Chapter 4: Amino Acids

Question 1

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

Answer 1

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

Question 2

Protein sequence is ultimately derived from what?

Answer 2

DNA Sequence

Question 3

What defines an alpha carbon?

Answer 3

It has 4 substituents and is tetrahedral

Question 4

What is connected to the alpha carbon in all proteins?

Answer 4

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

Question 5

What Amino Acids are non-polar and uncharged?

Answer 5

• Glycine
• Alanine
• Proline
• Valine
• Leucine
• Isoleucine
• Methionine

Question 6

What Amino Acids contain positively charged R groups?

Answer 6

• Lysine
• Arginine
• Histidine

Question 7

What Amino Acids contain negatively charged R groups?

Answer 7

• Aspartate
• Glutamate

Question 8

Which Amino Acids have Aromatic R Groups?

Answer 8

• Phenylalanine
• Tyrosine
• Tryptophan

Question 9

Which Amino Acids have Polar uncharged R groups?

Answer 9

• Serine
• Threonine
• Cysteine
• Asparagine
• Glutamine

Question 10

Which amino acids are chiral? which are not?

Answer 10

All amino acids are chiral, except for glycine

Question 11

Which wavelength is used by researchers to quantify proteins?

Answer 11

280 nm

Question 12

What is the charge of a Zwitterion?

Answer 12

0

Question 13

What is the Isoelectric Point?

Answer 13

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

Question 14

What is the formula to find pI?

Answer 14

pI = 0.5(pK1+pK2)

Question 15

From where do you start naming and numbering peptides?

Answer 15

The amino terminus

Question 16

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

Answer 16

Native Fold

Question 17

What are the 4 levels of protein structure?

Answer 17

Primary - Amino Acid Residues

Secondary - Alpha Helix

Tertiary - Polypeptide Chain

Quaternary - Assembled Subunits

Question 18

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

Answer 18

The C-N bond

Question 19

What are the properties of peptide bonds?

Answer 19

• 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

Question 20

What properties of peptides are attributed to their resonance?

Answer 20

• 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

Question 21

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

Answer 21

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

Question 22

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

Answer 22

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

Question 23

When is a secondary structure generated?

Answer 23

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

Question 24

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

Answer 24

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

Question 25

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

Answer 25

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

Question 26

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

Answer 26

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

Question 27

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

Answer 27

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)

Question 28

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

Answer 28

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

Question 29

What is a domain?

Answer 29

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

Question 30

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

Answer 30

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

Question 31

What is denaturation?

Answer 31

Loss of structural integrity with accompanying loss of activity

Question 32

What can cause proteins to denature?

Answer 32

- heat or cold - pH extremes - organic solvents - chaotropic agents: urea and guanidinium hydrochloride

Question 33

What are Chaotropic Agents?

Answer 33

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

Question 34

What are Reducing Agents? Can their actions be reversed?

Answer 34

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

Question 35

What is Dialysis used to do?

Answer 35

Selectively remove small molecules

Question 36

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

Answer 36

Exergonic and therefore has a -▲G value

Question 37

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

Answer 37

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

Question 38

By what does Ion-separation separate proteins?

Answer 38

It separates proteins based on their charge.

Question 39

What is Hydrophobic Chromatography?

Answer 39

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

Question 40

What is salting-in and salting-out?

Answer 40

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.

Question 41

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

Answer 41

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

Question 42

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

Answer 42

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)

Question 43

What is Yield?

Answer 43

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

Question 44

What is Specific Activity?

Answer 44

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

Question 45

What are the properties of SDS PAGE?

Answer 45

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