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Lecture 3 Flashcards

Amino Acids (58 cards)

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1
Q

Amino acid diversity?

A

Amino acids are incredibly diverse in nature. A great variety of amino acids have been identified on earth and in
materials from other sources. For example, the Murchison meteorite
has revealed many different amino acids.

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2
Q

Common features of amino acids?

A

Amino acids are smaller organic molecules that generally have the following:
- An amino group (NH2)
- A carboxylic acid group (COOH)
- A central alpha carbon
- An R (variable) group.

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3
Q

R groups of amino acids?

A

There are many different R groups that will result in district amino acids with different properties. They are anything that will covalently attach to the carbon.

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4
Q

Difference between often drawn amino acids and at neutral pH?

A

Often drawn - COOH and NH2
At neutral pH - COO^- and NH3

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5
Q

Why is it significant that they are drawn at neutral pH?

A

Because biological tissues are going to be at a neutral pH! The molecules are ionizable, meaning that they can give H and also have charges!

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6
Q

Amino acid stereochemistry?

A

The alpha carbon is oftentimes asymmetrical. Therefore, these are two enantiomeric forms.
- The NH3 can either be on there right or the left
- The NH3 being on the left is the L-amino acid and when NH3 being on the right is called D-amino acid.
- Amino acids in proteins are in the L configuration; D amino acids are less prevalent.

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7
Q

How many amino acids are there?

A

There are 20 genetically encoded amino acids
- These are amino acids that can be incorporated into proteins that are being synthesized according to the mRNA.

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8
Q

Differences in Amino acids are due to?

A

The only difference between them is the R group that they have. All amino acids (when free in sln and not incorporated into proteins with a peptide bond) have a carboxyl and amino group. The R groups infer the behaviour of the amino acid through its structure.

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9
Q

Types of amino acids? Common features?

A

Hydrophobic, polar, and charged amino acids.

Hydrophobic: The R group is non-polar
Polar: Don’t ionize. Functional R group has highly electronegative atoms, makes an uneven distribution of electron density, has slightly - and + ends.
Charged: Polar, but ionize (typically around physiological pH - 7). The carboxyl group is ionized at typical pH levels as does the carboxyl on the alpha carbon.

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10
Q

Proline?

A

Proline (Pro, P) forms a ring structure, having an R group that binds to the alpha carbon and the amino group. This changes how the protein is shaped. It is the only protein that does this!
HYDROPHOBIC

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11
Q

Gylcine?

A

Glycine (Gly, G) has an R group that is simply an H. We consider it POLAR. It is not capable of asymmetry - due to having two H’s. Can’t have L or D enantiomers and we cannot identify polarity in a completely definitive way.

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12
Q

Negatively charged amino acids?

A

Aspartate (Asp, D) and Glutamate (Glu, E) are negatively charged.

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13
Q

Positively charged amino acids?

A

Lysine (Lys, K) and Arginine (Arg, R) are positively charged.

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14
Q

Hydrophobic amino acids?

A

Hydrophobic amino acids are those with non-polar R groups. They are
typically found in the interior of folded proteins. They group together due to the hydrophobic effect and this can help to keep proteins properly folded.

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15
Q

What are proteins?

A

Proteins are amino acid chains that are folded to make their final form. This is done in a particular way to be able to perform its function.

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16
Q

Why are hydrophobic molecules found in the middle of proteins?

A

Hydrophobic amino acids partition out of the aqueous solution towards the middle of the folded protein. Therefore, hydrophobic groups are typically found in the middle of folded proteins. They stay away from water altogether - this helps keep proteins folded.

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17
Q

Aliphatic side chains?

A

Ala, Val, Leu and Ile all have
aliphatic side chains that are
hydrophobic.

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18
Q

Methionine?

A

Hydrophobic amino acid - one of two amino acids that contains sulfer

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19
Q

Tryptophan?

A

Tryptophan is the largest amino acid, and its UV absorbance 280 nm can be used to measure protein concentration.
HYDROPHOBIC

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20
Q

Phenylalanine?

A

Phenylalanine just like Ala with an added phenyl group. It also absorbs UV light at a slightly lower wavelength, but is not used to measure protein concentration.
HYDROPHOBIC

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21
Q

Proline?

A

Proline is the only imino (ringed) acid: The side chain loops around and connects to the amino group. This forces a forces a bend in proteins.
HYDROPHOBIC

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22
Q

The 8 hydrophobic amino acids?

A

Alanine (Ala, A)
Leucine (Leu, L)
Valine (Val, V)
Isoleucine (Ile, I)
Methionine (Met, M)
Tryptophan (Trp, W)
Phenylalanine (Phe, F)
Proline (Pro, P)

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23
Q

The 8 polar amino acids?

