The document discusses amino acids and protein structure and function. It begins by describing how amino acids are linked by peptide bonds to form polypeptide chains and proteins. It then explains that amino acids can be essential, nonessential, or conditionally essential depending on whether they must be obtained from diet. The document also discusses protein structure, the uses of proteins in the body, and how the body breaks down and uses amino acids for energy or biosynthesis through various pathways.
4. Peptide Bonds Link Amino Acids
• Form when the acid group (COOH) of one amino
acid joins with the amine group (NH2) of a second
amino acid
• Formed through condensation
• Broken through hydrolysis
8. Essential, Nonessential, and
Conditional
• Essential – must be consumed in the diet
• Nonessential – can be synthesized in the body
• Conditionally/Semi essential – cannot be
synthesized due to illness or lack of necessary
precursors
– Premature infants lack sufficient enzymes needed to
create arginine
9. What Are Proteins?
• Large molecules
• Made up of chains of amino acids
• Are found in every cell in the body
• Are involved in most of the body’s functions and
life processes
• The sequence of amino acids is determined by
DNA
10. Structure of Proteins
• Made up of chains of amino acids; classified by
number of amino acids in a chain
– Peptides: fewer than 50 amino acids
• Dipeptides: 2 amino acids
• Tripeptides: 3 amino acids
• Polypeptides: more than 10 amino acids
– Proteins: more than 50 amino acids
• Typically 100 to 10,000 amino acids linked together
• Chains are synthesizes based on specific bodily DNA
• Amino acids are composed of carbon, hydrogen,
oxygen, and nitrogen
11. How Does the Body Use Protein?
• Uses of protein
– Provide structural and mechanical support
– Maintain body tissues
– Functions as enzymes and hormones
– Help maintain acid base balance
– Transport nutrients
– Assist the immune system
– Serve as a source of energy when necessary
12.
13. Paper Chromatography
A method of partition chromatography using filter
paper strips as carrier or inert support.
The factor governing separation of mixtures of solutes
on filter paper is the partition between two
immiscible phases.
One is usually water adsorbed on cellulose fibres in the
paper (stationary phase).
The second is the organic solvent flows past the sample
on the paper (stationary phase).
14.
15. Partition occurs between the mobile phase and the
stationary aqueous phase bound by the cellulose.
Paper chromatography is used to separate amino
acids.
16. 16
Electrophoresis:
The transport of particles through a solvent by an electric field is called
electrophoresis.
In the biological system, many molecules are electrically charged and
will move if electric field is applied.
In electrophoresis, macromolecules are
characterized by their rate of movement in an
electric field.
This technique is used to (1) distinguish molecules
on the basis of charge and shape (2) to determine
molecular weight of proteins (3) to detect amino acid
changes from charged to uncharged residues & (4) to
separate different molecular species quantitatively.
17. 17
Types of Electrophoresis
Moving Boundary Zone
Paper
Gel
Polyacryalmide Agarose
Non Dissociating
(Native-PAGE)
Dissociating
(SDS-PAGE)
18. 18
Gel electrophoresis
* It is used for the separation of proteins and nucleic acids
* Many types of gels are used as supporting medium e.g. starch,
polyacrylamide and agarose
* Earliest work in gel electrophoresis was done with starch
* It provided the first evidence for the existence of isozymes.
* Generally polyacrylamide gels are used for proteins and agarose for
nucleic acids
19.
20. NITROGEN FIXATION
Nitrogen is found in many different organic
and inorganic forms in the atmosphere and
biosphere.
nitrate NO3
-
nitrite NO2
-
hyponitrite N2O2
2-
nitrogen N2 (80%of air)
ammonia NH3
amino acids
protein
purines
pyrimidines
biogenic amines
Inorganic organic
Inorganic nitrogen can be used by plants and bacteria.
Nitrogen used by animals exists in organic forms.
21. The nitrogen cycle
• Soil bacteria play a significant role in cycling
nitrogen through the biosphere:
• Nitrogenase containing bacteria N2 NH3
• Nitrite bacteria (Nitrosomonas) NH3 NO2
-
• Nitrate bacteria (Nitrobacter) NO2
- NO3
-
• Denitrifying bacteria NO3
- N2
22. N N + 3 H2 2 NH3
A bond very
difficult to break.
• This is a reduction reaction of N2, and is
thermodynamically unfavorable.
• 16 ATP is required to fix one molecule of N2.
Biological Nitrogen Fixation
• N2 is converted by some bacteria into ammonia
(NH3) that can be used by plants.
