Unit III week 1 Flashcards
Categorization of 20 Amino Acids
5 methods to do this
1) Acidic or basic
2) Polar or nonpolar
3) Ability to synthesize or not
4) Specific chemical constituents
5) Use in energy synthesis
Essential vs. non-essential vs. conditionally essential AAs
Essential: cannot be synthesized by body, obtained from diet
Non-essential: can be synthesized from other amino acids
Conditionally essential: can be made by the body, but capacity for their synthesis is limited (especially in state of high consumption - e.g. illness)
Specific chemical constituents in AAs can be… (4)
Sulfur containing AAs
AAs with nitrogen in side chain (involved in N transport)
Branched amino acids
Aromatic amino acids (precursors for NTs and hormones)
How are proteins broken down in the gut?
GI tract → Peptidases: activated in gut lumen
Different specificities for specific types of peptide bonds
Sequentially break down long peptide chains into component AAs → absorbed and enter circulation
How are proteins broken down in tissues? (2 ways)
protein within cells also need to be broken down
1) Ubiquitination: targets proteins for degradation in proteasomes
2) Degradation in lysosomes
Amino acids contain a _______ group.
This means it must first be removed before use as a precursor for ___________.
This means it must be added before _______ is made from a carbon skeleton.
NH2
gluconeogenesis
Amino acid
Transamination reactions:
1) L-Amino acid donates NH3 to ________ –> ________ + ___________
catalyzed by ___________
2) Ammonia released as NH3 with regeneration of _________ –> _________
(bidirectional depending on substrate / acceptor availability)
NO production of anything, just shuttling something
1) AA donates NH3 to a-ketoglutarate → L glutamate + a-keto acid
Catalyzed by aminotransferase
2) Ammonia released as NH3 with regeneration of a-ketoglutarate
→ Urea cycle
Urea cycle:
1) NH3 –> ___________
catalyzed by ____________
NH3 → carbamoyl phosphate
Catalyzed by carbamoyl phosphate synthase 1
*Key regulated step in protein catabolism
Urea cycle:
2) Carbamoyl phosphate + __________ –> _________
Carbamoyl phosphate + NH3 (from aspartate) → urea
Urea: marker of AA catabolism and oxidation
Glutamine
nitrogen containing AA, accepts nitrogen from other AAs in peripheral tissues and carries it to liver/kidney
→ donates N to glutamate
→ a-ketoglutarate + NH3
Glutamine donates N to _________
Glutamate –> _________ + ________
This reaction is catalyzed by __________
glutamate
Glutamate –> a-ketoglutarate + NH3
catalyzed by glutamate dehydrogenase
Second key regulated step
Two key regulated steps of urea cycle:
1) NH3 → carbamoyl phosphate
Catalyzed by carbamoyl phosphate synthase 1
2) Glutamate → a-ketoglutarate catalyzed by glutamate dehydrogenase
Sulfur containing amino acids (2)
cysteine (non-essential AA)
methionine (essential AA)
Cysteine
can form disulfide bridges (change protein conformation)
-SH group
unessential amino acid
Glutathione (GSH)
highly soluble tripeptide that contains cysteine
1) Redox buffer (SH buffer) that maintains proteins in reduced forms (EX - reduces Fe3+ → Fe2+)
2) ROS protection: reduces hydrogen peroxide (H2O2) → H2O
3) Cofactor for several enzymes
4) uses Cys to control redox potential via GSH ← → GSSG
A-adenosylmethionine (SAM)
Met used to produce SAM (produced during first step of methionine degradation)
- energy source for some biochemical reactions and important methyl donor
- Precursor for homocysteine (B1 and folate metabolism)
- SAM → S-adenosylhomocysteine (SAH)
Tetrahydrofolate
important one carbon methyl transfer reactions
Ring structure on side chains of what AAs? (3)
These are precursors for what important molecules? (7)
tryptophan, phenylalanine, tyrosine
Precursors for serotonin, niacin, dopamine, NE, epinephrine, tetrahydrobiopterin, thyroid hormone
Collagen
formation occurs via posttranslational modification from what 2 enzymes?
