USMLE (Fach) / Biochemistry - Molecular, Cellular, Techniques (Lektion)
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- Amino acids necessary for purine synthesis - Glycine - Aspartate - Glutamine
- Leflunomide Disrupt pyrimidine synthesis Inhibits dihydroorotate dehydrogenase.(Carbamoyl phosphate + Aspartate →| Orotic acid)
- Methotrexate (MTX), trimethoprim (TMP), pyrimethamine ... Disrupt pyrimidine synthesis Inhibit dihydrofolate reductase (↓ deoxythymidine monophosphate [dTMP]) in humans, bacteria, and protozoa, respectively
- 5-fluorouracil (5-FU) Disrupt pyrimidine synthesis - forms 5-F-dUMP, which inhibits thymidylate synthase (↓ dTMP)
- 6-mercaptopurine (6-MP) (and its prodrug azathioprine)Disrupt purine synthesis Inhibit de novo purine synthesisPRPP (phosphoribosyl pyrophosphate) →| IMP
- Mycophenolate and ribavirin Disrupt purine synthesis Inhibit iosine monophosphate dehydrogenase(IMP →| GMP)
- Hydroxyurea Disrupts purine and pyrimidine synthesis - inhibits ribonucleotide reductase
- Adenosine deaminase deficiency ADA is required for degradation of adenosine and desoxyadenosineConverts adenosine to inosine (which can be turned into hypoxanthine and used in the purine salvage pathway via HGPRT) - In ADA deficiency, ↑ ...
- Lesch-Nyhan syndrome Defective purine salvage due to absent HGPRT, which converts hypoxanthine to IMP and guanine to GMP. (Guanine, Hypoxanthine → Xanthine → Uric acid → Urine) - Results in excess uric acid production ...
- Probenecid Increasis uric acid secretion in the urine (Low-dose aspirin has the opposite effect --> decreases uric acid secretion --> promotes hyperuricemia)
- DNA polymerases DNA polymerase III: - Prokaryotes only- Elongates leading strand by adding deoxynucleotides to the 3' end (5' → 3' synthesis).- Elongates lagging strand until it reaches primer of preceding fragment.- ...
- DNA topoisomerases Create a single- or double-stranded break in the helix to add or remove supercoils. In eukaryotes: irinotecan/topotecan inhibit topoisomerase (TOP) I, etoposide/teniposide inhibit TOP II. In prokaryotes: ...
- Mutations in DNA Severity of damage: silent << missense < nonsense < frameshift. Transition = Purine to purine (eg, A to G) or pyrimidine to pyrimidine (eg, C to T).Transversion = Purine to pyrimidine (eg, A to T) or ...
- Nucleotide excision repair Single strand DNA repair - Specific endonucleases release the oligonucleotides containing damages bases.- DNA polymerase and ligase fill and reseal the gap.- Repairs bulky helix-distorting lesions, thymidine ...
- RNA polymerases Eukaryotes:RNA polymerase I makes rRNA (5.8S, 18S, 28S); present only in the nucleolus.RNA polymerase II makes mRNA, snRNA, hnRNA, miRNA.RNA polymerase III makes 5S rRNA, tRNA.- No proofreading function ...
- RNA processing (eukaryotes) Initial transcript is called heterogenous nuclear RNA (hnRNA). hnRNA is then modified and becomes mRNA. The following processes occur in the nucleus:- Capping of the 5' end (addition of the 7-methylguanosine ...
- Splicing of pre-mRNA 1. Primary transcript combines with small nuclear ribonucleoproteins (snRNPs) and other proteins to form spliceosome.2. Cleavage at 5' splice site; lariat-shaped (loop) intermediate is generated.3. Cleavage ...
- Protein synthesis Initiation:Eukaryotic initiation factors (eIFs) identify either the 5' cap or an internal ribosome entry site (IRES). IRES can be located at many places in an mRNA (most often 5' UTR). The eIFs then help ...
- Tumor suppressors p53 induces p21, which inhibits CDKs --> hypophosphorylation (activation) of Rb Hypophosphorylated Rb binds to and inactivates transcription factor E2F --> inhibition of G1-S progression. Mutations in ...
- I-cell disease Inclusion cell disease/mucolipidosis type II Inherited lysosomal storage disorder; defect in N-acetylglucosaminyl-1-phosphotransferase → failure of the Golgi to phosphorylate mannose residues (ie, ↓ ...
- Peroxisome Membrane-enclosed organelle involved in:- β-oxidation of very-long-chain fatty acids (VLCFA)- α-oxidation (strictly peroxisomal process)- Catabolism of branched-chain fatty acids, amino acids, and ...
- Vesicular trafficking proteins 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 ...
- Immunohistochemical stains for intermediate filaments ... Vimentin: Mesenchymal tissue (eg, fibroblasts, endothelial cells, macrophages)- Mesenchymal tumors (eg, sarcoma)- endometrial carcinoma- renal cell carcinoma- meningeoma Desmin: Muscle- Muscle tumors ...
- Drugs that act on microtubules - Mebendazole (antihelminthic) - Griseofulvin (antifungal) - Colchicine (antigout) - Vincristine/Vinblastine (anticancer) - Paclitaxel (anticancer)
- Kartagener syndrome (1° ciliary dyskinesia) Immotile cilia due to a dynein arm defect. - Autosomal recessive - Results in ↓ male and female fertility due to immotile sperm and dysfunctional fallopian tube cilia. - ↑ risk of ectopic pregnancy ...
