sakai-amino acids

Question 1

In the structure of -amino acids, does the -carbon represent carbon #1?

Answer 1

Alpha is the first letter of the alphabet, but the -carbon does not represent carbon #1 of amino acids.

Carbon #1 of amino acids is the carbon of the -COOH (-carboxyl) group.
With that, the -carbon is carbon #2.

The name amino acid indicates, that amino acids have an acidic group and an amino group. The - amino acids have an acidic group and an amino group both linked to their  carbon. The other two positions are held by hydrogen and a specific R-group.

Question 2

Which amino acid has an -carboxyl group and also a -carboxyl group?

Answer 2

The amino acid glutamate (Glu)

Question 3

In graphs you see structural features of amino acids shown in their fully protonated form. Is that the form that you find at physiological pH? Explain and give a range for the pKa -carboxyl-groups and pKa - amino groups

Answer 3

At physiological pH we find the -carboxyl group with a negative charge.
In general, the pKa for the -carboxyl group is about pKa 2, and the pKa for the amino groups is pKa 9-10.

The pKa is the pH where half of the group is charged and half uncharged. That means, the -carboxyl group is 50% charged at pH 2. At physiological pH of 7-7.4, the carboxyl group is negatively charged.

Question 4

Which amino acids of the 20 standard amino acids can contain 3 pKas? Explain the general concept!

Answer 4

Amino acids that contain a charged side chain contain three pKas, the pKa -carboxyl group, the pKa -amino group, and the pKa of the respective side chain

Question 5

Name the amino acids with a negatively charged side chain under physiological conditions! Name the amino acids with a positively charged side chain at pH 7!

Answer 5

The amino acids with a negatively charged side chains are glutamate and aspartate. The pKa for the negatively charged side chains are about pK4.

The amino acids with a positively charged side chains are lysine and arginine and histidine.

The His side chains have in free solution a pKa 6 and are not totally charged at physiological pH. Lys and Arg have a pKa larger than 10 for their side chains and are positively charged at pH7.

Question 6

Which amino acids are derivatives of glutamate (Glu) and aspartate (Asp) and contain polar uncharged side chains, respectively?

Answer 6

Glutamine (Gln) and asparagine (Asn)

Question 7

At the isoelectric point, do we find no charges in the molecule? Explain.

Answer 7

At the isoelectric point, both negative and positive charges are present but equal each other. For example, alanine contains both negative and positive charges in its structure, but the overall charge is zero at the isoelectric point.

Question 8

Why is it important to buffer a possible drop of pH in RBC especially in tissue capillaries? Which protein found in RBC contains many histidine residues and is able to prevent a dramatic drop of pH?

Answer 8

Carbon dioxide taken up from the tissue capillaries is substrate for the enzyme carbonic anhydrase in RBC which forms carbonic acid. This newly formed acid generates protons which need to be buffered, otherwise the dramatic drop of pH would destroy the RBC.

Hemoglobin is a histidine-rich protein found only in RBC. The side chains reaching outside of the -helices are able to buffer a possible drop of pH as the pKa of the side chains of histidine residues in hemoglobin are about 6-7.

The buffer capacity is highest at the pKa.

Question 9

Three unmodified amino acids contain a hydroxyl group in their side chain. Which one is also an aromatic amino acid with uncharged polar side chain? Name the two others and discuss possible function of the hydroxyl groups.

Answer 9

The amino acids containing a hydroxyl group are serine, threonine and tyrosine.
The amino acid which has an aromatic ring with a hydroxyl group is tyrosine.

  Serine and threonine residues are used for phosphorylation or glycosylation.

Question 10

In patients with Phenylketonuria, the hydroxylation of phenylalanine is defective. Which amino acid cannot be formed?

Answer 10

Hydroxylation of phenylalanine leads to tyrosine. Tyrosine is a non-essential
amino acid in healthy individuals, but becomes dietary essential in patients with
Phenylketonuria.

Question 11

In Maple Syrup Urine disease, the eventual degradation of the branched-chain amino acids is defective.
Into which group do branched-chain amino acids belong, amino acids with nonpolar, polar uncharged, or charged side chains?
Name the three branched-chain amino acids.

Answer 11

Branched-chain amino acids are grouped as amino acids with nonpolar side
chains. The branched-chain amino acids are valine (Val), leucine (Leu) and
isoleucine (Ile)

Question 12

Alanine and methionine both contain a methyl group. What is special in the methionine structure that allows methionine in its activated form to serve as the major methyl donor in metabolism?

