Step 1 Flashcards Excel 1 30 15
What makes up a nucleosome?
Negatively charged DNA loops twice around positively charged histone octamer.
Histones have a lot of what?
Rich in lysine and arginine
Purpose of H1
Binds to nucleosome and to linker DNA to stabilize the chromatin fiber: it is the only one NOT in the nucleosome core.
DNA and histone synthesis during what phase of mitosis
S phase
Nucleosome core histones
H2A, H2B, H3, H4 (each x2)
Heterochromatin
Highly condensed, not active
Euchromatin
Transcriptionally active
DNA methylation in prokaryotes
Template strand Cs and As are methylated to allow mismatch repair enzymes to distinguish parent from daughter strand.
DNA methylation in eukaryotes
CpG islands to repress transcription
What are CpG islands exactly?
Cytosine next to Guanine in a strand of DNA. The cytosine can be methylated, in fact most of the cytosines in CpG islands are.
Histone methylation
Usually reversible, represses transcription, but can occasionally activate it.
Histone acetylation
Relaxes DNA coiling, increasing transcription
What are the pyrmidines
Pyrimidines CUT
Thymine vs Uracil
Thymine has a methyl, uracil is a deaminated cytosine
Amino acids necessary for purine synthesis
GAG-Glycine, Aspartate, Glutamine
What makes up pyrimidines?
Carbamoyl phosphate and aspartate
Nucleoside vs. nucleotide
nucleoside is base + sugar, -tide has 3’-5’ phosphodiester bond linked phosphate(s)
Basic steps of Purine synthesis
- Star with sugar + phosphate (PRPP) 2. Add base
What is PRPP?
Phosphoribosyl pyrophosphate (it has a phosphate instead of a base attached to the ribose)
Basic steps of Pyrimidine synthesis
- Make temporary base (orotic acid) 2. Add sugar + phosphate (PRPP) 3. Modify base
What turns ribonucleotides to deoxyribonucleotides
Ribonucleotide reductase
Carbamoyl phosphate used in what metabolic pathways
De novo pyrimidine synthesis and the urea cycle
Purine base production steps
- Start with Ribose 5-P2. Turn to PRPP by PRPP synthetase3. Produce IMP through some steps4. AMP and GMP produced (GMP by IMP dehydrogenase?)
What does de novo purine synthesis require?
Aspartate, glycine, glutamine, and THF
Pyrimidine base production steps
- Combine Glutamine and CO2 with Carbamoyl phosphate synthetase II to produce carbamoyl phosphate (uses up two ATP)2. Carbamoyl phosphate + Asparate to produce Orotic Acid3. Orotic acid + PRPP to produce UMP4. UMP to UDP5. UDP to CTP or dUDP with ribonucleotide reductase6. dUDP to dUMP7. dUMP to dTMP by Thymidylate synthase8. Tetrahydrofolate in N5N10methyleneTHF is what is used to add the methyl group.
Draw out the pathways!
Writing them out isn’t very useful.
Leflunomide target
Inhibits dihydroorotate dehydrogenase
Mycophenolate and ribavirin target
Inhibit IMP dehydrogenase
Hydroxyurea target
Ribonucleotide reductase
6-mercaptopurine (6-MP) target AND its prodrug
Prodrug is azathioprine. They both inhibit de novo purine synthesis.
5-fluorouracil (5-FU) target
Inhibits thymidylate synthase (lowers deoxythymidine monophosphate (dTMP))
Methyotrexate (MTX), Trimethoprim (TMP), and pyrimethamine target
Inhibits Dihydrofolate reductase (lowers dTMP) in humans, bacteria, and protozoa, respectively. (MTX in humans, TMP in bacteria, Pyrimethamine in protozoa)
Does myophenolate/ribavirin only affect GMP production?
Yes, for de novo GTP production.
Guanine to Cuanylic acid (GMP)
HGPRT + PRPP
Hypoxanthine to Inosinic acid (IMP)
HGPRT + PRPP
Adenine to Adnylic acid (AMP)
APRT + PRPP
Adenosine to Inosine
Adenosine deaminase (ADA)
Hydroxanthine to Xanthine
Xanthine oxidase
Xanthine to uric acid
Xanthine oxidase
Draw out the purine salvage deficiencies
…
Adenosine deaminase deficiency path
Excess ATP and dATP imbalances nucleotide pool via feedback inhibition of ribonucleotide reductase leading to the prevention of DNA synthesis and thus lower lymphocyte count
Adenosine deaminase deficiency and what disease
Autosomal recessive SCID (one of the major causes)
Lesch-Nyhan path
Defective purine salvage from absence of HGPRT. Excess uric acid production and de novo purine synthesis.
Lesch-Nyhan genetics
X-linked recessive
Lesch-Nyhan presentation
Intellectual disability, self-mutilation, aggression, hyperuricemia, gout, dystonia.
Lesch-Nyhan tx
Allopurinol or febuxostate (2nd line)
Lesch-Nyhan Mnemonic
HGPRT: Hyperuricemia, Gout, Pissed off (aggressin,self-mutilation), Retardation, Dystonia
What is HGPRT?
Hypoxantine-Guanine Phosphoribosyltransferase
Degenerate code
Multiple codons for most amino acids
Methionine codon
AUG
Tryptophan codon
UGG
What is commaless, nonoverlapping code?
Commaless means that no codons are used as punctuation, it is read straight through (at least the exons, etc.). Nonoverlapping means one codon in a sequence leads to one amino acid. In viruses, the genes can overlap.
Universal code exception
Mitochondria in humans. The codons can be a little different.
Origins of replication in prok. and euk.
Prok. have 1! (theta-replication)Euk. have multiple (large chromosomes)
Single-stranded binding proteins
Prevent strands from reannealing
DNA topoisomerases
Create single or double-stranded breaks in helix to add or remove supercoils
Fluoroquinolones action
Inhibit DNA gyrase (prok. topoisomerase II)
Primase
RNA primer for DNA pol III initiation
DNA pol III
Prok. only, 5’-3’ replication, 3’-5’ exonuclease activity (proofreading). On lagging strand, reads until it gets to primer
DNA pol I
Prok. only. Replaces RNA primer with DNA. 5’-3’ exonuclease activity
DNA ligase
Joins Okazaki fragments
Telomerase
RNA-dependent DNA polymerase that adds DNA to 3’ ends of chromosomes to avoid loss of genetic material with every duplication.
HGPRT role
Recycling back to nucleic acids. Guanine to GMP, Hypoxanthine to IMP (moves away from xanthine and uric acid!!)
APRT role
It is the HGPRT for Adenine. Adenine to AMP.
