MCB 2000 CH 3: Amino Acids

What are the 5 major components of an amino acid?

• Amino group (NH2) = basic end

• Carboxyl group (COOH) = acidic end

• Alpha Carbon (α) = next to carboxyl group

• Hydrogen

• R group (side chain) = variable position

Amino acids are chiral: True/False

Which amino acid is the exception?

True

Glycine, R = H

What are the 2 isomers that amino acids exist in?

Which isomer is found in proteins?

L & D isomers = enantiomers

Only L isomers = found in proteins

What are the 4 major groups of amino acids + characteristics?

How many are there in each one?

What do the different groupings indicate?

Nonpolar → 9

• Hydrophobic

• Hydrocarbons → Neutral

Polar → 6

• Hydrophilic

• Neutral + H-bond

Positive → 3

• (+) charge @ pH = 7

Negative → 2

• (-) charge @ pH = 7

Groups = indicate side chain behavior @ pH = 7

• Δ pH → Δ charge (sometimes)

What are the 3 major categories of amino acids that depend on your body?

How many of them are in each?

Essential amino acids = must come from food

• 9 → His Ile Leu Lys Met Phe Thr Trp Val

Nonessential amino acids = built from body’s cells

• 11 → Ala Arg Asn Asp Cys Gln Glu Gly Pro Ser Tyr

Conditionally essential amino acids = built from cells when pathway works (can be blocked)

• 2 → Phe → Tyr, Met → Cys

What are the pH values of stomach lumen, lysosome, and mitochondrial matrix?

Stomach Lumen → pH = 2

Lysosome → pH = 4.5

Mitochondrial matrix → pH = 8

How many amino acids carry a ring?

Which group(s) is/are they a part of?

Nonpolar = Phe Trp

Polar = Tyr

Positive = His

What are the 5 nonpolar amino acids with hydrocarbon side chains? Use 3-letter code + 1 letter abbreviations.

Draw them

Glycine → Gly/G

• R = H

Alanine → Ala/A

• R = CH₃

Valine → Val/V

• R = CH(CH₃)₂

Leucine → Leu/L

• R = CH₂CH(CH₃)₂

Isoleucine → Ile/I

• R = CH(CH₃)CH₂CH₃

What are the 2 amino acids with sulfur in side chains? Draw them.

What families are they part of?

What is their H-bonding ability + how do you know?

What important covalent crosslink can 1 of the 2 amino acids form?

Methionine → Met/M

• Nonpolar

• R = CH₂CH₂SCH₃ = Thioether

• NOT an H-bond donor (No H on Sulfur)

Cysteine → Cys/C

• Polar

• R = CH₂SH = Thiol/Sulfhydryl

• H on Sulfur → H-bond donor

• Sulfur → H-bond acceptor (LPs on S)

Disulfide bridge = strong covalent bond b/w sulfur atoms of 2 cysteine amino acids

What is special to note about proline? Draw it.

What happens to the H-bonding ability of the amino group?

Proline → Pro/P

• R = CH₂CH₂CH₂

• Loops back to covalently bond w/ backbond amino

• Forms 5-membered ring → restricted rotation

Nitrogen of amino no longer donate H-bond (No free H)

What is collagen + its structure? What fits at crowded center?

What is the three amino-acid pattern in collagen?

Collagen = most abundant protein in body

• Three chains → triple helix

• Hydrogen

Gly - Pro - Y, Y = hydroxyproline

What is the importance of hydroxyproline in collagen peptide chain?

What element is necessary for the function of enzyme that forms hydroxyproline?

• What vitamin ensures that element keeps working?

Enzyme adds hydroxy (-OH) group to proline after chain = built

• Hydroxyproline → Locks helix → desired shape

Iron

• Vitamin C = ensures iron stays working

What is scurvy + symptoms?

How does the absence of vitamin C affect the structure of collagen?

How many mg of vitamin C a day is enough to prevent it?

