Biochemistry - First Aid Flashcards
Charges/Composition of DNA and histones
DNA: negatively charged; nucleic acids linked by phosphodiester bonds
Histones: positively charged; rich in amino acids lysine and arginine ;
8 subunits make up a nucleosome core (two each of 4 histone types - H2A, H2B, H3, H4)
Note that DNA loops around histones 2x.
Both DNA and histone synthesis occurs during S phase
DNA methylation
Represses transcription when methylated at CpG islands.
During replication, the template stand is IDed by the mismatch repair enzymes via methylation of A and C.
Nucleotide excision repair defect
xeroderma pigmentosum
predisposes to SCC, BCC, and melanoma
*Nucleotide excision repairs prymidine dimers during G1 phase because of UV light exposure; via specific endonucleases, DNA poly, and ligase;
Mismatch repair defect
HNPCC (hereditary nonpolyposis colorectal cancer (Lynch syndrome)
*mismatch repair fixes new strands during G2 phase
Base excision repair
Important in repair of spontaneous/toxic deamination throughout the cell cycle.
Via: base specific glycosylases remove altered base, endonuclease cleaves 5’ and lyase cleaves 3’, DNA poly, and ligase.
alpha-amanitin
found in amanita phalloides (death cap mushrooms) - inhibits RNA poly II (which makes mRNA, snRNA, microRNA)
RNA polymerase and rifampin
Prokaryotes only have 1 type of RNA poly that carries out the cell functions.
Note that rifampin inhibits it in prokaryotes
RNA polymerase and Actinomycin D
Inhibits RNA poly in both prokaryotes and eukaryotes
Splicing of pre-mRNA
- Primary transcript (heterogenous RNA) combines with snRNPs and other proteins to make spliceosome.
- lariat shaped (loop) intermediate is generated
- lariat released to precisely remove intervening introns and join 2 exons
Ab to spliceosome snRNPs (anti-smith ab) are highly specific for SLE.
Anti-U1 RNP ab are highly specific for mixed connective tissue disease.
tRNA structure
Acceptor stem: 3’ end CCA to carry amino acids via covalent bond
T arm: contains thymine, pseudouracil, cytosine sequences necessary for tRNA ribosome binding
D arm: contains dihydrouracil residues necessary for tRNA recognition by correct amino acyl tRNA synthetase
anticodon loop opposite the 3’ acceptor stem
Hydroxyurea
inhibits ribonucleotide reductase in pyrimidine production;
leads to inhibtoin of UDP to dUDP
Posttranslational modifications
Trimming: Removal of N or C terminal propeptides from zymogen to generate mature protein (ex. trypsinogen to tryspsin
Covalent alterations: phosphorylation, glycosylation, hydroxylation, methylation, acetylation, ubiquitination
Bonds in the primary structure of proteins
Peptide bonds
Typically the genetic code is considered universal (i.e., conserved throughout evolution). What is one noteworthy exception to this rule?
Human mitochondrial DNA, which is not conserved
Frameshift mutation
Deletion or insertion of number of nucleotides not divisible by 3 which leads to misreading of all nucleotides downstream, usually causing truncated, nonfunctional protein.
Ex. duchenne muscular dystrophy
DNA Polymerase 3
Prokaryote only
Elongates leading DNA strand adding to 3’,
elongates lagging DNA strand until it reaches primer of preceding fragment
3’ to 5’ exonuclease activity “proofreads” each added nucleotide
DNA polymerase1
Prokaryote only
Has same functions as DNA poly 3, but also excises RNA primer since it has 5’ to 3’ exonuclease activity, and replaces it with DNA
lac operon
Glucose normally surpresses adenylate cyclase.
If glucose absent, then increased AC, increased cAMP, increased CAP activation, and increased transcription (CAP acts as an activator for RNA poly)
High lactose unbinds the repressor (lactose acts as an inducer), so there is increased transcription.
Nonhomologous end joining
Brings together 2 ends of DNA fragments to repair ds breaks. No requirement for homology. Some DNA may be lost.
