DLAproperties Of Amino Acids

Question 1

Where are peptide bonds formed?

Answer 1

Between the a-carboxyl group of one amino acid and the amino group of another

Question 2

How are peptide bonds formed?

Answer 2

The process of translation

Exception is the synthesis o& the tripeptide glutathione

Question 3

What are the characteristics of the peptide bond?

Answer 3

• The peptide bond has partial (40%) double-bond character
• Peptide bond is rigid and planar
• the peptide bond is uncharged but polar
• The —C=O and —NH groups of the peptide bond May form hydrogen bonds
  
  • May form repetitive hydrogen bonds
  • Stabilizes the a-helical and B-sheet structures

Question 4

Describe the configuration of the peptide bond

Answer 4

• Trans configuration minimizes steric hindrance
• Side chains are in trans configuration
• Rotation is possible at the a-carbons
• Peptide bonds do not break during denaturation of proteins
  
  • Denaturation involves changing the conformational shape of a protein

Question 5

Aspartate and glutamate have…

Answer 5

Negative (acidic) side-chains at physiological pH (pk about 4)

Question 6

What are the precursors to biologically active amines?

Answer 6

The a-amino acids are precursors for many biological active amines

The amino group is retained (amines) and the a-carboxyl group is enzymatically removed as CO2 (decarboxylated)

Question 7

What is GABA?

Answer 7

A neurotransmitter

Question 8

What is histamine ?

Answer 8

Mediated allergic and inflammatory responses, gastric secretion and neurotransmission

Question 9

How is GABA formed?

Answer 9

GABA(y-aminobutyric acid) is formed by decarboxylation of the a-carboxyl group of glutamate

Question 10

How is histamine formed?

Answer 10

Formed by decarboxylation of histidine by histidine decarboxylase

Question 11

What are the functions of serotonin ?

Answer 11

• Pain perception
• Affective disorders
• Regulation of sleep, temperature and blood pressure

Question 12

Explain the transformation of tryptophan to serotonin

Answer 12

1. Tryptophan+ tetrahydrobiopterin —> 5-hydroxytryptophan and dihydrobiopterin (+H2O) by hydroxylase
2. 5-hydroxy-tryptophan —> serotonin by aromatic amino acid decarboxylase PLP

Question 13

How does Prozac (fluoxetine) work as an antidepressant?

Answer 13

• Prozac (fluoxetine) as a selective serotonin reuptake inhibitors (SSRI)
  
  • An antidepressant drug that blocks serotonin elimination from synaptic cleft

Enhances the action of the neurotransmitter

Question 14

What are the Catecholamines?

Answer 14

Dopamine, tyrosine, and epinephrine are formed from tyrosine

Question 15

Summarize dopamine formation

Answer 15

• Tyrosine is hydroxylated to dihydroxy-phenylalanine (L-DOPA)
• L-DOPA is decarboxylated to dopamine, the first Catecholamine

Question 16

What are dopamine functions?

Answer 16

Dopamine can act as neurotransmitter or it can be used as an intermediate for the synthesis of norepinephrine and epinephrine

Dopamine and norepinephrine are mainly neurotransmitters in the brain and the autonomic nervous system

Epinephrine and norepinephrine may also act as hormones

Question 17

What are the functions of epinephrine?

Answer 17

Epinephrine and norepinephrine are released inti the blood from the adrenal medulla during stress situations

Epinephrine (fight or flight) leads to:
-Release of glucose from the liver

• Release of fatty acids from fat cells
• Elevated blood pressure
• Increased heart output

Question 18

Describe positive and negative charges in amino acids at neutral pH

Answer 18

The a-amino acid carboxyl group is negatively charged at:
-physiological pH

-The pKa for the a-carboxyl groups is about 2

The amino group of the a-amino acids is positively charged

• At physiological pH
• The pKa for the a-amino group is about 9-10

Some amino acids have a side chain that may carry a charge at physiological pH

Question 19

How is a swifter ion formed?

