sequence of amino acids. They are crucial for ….

A
  1. The chemical reactivity of protein as enzyme
  2. The ability of a protein to fold into the correct shape (conforamtion) required to fulfill its function in the cell
74
Q

How strong are non-covalent forces compared to covalent bonds

A

Are individually weak but collectively strong and flexible
Numerous non-covalent and dynamic foces in and between macromolecules

75
Q

What are electrostatic (ionic) interactions

A

These occur between atoms that are oppositely charged
They are the strongest as ionic bonds form between fully charged ions
However hydration by water can weaken their strength

76
Q

Amino acids with charged amino acids can form electrostatic interaction
Which onces are these

A

Aspartate
Glutamate
Lysine
Arginine
Histidine

77
Q

What is the most important example of ionic bonds in proteins in human

A

ATPases
Lysine amino acid R-group bonds ionically to adenosine triphosphate

78
Q

What are polar bonds

A

Specialised type of polar interaction that involves a slightly electropositive hydrogen atom that interacts with a electronegative acceptor atoms
Most hydrogen bonds in proteins occur between hydrogen and oxygen/nitrogen

79
Q

What are polar bonds

A

Specialised type of polar interaction that involves a slightly electropositive hydrogen atom that interacts with a electronegative acceptor atoms
Most hydrogen bonds in proteins occur between hydrogen and oxygen/nitrogen

80
Q

Water forms two hydrogen bond per molecule
Why is water very important to protein function:

A

Provide a solvation shell around the protein
Control the ionic interactions between opposite charges by reducing them

Y1 Genes, Molecules and Cells (16 decks)

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