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First Aid Biochemistry > Biochem > Flashcards

Biochem Flashcards

1
Q

Walk through the pyrimidine and purine synthesis pathway in your head explaining the different points important for pathology.

A
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2
Q

Leisch Nyhan Syndrome is a deciciency in this enzyme which also acts as a mneumonic for the disease?

A

H - Hyperuricemia

G - Gout

P - pissed off (self mutilation, aggression)

R - retardation (intellectual disability)

T - DysTonia

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3
Q

What is a finding you will see in the diaper of a patient with Lesch Nyhan Sydrome?

A

Orange sand - sodium urate crystals

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4
Q

What are possible treatments for Lesch Nyhan Syndrome?

1st line vs. 2nd line?

A

1st - Allopurinol - Xanthine oxidase inhibitor

2nd - febuxostat - xanthine oxidase inhibitor

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5
Q

What is the sequence that marks off a Origin of replication or maybe a promoter region?

A

TATA

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6
Q

Telomerase functions to add a 6 nucleotide repeat to the end of these structures

A

TTAGGG to telomeres

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7
Q

Walk through purine salvage deficiencies in your head and the pathway!

A

Lesch Nyhan

ADA

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8
Q

Explain Lac Operon (E. Coli) – Genetic repsonse to environmental change

A
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9
Q

Nucleotide Excision Repair is defective in what dz?

A

Xeroderma Pigmentosum

Risk factor for melanoma.

Chacterized by dry skin, extreme light sensitivity, skin cancer

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10
Q

Mismatch repair (MMR) is defective in what dz?

A

Lynch Syndrome A.K.A.

HNPCC - hereditary nonpolyposis coloractal cancer

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11
Q

Nonhomologous end joining defective in what dz?

A

Ataxia Telangiectasia

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12
Q

Homologous Recombination is defective in what two dz?

A

breast/ovarian cancers with BRCA1

Fanconi anemia - Inhereited Aplastic anemia

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13
Q

Processing of hnRNA to mRNA involves three steps?

A
  1. Capping of 5’ methyl end (7 methylguanosine cap)
  2. Polyadenylation of 3’ end ( 200 base pairs )
  3. Splicing out of introns
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14
Q

Polymerase 1-3 in eukarytoes are responsible for the production of what? (Specifiy 1, 2, and 3)

A
  1. rRNA
  2. mRNA
  3. tRNA

It is in order dont miss this

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15
Q

Amanita phalloides is the deathcap mushroom and contains this toxin that inhibits this enzyme.

A

Toxin - alpha amanitin

Inhibits RNA polymerase 2

Severe hepatotoxicity

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16
Q

Splicing of pre-mRNA

A
  1. snRNPs combine with primary transcripts and other proteins to form spliceosome
  2. Cleavage of 5’ splice site -> Lariat-shaped loop (intermediate) is generated
  3. Cleavage of 3’ splice site -> Lariat released with introns and exons are joined.
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17
Q

What is a disease that has alteration in snRNPs ?

A

Spinal Muscular Atrophy (SMA)

decreased SMN -> congenital degeneration of anterior horns of spinal cord -> symmetric weakness

Floppy baby syndrome -> not related to honey

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18
Q

What are the functions of the following on tRNA?

  1. D-arm
  2. T-arm
  3. Anticodon
A
  1. Detected by aminoacyl tRNA synthetase
  2. tethers to ribosome
  3. pairs to correct sequence on mRNA
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19
Q

What is the function of Aminoacyl tRNA synthetase?

A

Correctly pairs and charges amino acid to tRNA if incorrect it is responsible for hydrolyzing the amino acid off.

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20
Q

What are the ribosomal subunits for Eukarytoes?

What are the ribosomal subunits for prokaryotes?

A

E - Even

40 and 60 - 80s

P - Prime

30 and 50 - 70s

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21
Q

Where does the initiator methionine bind for the start of translation of mRNA?

A

P site

all subsequent tRNA will load into the A site

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22
Q

Explain how the different amino acids move through the A site, P site, and E site?

A

A - load incoming tRNA

P - growing polypeptide chain

E - tRNA unbound to amino acid exits

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23
Q

Li-Fraumeni syndrome is a good example of a loss of this type of gene?

What are the characteristics of the dz?

A

Tp53 - Tumor suppressor gene

SBLA

S - Sarcoma

B - Breast

L - Leukemia

A - Adrenal glands

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24
Q

Growth factors (PDGF, TGF, etc..) bind to this type of receptor and transition the cells from which two phases?

A

Tyrosine kinase receptors

G1 –> S phase

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25
Q

What are the three general types of cells in the human body?

