Molecular Flashcards
What is a nucleosome
2 loops of negatively charged DNA around a positively charged histone
What amino acids are histones rich in?
Lysine and arginine
Which histone ties nucleosome beads together?
H1
Which histone is the only histone not in the nucleosome core?
H1
What is orotic aciduria?
Autosomal recessive disease with a defect in UMP synthase (defect in de novo pyrimidine synthesis pathway)
What would a patient with orotic aciduria have?
Increased orotic acid in urine
Megaloblastic anemia
Failure to thrive
What is the treatment for orotic aciduria?
Oral uridine administration
What disease has increased orotic acid with hyperammonemia?
OTC deficiency
Which nucleotide pairing has 3 H bonds?
G-C
Which 3 amino acids are necessary for purine synthesis?
Glycine
Aspartate
Glutamine
What does ribonucleotide reductase do?
It converts ribonucleotides to deoxyribonucleotides
What drug inhibits ribonucleotide reductase?
Hydroxyurea
What does HGPRT and PRPP do?
Converts guanine to GMP
Converts hypoxanthine to Inosinic acid (IMP)
What does APRT and PRPP do?
Converts adenine to AMP
What does adenosine deaminase do?
Converts adenosine to inosine
What does xanthine oxidase do?
Converts hypoxanthine or xanthine to uric acid
What does adenosine deaminase deficiency cause?
SCID - prevents DNA synthesis and thus decreases lymphocyte count.
What is the inheritance pattern of ADA deficiency?
Auto recessive
What was the first disease to be treated by experimental human gene therapy?
ADA deficiency
What is Lesch-Nyhan syndrome?
Absence of HGPRT - no purine salvage, excess uric acid, excess de novo purine synthesis.
What will a Lesch-Nyhan patient exhibit?
Retardation Self-mutilation Gout Hyperuricemia Aggression Choreathetosis
What is the inheritance pattern of Lesch-Nyhan syndrome?
X-linked
What is the severity of damage with point mutations in DNA in descending order?
Frame shift
Nonsense
Missense
Silent
What is a nonsense mutation?
Change resulting in a stop codon
What is a missense mutation?
Change resulting in a different amino acid that is similar to the original
What is a frame shift mutation?
Change resulting in misreading of all nucleotides downstream
How many origins of replication are seen in prokaryotes?
1
How many origins of rep are in eukaryotes?
2
What does helicase do?
Unwinds DNA at replication fork
What do single stranded binding proteins do?
Prevent strands from reannealing
What do DNA topoisomerases do?
Create a nick to relieve supercoiling
What drugs inhibit DNA topoisomerases?
Fluoroquinolones
What does primase do in DNA replication?
Makes an RNA primer for DNA polymerase III to initiate replication
What does DNA pol III do?
Adds nucleotides on leading and lagging strands from 3’ to 5’ using 5’ to 3’ synthesis
PROKARYOTIC ONLY
What does DNA pol I do?
PROKARYOTIC ONLY
Degrades the RNA primer and replaces it with DNA using 5’ to 3’ exonuclease
What does DNA ligase do?
Catalyzes formation of a phosphodiesterase bond within a strand of double-stranded DNA
What does telomerase do?
Adds DNA to 3’ ends of chromosomes to avoid loss of genetic material with every duplication
What is nucleotide excision repair?
Repairs bulky helix distorting lesions with endonucleases like pyrimidine dimers.
Endonucleases releases the oligonucleotide containing base
What disease has a defect in nucleotide excision repair?
Xeroderma pigmentosum - cant repair pyrimidine dimers caused by exposure to UV light
What is base excision repair?
Cut DNA at apurinic and a pyrimidine sites, empty sugar is removed, gap is filled and resealed
When would base excision repair be used?
To repair spontaneous/toxic deamination
What is mismatch repair?
Newly synthesized strand is recognized, mismatched nucleotides are removed and the gap is filled and resealed
In what disease is mismatch repair broken?
Hereditary nonpolyposis colorectal cancer
In what disease in no homologous end joining mutated?
Ataxia telangectasia
What is nonhomologous end joining?
Brings together 2 ends of DNA fragments to repair double stranded breaks
In what direction are DNA and RNA synthesized?
5’ to 3’
What does DNA synthesis require?
The triphosphate bond on the incoming 5’ base and a free OH on the 3’ base
In which direction is mRNA read?
5’ to 3’
In what direction is protein synthesis?
N to C
What is the most abundant type of RNA?
rRNA
What is the longest type of RNA?
mRNA
What is the mRNA start codon?
AUG
What amino acid does the start codon code for?
Methionine in euks
F-met in proks
What are the stop codons?
UGA
UAA
UAG
What is the promoter site?
Site where RNA polymerase and multiple other transcription factors bind to DNA upstream from a gene locus.
