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

aliphatic

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

Name, 3 letter abbreviation and Classification

special features?

Arginine

Basic and charged, 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 = deprotonated

1 = protonated

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?

pH will increase

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

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

it will decrease because the H from the carboxyl side chain will be given up.

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

A molecule containing an even # of positive and negative charged groups. At pH 7 a generic aa is a zwitterion.

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

negative and pH 14 an d positive at pH 1

In all cases, a protein’s function is determined

by its _______.

Structure

What do proteins do? Name 5 functions

1. Structure

2. Transport

3. catalysis

4. movement/contraction

5. communication

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

pH is a measure of the concentration of H+ in solution while pKa measures the strength of an acid

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?

The protonated form

When pH = pKa, what is true?

The concentration of HA = the Concentration of A-

What are the pHs of the following groups?

• SH-

• OH-

• COOH

• NH3

SH = 9

NH3+ = 9.5

COOH = 2 to 5

OH = highly variable

what is a chiral carbon? what are sterioisomers?

a carbon with 4 different groups attached. Stereoisomers = molecules with the same chemical formula and connectivity, but with different 3D arrangments of atoms

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

the alpha carbon

How are amino acids classified vs what are their properties?

Classification is based on Side chain but properties can be different.

What will happen to the pH of water (pH 7) if aspartate is added to it?

nothing

What are the characteristics of a peptide bond?

Rigid, planar, partial double bonds, polar

it is an amide/covalent bond, abs UV at 230 nm, neutral

made in a condensation rxn 

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

It has partial double bond character due to electron resonance

The bonds to the alpha carbon can rotate (Ca-N and C-Ca). However, they are limited by steric hindrance..

What is the directionality of polypeptides and peptide bonds?

polypeptides run N to C and Peptide bonds are C to N

Define Polypeptide and Protein

A polypeptide is a long chain of amino acids, usually natural

A protein is one or more polypeptides with biological function

What is van der Waals contact in the context of an alpha helix

The atoms on the inside of an alpha helix are said to be in van der Waals contact since they are closely packed to minimize empty space. 

Differentiate globular and fibrous tertiary structure

Fibrous = elongated filament, basically insoluble in aqueous solutions

Globular = hydrophobic interior, and normally hydrophilic side chains at the surface. soluble and compact

Define domains and motifs. Give an example of a motif.

A domain is segment of a polypeptide that folds into a single structural unit with a hydrophobic interior. It can often have independent function.

Motifs = a short region of a polypeptide with a recognisable 3D shape. It usually involves a common arrangement of secondary structures. Specific conserved function.

Example = The zinc finger motif

why are b-sheets not sequential? do antiparallel or parallel sheets have longer loops?

Strands are linked by loops which breaks up the sequence of amino acids involved in the sheet.

Parallel sheets have longer loops.

Define secondary structure. What about tertiary?

2 = the local arrangement/folding of a polypeptide backbone

3 = the arrangement of all the atoms in a single polypeptide

• R groups and backbone

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

they can typically be found at the surface but may be found in the interior if they are taking part in a hydrogen bond or a salt bridge (charged only)

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

Sequence of amino acid residues and the force is peptide bonds

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?

steric hindrance from bulky R groups and Carbonyl oxygens

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?

Regular structures form independently of the amino acid residues in the polypeptide. They include alpha helices and beta pleated sheets.

Irregular structure includes loops which do depend on the amino acid residues present.

What is the major stabilizing force in secondary structure?

Hydrogen bonds between atoms in the peptide bond

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

The major stabilising force is The Hydrophobic effect / hydrophobic interactions

Supplementary =

1. H bonds (between R groups and unused backbone groups)

2. Salt bridges (charged aminos and N and C terminals)

3. Disulphide bridges

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

A carbonyl group H-bonds with a N-H group 4 residues downstream.

the 1st 4 carbonyls at the C-terminus cannot Hydrogen bond since there are no N-H groups far enough downstream.

the 1st 4 N-H at the N-terminus cannot Hydrogen bond since there are no carbonyls far enough upstream.

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

For a membrane protein and for polypeptides with quaternary struture.

Why do loops tend to be located at the surface and regular structure in the center?

Residues in loops are more available for H bonding while in helices and sheets, many of the groups that can hydrogen bond are already doing so.