Mutated in ataxia telangiectasia and fanconi anemia
RNA polymerase 1
**Note the nucleolus is the primary site of ribosomal RNA transcription.
Also the nucleolus is involved in maturation of ribosomal subunits.
Ribosomal protein components are made in cytoplasm and then go to nucleolus where they combine with the rRNA to make the 40s and 60s . Then they go back to cytoplasm.
Generally as cells grow mature, they require less ribosomes and this process slows. But malignant cells with high metabolic activity use this process and have large numbers of active rRNA genes and prominent mucleoli.
ribosomal RNA (18s, 5.8s, 28S)
RNA polymerase 2
mRNA
snRNA
microRNA
RNA polymerase 3
tRNA
5S rRNA
P bodies
Where mRNA quality control occurs in the cytoplasm.
P bodies contain exonucleases, decapping enzymes, and microRNAs
mRNAs may be stored in P bodies for future translation
Rough ER function
The synthesis of secretory (exported) proteins and the addition of N-linked oligosaccharides to proteins
Goblet cells and plasma cells are very rich in RER!!
Nissl bodies
synthesis of peptide NTs for secretion
Free ribosome function
Unattached to any membrane; site of synthesis of cytosolic and organellar proteins
Smooth ER
Steroid synthesis; detoxification of drugs and poisons
adrenal cortex and hepatocytes are rich in SER!
Golgi
Distribution center for proteins and lipids from ER to vesicles and plasma membrane.
Modifies N oligosaccharides on asparagine.
Adds O oligosaccharides on serine and threonine.
Adds mannose 6P to proteins for lysosomal trafficking
Endosomes
sorting centers for material from outside the cell or from the golgi, sending it to lysosomes for destruction or back to the membrane / golgi for further use.
Signal recognition particles (SRPs)
abundant, cytosolic ribonucleoproteins that traffic proteins from ribosome to RER. Absent or dysfunctional SRP means that proteins accumulate in the cytosol!!
Vesicular trafficking proteins
COPI: golgi to golgi retrograde transport; cis golgi to ER
COPII: ER to cis golgi (anterograde)
Clathrin: trans-golgi to lysosomes; plasma membrane to endosomes
Microtubules
Movement and cell division; microtubules
cilia, flagella, mitotic spindles, centrioles, and axonal trafficking (ex. dynein and kinesin)
Intermediate filaments
maintain cell structure.
vimentin, desmin, cytokeratin, lamins, glial fibrillary acid proteins (GFAP), neurofilaments
Microfilaments
Muscle contraction, cytokinesis
Actin
Vimentin stains identify which type of cells?
Connective tissue
Desmin stains identify which type of cells?
Muscle
Cytokeratin stains identify which type of cells?
Epithelial cells
GFAP stains identify which type of cells?
Neuroglia
Neurofilaments stains identify which type of cells?
Neurons
Kartagener syndrome
Primary ciliary dyskinesia
immotile cilia due to dynein arm defect.
Results in male and female infertility due to immotile sperm and dysfunctional fallopian tube cilia; also increased risk ectopic pregnancy.
Can cause bronchiectasis, recurrent sinusitis, and situs inversus
Types of Collagen and location
Type 1: Bones, skin, tendons, dentin, fascia, cornea, mature scar
Type 2: cartilage (vitreous body, nucleus pulposus, hyaline cartilage, and articular surface of joints)
Type 3: reticulum (vessels, granulation tissue, keloid, etc)
Type 4: basement membrane, basal lamina, lens
Collagen synthesis
- Synthesis (RER) : Precollagen with peptides of Gly-X-Y
- Hydroxylation (RER): of proline and lysine (requires Vit C!! deficiency vitamin c = scurvy.)
- Glycosylation (RER): of pro-alpha-chain hydroxylysine residues and formation of procollagen via hydrogen and disulfide bonds. ie formation of triple helix. If problems with this, then osteogenesis imperfecta can result.
- Exocytosis: procollagen to extracellular space
- Proteolytic processing: cleave disulfide residues making insolule tropocollagen
- cross linking : covalent lysine-hydroxylysine cross linking by copper containing lysyl oxidase to make collagen fibrils. Problems with cross linking = Ehler Danlos sydrome, Menkes disease etc
Elastin
Stretchy protein within skin, lungs, large arteries, elastic ligaments, vocal cords, ligamenta flava.