These reactions are _______ dependent
most abundant protein in human body, forms triple stranded helix
1) Prolyl hydroxylase
2) Lysyl hydroxylase
Vitamin C dependent
Hydroxyproline (Hyp)
-use?
___________ converts _____ to Hyp
used in collagen for H-bonding → increase collagen strength
Prolyl hydroxylase converts Pro to Hyp
Hydroxylysine (Hyl)
-use?
___________ converts _____ to Hyl
used in collagen for interchain cross-links
Lysyl hydroxylase converts Lys to Hyl
Gamma-carboxyglutamate (Gla)
-use?
_________ converts ______ –> ______
This reaction is _______ dependent
used to target proteins to membranes via Ca chelation
Glutamyl carboxylase converts Glu → Gla (vitamin K dependent)
Scurvy
both prolyl hydroxylase and lysyl hydroxylase rely on Vit-C (ascorbate) as a coenzyme
No Vit C → scurvy (Reduced collagen strength)
Vitamin C
cofactor for prolyl hydroxylase and lysyl hydroxylase enzymes used in collagen synthesis and strengthening
Vitamin K
used as cofactor for glutamyl carboxylase
Vitamin B6
used to make pyridoxal phosphate (PLP) → used by aminotransferases to “hold” / transfer amino groups during transamination reactions
Ubiquitin-Proteasome System
ATP dependent cross-linking of protein to ubiquitin (done by E1, E2 and E3 types)
Ubiquitinated proteins sequestered to proteasome → cellular trash can with proteolytic activity
Protein degradation: Lysosomal path
ATP independent, engulfs extracellular proteins (or live pathogen) → broken down by acid hydrolysis and lysosomal proteins (cathepsin)
Proteases (6)
secreted as proenzymes and cleaved in order to be activated
1) Pepsin
2) Enteropeptidase
3) Trypsin
4) Chymotrypsin
5) Carboxypeptidase-A
6) Carboxypeptidase-B
Pepsin
stomach
pepsinogen cleaved by HCl → pepsin→ cleave proteins
Aspartic protease: hydrolyzes N-terminal side of aromatic residues (Phe, Trp, Tyr)
Enteropeptidase
(intestine): cleaves trypsin into active form
Trypsinogen cleaved by enteropeptidase → trypsin
Trypsin
produced in pancreas → small intestine
cleaved into active form by enteropeptidase
Serine protease - hydrolyze C-terminal side of basic AA (Arg, Lys)
Trypsin cleaves all other zymogens in SI (chymotrypsinogen → chymotrypsin, pro carboxypeptidases → carboxypeptidase)
Chymotrypsin
serine protease - hydrolyzes C-terminal side of aromatic and some hydrophobic residues (Phe, Trp, Tyr, Leu, Met)
cleaved into activated form by trypsin
Carboxypeptidase-A
metallocarboxypeptidase - hydrolyzes C- terminal of hydrophobic AAs (Ala, Ile, Leu, Val)
cleaved into activated form by trypsin
Carboxypeptidase-B
cleaved into activated form by trypsin
metallocarboxypeptidase - hydrolyzes C-terminal of basic residues AAs (Arg, Lys)
Liver problems –> build up of what two enzymes?
Liver problems → build up of aminotransferases (ALT and AST) in blood
Alanine aminotransferase (ALT)
catalyzes what reaction
alanine + a-ketoglutarate ← → pyruvate + glutamate
Aspartate aminotransferase (AST)
catalyzes what reaction
aspartate + a-ketoglutarate ← → oxaloacetate + glutamate
Glu dehydrogenase
catalyzes what reaction?
Glutamate → a-ketoglutarate + NH3+
NH3 –> enters urea cycle
Aminotransferases require coenzyme _________ derived from _______
require coenzyme pyridoxal phosphate (PLP)
PLP is a derivative of B6
pyridoxal phosphate (PLP)
PLP is a derivative of B6
PLP “holds” amino group during its transfer
Used by aminotransferases as a conenzyme
Urea Cycle general overview
get rid of ammonia by forming less toxic compounds (urea)
-We do NOT store ammonia, and it’s toxic
- Ornithine recycled in urea cycle
- Occurs in mitochondria for part and cytosol for part
Entry points for nitrogen: aspartate and free ammonia
Overall reaction of urea cycle
3ATP + HCO3- + NH4+ + aspartate → 2 ADP + AMP + 2Pi + PPi + fumarate + urea
Tyrosine
used to make…?
