Week 1

Proteins are made up of a series of amino acids.

Amino acids have an amino and acid group.
20 amino acids are available in the human body for the synthesis of proteins.
All 20 amino acids are alpha, L.

H
I
H2N---C---COOH - Typical amino acid
I
R

The R group (variable side chain) is the only difference between amino acids.

Amino acids are chiral molecules.

Protein functions:
- Structure building (collagen, elastin)
- Enzymes (amylase)
- Transport (haemoglobin, albumin, lipoproteins, transferrin, ceruloplasmin)
- Hormones (LH, FSH, TSH, Prolactin, Insulin)
- Neurotransmitters: Rhodopsin
- Contractility: Actin & Myosin
- Immunity: Antibodies

Ceruloplasmin transports copper

Transferrin transports ions.
Albumin is a general transport molecule. Transports ions, hormones, fatty acid

Amino Acids

1) Apolar, non aromatic side chain

- Gly - Glycine
- Ala - Alanine
- Val - Valine
- Leu - Leucine
- Ile - Isoleucine
- Pro - Proline

2) Aromatic side chain

- Phe - Phenylalanine
- Tyr - Tyrosine
- Trp - Tryptophan

3) Polar, no charge side chain

- Ser - Serine
- Thr - Threonine
- Cys - Cysteine
- Asn - Asparagine
- Gln - Glutamine
- Met - Methionine

4) Acidic Side Chain

- Asp - Aspartic Acid
- Glu - Glutamic acid

5) Basic Side Chain

- Lys - Lysine
- Arg - Arginine
- His - Histidine.

Post translational modification is done after the amino acid sequence has been made.

In proteins, amino acids are arranged in a linear chain and folded into globular form.
The amino group of one amino acid bonds with a acid group of another amino acid to
form a peptide bond. (CONH)
Peptide bond is between adjacent amino acids.

Structure and function of proteins are closely related.

There are 20 amino acids in human body

Proteins have primary, secondary, tertiary, quaternary structures.

Primary: Sequence of amino acids. (Contains all relevant info to build protein)
Secondary: Local 3 dimensional structure. Common ones are alpha helixes and beta
pleated sheet
Tertiary: 3D structure of proteins. Functional structure.
Quaternary: More than one chain/subunit. Combination of subunits.

Domains:
Structural, Functional unit of proteins

Function of proteins:
- Structure (collagen)
- Transport (albumin)
- Storage
- Signalling (glycine)
- Hormones (growth hormone)
- Enzymes (amylase)
- Immunity (Antibodies)
- Contraction (actin, myosin)

Enzymes are biological catalysts. Speed up biological reactions.

Precusor: Very first substance in a chain.

Steady state: There is a balance maintained in a series of reactions.

There is net zero change of a parameter in a system

Free Energy (G)

If energy of reactant is greater than energy of product then it is a spontaneous reaction

as energy is released.

If energy of reactant is less than energy of product then energy must be invested for the
reaction to happen.
Activation energy must be overcome for the reaction to take place.

Enzymes reduce the activation energy required for the reaction.

Enzymes are usually proteins but can be RNA too.
Enzymes have substrate and reaction specificity.
Enzymes do not change the direction of the reaction.
Enzymes are temperature and pH dependent.
Enzymes only speed up the reaction.
Denaturation van be reversible and irreversible.

Rate determining/Limiting Step is the weakest link in the reaction chain.

The speed of the whole reaction depends on this step. It is the slowest step and thus
acts as a bottleneck.

Commmitted Step:
After this step, molecules are fully committed to the certain pathway and will only end
up as the pathway end products.
It is an irreversible enzymatic reaction that occurs at a branch point.

Key step is the most regulated step.

Week 2
Blood is made up of cells (RBC, WBC, platelets) and plasma (water, electrolytes,
proteins).
Blood becomes serum after sedimentation and coagulation.
Cells fall down to the bottomdue to their weight.

There is delocalisation of electrons in the peptide bond.

Cu2+ ions can reaact with the deloclaised electrons in the peptide bond. Gives a violet -
blue color. This si the Biuret reaction (detects peptide bonds)

In colorometry the target can go from uncolored to colored or from one color to another
color.
Intensity of color change is proportional to the concentration of target.

Photometer measures color change intensity.

Albumin is the most abundant protein in blood plasma.

In photometry, there is a light source.

Due to the sample, the light can be reflected, scattered, absorbed or transmitted.

The amount of light transmitted is inversely proportional to the amount of light

absorbed. Knowing one can give the absorption value.

Since specific wavelengths are used in photometry, this process uses monochromator
(fliters)

Absorbance = molar absorption coefficient x Molar concentration x Optical path length

When using a standard solution, we know the concentration in this solution.

We compare this standard solution to the sample with unknown concentration then do
maths by comparing absorbance values of both.

Hypoalbuminemia - Less albumin in the blood than normal

Could be due to nephrotic syndrome.
This is a kidney disease in which the kidney podocytes malfunction and proteins are
filtered out of the body.
Enzymes have a 3D structure.
They have an active site which is responsible for substrate binding and catalysis.
The active site has 2 domains.
Substrate binding domain & Catalytic Domain
Domains are suprasecondary structures.

Substrate specificity by:

Lock & Key mechanism
Induced Fit model (used today):
The substrate can modify conformation of the enzyme and vice versa to find the best
fitting.

Sunstrate specificity can be wide. This means certain enzymes can act on various
similar substrates.
(Eg: Alcohol dehydrogenase, Cytochrome P450 are both liver enzymes)

Multienzyme complex:
Multiple enzymes work together like in a factory.
Due to this:
Diffusion distances between substrate and active site reduces.
Reaction rate increases
Chances of side reaction reduces.
There is coordinated control and regulation of reactions.

Eg:
Fatty Acid Synthetase (7 steps)
Glutamine synthetase (2 steps)
Pyruvate dehydrogenase (Pytuvate ----------> Acetyl CoA)

Isoenzymes: Same function but different structure.

Isooenzymes perform the same catalysis using the same substrates but have different
structures and work in different locations.
Eg: Creatine Kinase has 3 isoenzymes.

CPK1 (BB subunit) in brain

CPK2 (MB subunit) in heart
CPK3 (MM subunit) in skeletal muscle

For all 3, substrates and products are the same, just the enzyme structure is different.

Lactate dehydrogenase is also an isoenzyme.

Has 5 variations. PResent in heart, brain, kidney, liver, skeletal muscles.

Enzyme activity:
Consumption of substrate or Production of product over time
SI unit is Katal = mol/s
However we use: U = micromol/minute

Molecular mechanism of enzyme catalysis

Enzyme binds to substrate to form enzyme substrate complex.

This complex undergoes catalysis because enzyme substrate interaction align the
reactive chemical groups and hold them close together in an optimal geometry which
increases rate of reaction

Having the right orientation is crucial.

Catalysis can be:

acid base catalysis
metal ion catalysis
covalent.

To make the substrate more reactive, we can add or remove a proton. This is acid base
catalysis.
Many enzymes have metal ios. We could add or remove an electron to make the
substrate reactive. This is metal ion catalysis.

Covalent intermediates can be used to change the structure of substrates or eznyems.

This is covalent catalysis.
Kinetics looks at the speed of a reaction.
The Michaelis-Menten curve is linear, then saturates and then plateus.
It has velocity of the reaction (y axis) against the concentration of substrates (S)

Km value = S at which V=1/2 of Vmax and the Km value is constant for each enzymes.
The Km value describes the activity of the enymes.

V = Vmax x (S)/(S) + Km
Km = 1/2 Vmax

Mihaelis Mentes curve is a hyperbolic curve.

when number of substrate increases then:

Reaction speed increases
Number of products increase

Co enzymes are vitamin derivatives.

Enzymes almost always have -ase ending.

Pepsin is an exception

Enzymes have a systemic name which gives

substrate + function. Eg:
Creatin dehydrogenase

There is a special classification of enzymes.

Enzymes are written as classes.
Eg:
EC 1.1.1.1 is alcohol dehydrogenase

The very first number will indicate the enzyme class.

EC 1: Oxido-reductases
EC 2: Transferases
EC 3: Hydrolases
EC 4: Liases
EC 5: Isomerases
EC 6: Ligases
EC 7: Translocases

EC 1: Oxido-reductases
Enzynes that undergo oxidation or reduction
Oxidation is gain of oxygen, loss of hydrogen or electrons
Reduction is loss of oxygen, gaiin of hydrogen or electrons.

EC 2: Transferases
Enzymes that Transfers groups from one molecule to another.
Group could be phosphates, acyl, acetyl, amino, sulfur containing groups.

EC 3: Hydrolases
Enzymes that break bonds using the addition of water.

EC 4: Liases
Enzymes involved in Creating or destroying a double bond

EC 5: Isomerases
AB ----------> BA
No addition or removal of anything. Only internal structure changes. done by enzymes.

EC 6: Ligases
Enzymes that creates new compounds. Needs energy
A + B ------------> AB

EC 7: Translocases
Na+/K+ ATPase

Examples:

EC 1: Oxidoreductases

Lactic Acid (substrate) to Pyruvate (product)

Lactate dehydrogenase (enzyme)
NAD+ is the coenzyme ivloved.
NAD+ becomes NADH due to this reaction.

Phenyalanine (substrate) ---------> Tyrosine (product)

Enzyme used: Phenylalaninehydroxylase. Adds only one more O
THB ----> DP
THB is the coenzyme. (Tetrahydrobiopterin)

EC 2: Transferases

Glucose (substrate) ----------------> Glucokinase (product) {Glucose + P attached to carbon

6}
Source of phosphate group is ATP. ATP acts as coenzyme.
ATP ------> ADP
Enzyme is hexokinase

Kinase always means phosphotransferase.

Coenzyme for all kinase reactions is ATP (phosphate donor)

EC 3: Hydrolases

of esters: Esterases
of peptides: Peptidases
Digestive enzymes are hydrolases.

EC 4: Liases

2 Phosphoglucamate (substrate) ------------> phosphoenol pyruvate (product)

Enzymes is Enolase. Creates a double bond from a single bond.

Coenzymes are almost always necessary for reactions (except for hydrolases
enzymes).
Co enzymes are usually vitamin derivatives. They are removable and can be
interchanged.

NAD is Nicotinamide Adenine Dinucleotide

NAD+ ----------> NADH
NAD is a vitamin B3 derivative.
NAD/NADH is used in breaking down, catabolic reactions.
Proton carrier in Krebs cycle.

NADPH/NADP is used in anabolic, building up reactions.

FAD is Flavin Adenine Dinucleotide

Has the same function as NAD

NADH transports 3 ATP

FADH2 transports 2 ATP.

The enzyme class of hydrolases do not need or use coenzymes. Only class that does
so.
Week 3
All 20 amino acids in the human body are alpha amino acids.

Glutamate and Asparatate are the same as Glutamic Acid and Asprataic Acid.
Glutamate and Asparatate have (COO-) while the acids have (COOH)

Proteins in humans can be for:

Immunity
Enzymes
Contraction
Structure
Transport

Enzymes are biocatalysts.

