Biochemistry Flashcards
1
Q
How is G6PDH deficiency inherited? What are the histological findings? Is it common?
A
X-linked recessive, most common human enzyme deficiency Associated with Heinz bodies -> denatured “He”moglobin precipitates in RBCs due to oxidative stress “Bite cells” - result from phagocytic removal of Heinz bodies by splenic macrophages “bite into some Heinz ketchup”
2
Q
How is cysteine made? What co-factor is required?
A
Homocysteine + serine are combined via Cystathione synthase. Since we are adding two amino acids together, we require B6 to participate in the reaction.
3
Q
What are the causes of homocysteinuria?
A
- Cystathione synthase deficiency 2. Decreased affinity of cystathione synthase for B6 3. Methionine synthesis deficiency (too much homocysteine because it cannot be converted to methionine).
4
Q
What are the clinical features of homocysteinuria?
A
Elevated homocysteine in urine, Osteoporosis, Marfanoid habitus (features of Marfan, including long limbs, arachnodactyly, lens subluxation, and pectus excavatum), increased risk for stroke / MI from cardiovascular effects, intellectual disability
5
Q
How is homocysteinuria treated?
A
Supplement diet with B6 and cysteine, restrict methionine.
6
Q
During what phase of the cell cycle are histones synthesized?
A
S phase -> same as DNA
7
Q
What is the structure of a nucleosome, what links them together, and what amino acids are they rich in?
A
Octamer of histones, linked together by H1 histone to form the “beads” of nucleosomes with DNA twice wrapped around them. They are rich in positively charged lysine and arginine -> stabilize negatively charged DNA
8
Q
Is heterochromatin or euchromatin more likely to have histones methylated and why?
A
heterochromatin -> methylation will inactivate the DNA -> HeteroChromatin = Highly Condensed Euchromatin in expressed and acetylated
9
Q
How does mismatch repair occur in bacterial DNA replication?
A
DNA is normally methylated at specific C and A sites Newly replicated strand will not be methylated. Any mismatches can be repaired via mismatch repair enzymes using the methylated strand as a template (repair of hemimethylated DNA) Prior to replication, the new strand will finally be methylated via Dam methylase.
10
Q
Can regions of methylated histones be activated?
A
Sometimes yes, but histone methylation tends to reversible repress DNA transcription.
11
Q
What amino acids are necessary for purine synthesis?
A
Glycine, aspartate, glutamine
12
Q
How is Lesch-Nyhan inherited and what are the clinical findings?
A
X-linked, HGPRT deficiency H = hyperuricemia G = gout P = Pissed off R = Retardation T = dysTonia
13
Q
What are the two amino acids do not have a degenerate / redundant code?
A
Methionine and tryptophan Met = AUG start codon
14
Q
Why are telomeres added? Where are they added?
A
Added to the 3’ ends of chromosomes (with matching complementary DNA obviously) -> added so that when DNA polymerase starts synthesizing 5’ to 3’ it’s not losing any of its important genetic information when then required primer is excised, cutting some off on the 5’ end (template was the 3’ said of the parent gene).
15
Q
What type of protein is telomerase and how does it work?
A
RNA template-carrying reverse transcriptase, adds extra bases to the 3’ end of the parent strand so you don’t lose any important genetic information when 5’ to 3’ is synthesized.
16
Q
What is transition vs transversion point mutation?
A
Transition - purine to purine or pyrimidine to pyrimidine Transversion - purine to pyrimidine or pyrimidine to purine
17
Q
When is base excision repair needed and how does it work?
A
Needed whenever a base is damaged, most often deamination or depurination. Occurs throughout cell cycle GEL PLease Glycosylase -> cleaves off bad base Endonuclease -> cleaves phosphodiester backbone from 5’ end Lyase -> cleaves 3’ end Polymerase -> fills the gap with DNA Ligase -> seals it
18
Q
What DNA repair mechanism is defective in Lynch Syndrome?
A
Also known as hereditary nonpolyposis colorectal cancer (HNPCC) -> Defective mismatch repair in G2 phase of cell cycle. Deficiency will result in higher mutations due to slippage of DNA polymerase in DNA replication, leading to more microsatellite instability with frameshift mutations and duplications
19
Q
Give a condition where nonhomologous end joining repair is defective?
A
Ataxia-telangectasia -> failure to repair double-stranded breaks (ATM gene)
20
Q
At what sites do activator proteins and repressor proteins bind on the DNA? Where can these be located? How do they work?
A
Activator -> binds enhancer sequence Repressor -> binds silencer sequence These can be located upstream, downstream, or within the introns of the gene The activator / repressor proteins bend the DNA to interactive with the RNA polymerase II on the promoter, modifying transcription. UWorld 2025 has a great explanation
21
Q
How many RNA polymerases are in eukaryotes and what are their functions?
A
3 RNA polymerases Numbered in the same sequence as their functional products rRNA -> mRNA -> tRNA rRNA = RNA polymerase I - functions only in nucleolus mRNA = RNA polymerase II tRNA = RNA polymerase III
22
Q
What proteins are responsible for intron splicing in eukaryotes and what is the intermediate structure called?