Answer 12

Methionine contains sulfur and the methyl group is linked to it in the side chain.

The activated methionine is S-adenosyl-methionine (SAM) which is the major 	methyl-group donor for many reactions.

Question 13

Which amino acid side chain contains a sulfhydryl group that can form a disulfide bond with another amino acid residue of the same kind? Is a disulfide bond a covalent or a noncovalent bond? How many disulfide bonds are found in the insulin molecule?

Answer 13

Cysteine contains a sulfhydryl group in the side chain. Together with a sulfhydryl group of another Cys residue, a disulfide bond can be formed

  This is found often in extracellular proteins, like for example albumin. A disulfide 
  bond is a covalent bond!

  Insulin contains three disulfide bonds, two are linking the A and B polypeptide 
  chains together via disulfide bridges and one is found between cysteines of the A 
  chain. This leads to a structure that is recognized by the insulin receptor.

[in the primary sequence, the two cysteine residues in the A chain involved with the inter-chain disulfide bond or the intra-chain disulfide bond are following each other. The correct formation of the disulfide bonds is facilitated by the C-peptide which allows proper folding before the A and B chains are separated]

Question 14

What happens to the -amino acid or a modified -amino acid when it is used to form biological active amines?

Answer 14

Biological active amines are formed by decarboxylation of the carboxyl group.

[this process needs pyridoxal phosphate (PLP from vitamin B6) as cofactor and patients with this vitamin deficiency show less formation of biological active amines. PLP is needed for formation e.g. of histamine, GABA, serotonin]

Question 15

What is GABA? How is it formed? Explain the name.

Answer 15

GABA is an inhibitory neurotransmitter. It is formed in one step from glutamate
by decarboxylation of the carboxyl group. The carboxyl group in the side chain
is now the only carboxyl group in the molecule. With that the carbon of the
former -carboxyl group of glutamate becomes carbon #1 in GABA.

 The renaming following organic chemistry results in -aminobutyric acid, GABA

Question 16

How is histamine formed? Which responses or functions are mediated by histamine?

Answer 16

Histamine is formed in one step from histidine by decarboxylation.
This physiological active amine leads to gastric acid secretion.
Histamine mediates allergic and inflammatory responses and is a strong
vasodilator.

Question 17

Tryptophan is first hydroxylated and then decarboxylated to the physiological active amine serotonin. Which of the two reactions needs PLP? What is the biomedical importance of serotonin?

Answer 17

The decarboxylation of hydroxytryptophan to serotonin needs PLP.

Serotonin is needed for the regulation of sleep, temperature and blood pressure.
It is involved in pain perception and causes a feeling of well-being.
Serotonin blood levels are related to mood disorders.

[the hydroxylation of tryptophan to hydroxytryptophan needs tetrahydro-biopterin which can be synthesized in humans.]

Question 18

Catecholamines (dopamine, norepinephrine and epinephrine) have in common that they are physiological active amines and contain a catechol ring system in their structure.
Their synthesis needs tyrosine and the carboxyl group is decarboxylated. What is the main function of dopamine and norepinephrine?

Answer 18

Dopamine and norepinephrine function mainly as neurotransmitters in the brain
and the autonomic nervous system or they are intermediates in the synthesis of
epinephrine.

  Norepinephrine can also act as hormone when it is released together with 
  epinephrine from the adrenal medulla.

 [Norepinephrine is methylated to epinephrine using SAM  in the adrenal medulla]

Question 19

Dopamine is formed from DOPA. Sometimes the drug Levo-DOPA is given to patients. Why is it given as L-DOPA, meaning in its optical active form as L-amino acid? What does the abbreviation DOPA stand for?

Answer 19

The L-form of the amino acid dihydroxy-phenylalanine (DOPA) needs to be
given, as in humans the amino acids found are in the L-configuration which is
recognized by human enzymes.

  DOPA is formed by hydroxylation of L-tyrosine. Tyrosine is a hydroxylated 
  phenylalanine, and instead of hydroxy-tyrosine, the name refers to phenylalanine 
  and is named dihydroxy-phenylalanine.

Question 20

Which catecholamine acts mainly as hormone and is released from the adrenal medulla into the blood?

Answer 20

Epinephrine is mainly released from the adrenal medulla. Synthesis started with
tyrosine and forms dopamine and norepinephrine as intermediates.

  Epinephrine acts as flight and fight hormone, it leads to increase of blood glucose 
  and heart rate, and also leads to degradation of triacylglycerols in fat cells.