They speed up reactions by lowering the activation energy of the reaction.

When naming enzyme classes:

EC 1.4.2.5
The first number is the major class.

EC 1 - Oxido Reductases
EC 2 - Transferases
EC 3 - Hydrolases
EC 4 - Lyases
EC 5 - Ismoerases
EC - Ligases
EC 7 - Translocases

EC 3 - Hydrolases
Cleaves bonds with the help of a water molecule. One substrate becomes 2 products

EC 6 - Ligases
Uses energy to combine 2 or more products into 1 product

EC 5 - Isomerases
Number of atoms remain the same. Just the structure is changed.
EC 2 - Transferases
Adds a P atom to one substrate outta nowhere. ATP is required.

EC 1 - Oxido - Reductases
Number of O or H atoms increase or decrease between substrates and products.

EC 4 - Lyases
Produces new molecules by removing any random part of the old molecule.
Addition or removal of groups to form double bonds.

When naming proteins:

Substrate/Product + Nature of reaction. Eg:
Lactate Dehydrogenase
Glutamine synthetase
Glucokinase

Kinase is the term used for phosphotransferase.

Co enzymese are absoluteley necessary for enyme activity.

Co enzymes are removable.

EC 1: Oxido reductases
EC 2: Transferases
EC 3: Hydrolases
EC 4: Lyases
EC 5: Isomerases
EC 6: Ligases
EC 7: Translocases.

Coenzymes can only act within one class except for ATP.
ATP acts on transferases and Ligases.

Vitamin derivatives are often coenzymes

EC 1 (Oxido-reductases) coenzymes:
- NAD/NADH
- NADP
- FAD
- FMN
- THB

- NAD/NADH (Nicotinamide adenine dinucleotide)

NAD is the oxidized form. NADH is the reduced form.
Transports 2 protons and electrons.
Only present with oxidoreductase enzymes
eg: Lactate dehydrogenase. This catalyzes the conversion of pyruvate to lactate

-NADP/NADPH
Coenzyme used in anabolic Reactions

- FMN (Flavin Mononucleotide), FAD (Flavin Adenine Dinucleotde)

From Riboflaivn. Coenzyme used in transferring protons and electrons in Kreb cycle.
FAD-----> FADH2

- Tetrahydrobiopterin (THB)
Coenzyme used in aromatic amino acid hydroxylase
Tryptophan, Phenylalanine, Tyrosine hydroxylase.

EC 2: Transferases Coenzymes:
- Coenzyme A
- ATP
- SAM
- PAPS
- Cobalamine

- Coenzyme A
Transfers acetyl groups

- ATP (Adenosie Tri Phosphate)

High energy compound. Cleaving the high energy bond releases lots of energy.
- Cobalamine (Vitamine B12)
Coenzyme in Transfers of methyl groups.
Involved in DNA, Amino Acid, Fatty acid synthesis

- S-adenosyl Methionine (SAM)

Coenzyme in transfers of methyl groups. Transsulfuratiob.

- PAPS (3' Phosphoadenosine-5'-Phosphosulfate)

Coenzyme sulfurotransferase reactions.

Enzyme Regulation: How are enzymes regulated

1) Compartmentalization
Enzymes perform different reactions in different places (In compartments) Could be
blood, digestive system, cytosol, mitochondria

2) Milieu factors
How the environmental surroundings (temperature, pH) regulate and effect the
enzymes.

3) Reaction partners
presence and conc of products, coenzyme

4) Susbtrate
Substrate quantity.

5) Competitive Inhibitors
these inhibitors compete with substrate for enzymes active sites because they both
have similar structures.

6) Other Components that Influence enzyme activity.

(allosteric regulation, activators, feedback regulation)

7) Covalent Modification
Phosphorylation/Dephosphorylation. Limited proteolysis

Phosphorylation/Dephosphorylation is addition or removal of phosphate groups.

Phosphorylation requires protein kinase enzyme.
ATP acts as a coenzyme (Phosphate donor).
For depolarization: Dephosphatase is required.
Phosphate groups can activate or deactivate enymes (on or off switch)

Covalent modification could also be adenylation, acetylation

Pepsinogen, Fibrinogen are the inactive forms. Fibrin, Pepsin are active forms. From
inactive to active form it is irreversible reaction
Thus Limited Proteolysis is irreversible.

8) Enzyme Induction
(regulation at gene level). Modifies transciption factors, modifies transcription,
translation, enzyme shape, structure and quantity..

Michaelis Menten curve is a hyperbolic curve.

Steep then plateurs. Never touches Vmax.
Horizontal axis is Substrate concentration (S).
Vertical axis is velocity of reaction. (V)

V = Vmax x S/S+Km

Km is the Michaelis Menten constant

Km gives the slope of the curve.

Km is the substrate concentration at which V = 1/2 of Vmax

Allosteric regulation doesn't change Km. Changes Velocity

Competitve regulation doesn't change Velocity. Changes Km

Km and activity of enzyme are inversly proportional.

Allosteric regulation can be positive or negative.

Allosteric enzymes have a sigmoid Michaelis Menten curve. Not hyperblic.

Thermodynamics

1st law: energy is neither created nor destroyed.

2nd law: Transfer of energy is not 100% efficient.

G = H - TS
G = Gibbs Free Energy. H = Enthalpy. T = Absolute temperature. S = Entropy

Gases have the highest entropy.

More the number of molecules, higher the entropy.

ΔG = ΔH - TΔS
Gibbs Free Energy tells us whether the reaction will happen or not.

If ΔG is negative:
Reaction will happen spontaneously. Exergonic reaction. Happens during catabolic
(breaking down) reactions.

If ΔG is positive:
Reaction needs energy to proceed. Endergonic reaction. Happens during anabolic
(synthesis) reactions.
The required energy for endergonic reactions can be provided by coupling an exergonic
reaction to the endergonic reactions)

ΔG = Gproduct - Greactant

At chemical equilibrium: ΔG = 0
ΔG = -RT lnk
R = gas constant
T = absolute temperature
K = equilibrium constant.

If K is greater than 1 then ΔG is negative

If K is smaller than 1, then ΔG is positive.

There is less entropy in living systems compared to the environment.

Energy is needed in the cell for:

Movement (muscle contraction)
Transport across the cell membrane
Biosynthesis (protein synthesis)

ATP (adenosine-5-triphosphate) provides energy for most work in the cell.

ATP is a high energy compound.
ATP----->ADP. This reaction generates energy.
ADP---------->ATP. This reaction requires energy.

Phosphoenolpyruvate, 1,3 Bisphosphateglycerate, Creatine phosphate,

Coenzyme A are all macroenergy, high energy compounds. (>30kJ/mol)

CoA-S--R
The bond between S and R is high energy.

G = H - TS
ΔG = ΔH - TΔS
ΔG = Gproduct - Greactant
ΔG = -RT lnk
Week 4
Enzyme Activity is measured in Unit (micromol/minute)
or in Katal (mol/s)
Phosphotase cleaves phosphate groups.

Temperature, pH, Ion concentration, presence and concentration of substrates,

products, coenzyme all influence enzyme activity,

The optimum temperature for most enzymes in the human body is 37 degrees.

Km is the substrate concentration that half saturates the enzymes.

i.e. substrate concentration at which V = 1/2 Vmax.

Km describes the affinity of the enzyme to the substrate.

Lower the Km, higher the affinity between enzyme and substrate.
Higher the Km, lower the affinity between enzyme and substrate.

Increassing enzyme concentration will increase Vmax.

Increasing enzyme concentration is done by enzyme induction whereby the quantity of
enzymes is increased.

Michaelis Menten equation:

V = Vmax x S/ Km + S

Competitive Inhibitor: Vmax doesn't change but Km increases.

Non competitive inhibitor: V max reduces but Km doesnt change
Uncompetitive Inhibitor: Km increases but Vmax reduces. In uncompetitve inhibition,
the inhibitor binds to the enzyme substrate complex. Thus due to Le Chatelier
Princimple, more ES complex is produced so affinity between enzyme and substrate
increases.

Breakdown of organic compounds provides energy.

Once you oxidize organic compounds, then you get electrons and protons which have to
be taken up by carrier molecules.

NADH and FADH2 are the reduced forms. of coenzyme.

They are electron carriers and transfer electrons to the site of terminal oxidation.

Aerboic ATP synthesis happens in the mitochondria.

Mitochondria has an outer and inner membrane. Between them is an intermembrane
space.
Outer membrane is permeable to most ions.
Inner membrane is almost completely impermeable. Thus it has carrier/transport
systems instead.

Terminal oxidation is the same as cellular respiration.

Electron transport happens in the mitochondrial inner membrane.

ΔG = nFΔE

E = mid point potential. This is the potential where oxidant concentration equals the
reactant concentration for a half reaction.

Electron Transoprt Chain (ETC) has 4 different complexes.

Within the complex, there are several steps.

NADH, FADH2, Ubiquinone, Cytochromes (peptides with heme prosthetic groups) are
involved in electron transfer

If the electrons are coming from NADH then:

Electrons are donated to complex I
Complex I donates electrons to Coenzyme Q10.
Coenzyme Q10 transports electrons from complex I to Complex III
In complex III, electrons are transported to cytochrome C
Cytochrome C carries and donates electrons to complex 4.
At complex 4, electrons combine with Oxygen and H+ to form water

Complex II is only involved with FADH2 and not with NADH.

If the elctrons are from FADH2 then:

Electrons are donated to Complex II.
COmplex II donates the electrons to Coenzyme Q10.
Coenzyme Q10 transports electrons from Complex II to Complex III.
In complex III, electrons are transported to Cytochrome C.
Cytochrome C carries and donates electrons to complex 4.
At complex 4, electrons combine with oxygen and H+ to form water.

All complexes are located on the inner membrane.

Complexes I, III, IV can pump protons (H+) from the mitochondrial matrix to the
intermembrane space.

Coenzyme Q10 aka Ubiquinon.

Ubiquinone is a lipophilic molecule. Found in highest concentration in high energy
consuming organs (heart, brain)

Complex II only accepts electrons from FADH2.

Cant translocate protons. Succinate Dehydrogenase
Succinate ----------> Fumarate

Complex III shows proton pump activity.

Catalyzes the oxidation of ubiquinone.

Cytochrome C is the link between Complex III and IV.

Electrons are transported through the ETC components.

Protons carried by coeznymes are translocated from the mitochondrial matrix to the
intermembrane space via complex I, III, IV.
Translocation energy comes from electron transport across ETC>
Since the inner membrane is impermeable to protons, protons build up in the
intermembrane space.
Proton gradient is formed.
ATP Synthase complex utilizes the proton gradient to form ATP from ADP +Pi

Due to Inhibitors of ETC, ATP is not generated:

Compelx I - Amyral
Complex III - Antimycin A
Complex IV - Carbon Monoxide, Cyanide.
The proton gradient is used for oxidative phosphorylation to generate ATP.
ATP synthase allows protons to flow through itself from intermembrane space to the
mitochondrial matrix.