A
Small nuclear ribonuclear proteins (snRNPs) -> intermediate is a lariat structure (loop) formed by 3 phosphodiester bonds (one of which is via the 2’ hydroxyl of an adenine)
23
Q
Give two disorders with auto-antibodies to snRNPs?
A
SLE = anti-Smith = RNP mixed connective tissue disease = anti U1-RNP These are involved in splicing out introns via a lariat intermediate.
24
Q
How does a microRNA differ from siRNA?
A
MicroRNA -> interfere with translation via the 3’ UTR, forming loops or otherwise repressing the translation of the mRNA small interfering RNAs -> form double-stranded RNAs to interfere with translation
25
How is the amino acid attached to tRNAs? What is the sequence?
Attached via 3' hydroxyl of adenine in the sequence: 5'-CCA-3' CCA = Can Carry Amino (acids)
26
What are the two other main arms of tRNAs (other than acceptor stem for amino acid and the anticodon loop)? What is their function? What special amino acids do they contain?
T-arm = Tether tRNA molecule to ribosome, contains CYT - cytosine, pseudouridine, and ribothymidine D-arm = Detects the aminoacyl-tRNA synthetase, contains Dihydrouridine
27
How are tRNAs charged? What substrate is required?
Each amino acid has its own tRNA synthetase Amino acid is bound the enzyme, converts ATP to PPi and aminoacyl-AMP Amino acid is transfered from aminoacyl-AMP to 3' hydroxyl of acceptor arm of tRNA. Correct amino acid is determined by a single or few bases in the tRNA -\> no necessarily corresponding to a single arm.
28
What failsafes / ways to check are in place to prevent the wrong amino acid from binding the tRNA? What happens if the wrong amino acid is in the active site?
1. Steric hinderance of fitting into the active site 2. tRNA incoming does not match the amino acid in the active site. 3. Chemically related amino acids have an alternate hydrolysis site in enzyme which preferentially hydrolyzes the closely confused amino acid. In all cases, aminoacyl-AMP is hydrolyzed.
29
What is the energy source for initiation, elongation, and termination?
GTP
30
How does initiation occur (in prokaryotes)?
Initiation factors stabilize the small subunit (30S in bacteria) on the Shine-Dalgarno sequence. First tRNA carrying fMet binds the start codon, and IF-2 has GTP bound which is hydrolyzed to bring the large subunit (50S) in contact with the mRNA. fMET tRNA will be in the P site at this point.
31
What are the three sites on the ribosome?
APE A = Aminoacyl site P = Peptidyl site E = Exit site
32
What are the mRNA stop codons?
U Go Away U Are Away U Are Gone UGA UAA UAG
33
What catalyzes peptide bond formation and how does the ribosome move forward?
The ribozyme (23S of small subunit in prokaryotes) Amino acid in A site attacks carbonyl in P site to form peptide bond. Peptide always stays in P site, and the leaning of the tRNAs draws them one site forward, while moving mRNA one codon along
34
How does termination occur?
Release factor binds a stop codon (UGA, UAA, UAG), hydrolyzing bond in P site, causing dissociation of ribosome.
35
Where does N-glycosylation occur and how does it occur?
Occurs in the Rough ER, where a preformed oligosaccharide is transferred from dolichol phosphate to an asparginine side chain of the protein to be N-glycosylated
36
Where does O-glycosylation occur and how does it occur?
Occurs in the Golgi, where a sugar is transferred via a threonine or serine side chain and the sugars are added on one at a time (Dol-P not involved)
37
What causes I-cell disease and what are its symptoms very similar to?
I = inclusion cell disease, mucolipidosis type 2 Lysosomal storage disease due to failure of Golgi to phosphorylate mannose residues -\> no mannose-6-phosphate -\> acid hydrolases will end up extracellularly (diagnostic in plasma) Appears exactly like Hurler syndrome -\> course facial features, corneal clouding, restricted joint movement
38
What is the function of the signal recognition particle (SRP)?
Recognizes the signal sequence on nascent proteins from free ribosomes and causes translational arrests. Then drags them to the rough ER, allowing synthesis to continue through translocon channel (needed for RER-destined proteins)
39
What proteins mediate the trafficking of vesicles from the rough ER to the cis-Golgi?
Rough ER -\> cis-Golgi = anterograde = COPII cis-Golgi -\> Rough ER = retrograde = COPI II steps forward, I step back.
40
What protein is needed for LDL receptor endocytosis once it binds LDL?
Clathrin
41
What are plasmalogens? What is their physiologic significance?
Phospholipids with an ether backbone, similar to phosphoglycerols, which are synthesized in the peroxisome Significance -\> important phospholipid in myelin, explains why peroxisome dysfunction leads to neurologic disease
42
What are the functions of peroxisomes?
