The document provides information on a course covering nitrogen metabolism and related topics like amino acid metabolism, folate metabolism, and nucleotide metabolism. It discusses several key metabolic pathways including:
1) Transamination reactions that transfer amino groups between amino acids and alpha-ketoglutarate.
2) The urea cycle in the liver which involves ornithine, citrulline, arginine, and other intermediates to produce urea for excretion of ammonia.
3) The connection of the urea cycle to the TCA cycle through fumarate and other intermediates to allow disposal of excess nitrogen.
System response of metabolic networks in Chlamydomonas reinhardtii during Nit...Nishikant Wase
Nitrogen starvation induces a global stress response in microalga that results in the accumulation of triglycerides in lipid bodies. To identify components and mechanisms leading to lipid accumulation during nitrogen stress, we used GC-MS based metabolite profiling and iTRAQ based quantitative proteomics to examine Chlamydomonas reinhardtii cultured up to 144 hours without nitrogen. When nitrogen is limiting, starch and lipid accumulated rapidly, with lipid becoming the major storage compound by 144 hours. Our FAMEs data showed that the percentage of highly unsaturated fatty acids was reduced and the percentage of saturated and monounsaturated fatty acids were increased. Using information from the GC-MS based metabolite profiling; a Partial Least Squares Discriminant Analysis model was created to evaluate the role of different intracellular metabolites during lipid accumulation. We observed decreased abundance of key amino acids whereas some important metabolites including citric acid, trehalose, triethanolamine, nicotinamine, methnionine, citramalic acid and sorbitol were increased in abundance. Addition of citric acid (from 4 mM to 6 mM) to the growth media significantly improves the lipid yield in Chlamydomonas reinhardtii while growing in TAP media containing nitrogen. Examination of differentially expressed proteins revealed that 100 of 793 identified proteins were induced after 144 hours, while 77 proteins were reduced in abundance. Proteins involved in nitrogen assimilation, oxidative phosphorylation, the glycolytic pathway, TCA cycle, starch, and lipid metabolism were found to be higher in abundance than in non-stressed cultures. Another effect of nitrogen starvation was reduction of proteins of the photosynthetic apparatus (including PS-I and PS-II) and light harvesting complex proteins. We conclude that during nitrogen starvation, carbon availability is the most important factor controlling oil biosynthesis and that there is carbon partitioning between starch and oil synthesis.
System response of metabolic networks in Chlamydomonas reinhardtii during Nit...Nishikant Wase
Nitrogen starvation induces a global stress response in microalga that results in the accumulation of triglycerides in lipid bodies. To identify components and mechanisms leading to lipid accumulation during nitrogen stress, we used GC-MS based metabolite profiling and iTRAQ based quantitative proteomics to examine Chlamydomonas reinhardtii cultured up to 144 hours without nitrogen. When nitrogen is limiting, starch and lipid accumulated rapidly, with lipid becoming the major storage compound by 144 hours. Our FAMEs data showed that the percentage of highly unsaturated fatty acids was reduced and the percentage of saturated and monounsaturated fatty acids were increased. Using information from the GC-MS based metabolite profiling; a Partial Least Squares Discriminant Analysis model was created to evaluate the role of different intracellular metabolites during lipid accumulation. We observed decreased abundance of key amino acids whereas some important metabolites including citric acid, trehalose, triethanolamine, nicotinamine, methnionine, citramalic acid and sorbitol were increased in abundance. Addition of citric acid (from 4 mM to 6 mM) to the growth media significantly improves the lipid yield in Chlamydomonas reinhardtii while growing in TAP media containing nitrogen. Examination of differentially expressed proteins revealed that 100 of 793 identified proteins were induced after 144 hours, while 77 proteins were reduced in abundance. Proteins involved in nitrogen assimilation, oxidative phosphorylation, the glycolytic pathway, TCA cycle, starch, and lipid metabolism were found to be higher in abundance than in non-stressed cultures. Another effect of nitrogen starvation was reduction of proteins of the photosynthetic apparatus (including PS-I and PS-II) and light harvesting complex proteins. We conclude that during nitrogen starvation, carbon availability is the most important factor controlling oil biosynthesis and that there is carbon partitioning between starch and oil synthesis.