What is the order of severity of mutations to the genetic code
silent«frameshift. Transversions (purine to pyrimidine) is worse than transitions (purine to purine)
Most silent mutations found where in codon
In the 3rd position (wobble!)
Sickle cell caused by what mutation
Missense
How to get a frameshift
Delete or add nucleotides not a multiple of 3.
What mutation is duchenne’s
Frameshift
I have a bulky helix-distorting DNA lesion, what do I use?
Nucleotide excision repair. Removes an oligonucleotide containing the damage then DNA pol and ligase fills it in. Pyrimidine dimers and bulky chemical adducts.
I have an altered Base
Base excision repair
Base excision repair:
Base-specific glycosylase recognizes altered base and creates AP site (apurinic,apyrimidinic). One or more nucleotides are removed by AP-endonuclease, which cleaves the 5’ end. Lyase cleaves the 3’ end. DNA pol-beta fills the gap and DNA ligase seals it.
AP-endonuclease action
Forms a single strand break. DNA glycosylase just removes the base by cleaving the N-glycosidic bond. AP endonuclease cleaves the 5’ end of the AP site
Lyase action
Cleaves 3’ end of AP site
Mismatch repair vs. Nucleotide exicision repair
Nucleotide excision for bulky adducts or major distortions to the DNA helix.
Mismatch repair
Repairs errors that occur during DNA synthesis. Usually just transitional errors (laying a C instead of T)
Xeroderma pigmentosum problem
Nucleotide excision repair, prevents repair of pyrimidine dimers because of UV exposure
Spontaneous/toxic deamination repair
Base excision repair. It’s the reason why DNA has thymine, because when it deaminates it turns methylated cytosine which is recognizable. Not cytosine if we had uracil instead.
Hereditary nonpolyposis colorectal cancer problem
Mismatch repair
Ataxia telangiectasia problem
Nonhomologous end joining
Nonhomologous end joining problem
Repairs double stranded breaks. No requirement for homology.
Energy for DNA/RNA production
5’ end of incoming nucleotide bears the triphosphate
Protein synthesis direction
N-terminus to C-terminus
mRNA read
5’ to 3’
Phosphate bond reaction
Triphosphate bond targeted by the 3’ hydroxyl attack.
How to block DNA replication
Modified 3’ OH, preventing addition of the next nucleotide (chain termination)
mRNA start codons
AUG (rarely GUG):
AUG codes for
Euk. methionine which may be removed before translation ends. Prok. formylmethionine (f-met.)
mRNA stop codons
UAA, UGA, UAG (u are annoying, u go away, u are gone)
Promoter regions
TATA boxes and CAAT boxes (weak bonds, easy to open)
Enhancers bind
Transcription factors, may be found in introns
Silencers bind
Repressors, may be found far away, close to, or in an intron, like enhancers.
Most numerous RNA
rRNA (in ribosomes)
Largest RNA
mRNA
Smallest RNA
tRNA
RNA pol I
rRNA
RNA pol II
mRNA
RNA pol III
tRNA
Euk. or prok. have 3 RNA pol
Euk. have 3 RNA pol, prok. have just 1.
alpha-amanitin path
inhibits RNA pol II, severe hepatotoxicity, found in Amanita phalloides (death cap mushrooms)
Initial mRNA from transcription is called
Heterogenous nuclear RNA (hnRNA)
mRNA processing
- 5’ cap (7-methylguanosine cap)2. Polyadenylation at 3’ end (around 200 A’s)3. Splicing out introns
mRNA quality control
Cytoplasmic P-bodies, contain exonucleases, decapping enzymes, and microRNAs; mRNAs may be stored here for future translation
What are P-bodies?
Processing bodies. Decaps and degrades unwanted mRNAs. Stores mRNA for later translation. Aids in translation repression with miRNAs (like siRNAs)
Poly-A polymerase template
No template needed
Polyadenylation signal
AAUAAA
Splicing
- Primary transcript combines with small nuclear ribonucleoproteins (snRNPs) and other proteins to form spliceosome. 2. Lariat-shaped intermediate is generated 3. Lariat is released to precisely remove intron
Splicing mechanistically
A 3’ OH is formed during lariat formation which then allows for an attack at the phosphodiester bond at the 2nd exon leading to splicing out the intron.
anti-smith antibodies
Antibodies to spliceosomal snRNPs (anti-Smith antibodies). Highly specific for SLE.
Anti-U1 RNP antibodies
Highly associated with MCTD
Draw out splicing reaction
….
Abnormal splicing can cause what
Oncogenesis, Beta-thal
Exons vs. introns
Exons are coding
tRNA structure
75-90 nucleotides. Cloverleaf. CCA at 3’ end which binds the amino acid. Anticodon end is opposite 3’ aminoacyl end. The A in CCA binds the aminoacid.
T-arm of tRNA
Contains TPsyC (thymine, pseudouridine, cytosine) sequence necessary for tRNA-ribosome binding.
D-arm of tRNA
Contains dihydrouracil residues necessary for tRNA recognition by the correct aminoacyl-tRNA synthetase.
Acceptor stem of tRNA
The 3’ CCA is the amino acid acceptor site
tRNA charging
Aminoacyl-tRNA synthetase checks AA before and after binding to tRNA, if incorrect, it hydrolyzes it because you can’t fix it afterwards.
How many amino acids for each aminoacyl-tRNA synthetase
One synthetase for every AA
Aminoacyl-tRNA synthesis reaction energy
ATP used to make the bond, but the new bond is used to form the peptide bond.
Anticodon for start codon
UAC (binding to AUG)
tRNA wobble
Only first 2 nucleotide positions of an mRNA codon matter
Initiation of translation
GTP hydrolysis; initiation factors assemble 40S with initiator tRNA and are released when the mRNA and 60S assemble with the complex
Euk. ribosome
40S + 60S = 80S (Even (euk.))
Prok. ribosome
30S + 50S = 70S (Odd (prOk.))
ATP-tRNA
Activation (charging)
GTP-tRNA
Gripping and Going places (translocation)
Initiator methionine binds where
P site
Steps in translation
Aminoacyl-tRNA binds to A site, peptide bond forms, translocation 3 nucleotides over and repeat.
Stop codon reached, then what
Release factor comes in and releases the polypetide
A, P, and E sites
Aminoacyl, peptide, and exit.
Posttranslational modifications
Cleaving N- or C-terminus of zymogen. Phosphorylation, glycosylation, hydroxylation, methylation, acetylation, and ubiquitination.
What are heat shock proteins
e.g. Hsp60, in yeast, are chaperonins expressed at high temps to prevent protein denaturing/misfolding.
Chaperone proteins
Can facilitating or maintain protein folding.