Tyrosine → T4 (prohormone) → T3 (hormone)
Thyroid stimulating hormone (TSH)
stimulates iodide uptake + release of T4, T3
Thyroid peroxidase
oxidizes iodide (I-) → I2
Thyroglobulin (Tg)
contains Tyr residues iodinated to form T4, T3
Thyroxin binding globulin (TBG)
transports T3, T4
Porphyrin
cyclic molecules made of 4x pyrroles produced in liver
Bind Fe2+ (iron)
Heme synthesis
1) ______ + _______ –> __________
catalyzed by what enzyme
where in the cell does this occur?
Gly + succinyl CoA → d-Aminolevulinic acid (ALA)
Catalyzed by d-Aminolevulinate synthase
mitochondria
Heme synthesis
2) 2 d-Aminolevulinic acid (ALA) –> _______________
catalyzed by what enzyme
occurs where in the cell?
2 ALA → Porphobilinogen
Catalyzed by d-Aminolevulinate dehydratase
occurs in cytosol
Heme synthesis
3) Porphobilinogen –> –> –> –> __________ –> heme
the final step is catalyzed by what enzyme?
where in the cell does this occur?
Porphobilinogen → → → → Protoporphyrin → Heme
(catalyzed by ferrochelatase)
occurs in mitochondria
Porphyrin (heme) degradation:
1) Heme –> _______ –> _______
2) Bilirubin is transported in blood with ____________
3) Bilirubin is conjugated with ___________ in the _________ –> ______________
1) Heme → Biliverdin (green) → bilirubin (red-orange)
2) Albumin
3) Bilirubin conjugated with glucuronic acid in liver → bilirubin diglucuronide (conjugated bilirubin)
Porphyrin (heme) degradation:
4) Bilirubin diglucuronide (conjugated bilirubin) –> ________ –> _________
this occurs where?
→ bilirubin diglucuronide → urobilinogen → stercobilin (brown)
Occurs in intestine
Lead effect on heme - inhibits what two enzymes?
inhibits d-Aminolevulinate dehydratase and ferrochelatase
→ “Lead Poisoning”
Get Zn-protoporphyrin formation → fluorescent haze around RBCs
Urea cycle:
1) _______ + _________ –> Citrulline
catalyzed by what enzyme?
where in the cell?
Ornithine + Carbamoyl Phosphate → Citrulline
Catalyzed by Ornithine Transcarbamylase
Found in MITOCHONDRIA
Carbamoyl Phosphate Synthetase I
catalyzes what reaction?
located where in the cell?
activated by what?
uses what else in this reaction?
CO2 + NH3 → Carbamoyl Phosphate
**uses 2 ATP
MITOCHONDRIA
Activated by N-acetylglutamate**
N-acetylglutamate
Key activator required for carbamoyl phosphate synthetase I kick starting the Urea Cycle
How is N-acetylglutamate made?
______ + _______ –> N-acetylglutamate
catalyzed by _________
reaction is activated by ________
Acetyl CoA + Glutamate –> N-acetylglutamate
N-Acetylglutamate synthase
activated by Arginine
ORNT1
ornithine IN - citrulline OUT (of mitochondria)
antiporter
Urea Cycle
2) Citrulline + _________ –> _____________
catalyzed by what enzyme?
where in the cell does this take place?
what else is used in this reaction?
Citrulline + Aspartate → Argininosuccinate
Catalyzed by Argininosuccinate synthase (ASS)
Occurs in cytosol
uses ATP
Urea Cycle:
3) Arginosuccinate –> ________ + __________
catalyzed by what enzyme?
where in the cell does this take place?
what else is used in this reaction?
Argininosuccinate → Arginine + Fumarate
Catalyzed by Argininosuccinate lyase
Occurs in cytosol
doesn’t use anything else!
Arginine –> ______ + _______
catalyzed by what enzyme?
where in the cell does this take place?
what else is used in this reaction?
Arginine → Ornithine + Urea
Catalyzed by Arginase
Occurs in cytosol
doesn’t use anything else!