Question 21

Which parts of amino acids are normally involved with forming a peptide bond?

Answer 21

Normally, the -carboxyl group of amino acid #1 is forming a peptide bond with the -amino group of amino acid #2

Question 22

Why is the peptide bond rigid and planar? Explain.

Answer 22

The peptide bond has about 40% double-bond character. The polypeptide chain can rotate around the -carbon but cannot bend in the peptide bond.

Question 23

Name three (fibrous) structural proteins!

Answer 23

Collagen, elastin and keratin.

[Collagen is the most abundant fibrous protein and it has structural functions in bones and tendons. Together with elastin it is found in the skin and the extracellular matrix. Elastin is important for blood vessels.
Keratin is found in nails and hair and the outer layer of the skin.]

Question 24

Is albumin a fibrous or a globular protein? What is its function in addition to regulate osmolality? Would you expect disulfide bonds in its structure? Explain.

Answer 24

Albumin is a globular protein. It functions as transport protein in blood. One would expect disulfide bonds in its structure. Extracellular globular proteins are often stabilized by disulfide bonds.

Question 25

For eventual protein synthesis, is the process of translation performed before the process of transcription? Explain.

Answer 25

Protein synthesis involves first transcription and then the process of translation.
The information of DNA is transcribed to RNA which can leave the nucleus. Then the “nucleotide language” is translated to the “language” of amino acid sequence.

Question 26

What is the advantage to synthesize a larger precursor protein for eventual formation of short peptide hormones?

Answer 26

Peptide hormones are very powerful. It is necessary that they are only formed when needed and contain the correct amino acid sequence. The process of synthesis of a larger protein precursor is under genetic control and prevents formation of a faulty peptide hormone.

Question 27

Do all proteins have a primary and secondary structure? Do all proteins have a quaternary structure? Explain and give examples. Is hemoglobin formed by monomeric or multimeric proteins?

Answer 27

All proteins have a primary structure which is the amino acid sequence which also determines the secondary structure and tertiary structure.

Not all proteins have a quaternary structure. For example, myoglobin has only a tertiary structure whereas hemoglobin has a quaternary structure.
Hemoglobin is formed by multimeric proteins (dimer of  and - globin chains)

Question 28

Which bonds or forces are stronger, covalent bonds or Van der Waals forces? Compare to hydrogen bonds, ionic bonds and hydrophobic forces and give in general the ranges in kcal/mol.

Answer 28

Covalent bonds are stronger than Van der Waals forces which are very weak noncovalent bonds. Hydrogen bonds, ionic bonds and hydrophobic forces (bonds) are noncovalent bonds and they are much weaker than covalent bonds but they are also stronger than Van der Waals forces.

[General ranges are: covalent bonds >50 kcal/mol, ionic bonds 1-20 kcal/mol, hydrogen bonds 1-7 kcal/mol, hydrophobic forces 2-3 kcal/mol and the very weak van der Waal forces <1 kcal/mol.]

Question 29

Which amino acid side chains can form an ionic bond with a lysine residue?

Answer 29

An ionic bond with the positively charged side chain of lysine can be formed with the negatively charged side chain of aspartate or of glutamate

Question 30

Which weak noncovalent bonds are formed between side-chains of branched-chain amino acids? Would you find those side chains mainly inside of a globular protein or would they be directed to the outside water phase?

Answer 30

Hydrophobic forces (bonds) are formed between side-chains of branched-chain amino acids. These side chains are nonpolar and they would be normally mainly found inside of a globular protein.

Question 31

Insulin contains an A-chain and a B-chain. How are these polypeptide chains linked to each other? The A-chain has also an intra-chain bond. Is this bond a hydrogen bond or a disulfide bond?

Answer 31

The insulin A- and B-chains are linked to each other via two disulfide bonds.
The A-chain has also an intra-chain disulfide bond which leads to a specific configuration needed for the insulin receptor.

[inactivation of insulin in the liver cleaves the two interchain disulfide bonds]

Question 32

The secondary structures are stabilized by hydrogen bonds. Which part of the polypeptide chain is involved? Are hydrogen bonds covalent bonds?

Answer 32

Hydrogen bonds stabilizing the secondary structures are formed between peptide bonds. –C=O and –NH are involved. Hydrogen bonds are noncovalent bonds.

Question 33

Describe the direction of R-side chains for the -helix. Which amino acid side chains would interrupt the -helix when they would be 3-4 residues apart of glutamate residues?
Describe the concept and give an example. Name other side chains of amino acids that can disrupt the -helix.

