Biochemistry Flashcards
DNA methylation at CpG islands results in
Repression of transcription
Amino acids necessary for purine synthesis
- Glycine
- Aspartate
- Glutamine
“GAG”
Drugs that disrupt pyrimidine synthesis
- LEFLUNOMIDE (inhibits dihydroorate reductase)
- METHOTREXATE, TRIMETHOPRIM, PYRIMETHANAMINE (inhibit dihydrofolate reducts which results in decreased dexoythymidine monophosphase [dTMP] in humans, bacteria, and protozoa, respectively)
- 5-FLUOROURACIL (forms 5-F-dUMP, which inhibits thymidylate synthase and decreases dTMP)
Drugs that disrupt purine synthesis
- 6-MERCAPTOPURINE, AZATHIOPRINE (inhibit de novo purine synthesis)
- MYCOPHENOLATE, RIBAVIRIN (inhibit inosine monophosphate dehydrogenase)
Drugs that disrupt purine and pyrimidine synthesis
- HYDROXYUREA (inhibits ribonucleotide reductase)
Reaction catalyzed by HGPRT
Hypoxanthine + PRPP → IMP
Guanine + PRPP → GMP
DNA polymerase III
- Prokaryotic only
- Elongates leading strand by adding deoxynucleotides to the 3’ end
- Elongates lagging strand until it reaches primer of preceding fragment
- 3’→ 5’ exonuclease activty ‘PROOFREADS’ each added nucleotide
DNA polymerase I
- Prokaryotic only
- Degrades RNA primer and replaces it with DNA
- Has the same functions as DNA polymerase III but it also excises RNA primer with 5’→3’ exonuclease
N-formylmethionine stimulates
Neutrophil chemotaxis
RNA polymerase I
Makes rRNA (most numerous RNA, “r”ampant)
RNA polymerase II
Make mRNA (largest RNA, “m”assive)
RNA polymerase III
Makes 5S rRNA, tRNA (smallest RNA, “t”iny)
Eukaryotic RNA polymerases
- No proofreading function but can initiate chains
- RNA polymerase II opens DNA at promoter site
Prokaryotic RNA polymerase
1 RNA polymerase (multisubunit complex) makes all 3 kinds of RNA
α-amanitin
- Found in Amanita phalloides (death cap mushrooms)
- Inhibit RNA polymerase II
- Causes severe hepatotoxicity if ingested
Rifampin
Inhibits RNA polymerase in prokaryotes
Actinomycin D
Inhibits RNA polymerase in both prokaryotes and eukaryotes
Where does mRNA quality control occur
Cytoplasmic processing bodies (P bodies), which contain exonucleases, decapping enzymes, and miRNAs. mRNAs may be stored in P bodies for future translation.
Where are miRNA genes located
In introns
CDKs
Constitutive and inactive
Cyclins
- Regulatory proteins that control cell cycle events
- Phase specific
- Activate CDKs
Cyclin-CDK complexes
- Phosphorylate other proteins to coordinate cell cycle progression
- Must be inactivated and inactivated at appropriate times for cell cycle to progress
Tumor suppressors
- p53 induces p21, which inhibits CDKs → hypophosphorylation (activation) of Rb
- Hypophosphorylation of Rb binds to and inactivates transcrption factor E2F → inhibition of G1-S progression
- Mutations in these genes result in unrestrained cell division (eg Li-Fraumeni)
Permanent cells
- Neurons, skeletal and cardiac muscle, RBCs
- Remain in G0 and regenerate from stem cells
Stable (quiescent) cells
- Hepatocytes, lymphocytes
- Enter G1 from G0 when stimulated
Labile cells
- Bone marrow, gut epithelium, skin, hair follicles, germ cells
- Never go to G0, divide rapidly with a short G1
- Most affected by chemotherapy
Nissl bodies
- Rough endoplasmic reticulum in NEURONS
- Synthesize peptide neurotransmitters for secretion
Golgi protein modifications
- Modifies N-oligosaccharides on aspargine (initially added onto protein in the RER)
- Adds O-oligosaccharides on serine and threonine
- Adds mannose-6-phosphate to proteins for trafficking to lysosomes
Enzyme defect in I-cell disease
N-acetylglucosaminyl-1-phosphotransferase
Signal recognition particle (SRP)
- Abundant, cytosolic ribonucleoprotein that traffics proteins from the ribosome to the RER
