Download Amino Acids

Biochemistry-I
Spring Semester 2010
Course Outline
Chapters as in the text
Unit I: Protein Structure and Function
1: Amino acids
2: Structure of Proteins
3: Globular Proteins
4: Fibrous Proteins
5: Enzymes
Unit II: Intermediary Metabolism
6: Bioenergetics and Oxidative Phosphorylation
7: Introduction to Carbohydrates
8: Glycolysis
9: Tricarboxylic Acid Cycle
10: Gluconeogenesis
11: Glycogen Metabolism
12: Metabolism of Monosaccharides and Disaccharides
13: Pentose Phosphate Pathway and NADPH
14: Glycosaminoglycans and Glycoproteins
Textbook:
• Biochemistry, 3rd edition. Harvey and Champe (editors).
Champe, Harvey, and Ferrier. Lippincott Williams &
Wilkins (2005).
Grades
• Midterm exam
• Assignments, Participation & Quiz
• Final Exam
Contact details
• Prof. Dr. Fadel A. Sharif
• Medical Technology Department
• Genetics Lab
• [email protected]
35%
10%
55%
UNIT I:
Protein Structure and Function
Amino Acids
Overview
• Proteins: most abundant and functionally diverse
• Examples:
– Enzymes and polypeptide hormones  direct and
regulate metabolism
– Contractile proteins  movement
– Collagen + calcium phosphate crystals  bone
– Hemoglobin and plasma albumin in blood  shuttle
molecules
– Immunoglobulins  fight infectious agents
• All are polymers of amino acids
Structure of the amino acids
• More than 300 have been described in
nature
• Only 20 (encoded by DNA) are commonly
found in mammalian proteins
• Each (except proline) has a carboxyl
group, an amino group, and a distinctive
side chain (R-group)
• At physiologic pH (~ 7.4), -COOH  COOand NH2  NH3+
• In proteins, these groups are involved in
peptide linkage  not available for
chemical except for H-bonding
• Side chain dictates role of aa in a protein
• aa’s classified according to side chains
A. Amino acids with non-polar side chains
• R-group does not bind or give off protons
or participate in hydrogen or ionic bonds
• R-groups can be thought of as “oily” or
“lipid like”  a property that promotes
hydrophobic interactions.
Non-polar amino acids
1. Location in proteins:
• In proteins found in aqueous solutions, side chains
tend to cluster in interior of protein  i.e., fill up
interior of folded protein  help give 3D shape.
• In proteins located in membranes, non-polar R-groups
are on outside surface, interacting with lipid env.
2. Proline
• The side chain and α-amino group form a ring
• Thus it contains imino group, rather than amino
• Its unique geometry contributes to formation of fibrous
structure of collagen, and often interrupts α-helices found
in globular proteins
B. Amino acids with uncharged polar side chains
• Zero net charge at neutral pH
• Side chains of cysteine and tyrosine can lose protons at
alkaline pH
• Serine, threonine, tyrosine hydroxyl groups can
participate in H-bonding
• R-groups of asparagine and glutamine, containing a
carbonyl and amide group each, can also participate in
H-bonding
1. Disulfide bond
– R-group of Cys contains –SH group, an
important component of active site of many
enzymes
– In proteins –SH groups of two cysteines can
become oxidized to form a dimer, cystine,
which contains a covalent crosslink called a
disulfide bond (-S-S-)
2. Side chains as sites of attachment for
other compounds
– Ser, Thr, and rarely Tyr, contain a polar
hydroxyl group  as site of attachment for
structures e.g., phosphate group.
– Amide group of Asn, as well as hydroxyl
group of Ser or Thr, can be sites of
attachment for oligosaccharide chains in
glycoproteins
C. Amino acids with acidic side chains
• Amino acids Asp and Glu are proton donors
• At neutral pH, R-groups fully ionized, containing a
negatively charged carboxylate group (–COO-)
• Therefore called aspartate and glutamate to emphasize
that they are negatively charged at physiologic pH
C. Amino acids with basic side chains
• R-groups of basic aa’s accept protons
• At physiologic pH, R-groups of Lys, and Arg are fully
ionized and positively charged
• Histidine is weakly basic, free aa is largely uncharged at
physiologic pH. When in protein, His R-group can be
either positive or neutral depending on the ionic env.
provided by the polypeptide chains of the protein.
