CHAPTER 4 :

AMINO ACIDS, PROTEIN AND

PROTEIN METABOLISM
 Learning outcomes
Explain general features of amino acids.
Categorize the amino acids.
Understand zwitterion of amino acids.
Describe different levels of protein.
Compare protein folding with protein denaturation
 General features of amino acid

Amino acid includes

an amino group
a carboxyl group
a hydrogen
a side chain or R group bonded to
α-carbon.
Amino Acids
Building Blocks of Proteins
A chiral centre, a carbon with four
different groups bonded to it.

One chiral centre gives rise to two

stereoisomers, L and D-amino acids.

Protein, L amino acids only.

LO
 A malic acid with 1 chiral carbon atom has
21 = 2 stereoisomers:
Malic acid

An aldohexose with 4 chiral carbon atoms

has 24 = 16 stereoisomers:

Aldohexose
20 Common Amino Acids

Amino acids are classified according to the R side

chain group.

4 groups of amino acids:

Non-polar amino acids (8)
Polar, neutral/uncharged amino acids (7)
Polar, Acidic amino acids (2)
Polar, Basic amino acids (3)

LO
(a) nonpolar (hydrophobic)
(a) nonpolar (hydrophobic)
(b) polar, neutral
(b) polar, neutral
c) acidic
(d) basic
 ZWITTERION

 At a certain pH known as the isoelectric point (pI), an amino acid has

no net charge, because the number of protonated ammonium groups
and deprotonated carboxylate groups are equal.

 The ions produced at the pI have both positive and negative charges and
are known as zwitterion. LO
The ionization of amino acids
Titration of amino acid
When an amino acid
is titrated, its
titration curve
indicates the
reaction of each
functional group with
hydrogen ion.

pKa3 6.00
pKa2 9.17

1.92

pI = 7.59

LO
Amino Acids Can Join Via Peptide Bonds

LO
Amino acid,
Peptide bond,
N-terminal residue,
C-terminal residue.

N C
Disulphide bond

Disulphide bond) is a
covalent bond,
usually derived by
the coupling of two
thiol group.

Involved oxidation of
thiol/sulfhydryl
groups.
 Define amino acids.
Amino acids are the building blocks of all proteins. They are organic compounds
with an amino (-NH2) and a carboxylic acid group (-COOH).

List 3 amino acids you would expect to find at

the surface of the trans-membrane protein in
the part that lie within the cell membrane.
Explain your choice in a sentence.
The inner part of the cell membrane is hydrophobic /
nonpolar, therefore we would expect to find
nonpolar amino acids such as Ala, Val, Leu, Ile, Phe,
Met, Pro, Trp at the surface of the protein in this
region.
•State letter arrow that points to amine end.
A
• State letter arrow that points to carboxyl end.

C
•State letter arrow that points to peptide bond.
B
The mirror-image objects cannot be superimposed on
one another but are related are said to be chiral.

LO
Protein Structure
1° structure: the sequence of amino acids in a
polypeptide chain, read from the N-terminal end to
the C-terminal end
2° structure: the ordered 3-dimensional arrangements
in localized regions of a polypeptide chain (α-helix
and -pleated sheet).
3° structure: the arrangement in space of all atoms in
a polypeptide chain
three-dimensional arrangement of all the atoms in
the protein (fibrous and globular proteins).
4° structure: the association of polypeptide chains
into aggregations
LO
Primary structure

This is the sequence of amino acids, which

form a chain connected by peptide bonds.
Secondary structure

The secondary structure is the way the linear sequence of a

protein folds up into:
α- Helix: It has a rod shape. The peptide is coiled around an
imaginary cylinder and stabilized by hydrogen bonds between
amine and carbonyl groups of the same polypeptide chain.

ß - pleated sheets: The amino acids adopt the conformation of

a sheet of paper and the structure is stabilized by hydrogen
bonds between the amine groups of one chain and the
carbonyl groups of an adjacent chain in different polypeptide
strands. Note that some of the strands are parallel and some
are antiparallel.
back LO
 Helix vs beta-sheet
N N C

H
H

C C N
Tertiary structure
The tertiary structure (or conformation) is the way the secondary
structures, α-helixes and ß-pleated sheets fold in respect to each
other to form a protein or a subunit of a more complex protein.

Amino acids which are very distant in the primary structure might
be close in the tertiary because of the folding of the chain.

Tertiary structure is largely maintained by disulfide bonds. Disulfide

bonds are formed between the side chains of cysteine by oxidation
of two thiol groups (SH) to form a disulfide bond (S-S), also
sometimes called a disulfide bridge.
 Myoglobin

Myoglobin is the oxygen storage protein for tissues, present in

skeletal muscles as an extra storage protein to enable muscles
cells to have a readily available supply of oxygen.