Ruangpan, L., & Tendencia, E. A. (2004). Bacterial isolation, identification and storage. In
Laboratory manual of standardized methods for antimicrobial sensitivity tests for bacteria
isolated from aquatic animals and environment (pp. 3–11). Tigbauan, Iloilo, Philippines:
Aquaculture Department, Southeast Asian Fisheries Development Center.
http://hdl.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Nucleic Acid-its structural and functional complexity.
RLyons-AminoAcids-07-Proteins monomers.ppt
1. Unless otherwise noted, the content of this course material is
licensed under a Creative Commons Attribution – Share Alike 3.0
License.
Copyright 2007, Robert Lyons.
The following information is intended to inform and educate and is not a tool for self-diagnosis or a replacement for medical evaluation, advice,
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2. Nitrogen Metabolism (and Related Topics)
• Amino Acid Metabolism (Nitrogen metabolism)
• Folate Metabolism (“One-Carbon pathways”)
• Nucleotide Metabolism
Dr. Robert Lyons
Assistant Professor, Biological Chemistry
Director, DNA Sequencing Core
3. Supplementary study material on the Web:
http://seqcore.brcf.med.umich.edu/mcb500
There are also PDF’s of class
handouts with supplemental
information available in the
table of contents for this course.
4. Glu, Gln,
Asp, NH3
Amino Acid metabolism
Folate metabolism
Nucleic Acid metabolism
Methylene
THF
Met
Cycle
Purine s Py rim idine s
Uric Acid
Urea
Amino acids
DNA
RNA
(energy)
TCA Cycle
fumarat e
oxaloacetat e
5. Protein Degradation:
• Endogenous proteins degrade continuously
- Damaged
- Mis-folded
- Un-needed
• Dietary protein intake - mostly degraded
Nitrogen Balance - expresses the patient’s current
status - are they gaining or losing net Nitrogen?
6. Transaminases Collect Amines
General react ion overview:
C
H
R COO
NH2
amino
acid
C
H
R COO
NH
2
amino
acid
(typically glutamate)
1 2
C
R COO
O
-keto
acid
(typically
alpha-ketoglutarate)
(
-
)
+ +
2
C
R COO
O
-keto
acid
(
-
)
1
(
-
) (
-
)
Det ails of react ion mechanism:
C
H
R COO
NH
C
H
R COO
N
N
CH
O
CH
CH
OH
O
P
pyridoxal
phosphate
amino
acid
+
H O
2
3
2
CH
CH
CH
OH
O
P
3
2
2
C
H
R COO
N
CH
CH
CH
OH
O
P
3
2
+
H
+
+
C
H
R COO
N
CH
CH
CH
OH
O
P
3
2
+
C
R COO
NH
CH
O
CH
CH
OH
O
P
pyridoxamine
phosphate
+
3
2
2
+
H
-keto
acid
(
-
)
(
-
) (
-
) (
-
)
(
-
)
N
H
N
H
N
H N
H
8. Some amino acid + -ketoglutarate some alpha keto acid + Glutamate
In other words, alpha-ketoglutarate is the preferred
acceptor, and Glutamate is the resulting amino acid:
In peripheral tissues, transaminases tend to form
Glutamate when they catabolize amino acids
9. Glutamate can donate its amines to
form other amino acids as needed
Glutamate + oxaloacetate -ketoglutarate + aspartate
A specific example - production of Aspartate in liver
(described a few slides from now):
10. Ge t t ing Amines Int o t he Live r
OCCHCH C
H
NH
CO
glutamat
e
NAD(P)
NAD(P)H
OCCHCH C CO
-k
etogluta
rate
+ NH
am
monia
O
(mito)
C
H
OOC CH
NH
CH COO
glutamate glutamine
C
H
OOC CH
NH
CHC
O
NH
NH
ATP ADP P
Glutamate
Dehydrogenase:
Glutamine
Synthetase:
11. In t he Liver: Pre cursers for Urea Cycle
Glut amine is hydrolyzed t o glut amat e and ammonia:
C
H
OOC CH
NH
CHC
glutamate
O
OH
glutamine
C
H
OOC CH
NH
CHC
O
NH
HO
NH3
Glut amat e donat es it s amino group t o f orm aspart at e:
Gluta
mate aspa
rtate
oxal
oaceta
te
+ +
-keto
g
lutara
te
OCCHCH C
H
NH
CO OCCHC
H
CO OCCHCHC
O
CO OCCH C
H
NH
CO
O
Glut amat e-aspartat e aminot ransferase:
.