Oxidation of branched chain fatty acids and very long chain fatty acids, as well as amino acids / alcohol
43
Give two diseases which are caused by autosomal recessive mutation in proteins required for peroxisome biogenesis? Symptoms?
Neurologic symptoms 1. Zellweger syndrome - seizures, hypotonia, early death 2. Refsum disease - Blindness, ataxia, shortening of 4th toe
44
What are the functions of microfilaments vs microtubules vs intermediate filaments?
Microfilaments - muscle contraction, cytokinesis, i.e. actin Intermediate filaments - maintain cell structure, i.e. keratin, desmin, neurofilaments Microtubules - movement (cilia, flagella, axonal trafficking), cell division (mitotic spindle)
45
What type of tumor does vimentin identify?
viMEntin = mesenchymal, also other tumors including endoMEtrial carcinoma, and MEningioma
46
What type of tumor does desmin identify?
desmin = Muscle (Think fascia adherens of intercalated disc)
47
What type of tumor does GFAP immunohistochemistry help identify?
Neuroglial, especially astrocytoma and glioblastoma
48
What directions do dynein and kinesin help transport?
Kinesin = anterograde = kinetically forward = - to + Dynein = retrograde, towards nucleus = + to -
49
What anchors cilia into cell membrane? What is its microtubular structure?
The basal body, comprised of 9 triple microtubules (versus 9 doublets + a 2 singlet arrangement of cilia).
50
What is the base amino acid sequence of collagen? What is the first precursor of collagen?
Preprocollagen Sequence is Gly-X-Y X and Y are proline or lysine Thus, collagen will be 1/3 glycine
51
What is the next step after synthesis of preprocollagen? What disease is this deficient in?
Hydroxylation of lysine / proline -\> Required vitamin C -\> vitamin C deficiency will cause scurvy
52
After hydroxylation, how does preprocollagen become procollagen? What disease is marked by failure of procollagen formation?
N and O glycoylation occurs in the ER and Golgi, respectively, after which hydrogen and disulfide bonds help create the triple helix with disorganized ends of procollagen Osteogenesis imperfecta -\> failure of triple helices of 3 alpha procollagen chains due to replacement of Gly in Gly-X-Y with a bulky amino acid
53
What gets exocytosed in collagen synthesis? What happens next?
Procollagen Next: terminal regions are cleaved to insoluble tropocollagen
54
What disease is caused by impaired proteolytic processing of procollagen to tropocollagen?
Ehlers-Danlos
55
How is tropocollagen converted to collagen? What enzyme is required?
Via staggering and covalent lysine-hydroxylysine linkages by lysyl oxidase -\> lysyl oxidase requires copper
56
What two diseases are characterized by failure to crosslink tropocollagen?
Ehlers-Danlos (there are many variants) Menkes disease -\> impaired copper absorption and transport (required for lysyl oxidase activity)
57
What are the clinical features of Osteogenesis imperfecta and what is it commonly confused with?
Impaired Type 1 collagen synthesis: BITE Bones - multiple fractures I = Eye -\> blue sclera from choroidal veins showing (translucent connective tissue) T = Teeth, abnormal dentin E = Ears, hearing loss, due to abnormal ossicles Confused with child abuse -\> look for ITE signs
58
How is osteogenesis imperfecta inherited?
Autosomal dominant
59
What are the three presentations of Ehlers-Danlos syndrome, which is most common, and which is most severe?
Hypermobility Type - Most common, hyperextensible skin and hypermobile joints Classical Type - also join and skin symptoms, with easy bruising, due to Type V collagen mutation Vascular Type - Type III collagen defect, more severe, vascular and organ rupture, with aortic aneurysms
60
How is Menke's disease inherited, and what are its clinical features?
X-linked recessive -\> impaired copper absorption and transport with failed collagen production due to decreased lysyl oxidase activity (copper cofactor) Brittle, kinky hair, growth retardation, hypotonia in boys
61
What amino acids predominate in elastin?
Same as collagen -\> proline, glycine, and lysine, but they are not hydroxylated. However, not exclusively these residues
62
Where is elastin cross-linked and what accounts for its elastic properties?
Cross-linked extracellularly via lysyl oxidase -\> lysine residues will form desmosine / isodesmosine heterocyclic structures Elastic due to valine-rich hydrophobic domains.
63
How can an enzyme-deficiency cause emphysema?
Alpha-1-antitrypsin deficiency normally inhibits elastase -\> elastase will be overactive if deficient, breakdown of alveolar septae
64
How does UVA contribute to wrinkles?
Generates free radicals which decrease collagen production -\> wrinkles of aging due to decreased collagen and elastin production, allowing tonic contraction to have a greater effect (less ECM)
65
How is the subluxation of the lenses in marfinoid syndrome of homocysteinuria told apart from Marfan syndrome?
Homocysteinuria - downward (may be nasal or temporal) Marfan syndrome - upward (may be nasal or temporal)
66
What are the relative temperatures of Denaturation, Annealing, and Elongation in PCR?
