Biochem- Amino Acids

What is a semi-essential amino acid? Which one is the only amino acid with this characteristic?

A semi-essential amino acid is one that is only essential in periods of positive nitrogen balance. the only on is Arginine

Which amino acids are coded by codons in the mRNA?

All standard amino acids

Why is proline called an Imino acid?

Because its amino terminus is involved in ring formation.

Why are amino acids classified according to their side chains?

Because the side chain give the amino acid its chemical properties

Why are Arginine and lysine referred to as the basic amino acids?

Because they have an extra amino group (NH3+) leading to a positive charge under physiologic pH (basic = extra positive)

Which protein is made up of high amount of glycine?

Collagen is 33% glycine

What is the difference between the sulfur group in methionine and cysteine?

Cysteine has a "free" Sulfur atom which can therefore participate in disulfide bond formation

Which amino acid activated NMDA receptors in the brain?

D-serine

What is the only non-chiral amino acid?

Glycine

Which type of amino acids participate in o-linked glycosylation and other post-translational modifications?

Hydroxyl containing amino acids

What special property does having OH in the side chain confer to the amino acid?

In serine, threonine and tyrosine. OH groups are the sites for post-translational modifications such as phosphorylation and glycosylation

Why is histidine a good buffer amino acid?

Its structure contains an imidiazole ring which allows it to accept or donate protons depending on the local pH but under physiological pH (~7.4) it has a positive charge (so sometimes its classified as a basic amino acid)

What is arginine the precursor of?

Nitric oxide

Can the amino and carboxy groups undergo chemical reactions?

No, they are only available for peptide bond formation

What type of bonds occur in primary, secondary and tertiary structures?

Primary = peptide, secondary = hydrogen, tertiary = disulfide bonds

Which amino acid is the "helix breaker"? Why?

Proline, Because it has a very rigid ring structure and it can be accommodated in the alpha-helices breaking the helical structure of a protein.

What amino acids interrupts alpha helices by introducing bends? Why?

Proline, because of its side chain being too rigid to be accommodated in the helix.

What is methionine a precursor for?

SAM (S-adenosyl methionine) which is a methyl donor in the synthesis of creatine, epinephrine and other reactions.

What are the aromatic amino acids?

The amino acids that have benzene (aromatic) rings in the side chains. These are Phenylalanine, tyrosine and tryptophan.

What are essential amino acids?

The ones that cannot be synthesized by the body and need to be included in the diet

What are Asparagine and Glutamine derivates of? How did they become neutral?

They are derivatives of Aspartic and Glutamic acid and they became neutral due to the presence of an extra NH2 group which helps to stabilize the overall negative charge of their acid precursors

What are the three branched chain amino acids?

Valine, Leucine and Isoleucine (VIL)

What does tyrosine metabolism deficiency cause?

alkaptonuria and albinism

Which is the rate limiting enzyme in the metabolism of branched chain amino acids? Deficiency in this enzyme leads to what disease?

branched chain alpha-keto acid dehydrogenase complex, deficiency leads to maple syrup urine disease (can no longer degrade the branched chain amino acids leading to their buildup and their toxic byproducts in the blood and urine)

Which group of amino acids is used for treatment of patients who require total parenteral nutrition? Why?

branched chain amino acids, because these constitute 35% of muscle proteins and 40% of the preformed essential amino acids for humans

What is the function of NAC (N-acetyl cysteine)?

breaks S-S bonds, can be used in cough syrup to break mucus (liquifying it), helps cystic fibrosis patients to clear mucus, antidote in cases of acetaminophen overdose

What disease results from the defective transport of cysteine?

cystinuria

What chemical reaction occurs in the formation of a peptide bond?

dehydration reaction

What does the free sulfur participate in?

disulfide bond formation, formation of zinc fingers, and works as an antioxidant

What is tyrosine a precursor for?

dopamine, norepinephrine, epinephrine, melanin, T3 and T4

What is the special function of glutamic acid?

excitatory neurotransmitter (via NMDA receptors)

What are some functions of glycine?

is the precursor of heme, precursor of the purine ring (C4, C5 and N7), its an inhibitory neurotransmitter in the CNS

What two amino acids have sulfur in their side chain and how can you differentiate between the two?

methionine and cysteine. The main difference is that Sulfur is free in cysteine

What type of bonds do amino and carboxyl groups form?

peptide bonds (covalent = strongest bonds)

What is the enzyme that converts phenylalanine to tyrosine? What disease occurs in case of deficiency?

phenylalanine hydroxylase, deficiency leads to PKU (Cant metabolize phenylalanine)

At what pH do COOH and NH2 exist in ionized form? What are their ionized forms?

physiologic pH (~7.4), COO- and NH3+

What are some situations in which the body has positive nitrogen balance?

pregnancy, growth, recovery from surgery or injury, recovery from negative balance conditions

What is tryptophan a precursor for?

serotonin (neurotransmitter), melatonin (neurohormone) and niacin (vitamin)

What part of the amino acid structure dictates its function?

the side chain (R group)

What are non-polar amino acids?

the side chains of these amino acids don't have charge under any pH.

What are some special properties of the side chains of non-polar amino acids?

their side chains are "oily" and promote hydrophobic interactions, are usually found clustered in the inside of a globular proteins and are found in the membrane spanning regions of transmembrane proteins.

Why are aspartic acid and glutamic acid acidic amino acids?

they have an extra carboxy group which gives them an overall negative charge under physiological pH (acidic = extra negative)

What is phenylalanine a precursor for?

tyrosine, dopamine, norepinephrine, epinephrine, phenyletylamine, thyroxine, and melanin

What is negative nitrogen balance?

when your nitrogen output is higher than the input. This happens in protein malnutrition, dietary deficiency of one of the essential amino acids, starvation, uncontrolled diabetes and infection