ATP synthase has a F0 part and a F1 part.

F0 part is located within the inner membrane while the F1 part is in the mitochondrial
matrix.
F0 part has a,b,c subunits. F0 region acts as proton channel.
C subunit forms the rotor. A and B subunits are connected to the F1 region.

F1 part loosely binds ADP and Pi.

Tighter binding and conformational change in the catalytic site promotes ATP
synthesis.
Open conformation promotes release of ATP.

One full circular movement creates 3 ATP molecules.

Low pH is associated with high concentration of H+.

For ATP production, ADP, Pi and protons are required.

Oxidation per NADH molecule releases 2.5 mol of ATP

Oxidation per FADH2 molecule release 1.5 mol ATP

NADH generates more ATP because generates a greater proton gradient.

(NADH transports protons to intermembran space via Complex I,III,IV while FADH2 only
does so via complex III, IV)
Thus the difference in proton gradient generated is causing a difference in the amount
of ATP generated.

Terminal oxidation and Oxidative Phosphorylation are linked to each other as one
generates proton gradient an done uses proton gradient.

To create each ATP molecule, 30 kJ/mol is required'

Efficacy of ATP production is 35%.
Uncouoling proteins in the inner mitochndrial membrane destroy proton gradient as they
carry protons back into mitochondrial matrix prematurely.

C, O, H, N are responsible for macromolecules in the human body.

Macromolecules are carbohydrates, lipids, proteins, Nucleic Acids
Macromolecules are polymers, Dimers, Trimers, Tetramers, Oligomers.

Macromolecule --------------- Monomer

Carbohydrates Monosaccheride
Proteins Amino Acids
Lipids Fatty Acids + Glycerol
Nucleic Acids Nucleotides.

Macromolecules can be broken down to monomers (digestion).

Monomers can join together to form macromolecules.

Citric Acid Cycle:

Citrate - 6 carbons
Isocitrate - 6 carbon
Alpha Keto Glutarate - 5 carbons
Succinyl CoA - 4 carbons
Succinate - 4 carbons
Fumarate - 4 carbons
Malate - 4 carbons
Oxaloacetate - 4 carbons

Pyruvate (3 carbon) and Acetyl Coenzyme A (2 carbon) are common intermediates.

You can form Acetyl Coenzyme A from pyruvate.
Acetyl Coenzyme A goes to the Citric Acid cycle

Pyrucate can be broken down to monosaccharides. Pyruvate can be made from

monosaccharides
Acetyl Coenzyme A can be broken down to fatty acids. Acetyl Coenzyme A can be made
from fatty acids.
From amino acids, you can creat citric acid cycle components, pyruvate and Acetyl
Coenzyme A.
Nucleotides communicate with the citric acid cycle.
CO2 and H2O are formed in the citric acid cycle as a waste product.

When organic molecules go from a more reduced form to a more oxidized form it goes
from macromolecules to CO2. Oxidation is happening.

Common Intermediates --------(creation of energy)--------------> End products

1) Polymer ---------(Material)---------> Monomer

2) Monomer -----------(Material + Energy)-----------> Common interrmediates
3) Common intermediates -----(energy)------------> End products

Terminal Oxidation + Oxidative Phosphorylation go hand in hand.

Rotation of ATP Synthase rotor converts ADP + Pi to ATP
Electron Transport Chain transports protons to intermembrane space using energy from
transporting electrons.
Source of oxygen is air.
Source of hydrogen is NADH (3 ATP)and FADH2 (2 ATP)

Steps 2 and 3 produce NADH and FADH2.

Larger molecules become smaller molecules via catabolism.

Oxidation happens, ATP and NADH/FADH2 are produced.

For anabolism reactions, reduction happens.

ATP needs to be invested.
Uses NADPH instead.

The sum of catabolism and anabolism makes up metabolism.

Week 5
In covalent modification, limited proteolysis is irreversible.
Translocases (EC 7) also uses ATP. Eg: Na/K ATPase
- The glycolytic pathway (glucose ---------> 2 pyruvate) is found in all living organisms.
- Energy released by oxidation of glucose is stored as ATP and NADH. NADH gives 3
ATP.
- Conversion of: alkane--->alkene, alcohol---->ketone, aldehyde------>carboxylic acid and
NADH----->NAD+ are all oxidation reactions.
- Energy production involves conversion of compounds with high energy to those of low
energy initially; Transport of electrons on organic molecules; generation of a proton
gradient across membranes.
- Energy for the synthesis of ATP during oxidative phosphorylation is obtained form a
proton gradient across a membrane.
- The input of energy required to synthesize ATP from ADP + Pi is for the increasing
electrostatic repulsion in ATP and the resonance stabilization of the ADP form.

Week 6
Substrate level phosphorylation: Transfers phosphate group from a substrate to ADP to
generate ATP (energy).
Proton (H+) concentration is highest in intermembrane space.

ATP synthase is present on Mitochondrial inner membrane. Has F0 and F1 parts.

Protons pass through the ATP synthase to generate ATP.

To maintain proton gradients, pumping of protons is done by ETC. Protons move from
mitochondrial matrix to the intermembrane space.

Enzyme complexes I, III, IV are transmembrane protein. These complexes have proton
pump activity. Enzyme complex II (succinate dehydrogenase) does not have proton
pump activity.

Ubiquinone and Cytochrome C are mobile and transport electrons.

Ubiquinon transports electrons from I and II to III
Cytochrome C transports electrons from III to IV.

Electron movement generates energy for proton pumping.

Oxygen is the final acceptor of electrons. Source of oxygen is breathing.

NADH provides electrons to enyme complex I. Goes to ubiquinone, III, Cytochrome C, IV

and then oxygen.
FADH2 provides electrons to enzyme complex II. Goes to ubiquinone, III, Cytochrome C,
IV and then oxygen

NADH generates 3 ATP while FADH2 generates only 2 ATP. This is because electrons
from NADH go through 3 proton pumps (I,III,IV) and pump more protons.
Electrons from FADH2 go through only 2 proton pumps (III, IV) and thus pump less
protons.

Cyanide inhibits the 4th enzyme complex and thus blocks ATP production
Uncoupling agents /proteins disrupt proton gradient and bring protons back into the
mitochondrial matrix from the intermembrane space prematurely. This also interferes
with ATP formation and the efficacy of ATP production decreases.

Under aerobic conditions, macromolecules undergo hydrolysis and then biological

oxidation to give ATP, CO2, H2O
Glucose -------- (glycolysis)----------> Pyruvate
Pyruvate ------------(Pyruvate dehydrogenase enzyme)------> Acetyl Coenzyme A

In the above reaction, 1 CO2 and 1 NADH is produced.

Reduced coenzyme are needed for oxidative phosphorylation.

In the Kreb cycle, Acetyl Coenzyme A will be oxidized.

Enzymes of Kreb cycle are within the mitochondrial matrix except succinate
dehydrogenase
Thus Kreb cycle takes place in the mitochondrial matrix.

Both carbons in Acetyl Coenzyme A become CO2.

H atoms are used to form reduced coenzyme.
There are 4 carbon, 5 carbon and 6 carbon intermediates.

In the Kreb cycle, there is oxidation/reduction, condenstation and isomerization

reactions taking place.
Some steps of the Kreb cycle are irreversible and some are reversible.

Steps

1) Citrate (C6) formation

Oxaloacetate(4C) + Acetyl CoA(2C) ------------> Citrate (6C)
Enzyme: Citrate synthase
Intermediate: Citryl CoA
Irreversible reaction

2) Isocitrate(C6) formation
Citrate (6C) ------------------> Isocitrate (6C) [isomerization]
Enzyme: Aconitase
Intermediate: Cis-aconitase
Reversible

3) Alpha Ketoglutarate (C5) formation

Isocitrate(C6) -----------------> Alpha Ketoglutarate (C5) + CO2 + NADH
Enzyme: Isocitrate dehydrogenase
Irreversible reaction
CO2 produced and NAD+ converted to NADH
This is the determining step of the Kreb cycle.

4) Succinyl CoA (C4) formation

Alpha Ketoglutarate (C5) -----------------------> Succinyl CoA (C4) + CO2 + NADH
Enzyme: Alpha Ketoglutarate dehydrogenase
Irreversible reaction
CO2 produced, NAD+ converted to NADH.
Formation of high energy bond

5) Succinate (C4) formation

Succinyl CoA (C4) ---------------> Succinate (C4) + GTP
Enzyme: Succinyl CoA Synthetase
GTP synthesis is done here by coupling to the hydrolysis of CoA.
Substrate level phosphorylation.

6) Fumarate (C4) Formation

Succinate (C4) -------------------> Fumarate (C4) + FADH2
Enzyme: Succinate dehydrogenase
Enzyme is attached to mitochondrial inner membrane as its a part of Complex II of
electron transport chain.
FAD+ -------------> FADH2 happens in this step.

7) Malate (C4) formation

Fumarate (C4) -------------------> Malate (C4)
Enzyme: Fumarase
Addition of water

8) Oxaloacetate (C4) formation

Malate (C4) --------------> Oxaloacetate (C4) + NADH
Enzyme: Malate dehydrogenase
NAD+ converted to NADH in this step.

Oxaloacetate is now used to synthesize citrate with help of Acetyl CoA

Oxaloacetate + Acetyl CoA -------------------------> Citrate ----------------------------> Isocitrate

---------(CO2, NADH produced) -----------------> Alpha Ketoglutarate -------------(CO2, NADH
produced)---------> Succinyl CoA ------(GTP produced)-------------------> Succinate ---(FADH2
produced)----------------> Fumarate --------------------> Malate --------(NADH produced)------------->
Oxaloacetate
From 1 lap of the Kreb Cycle you get:
2 CO2
3 NADH
1 FADH2
GTP
CoA
Since 1 NADH gives 2.5 ATP and 1 FADH2 gives 1.5 ATP
1 lap of Kreb cycle provides 10 ATP
1 glucose molecule will lead to 2 Kreb cycles cuz 1 glucose gives rise to 2 pyruvates.

The generic condition of cell determines if TCA cycle is needed .

If there is a high ATP/ADP ratio (lots of ATP present) then cycle wont take place as there
is no need.
Intermediers are used for lipid, protein and glucose synthesis.
If there is a low ATP/ADP ratio (low levels of ATP present), Kreb cycle will take place.

Steps 1,3,4 are irreversible.

Citrate formation, Alphaketoglutarate formation, Succinyl CoA formation.
Allosteric regulation takes place at these steps.
ATP and NADH will allosterically inhibit all 3 steps. Succinly CoA can inhibit steps 1 and
3.

Anaplerotic reactions guarantees adequate oxaloacetate in the mitochondria.

Eg:
Conversion of pyruvate to oxaloacetate
Conversion of phoshoenolpyruvate to oxaloacetate
Pyruvate to Malate
Glutamate to alphaketoglutarate
Asparate to oxaloacetate.