Denaturation ~ 95 degrees C Annealing ~ 55 degrees C Elongation ~ 72 degrees C, a little hotter for the polymerase to run
67
How does a general southern / northern / western blot work? What is the mnemonic for knowing which corresponds to what?
Run the substance of interest through a gel, then blot the gel with a membrane, and use a labelled probe to detect the substance w/ respect to its presence and how far it migrated. Substances for each technique SNoW DRoP Southern - DNA, probe = cDNA Northern - RNA, probe = DNA or RNA Western - Protein probe = antibody
68
How does a southwestern blot work?
Like it sounds, you detect a protein (DNA-binding protein / transcription factor, western portion) using an oligonucleotide probe of DNA which it would normally bind (the southern portion)
69
What is used to confirm an HIV diagnosis after ELISA (the more sensitive test, but can give false +)?
Checking if patient has antibodies to protein components of HIV virus, via Western blot. Put the patient's serum on Western blot of HIV proteins, and use a probe to detect patient's antibodies to the relevant components antigens.
70
How does flow cytometry work and when is it typically used?
Can detect protein antigens on cells (i.e. CD4 and CD3 markers) via tagging those cells with fluorescent antibodies specific to those antigens, and measuring the fluorescent properties of cells in a sample one at a time -\> able to get an exact count of CD4+ cells or CD3+ cells in a sample -\> commonly used in hematalogic abnormalities
71
What are the applications of microarrays?
They are plentiful -\> profiling gene expression of thousands of genes simultaneously, detecting single nucleotide polymorphisms (SNPs) and copy number variants as well (array-CGH). Done by attaching nucleic acid probes onto a chip and measuring amount of hybridization.
72
How would a 22q11 deletion appear on a FISH?
Probe would fluoresce on the one normal copy of chromosome 22, but would be absent on the second chromosome (where the microdeletion occurred)
73
What is a dominant negative mutation?
A nonfunctional protein interferes with the function of wild type i.e. a malfunctioning transcription factor prevents the binding of the working, wild type transcription factor
74
What is McCune-Albright Syndrome a clinical example of in genetics? Give the clinical triad which accompanies it.
Somatic mosaicism -\> post-zygotic mutation in G-protein signalling, would be lethal if occurring in whole body. Triad: 1. Bony fibrous dysplasia 2. Cafe-au-lait spots, often unilateral (mosaicism) 3. Endocrinopathy -\> usually precocious puberty due to increased E2 or T secretion
75
In what stage of meiosis does heterodisomy and isodisomy occur via uniparental disomy?
heterodIsomy = Meiosis I IsodIsomy = Meiosis II If you think about why, having a nondisjunction in meiosis II means that the sister chromatids are inherited together. In Meiosis I, it would mean that homologous chromosomes are inherited together then segregated in meiosis II.
76
Calculate the carrier rate in females of an X-linked recessive disease with a 1/5000 rate in males. Disease rate in females?
1/5000 = q, since they only have one chromosome. 2pq = carrier rate 2(~1)(1/5000) = 1/2500 Disease rate = (1/5000)^2
77
How can you tell something is an X-linked dominant disorder?
Affected fathers transmit disease to all daughters and no sons
78
What causes hypophosphatemic rickets and how is it inherited?
X-linked dominant, caused by increased phosphate wasting at proximal tubule, results in rickets-like presentation
79
Why is thymidine synthesis so much more susceptible to low folate conditions than methionine synthesis?
In methionine synthesis, folate is kept in its fully reduced form: 5-Methyl-THF is converted to THF and donates its methyl to homocysteine In thymidine synthesis, the folate also becomes oxidized to DHF. It must be re-reduced to dihydrofolate reductase (inhibited by methotrexate) which is a very slow step
80
What is the function in inhibin B you goddamned idiot? What makes it?
Produced by Sertoli cells in response to FSH -\> feeds back on the hypothalamus to inhibit FSH release.
81
What causes Duchenne muscular dystrophy (DMD)? What is the most common mutation?
X-linked disorder due to defect in Dystrophin gene which links cardiac and skeletal muscle fibers to the ECM. Most common mutation is a frameshift mutation which causes a truncation of the protein -\> nonsense.
82
What are the clinical features of Duchenne and why? What causes death?
Pelvic girdle muscles become weak first -\> unable to stand without using hands (Gower maneuver) Will cause pseudohypertrophy of the calves due to fibrofatty replacement of muscle (with inflammation), and will be early onset. Dilated cardiomyopathy will be the cause of death -\> affects cardiac muscles as well
83
What markers are elevated in DMD and how is it confirmed?
CPK and aldolase (glycolysis enzyme which signifies muscle damage) Confirmed by genetic testing of the dystrophin gene
84
What causes Becker muscular dystrophy and what is the prognosis?
X-linked, non-frameshift mutations in dystrophin gene (Allelic heterogeneity of Duchenne) -\> less severe due to protein being partially functional instead of truncated -\> Onset in adolescence / early adulthood
85
What causes Myotonic dystrophy? What is the inheritance?