In nerves arginine can be converted directly into ________ and ______ via what enzyme?
Arginine → citrulline + NO (NO synthase)
In muscle, arginine can be converted directly into ________ and ________ for what purpose?
Arginine → ornithine → creatine phosphate for muscle energy
Four control points for protein catabolism:
1) Directionality of transamination (by ALT and AST) regulated by relative concentrations of “substrates” and “products”
2) N-acetylglutamate required activator of carbamoyl phosphate synthetase
Kick starts Urea Cycle
3) Directionality of oxidative deamination by Glu dehydrogenase depends on relative concentrations of Glu, a-ketoglutarate, NH3
4) ATP and GTP are allosteric inhibitors of Glu dehydrogenase, while ADP and GDP are activators
Ammonia is transported in the blood using ______ or _______
urea
glutamine
Glutamine
“holds” two ammonia groups
formed by glutamine synthetase
glutamine synthetase
converts glutamate → glutamine for transport to liver → enters urea cycle there
NOT in muscle
Glu dehydrogenase
why is it important?
what reaction does it catalyze?
what activates this reaction, what inhibits it?
control point for protein metabolism**
-Controls direction of nitrogen removal vs. incorporation into AAs
Glutamate + H2O ←→ a-ketoglutarate + NH4+
Inhibited by ATP and GTP
Activated by ADP and GDP
Cori Cycle
Pyruvate –> Lactate in muscle –> transported in blood to liver
Lactate –> pyruvate –> glucose in liver
Glucose sent to muscle for oxidation into pyruvate
Cahill Cycle - Alanine-Glucose Cycle
Glucose –> pyruvate –> alanine (transamination) in MUSCLE
Alanine transported in blood to liver
Alanine –> pyruvate (transamination) –> glucose in LIVER
glucose transported in blood to muscle
Gluconeogenic amino acids
-3 examples
produces pyruvate or TCA intermediates
Oxaloacetate (from aspartate transamination)
Asparagine
Aspartate
Ketogenic amino acids
-2 examples
no net production of glucose
Lysine and leucine → Acetyl CoA (2 carbons)
Maple Syrup Disease (MSUD)
deficiency in branched-chain a-ketoacid dehydrogenase complex
→ build up of a-keto acids in urine (“sweet smelling”)
leucine buildup is toxic
How are branched chain amino acids (leucine, valine, isoleucine) broken down?
(2 steps)
which one is deficient in MSUD?
1) Deaminated by branched-chain aminotransferase → a-keto acids
2) Decarboxylated by branched-chain a-ketoacid dehydrogenase
* *deficient in MSUD
Homocystinuria
defect where?
defect in cystathionine-b-synthase (CBS) or deficiency in Vit-B6
→ cannot convert homocysteine → cystathionine
Homocystinuria
presentation (4)
what are abnormal lab values? (2 key ones)
treatment (3) ?
Presentation:
1) DVT, stroke, atherosclerosis
2) Marfan-like habitus
3) Mental retardation
4) Joint contractures
Elevated homocysteine, elevated methionine (no megaloblastic anemia)
*on new born screening
TX:
- Vit-B6 to “force” CBS activity
- restrict methionine
- betaine treatment +/- folate and B12
Hyperhomocysteinemia
defect where?
causes what?
elevated levels of homocysteine due to low folate, B6, and B12 (vascular disease)
Cysteine is now essential and treat with folate, B6, and B12
Cystinuria
defect where?
treatment?
kidney stones due to defective transporter of cystine → crystallization in urea
TX: acetazolamide (make cystine more soluble)
Cys and Met Metabolism (4 steps for Met, 5 steps for Cys)
Met → SAM → SAH → homocysteine → Met
OR
Met → SAM → SAH → homocysteine → cystathionine → cysteine
Conversion of homocysteine –> Methionine requires _____ and _____ for CH3 transfer
Homocysteine → Met requires THF and VB12 for CH3 transfer
Tetrahydrofolate (THF)
synthesized in bacteria, Folate → THF
One-carbon donor for variety of biosynthetic reactions
(used in homocysteine –> Met reaction)
Trp Metabolism:
Trp –> ______ or _______
Trp hydrolyzed by ____________ which uses _______ has a cofator
Trp → pyruvate or acetyl-CoA
hydrolyzed by tryptophan hydroxylase
Uses Tetrahydrobiopterin (BH4) as cofactor
Tryptophan is important for the production of what 3 things?