What regulates cell cycle phases
Cyclins, cyclin-dependent kinseases (CDKs), and tumor suppressors.
Which phases are variable in time
G1 and G0. Not G2, when that begins, there is a set time for when it must go to mitosis.
Order of the phases
G1/G0 to S phase to G2 to Mitosis.
What regulates G1 to S phase progression.
Rb, p53
CDKs action
Constitutive and inactive…????
Cyclins
Regulatory proteins that control cell cycle events; phase specfic; activate CDKs
Cyclic-CDK complexes
Must be both activated and inactivated for cell cycle to progress
p53 and Rb
Hypophophorylated Rb and p53 normally inhibit G1-to-S progression
What happens if you mutate p53 or Rb
Unrestrained cell division (e.g. Li-Fraumeni)
What is interphase
G1, S, and G2
What cell lines are G0
Neurons, skeletal and cardiac muscle, RBCs. These are permanent
What cells go from G0 to G1
Hepatocytes, lymphocytes. These are quiescent.
What cells never go to G0
Bone marrow, gut epithelium, skin, hair follices, germ cells
Rough ER purpose
Site of synthesis of secretory (exported) proteins and of N-linked oligosaccharide addition to many proteins
Example of cells with lots of RER
Mucus-secreting goblet cells of the small intestine and antibody-secreting plasma cells
Nissl bodies
RER in neurons, synthesize peptide neurotransmitters for secretion
What do free ribosomes do
Site of synthesis of cytosolic and organella proteins
Smooth ER purpose
Steroid synthesis and detox of drugs and poisons.
Cells with lots of SER
Liver hepatocytes and steroid hormone-producing cells of the adrenal cortex and gonads
Golgi purpose
Movies proteins and lipids from the ER to vesicles and plasma membrane.
Example of specific effects of Golgi
Modifies N-oligosaccharides on asparagine. Adds O-oligosacchardies on serine and threonine. Adds mannose-6-phophate to proteins for trafficking to lysosomes.
Mannose-6-phosphate
…
Endosomes purpose
Take stuff from outside the cell or from the Golgi, sending it to lysosomes for destruction or back to the membrane/Golgi for further use.
Inclusion cell disease (I-cell disease) path
Inherited lysosomal storage disorder; defect in phosphotransferase. Golgi can’t phosphorylate mannose residues (i.e. dec. mannose-6-phosphate) on glycoproteins leading to extracellular excretion and not delivered to lysosomes.
I-cell disease presentation
Coarse facial features, clouded corneas, restricted joint movement, and high plasma levels of lysosomal enzymes. Often fatal in childhood.
Signal recognition particle (SRP)
Abundant, cytosolic ribonucleoprotein that traffics proteins from the ribosome to the RER. Absent or dysfunctional SRP leads to proteins accumulating in the cytosol.
Vesicular trafficking proteins
COPI, COPII, and Clathrin.
COPI functions
Golgi to Golgi (retrograde); Golgi to ER
COPII functions
Golgi to Golgi (anterograde); ER to Golgi
Clathrin functions
trans-Golgi to lysosomes; plasma membrane to endosomes (receptor mediated endocytosis (LDL receptor))
Peroxisome
Catabolism of very-long-chain fatty acids, branched-chain fatty acids, and amino acids
Proteasome
Breaks down damaged or ubiquitin tagged proteins. Defects in teh ubiquitin-proteasome system have been implicated in some cases of Parkinson’s.
Microtubule structure
Helical cylinder of polymerized heterodimers of alpha and beta-tubulin. Each dimer uses 2 GTP.
Microtubule location
Flagella, cilia, mitotic spindles
Microtubule growth
Grow slowly (at positive end), collapse quickly
Microtubule in neurons
Slow axoplasmic transport
Molecular motor proteins
Dynein (retrograde to microtubule (+ to -)Kinesin (anterograde to microtubule (- to +)
Drugs acting on Microtubules
Microtubules Get Poorly Very Poorly: Mebendazole, Griseofulvin, Colchicine, Vincristine/Vinblastine, Paclitaxel
Cilia structure
9+2 microtubule pair arragement with dynein ATPase linking peripheral 9 doublets
Kartageners syndrome presentation
Primary ciliary dyskinesia. Male and female infertility from immotile sperm and dysfunctional fallopian tube cilia. Increased risk of ectopic. Can cause bronchiectasis, recurrent sinusitus, and situs inversus.
Actin and Myosin found in
Muscles, microvilli, cytokinesis, adherens junctions.
Myosin structure
Dimeric, ATP driven motors
Intermediate filaments examples
Used for structure, vimentin, desmin, cytokeratin, lamins, glial fibrillary acid proteins (GFAP), neurofilaments.
Fungal membranes contain what
Ergosterol
What tissue stains vimentin
Connection
Tissue stain desmin
Muscle (desMin)
Tissue stain Cytokeratin
Epithelial Cells
GFAP tissue
NeuroGlia
Neurofilaments tissue
Neurons
Na/K ATPase
3 Na out, 2 K in. Net charge of 1 + out.
Toxins on Na/K ATPase
OuabainCardiac glycosides (digoxin and digitoxin)
Cardiac glycosides action
Directly inhibit the Na/K ATPase, which leads to indirect inhibition of Na/Ca exchange leading to increased intracellular calcium and increased cardiac contractility. Too much sodium in cell prevents movement of calcium into outside.
Oubain MOA
Inhibits K+ binding
ATP at what site of Na/K ATPase
Intracellular, fires when the sodium is released (first step). K+ comes in last
Which cartilage is the most common
Type I: 90%
Where do you find Type I, II, III, and IV cartilages (The Important Sites)
I: BoneII: Cartilage (cartwolage)III: Blood vessels (big one)IV: Under the floor (four/basement membrane)
Type I cartialge
Bone (osteoblasts), skin, tendon, dentin, fascia, cornea, late wound repair.
Type II cartilage
Cartilage (including hyaline), vitreous body, nucleus pulposus.
Type III cartilage
Reticulin: Skin, blood vessels, uterus, fetal tissue, granulation tissue
Type IV cartilage
Basement membrane, basal lamina, lens
Alport syndrome path
Defective Type IV collagen
Goodpasture path
Autoantibodies to Type IV
Vascular type of Ehlers-Danlos syndrome)
Type III; uncommon type!