All carbon atoms of glucose are oxidized to CO2.

Per glucose molecule (1 glucose leads to 2 pyruvate so 2 kreb cycle):
2 CO2 in acetyl CoA formation
4 CO2 in Kreb cycle.

Per glucose molecule there is:

2 NADH from glycolysis
2 ATP in glycolysis
2 NADH due to pyruvate dehydrogenase (Acetyl CoA formation)
6 NADH in Kreb cycle
2 FADH2 in Kreb cycle
2 GTP in Kreb cycle
Thus per glucose molecule maximum of 32-38 ATP is produced.
Its 32 ATP if you take NADH = 2.5 ATP and FADH2 = 1.5 ATP
Its 38 if you take NADH = 3 ATP and FADH2 = 2 ATP

Pyruvate dehydrogenase and alpha keto glutarate ate thiamine dependent.

Per mole of glucose:

under anaerobic conditions: 2 ATP
under aerobic conditions: 32-38 ATP

In glycolysis, 4 ATP is generated but 2 is used up so total of 2 ATP is made in

NADH can make 3 or 2.5 ATP each.
FADH2 can make 2 or 1.5 ATP each.
Thus aerobic respiration makes 32-38 ATP

Complex I,II, III,IV are in electron transport chain

Complex V is ATP synthase.

Pyruvate dehydrogenase works in the mitochondria so pyruvate has to go from the

cytosol to the mitochondria via the pyruvate transporter.

Redox Shuttles (intracellular electron transfer):

1) Glycerol Phosphate shuttle
2) Malate Aspartate shuttle

Glycerol Phosphate shuttle uses NADH as a donor to convert

glyceraldehyde-3-phosphate to 1-3, bisphosphoglycerate. Acceptor is FAD which
becomes FADH2. Loss of 1 ATP

Malate Aspartate shuttle uses NADH as donor and acceptor

Oxaloacetate is impermeable to mitochondrial membrane.
In this shuttle
Malate (intracellularly) ----> Malate (outercellularly) -----> Oxaloacetate (outercellularly)
-----------> Asparatate (outcellularly) ---------------> Asparatate (intracellularly) ------------>
Oxaloacetate (intracellularly) -----------> Malate (Intracellularly)

2-3 bisphoglycerate regulates the oxygen affinity and release with hemoglobin.
Higher the 2-3 bisphosphoglycerate, lower is the affinity of oxygen to hemoglobin (thus
oxygen is liberated)

From 3-phosphoglycerate you usually get 1-3 bisphosphoglycerate in gluconeogenesis

but you can get 2-3 bisphosphoglycerate

Gluconeogenesis - Production of glucose from non carbohydrate intermediates (usually

pyruvate)

Glycolysis: Glucose ----------> Pyruvate

Gluconeogenesis: Pyruvate -------------> Glucose

Glycolysis:
Glucose ---------------> Glucose-6-phosphate -----------> Fructose-6-phosphate---------->
Fructose-1,6-phosphate --------> GAP + DHAP -------------------- --------------------> (2) 1-3
bisphosphateglycerae ----------> (2) 3-phosphoglycerae -------------------------> (2) 2
phosphoglycerate --------------> (2) Phosphoenolpyruvate --------------------------> (2) Pyruvate

Steps 1,3,8 are irreversible

Steps 1,3,8. Glycolysis and Gluconeogenesis.

Glucose ----(hexokinase)-----> Glucose-6-phosphate -----(glucose-6-phosphatase)-------->

Glucose

Fructose-6-phosphate -----(phosphofructokinase 1)--------> Fructose-1,6-bisphosphate

----(Fructose-1,6-bisphosphatase)--------> Fructose-6-phosphate

Phosphenol pyruvate ---(pyruvate kinase)-------> Pyruvate -----(pyruvate

carboxylase)---------------------> Oxaloacetate ---(phosphoenolpyruvate
carboxykinase)--------------> Phosphoenolpyruvate

For pyruvate to phosphoenolpyruvate you need an intermediate (oxaloacetate) and the

investment of energy.
Oxaloacetate cant cross the mitochondrial membrane so it transforms into
something else (Malate)

For gluconeogenesis you need to invest 6 ATP and get only 2 ATP back.
Thus there is total consumption of 4 ATP

If glycolysis rate is high, then gluconeogenesis rate is low.

If glycolysis rate is low, then gluconeogenesis rate is high.

Inhibitor of glucogenesis is insulin.

Activator of glucogenesis is glucagon.

Precursor of gluconeogenesis is usually pyruvate.

Could be oxaloacetate, TCA cycle intermediates, Amino Acids, Lactate
(Acetyl CoA and fatty acids are not precursors for gluconeogenesis)

Pyruvate - 15 ATP
Lactate - 18 ATP

Citrate synthesis requires Acetyl CoA and oxaloacetate

Week 7
Glucose ------------> Pyruvate
This process is glycolysis. Invest 2 ATP and get 4 ATP.

Pyruvate ------------------> Glucose

This is gluconeogenesis. Invest 6 ATP and get back 2 ATP.
If you increase glycolysis, then decrease gluconeogenesis and vice versa.

PPP - Pentose Phosphate Pathway. Uses the HMP shunt. Gives NADPH
Has an oxidative and non oxidative phase.

Oxidative phase: Creates C5P and NADPH

Glucose-6-phosphate---------------------> 6-phosphogluconolactone -------------------------------------->

6-phosphogluconate ---------------------> Ribulose-5-phospphate.

Each step uses dehydrogenase enzyme.

Overall: C6P --------> C5P + CO2 + 2 NADPH

Non Oxidative phase: Creates monosaccharides with different carbon numbers

Ribulose-5-phosphate gives:
C5-----TK-----> C7---TA------->C4------TK--------> C6
C5------TK--------> C3
C5----TK------->C3-------TA---->C6

End products are 2 C6 (2 Fructose-6-phosphate) and 1 GAP

(Glyceraldehyde-3-phosphate)

The enzymes used in the non oxidative phase are transaldolase and transketolase.
Transaldolase transfers C3 fragments. Transketolase - C2 fragments.

Both the end products are a part of glycolysis.

HMP shunt does direct oxidation of glucose and gives NADPH. (from oxidative phase)
NADHP is a H donor for anabolism. (not used further in PPP)
The ribulose-5-phosphate from oxidative phase is used further (in non oxidative phase)
Thus HMP shunt is an important source of NADPH.

The oxidative phase is irreversible while the non oxidative phase is reversible.

---------------> = oxidative phase

<--------------- = non oxidative phase
------------> & ----------------> gives u NADPH only
-----------> gives you NADPH and ribulose-5-phosphate
<--------------- gives you ribulose-5-phosphate

Lipid synthesis is a major consumer of NADPH

In drug induced hemolytic anemia, RBC levels decrease.

In RBC there is a lot of oxygen thus oxidative stress is high.

To act against this oxidative stress, antioxidants are present (GSH)
Antixoidants undergo oxidation themselves and protect the body against oxidative
stress.
GSH becomes GS-SG.
To make GSH again, NADPH has to be used.

The human body always prefers the oxidized, low energy forms of molecules (NAD, FAD,
ADP, GS-SG)

Glucose is stored as glycogen (polysaccharide).

Liver glycogen is used to maintain blood glucose level.

For the synthesis of glycogen:

Glucose -----(+ ATP)----------------> Glucose-6-phosphate --------------> Glucose-1-phosphate

--(UTP enzyme)----------------------> Uridine diphosphate glucose ------------------> Glycogen

For breakdown:
Glycogen ------------(Glycogen phosphorylase, debranching enzyme)---------------------------->
Glucose-1-phosphate
Glycogen phosphorylase uses inorganic phosphate

Glycogen is very branched

Glycogen synthase - anabolism

Glycogen phosphorylase - catabolism
Both are dependent on phosphorylation and dephosphorylation.
Glycogen is regulated by hormones (glucagon, insulin). Hormones are linked to
glycogen by protein kinases and phosphorylase.

Glycogen <--------------------> Glucose

Activation of one reaction inhibits the other. Parallel combined regulation.

Insulin decreases the blood glucose level.

Steps for insulin function:
1) Increase activation of glucose transporters. Glucose goes into cells and becomes
glucose-6-phosphate
Glucose-6-phosphate can turn into (via activation reactions):
2) Glycogen
3) Pyruvate
4) Glycogen breakdown and
5) gluconeogenesis needs to be inhibited
From pyruvate you can get Acetyl Coenzyme A which gives
6) Fatty Acid
From pyruvate you can also get amino acids which gives
7) Proteins.

GSD (glycogen storage diseases). These affect liver and muscles.

GSD:
I - Von Gierke disease
IV - Anderson disease
V - McArdle disease

In Von Gierke disease, Glucose-6-Phosphatase (creates glucose from

glucose-6-phosphate) is missing
Hypoglycemia occurs (low blood glucose level). Happens in liver

In Anderson disease, branching enzyme is absent and liver failure occurs

In McArdle disease phosphorylase enzyme missing. Causes muscle weakness.

Glycolysis:
Glucose, Glucose-6-phosphate, Fructose-6-phosphate, Fructose-1,6-diphosphate,
glyceraldehyde-3-phosphate, 1,3-bisphosphoglycerate, 3 phosphoglycerate, 2
phosphoglycerate, phosphoenolpyruvate , pyruvate

G, G6P, F6P, F1-6P, GAP, 1-3BPG, 3PG, 2PG, PEP, pyruvate

Fructose ------------------(Fructokinase)-----------------> Fructose-1-phosphate-------------(Aldolase

B)-------> Glyceraldehyde --------(triokinase enzyme)---------> Glyceraldyhde-3-phosphate

Since Glyceraldyhyde-3-phosphate (GAP) is a part of glycolysis, it can be used to create

glucose. Thus fructose is converted to glucose indirectly.

3 possible diseases:
Fructose malabsorption
Fructosuria (fructose goes into urine) due to faulty fructokinase enzyme
Hereditary fructose intolerance (Aldolase B is faulty)

Galactose metabolism.

Galactose-----------(Galactokinase)-------------> Galactose-1-phosphate---(UTP)--------------->
UDPgalactose-------------(epimerization)------------> UDPglucose------------------------> glycogen by
glycogen synthesis.

Galactosemia - UTP not present.

Galactose comes from lactose in milk.

For full web check notes,

Glucose-6-Phosphate at the center. It has 7 metabolisms.

glycogenolysis
Glycogen --(glycogen phosphorylase)------------> G6P -----(phosphofructokinase)--------------->
Pyruvate
glycolysis
Glycogen <-------------- ------G6P <-------------------------- Pyruvate
glycogenesis gluconeogenesis

Glucose------(hexokinase)---------------> Glucose-6-phosphate
Glucose <----------(glucose-6-phosphatase)---------------------- Glucose-6-phosphate

Glucose-6-phosphate ------(Glucose-6-phosphate dehydrogenase)--------> HMP shunt

(PPP)

Products of the HMP shunt are NADPH and ribulose-5-phosphate.

