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Biochemistry > Chapter 4: Amino Acids > Flashcards

Chapter 4: Amino Acids Flashcards

1
Q

What properties do amino acids have that are well suited to carry out biological functions?

A
  • Capacity to polymerize
  • useful acid-base properties
  • varied physical properties
  • varied chemical properties
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2
Q

Protein sequence is ultimately derived from what?

A

DNA Sequence

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3
Q

What defines an alpha carbon?

A

It has 4 substituents and is tetrahedral

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4
Q

What is connected to the alpha carbon in all proteins?

A
  • An acidic carboxyl group
  • A basic amino group
  • A hydrogen
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5
Q

What Amino Acids are non-polar and uncharged?

A
  • Glycine
  • Alanine
  • Proline
  • Valine
  • Leucine
  • Isoleucine
  • Methionine
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6
Q

What Amino Acids contain positively charged R groups?

A
  • Lysine
  • Arginine
  • Histidine
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7
Q

What Amino Acids contain negatively charged R groups?

A
  • Aspartate
  • Glutamate
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8
Q

Which Amino Acids have Aromatic R Groups?

A
  • Phenylalanine
  • Tyrosine
  • Tryptophan
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9
Q

Which Amino Acids have Polar uncharged R groups?

A
  • Serine
  • Threonine
  • Cysteine
  • Asparagine
  • Glutamine
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10
Q

Which amino acids are chiral? which are not?

A

All amino acids are chiral, except for glycine

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11
Q

Which wavelength is used by researchers to quantify proteins?

A

280 nm

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12
Q

What is the charge of a Zwitterion?

A

0

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13
Q

What is the Isoelectric Point?

A

This is the characteristic pH at which the net electric charge is ZERO

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14
Q

What is the formula to find pI?

A

pI = 0.5(pK1+pK2)

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15
Q

From where do you start naming and numbering peptides?

A

The amino terminus

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16
Q

What is a protein’s specific 3-D structure called?

A

Native Fold

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17
Q

What are the 4 levels of protein structure?

A

Primary - Amino Acid Residues

Secondary - Alpha Helix

Tertiary - Polypeptide Chain

Quaternary - Assembled Subunits

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18
Q

Which bond within a polypeptide chain has a partial double-bond characteristic?

A

The C-N bond

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19
Q

What are the properties of peptide bonds?

A
  • Six atoms (C∝, C, O, N, H, C∝) of a peptide bonds lies in one plane, hence the peptide-bond is planer
  • The peptide-bond is uncharged; minimum charge repulsion b/w amino acids, hence large globular 3-D structure are possible
  • Oxygen attached to carbonyl is in trans to H of amide N
  • Virtually all peptide bonds occur in trans conformation
20
Q

What properties of peptides are attributed to their resonance?

A
  • to be less reactive compared to esters, for example
  • to be quite rigid and nearly planar
  • to exhibit a large dipole moment in the favored trans configuration
21
Q

Is rotation allowed around the alpha-carbon bonds? What about the peptide bond?

A

Rotation is allowed around bonds connected to the alpha-carbon. Rotations around the peptide bond are not allowed

22
Q

In order to know the 3D structure of the polypeptide, we must know what?

A
  • The sequence of amino acids in a polypeptide
  • the Psi and Phi for each alpha-carbon
23
Q

When is a secondary structure generated?

A

when Psi and Phi remains almost the same in a segment (Important to know)

24
Q

What are the two common regular arrangements of secondary structures? How are they stabilized?

A
  • Alpha Helix
    • stabilized by hydrogen bonds between nearby residues
  • Beta sheets
    • stabilized by hydrogen bonds between adjacent segments that may not be nearby
25
Q

Which helix structure (right-handed or left-handed) is more dominant? Why?

A

Right-handed dominates because of minimum steric hindrance when compared to left-handed

26
Q

What amino acids act as helix breakers? what about ones that favor alpha helixes?

A

Proline (roration around the N-Ca bond is impossible), Glycine (tiny R-groups favor other formations), and Glutamate (very charged and repels) act as helix breakers.
*Note: Bulky sidechains also disrupt helix formation
Alanine and Leucine favor helix formation

27
Q

What is the difference when ß sheets run in parallel vs antiparallel?

A

In parallel sheets, the H-bonded strands run in the same direction, which results in bent H-bonds (weaker)

In antiparallel sheets, the H-bonded strands run in the opposite direction, which results in linear H-bonds (stronger)

28
Q

When do ß turns occur? Over how many amino acids is it accomplished?

A

ß turns occur whenever strands in ß sheets change direction, and they are accomplished over 4 amino acids

29
Q

What is a domain?

A

Globular unit of protein structure that is a part of a larger protein

30
Q

Do domains retain their structure when separated from the rest of the protein?

A

They retain their structure even when separated from the rest of the protein

31
Q

What is denaturation?

A

Loss of structural integrity with accompanying loss of activity

32
Q

What can cause proteins to denature?

A
  • heat or cold
  • pH extremes
  • organic solvents
  • chaotropic agents: urea and guanidinium hydrochloride
33
Q

What are Chaotropic Agents?

A

They are small molecules that perturb (distort) the 3-dimensional structure by interfering with non-covalent interactions that stabilize the protein’s conformation

34
Q

What are Reducing Agents? Can their actions be reversed?

A

They are small molecules that reduce disulfide bridges, leaving the cysteines with their original sulfhydryl groups. Their actions can be reversed by their removal and introduction of oxidizing conditions

35
Q

What is Dialysis used to do?

A

Selectively remove small molecules

36
Q

What kind of process is protein folding? (exergonic or endergonic?)

A

Exergonic and therefore has a -▲G value

37
Q

What molecules help prevent misfolding? How do they do this?

A

Chaperones help prevent misfolding, and they do this by preventing aggregations of unfolded peptides.

38
Q

By what does Ion-separation separate proteins?

A

It separates proteins based on their charge.

39
Q

What is Hydrophobic Chromatography?

A

A separation technique that filters based on the solubility of the protein. Proteins that are more soluble will precipitate out first.

40
Q

What is salting-in and salting-out?

A

Salting-In - At low concentrations, the presence of salt stabilizes the various charged groups on a protein molecule, thus attracting protein into the solution and enhancing the solubility of protein

Salting-Out - At higher concentrations, there is less and less water available to solubilize a protein. This causes the proteins to precipitate because there is not enough water molecules to interact with.

41
Q

What is Gel Filtration Chromatography?
What are some of the properties?

A

A separation method based on the size and shape of proteins. Larger proteins are eluted out first.

*Properties:
- Leaves Proteins Intact
- Good Resolutions
- Not Efficient with Crude Solutions
- Relatively Slow Flow Rates

42
Q

What is Affinity Chromatography?
What are some of the properties?

A

A separation method based on activity/function. First unwanted proteins are eluted out and then a solution of ligand is pumped in to have the protein of interest bind to it. They are then eluted out.

*Properties:
- Unparalleled Potency (fold-purification)
- Leaves Proteins Intact
- Requires prior knowledge of biologicalproperties and availability of an interacting species (ligand, substrate analog, antibody)

43
Q

What is Yield?

A

Yield - percent of the initial activity at the end of each purification step

44
Q

What is Specific Activity?

A

Specific Activity - the total activity divided by the total amount of protein (number of total enzyme units per mg of total proteins)

45
Q

What are the properties of SDS PAGE?

A
  • Unparalleled Resolution
  • Fast
  • Denatures proteins
  • Samples are treated with a reducing agent (DTT or ß-mercaptoethanol)

Biochemistry (11 decks)

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