Autosomal dominant CTG repeat disorder in DMPK gene leading to abnormal epression of myotonin protein kinase
86
What are the clinical signs of myotonic dystrophy?
Muscular dystrophy so there will be muscle signs, which include myotonia (i.e. dystonia, unable to loosen grip after handshake), and muscle weakness Other strange signs can be remembered via the trinucleotide repeat mnemonic C - Cataracts T - Toupee - frontal balding in men G - Gonadal atrophy
87
What is the 5p microdeletion syndrome and its clinical signs/symptoms?
Cri du chat = cry of the cat High-pitching meowing or crying, microcephaly, intellectual disability, ventricular septal defect (VSD)
88
What causes Williams syndrome and what are the characteristic features?
Chromosome 7 microdeletion, including elastin gene -\> same chromosome as CF Elastin problems: Elfin faces, supravalvular aortic stenosis - Hypercalcemia (opposite of DiGeorge) - Extreme friendliness to strangers (remember Dr. Sandall telling me about this)
89
How is B1 deficiency definitively diagnosed?
Increased RBC transketolase activity following B1 administration.
90
What vitamin can be made from tryptophan? What vitamins does this process depend on?
Niacin (B3) Depends on vitamins B2 (flavin) and B6 (pyridoxine)
91
What causes Hartnup disease and what symptoms will precipitate?
Autosomal recessive disorder causing deficiency of neutral amino acid reuptake in kidney proximal tubules and enterocytes. -\> aminoaciduria and decreased gut absorption -\> manifests primarily as tryptophan deficiency leading to pellagra-like symptoms
92
What type of anemia does B6 deficiency cause?
Sideroblastic anemia -\> abnormal ringed sideroblasts accumulate in periphery since heme cannot be synthesized, despite excess iron
93
Where are iron, folate, and cobalamin absorbed?
Dude Is Just Feeling Ill, Bro Duodenum - Iron Jejunum - Folate Ileum - B12
94
What parasite is known to cause a cobalamin deficiency?
Fish tapeworm - diphyllobothrium latum -\> must B12 to buy fireworks -\> guy running to the bathroom throwing a tray of fish
95
What are the two main adverse effects possible with vitamin C overdose?
1. Calcium oxalate nephrolithiasis - vitamin C is broken down and excreted as oxalic acid, can cause kidney stones 2. Iron toxicity - in those predisposed, since it helps reduce iron to its ferric form for better absorption.
96
How do high doses of vitamin E affect Warfarin efficacy?
Enhances the anti-coagulant effects -\> probably fight for vitamin K y-carboxylation proteins active site (competitive)
97
Other than factors 2, 7, 9, and 10, what other proteins have gamma-carboxylation assisted by vitamin K?
Proteins C and S -\> think of Corporal and Sergeant in Sketchy -\> These inactivate factors 5a and 8a in the clotting cascade after being activated by thrombin when held by thrombomodulin
98
What is the primary change that occurs in the liver as result of the ethanol metabolism (in terms of metabolic levels)?
Increased NADH to NAD ratio, since both alcohol dehydrogenase and acetaldehyde dehydrogenase produce NADH from oxidation of ethanol to acetate
99
Why does alcoholism cause fasting hypoglycemia?
Pushes oxaloacetate to malate due to increased NADH levels. -\> need oxaloacetate from pyruvate via pyruvate carboxylase Also, DHAP is pushed to glycerol 3 phosphate from increased NADH levels.
100
Why does alcoholism cause ketoacidosis and hepatosteatosis longterm?
Increased NADH levels disfavor TCA production of NADH -\> increased usage of acetyl-CoA for ketogenesis and lipogenesis
101
What metabolic processes take both mitochondria and the cytoplasm to do?
HUGs take two H - Heme synthesis U - Urea cycle G - Gluconeogenesis (oxaloacetate transported out) In normal oxidation, pyruvate is transported into mitochondria via pyruvate translocase
102
What is the difference between a phosphorylase and a phosphatase?
PhosphaTase -\> Takes off the phosphate Phosphorylase -\> Cleaves a substrate using inorganic substrate, leaving phosphate on (i.e. glycogen phosphorylase)
103
What two amino acids are good for a ketogenic diet and why?
Leucine and lysine -\> only two amino acids which cannot be used for gluconeogenesis
104
What is the purpose of the citrate shuttle? How does it work?
Need Acetyl-CoA in the cytosol for fatty acid synthesis, but it is produced in the mitochondria Oxaloacetate + citrate are made via citrate synthase, citrate shuttled out, citrate is split back into oxaloacetate in cytoplasm, made into malate and antiported with alpha-ketoglutarate, then malate DH'd back to oxaloacetate alpha-ketoglutarate is kept the same with an obnoxious glutamate aspartate antiporter which does some deaminations
105
How is ornithine transcarbamylase deficiency inherited and what will be seen in this disorder?