• This contributes to role of His in functioning of proteins
such as Hb
E. Abbreviations and symbols for the commonly
occurring amino acids
•
•
Three-letter abbreviation and one-letter symbols
The one-letter codes are determined by following
rules:
1.
2.
3.
4.
–
Unique first letter: if only one aa begins with a particular letter
e.g., I = ileucine
Most commonly occurring aa’s have priority e.g., gly is more
common than glutamate, so G = glycine
Similar sounding names: e.g., F = phenylalanine, W =
tryptophan
Letter close to initial letter: for remaining aa’s symbol is the
letter as close in alphabet as possible to the initial of the aa
e.g., K = lysine.
Further, B is assigned to Asx, Z to Glx, and X to unidentified
aa.
Figure 1.7. Abbreviations and symbols for the commonly occurring amino acids.
F. Optical properties of amino acids
•
The α-carbon of each aa is attached to 4 different
chemical groups i.e., a chiral or optically active carbon
atom
Gly is an exception why? It is optically inactive
aa’s that have an asymmetric center at the α-carbon
can exist in two forms D and L
•
•
–
–
–
The two forms in each pair termed stereoisomers, optical
isomers, or enantiomers
All aa’s found in proteins are of the L-form
D-aa’s are found in some antibiotics and in bacterial CW
Figure 1.8: D and L forms of alanine are mirror images.
III. Acidic and Basic Properties of amino acids
• aa’s in aqueous solution contain weakly acidic αcarbonyl and weakly basic groups α-amino
groups
• Additionally, acidic and basic aa’s contain
ionizable groups
• Thus, free aa’s and some aa’s in peptide
linkages can act as buffers
• The quantitative relation b/w the conc. of weak
acid (HA) and weak base (A-) is described by
Henderson-Hasselbalch equation
A. Derivation of the equation
• HA
H+ + A-
• Ka = [H+] [A-]
[HA]
• The larger the Ka, the stronger the acid and vice versa
• By solving the above equation, you obtain the
Henderson-Hasselbalch equation
• pH = pKa + log [A-]
[HA]
B. Buffers
• Resist change in pH following addition of an acid
or base
• Created by mixing weak acid (HA) with its
conjugate base (A-)
• If acid (e.g., HCl) is added, A- can neutralize it,
being converted into HA
• If base is added, HA can neutralize it, being
converted into A• Maximum buffering capacity occurs at pH = pKa,
but still HA/A- pair can serve as an effective
buffer when pH is within ~ ± 1 pH unit of the pKa
Figure 1.9: Titration curve of acetic acid
C. Titration of an amino acid
1. Dissociation of the carboxyl group:
–
–
–
As for other weak acids
e.g., Ala with an α-carboxyl and an α-amino group:
at a low (acidic) pH, both groups are protonated
As pH raised, -COOH group of form I can dissociate
by donating a proton to medium  COO- (form II, a
dipolar form) this form is a.k.a zwitterion, the
isoelectric form of Ala
Figure 1.10. Ionic forms of alanine in acidic, neutral, and basic solutions.
2. Application of the Henderson-Hasselbalch eq.
• Dissociation constant of carboxyl group is called
K1
• The Henderson-Hasselbalch eq.
K1 = [H+] [II]
[I]
pH = pK1+ log [II]
[I]
3. Dissociation of the amino group:
– The second titratable group of Ala is -NH3+
– A much weaker acid than the –COOH,
therefore a much smaller dissociation
constant K2 (i.e., pK2 is larger)
– Release of a proton from -NH3+  fully
deprotonated form of Ala (form III)
4. pKs of alanine
• Each titratable group has a pKa that is
numerically equal to the pH at which
exactly one half of the protons have been
removed from that group
5. Titration curve of alanine
Figure 1.11. The titration curve of alanine.
