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Chapter 5
Amino Acids and
Proteins
Structural Differences Between Carbohydrates, Lipids, and Proteins
Figure 6.1
The Anatomy of an Amino Acid
Figure 6.2b
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
Condensation and Hydrolytic Reactions
Figure 6.3
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
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
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
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
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).
Partition occurs between the mobile phase and the
stationary aqueous phase bound by the cellulose.
Paper chromatography is used to separate amino
acids.
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
Types of Electrophoresis
Moving Boundary Zone
Paper
Gel
Polyacryalmide Agarose
Non Dissociating
(Native-PAGE)
Dissociating
(SDS-PAGE)
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
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.
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
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.
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.
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.
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.
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
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
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
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.
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.
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.
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
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
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
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.
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
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
+
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.
• 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.
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.
• 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.
For example
+NH3
|
H-C-COO-
|
H-C-H
|
H
O
||
C-COO-
|
H-C-H
|
H-C-H
|
COO-
O
||
C-COO-
|
H-C-H
|
H
+NH3
|
H-C-COO-
|
H-C-H
|
H-C-H
|
COO-
+ +
alanine -ketoglutarate pyruvate glutamate
to the
citric acid cycle
on to the
next step
The amino group receiver is
usually -ketoglutarate.
alanine
aminotransferase
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+.
Oxidative deamination example
NADH
+
H+
+
NH4
+
+
off to the
urea cycle
O
||
C-COO-
|
H-C-H
|
H-C-H
|
COO-
+NH3
|
H-C-COO-
|
H-C-H
|
H-C-H
|
COO-
+ NAD+ + H2O
glutamate -ketoglutarate
Energy
Summary
transamination
oxidative
deamination
-amino acid
-keto acid
-ketoglutarate
glutamate
NAD+ + H2O
NADH + NH4
+
oxaloacetate
aspartate
To the urea cycle
(1) (2)
• 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
• 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.
COO-
C
H3
+
N
CH
H3C
CH3
H
COO-
C
H3
+
N
CH
H3C
CH2
H
CH3
COO-
C
H3
+
N
CH2
CH
H
CH3
H3C
COO-
C
CH
H3C
CH3
O
COO-
C
CH
H3C
CH2
O
CH3
COO-
C
CH2
CH
O
CH3
H3C
C
CH
H3C
CH3
O SCoA
C
CH
H3C
CH2
CH3
O SCoA
C
CH2
CH
CH3
H3C
O SCoA
CoASH CO2
-keto acid
dehydrogenase
complex
branched-
chain
amino
transferase
valine
isoleucine
leucine
Acyl-CoA
derivatives
• 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
p-hydroxyphenypyruvate
homogentisate
CH2
C
O
COO-
OH
OH
OH
CH2
COO-
4-maleylacetoacetate
-
OOC
C
H
C
C
H
C
H2
O
C
O
C
H2
COO-
-
OOC
C
H
C
C C
H2
C
O
C
H2
COO-
H
O
4-fumarylacetoacetate
C C
-
OOC H
H COO-
H3C C
O
C
H2
COO-
fumarate
acetoacetate
+
homogentisate
oxidase
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
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).
• 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
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
• 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
Biosynthesis of Chlorophyll
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.
Reaction pathway
Enzyme structure
• Enzymes are
proteins
• They have a globular
shape
• A complex 3-D
structure
Human pancreatic amylase
The active site
• One part of an enzyme,
the active site, is
particularly important
• The shape and the
chemical environment
inside the active site
permits a chemical
reaction to proceed
more easily
© H.PELLETIER, M.R.SAWAYA
ProNuC Database
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
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
• 1. Oxidoreductases
• 2. Transferases
• 3. Hydrolases
• 4. Lyases
• 5. Isomerases
• 6. Ligases
Classification and Nomenclature of
Enzymes
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.
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
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
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.
5. Isomerases
• 5. Isomerases – catalyzes isomerization
reactions, including racemizations and cis-
tran isomerizations.
