lecture 2 outline - university of texas at...

Lecture 2 Outline

Chapter 2 Aqueous solutionsAcids and Bases

pHpH

Henderson Hasselbalch

Chapter 4 Amino Acids and PeptidesStructure

Chirality

Non-protein amino acids

Peptide bond

What is the typical molarity of the H+ for maximal

activity in animal tissues?

i.e. ~ pH 7

However a few physiological surroundings are far

from neutrality. Name one: Stomach Contents

Acid Ka p Ka

HCOOH (formic) 1.8 x 10-4 3.75

CH3COOH (acetic) 1.74 x 10-5 4.76

Dissociation of common acids

CH3COOH (acetic) 1.74 x 10-5 4.76

H3PO4 (phosphoric) 7.25 x 10-3 2.14

NH4+ (ammonium) 5.62 x 10-10 9.25

It is important to note that all of the pK values we have talked about

refer to measurements carried out in water.

In biological systems not all of the reactants operate in a purely

aqueous environment.

Box 2-B Acid-base balance in humans.

Table 2-3 (bottom) Dissociation Constants and pK’s at

25°C of Some Acids in Common Laboratory Use as

Biochemical Buffers.

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For reviews of pH and buffers see

http://www.boyerbiochem.com/

and go to Concept Reviews

Deep Diving Apparatus

Chapter 4 Voet & Voet

Figure 4-1General structural

formula for α-amino acids.

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Figure 4-2 Zwitterionic form of the α-amino acids that

occur at physiological pH values.

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Table 4-1 (left)Covalent Structures and Abbreviations of

the “Standard” Amino Acids of Proteins, Their Occurrence,

and the pK Values of Their Ionizable Groups.

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Table 4-1 (right) Covalent Structures and Abbreviations of

the “Standard” Amino Acids of Proteins, Their Occurrence,

and the pK Values of Their Ionizable Groups.

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Ways in Which Amino Acids Differ

• Polarity

• Acidity, Basicity

• Aromaticity

• Bulk• Bulk

• Conformational Flexibility

• Ability to Crosslink

• Ability to Hydrogen Bond

• Chemical Reactivity

Figure 4-9 Greek lettering scheme used to identify

the atoms in the glutamyl and lysyl R groups.

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Figure 4-5 Structure of cystine.

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cystine

Figure 4-4a Structure of

phenylalanine. (a) Ball and stick form.

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Figure 4-4b Structure of

phenylalanine. (b) Space-filling model.

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Figure 4-3 Condensation of two α-

amino acids to form a dipeptide.

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Figure 4-6 Titration curve of glycine.

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Figure 4-7 Titration curves of the

enzyme ribonuclease A at 25°C.

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KCl concentratoion = 0.01M blue, 0.03 red, 0.15 green

Figure 4-8The tetrapeptide Ala-

Tyr-Asp-Gly.

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Figure 4-10 The two enantiomers of

fluorochlorobromomethane.

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Figure 4-11 Schematic diagram of a

polarimeter.

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Figure 4-12 Fischer convention configurations for naming the enantiomers of

glyceraldehyde.

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Figure 4-13 Configuration of L-glyceraldehyde and

L-αααα-amino acids.

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Figure 4-14 “CORN crib” mnemonic for the

hand of

L-amino acids.

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Figure 4-15 Fischer projections of

threonine’s four stereoisomers.

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Only the L-Threonine isomer is found in proteins. Isoleucine is

the only other amino acid found in proteins which has 2

asymmetric centers.

Ways in which an enzyme can interact with substrate

Interaction of prochiral compound with enzyme

Figure 4-20 Views of ethanol.

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Note: The conversion of the serine to selenocysteine

occurs on the tRNA

Figure 4-22 Some uncommon amino acid residues that are components of certain

proteins.

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Figure 4-23: Some biologically produced

derivatives of “standard” amino acids and amino

acids that are not components of proteins.

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Figure 4-3 Condensation of two αααα-amino acids

to form a dipeptide.

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