Too little G6PDH is drug induced hemolytic anemia.

Phosphoenol pyruvate --(pyruvate kinase, ATP made)---------> Pyruvate ---(pyruvate

dehydrogenase enzyme, CO2, NADH made)----------> Acetyl CoA

This is part of gluconeogenesis:

Pyruvate ---(pyruvate carboxylase, need ATP, biotin)---------> Oxaloacetate
----(phosphoenolpyruvate carboxykinase, need GTP)---------> Phosphoenolpyruvate

Also for pyruvate

Lactate<------------------------->Pyruvate <--------------------> Alanine

Glycogen --(glycogen phosphorylase)------------> Glucose

Glucose -(UDP glucose phosphorylase)-----------> UDP Glucose --(glycogen

synthase)------------> Glycogen

UDP glucose can form

UDP galactose (epimerization)
Amino Sugars
Glucorinic Acid
Week 8
High substrate specificty - only binds to one substrate. (glucokinase)
Low substrate specificity - binds to many similar substrates (hexokinase)
Lipids

Lipids are apolar, hydrophobic and lipophilic.

Lipid functions:
- Energy Source (triacyl glycerol) Daily Lipid requirement is 90 g.
- Energy Storage (triacyl glycerol). Done by adipose tissue. 15-20% of human weight is
adopise tissue. Adipose tissue is a better energy store than glycogen due to its higher
mass and higher energy concentration.
- Structure formation (phospholipids, cholesterol)
- Bioactive properties (regulatory function - steroid hormones) !!!!!
Above 4 are crucial
- Isolation (myelin sheaths)
- Lipid soluble vitamin storage (ADEK)
- Helps in digestion (bile acids)
- Nutritional function (fatty acids)

Lipid classification

Lipids:
a) Saponification (fatty acid derivatives)
b) No saponification (isoprene)

Dividing fatty acid derivatives

a1) Glycerol derivatives
a2) Sphingosine derivatives

Dividing glycerol derivatives

a1i) Neutral lipids, Triacylglycerol
a1ii) Phospholipids

Phospholipids are amphipathic.

Triacylglycerol = Glycerol + 3 Fatty Acids
broken by esterase.
Fatty Acid classification
1) By carbon number
Fatty acids are long. Have 14, 16, 18 carbons usually.
Always have even number of carbons because they are made up from acetyl coenzyme
A
2) Presence of double bond or not.
If no double bond present - saturated fatty acid
If 1 double bond present - monounsaturated fatty acid
If multiple double bond present - polyunsaturated fatty acid
3) Trans/Cis
Trans fatty acid means opposite sides on double bond.
Cis means same side on double bond.
Trans fatty acids are unhealthy.
4) Essential or non essential

Essential fatty acids always have cis configuration.

If it is a polyunsaturated fatty acid then double bond is every 3 carbons.

There are omega 3, omega 6, omega 9 polyunsaturated fatty acid families..

Omega 3 and Omega 6 fatty acids are essential.

Carbons: Double bonds - Name

16:0 - Palmitic Acid
18: 0 - Stearic Acid
18: 2 - Linoleic Acid (is omega 6)
18: 3 - Linolenic acid
20: 4 - Arachidonic Acid

Ecosinoids are fatty acid derivatives with 20+ carbons.

Arachidonic Acid is a polyunsaturated fatty acid. Is non essential. Derivative of linoleic
acid which is essential.

Prostanoids are a subclass of ecosinoids. Contains prostaglandins.

functions of prostanoids:
- Inflammatory
- Blood flow regulation
- Smooth muscle contraction
- Gastrointestinal tract protection
- Reproductive physiology
- Respiratory function
- Pain sensation
- Platelet function
- Kidney function
Prostoglandings are inflammation mediators

Anilin derivative: Paracetamol

Propionic acid derivative: Ibuprofen
Salicylates: Aspirin

Arachnoid Acid -------(COX)-------------> Prostoglandin G2

Week 9
Prostoglandins have many, many functions.
In nomenclatur of prostoglandings, the number in the name indicates the number of
double bonds.
prostaglandins used in female and male reproductive organs, cardiovascular,
respiratory, renal, GI, immune and CNS systems.
Lipids are hydrophobic
Bile acids are cholesterol derivatives.
Bile acids are produced in the liver and they emulsify lipids.

Lipases digest lipids.

Triacylglycerol becomes free fatty acid, diacylglycerol, monoacylglycerol and glycerol.
Lipases are EC 3 (hydrolase) - esterase. No coenzyme
Lipases are produced by the pancreas and small intestine.

After absorption into cell, monoacylglycerol and fatty acid becomes a chylomicron
which goes into lymphatic circulation via exocytosis.

Lipoproteins are used for the transport of lipids in the blood stream. Lipoproteins are
spherical and have a surface and core part.
On the surface are apolipoprotein. These have structural function and stabilize the
lipoproteins. These apolipoprotein also have recognition and enzymatic function (they
activate other enzymes).
In lipoproteins, lipids are in the core (being transported) or in the periphery as
phospholipids + Cholesterol.

Cholesterol is mainly a membrane component. Is amphipathic

When making a cholesterol ester, you remove OH (hydrophilic part of cholesterol) and
create an ester bond. This makes cholesterol esters completely hydrophobic while
cholesterol itself is hydrophilic.
Cholesterol is unbreakable

To move triacylglycerol from chylomicron to cells, use lipoprotein lipase.

These digest triacylglycerol in the chylomicron and becomes free fatty acid and
glycerol.
Free fatty acid go into the cell and glycerol goes to the liver and joining glycolysis

Highest consumer of fatty acids is heart and skeletal muscle.

Lipoproteins:
Chlyomicron: Transports triacylglycerol from GI tract to cells
VLDL: Transports triacylglycerol from the liver to the cellss
LDL: Transports cholesterol from liver to cells (bad cholesterol)
HDL: Trabsports cholesterol from cells to liver (good cholesterol)
The liver converts cholesterol to bile acids
LDL : HDL in the blood
4:1

Name Lipid Content Protein Content

Chylomicron 98% 2%
VLDL 90% 10%
LDL 80% 20%
HDL 50% 50%

LDL causes cells to have increased cholesterol storage and decreased cholesterol
synthesis.

Week 10
Cholesterol is ampipathic.
Important membrane component.

Formation of atherosclerotic plaques (blockage of circulation) is due to high cholesterol

in the blood stream.

Cholesterol is enzymatically unbreakable.

Elimination of cholesterol is done by the bile. Used in creation of bile acids.

Sources of cholesterol:
Diet
Created by the body.

Cholesterol can be synthesized by any cell in the body. However the main source is the
liver. Cholesterol is transported from the liver to cells by LDL.

Acetl CoA is a precursor for cholesterol.

Acetyl CoA (2 carbon) ------------> Aceto Acetyl CoA (4 carbon [2 Acetyl CoAs]) ---------(HMG
CoA Synthase)--------> HMG CoA (6 carbon [3 Acetyl CoAs]) -------------------------------------(
HMG CoA reductase + NADPH) ---------> Mevalonate-5-kinase ------> Cholesterol

HMG CoA reductase uses NADPH as a coenzyme.

HMG CoA to Mevalonate-5-kinase is the rate limiting step in cholesterol synthesis.
It is the committed, irreversible, most regulated step.

HMG CoA reductase enzyme can be covalently modified and inhibited.

Hormonal control is done by insulin and glucagon.
The enzyme activity can be modified at the gene level (enzyme induction)

HMG CoA reductase is the key enzyme in cholesterol synthesis.

Conversion of lanostel to cholesterol requires NADPH, O2 at every step. Due to such

requirements cells don't tend to make cholesterol on their own.

Cholesterol derivatives:
Bile Acids
Vitamin D
Steroid Hormones: Mineralocorticoids, Glucocorticoids, Androgens: Estrogen,
Progesterone, Testosterone.

Ketone bodies act as an alternative source of energy for the brain.

Made in the mitochondira, it is a liver specific process.
Ketosis (high ketone body concentration in the blood) is not good.
Acetyl CoA + Acetyl CoA ----------> Aceto Acetyl CoA ------------( HMG CoA Synthase)
-----------> HMG CoA -----------(HMG CoA lyase)----------> Acetoacetate (ketone body)

HMG CoA could form cholesterol or acetoacetate (ketone body) depending on which
enzyme acts on it.

Lipolysis is induced by high glucagon and low insulin levels.

Adipocytes are under hormonal control.
Glucagon causes the release of free fatty acid (lipid mobilization)

Lipids store more energy than carbs because lipids are more reduced and contain more
hydrocarbons. Lipids give rise to more NAD and FAD

Lipids are polar. Insoluble in water.

90% of dietary lipids are triacylglycerol. Cholesterol and fat soluble vitamins also come
from diet.
Essential fatty acids must come from the diet as they cant be produced by the body.

Lipids are digested by lipases.

Lipases only act on small lipid droplets.
Bile emulsifies (turns large fat globules into small lipid droplets).
Bile contains bile acids and bile salts.
After digestion, free fatty acids and monoacyl glycerol are absorbed in the small
intestine.
Lipids are transported in the body by lipoprotein complexes (lipid core surrounded by
phospholipid monolayer. Proteins embedded in the phospholipid layer). Transported
lipids are in the core.

Lipoproteins can be classified based on their densities and size.

HDL: Small, compact and has highest relative protein content
VLDL: Large and has lowest relative protein content.

Chylomicron in made in the small intestine.

Chylomicron transports Triacylglycerol.
Chylomicrons go to the lymphatic system and then enters the blood..

Young chylomicron contains B48 apolipoprotein

In plasma, mature chylomicron contains B48, E and CII apolipoprotein
CII apolipoprotein activates lipoprotein lipase which digests triactlglycerol of
chylomicron to monoacylgylycerol
Once digestion happens, remenant chylomicron loses CII apolipoprotein and goes to
liver.

VLDL is a large lipoprotein.

VLDL is produced in the liver and carries triacylglycerol in blood.
Young VLDL contains B100 apolipoprotein.
In blood, VLDL also picks up E and CII apolipoprotein and becomes mature VLDL

LDL transports cholesterol from the liver to the periphery.

LDL has B100 apolipoprotein. This causes receptor mediated endocytosis if cells have
LDL receptors.
If there is a lack of LDL receptors then LDL containing cholesterol remains and
accumulates in the blood

HDL has A, E, C apolipoprotein

HDL transports cholesterol from the periphery and cells to the liver..
Thus HDL is called good cholesterol.
A apolipoprotein is specific for HDL

Triacylglycerol is made up of 3 fatty acid chains and 1 glycerol backbone. Storage form
of lipids. Found in adipose tissue.
Triacylglcyerol ------------------> Free fatty acid
This process is called lipid mobilization (lipolysis)
Fatty acids are broken down by oxidation. This gives acetyl coenzyme A which is used in
kreb cycle onwards.
Oxidation of fatty acids happens in the mitochondria.