23. Biological significance of nitrogen fixation
- a self fertilization system for plants.
Some bacteria can develop specific association with
certain plants.
Legume plants, after being infected by bacteria
(Clostridia) will form tumor-like nodules on their roots,
which allows cooperative association between bacteria
and plants.
The plants produce carbohydrate for bacteria; and bacteria
provide ammonia to plants by carrying out N fixation.
24. Biosynthesis of amino acids
• While each amino acids has a unique
biosynthetic pathway, each shares several
common features:
– There are six biosynthetic families based on
common precursors.
– Amino acids obtain their carbon skeletons from
an intermediate of glycolysis, citric acid cycle or
phosphogluconate pathway.
– -NH2 usually comes from glutamate.
25. Essential amino acids
• Produced by plants and bacteria.
• Biosynthesis involves longer and more complex
pathways.
• Example
• Synthesis of phenylalanine, tyrosine and
tryptophan.
• They share two to three common steps.
26. Essential amino acids
COO-
OH
O C
COO-
O
P C
H2
C
OH
H
C
OH
H
C
O
H
H2C C
P
COO-
+
erythrose
4-phosphate
phosphoenol-
pyruvate
several
steps
2 Pi
Chorismate
to tryptophan to tyrosine &
phenylalanine
27. COO-
OH
O C
COO-
O
Chorismate
COO-
H2N
N
H
C C H
H
H
NH3
+
COO-
Anthranilate
Tryptophan
CH2
C
COO-
O
CH2
C
COO-
H
+
H3N
CH2
C
COO-
O
OH
CH2
C
COO-
H
+
H3N
OH
Phenylpyruvate Phenylalanine
p-Hydroxyphenyl
pyruvate
Tyrosine
28. Six biosynthetic families based on
common precursors.
Pyruvate
Alanine
Valine
Leucine
Oxaloacetate
Aspartate
Asparagine
Methionine
Lysine
Threonine
Isoleucine
Ribose-5-phosphate
Histidine
-Ketoglutarate
Glutamate
Glutamine
Proline
Arginine
3-Phosphoglycerate
Serine
Cysteine
Glycine
Phosphoenolpyruvate
Tryptophan
Phenylalanine
Tyrosine
29. pyruvate + glutamate alanine + -ketoglutarate
oxaloacetate +glutamate aspartate +-ketoglutarate
alanine
aminotransferase
aspartate
aminotransferase
Alanine can be synthesized from the interaction between
pyruvate and glutamate. Pyruvate gains an amino group
to become alanine, and glutamate loses –NH2 and
oxidized to become a-ketoglutarate.
30. Glutamate synthesis
COO-
C O
CH2
CH2
COO-
+ NH4
+
+ NADPH + H
+
COO-
C H
CH2
CH2
COO-
H3N+
+H2O +NADP
+
glutamate
dehydrogenase
-ketoglutarate glutamate
The process of amino group addition is called
amination.
-ketoglutarate ties this process to the citric acid cycle.
31. Glutamine synthesis
+ NH4
+
+ ATP
COO-
C H
CH2
CH2
C
H3N+
+ ADP + Pi
glutamine
synthetase
COO-
C H
CH2
CH2
COO-
H3N+
O
NH2
Glutamate can be further aminated to form glutamine.
32. Glutamate and glutamine
• All life has the glutamate dehydrogenase
and glutamine synthetase.
• In addition, higher plants and prokaryotes
have glutamate synthase.
-ketoglutarate + glutamine + NADPH + H+
• 2 glutamate + NADP+
glutamate synthase
33. Nonessential amino acids
• Those that can be produced by animals.
• Pathways are relatively straightforward.
• pyruvate + glutamate alanine + -ketoglutarate
• oxaloacetate + glutamate aspartate +-ketoglutarate
• Some pathways are more complex, like the one
for serine.
alanine
aminotransferase
aspartate
aminotransferase
34. Biosynthesis of serine
COO-
C
H OH
CH2
OPO3
2-
COO-
C O
CH2
OPO3
2-
COO-
C H
CH2
OPO3
2-
H3
+
N
COO-
C H
CH2
OH
H3
+
N
hydrolysis
NAD+ NADH + H+
glutamate
-ketoglutarate
H2O
Pi
oxidation-reduction
transamination
3-phosphoglycerate
3-phospho-
hydroxy-
pyruvate
3-phospho-
serine
serine
35. Biosynthesis of glycine
• Glycine is synthesized from serine.
• It uses an unusual process - a one carbon
transfer.
• Tetrahydrofolate (FH4) is an essential cofactor
for this reaction.