Scurvy = disease caused by severe lack of vitamin C (ascorbic acid) in diet

• Bleeding gums

• Loose teeth

• Non-healing wounds

No vitamin C → no iron → no enzyme to add hydroxy group → no hydroxyproline

• Collagen triple helix does not hold together @ body temperature → tissues unable to be held together

10 mg Vitamin C/day → prevents scurvy

What amino acid swap in collagen peptide pattern leads to osteogenesis imperfecta or brittle bone disease + why?

Glycine = smallest amino acid (R = H)

• Replacement to bigger amino acid → triple helix cannot close → bones break easily

What are the 3 amino acids with aromatic rings in side chains? Draw them.

Identify:

• Abbreviations

• Group

• Essentiality

Phenylalanine → Phe/F

• Nonpolar

• Essential

Tyrosine → Tyr/Y

• Polar

• Nonessential

Tryptophan → Trp/W

• Nonpolar

• Essential

• Indole = largest side chain → resonance delocalization

What enzyme converts phenylalanine to tyrosine?

What is the name of the disorder that results when that enzyme is nonfunctional?

Phenylalanine hydroxylase = adds hydroxy (-OH) group to phenylalanine → tyrosine

Phenylketonuria = metabolic disorder → body CANNOT break down phenylalanine → toxic buildup in blood + brain

What amino acid is Tyrosine structurally similar to and how?

How does this affect polarity?

Tyrosine = Phenylalanine + hydroxyl

• Tyrosine = polar

• Phenylalanine = nonpolar

What are the 2 amino acids with hydroxyl groups? Draw them.

Serine → Ser/S

• Polar neutral

Threonine → Thr/T

• Polar neutral

What are the 2 amino acids with amide groups? Draw them.

Why is the amide nitrogen of side chain NOT protonated @ pH = 7?

Amide = -CO-NR₂ = carboxylic acid derivative

Asparagine → Asn/N

• Polar neutral

Glutamine → Gln/Q

• Polar neutral

Carbonyl = EWG → resonance → does NOT allow amide nitrogen to be protonated @ pH = 7

What are the 2 negative amino acids? Draw them.

What 2 other amino acids are they similar to?

Aspartate → Asp/D

• Negative

Glutamate → Glu/E

• Negative

Similar relationship to Asn and Gln → Difference of 1 CH₂ in chain

What is the difference between aspartic or glutamic acid and aspartate or glutamate? What is the charge?

Aspartic acid/Glutamic acid = carboxylic acid form = neutral

Aspartate/Glutamate = carboxylate form = (-) charge

What amino acid is involved in MSG or umami flavor?

MSG = Monosodium Glutamate = sodium salt form of glutamic acid → umami flavor

What is glutamate’s role in central nervous system?

What barrier prevents the dietary glutamate out?

Glutamate = main excitatory neurotransmitter → must be tightly regulated to avoid neuroinflammation or oxidative stress

Blood-brain barrier = semi-permeable border of cells b/w circulating blood from brain & CNS extracellular fluid

What is aspartame?

Which amino acid(s) make up aspartame?

People with what condition must be weary of diet sodas with warnings of aspartame?

Aspartame = artificial, low-calorie sweetener = 200x sweeter than sugar

• Dipeptide = aspartate + phenylalanine + CH₃

• PKU Phenylketonuria = phenylalanine buildup → neurological issues

What are the 3 positive amino acids? Draw them.

List important characteristics for each

Which amino acid has a guanidinium and an imidazole?

Lysine → Lys/K

• R = 4 CH₂ + NH₃⁺

Arginine → Arg/R

• 3 CH₂ + Guanidinium

• Guanidium = holds (+) charge very tightly

Histidine → His/H

• Imidazole = 5-membered ring w/ 2 N

• *Partial charge @ pH = 7

  • 1 N LP → resonance

  • 1 N LP → protonated

What are the 4 questions to identify each amino acid?

