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Biochemistry > Chapter 3; Amino Acids (New) > Flashcards

Chapter 3; Amino Acids (New) Flashcards

1
Q

What are the common features of all amino acids?

A
  1. All contain an alpha amino group and alpha carboxyl group
  2. All are L isomers in proteins
  3. contain an alpha carbon
  4. Are dipolar (zwitterion) at a neutral pH
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2
Q

________ are the building blocks of proteins & have 20 different variation

A

Amino acids

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3
Q

What are some roles of proteins?

A

Proteins are the workhorses of the cell where they storage and transport, support the shape of cells, help mechanical movement, factors/regulate different hormones, recptors, etc

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4
Q

What are the 4 levels to protein structure?

A
  1. Primary structure
  2. Secondary structure
  3. Tertiary structure
  4. Quaternary structure
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5
Q

Are amino acids chiral or achiral?

A

Chiral

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6
Q

Proteins are formed from what type of isomer of amino acids L or D?

A

L amino acids

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7
Q

What amino acids is achiral?

A

Glycine since it has a hydrogen atom as its side chain

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8
Q

What amino acids have chiral carbons in their side chain?

A

Threonine & Isoleucine

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9
Q

When the alpha amino group is on the left what stereoisomer is the amino acid?

A

L (& if it was on the right it would b D)

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10
Q

Nonpolar (alipathetic & aromatic) amino acids like to do what?

A

They are hydrophobic & bury away from water

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11
Q

Polar uncharged amino acids like to do what?

A

They are hydrogen bond donors & acceptors & interact with water

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12
Q

Polar charged amino acids like to do what?

A

They are cationic & anionic groups at neutral pH

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13
Q

What are the two amino acids that contain sulfur?

A

Cysteine & methionine

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14
Q

Name all the aliphatic amino acids?

A
  1. Glycine
  2. Alanine
  3. Leucine
  4. Valine
  5. Isoleucine
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15
Q

Name all the aromatic amino acids

A
  1. Methionine
  2. Proline
  3. Phenylalanine
  4. Tryptophan
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16
Q

What aromatic amino acids can absorb UV light?

A
  1. Tyrosine (280 +nm)
  2. Tryptophan (280 +nm)
  3. Phenylalanine (270nm)
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17
Q

What are the polar uncharged amino acids?

A
  1. Serine
  2. Threonine
  3. Asparagine
  4. Glutamine
  5. Tyrosine
  6. Cysteine
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18
Q

Which of the polar uncharged amino acids has a hydroxyl side chain? (make a strong nucleophile)

A
  1. Serine
  2. Threonine
  3. Tyrosine
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19
Q

Which of the polar uncharged amino acids has a amide side chain?

A
  1. Glutamine
  2. Asparagine
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20
Q

Cysteine side chains can be cross-linked if oxidized to form a _______ bridge that stabilize the 3D structure

A

Disulfide bridge

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21
Q

What amino acids are polar charged

A
  1. Lysine
  2. Argine
  3. Histidine
  4. Aspartic acid
  5. Glutamic acid
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22
Q

Within the charge polar amino acids which are the basic (+) charge?

A
  1. Histidine
  2. Lysine
  3. Arginine
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23
Q

Within the charge polar amino acids which are the acidic (-) charge?

A
  1. Aspartate
  2. Glutamate
24
Q

What are the ionizable amino acid groups?

A
  1. C-terminus
  2. N-terminus
  3. Glu
  4. His
  5. Cys
  6. Tyr
  7. Lys
  8. Arg
25
Q

Delocalized electron density (resonance) stabilizes __________
(protonated form of glutamate side chain) & stabilizes __________
(arginine side chain)

A

carboxylate, guanidium ion

26
Q

If the pH below the pKa, then the _________ form of the group dominates

A

protonated (acid)

27
Q

If the pH is above the pKa, the ___________ form of the group dominates

A

Deprotonated

28
Q

Zwitterionic form can act as what?

A

Acid or base

29
Q

pH = pI when what?

A

Between 2 pKa values when the net charge is zero

30
Q

__________ amino acids have ionizable side chains

A

Polar charge

31
Q

In a titration curve if an amino acid has an ionizable R group how many stage will it have on the titration curve?

