Chapter 4: Amino Acids Flashcards
What properties do amino acids have that are well suited to carry out biological functions?
- Capacity to polymerize
- useful acid-base properties
- varied physical properties
- varied chemical properties
Protein sequence is ultimately derived from what?
DNA Sequence
What defines an alpha carbon?
It has 4 substituents and is tetrahedral
What is connected to the alpha carbon in all proteins?
- An acidic carboxyl group
- A basic amino group
- A hydrogen
What Amino Acids are non-polar and uncharged?
- Glycine
- Alanine
- Proline
- Valine
- Leucine
- Isoleucine
- Methionine
What Amino Acids contain positively charged R groups?
- Lysine
- Arginine
- Histidine
What Amino Acids contain negatively charged R groups?
- Aspartate
- Glutamate
Which Amino Acids have Aromatic R Groups?
- Phenylalanine
- Tyrosine
- Tryptophan
Which Amino Acids have Polar uncharged R groups?
- Serine
- Threonine
- Cysteine
- Asparagine
- Glutamine
Which amino acids are chiral? which are not?
All amino acids are chiral, except for glycine
Which wavelength is used by researchers to quantify proteins?
280 nm
What is the charge of a Zwitterion?
0
What is the Isoelectric Point?
This is the characteristic pH at which the net electric charge is ZERO
What is the formula to find pI?
pI = 0.5(pK1+pK2)
From where do you start naming and numbering peptides?
The amino terminus
What is a protein’s specific 3-D structure called?
Native Fold
What are the 4 levels of protein structure?
Primary - Amino Acid Residues
Secondary - Alpha Helix
Tertiary - Polypeptide Chain
Quaternary - Assembled Subunits
Which bond within a polypeptide chain has a partial double-bond characteristic?
The C-N bond
What are the properties of peptide bonds?
- 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
What properties of peptides are attributed to their resonance?
- 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
Is rotation allowed around the alpha-carbon bonds? What about the peptide bond?
Rotation is allowed around bonds connected to the alpha-carbon. Rotations around the peptide bond are not allowed
In order to know the 3D structure of the polypeptide, we must know what?
- The sequence of amino acids in a polypeptide
- the Psi and Phi for each alpha-carbon
When is a secondary structure generated?
when Psi and Phi remains almost the same in a segment (Important to know)
What are the two common regular arrangements of secondary structures? How are they stabilized?
- Alpha Helix
- stabilized by hydrogen bonds between nearby residues
- Beta sheets
- stabilized by hydrogen bonds between adjacent segments that may not be nearby
Which helix structure (right-handed or left-handed) is more dominant? Why?
Right-handed dominates because of minimum steric hindrance when compared to left-handed
What amino acids act as helix breakers? what about ones that favor alpha helixes?
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
What is the difference when ß sheets run in parallel vs antiparallel?
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)
When do ß turns occur? Over how many amino acids is it accomplished?
ß turns occur whenever strands in ß sheets change direction, and they are accomplished over 4 amino acids
What is a domain?
Globular unit of protein structure that is a part of a larger protein
Do domains retain their structure when separated from the rest of the protein?
They retain their structure even when separated from the rest of the protein
What is denaturation?
Loss of structural integrity with accompanying loss of activity
What can cause proteins to denature?
- heat or cold
- pH extremes
- organic solvents
- chaotropic agents: urea and guanidinium hydrochloride
What are Chaotropic Agents?
They are small molecules that perturb (distort) the 3-dimensional structure by interfering with non-covalent interactions that stabilize the protein’s conformation
What are Reducing Agents? Can their actions be reversed?
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
What is Dialysis used to do?
Selectively remove small molecules
What kind of process is protein folding? (exergonic or endergonic?)
Exergonic and therefore has a -▲G value
What molecules help prevent misfolding? How do they do this?
Chaperones help prevent misfolding, and they do this by preventing aggregations of unfolded peptides.
By what does Ion-separation separate proteins?
It separates proteins based on their charge.
What is Hydrophobic Chromatography?
A separation technique that filters based on the solubility of the protein. Proteins that are more soluble will precipitate out first.
What is salting-in and salting-out?
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.
What is Gel Filtration Chromatography?
What are some of the properties?
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
What is Affinity Chromatography?
What are some of the properties?
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)
What is Yield?
Yield - percent of the initial activity at the end of each purification step
What is Specific Activity?
Specific Activity - the total activity divided by the total amount of protein (number of total enzyme units per mg of total proteins)
What are the properties of SDS PAGE?
- Unparalleled Resolution
- Fast
- Denatures proteins
- Samples are treated with a reducing agent (DTT or ß-mercaptoethanol)