.
Ammonia can also be formed by the glutamate dehydrogenase reaction
and several other reactions as well.
12. Liver mitochondrion
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH3
(
+
)
Ornit hine
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH3
(
+
)
Ornit hine
C
H
OOC CH
2
NH
3
(
+
)
(
-
) CH2
CH2
NH C
(
+
)
Arginine
C
H
OOC CH2
NH3
(
+
)
(
-
) CH
2CH
2
NH C
O
Cit rulline
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH C
O
Cit rulline
2ATP + HCO +
3
NH2C
O
3
OPO(
-
)
Carbamoyl
phosphat e
Pi
2ADP + Pi
O CCH C
H
2 2 2
aspartate
(
-
) (
-
)
CO
i
ATP
AMP + PP
C
H
OOC CH
2
NH
3
(
+
)
(
-
)
CH2
CH2
NH C
O CCH C
H
2 2 2
(
-
) (
-
)
CO
(
+
)
Argininosuccinat e
Liver cyt oplasm
O C C C
H
2 2
(
-
) (
-
)
CO
H
Fumarat e
H O
2
C
O
Urea
NH2
NH2
NH2
NH3
NH2
NH2
NH2
NH2
NH2
NH2
1
5
4
3
2
13. Ca r b a m o y l p h o s p h a t e sy n t h e t a s e I
HO C
O
O
ATP
ADP
P
NH
P
HO C
O
O
bicarbonate carbonyl
phosphate i
HO C
O
NH
carbamate
ATP
ADP
O C
O
NH
P
carbamoyl
phosphate
14. O r n it h in e T r a n s c a r b am o y las e
C
H
OOC CH
NH
CH CHNH
O r n it h in e
C
H
OOC CH
NH
CH CHNH NH
C
O
C it r ullin e
NH C
O
OPO
C ar b am o y l p ho s p hat e
P
CHNH
15. A r g in in o su c c in a t e s y n t h e t as e
O CC
H
C
H
NH
2
2 2 2
aspartate
(
-
) (
-
)
CO
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH 2
NH
C
O
Cit rulline
i
ATP AMP + PP
C
H
OOC CH
2
NH
3
(
+
)
(
-
)
CH2
CH2
NH C NH
O CCH C
H
NH
2
2 2 2
(
-
) (
-
)
CO
2
(
+
)
Argininosuccinat e
16. A r g in in o s u c c in a t e ly a se
C
H
OOC CH
2
NH
3
(
+
)
(
-
)
CH2
CH2
NH NH2
C
NH2
(
+
)
Arginine
C
H
OOC CH
2
NH
3
(
+
)
(
-
)
CH2
CH2
NH C NH
O CCH C
H
NH
2
2 2 2
(
-
) (
-
)
CO
2
(
+
)
Argininosuccinate
O C C C
H
2 2
(
-
) (
-
)
CO
H
Fumarate
17. A r g in as e
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH3
(
+
)
Ornit hine
C
H
OOC CH
2
NH
3
(
+
)
(
-
)
CH2
CH2
NH NH2
C
NH2
(
+
)
Arginine
NH2C
O
NH2
Urea
H2
O
18. Liver mitochondrion
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH3
(
+
)
Ornit hine
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH3
(
+
)
Ornit hine
C
H
OOC CH
2
NH
3
(
+
)
(
-
) CH2
CH2
NH C
(
+
)
Arginine
C
H
OOC CH2
NH3
(
+
)
(
-
) CH
2CH
2
NH C
O
Cit rulline