A

3 (pKa 1, pKa 2, pKar)

32
Q

How would you calculate the partial charge on an amino acid at a particular pH?

A

Use the henderson hasselbatch equatin (pH = pKa + log [A]/[HA]) & then solve it for [A]/[HA] & [HA] charge will be its value / its value + 1 & [A] fraction charge will be 1- charge of HA & to calculate its pI its is pKa 2 + pKr)

33
Q

________ bonds form between amino acids

A

Peptide bonds

34
Q

What type of reaction occurs to form a peptide bond?

A

Condensation reaction where the O atom is lost on the alpha carboxyl group & two hydrogen atoms are lost from the alpha amino group on the other amino acid that its connecting to

35
Q

What is the Primary structure of a protein?

A

Its the linear sequence of amino acids in a polypeptide

36
Q

What is an oligopeptide?

A

Has 3 - 10 or 20 amino acids

37
Q

What is a polypeptide?

A

Has many amino acids up to 1000s

38
Q

Polypeptide chains are read & numbered in what order?

A

From the N- terminus to the C-terminus

39
Q

Peptide formation eliminates ________ alpha carboxyl & alpha amino groups of free amino acids

A

Ionizable

40
Q

What are the rules for naming peptides?

A

Name from N-terminus to C- terminus & at the end replace the end with yl (ex. ala-tyr-asp-gly) (instead of glu)

41
Q

Isopeptide bonds

A

Form between side chains carboxyl or amino groups and alpha-amino or carboxyl group through disulfide bridge

42
Q

At certain pH values these ionizable side chains groups will be able to exchange hydrogen atoms & that will allow them to form ______ bonds

A

Ionic bonds

43
Q

What are the protein purification techniques?

A
  1. Dialysis
  2. Salting out
  3. Gel fraction chromatography
  4. Ion exchange chromatography
  5. Affinity chromatography
  6. Gel electrophoresis
  7. Isoelectric focusing
  8. 2D electrophoresis
44
Q

What is dialysis

A

Separates proteins from small molecules & ions

45
Q

What is salting out?

A

Using salt concentration to cause precipitation of proteins (if it doesn’t precipitate means the salt concentration too low for the protein & need to be higher)

46
Q

What is Gel fraction chromatography?

A

Separates proteins based on size (it contains a tube with beads & the proteins move thru the beads & the proteins thar largest move faster & the smaller ones get trapped in the beads)

47
Q

What is ion exchange chromatogrpahy?

A

Separates proteins based on charge (if the column is an anion column then positively charge proteins will move faster & negatively charge will move slower & vis versa if its a cation column)

48
Q

What is an affinity chromatography?

A

Separates proteins based on their affinity for a certain molecule

49
Q

Gel electrophoresis

A

Separates proteins based on size

50
Q

Isoelectric focusing

A

Separates based on their isoelectric point

51
Q

2D electrophoresis

A

Combines isoelectric focusing & gel electrophoresis

52
Q

Specific activity

A

Used to determine the purity of the sample (enzyme activity/ concentration)

53
Q

What is the difference between gel electrophoresis & gel chromatography

A

In gel electrophoresis all proteins move along in it but in gel chromatography small proteins get trapped in the beads

54
Q

_________ allows us to purify a mixture of proteins that contain nonproteins. Substances where small molecules move outwards through the insoluble membrane but the large proteins can’t

A

Dialysis

55
Q

What are the conditions used to determine the pI of an amino acid?

A
  1. If the side chain is not ionizable then the pI is the average of the pKa values of the terminal alpha amino & alpha carboxyl group
  2. If the side chain is ionizable & acidic then the pI is the average of the pKa value of the terminal alpha carboxyl group & the side chain
  3. If the side chain is ionizable & basic the pI is the average of the pKa values of the terminal alpha-amino group & the side chain
  4. For all other ionizable groups, we must determine the middle pKa value & average it with the terminal alpha carboxyl group
56
Q

How do you calculate the pI of a protein?

A
  1. Estimate the pH at which the net charge on the proteins will be zero
  2. Find the average of the two pKa values directly above & directly below the estimate

Biochemistry (26 decks)

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