1. Ring?

   1. Phe = 1 ring

   2. Tyr = 1 ring + OH

   3. Trp = 2 fused rings

   4. His = 5-membered ring + 2 N

2. Charge?

   1. NH3⁺ → Lys

   2. 3 N on 1 carbon → Arg

   3. -COO^-

      1. Short → Asp

      2. Long → Glu

3. O, N, or S in side chain?

   1. -OH → Ser or Thr

   2. -SH → Cys

   3. S in chain → Met

   4. Amide

      1. Short → Asn

      2. Long → Gln

4. Only C and H?

   1. Count #C’s → find branch

      1. Gly, Ala, Val, Leu, Ile

   2. Ring → backbone → Pro

What is the relationship between protonation state and actual charge? Same or different?

THEY ARE NOT THE SAME

Protonation state = protonated/deprotonated

Actual charge = depends on pKa of α-amino, α-carboxyl, and side chain

What is a zwitterion?

Why are most free amino acids zwitterions in body?

Zwitterion = molecule with both ± charge @ same time & net 0 charge

Neutral conditions, pH = 7:

• α-amino (basic) → protonated → +1

• α-carboxyl (acidic) → deprotonated -1

What is the net charge of free amino acid @ low pH? Why?

What is the net charge of free amino acid @ high pH? Why?

Low pH → ↑[H⁺]

• α-amino (basic) → protonated → +1

• α-carboxyl (acidic) → protonated → 0

• Net charge = +1

High pH

• α-amino (basic) → deprotonated → 0

• α-carboxyl (acidic) → deprotonated → -1

• Net charge = -1

What is pKa?

How can you determine pKa on a titration curve? (3 steps)

Why are there flat regions on a titration curve?

pKa = pH @ which ½ molecules = deprotonated, ½ molecules = protonated

1. Find equivalence point → find sharp, vertical jump on graph & find total volume on x-axis

2. Half volume

3. Read pH following ½ volume on x-axis and pH on y-axis

Buffer regions = nearly flat section where pH changes very slowly despite more acid/base

• Absorbs added ions → resistance = buffer

What is the pH and pKa rule?

pKa > pH by 1 or MORE → protonated

pKa = pKa → ½ charge

• Acidic → -½

• Basic → +½

pKa < pH by 1 or MORE → deprotonated

1 unit difference b/w pKa and pH is truly 1 unit away (True/False)

What is 1 unit and 2 units away equivalent to?

False → 1 unit away = 90/10, 2 units away 99/1

What is the alpha group and 4 amino acids that act as acid groups?

α-carboxyl

• Aspartate (Asp)

  • R = -CH₂-COOH

• Glutamate (Glu)

  • R = -CH₂-CH₂-COOH

• Cysteine (Cys)

  • R = -CH₂-SH

• Tyrosine (Tyr)

  • R = CH₂-C₆H₄-OH

What is the alpha group and 3 amino acids that act as basic groups?

α-amino

• Lysine (Lys)

  • R = -(CH₂)₄-NH₂

• Arginine (Arg)

  • R = -(CH₂)₃-NH-C(=NH)-NH₂

• Histidine (His)

  • R = -CH₂-C₃H₃N₂

What is the charge of deprotonated and protonated forms of acid groups?

What is the charge of deprotonated and protonated forms of basic groups?

ACIDS

• Protonated → 0

• Deprotonated → -1

BASES

• Protonated → +1

• Deprotonated → 0

What is the pKa of an α-amino and α-carboxyl groups of free amino acid?

α-amino (basic) → pKa = 9.5

α-carboxyl (acidic) → pKa = 2.2

What are the 3 steps to determine net charge?

1. List ionizable groups

2. pKa vs. pH

   1. pKa > pH (by more than 1) → protonated

   2. pKa = pH → +/- ½

   3. pKa < pH (by more than 1) → deprotonated

3. Convert state to charge → add total

   1. Free amino acid cannot be more than +2 or less than -2

What are the 4 acidic ionizable amino acids?

What are the protonated forms and charges?