Mnemonic for cartilage
Be So Totally Cool, Read Books. BST C R B
Osteogenesis imperfecta type I
Type I cartilage decreased production
Collagen synthesis steps
- Synthesis 2. Hydroxylation 3. Glycosylation 4. Exocyotosis 5. Proteolytic processing 6. Cross-linking
- Collagen Synthesis step
Translation of collagen alpha chains (preprocollagen): Gly-X-Y (X and Y are proline or lysine)
Amino acids that make up collagen
Glycine, proline, and lysine
- Collagen hydroxylation step
Hydroxylation of specific proline and lysine residues requiring vit C
- Collagen glycosylation step
Glycosylation of pro-alpha-chain hydroxyline residues and formation of procollagen via hydrogen and disulfide bonds (triple helix of 3 collagen alpha chains). Then leads to 4. Exocytosis
Osteogenesis imperfecta path
Can’t form triple helix of procollagen.
What steps happen in the RER
Synthesis, hydroxylation, and glycosylation.
Look at a figure for Collagen synthesis steps
….
- Proteolytic processing of collagen
Cleavage of disulfide-rich terminal regions of procollagen, transforming it into insoluble tropocollagen.
- Cross linking of collagen
Staggered tropocollagen molecules reinforced by covalent lysine-hydroxylysine cross-linkage (by Cu2+-containing lysyl oxidsae) to make collagen fibrils.
Ehlers-Danlos path
You can’t cross link collagen properly.
Osteogenesis imperfecta presentation
Brittle bone disease. Multiple fractures from minimal trauma. Blue sclerae because of translucency over the choidal veins. hearing loss (abnormal ossicles). Dental imperfections due to lack of dentin. May be confused with child abuse.
Osteo. Imp. genetics
Most common form is Aut. dom. with decreased production of otherwise normal type I collagen.
Ehlers-Danlos presentation
Hyperextensible skin, tendency to bleed (easy bruising), and hypermobile joints. May be associated with joint dislocation, berry and aortic aneurysms, and organ rupture.
Ehlers-Danlos types
6+ types. May be aut. dom. or rec. Hypermobility type: Most COMMON. Classical type (joint and skin symptoms): Mutation in type V collagen. Vascular type (vascular and organ rupture): Deficient type III collagen
Menkes disease
Connective tissue disease caused by impaired copper absorption and transport. Leads to decreased activity of lysyl oxidase (copper is a necessary cofactor). Results in brittle, kinky hair, growth retardation and hypotonia.
Elastin is found where
Skin, lungs, large arteries, elastic ligaments, vocal cords, ligamenta flava
Elastin structure
Rich in proline and glycine, nonhydroxylated forms. ????
Tropoelastin with fibrillin scaffolding?
….??
Elastin cross-linking
Takes place extracelluarly and gives elastin its elastic properties
What breaks down and prevents breakdown of elastin?
Elastase breaks down, inhibited by alpha1-antitrypsin.
Marfan syndrome
Defect in fibrillin, a glycoprotein that forms a sheath around elastin
Emphysema
Can be caused by alpha1-antitrypsin deficiency
Wrinkles of aging caused by
Lower collagen and elastin production
Diagnosing neonatal HIV or herpes encephalitis
PCR
Southern blot steps
DNA electrophoresed on gel then transferred to filter. Then denatured and exposed to radiolabeled DNA probe.
Northen blot
RNA
Western blot
Protein with antibody probe
Confirmatory test for HIV
Western blot after + ELISA
Southwestern Blot
DNA-binding proteins (Transcription factors) using labeled oligonucleotide probes
Microarrays benefits
Can profile gene expression levels of thousands of genes simultaneously to study diseases and treatments. Can detect SNPs and copy number variations (CNVs) for genotyping, clinical genetic testing, forensic analysis, cancer mutations, and genetic linkage analysis.
Collagenases are what kind of enzyme
MMP matrix metalloproteinases
Marfan’s gene
Fibrillin-1 gene
The PI3K/Akt/mTOR pathway
anti-apoptosis, cellular proliferation, and angiogenesis. mutations in these lead to cancer pathogenesis
IP3
activates Protein Kinase C
Branched chain fatty acids undergo what for breakdown
Alpha-oxidation
problems with ubiquitin-proteasome system can lead to
Parkinson and Alzheimer’s
Mousy odor in a child with fair colored features
Phenylketonuria. Tyrosine is an essential enzyme because they can’t make it from phenylalanine anymore. Can’t produce melanin either.
PKU caused by
mutation in phenylalanine hydroxylase enzyme
Nitrates in diet do what to DNA
deaminate cytosines, adenines, and guanines
In base excision repair….
AP endonuclease cleaves 5’ side before lyase cleaves 3’ side
Iron deficient anemia can present with
Dysphagia (esophageal webs) and dysfigured fingernails (spoon nails (koilonychia))
Plummer-Vinson or Patterson Kelly syndrome
Iron deficiency anemia with dysphagia from esophageal webs??
Pernicious anemia classic presentation
Older, mentally slow woman of northern European descent who is “lemon colored” (anemic and icteric) with a smooth shiny tongue of atrophic glossitis and a broad shuffling gait.
Cobalamin deficiency path
Homocystinemia due to impaired methionine re-synthesis.
Maturing erythrocytes lose the ability to synthesize heme when what happens…
When they lose their mitochondria
HbC is made of what
Lysine instead of glutamate residue so the Hb molecule is more positive and does not electrophorese as far compared to even HbS (valine is nonpolar)
ELISA stands for
Enzyme-linked immunosorbent assay
Indirect ELISA
A test antigen used to determine if an antibody is in the patient’s blood, second antibody used to detect the first antibody.
Direct ELISA
Test antibody used to detect antigen in patient’s blood, second antibody is used to detect the antigen
Positive ELISA result
Lights up brightly
Indirect ELISA test
anti-HIV antibody detection
Fluorescent in situ hybridization.
Using fluorescent DNA or RNA probe to bind specific gene site of interest on chromosomes.
Uses of FISH
Microdeletions that can’t be detected by karyotype
Steps of cloning
Isolate euk. mRNA, use reverse transcriptase to make cDNA, insert cDNA into bacterial plasmids with ABx resistance genes, transform recombinant plasmid into bacteria, grow on Abx medium to get the bacteria that produces the cDNA.
How to get DNA into a mouse
- Random insertion into mouse genome. 2. Trageted insertion or deletion of gene through homologous recombination with mouse gene.
What is homologous recombination
Uses a complementary dsDNA template (like the other chromosome) to fix dsDNA breaks. Can also be used for cloning………
Cre-lox system
Can induce genes at specific developmental points……………………………..
RNA interference (RNAi)
dsRNA complementary to target mRNA used to degrade target mRNA
What tissues can be karyotypes
blood, bone marrow, amniotic fluid, or placental tissue.
alpha1-antitrypsin deficiency is inherited in what way
Codominance………….