36. Biosynthesis of glycine
COO-
C
CH2OH
H3
+
N H
C
C
N
H
CH2
H
N
CH2
H
N
H
COO-
C
H
H3
+
N H
N
CH2
H
N
CH2
H
N
C
H2
+
+
Serine
Glycine
Tetrahydrofolate
N5,N10-Methylene-
tetrahydrofolate
37. Major metabolic pathways
of amino acids
Dietary
protein
Body
protein
Amino acid
pool
Liver
synthesis
Nitrogen
Compounds
citric acid
cycle
urea
cycle
turnover
catabolism
digestion
carbon
skeleton
NH4
+
38. Amino acid Catabolism
• Amino acids cannot be stored.
• If there is an excess of amino acids or a lack
of other energy sources, the body will use
them for energy production.
Amino acid degradation requires the
removal of the amino group as ammonium.
• Ammonium must then be disposed of as it is
toxic to the body.
39. • Amino acids are only used as fuel when:
• Too much protein is ingested
• Normal recycling of protein
• Starvation/diabetes.
• Catabolic pathways
• Each amino acid has a unique pathway.
• All are converted to mainstream metabolites.
40. Catabolism of amino acids starts with
deamination.
After losing the amino group the rest of the
carbon skeleton can usually enter TCA cycle as
intermediate molecules for energy production.
41. • Removal of amino group is a two step
process.
–Transamination reaction
• Aminotransferase moves the amino group to
to a -Keto acid to form another amino acid.
The amino group receiver is usually -
ketoglutarate to produce glutamate.
–Oxidative deamination
• Removal of the amino group from glutamate
producing an ammonium ion.
43. The purpose of transamination is to transfer the
amino groups to one species of a.a. (glutamate)
that can be used for further nitrogen metabolism,
either synthesis of other amino acid or elimination
of NH4+.
46. • Ketogenic amino acids (Isoleucine, leucine, isolucine and
tyrosine…)
• Degraded to acetyl CoA or acetoacetyl CoA
• Produce ketone bodies.
• Glucogenic amino acids (argenine, glutamate, valine
aspartate…)
• Degraded to pyruvate, -ketoglutarate, succinyl
CoA, fumarate or oxaloacetate.
• They can then be used for glucose synthesis.
Catabolism of the carbon skeleton
47. • Isoleucine, leucine and valine share some
steps in their catabolism.
• Transamination is catalyzed by branched-chain
aminotransferase.
• After transamination, ketoproducts are then
decarboxylated via a complex similar to the
pyruvate dehydrogenase complex.
• Their catabolism then proceeds in different
directions.
49. • Phenylalanine catabolism
• Transamination does not occur as the first step. It is
initially hydroxylated to tyrosine
CH2
C
H +
NH3
COO-
CH2
C
H +
NH3
COO-
OH
phenylalanine
hydroxylase
phenylalanine tyrosine
p-hydroxyphenypyruvate
CH2
C
O
COO-
OH
Transamination
51. Where amino acids enter cycle
tyrosine
phenylalanine
aspartate
oxaloacetate
citrate
-ketoglutarate
succinyl
CoA
fumarate
pyruvate
acetyl
CoA
acetoacetyl
CoA
glutamate, glutamine
proline, arginine
isoleucine
leucine
tryptophan
leucine
lysine
phenylalanine
tryosine
tryptophan
isoleucine
methionine
valine
asparagine
aspartate
alanine, glycine
serine, threonine
tryptophan
52. Elimination of ammonium ion
• NH4+ is produced from amino acid catabolism is toxic
and must be eliminated.
• NH4+ is eliminated through the urea cycle
that occurs in the liver.
• The urea cycle
–Occurs in the liver.
–Results in the formation of urea.
–Urea is eliminated by excretion (urine).
53. • Urea cycle is a five-step pathway carried out by
liver cells.
• The strategy is to synthesize arginine that is
then hydrolyzed to release urea and L-ornithine
54. COO- NH2 COO-
| | |
-OOC-CH2CH-N=C-NH-(CH2)3CH
L-argininosuccinate
NH4
+ + CO2 carbamoyl
phosphate
O O
| | | |
H2N-C-O-P-O-
|
O-
O NH3
+
| | |
H2N-C-NH-(CH2)3CH-COO-
L-citrulline
NH3
+
|
-OOCCH2CH-COO-
L-aspartate
NH3
+
|
+H3N-(CH2)3CH-COO-
L-ornithine
-OOC-CH=CH-COO-
fumarate
NH2 NH3
+
| |
+H2N=C-NH-(CH2)3CH-COO-
L-arginine
O
| |
H2N-C-NH2
urea
ATP
AMP
+ PPi
H2O
Pi
2 ATP + 2 H2O
2 ADP
+ Pi
Urea
Cycle
55. • A complete block of any step of the urea
cycle is incompatible with life.