Answer 33

The R-side chains of the -helix are directed to the outside of the helix.

Glutamate residues are negatively charged, and any amino acid residue with a charged side chain 3-4 residues apart would disrupt the -helix.
So it could be by Asp or Glu, or also by Lys, Arg and His.

Also, in general, bulky side chains 3-4 residues apart in the primary structure do not allow formation of the helix as they are too close above each other.

Proline (imino acid) and glycine (smallest side chain) also disrupt the -helix.

Question 34

How can proline residues in the primary structure affect the respective secondary structure of the helix?

Answer 34

The peptide bond formed with proline leads to a “kink” in the polypeptide chain. This disrupts and ends the secondary structure of the -helix.

[proline is not an amino acid but actually an imino acid. It is still generally grouped as amino acid. Proline is found in high concentration in collagen, where the “kink” formation is of advantage in order to wind three “kinked” strands around each other. A triple helix is formed which is NOT an -helix.]

Question 35

Describe and compare the structures of the -helix and of the -pleated sheet. The structures are highly specifically described, not any helix is an -helix.

Answer 35

helix:
one polypeptide chain wound around an imaginary axis,
hydrogen bonds formed from peptide bonds in the direction of the axis,
amino acid side chains oriented to the outside of the spiral,
it is a very special helix right handed with 3.6 residues per turn

-pleated sheet:
at least two polypeptide chains linked to each other via hydrogen bonds formed with peptide bonds of the other chain, (it can also be the same chain after a bend)
side chains are alternately above and below the plane,
pleated structure due to the rigid peptide bonds,
strands can run parallel or anti parallel.

[In 1951, the -helix and the -sheet were correctly proposes as forming the protein secondary structures. This work of Linus Pauling, Robert Corey and Herman Branson was based on the knowledge of the structures of amino acids and the planar peptide bond. Linus Pauling received the Nobel Prize in Chemistry 1954 and also the Peace Nobel Prize in 1952.]

Question 36

Name two diseases where an abnormal protein is not degraded but accumulates and damages the brain.

Answer 36

Alzheimer’s disease and Prion disease (transmissible spongiform encelphalopathy, Creutzfeld-Jacob disease, scrapie and mad-cow disease).

Question 37

Does Prion disease show a change from an -helix to a -pleated sheet or is it the other way round? Is the amino acid sequence of the abnormal PrPsc different from the amino acid sequence of normal PrPc? How can this disease be acquired?

Answer 37

Prion is a normal part of brain tissue that is found on the surface of neurons. This protein has an abundance of the secondary structure of -helices. In prion disease, it can trigger the change to an abnormal protein.

Prion disease shows an abnormal change from the -helix to the -pleated sheet. The amino acid sequence is the same, only the secondary structure is changed and leads to the disease. This process is not well understood.

Prion disease can be acquired by eating infected tissue that contains abnormal prion protein and it can also sporadically develop.

Question 38

What are heat shock proteins? What is the function of Hsp 70? Describe shape and function of Hsp60.

Answer 38

Heat shock proteins are chaperones for specific folding of proteins.

Hsp 70 mostly prevents incorrect aggregation of unfolded protein.

Hsp60 have a barrel shape and have the function of folding and refolding of proteins.

Question 39

What is changed during denaturation of proteins in the stomach or in the laboratory?

Answer 39

Denaturation of proteins leads to the disorganization of its secondary and tertiary structures. It does not involve the hydrolysis and destruction of the peptide bonds.

[Dietary proteins are denatured under the strong acid condition in the stomach lumen. It is special that the protein structure of the enzyme pepsin itself is not denatured and that this enzyme can perform catalysis at high proton concentration and that it can cleave denatured dietary proteins.]

Question 40

What is used in the laboratory to break in proteins hydrogen bonds, hydrophobic interactions and what is used to break ionic bonds? How are disulfide bonds broken?

Answer 40

Hydrogen bonds are broken by heat, 5-10 M urea or salts

Hydrophobic interactions are broken by detergent (SDS)

Ionic bonds in proteins are broken by strong acids or strong bases.

Disulfide bonds are broken using mercaptoethanol.

Question 41

EXTRA:

Answer 41

• The dipeptide aspartame is a methyl ester of aspartylphenylalanine. It is sweet tasting and used as artificial sugar substitute.
• Dietary essential amino acids are found with the most perfect protein score in the food groups of eggs, milk and soy protein.