What phase do they operate in?

A
  1. Permanent (G0) regenerate from stem cells
  2. Stable (quiescent) (enter G1 when stimulated from G0)
  3. Labile - (Never go to G0 always in G1 divide rapidly) most susceptible to chemo
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26
Q

What type of proteins are sythesized on the RER?

A

secretory (exported) proteins and N-linked oligosaccharide addition to lysosomal and other proteins.

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27
Q

Smooth endoplasmic reticulum is responsible for what?

What special enzyme is located here?

A
  1. Synthesis of steroid hormones
  2. detoxification of drugs and poisons (liver)
  3. Glucose-6-phosphate
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28
Q

What is I-Cell disease?

A

Lysosomal storage disorder

defect in

N-acetylglucosaminyl-1-phosphotransferase

Golgi fails to phopshorylate Mannose binding lectine leading to decreased mannose-6-phosphate This further results in proteins being secreted rather than delivered to the lysosome

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29
Q

What are symtpoms of I-cell disease and when is it fatal?

A

coarse facial hair

gingival hyperplasia

clouded corneas

restricted joint movements

claw hand deformities

kyphoscoliosis

High plasma lysosomal enzymes

fatal during childhood

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30
Q

What is the function of Signal recognition peptides (SRP) what happens if they are defective?

A

transports proteins from cytosol to RER if absent buildup of protein in cytosol

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31
Q

Vesicular Trafficking Functions of

  1. COPI
  2. COPII
  3. Clathrin
A
  1. Golgi - Cis golgi - ER (retrograde)
  2. ER -> Golgi (anterograde)
  3. Trans golgi -> lysosome

Plasma membrane -> endosome

Note: Clathrin is responsible for endocytosis (ex. LDL receptor activity)

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32
Q

What is Zellweger syndrome?

A

AR dz of peroxisome biogenesis due to mutate PEX genes.

Causes: Hypotonia, seizures, hepatomegaly, early death

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33
Q

What is Refsum disease? (peroxisome)

A

AR dz of alpha-oxidation in peroxisome

phytanic acid not metabolized to pristanic acid

Scaly skin, ataxia, cataracts/night blindness, shortening of 4th toe, epiphyseal syplasia.

Tx: diet, plasmaphoresis

34
Q

What is Adrenoleukodystrophy?

inheritance?

gene?

A

X-linked disorder of beta-oxidation due to a mutation in the ABCD1 gene -> VLCFA buildup in adrenal glands, white (leuko) matter of brain, testes. Progressive disease that can lead to adrenal gland crisis, coma, and death.

35
Q

Microfilaments

  • function
  • examples
A

muscle contraction, cytokinesis

Actin, microvilli

36
Q

Intermediate filaments

  • function
  • examples
A

maintain cell structure

vimentin, desmine, cytokeratin, lamins, glial fibrillary acidic protein GFAP, neurofilaments

37
Q

Microtubules

  • function
  • examples
A

movement, cell division

cilia, flagella, mitotic spindles, axonal trafficking, centrioles

38
Q

Two motor proteins that move on microtubules and direction.

A

Dynein - retrograde + -> -

Kinesin - Anterograde - -> +

39
Q

What are four microorganisms that Dynein to get to neuronal cell body?

A

C. Tetani

HSV, Polio virus, Rabies lyssavirus

40
Q

What are drugs that act on Microtubules?

“Microtubules Get Constructed Very Poorly”

A

Mebendazole (antihelminthic)

Griseofulvin (antifungal)

Colchicine (antigout)

Vincristine/Vinblastine (anticancer)

Paclitaxel (anticancer)

41
Q

Exlain the relationship of the - and + end of the microtubules?

A

Negative end points toward Nucleus

Positive end points toward Periphery

42
Q

What structure coordinates ciliary movement?

A

Gap Junctions

43
Q

What is Kartagener Syndrome?

A
  • immotile cilia due to dynein arm defect
  • Infertility (male sperm dont move) female fallopian tube cilia dysfunction (increased ectopic risk)
  • Situs inversus
  • recurrent sinus/pulmonary infections
44
Q

What is a laboratory test for Kartagener Syndrome?