Note the following:
a.
b.
c.
Buffer pairs: the –COOH/-COO- pair can serve as a
buffer in the pH region around pK1, and the –NH3/ NH2 pair can buffer in the region around pK2
When pH=pK: when pH = pK1(2.3), equal amounts of
forms I and II exist in solution. When pH = pK2 (9.1),
equal amounts of form II and form III.
Isoelectric point: at neutral pH, alanine exists as the
dipolar form II, net charge is zero.
Isoelectric point (pI) is the pH at which aa is electrically
neutral.
For aa that has only two dissociable hydrogens, pI =
(pK1 + pK2)/2, i.e., (2.3 + 9.1)/2 = 5.7.
pI corresponds to pH at which structure II
predominates, and at which equal amounts of form I
(net charge of +1) and III (net -1) exist
6. Net charge of amino acids at neutral pH
• At physiologic pH, all aa’s have a negative
–COO- and a positive –NH3+ group, both
attached to the α-carbon
• Glu, Asp, His, Arg, Lys have additional
potentially charged groups
• Substances, e.g., aa’s, that can act as an
acid and a base are defined as
amphoteric, and are referred to as
ampholytes (amphoteric electrolytes)
D. Other applications of Henderson-Hasselbalch eq.
• Can be used to calculate how the pH of a
physiologic solution responds to changes
in the conc. weak acid and/or its
corresponding “salt” form.
• E.g., in bicarbonate buffer system, the
equation predicts how shifts in [HCO3-]
and pCO2 influence pH
Figure 1.12 A. changes in pH as the concentrations
of HCO3- or CO2 are altered;
• The
eq. is also useful for
calculating the abundance of ionic
forms of acidic and basic drugs.
E.g., most drugs are either weak
acids or weak bases.
• Acidic drugs (HA): HA ↔ H+ + A• Weak bases (BH+) can also
release a H+. The protonated form
of a basic drug is usually charged,
and loss of a H+  uncharged
base (B): BH+ ↔ B + H+
• A drug passes through
membranes more
readily if uncharged.
• For a weak acid, the
uncharged (HA) can
permeate through
membranes and Acannot.
• For a weak base, such
as morphine, the
uncharged, B,
penetrates and BH+
does not
• The effective conc. of permeable form at its
absorption site is determined by relative conc. of
charged/uncharged forms.
• The ratio is determined by pH at site of
absorption, and by strength of the weak acid or
base which is represented by pKa of the
ionizable group
• The eq. is useful in determining how much drug
found on either side of a membrane separating
two compartments that differ in pH e.g., stomach
(pH 1.0-1.5) and blood plasma (pH 7.4)
IV. Concept Maps
• Biochemistry is a body of concepts
• Biochemical concept maps graphically illustrates
relationships between ideas presented, and
show how info. organized
• A concept map is a tool for visualizing
connections b/w concepts
• Material presented in hierarchical fashion: most
inclusive/general concepts at top of the map 
 more specific/less general concepts.
• Should not be memorized, they are guides for
organizing info. so that you can find best ways to
integrate new info. into knowledge you already
possess.
Figure 1.13. Symbols used in concept maps.
Summary
• Each aa has an α-carboxyl and an α-amino group (except Pro, has
an imino group)
• At physiologic pH: α-carboxyl  COO-, α-amino  NH3+
• Each aa contains one of 20 side chains
• The chemical nature of side chain determines function of aa in a
protein, and classifies aa as nonpolar, uncharged polar, acidic, or
basic
• All free aa’s plus charged aa’s in peptide chains serve as buffers
• Relation b/w the conc. of weak acid and its conjugate base is
described by Henderson-Hasselbalch eq.
• Buffering occurs within ±1 pH, and max when pH = pKa at which
[HA] = [A-]
• The α-carbon of each aa (except Gly) is attached to 4 different
chemical groups i.e., a chiral or optically active carbon atom
• Only L-form of aa’s is found in proteins synthesized by human body