Amino acids and Proteins

Name, 3 letter abbreviation and Classification

special features?

Glycine. Gly. Polar (up for debate)

Achiral and very small

Which amino acid may be found at tight turns in a protein due to its flexibility?

Glycine

Name, 3 letter abbreviation and Classification

special features?

Alanine. Ala. Non-polar/hydrophobic

Would alanine or valine be more hydrophobic?

valine since it has a larger non-polar side chain 

Name, 3 letter abbreviation and Classification

special features?

Proline. Pro. Non-polar/Hydrophobic.

Cyclic but not aromatic.

Is the amino group primary, secondary or tertiary in proline?

secondary

Name, 3 letter abbreviation and Classification

special features?

Valine. Val, Non-polar/hydrophobic

What are aliphatic amino side chains?

Aliphatic amino acids are non-polar and hydrophobic. contain only carbon and hydrogen.

Name, 3 letter abbreviation and Classification

special features?

Leucine. Leu. Hydrophobic/Non-polar

Name, 3 letter abbreviation and Classification

special features?

Isoleucine. Ile. Hydrophobic/Non-polar

2 chiral carbons!

What are all the aromatic aminos?

Tryptophan, Histidine, Tyrosine, Phenylaline

Which 2 aminos have >1 chiral carbon

isoleucine and threonine

Name, 3 letter abbreviation and Classification

special features?

Methionine. Met. Hydrophobic

even though sulfur is present (thioether), it is a non-polar side chain.

Unlikely to form H bonds.

Name, 3 letter abbreviation and Classification

special features?

Phenylalanine. Phe. Hydrophobic

Aromatic R group: absorbs UV very weakly at 280nm

Name, 3 letter abbreviation and Classification

special features?

Tyrosine. Tyr. Polar.

Can form H-bonds but also participate in hydrophobic interactions!!

Absorbs UV at 280nm

due to OH group, it can be phosphorylated

pKa = 10.5 therefore has H under biological conditions (negative charge at pH 14)

Which 7 aminos have ionizable R groups?

Glutamate, Aspartate, Lysine, Arginine, Tyrosine, Histidine, Cytsteine

Name, 3 letter abbreviation and Classification

special features?

Tryptophan. Trp. Hydrophobic.

Biggest and bulkiest side chain. Hydrophobic but can form an H bond.

Heterocyclic and Absorbs UV Strongly at 280nm

Name, 3 letter abbreviation and Classification

special features?

Serine. Ser. Polar

Can be phosphorylated due to OH group.

Participates in H bonding.

Name, 3 letter abbreviation and Classification

special features?

Threonine. Thr. Polar

2 chiral carbons!

Can be phosphorylated

H-bonds as donor and acceptor

Name, 3 letter abbreviation and Classification

special features?

Cysteine. Cys. Polar.

Can form disulphide bridges/bonds with other Cys.

Can form H-bonds but doesn't act as an acceptor

pKa = 8.5 can give up H at pH 14

What are the necessary conditions to form a disulphide bridge and where can this occur?

1. Two Cys residues must be close enough to form a bond

2. Oxidizing environment such as the mitochondria or the extracellular fluid

If S-S bonds are formed in an oxidizing environment, what breaks a disulphide bond?

A reducing env.

What is Cystine? Is it polar or hydrophobic?

Two cysteine side chains interacting in a disulphide bond. 

Relatively hydrophobic (S-S bond not S-H)

Name, 3 letter abbreviation and Classification

special features?

Asparagine. Asn. Polar.

Amide group and forms hydrogen bonds (O acceptor, N donor)

Name, 3 letter abbreviation and Classification

special features?

Glutamine. Gln. Polar

Amide group, forms H-bonds

Name, 3 letter abbreviation and Classification

special features?

Lysine. Lys. Charged.

Positive charge from NH3 at pH 7

pKa = 10.5 therefore neutral/loses H at pH 14. Basic amino acid

Long CH chain is hydrophobic?

Name, 3 letter abbreviation and Classification

special features?

Arginine

Basic, but never deprotonated under biological conditions

pKa = 12.5

H bond donor only!

Name, 3 letter abbreviation and Classification

special features?

Histidine. His. Polar

Aromatic - abs weakly at 280nm

pKa = 6 therefore neutral at 7 but becomes protonated at pH 1 with a positive charge!

Histidine can act as an acid or a base in reactions and also participates in H-bonding. 

At pH 10 and 1 is histidine protonated or not? what is its pKa

pKa = 6 therefore;

10 = no

1 = yes

Name, 3 letter abbreviation and Classification

special features?

Aspartate. Asp. Charged

acidic amino acid. pKa = 4.0

Negative charge at pH = 7 but called aspartic acid at pH 1 since it becomes protonated

Negatively Name, 3 letter abbreviation and Classification

special features?

Glutamate. Glu. Charged. 

pKa = 4: Negative at pH 7 

acidic amino acid

called glutamic acid at pH 1 since becomes protonated

What will happen to the pH of water (pH 7)

if the fully deprotonated form of lysine is

dissolved in it?

what is a zwitterion? at what pH is a free generic amino acid a zwitterion?

what pH does a free generic amino acid have a positive charge? Negative charge?

In all cases, a protein’s function is determined

by its _______.

Structure

What do proteins do? Name 5 functions

What is pH and what is pKa? What do their high and low values mean?

At a pH above pKa, the acid exists predominately as?

The conjugate base/deprotonated form

At a pH below pKa, the acid exists predominately as?

When pH = pKa, what is true?

What are the pHs of the following groups?

• SH-

• OH-

• COOH

• NH3

what is a chiral carbon? what are sterioisomers?

What is the major chiral carbon in 19/20 amino acids?

How are amino acids classified vs what are their properties?

What will happen to the pH of water (pH 7)

if the fully protonated form of lysine is dissolved in it?

What will happen to the pH of water (pH 7) if

aspartate is dissolved in it?

What are the characteristics of a peptide bond?

Why cant a peptide bond rotate? Which bonds in the backbone can rotate?

What is the directionality of polypeptides and peptide bonds?

Where can polar and charged side chains be found in a protein?

what is the primary structure of proteins? What is the major stabilising force?

What atoms make up the backbone of a polypeptide?

The backbone of a polypeptide includes the

alpha carbon atoms and those atoms involved in the peptide bond

What limits rotation of the backbone?

What determines the 3D structure of a protein?

Primary structure determines the 3-D structure. Specifically where the hydrophobic amino acid residues are located influences folding. 

Can the alpha carbon participate in H-bonding?

No

what is regular vs irregular secondary structure?

What is the major stabilizing force in secondary structure?

What drives the formation of tertiary structure/what is the major stabilising force? What are the supplemental forces?

What is the H bonding pattern in an alpha helix? Which groups cannot H-bond?

In what 2 scenarios would hydrophobic side chains be found on the surface of a protein?