6. Ligases
• 6. Ligases -- catalyzes the synthesis of various
(mostly C-X) bonds, coupled with the
breakdown of energy-containing substrates,
usually ATP
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
The Lock and Key Hypothesis
Enzyme
may be
used again
Enzyme-
substrate
complex
E
S
P
E
E
P
Reaction coordinate
The Lock and Key Hypothesis
• This explains enzyme specificity
• This explains the loss of activity when
enzymes denature
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)
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
Factors affecting Enzymes
• Substrate concentration
• pH
• Temperature
• Inhibitors
Substrate concentration: Non-enzymic reactions
• The increase in velocity is proportional to the
substrate concentration
Reaction
velocity
Substrate
concentration
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
The effect of pH
Optimum pH
values
Enzyme
activity Trypsin
Pepsin
pH
1 3 5 7 9 11
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.
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.
The effect of temperature
Temperature / °C
Enzyme
activity
0 10 20 30 40 50
Denaturation
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.
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.
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.
The effect of enzyme inhibition
• Reversible inhibitors: These can be washed
out of the solution of enzyme by dialysis.
There are two categories.
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
The effect of enzyme inhibition
Succinate Fumarate + 2H++ 2e-
Succinate dehydrogenase
CH2COOH
CH2COOH CHCOOH
CHCOOH
COOH
COOH
CH2
Malonate
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.
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
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
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
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
Examples of isoenzymes commonly assayed for diagnostic purposes
Enzyme Location Cause of elevated plasma level
Creatine kinase – CK
CK-MB Heart Myocardial infarction
CK-MM Skeletal muscle Muscular dystrophy
Lactate dehydrogenase – LD
LD1 > LD2 Heart, kidney, Myocardial infarction, kidney
blood cells disease, megaloblastic anemia,
leukemia
LD2, LD3 Leukemia
LD5 Liver, muscle Liver disease, muscle damage
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Amino Acids and Proteins Explained: Structures, Functions, Biosynthesis

  • 1. Chapter 5 Amino Acids and Proteins
  • 2. Structural Differences Between Carbohydrates, Lipids, and Proteins Figure 6.1
  • 3. The Anatomy of an Amino Acid Figure 6.2b
  • 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
  • 5. Condensation and Hydrolytic Reactions Figure 6.3
  • 6.
  • 7.
  • 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.
  • 42. For example +NH3 | H-C-COO- | H-C-H | H O || C-COO- | H-C-H | H-C-H | COO- O || C-COO- | H-C-H | H +NH3 | H-C-COO- | H-C-H | H-C-H | COO- + + alanine -ketoglutarate pyruvate glutamate to the citric acid cycle on to the next step The amino group receiver is usually -ketoglutarate. alanine aminotransferase
  • 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+.
  • 44. Oxidative deamination example NADH + H+ + NH4 + + off to the urea cycle O || C-COO- | H-C-H | H-C-H | COO- +NH3 | H-C-COO- | H-C-H | H-C-H | COO- + NAD+ + H2O glutamate -ketoglutarate Energy
  • 45. Summary transamination oxidative deamination -amino acid -keto acid -ketoglutarate glutamate NAD+ + H2O NADH + NH4 + oxaloacetate aspartate To the urea cycle (1) (2)
  • 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.
  • 59. Enzyme structure • Enzymes are proteins • They have a globular shape • A complex 3-D structure Human pancreatic amylase
  • 60. The active site • One part of an enzyme, the active site, is particularly important • The shape and the chemical environment inside the active site permits a chemical reaction to proceed more easily © H.PELLETIER, M.R.SAWAYA ProNuC Database
  • 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
  • 63. • 1. Oxidoreductases • 2. Transferases • 3. Hydrolases • 4. Lyases • 5. Isomerases • 6. Ligases Classification and Nomenclature of Enzymes
  • 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
  • 75. Factors affecting Enzymes • Substrate concentration • pH • Temperature • Inhibitors
  • 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
  • 87. The effect of enzyme inhibition Succinate Fumarate + 2H++ 2e- Succinate dehydrogenase CH2COOH CH2COOH CHCOOH CHCOOH COOH COOH CH2 Malonate
  • 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
  • 94. Examples of isoenzymes commonly assayed for diagnostic purposes Enzyme Location Cause of elevated plasma level Creatine kinase – CK CK-MB Heart Myocardial infarction CK-MM Skeletal muscle Muscular dystrophy Lactate dehydrogenase – LD LD1 > LD2 Heart, kidney, Myocardial infarction, kidney blood cells disease, megaloblastic anemia, leukemia LD2, LD3 Leukemia LD5 Liver, muscle Liver disease, muscle damage