Neurofibromatosis type 1 inheritance
variable expressivity
Example of pleiotropy
PKU with light skin, retardation, and musty body odor
what diseases have anticipation
Huntington, fragile x, myotonic dystrophy
Do oncogenes need loss of heterogeneity
No, loss of heterogeneity only applies to tumor suppression genes
Explain dominant negative mutation
It’s a dominant mutation but it has the the negative, suppressive effect. Like a nonfunctional transcription factor preventing the functional wildtype protein from working.
Linkage disequilibrium for individuals or population
Measured in a population, not in a family
When is McCune-Albright a viable condition
Only if it is inherited mosaically
What is McCune-Albright syndrome
Genetic syndrome with 2 out of 3 of following: autonomous endocrine excess (e.g. precocious puberty), polyostotic fibrous dysplasia, unilateral cafe au lait spots.
What is locus heterogeneity
Mutations at different loci producing the same phenotype
What is allelic heterogeneity
Different mutations in the same locus produce the same phenotype
Heteroplasmy
Having normal and mutated mtDNA, causes variable expression in mitochondrial inherited disease.
How is homologous recombination used in cloning
…..
Uniparental disomy
Receiving 2 copies of a chromosome from one parent. and 0 from the other.
Hetero vs. isodisomy
Hetero occurs in meiosis I, iso in meiosis II. Iso can also happen post-zygotically with a chromosomal duplication and loss of the other chormosome.
When to consider UPD
When an individual has a recessive disorder but only one parent is carrying the trait.
How bad is UPD usually
Usually normal phenotype
Frequency of an X-linked recessive disease in males and females
males: qfemales: q^2
Hardy-Weinberg equillibrium requires
No mutation occurring at the locus, natural selection is not occuring, completely random mating, no net migration
Prader-Willi and Angelman on what chromosome
15
Prader-Willi inheritance
Prader lacks Faddah. Maternal imprinting: maternal gene is silent and paternal gene is deleted/mutated
AngelMan inheritance
Misses Muddah. Dad gene is normally silent and maternal gene is deleted/mutated.
P-W presentation
Hyperphagia, obesity, intellectual disability, hypogonadism, and hypotonia
Angelman presentation
Inappropriate laughter (happy puppets, seizures, ataxia, and severe intellectual disability)
Specific genetics about P-W
25% of cases due to maternal UPD, remaining are mutuation or deletion
Specific genetics about Angelman
5% of cases due to paternal UPD, remaining are mutuation or deletion
Are P-W and Angelman genes on maternal and paternal side both normally silent????
No…one is usually active. So if you lack the father’s chromosome from deletion but the maternal side is not imprinted…will you not have the disease. Or is one or the other imprinted……………………
Which diseases tend to be worse, aut. rec or aut. dom.
Aut. rec., they tend to pop up in childhood, aut. dom. are often pleiotropic
Why aren’t x-linked recessive passed male to male
Because the father gives the son the Y chromosome
X-linked dom. inheritance
Mothers pass on to 50% of sons AND daughters, fathers transmit to all daughters but no sons
Example of x-linked dom. inheritance
Hypophosphatemic rickets
Hypophosphatemic rickets
vitamin-D resistant rickets. Increased phosphate wasting and proximal tubule.
Mitochondrial myopathies presentation
Myopathy, lactic acidosis, and CNS disease, secondary to failrue in ox phos
Muscle biopsy of mitochondrial myopathies
Ragged red fibers
Autosomal dominant polycystic kidney disease genetics
85% of cases due to mutation in PKD1 (chromosome 16); remainder due to mutation in PDK2 (chrom. 4)
Familial adenomatous polyposis genetics
APC gene, chrom. 5
Familial hypercholesterolemia
Defective/absent LDL receptor, can have tendon xanthomas (Achilles!!)
Hereditary hemorrhagic telangiectasis
Telangiectasia, recurrent epistaxis, skin discolorations, AVMs, GI bleeding, hematuria.
Hereditary spherocytosis genetics
spectrin or ankyrin defects
Hereditary spherocytosis CBC w/ diff results
Elevated MCHC
Huntington genetics
Chrom 4, trinucleotide repeat disorder (CAG)n.
Marfan’s genetics
fibrillin-1 gene mutation
Marfan syndrome presentation
Tall with long extremities, pectus excavatum, hypermobile joints, and long, tapering fingers and toes (arachnodactyly), cystic medial necrosis of aorta leading to aortic incompetance and dissecting aortic aneurysms, floppy mitral valave. Subluxation of lenses upward and temporally.
MEN2 gene
ret gene
NF1 (von Recklinghausen disease)
Neurocutaneous: cafe-au-lait spots, cutaneous neurofibromas, aut. dom., 100% penetrance, variable expression. CHROMOSOME 17
NF2
Bilateral acoustic schwannomas, juvenile cataracts, meningiomas, and ependymomas. CHROMOSOME 22
Tuberous sclerosis
neurocutaneous disorder with numerous benign hamartomas, incomplete penetrance, variable expression
von Hippel-Lindau disease
VHL gene (tumor suppressor) on chromosome 3 (3p).
Cystic fibrosis genetics
Aut. rec, CFTR gene on chrom. 7, most commonly a deletion of Phe508, most common lethal genetic disease in caucasians
Function of CFTR gene
ATP-gated Cl- channel that secretes cl- in lungs and GI tract and reabsorbs Cl- in sweat glands.
CF patho
mutations cause misfolded protein that is retained in RER and not transported to cell membrane leading to less Cl- (and H2O) secretion and more Na+ reabsorption to compensate for incrased ICF cl- leading to even less ECF water causing very thick mucus
CF membrane potential
Increased Na+ reabsorption causes mroe negative transepithelial potential difference….how….I thought the inside is negative because the na/k atpase pushes an extra cation out, wouldn’t this just ruin the membrane potential.
CF diagnosis
Cl- conc. >60 mEq/L in sweat is diagnostic, can cause a contraction and hypokalemia (ECF effects like taking a loop diuretic) Renal K+/H+ wasting
CF CXR
Reticulonodular pattern
CF genitals
Infertile men (no vas deferens, no sperm)
CF PNA
recurrent Pseudomonas
CF tx
N-acetylcysteine to loosen mucus plugs (cleaves disulfide bonds within mucus glycoproteins). Dornase alfa (DNAse) to clear leukocytic debris
X-linked recessive disorders
Be Wise, Fool’s GOLD Heeds Silly HOpe.Bruton agammaglobulinemia, Wiskott-Aldrich syndrome, Fabry disease, G6PD deficiency, Ocular albinism, Lesch-Nyhan syndrome, Duchenne (and Becker) muscular dystrophy, Hunter Syndrome, Hemophilia A and B, Ornithine transcarbamoylase deficiency
CF transepithelial potential difference
More negative because more sodium is being reabsorbed. This is different from membrane potential because I think that actually goes up because of the sodium rushing in, unless the Cl- still makes it more negative.