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH C
O
Cit rulline
2ATP + HCO +
3
NH2C
O
3
OPO(
-
)
Carbamoyl
phosphat e
Pi
2ADP + Pi
O CCH C
H
2 2 2
aspartate
(
-
) (
-
)
CO
i
ATP
AMP + PP
C
H
OOC CH
2
NH
3
(
+
)
(
-
)
CH2
CH2
NH C
O CCH C
H
2 2 2
(
-
) (
-
)
CO
(
+
)
Argininosuccinat e
Liver cyt oplasm
O C C C
H
2 2
(
-
) (
-
)
CO
H
Fumarat e
H O
2
C
O
Urea
NH2
NH2
NH2
NH3
NH2
NH2
NH2
NH2
NH2
NH2
1
5
4
3
2
19. Urea Cycle Connect s t o TCA Cycle
Arginine
Citrulline
O CCH C
H
NH
2
2 2 2
Aspartate
(
-
) (
-
)
CO
Argininosuccinate
OC C C
H
2 2
(
-
) (
-
)
CO
H
Fumarate
Malate
Oxaloacetate
TCA Cycle
-Ketoglutarate
Citrate
Urea
Ornithine
Urea Cycle
20. Ge t t ing Amines Int o t he Live r
OCCHCH C
H
NH
CO
glutamat
e
NAD(P)
NAD(P)H
OCCHCH C CO
-k
etogluta
rate
+ NH
am
monia
O
(mito)
C
H
OOC CH
NH
CH COO
glutamate glutamine
C
H
OOC CH
NH
CHC
O
NH
NH
ATP ADP P
Glutamate
Dehydrogenase:
Glutamine
Synthetase:
21. Liver mitochondrion
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH3
(
+
)
Ornit hine
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH3
(
+
)
Ornit hine
C
H
OOC CH
2
NH
3
(
+
)
(
-
) CH2
CH2
NH C
(
+
)
Arginine
C
H
OOC CH2
NH3
(
+
)
(
-
) CH
2CH
2
NH C
O
Cit rulline
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH C
O
Cit rulline
2ATP + HCO +
3
NH2C
O
3
OPO(
-
)
Carbamoyl
phosphat e
Pi
2ADP + Pi
O CCH C
H
2 2 2
aspartate
(
-
) (
-
)
CO
i
ATP
AMP + PP
C
H
OOC CH
2
NH
3
(
+
)
(
-
)
CH2
CH2
NH C
O CCH C
H
2 2 2
(
-
) (
-
)
CO
(
+
)
Argininosuccinat e
Liver cyt oplasm
O C C C
H
2 2
(
-
) (
-
)
CO
H
Fumarat e
H O
2
C
O
Urea
NH2
NH2
NH2
NH3
NH2
NH2
NH2
NH2
NH2
NH2
1
5
4
3
2
22. CPS I is St im u la t e d b y N A G
HO C
O
O
ATP
ADP
P
NH
P
HO C
O
O
bicarbonate
carbonyl
phosphate i
HO C
O
NH
carbamate
ATP
ADP
O C
O
NH
P
carbamoyl
phosphate
g lu t am at e
C
H
OOC CH
NH
CH C
O
OH
+ Co A -
C
H
OOC CH
NH
CH C
O
OH
C O
CH
C O
CH
a c et y l Co A
N - ac et y l g lu t am a t e
( N A G)
N -a c e t y l
g lu t a m a t e
s y n t h e t as e
( r e p e a t in g t h e f ig u r e f r o m p a g e 3 o f y o u r h an d o u t )
26. Why is Ammonia Toxic?
• Possible neurotoxic effects on
glutamate levels (and also GABA)
(due to shifting equilibria of reactions
involving these compounds)