• No alternate pathway for NH4
+ elimination.
• Some genetic disorders will affect
arginase
carbamoyl phosphate synthase
ornithine transcarbamoylase
57. Enzymes - Introduction
• A protein with catalytic properties due to its power
of specific activation
• Chemical reactions need an initial input of energy =
THE ACTIVATION ENERGY
• During this part of the reaction the molecules are
said to be in a transition state.
61. Coenzymes
• An additional non-
protein molecule that is
needed by some
enzymes to help the
reaction is cofactor
• Tightly bound cofactors
are called prosthetic
groups
• Cofactors that are bound
and released easily are
called coenzymes
• Many vitamins are
coenzymes (eg) Biotin
Nitrogenase enzyme with Fe, Mo and ADP cofactors
62. The substrate
• The substrate of an enzyme are the reactants
that are activated by the enzyme
• Enzymes are specific to their substrates
• The specificity is determined by the active site
64. 1. Oxidoreductases
• Oxidoreductases :catalyze the transfer of
hydrogen or oxygen atoms or electrons from
one substrate to another, also called
oxidases, dehydrogenases, or reductases.
Note that since these are ‘redox’ reactions,
an electron donor/acceptor is also required
to complete the reaction.
65. 2. Transferases
• 2. Transferases – catalyze group transfer
reactions, excluding oxidoreductases (which
transfer hydrogen or oxygen and are EC 1).
These are of the general form:
• A-X + B ↔ BX + A
66. 3. Hydrolases
• 3. Hydrolases – catalyze hydrolytic reactions.
Includes lipases, esterases, nitrilases,
peptidases/proteases. These are of the
general form:
• A-X + H2O ↔ X-OH + HA
67. 4. Lyases
• 4. Lyases – catalyze non-hydrolytic (covered in
EC 3) removal of functional groups from
substrates, often creating a double bond in the
product; or the reverse reaction, ie, addition of
function groups across a double bond.
• A-B → A=B + X-Y
X Y
• Includes decarboxylases and aldolases in the
removal direction, and synthases in the addition
direction.
68. 5. Isomerases
• 5. Isomerases – catalyzes isomerization
reactions, including racemizations and cis-
tran isomerizations.
69. 6. Ligases
• 6. Ligases -- catalyzes the synthesis of various
(mostly C-X) bonds, coupled with the
breakdown of energy-containing substrates,
usually ATP
70. Mechanism of Action of Enzymes
1. The Lock and Key Hypothesis
• Fit between the substrate and the active site of the enzyme is
exact
• Like a key fits into a lock very precisely
• The key is analogous to the enzyme and the substrate
analogous to the lock.
• Temporary structure called the enzyme-substrate complex
formed
• Products have a different shape from the substrate
• Once formed, they are released from the active site
• Leaving it free to become attached to another substrate
71. The Lock and Key Hypothesis
Enzyme
may be
used again
Enzyme-
substrate
complex
E
S
P
E
E
P
Reaction coordinate
72. The Lock and Key Hypothesis
• This explains enzyme specificity
• This explains the loss of activity when
enzymes denature
73. 2. The Induced Fit Hypothesis
• Some proteins can change their shape
(conformation)
• When a substrate combines with an enzyme, it
induces a change in the enzyme’s conformation
• The active site is then moulded into a precise
conformation
• Making the chemical environment suitable for the
reaction
• The bonds of the substrate are stretched to make the
reaction easier (lowers activation energy)
74. The Induced Fit Hypothesis
• This explains the enzymes that can react with a range
of substrates of similar types
Hexokinase (a) without (b) with glucose
substrate
76. Substrate concentration: Non-enzymic reactions
• The increase in velocity is proportional to the
substrate concentration
Reaction
velocity
Substrate
concentration
77. Substrate concentration: Enzymic reactions
• Faster reaction but it reaches a saturation point when all the
enzyme molecules are occupied.
• If you alter the concentration of the enzyme then Vmax will
change too.
Reaction
velocity
Substrate
concentration
Vmax
78. The effect of pH
Optimum pH
values
Enzyme
activity Trypsin
Pepsin
pH
1 3 5 7 9 11
79. The effect of pH
• Extreme pH levels will produce denaturation
• The structure of the enzyme is changed
• The active site is distorted and the substrate
molecules will no longer fit in it
• At pH values slightly different from the enzyme’s
optimum value, small changes in the charges of the
enzyme and it’s substrate molecules will occur
• Optimum pH: The pH at which the given enzyme
exhibits maximum activity is called as Optimum pH.