A

Decreased Nasal nitric oxide

45
Q
  1. MOA of Ouabain
  2. MOA Digoxin and Digitoxin
A
  1. inhibits K+ entry with Na/K ATPase by binding to the K+ site.
  2. Directly inhibits Na/K ATPase leads to indirect inhibition of Na/Ca exchanger whcih increases cytosolic Ca+ and increases inotropy on cardiac myocytes
46
Q

Type 1 collagen

  • found where
  • Dz?
A

bone, skin, tendons

decreased in osteogenesis imperfecta type 1

47
Q

Type 2 collagen

  • found where
A

Cartilage

48
Q

Type 3 collagen

  • found where
  • dz?
A

Vessels

Vascular form of Ehlers-Danlos

49
Q

Type 4 collagen

  • found where
  • dz?
A

Basement membrane (4 - floor)

Alport syndrome

Goodpasture - Abs target collagen

50
Q

Collagen and wound repair late vs early?

A

Type 3 in early wound repair that is replaced by Type 1 collagen to thicken and strenghten scar in wound healing.

51
Q

Briefly explain Collagen synthesis and formation

A

synthesis - Gly-X-Y (GLY most abundant) of procollagen

Hydroxylation - proline lysine residues (requires Vit. C) without this leads to scurvy

Glycosylation - of hydroxylysine residues (OIM) and formation of procollagen (triple helix 3 alpha)

Exocytosis

Proteolytic processing - Cleave terminals

Cross Linking - lysine hydroxylysine linkages by copper containing lysyl oxidase to make collagen fibrils.

52
Q

What is Menkes Dz?

  1. inheritance?
  2. Gene?
  3. Copper levels?
  4. Enzyme effected?
  5. Symptoms
A
  1. X-linked
  2. ATP7A - (contrast this with ATP7B in wilsons)
  3. Low (wilsons has high)
  4. Lysyl Oxidase activity decreases
  5. kinky hair, growth retardation, hypotonia, cerebral aneurysm
53
Q

Osteogenesis Imperfecta

  1. Collagen defect?
  2. Gene?
  3. BITE mneumonic
A
  1. No defect just decreased normal type 1 collagen
  2. COL1a1 COL1a2
  3. Bone fractures, blue sclera (eye = I), teeth, ear (hearing loss) abnormal ossicles
54
Q

Ehlers Danlos Syndrome

  1. Common collagen defect type
  2. Uncommon collagen defect type
A
  1. Type 5 collagen (COL5A1, COL5A2) Joints and skin hypermobile
  2. Type 3 Collagen (COL3A1) Vascular type
    - fragile muscle, vessels (aorta), and organs prone to rupture (gravid uterus)
55
Q

Marfan Syndrome

  1. Inheritance
  2. Gene, product, chromosome
  3. Findings
A
  1. AD
  2. FBN1, Fibrillin, 15
  3. Tall, long extremities, pectus carinatum (more specific) or pectus excavatum, cystic medial necrosis of aorta, aortic root aneurysm, rupture, dissection. Subluxation of lens upward and temporally
56
Q

Step of PCR

A
  1. Denature - 95
  2. Annealing - 55 DNA primers, TAQ polymerase, dNTPs
  3. Elongation - 72 - DNA polymerase attaches dNTPs
57
Q

Crispr/Cas9

1 & 2 steps to break

3 & 4 two repair pathways

A
  1. gRNA (guideRNA) - for a specific target DNA seqeunce
  2. Cas9 - endonuclease single or double stranded break at target site
  3. NHEJ imperfectly repairs, knock out
  4. Homology directed repair w/ donor sequence, knock in
58
Q

Flow Cytometry

  • How is it done?
A
  1. Cells are tagged with antibodies against a specific surface marker
  2. They are then ran through one by one and a lasor detects labeled cells
59
Q

What are some dz we might use flow cytometry for?

A

PNH, leukemia, immunodeficiencies

60
Q
  1. What is microRNA (miRNA)
  2. What is Small interfering RNA (siRNA)
A
  1. naturally produced by cells hairpin that blocks RNA translation leading to quicker degredation.
  2. usually derived from exogenous dsRNA source like virus. Once inside cell highly specific mRNA trageting. Can be used for knock down experiments.
61
Q
  1. What is Codominance?
  2. What is Variable Expressivity?
A
  1. Both alleles contribute equally - HLA, alpha1antitrypsin, A, B, AB blood types
  2. same genotype variable phenotype - NF1
62
Q

Incomplete Penetrance

  • equation
A

Not all individuals with a mutant genotype show the mutant phenotype.

% penetrance x probability of inheriting genotype = risk of expressing phenotype.

BRCA1 - do not always result with breast/ovarian cancer

63
Q

Pleiotropy

A

one gene contributes to multiple phenotypic effects

PKU - light skin, intellectual disability, musty body odor

64
Q

Loss of Heterozygosity

A

If a patient inherits or develops a mutation in a tumor suppressor gene, the complementary allele must be deleted/mutated before cancer develops. this is not true of oncogenes.