27. Why is Ammonia Toxic?
• Possible neurotoxic effects on
glutamate levels (and also GABA)
(due to shifting equilibria of reactions
involving these compounds)
• Possible metabolic/energetics effects:
- alpha-ketoglutarate levels
- glutamate levels
- glutamine
28. Liver mitochondrion
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH3
(
+
)
Ornit hine
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH3
(
+
)
Ornit hine
C
H
OOC CH
2
NH
3
(
+
)
(
-
) CH2
CH2
NH C
(
+
)
Arginine
C
H
OOC CH2
NH3
(
+
)
(
-
) CH
2CH
2
NH C
O
Cit rulline
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH C
O
Cit rulline
2ATP + HCO +
3
NH2C
O
3
OPO(
-
)
Carbamoyl
phosphat e
Pi
2ADP + Pi
O CCH C
H
2 2 2
aspartate
(
-
) (
-
)
CO
i
ATP
AMP + PP
C
H
OOC CH
2
NH
3
(
+
)
(
-
)
CH2
CH2
NH C
O CCH C
H
2 2 2
(
-
) (
-
)
CO
(
+
)
Argininosuccinat e
Liver cyt oplasm
O C C C
H
2 2
(
-
) (
-
)
CO
H
Fumarat e
H O
2
C
O
Urea
NH2
NH2
NH2
NH3
NH2
NH2
NH2
NH2
NH2
NH2
1
5
4
3
2
29. Defects are diagnosed based on the metabolites seen
in the blood and/or urine.
CPSD
OTCD
ASD
ALD
AD
No elevation except ammonia; diagnosed by elimination.
Elevated CP causes synthesis of Orotate
Elevated citrulline
Elevated argininosuccinate
Elevated arginine
Inherited Defects of Urea Cycle Enzymes: Diagnosis
30. Liver mitochondrion
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH3
(
+
)
Ornit hine
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH3
(
+
)
Ornit hine
C
H
OOC CH
2
NH
3
(
+
)
(
-
) CH2
CH2
NH C
(
+
)
Arginine
C
H
OOC CH2
NH3
(
+
)
(
-
) CH
2CH
2
NH C
O
Cit rulline
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH C
O
Cit rulline
2ATP + HCO +
3
NH2C
O
3
OPO(
-
)
Carbamoyl
phosphat e
Pi
2ADP + Pi
O CCH C
H
2 2 2
aspartate
(
-
) (
-
)
CO
i
ATP
AMP + PP
C
H
OOC CH
2
NH
3
(
+
)
(
-
)
CH2
CH2
NH C
O CCH C
H
2 2 2
(
-
) (
-
)
CO
(
+
)
Argininosuccinat e
Liver cyt oplasm
O C C C
H
2 2
(
-
) (
-
)
CO
H
Fumarat e
H O
2
C
O
Urea
NH2
NH2
NH2
NH3
NH2
NH2
NH2
NH2
NH2
NH2
1
5
4
3
2
31. CPS I is St im u la t e d b y N A G
HO C
O
O
ATP
ADP
P
NH
P
HO C
O
O
bicarbonate
carbonyl
phosphate i
HO C
O
NH
carbamate
ATP
ADP
O C
O
NH
P
carbamoyl
phosphate
g lu t am at e
C
H
OOC CH
NH
CH C
O
OH
+ Co A -
C
H
OOC CH
NH
CH C
O
OH
C O
CH
C O
CH
a c et y l Co A
N - ac et y l g lu t am a t e
( N A G)
N -a c e t y l
g lu t a m a t e
s y n t h e t as e
( r e p e a t in g t h e f ig u r e f r o m p a g e 3 o f y o u r h an d o u t )
32. Liver mitochondrion
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH3
(
+
)
Ornit hine
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH3
(
+
)
Ornit hine
C
H
OOC CH
2
NH
3
(
+
)
(
-
) CH2
CH2
NH C