X-linked defect in ornithine transcarbamylase. Excess carbamoyl phosphate leaks from mitochondria into cytoplasm, where it is used for increased pyrimidine synthesis. Findings: Increased orotic acid in blood and urine, and symptoms of hyperammonemia
106
What causes orotic aciduria and how is it told apart from ornithine transcarbamylase deficiency?
Defect in conversion of orotic acid to UMP. Autosomal recessive. Will still have increased blood orotic acid. Major difference: No hyperammonemia (OTCase 1 still working fine), and will cause megaloblastic anemia which is refractory to B9/B12 (impaired UMP synthesis, dTMP and dCTP cannot be made)
107
What steps of glycolysis make and require ATP?
Require: PFK-1, hexokinase Make: (steps losing phosphates, as it is substrate-level phosphorylation) -\> Phosphoglycerate kinase (1,3-BPG-\>3-PG) -\> Pyruvate kinase (PEP -\> pyruvate)
108
What cofactors are used by the pyruvate dehydrogenase complex, and what substance inhibits it? What poisoning findings are there?
Thiamine (TPP) Lipoic acid B5 - CoA B2 - FAD+ B3 - NAD+ Inhibited by Arsenic -\> binds lipoic acid. Findings of poisoning include GI distress and garlic breath
109
What two enzymes are very structurally and functionally similar to pyruvate dehydrogenase?
1. Alpha-ketoglutarate DH (TCA cycle) 2. Branched-chain amino acid DH
110
How is PDH deficiency inherited and what are its clinical symptoms? How is it treated?
X-linked Neurologic defects, with lactic acidosis and increased serum alanine starting in infancy Treatment: Ketogenic diet, with increased lysine and leucine (purely ketogenic)
111
What cofactors are used by alanine aminotransferase?
B6 only - allows amino groups to be carried to the liver from muscle
112
What enzymes of the TCA cycle are on tight control and why?
The irreversible ones 1. Citrate synthase 2. Isocitrate dehydrogenase 3. Alpha-ketoglutarate dehydrogenase
113
Give the steps in the TCA cycle (intermediates only, no enzymes)
Oxaloacetate -\> citrate -\> isocitrate -\> alpha-ketoglutarate -\> succinyl-CoA -\> succinate -\> fumarate -\> malate -\> oxaloacetate
114
What complexes do Rotenone and antimycin inhibit?
RotenONE - complex one An-t3-mycin - Complex 3
115
Give three uncouplers of the ETC which cause increased generation of heat and oxygen consumption with dissipation of the proton gradient.
1. 2,4-DNP - dinitrophenol 2. Aspirin - fevers after aspirin overdose 3. Thermogenin
116
What enzyme is used to converted Oxaloacetate to PEP for gluconeogenesis? What substrate is required?
phosphoenolpyruvate carboxykinase, in cystol GTP is required
117
What are the four irreversible enzymes of gluconeogenesis?
Pathway Produces Fresh Glucose Pyruvate carboxylase PEP carboxykinase Fructose-1,6-bisphosphatase Glucose-6-phosphatase
118
Can fatty acids be used for gluconeogenesis?
Only odd-chain ones, which will produce propionyl-CoA as their final product -\> can enter TCA cycle as succinyl-CoA and serve as a glucose source (requires B12 with a methylmalonyl-CoA intermediate) Glycerol component of the triglycerides is also gluconeogenic substrate
119
What causes essential fructosuria and what are the symptoms?
Defect in fructokinase -\> no symptoms due to fructose not being trapped in cells -\> fructose appears in blood / urine (uria)
120
What causes fructose intolerance? What accumulates?
Remember FAB GUT Deficiency of aldolase B, which converted Fructose-1-phosphate to DHAP and glyceraldehyde (vs aldolase A which converts F-1,6-BP to DHAP and glyceraldehyde-3-P) Accumulates fructose-1-phosphate
121
What causes onset of symptoms of fructose intolerance? What are they?
High fructose or sucrose (fructose + glucose) foods, appearing when food is introduced in diet -\> treatment is to avoid Due to usage of phosphate in cell, impairs gluconeogenesis -\> hypoglycemia, vomiting. Jaundice / cirrhosis from fructose buildup in liver.
122
How do Galactose vs Fructose conditions differ in terms of time of onset and severity?
Galactose buildup -\> more severe, due to alcohol pathway Galactose conditions -\> appear sooner, because lactose is in breast milk. Fructose is not until baby is weaned onto real foods later.
123
What is the cause of classic galactosemia? What are the main presenting symptoms? Which one is shared with galactokinase deficiency?
Typically Galactose-1-phosphate uridyltransferase deficiency Symptoms: E. coli sepsis Hepatomegaly Failure to thrive Infantile cataracts (Also shared with galactokinase deficiency)
124
Why do infantile cataracts occur in galactokinase deficiency?
Galactose is converted to galactilol via aldose reductase, which accumulates in lens of the eye
125
What is the function of sorbitol formation and why are diabetics particularly susceptible?
It is a method of trapping glucose in the cell. Diabetics are susceptible because the enzyme which does this has a high Km (aldose reductase)
126
What tissues are most susceptible to sorbitol accumulation and why?