80. The effect of temperature
• The temperature coefficient = the increase in
reaction rate with a 10°C rise in temperature.
• Enzyme-controlled reactions follow this rule as they
are chemical reactions
• BUT at high temperatures proteins denature
• The optimum temperature for an enzyme controlled
reaction will be a balance between the starting and
denaturation.
81. The effect of temperature
Temperature / °C
Enzyme
activity
0 10 20 30 40 50
Denaturation
82. The effect of temperature
• For most enzymes the optimum temperature is about
30°C
• Many are a lot lower, cold water fish will die at 30°C
because their enzymes denature
• A few bacteria have enzymes that can withstand very
high temperatures up to 100°C. Most enzymes however
are fully denatured at 70°C.
• Optimum temperature: The temperature at which the
given enzyme exhibits maximum activity is called as
Optimum pH.
83. Inhibitors
• Inhibitors are chemicals that reduce the rate
of enzymic reactions.
• The are usually specific and they work at low
concentrations.
• They block the enzyme but they do not usually
destroy it.
• Many drugs and poisons are inhibitors of
enzymes in the nervous system.
84. The effect of enzyme inhibition
• Irreversible inhibitors: Combine with the
functional groups of the amino acids in the
active site, irreversibly.
Examples: Nerve gases and pesticides,
containing organophosphorus, combine with
serine residues in the enzyme acetylcholine
esterase.
85. The effect of enzyme inhibition
• Reversible inhibitors: These can be washed
out of the solution of enzyme by dialysis.
There are two categories.
86. The effect of enzyme inhibition
1. Competitive: These
compete with the
substrate molecules for
the active site.
The inhibitor’s action is
proportional to its
concentration.
Resembles the substrate’s
structure closely.
Enzyme
inhibitor
complex
Reversible
reaction
E + I EI
88. The effect of enzyme inhibition
2. Non-competitive: These are not influenced by the
concentration of the substrate. It inhibits by binding
irreversibly to the enzyme but not at the active
site.
Examples
• Cyanide combines with the Iron in the enzymes
cytochrome oxidase.
• Heavy metals, Ag or Hg, combine with –SH groups.
These can be removed by using a chelating agent such
as EDTA.
89. Applications of inhibitors
• Negative feedback: end point or end product
inhibition
• Poisons snake bite, plant alkaloids and nerve
gases.
• Medicine antibiotics, sulphonamides,
sedatives and stimulants
90.
91. ENZYMES IN MEDICINE
• Diagnostic indicators – the activities of many enzymes are
routinely determined in plasma ( rarely in tissue biopsies) for
diagnostic purposes in diseases of the heart, liver, skeletal muscle,
pancreas and other tissues - enzyme diagnostics
• Therapeutic agents – several enzymes are used as drugs; new
approach - enzymotherapy
• Diagnostic tools – use as chemicals in clinical laboratory assays
92. ENZYMES IN CLINICAL DIAGNOSIS
secretory - produced by tissues (namely liver), acting in plasma –
prothrombin, plasminogen, cerruloplasmin, choline
esterase; lipoprotein lipase
Enzymes
intracellular – function intracellulary, have no physiological use in
plasma
- membrane bound – ALP, GMT
- cytosolic – ALT, AST, LD, MDH
- mitochondrial – AST, GMDH
- lysosomal - ACP
- tissue specific – glucose-6-phosphatase – liver
amylase – pancrease
LD1 – heart
93. Examples of enzymes commonly assayed for diagnostic purposes
Enzyme Location Cause of elevated plasma level
Acid phosphatase - ACP Prostate Prostatic cancer
Alkaline phosphatase – ALP Bone, liver Rickets, hypoparathyroidism,
osteomalacia, obstructive
jaundice, cancer of bone/liver
Alanine aminotransferase – ALT Liver (muscle, Hepatitis, jaundice, circulatory
heart, kidney) faillure with liver congestion
Aspartate aminotransferase – AST Heart, muscle, Myocardial infarction, muscle
red cells, liver damage, anemia, hepatitis,
circulatory faillure with liver
congestion
Amylase - AM Pancres Acute pancreatitis, peptic ulcer
-Glutamyl transferase – GMT Liver, kidney, Hepatitis, alcoholic liver
pancreas damage, cholestasis