Duchenne mutation
X-linked frameshift
Gower manuever
using upper extremities to help kids stand up
Duchenne age of onset
Before 5 yrs
MCC of death in Duchenne’s
dilated cardiomyopathy
Dystrophin purpose
connects intracellular cytoskeleton (actin) to the transmembrane proteins alpha and beta-dystroglycan, which are connected to the ECM. without in you get myonecrosis
Duchenne’s bloodwork
Increased CPK and aldolase scene
Duchenne’s dx
Western blot and muscle biopsy confirm diagnosis
Becker mutation
X-linked point mutation
Becker onset
Adolescene or early adulthood
Myotonic dystrophy type 1 genetics
CTG trinucleotide repeat expansion in the DMPK gene leading to abnormal expression of myotonin protein kinase
Myotonic type 1 presentation
Myotonia, muscle wasting, frontal balding, cataracts, testicular atrophy, and arrhythmia
Myotonia is
Delayed relaxation with prolonged contraction, muscle may be warmed up to limit the myotonia
Fragile X genetics
FMR1 gene on X chrom. affecting the methylation and expression of the FMR1 gene.
Fragile X epidemiology
2nd MCC of genetic intellectual disability (after Down’s)
Fragile X presentation
Post-pubertal macroorchidism (enlarged testes), long face with a large jaw, large everted ears, autism, mitral valve prolapse
Fragile X genetic path
Trinucleotide repeat disorder (CGG)
Fragile X mnemonic
eXtra large testes, jaw, and ears
GAA
Friedreich ataxia
CAG
Huntington
CTG
Myotonic dystrophy
CGG
Fragile X
Mnemonic for Trinucleotide repeat disorders
X-Girlfriend’s First Aid Helped Ace My Test (the middle letter of each repeat)
Down syndrome presentation
MR, flat facies, epicanthal folds, palmar crease, gap between 1st 2 toes, duodenal atresia, Hirschsprung’s, congenital heart disease (ostium primum-type ASD), Brushfield spots. Inc. risk of ALL, AML< and Alzheimer’s (>35 years old)
Down’s genetics
1:700. 95% due to nondisjunction. 4% due to reobersonian translocation. 1% due to mosaiciism (post-fertilization mitotic error)
Down syndrome First trimester diagnosis
US: Inc. nuchal translucency and hypoplastic nasal boneSerum: PAPP-A is down, betahCG is up
Down syndrome Second trimester diagnosis
Serum: low AFP, high beta-hCG, low estriol, inc. inhibin A
Edwards syndrome presentation
Severe MR, rocker-bottom feet, micrognathia, low set Ears, clenched hands, prominent occiput, cong. heart disease, death within 1 yr
Edwards syndrome genetics
(E)lection age (18)1:8000, most common trisomy resulting in live birth after Down’s
Edwards serum
PAPP-A and free betahCG down in first trimester. Quad screen: low AFP, low betahCG, low estriol, low or normal inhibin A
Patau syndrome presentation
severe MR, rocker bottom feet, microphthalmia, microcephaly, cleft liP/Palate, holoProsencephaly, Polydactyly, congenital heart disease, death within 1 yr
Patau genetics
(P)uberty 13
Patau serum
First-trimester: low betahCG, low PAPP-A and increased nuchal translucency
Draw out a table of the three viable trisomies bloodwork in pregnancy
….
Draw out nondisjunction
…..
What are acrocentric chromosomes
have centromeres near the ends
Robertsonian translocation
Acrocentric chromosomes fuse with loss of both short arms, can be balanced or unbalanced
Which chromosomes can undergo robertsonian translocation
paris 13, 14, 15, 21 and 22
What happens to the short arms in a robertsonian translocation
The reciprocal product is formed from the long armed chromosome but because they have useless genes they are usually lost quickly.
Cri-du-chat syndrome genetics
Congenital microdeletion of short arm of chrom. 5 (46,XX or XY, 5p-)
Cri-du-chat presentation
Microcephaly, moderate to severe MR, high-pitched crying/mewing, epicanthal folds, cardiac abnormalities (VSD)
Williams syndrome genetics
Congenital microdeletion of long arm of chrom. 7 (deleted region includes elastin gene)
Williams presentation
Elfin facies, MR, hypercalcemia (incr. sensitivity to vit. D), well developed verbal skills, extremely friendly, CV problems
What are the 22q11 deletion syndromes
DiGeorge and Velocardiofacial syndromes
CATCH-22
Cleft palate, abnormal facies, thymic aplasia, cardiac defects, hypocalcemia secondary to parathyroid aplasia, due to microdeletion at chromosome 22q11.
22q11 deletion path
Aberrant development of 3rd and 4th branchial pouches
DiGeorge syndrome presentation
thymic, parathyroid, and cardiac defects
Velocardiofacial syndrome
palate, facial, and cardiac defects
B1
thiamine (TPP)
B2
riboflavin (FAD,FMN)
B3
niacin: NAD+
B5
pantothenic acid (CoA)
B6
pyridoxine (PLP)
B7
biotin
B9
folate
B12
cobalamin
What B vitamins stored in liver
B12 and folate, the rest are peed out
B-complex deficiencies typical presentation
Dermatitis, glossitis, and diarrhea
Vitamin A is used as treatment for
Treats measles and AML, subtype M3. Retin-A for wrinkles and acne
Vitamin A phys
Antioxidant, visual pigments (retinal), normal differentiatino of epithelial cells into specialized tissue (pancreatic cells, mucus cells), prevents squamous metaplasia
Vit A Deficiency
Night blindness (nyctalopia); dry, scaly skin (xerosis cutis); alopecia; corneal degeneration (keratomalacia); immune suppression
Vit A Excess
Arthralgias, skin changes (scaly), alopecia, pseudotumor cerebri, cerebral edema, osteoporosis, hepatic abnormalities, teratogenic (cleft palate, cardiac abnormalities), so a negative preg. test and relaiable contraception are needed before isotretinoin is prescribed for severe acne
Thiamine function
Thiamine pyrophosphate (TPP): cofactor for several dehydrogenase enzyme reactions: pyruvate dehydrogenase, alpha-ketoglutarate dehydrogenase (TCA cycle), transketolase (HMP shunt), Branched chain ketoacid dehydrogenase
Thiamine mnemonic
ATP: alpha-ketoglutarate dehyd., transketolase, pyruvate dehydroganase ….and throw in branched chain ketoacid dehydrogenase
Thiamine deficiency presentation
Wernicke-Korsakoff: triad (confusion, ophthalmoplegia, ataxia); confabulation, personality change, memory loss (permanent).Ber1Ber1: Dry: polneuritis, symmetrical muscle wasting. Wet: high output cardiac failure (dilated cardiomyopathy), edema.