- Absent or dysfunctional SRP → proteins accumulate in the cytosol
COPI
- Golgi → golgi (retrograde)
- cis-Golgi → ER
COPII
ER → cis-Golgi (anterograde)
Clathrin
- trans-Golgi → lysosomes
- Plasma membrane → endosomes (receptor mediated endocytosis, eg LDL receptor activity)
Microfilaments
- Muscle contraction, cytokinesis
- Actin, microvilli
Intermediate filaments
- Maintain cell structure
- Vimentin, desmin, cytokeratin, lamins, glial fibrillary acid proteins (GFAP), neurofilaments
Microtubules
- Movement, cell division
- Cilia, flagella, mitotic spindle, axonal trafficking, centrioles
Vimentin stain
- Mesenchymal tissue (eg fibroblasts, endothelial cells, macrophages)
- Identifies mesenchymal tumors (eg sarcoma) but also many other tumors (eg endometrial carcinoma, renal cell carcinoma, and meningiomas)
Desmin stain
- Muscle
- Identifies muscle tumors (eg rhabdomyosarcoma)
Cytokeratin stain
- Epithelial cells
- Identifies epithelial cell tumors (eg squamous cell carcinoma)
GFAP stain
- Neuroglial cells (eg astrocytes, Schwann cells, oligodendrogia)
- Identifies astrocytoma and glioblastoma
Neurofilament stain
- Neurons
- Identifies neuronal tumors (eg neuroblastoma)
Drugs that act on microtubules
- Mebendazole (antihelminthic)
- Griseofulvin (antifungal)
- Colchicine (antigout)
- Vincristine/ Vinblastine (anticancer)
- Paclitaxel (anticancer)
“Microtubules Get Constructed Very Poorly”
Types of collagen
- TYPE I → most common, Bone, Skin, Tendon, dentin, fascia, cornea, late wound repair
- TYPE II → Cartilage (including hyaline), vitreous body, nucleus pulposus
- TYPE III → Reticulin - skin, BLOOD VESSELS, uterus, fetal tissue, granulation tissue
- TYPE IV → Basement membrane, basal lamina, lens
“Be So Totally Cool Read Books”
(bone, skin, tendon, cartilage, reticulin, basement membrane)
Problems with formation of triple helix of collagen is associated with what disease
Osteogenesis imperfecta
Problems with cross-linking of tropocollagen in the extracellular space is associated with which diseases
- Ehlers-Danlos syndrome
- Menkes disease
Describe the most common type of Ehlers-Danlos syndrome
Hypermobility type (joint instability)
Describe the classical type of Ehlers-Danlos syndrome
- Involves joint and skin symptoms
- Caused by a mutation in type V collagen
Describe the vascular type of Ehlers-Danlos syndrome
- Involves vascular and organ rupture
- Deficient type III collagen
Menkes disease
- X linked recessive connective tissue disease cause by impaired copper absorption and transport due to defective Menkes protein (ATP7A) [ATP7B is the gene implicated in Wilson’s disease]
- Leads to ↓ activity of lysyl oxidase (copper is a necessary cofactor)
- Results in brittle, kinky hair, growth retardation, and hypotonia
How is Marfan syndrome related to elastin
Marfan syndrome is caused by a defect in fibrillin, a glycoprotein that forms a sheath around elastin
What causes the wrinkles of aging
↓ collagen and elastin production
How do collagen and elastin differ
- Elastin is rich in NONhydroxylated proline, glycine and lysine residues
- Tropoelastin has fibrillin scaffolding
Southwestern blot
Identifies DNA-binding proteins (eg transcription factors) using labeled oligonucleotide probes
Cre-lox system
Gene expression modification whereby one can inducible manipulate genes at specific developmental points (eg to study a gene whose deletion causes embryonic death)
RNA interference
Gene expression modification whereby dsRNA is synthesized that is complementary to the mRNA sequence of interest. When transfected in human cells, dsRNA separates and promotes degradation of target mRNA, “knocking down” gene expression.