(
+
)
Arginine
C
H
OOC CH2
NH3
(
+
)
(
-
) CH
2CH
2
NH C
O
Cit rulline
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH
2
NH C
O
Cit rulline
2ATP + HCO +
3
NH2C
O
3
OPO(
-
)
Carbamoyl
phosphat e
Pi
2ADP + Pi
O CCH C
H
2 2 2
aspartate
(
-
) (
-
)
CO
i
ATP
AMP + PP
C
H
OOC CH
2
NH
3
(
+
)
(
-
)
CH2
CH2
NH C
O CCH C
H
2 2 2
(
-
) (
-
)
CO
(
+
)
Argininosuccinat e
Liver cyt oplasm
O C C C
H
2 2
(
-
) (
-
)
CO
H
Fumarat e
H O
2
C
O
Urea
NH2
NH2
NH2
NH3
NH2
NH2
NH2
NH2
NH2
NH2
1
5
4
3
2
33. Clinical Management of Urea Cycle Defects
• Dialysis to remove ammonia
• Provide the patient with alternative ways to excrete
nitrogenous compounds:
• Levulose - acidifies the gut
• Low protein diet
* Intravenous sodium benzoate or phenylacetate
* Supplemental arginine
O
rnithine
A
rgin
in
e
C
itrulline
i
A
T
P
A
M
P+P
P
A
rgin
inosuccinate
HO
2
C
O
U
rea
N
H
2
N
H
2 A
spa
rta
te
Excreted by kidney
Excreted by kidney
X
D
ieta
ry
A
rg
in
in
e
carbam
oyl phosphate
XASD
ALD
35. Easily-degraded products after transamination:
O CCH C
H
NH3
2 2 2
aspartate
(
-
)
CO
transamination
O CCH C
O
2 2 2
(
-
)
CO
oxaloacetate
(
-
) (
-
)
(
+
)
O C CH C
H
NH
3
2 2 2
glutamate
(
-
)
transamination
CH C
O
2 2
(
-
)
-ketoglutarate
CH2 O C
2 CH2
CO CO
(
-
) (
-
)
(
+
)
CH C
H
NH
3
3 2
alanine
(
-
)
CO
transamination
CH C
O
3 2
(
-
)
CO
pyruvate
(
+
)
We also already know how to degrade Glutamine:
Glutamine ----------------> glutamate + ammonia
Asparagine ---------------> aspartate + ammonia
…and by analogy, how to degrade Asparagine:
glutaminase
asparaginase
glutaminase
36. Many amino acids are purely glucogenic:
Glutamate, aspartate, alanine, glutamine,
asparagine,…
Some amino acids are both gluco- and ketogenic:
Threonine, isoleucine, phenylalanine,
tyrosine, tryptophan
Amino Acids are categorized as ‘Glucogenic’
or ‘ketogenic’ or both.
The only PURELY ketogenic Amino Acids:
leucine, lysine
37. C
H
OOC CH
2
NH
3
(
+
)
(
-
)
CH2
CH2
NH NH2
C
NH2
(
+
)
Arginine
Urea (via
t he urea cycle)
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
CH2
NH3
(
+
)
Ornit hine
-ket oglut arat e
glutamat e
C
H
OOC CH2
NH3
(
+
)
(
-
)
CH
2
C
glut amat e - 5 - semialdehyde
O
H
NAD(P)
NAD(P)H
(
+
)
C
H
OOC CH
2
NH
3
(
+
)
(
-
)
CH2
C
glut amate
O
OH
- ketoglutarate
N
H
(
+
)
OOC
(
-
)
Proline
glutamine
C
H
OOC CH
2
NH
3
(
+
)
(
-
)
CH2
C
O
NH
2
H O
2
NH
3
Amino acids with 5-carbon
backbones tend to form
-ketoglutarate
38. C
H
OOC NH3
(
+
)
(
-
)
H
Glycine
NAD NADH
(
+
)
THF N -N - methylene THF
5 1
0
+
CO NH
4
(
+
)
2
C
H
OOC NH
3
(
+
)
(
-
)
2
Glycine
THF N -N - methylene THF
5 1
0
Serine
CH
OOC NH
3
(
+
)
(
-
)
CH OH
2
Glycine