Myoglobin is comprised of a single

polypeptide chain of helical
secondary structure, which is
wrapped around a functionally
essential prosthetic group called a
heme.

The heme molecule is a porphyrin ring

complexed with Fe(II), and is responsible
for the oxygen-binding properties of
myoglobin. ferrous
 Heme
At the center of the heme is
an Fe(II) atom.
Four of the six coordination
sites around this atom are
occupied by nitrogen atoms
from a planar porphyrin ring.
The fifth coordination site is
occupied by a nitrogen atom
from a histidine side chain on
one of the amino acids in the
protein.
The last coordination site is
available to bind an O2 molecule.
Quaternary structure

The quaternary structure is the arrangement of polypeptide

subunits within complex proteins.
The interaction between subunits in proteins that consists of
more than one polypeptide.
The chains interact with each other non covalently via
electrostatic attractions, hydrogen bonds and hydrophobic
interactions.
Hydrophobic interaction is the main stabilizing force for
subunits in quaternary structure.
Hemoglobin is used to transport
oxygen in the blood in red blood
cells to tissue cells where it is used
directly. Hemoglobin
Function: O2 transport, able to bind
and release O2 easily depending
upon conditions
A tetramer, four polypeptide
chains, 2 α-chains and 2 ß-chains.

Hemoglobin has four separate

heme groups that can bind a
molecule of O2.
4 molecules of O2 can bind to one
molecule of hemoglobin, positive
cooperative.
 Fibrous vs Globular

keratin enzyme

collagen transporter

elastin regulatory protein

LO
 Fibrous vs Globular

Fibrous Globular
Elongated Compact spheroidal
Secondary structure Tertiary and quartenary
α-heliks structure (primary and
β-pleated sheets secondary)
Soluble
Insoluble
Enzymes, biological
Structural/supportive role
messengers and transport
mechanisms
 3-D
arrangement of
amino residues
HSTYHSTYHH..

10 20 30 40
Structure of silk

Its primary structure mainly consists of the

recurrent amino acid sequence (Gly-Ser-Gly-Ala-
Gly-Ala)n.

The fibroin protein consists of layers of antiparallel

β sheets.
Protein folding vs Protein denaturation
 Protein folding: the folding of polypeptide into functional 3D
structure.

 Proteins may begin to fold incorrectly or may associate with other

proteins before folding is completed.

 The incorrect protein folding is due to the hydrophobic regions that

should be buried inside the protein remain exposed.

 Protein denaturation: the loss of the structural order (2°, 3°, 4°, or a
combination of these) that gives a protein its biological activity.

 Denaturation can be brought about by heat, pH, detergent and urea.

LO
LO
Abnormalities in
Unfolded
protein folding

Folded
incorrectly

Misfolded

ABCDEFGHI Normal amino acid sequence

ABCDDDGHI Mutated amino acid sequence

p53 (also known as protein 53 or tumor protein 53), is a
tumor suppressor protein
p53 is crucial in multicellular organisms, where it
regulates the cell cycle and, thus, functions as a tumor
suppressor that is involved in preventing cancer.
its role in conserving stability by preventing genome
mutation.[5]
In the normal protein, hydrophobic (water-repelling) amino acids
bury themselves inside the protein right from the start of folding.
However, if the protein folds wrongly, these hydrophobic amino
acids are exposed and they rapidly seek out and bind to
hydrophobic groups on other protein molecules, forming the
insoluble aggregates or plaques that are found in Alzheimer�s
patients.

Protein folding technology
Joaquim Pietzsch
 Figure 1 | b-amyloid and Alzheimer�s disease.
a | b-amyloid peptide (Ab42; red) is released by the cleavage of amyloid precursor
protein (purple bar) by b-secretase at the amino terminal end of the b-amyloid peptide,
followed by cleavage involving g-secretase at the carboxy terminal.
b | Ab42 is then thought to self associate under certain circumstances to form
aggregates called b-amyloid in the brain. c | These plaques occur in high density in
many parts of the brain in Alzheimer �s disease and are thought to cause the shrunken
appearance of the brain and the clinical symptoms of dementia seen in Alzheimer �s
patients. Part b reproduced with permission from Sisodia, S. S. & St George-Hyslop, P.
H. Nature Rev. Neurosci. 4, 281�290 (2002) © Macmillian Magazines Ltd.
Learning outcomes

Describe nitrogen cycle, amino acid biosynthesis

and urea cycle.
Major Pathways for N Acquisition
All biological compounds contain N in a reduced form .
The principal inorganic forms of N are in an oxidized state
.
Thus, N acquisition must involve reduction of the
oxidized forms (N2 and NO3-) to NH4+ .