Answer 19

At physiological pH, a possible charge of the side chain will determine the overall charge of an amino acid

If the side chain doesn’t have a dissociable proton, then a zwitterion is formed at ~neutral pH; the amino acid carries no net charge

Question 20

What are the positive/basic side chains amino acids?

Answer 20

Sometimes histidine, dependent on exact pH

Arginine (Arg)and lysine (Lys)(pKa for both above 10)

Histidine (his) pKa about 6

Question 21

Explain the titration curve of alanine

Answer 21

Alanine has two ionizable groups= two pkas

Two pKa gives two buffering regions

Some aa will have 3 pKas due to the ionizable nature of their side chains

• aa capable of acting as either an acid or base - amphoteric
• Most aa are not soluble as physiological buffers as pKas are too high or low I.e. ~2.3 or 8-9

Question 22

What defines the buffer region of an amino acid?

Answer 22

The pKa defines the buffer region

The pI is the isoelectric point- no net charge

Question 23

Explain the histidine side chain buffer

Answer 23

-The histidine side chain has an imidiazole ring (pKa 6) which allows buffering of a possible drop in intracellular pH, which is normally about pH 7

• The pKa of histidine May be shifted in proteins to 6-7 due to local chemical environment of the protein
  
  • Histidine would then be even more favorable to buffer the normal pH inside of cells

Question 24

What are the main blood buffer systems?

Answer 24

• Phosphate buffer
• Hb buffer in RBC (hemoglobin is rich in histidine side chains)
• Bicarbonate buffer in plasma

Question 25

What are the general structure of amino acids?

Answer 25

An a-carbon atom -assymetric (except in glycine)-linked to: -A Carboxylic acid group - An amino group - An H atom - A variable R group (side chain): any molecule can replace the ‘R’. For instance glycine simply has an -H instead and alanine a -CH3 - In total there are 22 different R-groups and different three letter abbreviations to represent the amino acid (Asn, Glu)

Question 26

Explain the stereochemistry of Amino Acids

Answer 26

19 of the common amino acids are chiral (glycine aren’t chiral) 2 non-superimposable mirror images -stereoisomers - D & L forms based on the glyceraldehyde rule - Determined by the position of the -amino group, instead of -OH - Naturally occurring proteins are L-amino acids - Rare-D-amino acids in some antibiotics & peptidoglycan of bacterial cell wall

Question 27

How is proline different from amino acids ?

Answer 27

It has secondary amino group and it’s side chain forms a rigid ring structure

Question 28

How do peptide bonds formed with proline take a specific shape?

Answer 28

- Lead to bends in the protein chain - Collagen is rich in proline residues - Interrupt the a-helical structure - Proline is an a-helix breaker

Question 29

What amino acids have nonpolar, aliphatic side chains?

Answer 29

Glycine, alanine and proline

Question 30

What amino acids have nonpolar, aliphatic side chains(branched ) ?

Answer 30

Valine, leucine, and isoleucine

Question 31

What amino acids have aromatic side chains ?

Answer 31

Phenylalanine, tryptophan, and tyrosine

Question 32

Contrast Trp and Tyr have UV light absorbance.

Answer 32

UV light absorbance by aromatic amino acids Absorbance at 280 no is approximately 4x higher for TRP than for TYR -Phenylalanine doesn’t show much absorbance

Question 33

What are the sulfur containing methionine and cysteine ?

Answer 33

Methionine and cysteine Methionine is also grouped under nonpolar side chains Cysteine is grouped under uncharged polar side chains at neutral pH

Question 34

Describe cysteine

Answer 34

Contains a sulfhydryl group 2 cysteine residues can be used to form a disulfide bond 2 “free” cysteine May oxidize to form cystine

Question 35

What are the polar uncharged amino acids:

Answer 35

asparagine and glutamine Asparagine is a derivative of Aspartate Glutamine is a derivative of glutamine

Question 36

What are the polar, uncharged amino acids?

Answer 36

Serine, threonine Serine & threonine residues contain a hydroxyl group May be: - Phosphorylated - Glycosylation