A

Glycine (Gly, G)
Serine (Ser, S)
Threonine (Thr, T)
Histidine (His, H)
Tyrosine (Tyr, Y)
Asparagine (Asn, N)
Glutamine (Gln, Q)
Cysteine (Cys, C)

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24
Q

Glycine?

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A

Glycine is the simplest amino acid
with an H as the R group. It is
the only one that is not chiral at
the alpha carbon.

POLAR

25
Serine and Threonine?
Serine and Threonine have hydroxyl (-OH) groups. POLAR
26
Histidine?
Histidine has an imidazole side chain. This amino acid is considered as uncharged in this list. However, it can be charged at slightly acidic pH. POLAR
27
Tyrosine?
Tyrosine is a derivative of Phe that has a hydroxyl group. Tyr also absorbs UV light at 280 nm, but is not typically used to detect or quantify proteins. POLAR
28
Cysteine?
Cysteine has a sulfhydryl group (-SH). This can form a disulfide bond. POLAR
29
Cysteine residues can form?
Cysteine residues can form disulphide bonds. It can be found on its own or in proteins. - When separate these amino acids are each called cysteine. - When two cysteines are joined through a disulphide bond, the entire thing is called cystine.
30
Cystine?
Occur in proteins and can fold the chain over.
31
How does Cystine form?
The sulfhdryl (SH) group of Cys can be oxidized to form a covalent disulfide bond (S-S) with another Cys, resulting in cystine. - when the bond needs to be broken, reducing agents ae added!
32
The 4 charged amino acids?
Aspartate (Asp, D) Glutamate (Glu, E) Lysine (Lys, K) Arginine (Arg, R)
33
Negatively charged amino acids?
Asp and Glu have negatively-charged carboxyl side chains at pH 7 (often referred to as acidic amino acids)
34
Positively charged amino acids?
Lys and Arg have positively-charged side chains at pH 7 (often referred to as basic amino acids)
35
Aromatic amino acids?
Trp, Phe and Tyr are amino acids that all have a benzene ring. Thus, they are commonly called aromatic amino acids. * These amino acids differ in other ways, and are in different categories, as seen above. However, they have some shared properties due to the aromatic (benzene) ring. * All absorb UV at about 280 nm
36
Where do peptide bonds form?
Peptide bonds can form between amino acids.
37
What are peptide bonds?
Peptide bonds are covalent bonds that can form between any of the 20 genetically-encoded amino acids. Proteins are formed when a series of amino acids are linked in this way. - Commonly, the bond occurs between the amino group of one amino acid and the carboxyl group of the other amino acid - independent of the R group.
38
How do peptide bonds form?
The carboxyl group of one amino acid and the amino group of the pother amino acid go through a dehydration reaction (loss of water) to form a peptide bond. - Leaves a free amino end of one peptide called the N-terminus - Leaves a free carboxyl end of the other peptide called the C-terminus
39
Where do protein sequences begin?
Protein sequences always begin at the N terminus and end at the C-terminus.
40
Terminology (residues and terminals)?
Protein sequences are written from the N- to C- terminus. Amino acids linked by peptide bonds are called residues.
41
Sequence and size notation example?
If the word SCIENCE were a peptide sequence, the whole name would be as follows: serine-cysteine-isoleucine-glutamate-asparagine-cysteine-glutamate or Ser-Cys-Ile-Glu-Asp-Asn-Cys-Glu However, it is much easier to write and analyze SCIENCE, using the single letter amino acid code. The molecular mass of this peptide would be 797 g/mol. For proteins, the molecular mass is normally called "molecular weight" and it is given in Daltons. So, this would be 797 Daltons. (Most proteins are far larger and the molecular weight, as it is called, is expressed in kiloDaltons (kDa).
42
Leucine and isoleucine share an important feature that distinguishes them from other amino acids. What is it?
Leucine and isoleucine have the same molecular mass: 131.18 g/mol. Until recently, it was not possible to distinguish them by mass spectrometry. (New MS methods do allow them to be distinguished.) - They just have different connectivities!
43
Which amino acid is a common flavour additive in foods?
A common flavour additive in foods is monosodium glutamate. It imparts umami flavour to savoury foods.
44
Are there other common amino acids besides the 20 found in proteins?
Yes. There are several non-protein amino acids. (Any compound with a carboxyl group and an amine would be an amino acid by definition.) - Citrulline is abundant in watermelon. After ingestion, it is converted to arginine. It is sometimes used as a sports supplement - BMAA is an amino acid neurotoxin that is found in blue-green algae. They are cyanobacteria and grow in warm waters that contain necessary nutrients.
