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BIOCHEM*2580 > Lecture 3 > Flashcards

Lecture 3 Flashcards

1
Q

What are hydrogen bonds?

A

Electrostatic attractions between a H-bond donor and an acceptor.

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2
Q

What is a donor?

A

Highly polar -OH or -NH groups are good H-bond donors (a H-atom that is covalently bonded to another EN atom)

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3
Q

What is an acceptor?

A

An electronegative atom with available lone pairs of electrons, such as O or N

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4
Q

How strong is the hydrogen bond to a covalent bond?

A

About 5-10% strong, enough to make molecule R1 stick to R2 but not form a permanent link

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5
Q

What are H-bonds?

A

Directional - stronger if donor and acceptor line up with one another.

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6
Q

What are the amino acids with positive side chains?

A

His, Lys, Arg

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7
Q

What are the characteristics of positively charged side chains? d

A
  • The side chains contain weak bases that gain H+ (become protonated) and so are positively charged in aqueous solution at neutral pH
  • The charge makes them very polar, overriding the non-polar hydrocarbon side chain.
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8
Q

What amino acids have negatively charged side chains?

A

Asp and Glu

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9
Q

What are the characteristics of the negatively charged side chains?

A

They have carboxylic acid groups R-COOH that lose H+ (become protonated) at neutral pH

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10
Q

What is COOH deprotonated?

A

Described as carboxylate groups R-COO-

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11
Q

What are carboxylate groups?

A

Negative and very polar

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12
Q

What is the Asp side chain?

A

-CH2-COO-

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13
Q

What is the Glu side chain?

A

-CH2-CH2-COO-

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14
Q

What can amino acids act as?

A

Acids and Bases

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15
Q

What does an acid do?

A

Donote a proton

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16
Q

What does a base do?

A

Gain a proton

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17
Q

What will the acids and bases do?

A

Gain (protonate) or lose (deprotonate) H+ depending on availability of H+ in solution.

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18
Q

What do natural biochemical occur close to?

A

pH 7

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19
Q

What is the equation for how pH express availability of H+:

A

pH = -log10[H+]

at pH = 7, [H+] = 10-7 M

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20
Q

What does the Henderson-Hasselbalch equation relate?

A

pH, pKa and the state of ionization of a given group.

21
Q

What is the Henderson-Hasselbalch equation?

A

pH = pKa + log[deprotonated]/[protonated]

22
Q

What do the vast majority of molecules for the a-carboxylate group at pH 7 exist as?

A

As carboxylate -COO NOT as carboxylic acid - COOH (in deprotonated form)

23
Q

What do the vast majority of molecules for the a-amino group at pH 7 exist as?

A

As protonated RNH3+ rather than as RNH2

24
Q

What is the correct structure to represent an individual amino acid at neutral pH?

A

A dipolar ion (zwitterion)

25
Q

What happens when the amino acid is part of a peptide chain?

A

The a-amino groups and the a-carboxylate groups are linked as uncharged amide (except for the ones at the N and C termini, which are also NH3+ and COO- at pH 7)

26
Q

Which amino acids have ionizable side chains?

A

There are SEVEN amino acids with side chains that have acid/base properties.

27
Q

What are the amino acids that have acid/base properties for side chains?

A

Aspartate, Glutamate, Tyrosine, Cysteine, Arginine, Histidine, Lysine

28
Q

What are the side chains of Arg, His and Lys?

A

Neutral when deprotanted and positive when protonated

29
Q

What does the value of pKa tell you?

A

Where in the pH scale a group undergoes deprotonation

30
Q

What can a molecule have?

A

Several ionizable groups, that has its own Pka value dependent on its chemical context.

31
Q

When an amino acid is part of a peptide chain, what will happen?

A

It will have a slightly different pKa

32
Q

What happens if the pH is one unit or more below the pKa:

A

The group is fully protonated

33
Q

What happens if the pH is one unit or more higher than pKa?

A

The group is fully deprotanated

34
Q

What happens if the pH is equal to pKa?

A

The group is 50% deprotonated and 50% protonated

35
Q

What happens if the pH is less then one unit away from pKa?

A

Use the Henderson-Hasselbalch equation

36
Q

What can amino acid analysis determine?

A

Help to determine protein structure

37
Q

What does analysis of amino acids involve?

A

1.) Separation of a mixture into components

2.) Detection of the components of interest
- Can be qualitative (tells you what’s present)
- Can be quantitivate (tells you how much is present)
- Can be preparative (separated components can be recovered for further experiments)

38
Q

Particles of a solid are chosen with a specific property (eg, silica gel)

A

Known as the stationary phase - polar.

39
Q

Liquid solvent or buffer flows past the particles and is non-polar

A

Mobile phase

40
Q

Amino acids exchange (partition) between phases

A
  • Polar amino acids P spend more of their time hydrogen bonded to silica and move slowly
  • Non-polar amino acids N spend more time in solvent, and move almost as fast as solvent
41
Q

What is the highest point reached by solvent?

A

Solvent Front

42
Q

What do very polar amino acids have?

A

Low Rf

43
Q

What do non-polar amino acids have?

A

High Rf - Run with the gel

44
Q

How can amino acids be detected?

A

Adding ninhydrin which reacts with secondary and primary amines.

Alternate is adding fluroscamine, giving yellow fluroscence under UV light.

45
Q

What does Ion exchange chromatography do?

A

Separates on the basis of charge
- Uses charged resins as stationary phase

46
Q

What do cation exchange resins contain?

A

Negative groups, which bind positive molecules (cations) - Cation Exchange

47
Q

What do anion exchange resins contain?

A

Negative molecules, which bind negative molecules (anions) - Anion Exchange

48
Q

What is Elution by?

A
  • Competition with a high ion concentration (usually NaCl), which displaces the amino acid from the resin
  • Changing the pH to alter the charge on the amino acid, so it no longer binds to the resin.

BIOCHEM*2580 (21 decks)

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