Wernicke-Korsakoff path
Damage to medial dorsal nucleus of the thalamus, mammillary bodies
Thiamine deficiency path
Impaired glucose breakdown, ATP depeltion worsened with glucose infusion; highly aerobic tissues (brain, heart) affected first.
Thiamine def. cause
Malnutrition and alcoholism
Thiamine def. diagnosis
Increased RBC transketolase activity following thiamine administration
Thiamine is what B vitamin
B1
Riboflavin function
Part of FAD and FMN, used as cofactors in redox reactions, e.g. succinate dehydrogenase reaction in the TCA cycle
Riboflavin deficiency
Cheilosis and Corneal vascularization (2 C’s of B2)
Niacin function
NAD+, NADP+.
Niacin tx
dyslipidemia, lowers VLDL and raises HDL
Niacin synthesis
Need tryptophan, synthesis requires B2 and B6
Niacin deficiency
Glossitis. Severe is pellagra (caused by Hartnup disease and malignant carcinoid syndrome), and isoniazid.
Pellagra presentation
3 D’s of B3: diarrhea, dementia, dermatitis
Dermatitis in pellagra
Casal necklace or hyperpigmentation of sun-exposed limbs
Tryptophan metabolism in Hartnup, carcinoid, and isoniazid
Hartnup: dec. trypt absorptionCarcinoid: Inc. trypt metabolismIsoniazid: decreased B6
Niacin excess
Facial flushing (prostaglandin, not histamine), hyperglycemia, hyperuricemia
Pantothenate function
Coenzyme A and fatty acid synthase
B5 is
“pento”thenate
Pantothenate deficiency
Dermatitis, enteritis, alopecia, adrenal insufficiency
Pyridoxine function
Converted to pyridoxal phosphate, used in transamination (ALT and AST), decarboxylation reactions, glycogen phosphorylase. Synthesis of cystathionine, heme, niacin, histamine, serotonin, epinephrine, norepinephrine, dopamine, and GABA
Pyridoxin deficiency
Convulsions, hyperirritability, peripheral neuropathy (isoniazid and oral contraceptives), sideroblastic anemias due to impaired hemoglobin synthesis and iron excess
Biotin Function
Cofactor for carboxylation enzymes (which add 1-carbon group)
Biotin mnemonic
Avidin in egg whites avidly binds biotin
Biotin reactions
Pyruvate carboxylaseAcetylCoA carboxylasePropionyl-CoA carboxylase
Biotin deficiency
Rare. Dermatitis, alopecia, enteritis. Caused by abx or excessive ingestion of raw egg whties
folate function
Turned into tetrahydrofolate for 1-carbon transfer/methylation reactions. Synthesizing nitogenous bases in DNA and RNA
Folate sources
Leafy green vegetables, absorbed in jejunum. Folate from Foliage.
Folate deficiency
macrocytic, megaloblastic anemia; hypersegmented PMNs, glossitis, no neurologic symptoms
folate def. labs
increased homocysteine, normal methylmalonic acid
folate def. in US
most common vit. deficiency, seen in alcoholics and pregnancy
folate def. causes
Phenytoin, sulfonamides, methotrexate
Cobalamin function
cofactor in homocysteine methyltransferase (transfers methyl groups as methylcobalamin) and methlmalonyl-CoA mtuase
Cobalamin deficiency
macrocytic, megaloblastic anemia; hypersegmented PMNs, paresthesias, subacute combined degeneration due to abnormal myelin
What is subacute combined denegeration
degeneration of dorsal columns, lateral corticospinal tracts, and spinocerebellar tracts.
Cobalamin blood work
elevated serum homocysteine and methylmalonic acid levels
Permanent effect of prolonged B12 deficiency
irreversible nerve damage
Cause of B12 deficiency
Only made by microorganisms, only from animal products. Veganism, malabsorption (Diphyllobothrium latum), lack of intrinsic factor (pernicious anemia, gastric bypass surgery), or absence of terminal ileum (Crohn’s).
Diagnosis of pernicious anemia
Anti-intrinsic factor antibodies
Draw out reactions for B12 and B6
….
What are the B12 reactions
Homocysteine to Methionine via Homocysteine methyltransferase AND methylmanolyl-CoA to succinyl-CoA via methylmalonyl-CoA mtuase
What are the B6 reactions
Homocysteine to cysteine and Succinyl-CoA to Heme….but not all of them??
Folates (B9) reactions
Used in reaction from homocysteine to methionine but not in forming succinyl-CoA (which is used for myelin synthesis)
Vit C functions
helps iron absorption by reducing to Fe2+ stateHydroxylating proline and lysine in collagenNeeded for dopamine Beta-hydroxylase to convert DA to NE
Treatment for methemoglobinemia
Vit C is ancillary tx by reducing Fe3+ to Fe2+
Scurvy presentation
swollen gums, bruising, hemarthrosis, anemia, poor wound healing, perifollicular and subperiosteal hemorrhages, corkscrew hair, weakened immune systhem
Vit. C excess
N/V/D, fatigue, calcium oxalate kidney stones. Increased risk of iron toxicity for people who receive transfusions, hereditary hemochromatosis
D2
ergocalciferol: from plants
D3
cholecalciferol: milk, sun-exposed skin (stratum basale)
Vit D storage form
25-OHD3
Vit D active form
1,25-(OH)2D3 (calcitriol)
Vit D function
Inc. intestinal absorption of calcium and phosphate, inc. bone mineralization
Vit D def.
Rickets in kids, osteomalacia in adults, hypocalcemic tetany
Breastmilk and Vit D
Low in Vit D, breastfed babies need oral vitamin D
Vit D Excess
HyperCa, hypercalciuria, loss of appetite, stupor
Causes of Vit D excess
Sarcoid (inc. activation of vitamin D by epitheliod macrophages)
Vit E is also called
tocopherol and tocotrienol
Vit E function
Antioxidant (protects RBCs and membranes from free radical damage)
Vit E and blood thinners
Can enhance anticoagulation due to warfarin
Vit E Def.
hemolytic anemia, acanthocytosis, muscle weakness, posterior column and spinocerebellar tract demyelination
Vit E def. simply explained
Like B12, with no anemia, PMN changes, or increased serum methylmalonic acid levels
Vit K function
Cofactor for gamma-carboxylation of glutamate residues on proteins for blood clotting (II, VII, IX, X) and proteins C and S
Vit K def. presentation
Inc. PT and aPTT with normal bleeding time
Vit K def. causes
Neonates (no bacteria in gut), prolonged use of broad-spectrum antibiotics
Vit K and breast milk
Not in breast milk, neonates need an injection at birth
Zinc function
Essential for the activity of 100% enzymes. Zinc fingers (transcription factor motifs)
Zinc def.