Aspartate

• -COOH

• 0

Glutamate

• -COOH

• 0

Cysteine

• -SH

• 0

Tyrosine

• -OH

• 0

What are the 3 basic ionizable amino acids?

What are the protonated forms and charges?

Histidine

• -Imidazole ring-H⁺

• +1

Lysine

• -NH₃⁺

• +1

Arginine

• -Guanidine⁺

• +1

What is special about net charge of histidine?

What is it’s pH?

Histidine = basic group = only side chain w/ pKa close to pH = 7

• pKa = 6

• Present @ active enzyme sites → easily protonated/deprotonated

What is pI?

What are the 2 cases used to calculate pI?

Which amino acid is the exception to case 2?

pI = Isoelectric point = pH where molecule has no net charge

• Case 1: No ionizable side chain

  • pI = (2.2+9.5/2 = 5.85

• Case 2: Ionizable side chain

  • pI = average of 2 alike-charged groups

    • Asp = (2.2+4.1)/2 = 3.15

    • Lys = (9.5+10/8)/2 = 10.15

Tyrosine → case 1 → pI = 5.85

What are the pKa values of the 7 ionizable side chains?

Asp

• pKa = 4.1

Glu

• pKa = 4.1

Cys

• pKa = 8.3

Tyr

• pKa = 10.9

His

• pKa = 6.0

Lys

• pKa = 10.8

Arg

• pKa = 12.5

What is the folding rule in water?

What happens to nonpolar, polar, and charged groups?

Nonpolar/hydrophobic groups → inside

Polar/hydrophilic + charged groups → outside

What is the folding rule in lipid membrane?

What happens to nonpolar, polar, and charged groups?

Nonpolar/hydrophilic groups → out

Polar/hydrophilic + charged groups → in

How many amino acid side chains face the water?

Name them according to group + main roles

11 = 6 polar + 3 positive + 2 negative

• Polar → -OH, -SH, or amide

  • Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine

  • Ser, Thr, Tyr → @ enzyme active sites

    • -OH → reactive to attack substrate

• Positive

  • Lysine, Arginine, Histidine

    • TFs, histones

    • Bind nucleic acids (DNA Backbone = (-) charged)

• Negative

  • Aspartate, Glutamate

  • Carboxylate groups → hold metal ions in place @ enzyme active sites

What is TRPV5?

What is the polarity of the top, middle, and bottom parts?

TRPV5 = transmembrane protein = ion channel

• Top = polar = hydrophilic

• Middle = nonpolar = hydrophobic

• Bottom = polar = hydrophilic

What is p53?

What is the mutation that causes p53 to be nonfunctional?

How does the difference in properties of amino acids change p53 ability?

p53 = tumor suppressor protein → binds DNA (Negatively charged) to control cell division

Mutation Arg-248 → Gln-248

• Healthy p53: Arginine → (+) charge → able to grip DNA

• Cancer mutation p53: Glutamine → polar neutral → unable to grip DNA → unable to suppress tumor → cancer

What types of problems is the Henderson-Hasselbach equation used for?

What are the 3 steps to answer the problem type?

Percentage questions

• Ex. What is the percentage of neutral molecules of aspiring in the stomach, pH = 1.5 and pKa = 3.5?

Steps:

1. Plug in

2. Solve for ratio

3. Convert to percentage

   1. Neutral percentage = (Denom)/(Num + Denom)

If aspirin has a pKa of 3.5, stomach has a pH of 1.5, and the small intestine has a pH of 6.5, where is the aspiring expected to be absorbed (according to pKa rule)?

What win, chemistry or anatomy (SA)?

Aspirin = acidic

• Stomach → pKa > pH → protonated, neutral → nonpolar, hydrophobic

  • Easily cross cell membrane → absorbed in stomach

• Small intestine → pKa < pH → deprotonated, charged → polar, hydrophilic

  • Water soluble but blocked from membranes

Anatomy wins → greater surface area