Pleiotropy
- One gene contributes to multiple phenotypic effects
- Example: untreated phenyketonuria (PKU) manifests with light skin, intellectual disability and musty body odor
Dominant negative mutation
- Exerts a dominant effect
- A heterozygote produces a nonfunctional altered protein that also prevents the normal gene product from functioning
- Example: mutation of a transcription factor in its allosteric binding site; nonfunctioning mutant can still bind DNA, preventing wild-type transcription factor from binding
Hypophosphatemic rickets
- X linked dominant
- Formerly known as vitamin D resistant rickets
- Inherited disorder resulting in ↑ phosphate wasting at proximal tubule
- Results in rickets-like presentation
Examples of X linked dominant disorders
- Hypophosphatemic rickets
- Rett syndrome
- Fragile X syndrome
- Alport syndrome
Mitochondrial myopathies
- Often present with myopathy, lactic acidosis, and CNS disease
- MELAS syndrome (mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes)
- Secondary to failure in OXPHOS
- Muscle biopsy often shows “ragged red fibers”
Cystic fibrosis pathophysiology
- CFTR encodes an ATP-gated Cl- channel that secretes Cl- in lungs and GI tract and reabsorbs Cl- in sweat glands
- MOST COMMON MUTATION: misfolded protein → protein retained in RER and not transported to cell membranes, causing ↓ Cl- (and H2O) secretion
- ↑ intracellular Cl- results in compensatory ↑ Na+ reabsorption via epithelial Na+ channels → ↑ H2O reabsorption → abnormally thick mucus secreted into lungs and GI tract
- ↑ Na+ reabsorption also causes more negative transepithelial potential difference
Cystic fibrosis diagnosis
- ↑ Cl- concentration in sweat (>60 mEq/L)
- Can present contraction alkalosis and hypokalemia (ECF effects analogous to a patient taking a loop diuretic) because of ECF H2O/Na+ losses and concomitant renal K+/H+ wasting
- ↑ immunoreactive trypsinogen (newborn screening)
What is used as an anti-inflammatory agent in cystic fibrosis
Azithromycin
X-linked recessive disorders
- Ornithine transcarbamylase deficiency
- Fabry disease
- Wiskott-Aldrich syndrome
- Ocular albinism
- G6PD deficiency
- Hunter syndrome
- Bruton agammaglobulinemia
- Hemophilia A and B
- Lesch-Nyhan syndrome
- Duchenne (and Becker) muscular dystrophy
“Oblivious Females Will Often Give Her Boys Her x-Linked Disorders”
Causes of muscular dystrophies
- Duchenne → frameshift, nonsense mutation, deletion
- Becker → non-frameshift insertion or deletion
- Myotonic type 1 → CTG expansion of DMPK gene (myotonin protein kinase)
Most common cause of death from Duchenne muscular dystrophy
Dilated cardiomyopathy
Function of dystrophin
Helps anchor skeletal muscle fibers, primarily in skeletal and cardiac muscle
Lab findings for Duchenne muscular dystrophy
- ↑ CK and aldolase
- Western blot and muscle biopsy confirm diagnosis
Cause of Fragile X syndrome
- X linked dominant inheritance
- Trinucleotide repeat in FMR1 gene (CGG) → METHYLATION → ↓ expression
Heart condition found in Fragile X syndrome
Mitral valve prolapse
Laboratory screens for trisomies
DOWN SYNDROME 1st TRIMESTER:
- ↓ serum PAPP-A
- ↑ free β-hCG
DOWN SYNDROME 2nd TRIMESTER:
- ↓ α-fetoprotein
- ↑ β-hCG
- ↓ estriol
- ↑ inhibin A
EDWARDS SYNDROME 1st TRIMESTER:
- ↓ PAPP-A
- ↓ β-hCG
- ↓ α-fetoprotein
- ↓ estriol
- ↓ or normal inhibin A
PATAU SYNDROME 1st TRIMESTER:
- ↓ β-hCG
- ↓ PAPP-A
3 ways to convert ethanol → acetaldehyde
- CYTOSOL via alcohol dehydrogenase, generates NADH
- MICROSOME via CYP2E1, consumes NADPH and generates ROS
- PEROXISOME via catalase, generates H2O from H2O2
Location of acetaldehyde dehydrogenase
Mitochondria
Limiting reagent of alcohol metabolism
NAD+
Ethanol metabolism ↑ NADH/NAD+ ratio in liver causes
- Pyruvate → lactate (lactic acidosis)
- Oxaloacetate → malate (prevent gluconeogenesis → fasting hypoglycemia)
- Dihydroxyacetone phosphate → glycerol-3-phosphate (combines with fatty acids to make triglycerides → hepatosteatosis)
- Disfavors TCA production of NADH
- ↑ utilization of acetyl-CoA for ketogenesis (→ ketoacidosis) and lipogenesis (→ hepatosteatosis)
Mitochondria is site for
- Fatty acid oxidation (β oxidation)
- Acetyl-CoA productino
- TCA cycle
- OXPHOS
- Ketogenesis
Cytoplasm is site for
- Glycolysis
- HMP shunt
- Synthesis of steroids (SER)
- Proteins (ribosomes, RER)
- Fatty acids
- Cholesterol
- Nucleiotides
Mitochondria and cytoplasm are both sites for
- Heme synthesis
- Urea cycle
- Gluconeogenesis
“HUGs take 2”
Kinase vs phosphorylase
Kinase catalyzes transfer of a phosphate group from a HIGH-ENERGY MOLECULE (usually ATP) to a substrate (eg phosphofructokinase)
Phosphorylase add inorganic phosphate onto substrate WITHOUT USING ATP (eg glycogen phosphorylase)
Carboxylase
Transfers CO2 groups with the help of BIOTIN
Mutase
Relocates a functional group within a molecule
de novo synthesis of pyrimidine base production requires
Aspartate
de novo synthesis of purine base production requires
- Apartate
- Glycine
- Glutamine
- THF
Peroxisome
- Membrane enclosed organelle involved in catabolism of very-long-chain fatty acids (through beta-oxidation), branched chain fatty acids, amino acid and ethanol
- Refsum disease, Adrenoleukodystrophy – inability to metabolize long chain FAs
Defects in the ubiquitin proteasome system have been implicated in some cases of
Parkinson disease
