Amino acids and proteins: Primary structure

Approximately how many genes in our genome? Is it static or dynamic?

21 000 genes and static

How many chemically distinct proteins in our proteome? Is it static or dynamic?

More than 1 million and dynamic since lots of modifications can occur

What are many diseases due to? What is an example?

They are due to proteins having one incorrect amino acid such as sickle cell anemia which has a single AA mutation in hemoglobin (glutamate to valine)

What are the four different levels of protein structure?

1. Primary structure

2. Secondary structure

3. Tertiary structure

4. Quaternary structure

What is primary structure and secondary structure?

Primary: It is the sequence of amino acids

Secondary: It is localized folding

What is tertiary structure and quaternary structure?

Tertiary is complete fold and quaternary is multiple proteins coming together to make one functional protein

What are the common features of amino acids?

1. Have an amine group

2. Have a carboxylic group

3. Have a central carbon known as alpha carbon where an R group is attached and a hydrogen

What are all proteins linear polymers of?

alpha amino acids (residues in proteins)

What makes each of the 20 amino acids distinct from one another? What are the two main amino acid categories?

Each have a different R group. Two main categories are non-polar (hydrophobic) and polar (neutral or charged)

At neutral pH, what form would the amino acid be in?

The zwitterionic form where the amino group is protonated and the carboxyl group is deprotonated

Are most amino acids chiral?

Yes they are except for glycine which is achrial

Are most amino acids in the L or D form? Are most amino acids R or S?

L configuration as D amino acids are less prevalent (seen in bacteria in peptidoglycan). Most amino acids are S.

Due to entropy, what happens to amino acids in proteins in the L-form?

They begin to slowly racemize over time (convert to their D forms)

What four amino acids have alipathic side chains and are hydrophobic?

Ala, Val, Leu, and Ile

What is alanine often chosen for?

It is chosen as a replacement to determine amino acid function using site-directed mutagenesis

Where are hydrophobic amino acids found? Why?

In the protein interior because they need to pack together well and don’t like to mix with water/aqueous environment

What hydrophobic amino acids contains sulfur? What can sulfur be oxidized to?

Methionine and it can be oxidized to S double bonded to O or O double bonded to S double bonded to O

What is the largest amino acid? What is a property of it?

Tryptophan and its UV absorbance 280 nm can be used to measure protein concentration (can monitor protein purification)

What does phenylalanine resemble?

Alanine but has a phenyl group on it

What is the only imino acid? What is a property of it? Can it hydrogen bond?

Proline and its side chain is connected to an NH group that forces a kink into polypeptide chains. No

What is the simplest amino acid?

Glycine

What is a property of asparagine (Ash) and glutamine (Gln)? Are they polar, charged, or non-polar?

They are polar amino acids and are the corresponding uncharged amides of the acidic amino acids Asp and Glu. They can also be H bond donors or acceptors

What type of side chain does histidine have?

It has an imidazole side chain that can be positively charged at acidic pH

What three amino acids have hydroxyl groups? What can they act like?

Serine, threonine, and tyrosine. They act as nucleophiles in biochemical reactions

What can the hydroxyl groups of tyrosine, serine, and threonine be covalently attached to?

Other groups such as reversible phosphorylation to change protein function

What is tyrosine a derivative of? What are they both precursors of?

Derivative of phenylalanine and both are precursors of amino acid neurotransmitters

What is a second amino acid that absorbs light at 280 nm?

Tyrosine and can measure protein concentration through absorption of light at 280 nm

What two amino acids have two chiral centres?

1. Isoleucine

2. Theronine

What can cysteine residues form? How?

Disulfide bonds. The sulfhydryl (SH) group of Cys can be oxidized to form a disulfide bond (S-S) with another cys

Is intracellular environment reducing or oxidizing? Extraceullular environment?

Intra: Reducing (SH)

Extra: Oxidizing (S-S)