LO
 Nitrogen cycle

Nitrogen cycle is the movement of nitrogen through the food chain from simple
inorganic compounds to complex organic compounds
 Amino Acid Biosynthesis
Amino acids are synthesized from α-ketoacids.
Transaminated from another amino acid, glutamate

The enzyme involved in this reaction is an

aminotransferase, transamination.
α-ketoacid + glutamate ⇄ amino acid + α-ketoglutarate

Glutamate itself is formed by amination of α-ketoglutarate :

α-ketoglutarate + NH+4 ⇄ glutamate

Glutamate is the major donor of amino groups for amino acid

biosynthesis.
Amination
Amino Acid Biosynthesis

transamination

LO
 Amino Acid Synthesis
*One-carbon Transfers Hydrolisis of phosphate group

Transamination process
Glutamate as a nitrogen donor

C2-hydroxyl group is oxidized THF

*
to a keto group
Methylene-THF
 Amino Acid Synthesis

*One-carbon Transfers
themedicalbiochemistrypage.org/amino-acid-metabolism.php
 Amino Acid Requirements in Humans
Essential Nonessential
(Cannot be Synthesizesd)
Arginine Alanine
Histidine Asparagine
Isoleucine Aspartate
Leucine Cysteine
Lysine Glutamate
Methionine Glutamine
Phenylalanine Glycine
Threonine Proline
Tryptophan Serine
Valine Tyrosine
The body can synthesize some of these AA but not in sufficient quantities, need to obtain from diet.
 Amino acids Catabolism
The amino nitrogen of the amino acid is transferred to α-
ketoglutarate to produce glutamate, leaving behind the
carbon skeleton.
The carbon skeleton follows two general pathways,
depending on the end product.
Amino acids are grouped into two classes, based on whether or not
their carbon skeletons can be converted to glucose:
Glucogenic amino acids: Their carbon skeletons are degraded to
pyruvate, or to one of the 4- or 5-carbon intermediates of Krebs
Cycle that are precursors for gluconeogenesis. Glucogenic amino
acids are the major carbon source for gluconeogenesis when
glucose levels are low. They can also be catabolized for energy or
converted to glycogen or fatty acids for energy storage.
Ketogenic amino acids: Their carbon skeletons are degraded to
acetyl-CoA or acetoacetyl-CoA. For every 2-C acetyl residue
entering Krebs Cycle, two carbon atoms leave as CO2. Carbon
skeletons of ketogenic amino acids can be catabolized for energy
in Krebs Cycle, or converted to ketone bodies or fatty acids. They
cannot be converted to glucose.
LO
Excess nitrogen is excreted in one of
three forms:
Ammonia (as ammonium ion) eg. fish.
Uric acid eg. bird & other desert animals.
Urea eg. mammals – have bladders & adequate
water is available.

LO
Urea cycle describes the conversion reactions of ammonia
into urea.

Urea is the major end product of nitrogen metabolism in

humans and mammals.
Ammonia, the product of oxidative deamination reactions, is
toxic in even small amounts and must be removed from the
body.
Breakdown of Arg in the urea cycle releases two N and one C
as urea
4 high energy phosphate group are required. Because it takes 2 ATP to
regenerate one ATP from one AMP, four high energy phosphates are consumed in each turn of the cycle.

Urea cycle is linked to TCA by fumarate

LO
 CO2 +NH4+
2ATP + H2O

2ADP + P
See what you learned. Click for the answer after reading the question.

1. Name 5 -amino acids that are required in the urea cycle.

There are 3 traditional, arginine, aspartate, and glutamate, as well 2

non-traditional: ornithine and citrulline. By traditional is meant
amino acids that appear in proteins.

2. What is the function of glutamate in the cycle?

Glutamate is needed to regenerate aspartate from OAA.

3. All told, how may ATPs are needed to make one molecule of urea?
Three are needed . Two to make carbamoyl-PO 4 and one to provide
energy for the aspartate condensation with citrulline.
4. Why is the urea cycle referred to as a “bicycle”?
There are actually 2 cycles going on. One takes ornithine to
arginine and returns arginine to ornithine. The second takes
fumarate from the argininosuccinate and returns it to aspartate.
Calculate the concentrations of all ionic species
in a 0.25 M solution of histidine at
pH 2, pH 6.4, and pH 9.3.
Serine Family

Pyruvate Family
Aromatic Family

Glutamate & Histidine Families

Aspartate Family