“two hit”

  • lynch syndrome (HNPCC), Li-Fraumeni
65
Q

What is Mosaicism?

somatic vs. gonadal

A

Genetically distinct cell lines in same individual

  • somatic - mitotic errors after fertilization, propogates through multiple tissues
  • gonadal - only in egg or sperm
66
Q

McCune Albright syndrome

symptoms?

example of what genetic phenomena?

A
  • Gs protein activating mutation
  • Cafe au laut spots, polyostotic fibrous dysplasi (bone replaced by collagen), and one endocrinopathy.
  • Mosaicism, lethal if it occurs before fertilization
67
Q

Prader-Willi and Angelman Syndrome are examples of what genetic phenomena?

A

Uniparental Disomy

68
Q

Hardy-Weinberg population Genetics

  1. Equations
  2. What variables mean
A

p + q = 1

p2 + 2pq + q2 = 1

p2 = frequency of homozygosity for allele A

q2 = frequency of homozygosity for allele a

2pq = frequency of heterozygosity (carrier frequency)

69
Q

Angelman syndrome

Silent gene?

deleted/mutated gene?

Signs and Symptoms?

A

Paternally derived UBE3A (15) is silenced

Maternal allele mutate/deleted

MD’s are Angels

SAIL - Seizures, Ataxia, intellectual disability, inappropriate laughter (happy puppet)

70
Q

Prader Willi

gene silence?

gene mutated?

Signs and symptoms?

A

Maternally derived allele silenced

disease of paternal allele is deleted/mutated

Hyperphagia, obesity, intellectual disability, hypogonadism, hypotonia

Prader has no Dad (Paternal deletion)

71
Q

What is MELAS an example of?

Signs and Symptoms?

A

Mitochondrial Inheritance Disease

MELAS

ME - mitochondrial encephalomyopathy

LA - Lactic Acidosis

S - Stroke like episodes

“ragged red fibers”

72
Q

Cystic Fibrosis

  1. Gene, chromosome, deletion
  2. Channel type - what it does in sweat glands vs lungs
  3. How do we diagnose?
  4. Newborn screen?
  5. Tx
A
  1. CFTR, 7, ^F508
  2. ATP-gated Cl- channel lungs causes chloride to move out, sweat glands chloride moves in ENaC responds accordingly
  3. Pilocarpine sweat test - increased Cl-
  4. increased immunoreactive trypsinogen
  5. Lumacaftor - corrects misfolded protein

ivacaftor - opens Cl- channels

73
Q

DMD vs. BMD. vs. Myotonic Dystophy

A

DMD - Frameshift

BMD - Non-frameshift

Myotonic - CTG repeat abnormal DMPK gene

74
Q

What is the mneumonic for CTG repeat in Myotonic dystrophy?

A

C - Cataracts

T - Toupee - early balding

G - Gonadal atrophy

75
Q

What is Rett Syndrome?

A

occurs in girls (x-linked) males die in utero

MECP2 gene

between ages 1-4 children regress with stereotypical hand wringing

76
Q

Fragile X-Syndrome

Gene?

Repeat?

Findings?

A
  • FMR1

CGG

post-pubertal macroorchidism, long face with large jaw, large everted ears, autism, mvp, hypermobile joints.

77
Q

Huntingtons Disease

repeat?

Mnemonic?

A

CAG

Caudate has decreased ACh and Gaba

78
Q

Down Syndrome

1st trimester Ultrasound findings?

Markers?

A

Increaces nuchal translucency

Increased hCG and Inhibin

“Down syndrome markers are HI up”

79
Q

Edwards Syndrome

chromosome?

Findings?

A

Chromosome 18

mneumonic is “prince edward”

P - prominent occiput

R - Rocker-bottom feet

I - intellectual disability

N - Nondisjunction

C - clenched fists overlapping fingers

E - low set ears

80
Q

Patau Syndrome

chomosome?

Findings?

A

chromosome 13

  • severe intellectual disability
  • microphthalmia, microcephaly
  • cleft lip/palate
  • holoprosencephaly
  • polydactyly
  • cutis aplasia
  • polycystic kidney disease
81
Q

1st Trimester vs 2nd Trimester Screen markers

Down

Edward

Patau

A

Down 1st - increased hCG and decreased PAPP-A

Down 2nd - Increased hCG/Inhibin A, decreased estriol AFP

Edward 1st - decreased hCG/PAPP-A

Edward 2nd - everything decreased

Patau 1st - decreased hCG/PAPP-A

Patau 2nd - None

82
Q
A

First Aid Biochemistry (2 decks)

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