Acetyl CoA is used to build up fatty acids.

Fatty acid synthesis (lipogenesis) happens in the liver and adipose tissue

Acetyl CoA can be converted to ketone bodies. (ketogenesis)

Ketone bodies are water soluble so they can be transported easily.
Since ketone bodies can penetrate the blood brain barrier, it can supply the brain.

Degradation of ketone bodies gives Acetyl CoA (ketolysis).

Insulin positively modulates Fatty Acid and triacylglycerol synthesis.

Insulin can negatively modulate fatty acid and triacylglycerol breakdown.(Insulin is
secreated when blood glucose levels is high).
Glucagon positively modulates Fatty Acid and triacylglycerol breakdown. Glucagon can
negatively modulate fatty acid and triacylglycerol synthesis.
Both modulations are done by phosphorylation the enzymes used.

There is beta oxidation and alpha oxidation.

alpha oxidation for phytanic acid breakdown in the CNS.

Beta oxidation is the degradation of saturated fatty acids to Acetyl CoA

1) Activation of fatty acid (by adding CoA) ------------> Acyl CoA

Enzyme: Acyl CoA snythetase
On the outer mitochondrial membrane. Uses 2 ATP.
2) Transport to the mitochondrial matrix by Carnithine shuttle
This step is regulatory.
Acyl binds to carnithine, goes through mitochondrial membranes and once in the
mitochondrial matrix separates from carnithine and binds to matrix CoA
3) Oxidation of Acyl CoA (in the matrix)
i) Dehydrogenation (gives FADH2)
ii) Hydration
iii) Dehydrogenation (gives NADH + H+)
iv) Cleavage (release of acetyl CoA)
All this is 1 cycle.
Each cycle releases 1 acetyl CoA which goes into Kreb cycle.
1 cycle gives 17 ATP but because 2 ATP are used up in the activation,
Beta oxidation of one saturated fatty acid gives net 15 ATP.
Beta oxidation of an unsaturated fatty acid (with the same carbon number as a
saturated one) will give less ATP.

Fatty Acid synthesis

Happens in the cytosol.
Acetyl CoA used to build up fatty acids.
Acetyl CoA is in the mitochondria but CoA cant go through mitochondrial membranes.
Thus Acetyl CoA becomes citrate in the mitochondria.
Citrate goes through mitochondrial membrane to cytosol and in cytosol, citrate
becomes Acetyl CoA once again.

1) Acetyl CoA (2 C) -----(Acetyl CoA carboxylase, +CO2)----------> Malonyl CoA (3 C)

Acetyl CoA carboxylase is a key enyme of fatty acid synthesis. It is regulated by insulin
(dephosphorylation) and by glucagon (phosphorylation)

Malonyl CoA regulates beta oxidation of fatty acids.

2) Acetyl combines with Malonyl -----(beta ketoacyl synthase)------> Acetoacetyl

3) Acetoacetyl undergoes Reduction, Dehydration, Reduction
NADPH used in both the reduction reactions.

This is 1 cycle.

Ketone body formation is called ketogenesis.

From acetyl CoA. Happens in the liver, in mitochondrias.
Each amino acid contains a nitrogen.
Amino acids are not a major source of energy. They are only used if lipids and
carbohydrates are not available.

Some amino acids can be synthesized in the human body.

Amino acids are used in protein synthesis.

Carbohydrates and lipids can be stored in the human body but we cannot store proteins
in the human body.

Amino acids are precursors for biologically active N containing substances.

Essential amino acids must be taken up in the diet because the body cant make them.
Eg: His, Ile, Lys, Leu, Met
Non essential amino acids (body can make these) :Ala, Glu, Gly, Pro, Asn, Asp

Animal sources of proteins are better than plant sources as animal sources provide all
essential amino acids while plant sources provide a few.

All Amino Acids have a alpha carbon atom, amino group (NH3+), Carboxyl group (COO-).
The R group (the side chain) is the only thing that differs between amino acids.
There is nitrogen balance in the human body. The amount of nitrogen we uptake and
excreate is equal under normal conditions.
Negative N balance: Protein intake deficiency or increased N loss.
Positive N balance: Growing body, muscle development, pregnancy, breastfeeding.

Digestion and absorption of proteins happens in the GI tract.

Exopeptidases cleaves proteins from one of its ends.
Endopeptidases cleaves proteins from somewhere in the middle.

Proteases are produced in an inactive form (zymogen)

They are activated once in the GI tract.

Digestion

In Stomach: Pepsin and HCl used for protein digestion

Here polypeptides -------------------> Oligopeptides

In intestine: Trypsin, Kinotrypsin, Elastase (all come from pancreas)

Here oligopeptide ---------------> shorter polypeptides

Intestinal epithelial cells: Endopeptidases, Dipeptidases, Amino peptidases

Here free amino acids are produced.

Protease inhibitors: For protection.

Eg: Pancreatic trypsin inhibitor

Absorption happens in the intestine.

Free amino acids go from lumen into cells because of Na+ coupled secondary active
symport.
Dipeptides and tripeptides are transported due to H+ coupled symport and then
digested in the cells by dipeptidases and tripeptidases.

Amino acids move via passive transport.

From intestinal epithelial cell to capillary to site of use in the body.

Amino acid uptake into the cell is due to gamma glutamyl cycle. Glutathione is involved.
Endogenous proteins come from extracellular or intracellular compartmetns.
For extracellular protein degradation: Matrix metalloproteases are secreated into the
ECM. TIMPs inhibits these enzymes
For intracellular protein degradation:
- In lysosomes (receptor mediated endocytosis associated proteolysis)
- ATP dependent proteolysis (uses ubiquitination)
- Autophagy (autophagosome + Lysosome)

Once we have free amino acid pool, we can make many things from them.

Removal of amino acid nitrogen

1) Transamination
Amino group is transferred to another molecule.
You need the amino acid, an alpha keto acid.
The amino group and the alpha keto group switch so we get a different amino acid.
2) Deamination
Amino group is eliminated.
Ammonia produced and released.
a) oxidative deamination: oxidize the carbon which has amino group
enzyme is glutamate dehydrogenase, coenzyme is NAD
b) Non oxidative decarboxylation: Uses ammonia lyase.
3) Hydrolysis.
Only for Asn, Gln amino acids.

Ammonia is necessary for synthesis of amino acids and nucleic acids.

If ammonia level is too high, it could be toxic.

Human Nitrogen elimination:

Urea (made in liver, excreated by the kidney)
AA derivatives (creatinine)
Uric Acid (Purine degradation)

Glutamate has a central role. It is used in:

- Glutamine synthesis
- Transamination (alpha keto glutarate synthesis)
Urea synthesis

1) Free Ammonia + CO2---------(Carbamoylphosphate synthase + 2 ATP, )------->

Carbamolyphosphate
2) Carbamoylphosphate + Ornithine -----(ornithine transcarbamoylase)----------> Citrulline
3) Citrulline + Asparate -----(Argininosuccinate synthetase + ATP) ---------------->
Argininosuccinate
4) Argininosuccinate ---------------( Argininosuccinate lyase) ---------------------------> Arginine &
Fumarate
5) Arginine ---(Arginase)---------> Urea and Ornithine.

The first step is the rate limiting step of urea synthesis

Steps 1 and 2 are in the mitochondria
Step 3 onwards is in the cytosol
3 ATP used up in the urea synthesis cycle.
Allosteric regulation of urea cycle is possible.

Amino acids can undergo decarboxylation to form amine using the decarboxylase
enzyme.

Week 11
Cholesterol have a sterol group.
Cholesterol can exist in the free form and esterified form.

Free cholesterol is used in membranes.

Derivatives of free cholesterol are steroid hormones, vitamin D and bile salts.
Cholesterol is transported by LDL, HDL
Cholesterol cannot be broken down to make energy.
Normal cholesterol levels is less than 5.2 mmol/l
Esterified cholesterol is cholesterol + fatty acid (present in blood plasma

Triacylglycerides are used in energy production.

Triacylglycerides are transported by VLDL, chylomicron.
Normal levels are less than 2.3 mmol/l

Cholesterol has 27 carbons.

Acetyl CoA used to build up cholesterol. Energy is required for this anabolic process.
Energy comes from hydrolysis of ATP or removal of CoA bond. NADPH is used.

Cholesterol synthesis happens in the cytosol.

Acetyl CoA is in the mitochondria. It crosses the mitochondrial membrane as citrate.

Formation of mevalonate requires 3 Acetyl CoA, 2 NADPH, Thiolase enzyme, HMG CoA
synthase enzyme, HMG CoA reductase enzyme.
HMG CoA reductase is the key enzyme.
After formation of one mevalonate, 3 CoA and 2 NADP+ are released.

Insulin and glucagon regulate HMG CoA reductase enzyme.

Insulin will positively regulate HMG CoA reductase enzyme and cholesterol synthesis.
Glucagon will negatively regulate HMG CoA reductase enzyme and cholesterol
synthesis.
Allosteric regulation of this enzyme is done by phosphorylation and dephosphorylation.
The dephosphorylated form of HMG CoA reductase is the active form.
The phosphorylated form of HMG CoA reductase is inactive.
Thyroid hormones increase the amount of the HMG CoA reductase enzyme by
enhancing its transcription.
Cholesterol can also regulate HMG CoA reductase enzyme levels (feedback control)
Statins are competitive inhibitors of HMG CoA reductase.

Triacylglycerol - 1 glycerol backbone and 3 fatty acid chains

Fatty acids come from liver and adipose tissue.
Glycerol phosphate comes from glucose or glycerol (liver)
Glycerol phosphate -----(acyltransferase)-----------> Lysophosphatidic Acid
-----(acyltransferase)----------> Phosphatidic Acid --------------> Diacylglycerol
-----(acyltransferase) ------------> Triacylglycerol.
Hormone sensitive lipase is responsible for the removal of the first fatty acid.
Fatty acids can be oxidized to give energy.

Synthesis of bile is in the liver.

Rate limiting step is cholesterol-7-hydroxylase.

Bile acid is the derivative of cholesterol

Conjugated primary bile acid = bile salts
Conjugation of primary bile acid happens with glycine or taurine.

Bile salts are amphipathic and thus are effective detergents.

Decreased amounts of bile acids in the bile can result in the formation of gallstones.

Ketone bodies: Alternative sources of energy for CNS.

Produced from acetyl CoA
Synthesis of ketone body is in the mitochondria in the liver only.
Same process until HMG CoA reductase as cholesterol synthesis.
Ketone body breakdown can provide Acetyl CoA which goes into TCA cycle.