- Sodium-potassium pump Na+-K+ ATPase is located in the plasma membrane with ATP site on cytosolic side. For each ATP consumed, 3Na+ go out of the cell (pump phosphorylated) and 2K+ come into the cell (pump dephosphorylated).Plasma ...
- Collagen Most abundant protein in the human body.Extensively modified by posttranslational modification.Organizes and strengthens extracellular matrix. Type I: Most common (90%) – bone (made by osteoblasts), ...
- Collagen synthesis and structure 1. Synthesis – translation of collagen α chains (preprocollagen) – usually Gly-X-Y (X and Y are proline or lysine). Glycine content best reflects collagen synthesis. 2. Hydroxylation – hydroxylation ...
- Osteogenesis imperfecta Genetic bone disorder (brittle bone disease) caused by a variety of gene defects (most commonly COL1A1 and COL1A2). - Most common form is autosomal dominant with ↓ production of otherwise normal type ...
- Ehlers-Danlos syndrome Faulty collagen synthesis causing hyperextensible skin, tendency to bleed (easy bruising), and hypermobile joints.- Multiple types.- Inheritance and severity vary.- Can be autosomal dominant or recessive. ...
- Menkes disease X-linked recessive connective tissue disease caused by impaired copper absorption and transport due to defective Menkes protein (ATP7A).- Leads to ↓ activity of lysyl oxidase (copper is a necessary ...
- Elastin Stretchy protein within skin, lungs, large arteries, elastic ligaments, vocal cords, ligamenta flava (connect vertebrae → relaxed and stretched conformations).- Rich in nonhydroxylated proline, glycine, ...
- Blotting procedures Southern blot: DNA is electrophoresed Northern blot: RNA is electrophoresed Western blot: protein is electrophoresed- eg, confirmatory test for HIV after positive ELISA Southwestern blot: identifies ...
- Zellweger syndrome Disorder of peroxisome biogenesis due to mutated PEX genes. - Autosomal recessive - Hypotonia- Seizures- Hepatomegaly- Craniofacial abnormalities (eg, widened sutures, large anterior fontanelle)- Early ...
- Refsum disease Peroxisome disorder. Disorder of α-oxidation → phytanic acid not metabolized to pristanic acid. - Autosomal recessive - Scaly skin- Ataxia- Cataracts/night blindness- Shortening of 4th toe- Epiphyseal ...
- Adrenoleukodystrophy Peroxisome disorder. Disorder of β-oxidation → VLCFA buildup in adrenal glands, white matter of brain, testes. - X-linked recessive - Progressive disease that can lead to adrenal gland crisis, coma, ...
- Cytoskeletal elements A network of protein fibers within the cytoplasm that supports cell structure, cell and organelle movement, and cell division. Microfilaments: Muscle contraction, cytokinesisEg, actin, microvilli Intermediate ...
- Telomerase Eukaryotes only. A reverse transcriptase (RNA-dependent DNA polymerase) that adds DNA (TTAGGG) to 3' ends of chromosomes to avoid loss of genetic material with every duplication. Often dysregulated in ...
- Nucleolus - Transcription of rRNA - Maturation and assembly of ribosomal subunits
- Chromatin structure DNA exists in the condensed, chromatin form to fit into the nucleus.DNA loops twice around a histone octamer to form a nucleosome. A nucleosome consists of 2x (H2A, H2B, H3, H4) H1 binds to the nucleosome ...
- Heterochromatin Condensed, appears darker on EM. Transcriptionally inactive, sterically inaccessible. ↑ methylation, ↓ acetylation. Barr bodies (inactive X chromosomes) may be visible on the periphery of nucleus. ...
- Euchromatin Less condensed, appears lighter on EM. Transcriptionally active, sterically inaccessible.
- DNA methylation Changes the expression of a DNA segment without changing the sequence. Involved with genetic imprinting, X-chromosome inactivation, repression of transposable elements, aging, and carcinogenesis. DNA ...
- Histone methylation/acetylation Histone methylation: Usually causes reversible transcriptional suppression, but can also cause activation depending on the location of methyl groups. Histone acetylation: Relaxes DNA coiling, allowing ...
- Nucleotides Nucleoside = base + (deoxy)riboseNucleotide = base + (deoxy)ribose + phosphate; linked by 3'-5' phosphodiester bond. 5' end of incoming nucleotide bears the triphosphate (energy source for the bond).Triphosphate ...
- Origin of replication Particular consensus sequence of base pairs in genome where DNA replications begins. - Single in prokaryotes- Multiple in eukaryotes AT-rich sequences (such as TATA box regions) are found in promotors ...
- Primase Makes an RNA primer on which DNA polymerase III can initiate replication.
- DNA ligase Catalyzes the formation of a phosphodiester bond within a strand of double-stranded DNA. Joins Okazaki fragments.
- Base excision repair Single strand DNA repair - Important repair of spontaneous/toxic deamination. - Base-specific glycosylase removes altered base and creates AP (apurinic/apyrimidinic) site.- One or more nucleotides are ...
- Mismatch repair Single strand DNA repair - Fixes DNA copy errors - Newly synthesized strand is recognized, mismatched nucleotides are removed, and the gap is filled and resealed.- Occurs predominantly in S phase of ...