Rich in nonhydroxylated proline, glycine, and lysince residues.
Tropoelastin w/fibrillin scaffolding.
Cross linking takes place extracellularly and gives elastin its elastic properties.
Broken down by elastase, which is normally inhibited by alpha1 antitrypsin
I-cell disease results in ____ (increased/decreased) phosphorylation of mannose residues on glycoproteins. What enzyme defect contributes
Decreased; defect in N-acetylglucosaminyl-1-phosphotransferase
It’s an inherited lysosomal storage d/o. Enzyme deficiency leads to proteins being secreted extracellularly since they can’t be sent to lysosomes for lack of golgi to phosphorylate mannose residues
Features: coarse facial features, clouded corneas, restricted joint movement, and high plasma levels of lysosomal enzymes. Often fatal in childhood
A 13-year-old boy presents with hearing loss, hematuria, and end-stage kidney disease. What type of collagen is most likely defective?
Type IV—disease is Alport syndrome
A boy exhibits hyperphagia, obesity, intellectual disability, hypogonadism, and hypotonia from birth. How is this condition inherited?
Prader-Willi is due to deletion or mutation of Paternal copies of genes on chromosome 15—25% of cases from maternal uniparental disomy
McCune Albright syndrome
Due to mutation affecting G protein signaling.
Presents with unilateral cafe-au-lait spots, polyostotic fibrous dysplasia, precocious puberty, multiple endocrine abnormalities.
Letal if mutation occurs before fertilization (affecting all somatic cells); Survivable in pts with mosaicism.
vitamin D̫ resistant rickets / Hypophosphatemic rickets
X-linked dominant disorder; inherited from the father, as no sons affected.
Ex. A girl has proximal tubule phosphate wasting. All of her sisters, but no brothers, have this issue.
What findings in the prenatal quad screen indicate possible Down syndrome?
Decreased α-fetoprotein and estriol, increased β-human chorionic gonadotropin, and inhibin A
Hereditary hemorrhagic telangiectasia
Osler-Weber-Tendu syndrome.
Autosomal Dominant
Inherited d/o of blood vessels.
Findings include: branching skin lesions (telangiactasias), recurrent epistaxis, skin discoloration, AVMs, GI bleeding, hematuria.
X linked recessive Disorders
“Be Wise, Fool’s GOLD Heeds silly HOpe”
Bruton (X linked) agammaglobulinemia, Wiskott Aldrich sydrome, Fabry’s disease, G6PD deficiency, OTC deficiency, Lesch-Nyhan syndrome (HGPRT), Duchenne’s (and becker’s) MD, Hunter’s syndrome, Hemophilia A and B, Ocular Albinism
Trinucleotide Repeat Disorders
Huntingtons (Auto dom, CAG) Fragile X (X linked, CGG) Myotonic type 1 (Auto dom, CTG) Friedreich Ataxia (GAA)
Robertsonian translocation
Acrocentric chr. 13,14,15,21,22
What chromosome is implicated in Wilson disease
Chromosome 13
What chromosome is implicated in Wilms tumor
Chromosome 11
What chromosome is implicated in Prader Willi and Angelman syndromes?
Chromosome 15
What chromosome is implicated in Williams syndrome?
Chromosome 7
same as with CF
What chromosome is implicated in VHL/RCC
Chromosome 3
Fat soluble vitamins
ADEK
Water soluble vitamins
B1, thiamine B2, riboflavin B3, niacin B5, pantothenic acid B6, pyridoxine B7, biotin B9, folate B12, cobalamin C, ascorbic acid
B complex defieciencies
Generally result in dermatitis, glossitis, diarrhea
Note that B12 (years) and B9 (months) can be stored for a long time in the liver
Antioxidant Vitamins
A, C, E
BeriBeri
B1 deficiency
Dry beriberi: polyneuritis, symmetrical muscle wasting
Wet beriberi: high output cardiac failure (dilated cardiomyopathy), edema
Vitamin B2 or riboflavin deficiency
Important for FAD and FMN, used as cofactors in redox reactions.