Trp → serotonin, melatonin, niacin
Phe and Tyr metabolism:
Phe, Tyr →_____________ or _________
fumarate or acetoacetate
Phe (hydroxylated by _________) → ______
Uses ______ cofactor
Phe (hydroxylated by phenylalanine hydroxylase) → Tyr
Uses BH4 cofactor
Tyr (hydroxylated by ________) → _______
Uses ______ as cofactor
Tyr (hydroxylated by tyrosine hydroxylase) → DOPA
Uses BH4 as cofactor
DOPA –> _________ or ________
uses _____ as cofactor
DOPA → catecholamines (dopamine, NE, epinephrine) or melanin
Uses BH4 as cofactor
BH4
cofactor for…(3)
1) Phenylalanine hydroxylase
2) Tyrosine hydroxylase
3) Tryptophan hydroxylase
Phenylketonuria (PKU)
defect in phenylalanine hydroxylase (convertes Phe–> tyrosine)
→ buildup of alternative byproducts (phenyllactate, phenylacetate, phenylpyruvate)
Tyrosinemia
defects in multi-step tyrosine degradation
Purines vs. Pyrimidines
Purines: guanine, adenine - 2 ringed base
Pyrimidines: uracil, thymine (DNA), cytosine (RNA) - 1 ring base
Nucleoside vs. nucleotide
Base = single or double ringed, contains N, C, O, and H
Nucleoside = base + pentose sugar
Nucleotide = base + ribose sugar + phosphate
Purine nucleotide synthesis overview
start with sugar, add phosphate (PRPP) to activate sugar –> add base
–> ends at IMP –> AMP, GMP
Pyrimidine nucleotide synthesis overview
start by making base –> add activated sugar (PRPP) –> ends at UMP –> UTP or dTMP
Unlike purines, pyrimidine base ring NOT made on ribose sugar - made separately and then base ring is added to sugar
Purine nucleotide synthesis:
1) Ribose -5-Phosphate –> __________
catalyzed by _________
uses _____
activated by ______
Inhibited by _______
1) Ribose 5-phosphate → 5-Phosphoribosyl-1-pyrophosphate (PRPP, ACTIVATED SUGAR)
Catalyzed by PRPP Synthetase
Uses ATP
Activated by Pi
Inhibited by purine ribonucleotides
Purine nucleotide synthesis:
2) PRPP + _______ –> adds first N to PRPP
catalyzed by \_\_\_\_\_\_\_\_\_\_\_ inhibited by (3) activated by (1)
RPP (contains ribose sugar) + Glutamine → add first N to PRPP
Via glutamine Phosphoribosylpyrophosphate amidotransferase
KEY STEP
Inhibited by AMP, GMP, IMP
Activated by PRPP
What is required for purine synthesis (4)
glycine
glutamine
THF
aspartate
What is required for pyrimidine synthesis (1)
aspartate
Purine synthesis:
after N is added to PRPP –> –> a few steps later you make _________ which can then generate ______ and _______
Inosine Monophosphate (IMP)
→ GMP + AMP
AMP –> ATP how?
GMP –> GTP how?
AMP* + ATP ← → 2 ADP* (via adenylate kinase)
ADP + CTP ← → ATP* + CDP
GMP* + ATP ← → GDP* + ADP (via guanylate kinase)
GDP + ATP ← → GTP* + ADP
Pyrimidine synthesis:
1) ______ + CO2 –> ________
catalyzed by ___________ where in the cell?
inhibited by _____
activated by _______
Glutamine + CO2 –> carbamoyl phosphate
Via Carbamoyl Phosphate Synthetase II: in cytosol
Activated by PRPP
Inhibited by UTP
Pyrimidine synthesis:
2) Carbamoyl phosphate + _________ –> –> –> eventually generates _________
Aspartate
Generates Uracil Monophosphate (UMP)
Pyrimidine synthesis:
3) Once UMP is made, it can generate…(2 pathways)
1) UMP → UDP –> UTP → CTP (Via CTP synthase)
2) UMP –> UDP –> dUTP (via ribonucleotide reductase) –> dUMP –> dTMP
Purine breakdown overview
base removed from sugar → free base (adenosine/guanine)
Bases broken down to uric acid → excreted in urine
Purine breakdown:
1) AMP –> ______
2) Adenosine –> ________
- what enzyme?