Delayed wound healing, hypogonadism, less adult hair, dysgeusia, anosmia, acrodermatitis enteropathica, may predispose to alcoholic cirrhosis
What reactions happen in the mitochondria
Beta-oxidation, acetyl-CoA production, TCA cycle, Ox phos
What reactions happen in the cytoplasm
Glycolysis, fatty acid synthesis, HMP shunt, protein synthesis (RER), steroid synthesis (SER), cholesterol synthesis
What happens in both mitochondria and cytosol
Heme synthesis, Urea cycle, Gluconeogenesis (HUGs take two)
What is a phosphorylase
Adds phosphate without ATP (e.g. glycogen phosphorylase)
What is a carboxylase
Transfers CO2 groups with the help of biotin (e.g. pyruvate carboxylase)
Mutase does
relocates a functional group within a molecule
Know what type of enzyme specific ones are??
????
What cofactor is needed for ethanol metabolism
NAD+ (turned into NADH)
limiting reagent in ethanol metabolism
NAD+
Kinetics of alcohol metabolism
zero-order kinetics
NADH/NAD+ ratio in alcohol metabolism
Increases in liver
What is the effect of the NADH/NAD+ ratio on pyruvate, oxaloacetate, and glyceraldehyde-3-phosphate
Lactate, malate and glycerol-3-phosphate
Fomepizole
Inhibits alcohol dehydrogenase (used to treat methanol or ethylene glycol poisoning)
Disulfiram
Inhibits acetaldehyde dehydrogenase (acetaldehyde accumulates, contributing to hangover sxs)
Elevated NADH/NAD+ prevents TCA production of NADH causing increased utilization of acetyl-CoA for ketogenesis (ketoacidosis) and lipogenesis (hepatosteatosis)
….
Kwashiorkor….
…..
Kwashiorkor
Protein malnutrition! Skin lesions, edema, liver malfunction (fatty change due to dec. apolipoprotein synthesis). Small child with swollen belly.
Kwashiorkor mnemonic
MEAL: Malnutrition (protein), Edema, Anemia, Liver (fatty)
Marasmus
Total calorie malnutrition resulting in tissue and muscle wasting, loss of SubQ fat, and variable edema
How much net ATP via malate-aspartate shuttle
- because NADH is used in cytosol and matrix so you don’t lose anything.
Net ATP via glycerol-3-phosphate shuttle
- because you end up with reduced FADH2, so you end up losing 2 ATP per glucose (2.5(NADH)-1.5(FADH2)=1 (the loss of energy from one pyruvate formed)
Malate-aspartate shuttle
Needed because NADH can’t cross the inner mitochondrial membrane. In cytosol OAA is converted to malate and this then enters matrix to produce a new NADH in the TCA cycle. Aspartate is the way OAA can move from matrix to cytosol.
Glycerol-3-phosphate shuttle
DHAP formed in glycolysis is reduced to glycerol-3-phosphate which is then oxidized by glycerol-3-phosphate dehydrogenase which gives its electrons to FADH2, hence the loss. It also is a way of regenerating NAD+ for glycolysis.
Glycolysis net ATP production
2 net
Arsenic effect
Causes glycolysis to produce 0 net ATP
What does CoA and lipoamide carry
Acyl groups
What does Biotin carry
COOH (carboxylic acid group)
What does THFs carry
1-carbon units
What does SAM carry
Methyl (CH3) groups
What does TPP carry
Aldehydes
What family of molecules in NAD+ and NADP+
Nicotinamides from vitamin B3 (Niacin)
What family is FAD+
Flavins (Riboflavin B2)
NAD+ for what general reactions
Catabolic (for energy production)
NADPH+ for what general reactions
Anabolic processes (steroid and fatty acid synthesis), Respiratory burst, Cytochrome P-450 systemGlutathione reductase
First step of glycogen synthesis in the liver?
Glucose to glucose-6-phosphate
Know all the differences between Hexokinase vs. Glucokinase…
Location, Km, Vmax, Induced by Insulin, Feedback-inhibited by glucose-6-P, gene mutation associated with maturity onset diabetes of the young (MODY)
What does it mean that hexokinase is feedback-inhibited by glucose6P
Excess glucose-6-P will stop hexokinase which makes sense in muscles where you only use the pathways to make energy. In liver, you’ll have excess glucose-6-P but you don’t want to slow it down so it does not feedback-inhibit.
What is MODY
Aut. dom. gene disrupting insulin production. (monogenic diabetes) Type I and Type II are multigenic
What does phosphofructosekinase-1 reaction do
Fructose-6-P to Fructose-1,6-bisphosphate
What reactions in glycolysis produce ATP?
1,3-BPG to 3-PG by phosphoglycerate kinase ANDPhosphoenolpyruvate to pyruvate by Pyruvate Kinase
Why does fructose-2,6-BP induce PFK-1?
Because when glucose is in high supply it is produced by PFK-2 and activates PFK-1
Why does alanine slow down pyruvate kinase?
alanine is made from pyruvate so if you have too much alanine, you probably have a lot of pyruvate, hence pyruvate kinase not needed.
Know regulation by F2,6BP
…..
Are Fructose bisphosphatase-1 and PFK-1 the same enzyme with different phosphorylations too?
No. They are not the same. PFK-1 reaction is unidirectional.
Where is pyruvate dehydrogenase complex and what does it do?
it is mitochondrial and links glycolysis to TCA cycle
When is PDH active?
In fed state
PDH has how many enzymes
3
Name the PDH cofactors
- Pyrophosphate (B1, thiamine; TPP)2. FAD (B2, riboflavin)3. NAD (B3, niacin)4. CoA (B5, pantothenate)5. Lipoic acid
What activates PDH
Exercise which also increases Ca2+, ADP, and NAD+/NADH ratio which all increase PDH
What is the basic reaction for PDF
pyruvate+NAD+ +CoA leads to acetyl-CoA+CO2+NADH
PDH is like what TCA cycle complex
alpha-ketoglutarate dehydrogenase complex (same cofactors, simlar substrate and action)
Arsenic does what to PDH
Inhibits lipoic acid
Arsenic presentation
Vomiting, rice-water stools, garlic breath