Cholesterol synthesis

1) Acetyl CoA (2C) + Acetyl CoA (2C) -------------(Thiolase)--------------------------------------------->

2) Acetoacetyl CoA (4C)
3) Acetoacetyl CoA (4C) + Acetyl CoA (2C) -------------(HMG CoA synthase)----------------->
4) HMG CoA (6C)--------------------(HMG CoA reductase, 2 NADPH + H+) -------------------------->
Mevalonate (6C)

key enzyme is HMG CoA reductase

PP = pyrophosphate
Mevalonate (6C) -------------> isopentylPP (5C) -------(isomerization)-------> dimethylallylPP
(5C) ----(+ IPP)--------> geranylPP (10C)--------(+IPP)-------------------> farnesylPP (15C)
------------(FPP)-------> Squalene (30C) ----(NADPH used)--------> Lanesterol (30C) ---------------->
Cholesterol (27 C)
6 isoprene units needed for 1 cholesterol.
3 acetyl CoA in 1 isoprene unit.
18 acetyl CoA needed for 1 cholesterol.

Catabolism: Oxidation, ATP & NADH formation.

Anabolism: Reduction. ATP and NADPH usage.

Amino Acids can be glucogenic, ketogenic or both.

Glucogenic - Amino acids degrade to glucose via phosphoenolpyruvate
Ketogenic - Amino acids degrade to ketone bodies or fatty acids.

Amino acids can turn into pyruvate, Acetyl CoA, alpha keto glutarate, fumarate,
oxaloacetate to enter the metabolic pathways.

Arginine is a semi essential amino acid. It can be synthesized in the urea cycle.
There are 10 essential amino acids. (PVT. TIM HALL)
Phenylalanine, Valine, Threonine, Tryptophen, Isoleucine, Methionone, Histidine,
Arginine, Leucine, Lysine.

Thus amino acids can be classified as essential/non essential or as

glucogenic/ketogenic/both.

Glucogenic amino acids:

Alanine, Glycine, Serine, Cysteine, Asparate, Arginine, Asparagine, Proline, Histidine,
Glutamine, Methionine, Valine.
These amino acids can be converted to glucose and thus they are an energy source
during starvation.

Both glucogenic & ketogenic amino acids:

Threonine, Tryptophan, Tyrosine, Phenylalanine, Isoleucine

Ketogenic amino acids:

Leucine, Lysine

Note: Acetyl CoA cannot become glucose. It can only be used in TCA cycle or lipid
synthesis.

Individual amino acid metabolism.

(Note: All transaminase enzymes require PLP as a coenzyme)
Pyridoxial-5-phosphate acts in transamination & deamination reacttions

1) Alanine.
Pyruvate + Glutamate <-----(alanine transaminase)------------> Alanine

You can create alanine from pyruvate (transamination). This alanine can become
pyruvate once again in the liver (transamination)

Lactic Acid: End product of anaerobic respiration. Used by heart & skeletal muscle.

2) Glutamate
It can be produced from:
- Glutamine (glutaminase enzyme)
- alpha ketoglutarate + NADPH + NH4+ (glutamate dehydrogenase enzyme)
- alpha ketoglutarate + alpha amino acid (transaminase enzyme)

Glutamate dehydrogenase acts on both directions.

Can create alpha ketoglutarate from glutamate and glutamate from alphaketoglutarate.

Alpha ketoglutarate <---(glutamate dehydrogenase)--------> Glutamate

Glutamate is he most abundant excitatory neurotransmitter in the CNS.
3) Glutamine
Produced from glutamate in 2 steps. Glutamine synthase.

Glutamate ----------(glutamate synthetase)----->gamma glutamyl phosphate (intermediate)

--(glutamate synthetase)--------> Glutamine

From glutamine
Glutamine -----(Glutaminase enz)--------> Glutamate + NH4+

Glutaminase is an important kidney tubule enzyme involved in the process of renal

ammoniagenesis.

Glutamine, just like every other amino acid, is used in protein synthesis.
Glutamine is also used for nitrogen & carbon donation, providing cellular energy,
providing cellular energy (gluconeogenesis) lipid synthesis.

Note: Reccommended daily intake of proteins is less than 1g per kg.

Excess amino acid intake will negatively affect the kidney.

4) Asparatate
Glutamate + Oxaloacetate <----(asparatate transaminase)-------> Asparatate

Asparatate transaminase enzyme (PLP dependent cux transaminase) can act both ways
and can form oxaloacetate from asparatate.
Asparatate is a neurotransmitter.

Asparatate serves as an amino donor in the urea cycle and in transamination reactions
(this yields oxaloacetate which follows gluconeogenesis pathway)

5) Asparagine
Asparatate + Glutamine----(asparagine synthetase)-->Asparagine + Glutamate
Asparagine -----(asparaginase)----------> Asparatate

6,7,8) Branched Chain Amino Acids:

Leucine, Valine, Isolecuine
From these 3 amino acids we can make tRNA or fatty acids.
Fatty acid ---> Acyl CoA ---> Acetyl CoA
The branched chain amino acids undergo transamination and then oxidative
decarboxylation to give Acyl CoA.
The enzyme at the oxidative decarboxylation stage is BCKDC enzyme which is similar to
PDH enzyme.

9) Glycine
Glycine -----(glycine cleavage complex)----------------> N5, N10 methylene THF + CO2 +
NH4+
NAD+ -----> NADH

Glycine <---------(serine hydroxymethyltransferase)--------------------------------> Serine

Folate ----(dihydrofolate reductase)-------> Dihydrofolate ------> (dihydrofolate reductase)

---------> Tetrahydrofolic acid

10) Serine
3-phosphoglycerate --(PGHdehydrogenase)--------> 3-phosphohydroxypyruvate
---(phosphoserine aminotransferase 1)----------------> Phosphoserine ----(phosphoserine
phosphatase)------------------------> Serine

Serine gives rise to sphingosine.

11) Cysteine
Cysteine ---(cysteine diosxygenase)----------> Cyestein sulfinate
1) Cysteine Sulfinate ---(cysteine decarboxylase)---------> Hypotaurine ---------> Taurine
2) Cystein sulfinate ----(asparatate transaminase)--------> 3-sulfinyl pyruvate ----------->
pyruvate

Serine + homocysteine ---(cystathione beta synthase)--------> cystathione -----------(cysteine

lyase)-------> Cysteine + alpha keto butarate

Cysteine gives rise to: Glutathione, Biotin, Taurine, Coenzyme A, protein synthesis
12) Methionine
Serine + homocysteine ----(methionine synthase)-------------> Methionine
Methionine ---(methionine adenosyltrasnferase)------------> S-adenosyl methionine
-----(adenosyl homocysteine)------------> Serine + homocysteine

13 & 14)
Phenyalanine --(phenylalanine hydroxylase)-------------> Tyrosine

Phenyalanine ----( phenylalanine hydroxylase & PCBD 1)

----dihydrobiopterine---(dihydrobiopterine reducatse)-----> Tetrahydrobiopterine (BH4)

Phenylalanine ----------> Tyrosine ----------> DOPA ---------> Dopamine -------> Noradrenaline

-------> Adrenaline
All steps use hydroxylase enzymes except last step which has N-methyltransferase

15) Lysine
Lysine eventually becomes Acetyl CoA
Lysine --(AASS)--------> Saccharopine ---(AASS)--------> aminoadipic-6-semialdehyde
--(AASD)-------> aminoadipic acid --(PLP-AT)---------> alpha ketoadipate ----(OADHc)------->
glutaryl CoA - - - - - - - - -> Acetyl CoA

16) Proline
Glutamate serves a the precursor of proline

Gluatmate ----(ALDH18A1)----------> Glutamyl gamma phosphate ----(ALDH18A1)-------->

pyrroline 5 carboxylase --(PYCR 1)----------> Proline

17) Threonine is converted to alpha ketobutyrate

18) Histidine is used to make glutamate, histamine

19) Tryptophan is used to make serotonin, melatonin, Acetacetate CoA

20) Arginine is a precursor in creatine synthesis.

Week 12
Amino Acid metabolism

Amino acids can be apha, beta, gamma, delta

Only alpha amino acids are protein building blocks.
In alpha amino acids, the amino group is attached to the alpha carbon.

Amino acids are needed for protein synthesis, as an energy source (during starvation)
and for creating nitrogen containing compounds.
Arginine (using NADPH) -----------> Citruline + NO
Nitrogen monoxide is used in vasodilation and in reducing blood pressure.

Heme synthesis:
Glycine + Succinyl CoA ---(alpha aminolevulnic acid synthase)-->alpha aminolevulnic
acid
Succinly CoA comes from TCA cycle components, Isoleucine, Methionine, Valine,
Threonine.

Branched Chain Amino Acids are used by muscles but they are not high energy
compounds.
Creatine phosphate is a high energy store in the muscles.

Arginine + Glycine ----------> Ornithine --(S-adenosyl Methionine)---------> Creatine

Tyrosine is used to make catecholamines (neurotransmitters dopamine, norepinephrine,

epinephrine)
Tryptophan used to make serotonin, melatonin
Glutamate used to make GABA
Arginine used to make Nitrogen monoxide
Histidine used to make histamine
Cysteine used to make Disulfide bridges
Glycine used to make heme (porphyrin ring)
Methionine used to make S-Adenosyl Methionine (SAM)
Serine used to make Choline

Tyrosine ----(tyrosine hydroxylase)---------> DOPA ----(aromatic amino acid

decarboxylase)------------> Dopamine ---(dopamine beta hydroxylase)-------> Noradrenaline
----(N-Methyltransferase)---------> Adrenaline

Tryptophan ---(oxidation)-------> 5-hydroxy-L-tryptophan ----(decarboxylation)-------->

Serotonin

All decarboxylase enzymes use PLP as a coenzyme.

Glutamate ------(glutamate decarboxylase)----------> GABA + CO2

Histidine ---(decarboxylation)-----------> Histamine

Glutathione is a tripeptide.
Glutamate + Cysteine ----------> GSH (reduced form)
GS-SG is the oxidized form.
Glutathione is an antioxidant (catches free radicals), scavenged H202 and is used in
conjugation (eg: paracetamol conjugation thus inactivates paracetamol)
To make GSH from GS-SG, we use NADPH.

Glucose-6-phosphate dehydrogenase is used in Pentose Phosphate pathway which

gives rise to NADPH.
Lack of G6PDH will cause drug induced hemolytic anemia

In the gamma glutamyl cycle, gluathione is produced.

This cycle transports amino acids into the cell across cell membrane.
The enzyme used in this cycle is gamma glutamyl transpeptidase.

Bile has cholesterol, bile salts, phospholipids.

Bile salts are made from cholesterol.
Glycine can conjugate (inactivate) primary bile acid to give bile salts.

SAM (S adenosyl methionine) is a methyl group donor.

Thus its a cofactor for the synthesis of catecholamines, creatine phosphate, choline
synthesis.

Serine ------> Choline by decarboxylation

Serine is sued in phospholipid and sphingolipid synthesis. (serine gives rise to
sphingosines)

Phenylketonuria is a hereditary disease. Phenylalanine is not broken down by

phenylalanine hydroxylase.
In this disease, melanin is not produced leading to paler skin and there is ketone build
up in brain which damages brain causing mental retardation.