3) -> hypoxanthine –> __________
- what enzyme?
4) Xanthine –> ________
- what enzyme
AMP → Adenosine
Adenosine→ Inosine (Adenosine deaminase)
→ hypoxanthine → xanthine (xanthine oxidase)
Xanthine → uric acid (xanthine oxidase)
Pyrimidine breakdown
base ring removed from ribose (same as purines)
→ base ring OPENED UP → Succinyl-CoA, Malonyl-CoA, Acetyl-CoA
NO toxic intermediates
Salvage Pathways
-two main enzymes used?
nucleotides made from partially degraded, reused nucleotides
-Free bases attached to ribose sugar (PRPP)
1) Guanine + PRPP → GMP (by HGPRT)
2) Hypoxanthine + PRPP → IMP (HGPRT)
3) Adenine + PRPP → AMP (by adenine phosphoribosyl transferase (APRT))
Ribonucleotide Reductase
converts ribose to deoxyribose
Operates on diphosphates (NDPs, ADP, GDP, CDP, UDP)
Regulation of ribonucleotide reductase
Primary regulation site (“on/off” switch) for overall enzyme activity → active in presence of ATP, inactive with high dATP
Substrate specificity site (“dial”): sensitive to concentrations of individual dNTPs → enzyme changes specificity based on what NDP is in highest concentration
→ equal amounts of each NDP → dNDP
Gout
buildup of uric acid in blood due to deficiency or hyperactivity of enzymes in purine degradation pathway
Severe Combined Immunodeficiency Syndrome (SCID)
mutation in adenosine deaminase gene
→ build up of dATP → inhibits ribonucleotide reductase → prevents enough dNTPs from being made
Lesch-Nyhan Syndrome
deficiency in what?
presentation? (3)
deficiency in purine salvage pathway (HGPRT) → higher rates of de novo purine synthesis
Presentation: gout symptoms, self-mutilating behavior, severe mental disorders
5-Fluorouracil targets _______ and Methotrexate targets __________
targets thymidylate synthase (5-FU)
targets folate metabolism cycle (Methotrexate
6-mercaptopurine inhibits ________
inhibits de novo purine synthesis (inhibits AMP synthesis)
Azidothymidine (AZT) inhibits ___________
viral polymerase
Cytosine arabinoside (araC) targets __________
targets DNA polymerase (anti leukemia)
Acyclovir (ACV) targets _______ and _________
targets viral DNA polymerase and reverse transcriptase (anti HSV)
Hydroxyurea inhibits __________
ribonucleotide reductase
Acute intermittent porphyria is a deficiency in ___________ enzyme.
Inheritance?
Problem with porphobilinogen deaminase (converts porphobilinogen → hydroxymethylbilane)
AD, episodic, variable expression
Acute intermittent porphyria
Presentation (5)
1) Late onset
2) Anxiety, confusion, paranoia
3) Acute abdominal pain
4) NO photosensitivity
5) Port-wine urine
What should you NEVER give a patient with Acute intermittent porphyria? Why?
NEVER give barbiturates (induce CYP450 → increase heme consumption → decrease [heme] → no ALA synthetase inhibition → build up of heme synthesis intermediates)
Porphyria Cutanea Tarda is a deficiency in _________ enzyme
inheritance?
Problem with uroporphyrinogen decarboxylase (converts uroporphyrinogen → coproporphyrinogen)
Most common Porphyria
AD
Porphyria Cutanea Tarda
Presentation (5)
1) Late onset
2) Photosensitivity - inflammation, blistering, shearing of skin with sun exposure
3) Hyperpigmentation
4) Exacerbated by alcohol
5) Red/brown urine
Albinism is a defect in ________ enzyme, a part of ________ metabolism that produces melanin
defect in tyrosinase (converts tyrosine → melanin)