Cheilosis (inflammation of lips, scaling and fissures at corners of mouth).
Corneal vascularization
A man presents with dementia, diarrhea, and skin darkening in sun-exposed areas. What characteristic cervical-area finding might he have?
This is B3 (niacin) deficiency, which may present with a C3/C4 dermatome circumferential “broad collar” rash (Casal necklace)
Niacin is derived from tryptophan and synthesis requires vitamins b2 and b6
Niacin can be used to treat dylipidemia since it raises HDL and lower VLDL
Pantothenate (vitamin B5) deficiency
Adrenal insufficiency, hair loss, dermatitis, and diarrhea
Enzymes affected: coenzyme A and fatty acid synthase
Vitamin B6 (pyridoxine) deficiency
Note isoniazid and contraceptives can induce deficiency.
Convulsions, hyperirritability, peripheral neuropathy, sideroblastic anemia.
Biotin (B7) is a cofactor for which enzymes
Carboxylation enzymes.
Biotin and pyruvate carboxylase catalyze what reaction? Conversion of pyruvate to oxaloacetate
Biotin and acetyl-CoA carboxylase? acetyl-CoA to malonyl-CoA
Biotin and propionyl-CoA carboxylase? propionyl-CoA to methylmalonyl-CoA
Where are Vitamins A and B9 found?
Vitamin A: liver and leafy vegetables
Folate: Leafy green vegetables
Folate (B9) deficiency
mc vitamin deficiency in US - seen with alcoholism and pregnancy
*see increased homocysteine levels
Folate is required for THF synthesis. THF is coenzyme of 1-carbon transfer/methylation reactions, needed for nitrogenous base synthesis in RNA/DNA
Wernicke-Korsakoff syndrome
Confusion, ophthalmoplegia, ataxia = classic triad
Also confabulation, personality change, memory loss.
Due to medial dorsal nucleus of thalamus, mammillary bodies.
Commonly seen as Vitamin B1/thiamine deficiency in alcoholics
Vitamin B12/ cobalamin deficiency
Found in animal products.
Macrocytic, megaloblastic anemia; subacute combined degeneration, paresthesias, optic neuropathy
*see increased homocysteine and methylmalonic acid levels
Vitamin C (ascorbic acid) deficiency
Scurvy, due to decreased hydroxylation of collagen. A patient presents with swollen gums, bruising, anemia, poor wound healing, hemarthrosis, recurrent infections, and “corkscrew hair.
Also necessary for DA ßhydroxylase (DA to NE)
Glucose infusion and B1 deficiency
Worsened by glucose infusion because whatever thiamine was left in the system gets depleted.
Vitamin D (names)
D2: ergocalciferol
D3: cholecalciferol
25 OH D3: storage form
1,25 (OH)2 D3: calcitriol
Vitamin E (names)
Tocopherol/tocotrienol
- Note that vitamin E can enhance the anticoagulant effects of warfarin
- Note that in deficiency neuro presentation may mimic B12 deficiecy ( with posterior column and spinocerebellar tract demyelination), but w/o megaloblastic anemia, hypersegmented PMNs, or increased serum methylmalonic acid levels
Neonatal hemorrhage
Most likely due to Vitamin K (phytomenadione, phylloquinone, phytonadione) deficiency - esp if neonates not given K injection at birth. Neonates have sterile intestine initially and are unable to synthesis vitamin K.
Note there is increased PT and aPTT, but nl bleeding time in neonates.
Kwashiorkor
MEAL: Malnutrition (protein) Edema Anemia Liver (fatty)
Marasmus
Total calorie malnutrition resulting in tissue and muscle wasting, loss of subcutaneous fat, and variable edema
*Marasmus results in muscle wasting
Hartnup disease and pellagra
Impaired absorption of tryptophan, which is used to synthesize niacin (needs B2 and B6 to synthesize)
Where is folate absorbed?
Jejunum
Malignant carcinoid syndrome and pellagra
Through increased metabolism of tryptophan, which is used to synthesize niacin
Which 2 vitamins does breast milk not provide?
Vitamin K
Vitamin D