Urea cycle happens in the mitochondria (first 2 steps) and then cytoplasm of
hepatocytes.
Carbamoyl phosphate synthetase is the rate limiting step of urea cycle.
CO2 + NH4+ ----------------> Carbamoyl phosphate

All decarboxylation and transamination reactions use PLP as a coenzyme.

Alanine and Asparatate both have aminotransferase enzymes.

Pyruvate is an alphaketo acid
following 2 reactions occur at the same time:
Pyruvate <-----------> Alanine
Glutamate <------------> alpha keto glutarate

Also
Oxaloacetate <------------> Asparatate

Alanine is glucogenic (glucose source)

Isoleucine, Leucine,, Lysine, Tyrosine, Threonine, Tryptophan are all ketogenic (ketone
body source)

Phenylalanine & Tyrosine

Tyrosine is non essential

Tyrosine can be made from phenylalanine.
Tyrosine breakdown gives acetoacetate and fumarate (ketogenic and glucogenic amino
acid)
Phenylalanine --(phenylalanine hydroxylase)------> Tyrosine
coenzyme used is BH4

Tyrosine (and phenylalanine indirectly) gives rise to catecholamines (dopamine,

norepinephrine, epinephrine)
Thyroid hormones (T3, T4)
Melanin

Accummulation of phenylalanine (due to disfunction of phenylalanine hydroxylase)

causes phenylketonuria (PKU). Mental retardation is caused.

Phenylalanine can be transaminated to phenylpyruvate

MAO and COMT regulate the amount of catecholamines.

Pyruvate -----> Acetyl CoA <------ Acetoacetate

Breakdown of amino acid carbon skeletons gives:

Acetyl CoA
Acetoacetate
Pyruvate
Alpha keto glutarate
Succinly CoA
Fumarate
Oxaloacetate

Any amino acid that breaks down and gives acetyl CoA and acetoacetate is ketogenic.
If an amino acid gives any of the other products, it is glucogenic.

Lysine - Essential amino acid

Is ketogenic. Breakdown of lysine gives acetoacetate, Aceteyl CoA'
Lysine derivatives are: carnitine.
Carnitine is used in the 2nd step of beta oxidation of fatty acids when transporting fatty
acids across the mitochondrial membrane.

Proline - non essential amino acid.

Is glucogenic.
Breakdown and synthesis of proline is linked to glutamate.
Glutamate in turn is linked to alpha keto glutarate

Threonine - Essendial amino acid

Glucogenic and KEtogenic.
Brekadown of threonine gives 2-oxobutyrate which is eventually linked to succinyl CoA
Threonine can also be claved to form glycine + acetaldehyde
Glycine is linked to pyruvate and acetaldehyde is oxidized to acetate.
Threonine is a target for phosphorylation in the protein sequences due to its -OH group.

Histidine
Is glucogenic.
Like proline, its breakdown is linked to glutamate which in turn is linked to alpha
ketoglutarate.
First step of histidine metabolism uses a lyase enzyme - histidinase.
Histidine ----(histidine decarboxylase)----------> Histamine
Histamine is the most important derivative of histidine.
Tryptophan - Essential amino acid
Glucogenic and Ketogenic
The end product of tryptophan metabolism is pyruvate and acetoacetate CoA.
Derivative: Serotonin, melatonin.

Tryptophan ---(hydroxylation, decarboxylation)-----------> Serotonin

----------------------(methylation, acetylation)---------> Melatonin

Arginine - semi essential amino acid

Glucogenic
Present in the urea cycle.
Eventually gives off alpha keto glutarate
Arginine -----(arginase)----------> urea + ornithine
Ornithin can be used in the creation of proline and thus glutamate which is linked to
alpha keto glutarate.
Arginine is called a semi essential amino acid because it is produced in the urea cycle)

Arginine gives rise to NO using nitrogen oxide synthase.

NO induces smooth muscle relaxation.

Nucleotides

Nucleotides are made from:

organic bases (purines or pyrimidnes)
sugars (ribose or deoxyribose)
Phosphate group
Nucleotides are components of DNA, RNA, can give ATP, GTP (energetics). Atp gives
rise to cAMP (signalling function). Nucleotids also give rise to UDP-glucose (used in
glycogen synthesis)

Purines:
Adenine (NH2 on backbone)
Guanine (double bond O and NH2 on backbone)

Pyrimidines:
Uracil (2 double bond O on backbone)
Thymine (2 double bond O and 1 CH3 on backbone)
Cytosine (double bond O and NH2 on backbone)

In DNA, A binds with T, G binds with C

Organic base is always bound to the glycosidic bond of sugars. Phosphate group binds
to carbon 5 of sugar.

The last oxygen between the 2 last phosphate groups is high energy.

Phosphate
\
Sugar --- Base
/
Phosphate
\
Sugar ---- Base
/
Phosphate

Nucleotides can be synthesised by our bodies from broken cells.

Ribose is always phosphorylated on the 5th carbon (Ribose-5-phosphate)

for nucleotide synthesis.

R5P comes from HMP shunt

Ribose-5-phosphate ------------------> PRpyrrophosphate (high energy compound) ----(pyrro
phosphate removed)-----------> PRNH2 (phosphor reibosyl amide) ----(glycine)------->
Phospho ribosine glycine amide ----------(Formylation occurs using formyl TH4) --------->
(Formylation gives the purine ring) ----------(ATP used, NH2 added)-----> -------------(ATP
used)----> ----(HCO2- removed)-------> ----(ATP used)--------> AICAR -------------> IMP
(inozin mono phosphate)

Formation of PRNH2 is the key step in nucletoide synthesis.

N atoms in purines come from glycine, glutamate, PRNH2.
2 formyl TH4s, HCO3-, Asparatate is also used in nucleotide synthesis.
4 ATP required for the synthesis of 1 purine structure

Inozin mono phosphate (IMP) is an intermediate which can be converted to either

adenine or guanine.

Asparatate + NH2 ----(ATP used)------------> Fumarate

For adenine:
IMP ---(asparatate, ATP used)------------> Adenylo succinate -----(fumarate given off)-------->
AMP ----(ATP used)-------> ADP -----(ATP used)------> ATP

For guanine:
IMP --(NADPH used)---------> XMP --(ATP, glutamate/glycine used)-------> GMP

Hypoxanite --(xantine oxidase)------> Xanite --(xantine oxidase)-----> Urate

Urate cant be degraded by humans, it can only be secreated.

Salvage pathway of purine nucleic acids:

PRPP ---(adenine becomes AMP by APRT, Guamine becomes GMP by

HGPRT)-------------------> Pyrrophosphate
Week 13
Nucleotdies are:
AMP/ADP/ATP
GMP/GDP/GTP
CMP/CDP/CTP
UMP/UDP/UTP

Its only called a nucleotide when we have sugar + base + phosphate.

Bases
Purines: Adenine, Guanine
Pyrimidines: Cysteine, Thymine, Uracil.

Base - Adenine
Nucleoside = Adenine + Sugar = Adenosine
Nucleotide = Adenosine + Phosphate = AMP

Nucleotides are needed for RNA production.

Deoxynucleotides are needed for DNA production.
Cyclic nucleotides (cAMP, cGMP) are used as cofactors, enzymes.

HMP Shunt/PPP needed to make sugars of nucleotides.

Base production requires Asparatate, CO2, Glycine, Formate, Amide and N of glutamate.

For purines and pyrimidines:

Ribose-5-phosphate ---(ribose phosphate pyrophosphate kinase)---------> PRPP
(phosphoribosyl pyrophosphate)

Regradation of nucleotides is done by nucleotidase (unspecific)

Xanthin oxidase is a crucial enzyme in urate production.

HGPRT is the key enzyme of the salvage pathway.

Urea concentrations:
Men: 200-400 micromol/L
Women: 140-340 micromol/L

Too much urine - hyperuricemia

This can cause gout, kidney stones.

Ribulose-5-phosphate ---------> IMP -------> AMP or GMP

AMP/GMP can become ADP/ATP or GDP/GTP.
All of the nucleotides negatively modulate the step:
R5P --------> PRPP

DNA has deoxyribose sugar. RNA has ribose sugar.

The main difference is carbon number 2. It could have oxygen or not.
DNA has NDP. RNA has dNDP
NDP -------> dNDP is due to ribonuclic reductase.

Carbamoyl phosphate --(dehydrogenase enzyme)------> Dehydroratate ----(NADH

used)-----> Orotate ---(PRPP)-----> OMP --(decarboxylation so CO2 cleaved. Enzyme: UMP
synthase)-------> UMP

Uracil can become Thymine.

UMP----> UDP ------> dUDP ----(loss pf Pi)-------> dUMP --(methylated. TH4 used)-----> dTMP
--------> dTDP -----------> dTTP

TH4 is used in both purine and pyrimidine synthesis.

Pteridin --(Ser --> Gly)-------> 5'10'N CH2 TH4 ---------> CH3TH4 -------> TH4 (B12)

Homocystein eventually becomes SAM using ATP

Activated methyl cycle: SAM------> SAH ------> Homocysteine -----> SAM.

Glycine + Succinyl CoA needed for heme synthesis.

Heme is found in hemoglobin (95%), myoglobin (1%), cytochrome C oxidase [ETC] and
cytochrome P450 [detoxification in liver] (1%)

Most hemoglobin is in red blood cells. About 130g/L or 2.2 mmol/L.

Hemoglobin in plasma is practically 0 normally.

Porphyrin is a collective term. Heme comes under this collective term.

If iron is in the center of the porphyrin ring - heme.
If any other metal in the center - porphyrin ring.

Heme synthesis.
Glycine + Succinyl CoA ----(ALA synthase, CO2, CoA given out)--------------------->
5-Aminolevulinic Acid
This first step is the key step, committed step, most regulated step. Happens in the
mitochondria.
Following steps happen in cytoplasm.

5-Aminolevulinic Acid -----(ALA dehydratase, -2H2O)-------> Porphobilinogen -------(PBG

deaminase)---------> Linear tetra pyrrole (porphyrin ring now formed) ---------(UPG III
synthase, -H2O)-------------> Uroporphinogen III -------(UPG III decarboxylase.
-4CO2)------------------------> Coproporphyrinogen ---(CPG oxidase, -2CO2)---------------->
Protoporphyrinogen IX ------(PPG oxidase, -6H)--------------> Protoporphrin IX
-------(Ferrorductase, Fe2+ --> 2H+)-------> Heme B

Key enzyme of heme synthesis: ALA synthase.

Heme itself is the best regulator of heme synthesis.

Porphyria is a hereditary rare disease due to insuffiencent [production of hemoglobin.

Also due to stress, alcohol consumption, low energy diet. Leads to pale skin,
photosensitivity, urea becomes dark after prolonged exposure to sunlight.

Heme degradation is in the macrophage.

Heme --(heme oxygenase)----> Biliverdin --(biliverdin reductase)------> Bilirubin

---(glucoronic acid removal)-------> Urobilinogen/Stercobilinogen