Tissues which have an aldose reductase to make sorbitol, but not sorbitol dehydrogenase to make sorbitol -\> fructose are susceptible These include: Lens, Retina, Kidneys, Schwann cells
127
What are the manifestations of sorbitol excess in diabetic patients and why?
Sorbitol accumulates in the susceptible tissues -\> cataracts (lens), retinopathy (Retina), peripheral neuropathy (schwann cells). Aldose reductase requires NADPH and sorbitol DH makes NADH -\> pushes more electrons to NADH and thus ETC, causing ROS damage. Also, sorbitol is osmotically active and causes osmotic damage in hyperglycemia.
128
What is the Cahill cycle?
Way of disposing of nitrogen, pyruvate accepts amino group to make alanine in muscle. Alanine transported to liver for urea cycle, with pyruvate made back to glucose for shipment back to muscle. Pg. 78
129
What are the clinical features of hyperammonemia?
Alpha-ketoglutarate is made to glutamate, and glutamate is made to glutamine in neurons Features: Asterixis (flapping tremor) Vomiting Somnolence Cerebral edema
130
How is Hyperammonemia treated?
Limit protein in diet Rifaximin antibiotic to limit colonic ammonia generation Lactulose to acidify GI tract and prevent NH4+ reuptake Benzoate / phenylbutyrate to react with amino acids and scavenge nitrogen into products excreted renally.
131
What condition does congenital deficiency of homogentisate oxidase cause? How is it inherited?
Alkaptonuria -\> accumulation of homogentisic acid in tissue, in conversion of tyrosine to fumurate
Autosomal recessive
132
What are the signs and symptoms of alkaptonuria?
Ochronosis - Bluish-black connective tissue, ear cartilage, and sclerae
Urine turns black when exposed to air over time (spontaneous oxidation)
Ochronotic arthropathy - due to toxicity to cartilage. Debilitating arthralgias later in life.
133
What are the three enzymatic causes of homocystinuria?
1. Cystathione synthase deficiency 2. Decreased affinity of cystathione synthase for B6 cofactor (treat by increasing intake) 3. Methionine synthase deficiency
134
What are the important consequences of homocystinuria?
1. Atherosclerosis -\> increased stroke and MI risk 2. Marfanoid habitus -\> looks like Marfan syndrome 3. Ocular changes -\> downward and inward lens subluxation (Marfan = upward and temporally)
135
What causes Cystinuria and what is its primary complication?
Defect in renal PCT amino acid transporter of COLA -\> Cystine, ornithine, lysine, arginine Excess cystine in urine (2 cysteines connected by disulfide bond) forms HEXAGONAL cystine stones.
136
Why does von Gierke precipitate gout?
Increased G6P levels will decrease phosphate supplies -\> AMP is degraded to uric acid. Also, elevated lactate from glucose accumulation prevents uric acid excretion in kidney
137
What is the early triad of Fabry disease?
1. Peripheral neuropathy (acroparesthesia, pain in hands / feet) 2. Angiokeratomas 3. Hypohidrosis Angiokeratoma is a Fabric (Fabry) of blood vessels and Galaxy of red spots (Alpha-Galactosidase deficiency)
138
What causes Krabbe disease and what disorder is it related to?
Galactocerebrosidase deficiency -\> accumulation of galactocerebroside Related to metachromatic leukodystrophy which is caused by Arylsulfatase A deficiency, which would normally make the galactocerebroside -\> these tend to be a major part of the myelin sheath
139
How is Krabbe disease diagnosed / what are the symptoms?
Central and peripheral neuropathy (demyelinating, like metachromatic leukodystrophy) \*\*Globoid cells -\> macrophages in globoid shape from lipid accumulation
140
What are the clinical symptoms of MCAD deficiency and how is it treated?
Episodes of vomiting, lethargy, seizures, and coma with fatty-acyl carnitines in blood and \*\*hypoketotic hypoglycemia\*\* Treatment - frequent feedings
141
Why does ketoacidosis occur in both alcoholism and diabetes?
Alcoholism - excess NADH shunts oxaloacetate to malate DKA - oxaloacetate is depleted for gluconeogenesis -\> acetyl-CoA builds up from inability to use TCA cycle -\> production of ketone bodies
142
How soon into starvation are glycogen stores exhausted? Why does protein and not just fat need to be broken down during starvation?
About 1 day Even though most of the body can run on ketone bodies, protein needs to be broken down for glucose use by RBCs -\> lack mitochondria and thus cannot use ketones
143
What is the function of LCAT?
LCAT = Lecithin cholesterol acyltransferase Esterifies plasma cholesterol released from tissues so they can be uptaken by HDL (they will be hydrophobic enough)
144
On what particles does ApoE exist and what is its function?
"E"verything "E"xcept LDL -\>LDL doesn't have one because liver has LDL scavenger receptor -\> ApoE is used to pick up remnants of other lipoproteins
145
What is the primary apolipoprotein on chylomicrons and its function?