Synthase:
Serine
Hydroxymethyl-
transferase:
Serine
CH
OOC NH3
(
+
)
(
-
)
CH OH
2
H O
2
C
OOC NH3
(
+
)
(
-
)
CH2
C
OOC NH
2
(
+
)
(
-
)
CH
3
C
OOC
(
-
)
CH
3
H O
2
NH4
(
+
)
O
Serine
Dehydratase:
Degradation and Biosynthesis of Serine and Glycine
39. C
H
C
OO
C
H
N
H
C
H
Methionine
Serine
C
H
C
OO
C
H
N
H
HO
S
C
H
C
H
C
OO
C
H
N
H
C
H
S-Adenosyl Met hionine
S
C
H
ATP +
H O
PPi +
Pi
C
H
O
H
H H H
OH OH
Adenine
C
H
CO
O
CH
NH
CH
Homocysteine
HS
C
H
C
OO
C
H
N
H
C
H
S-Adenosyl Homocyst eine
H
S
C
H
O
H
H H H
OH OH
Adenine
Bios ynt het ic
Met hy lat ion
react ion
Met hyl accept or
Met hylat ed acc eptor
* see exam ples
C
H
CO
O
CH
NH
Cyst eine
H
S
(remainder of
homocysteine
degraded
for energy)
tet rahydrofolat e
N5 methyl
t et rahydrofolate
Methionine Cycle
And Biological
Methyl Groups
40. Phenylalanine and Tyrosine
CH2 CH COO
NH3
(+)
(-)
Phenylalanine
Tetrahydrobiopterin + O2
Dihydrobiopterin + H2O
CH2 CH COO
NH3
(+)
(-)
Tyrosine
HO
Homogent isat e
Enzyme:
Phenylalanine
hydroxylase
Enzyme:
homogent isat e
dioxygenase
CH2 C COO
(-)
Phenylpyruvat e
O
Phenylketonuria
(no phenylalanine
hydroxylase)
(Normal path shown in black, pathological reaction shown in red)
(you don’t need to
know the rest)
Deficiency:
Alkaptonuria
“Ochronosis”
41. Branched Chain Amino Acids
Isoleucine Leucine Valine
CH COO
(
-)
NH3
(+
)
CH
CH2
CH3
CH3
CH COO
(
-
)
NH3
(
+)
CH
CH 2
CH3
CH3
CH COO
(-
)
NH3
(+
)
CH
CH3
CH3
C COO
(
-)
O
CH
CH2
CH3
CH3
C COO
(-
)
CH
CH 2
CH3
CH3
C COO
(
-
)
CH
CH3
CH3
O O
C
O
CH
CH2
CH3
CH3
C
CH
CH 2
CH3
CH3
C S-CoA
CH
CH3
CH3
O O
NAD, CoASH
+
NADH +
CO
2
NAD, CoASH
+ NAD, CoASH
+
NADH + CO
2 NADH + CO2
S-CoA
S-CoA
-KG -KG -KG
Glu Glu Glu
---------------- Transamination ----------------
--- Branched-chain -keto acid dehydrogenase ---
(continues on to degradation path similar to -oxidation of fatty acids)
42. Synthesis of Bioact ive Amines
CH 2 CH COO
NH 3
(+)
(-)
Tyrosine
HO CH 2 CH COO
NH 3
(+)
(-)
HO
HO
Dihydroxypheny lalanine
Tyrosine
hydroxylase
( L-DOPA)
HO
HO
CH 2CH NH 3
(+)
2
Dopam ine
CH CH NH 3
(+)
2
Norepinephrine
OH
H
HO
HO
CH CH N
H
2
Epinephrine
OH
H
HO
HO
CH 3
43. N
CH 2 CH COO
NH3
(+)
(-) HO
N
CH2 CH COO
NH3
(+)
(-)
Tryptophan 5-hydroxytryptophan
Tryptophan
hydroxylase
CO2
HO
N
CH 2 CH NH3
(+)
Serotonin
2
PLP-dependent
decvarboxylat ion
NAD+
Synthesis of Bioactive Amines
44. CH2 CH COO
NH3
(+)
(-)
CH 2
COO
(-)
Glut amate
Glutamate
decarboxylase
( PLP-dependent )
CH 2 CH NH3
(+)
CH 2
COO
(-)
-aminobut yric acid
(GABA)
2
N
N
H
CH2 CH COO
NH3
(+)
(-
)
Hist idine
Hist idine
decarboxylase
( PLP-dependent )
N
N
H
CH2 CH NH3
(+)
Hist amine
2
Synthesis of Bioactive Amines