45
Where in a protein is this amino acid likely to be found? A. At the surface of a protein B. Near the N-terminus of a protein C. Near the C-terminus of a protein D. Buried in the interior of a protein E. This amino acid does not preferentially locate to any particular region of a protein NOTE: No electronegative side chain
The answer is D. Notice that the R group of this amino acid (leucine) is non-polar. So, it would tend to group with others at the centre of a folded protein, where it would be buried away from the aqueous solvent.
46
Amino acids are...?
Amino acids are weak acids/bases
47
Titration of glycine with base?
For every amino acid (peptide, protein) there is an isoelectric point (pI), a pH value where the net charge of the molecule is zero Starting from a low pH, each time we ‘cross’ a pKa, a proton is released (amino acid charge decreases by 1). * When the pH is above the pKa, the proton is released. * When the pH is below the pKa, the proton is retained.
48
Titration of histidine?
Charge decreases by 1 each time a pKa is crossed. To estimate pI: Find the two pKa values surrounding the net charge 0 species, then average them! Basic amino acids have basic pIs (and vice versa). This can be extended to proteins.
49
Calculating/estimating pH?
pl = pk1 + pk2 / 2
50
Table method for pl?
When a rising pH crosses the pKa of an ionizable group, the group loses a proton. Knowing this, we can complete the charge table for –COOH, which has a pKa = 1.8. Complete table with charge changes across each group at its pKa. The net (overall) charge is 0 where indicated. This allows students to avoid mistakes. Then, the pI can be calculated. pH 4 is between the two pKas of 1.8and 6. The net charge on His is +1 in that interval. So, the charge on His at pH 4 is +1. See slide #33!
51
Estimating protein charge?
What is the net charge of the peptide Leu-Arg-Asp-Lys-Glu at pH 7.0? - First, identify the ionizable groups (charged molecules and those on C and N terminus') - Second, refer to the table of pkas in proteins. - Third, complete the table. Ex. Our pH of interest, 7, falls in the interval between the pKas of 4.1 and 9. In that interval, the charge on the protein is 0.
52
Shortcut method?
What is the net charge of the peptide Leu-Arg-Asp-Lys-Glu at pH 7.0? - Remember that groups have an extra H below their pKa and lost it when they cross it to be above. Refer to table: N terminus: pH 7.0 is below its pKa so it has an extra proton and it is positively charged (+1) Leu: hydrophobic (no charge) Arg: pH 7.0 is below its pKa so it has an extra proton and it is positively charged (+1) Asp: pH 7.0 is above its pKa so it has one less proton and it is negatively charged (-1) Lys: pH 7.0 is below its pKa so it has an extra proton and it is positively charged (+1) Glu: pH 7.0 is above its pKa so it has one less proton and it is negatively charged (-1) C terminus: pH 7.0 is above its pKa so it has one less proton and it is negatively charged (-1) Adding the charges indicated gives 0. That is the net charge on the protein at 7.0.
53
Estimating protein pl?
What is the approximate isoelectric point of this peptide? Leu – Arg – Asp – Lys - Glu Use the same table: - The charge on the protein is 0 between the pKa values of 4.1 and 9.0. Therefore, the average between those values is the estimated pI. pI = 4.1 + 9.0 / 2 = 6.6 The pI is 6.6.
54
Estimating protein pl - shortcut?
What is the approximate isoelectric point of this peptide? (Leu – Arg – Asp – Lys - Glu) / | | | | \ NH2 NH2 COOH NH2 COOH COOH From table, the pKa values across the peptide are: 9.0 (N terminus), 12.5, 3.9, 10.5, 4.1, 3.5 (C terminus) Placed in order, the pKa's are: 3.5 3.9 4.1 9.0 10.5 12.5 . Charges are: +3 +2 +1 0 -1 -2 -3 Overall charge = 0 between 4.1 and 9. So, take the average of those pKa values for an estimate of the pI. pI = 4.1 + 9.0 / 2 = 6.6
55
Protein solubility depends on pH?
pH < pl (soluble) pH >pl (soluble) pH = pl (low solubility) - Proteins repel each other when carrying a net charge, making them more soluble.
56
What are the hydrophobic amino acids?
Alanine Valine Phenylalanine proline methionine tryptophan leucine isoleucine
57
What are the polar amino acids?
serine threonine tyrosine asparagine glutamine cysteine glycine histidine
58
What are the negatively and positively charged amino acids?
Negative: glutamate and aspartate Positive: lysine and arginine
BIOC2300
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