Lecture 6: proteins Flashcards
What are the two types of isomers in amino acids?
- L isomer: left handed turn
- D isomer: right handed turn
All amino acids in proteins are _____isomers?
L
What is the isoelectric point?
The pH at which the amino acid carries a net charge of zero
How do you calculate the isoelectric point (pI)?
- If the amino acid does not have an ionisable R group:
pI = the average of the pKa of the amino and carboxylic group - If the amino acid has an ionisable R group:
- locate the pKa for which the amino acid has a net charge of +1 and -1
- Take the average of the 2 pKa values
What are the 4 classifications of amino acids?
- Non polar aliphatic
- Aromatic
- Uncharged polar
- Charged polar
Which type of amino acid has a UV absorbing property?
Aromatic
What are the intermolecular forces that can be formed between R groups of amino acids?
- Hydrogen bonds
- Hydrophobic interactions
- Disulfide bonds
- Ionic bonds
Which proteogenic amino acid is not coded by standard codons but can be incorporated into the polypeptide though a stop codon?
Selenocysteine
(stop codon: UGA)
What makes amino acids non-proteogenic?
There is no codon coding for them
A polypeptide made up of ____ or more amino acids is called a protein.
50
What are the types of secondary structures?
- Alpha helix
- Beta sheet
- Beta turn
What is the pattern of intermolecular forces found in alpha helixes?
Hydrogen bonding between carbonyl group of an amino acid and amino group of an amino acid 4 residues away from it.
Is the alpha helix right or left handed?
right
Which amino acids tend to not form alpha helixes and why?
- Glycine: it is too flexible, alpha helix needs rigidity
- Proline: structure too short, alpha helix will break
How are hydrogen bonds formed in the beta sheet?
Formed across adjacent segments of the polypeptide chain, in right angles to the direction of the polypeptide strands
What is a beta turn?
It is a segment of the polypetide forming a beta sheet that abruptly reverses the direction
How many amino acids is a beta turn made out of?
4
Where does protein folding most commonly occur in mammalian cells?
Endoplasmic reticulum
What are factors that cause protein unfolding?
- pH changes
- High temperatures
- Organic solvents
- Denaturing agents
What are the types of post translational modifications to proteins?
- Phosphorylation
- Carboxylation
- Glycosylation
4.Conjugation with lipids - Hydroxylation
- Oxidation
- Hydrolysis
Which amino acid is subjected to carboxylation?
glutamate
Where does N linked glycosylation occur, and which residues are glycosylated?
- RER and Golgi apparatus
- N atom in side chain of asparagine residues
Where does O linked glycosylation occur, and which residues are glycosylated?
- Golgi apparatus
- O atom in side chains of Serine and Threonine residues
How are lipids conjugated to proteins?
Polar group of the lipid is attached to:
1. N terminal
2. Cysteine reside through a thioester linkage
On which amino acid does hydroxylation occur?
Proline
On which amino acid does oxidation occur and why is it important?
- Cysteine
- Important as it allows for the formation of the disulfide bond between 2 cysteine residues.
What is the function of hydrolysis?
- Convert pro-active proteins into active form by removal of a certain peptide fragment
- Degrade proteins into amino acids/peptides
What kind of amino acids can be phosphorylated?
Serine, threorine and tyrosine
because they have hydroxyl groups
What are the aromatic amino acids?
tyrosine, phenylalanine, typtophan
What are the aliphatic non polar amino acids?
glycine, valine, alanine, leucine, isoleucine
What are the hydroxyl containing aliphatic amino acids?
serine, threorine
What are the acidic amino acids?
aspartic acid, glutamic acid
What are the basic amino acids?
arginine, lysine, histidine
What are the amino acids containing amide groups?
asparagine, glutamine
What are the sulfur containing amino acids?
methionine, cysteine