Apo B-48 -\> mediates its secretion into lymphatics
146
What is the function of Apolipoprotein C-II and what particles is it present on?
VLDL, HDL, Chylomicrons -\> "C"ofactor for "C"leavage -\> required for activity of vascular endothelial lipoprotein lipase to free fatty acids for tissue uptake
147
What apolipoprotein activates LCAT?
A-I "A"ctivates
148
What is the function of B100?
Packaged with VLDL by liver, it will also be present in IDL and LDL. Function: Binds the LDL receptor on liver (since no Apo-E is present). Receptor is the apo B/E receptor
149
What causes abetalipoproteinemia? What are the symptoms?
Deficiency in Apo B48 (Chylo) and ApoB100 (VLDL and others) -\> severe fat malabsorption & failure to thrive -\> vitamin E deficiency -\> spinocerebrellar degeneration, retinitis pigmentosa, progressive ataxia -\> restrict fats from diet, use large doses of vitamin E
150
There are four familial dyslipidemias. Which are autosomal dominant vs recessive? 1. Hyperchylomicronemia 2. Familial hypercholesterolemia 3. Dysbetalipoproteinemia 4. Hyper triglyceridemia
1. Hyperchylomicronemia - recessive 2. Familial hypercholesterolemia - dominant 3. Dysbetalipoproteinemia - recessive 4. Hyper triglyceridemia - dominant
151
There are four familial dyslipidemias. What causes each of these? 1. Hyperchylomicronemia 2. Familial hypercholesterolemia 3. Dysbetalipoproteinemia 4. Hyper triglyceridemia
There are four familial dyslipidemias. Which are autosomal dominant vs recessive? 1. Hyperchylomicronemia - LPL or apo C-II deficiency (cofactor for LPL) 2. Familial hypercholesterolemia - LDL receptor defect 3. Dysbetalipoproteinemia - defective ApoE 4. Hyper triglyceridemia - hepatic overproduction of VLDL
152
There are four familial dyslipidemias. Which ones predipose to atherosclerosis? 1. Hyperchylomicronemia 2. Familial hypercholesterolemia 3. Dysbetalipoproteinemia 4. Hyper triglyceridemia
1. Hyperchylomicronemia - no (only elevates TGs) 2. Familial hypercholesterolemia - yes - elevates VLDL 3. Dysbetalipoproteinemia - yes - all particles harder to uptake 4. Hyper triglyceridemia - no (only elevates TGs)
153
What are the clinical features of hyperchylomicronemia?
Pancreatitis (elevated TGs), hepatosplenomegaly, eruptive xanthomas (but no increased atherosclerosis) -\> lab \*\*creamy layer in supernatant\*\*
154
What are the clinical features of familial hypercholesterolemia?
Homozygotes way worse than heterozygotes Acellerated atherosclerosis & MIs Tendon xanthomas (Especially Achilles) Corneal arccus
155
What are the clinical features of dysbetalipoproteinemia?
Premature atherosclerosis with tuberoeruptive xathomas (red and tuberous), and xanthomas on palms of hands
156
What are the clinical features of hypertriglyceridemia?
Elevated TGs (\>1000 mg/dL) which can cause acute pancreatitis (as in elevated TGs in hyperchylomicronemia)
157
What is the primary stimulus for increasing the activity of glycogen phosphorylase in the liver and skeletal muscle?
Liver - glucagon and epinephrine -\> activate phosphorylation kinase via cAMP
Skeletal muscle - Ca+2 is the primary activator phosphorylase kinase -\> increase glucose with muscle contraction, secondary activation via epinephrine (cAMP)
158
How can deficiency in dihydropteridine reductase cause problems outside of the phenylalanine/tyrosine pathway?
BH4 is also needed as a cofactor for the production of serotonin from Tryptophan and Nitric oxide from arginine.
159
Is Hexokinase or Glucokinase (Hexokinase IV) induced by insulin?
Glucokinase -\> allows Vmax to overall increase in response to increasing blood glucose levels, since glucokinase is the key glucose response element in pancreatic Beta cells + hepatocytes.
160
What occurs if you have a defect in the glucokinase gene which decreases its ability to phosphorylate glucose?
Maturity-Onset Diabetes of the Young - most common form. Increased glucose levels are required to produce the same insulin (glucokinase is the enzyme present in beta cells).
161
What are the four important reactions the BH4 is a cofactor for? What enzyme regenerates this BH4 after usage?
1. Phenylalanine to tyrosine (Phenylalanine hydroxylase)
2. Tyrosine to L-dopa (Dopa decarboxylase)
3. Tryptophan to Serotonin
4. Arginine to nitric oxide
Dihydrobiopterin reductase regenerates BH4 from BH2 -\> deficiency can cause PKU #1501
162
How does blood acidity affect the urea cycle?
Acidosis -\> inhibition of urea cycle and hyperammonemia
-\> due to protonation of ammonia to ammonium so it can't be used by carbamoyl phosphate synthetase 1.