Rich in A-T
What would a mutation in the promoter site result in?
A decrease in the amount of gene transcribed
What is the enhancer/silencer?
Stretch of DNA that alters gene expression by binding transcription factors
What does RNA pol I do?
Makes rRNA in euks
What does RNA pol II do?
Makes mRNA in euks
What does RNA pol III do?
Makes tRNA in euks
What does alpha-amanitin do?
It is a poison found in Amanita phalloides.
It inhibits RNA polymerase II - causes hepatotoxicity if ingested.
What is the initial transcript in RNA processing?
Heterogenous nuclear RNA
Where does RNA processing occur?
In the nucleus
What are the post translation modifications to make mRNA?
Capping of 5’ end
Polyadenylation tail on 3’ end
Splicing out of introns
What are the steps of splicing?
- Make spliceosome with snRNPs and the primary transcript
- Lariat intermediate made
- Lariat released to remove intron
What patients make antibodies to snRNPs?
Lupus patients
What enzyme checks the amino acids binding to the 3’ end of tRNA?
Amino-acyl tRNA synthetase
Which DNA polymerase has 5’ to 3’ exonuclease activity?
DNA pol I
What kind of exonuclease activity does DNA pol III have?
3’ to 5’
Which antibiotic class inhibits the binding of aminoacyl-tRNA?
Tetracyclines by binding the 30S subunit
What happens if aminoacyl tRNA synthetase recognizes that the tRNA has bound the wrong amino acid?
The bond is hydrolyzed
What is protein synthesis initiation activated by?
GTP hydrolysis
What catalyze a the peptide bond formation during elongation?
RRNA - ribozymes
What does the “A” site of the ribosome do?
It binds to the aminoacyl-tRNA
What is the “P” site of the ribosome for?
Accommodating the growing peptide
What is the E site for?
Holding th empty tRNA as it exits
What recognizes the stop codon?
Release factor
What do p53 and hypophosphorylated RB do?
Inhibit the progression from G1-S
What are the permanent cells and what cell cycle do they stay in?
Neurons
Skeletal and cardiac muscle cells
RBCs
They stay in G0 and regenerate from stem cells
What are the stable cells?
Hepatocytes
Lymphocytes
They enter G1 when stimulated
What are the labile cells?
Bone marrow Gut epithelium Skin Hair follicles Germ cells These are always in G1. Never go to G0
What cells are rich in RER?
Goblet cells
Plasma cells
What does the smooth ER do?
Steroid synthesis and detox of poisons and drugs
What does the RER do?
Synthesize secretory proteins and N-oligosaccharides
Which cells are rich in smooth ER?
Hepatocytes
Cells of the adrenal cortex
What does the Golgi apparatus do?
Modifies N-oligosaccharides on asparagine
Adds O-oligosaccharides on serine and threonine
Adds mannose-6-phosphate to proteins for trafficking to lysosomes
What is I-cell disease?
Inherited condition where mannose-6-phosphate is not being added to proteins so they don’t end up in lysosomes where they belong. They are dumped outside the cell
What are the features of I-cell disease?
Coarse facial features Clouded corneas Restricted joint movement High plasma levels of Lysosomal enzymes Often fatal in childhood
What is COPI?
The retrograde vesicular trafficking protein - tells the protein to go from the Golgi to the ER
What is COPII?
The anterograde vesicular trafficking protein telling the proteins to go from the ER to the Golgi
What is Clathrin?
It is the vesicular trafficking protein that does receptor-mediated endocytosis .
What is the fxn of a peroxisome?
Catabolism of long chain fatty acids and amino acids
What is a proteasome?
Barrel-shaped protein complex that degrades damaged or unnecessary proteins tagged for destruction by ubiquitin
What is a microtubule?
Tubes of polymerized dimers of alpha and beta Tubulin used for axoplasmic transport and locomotion.
Examples: dynein (retrograde transport from positive to negative end)
Kinesin (anterograde)
What is chediak-higashi syndrome?
Mutation in lysosomal trafficking regulator gene - have problems With the microtubule dependent sorting of the endosomal proteins and with lysosomes-phagosome fusion.
What is the presentation in chediak-higashi syndrome?
Partial albinism
Pyogenic infections
Peripheral neuropathy
Will see giant granules in the neutrophils
What is the structure of cilia?
9 doublets of microtubule
Axonemal dynein causes bending of the cilium by differential sliding of the doublets
What is axonemal dynein?
An ATPase that causes the differential sliding of the doublets so the cilia can bend
What is Kartagener’s syndrome?
Defect in dynein arm –> immotile cilia
Male infertility, decreased female fertility, bronchiectasis, recurrent sinusitis
What is Kartagener’s associated with?
Situs in versus
What are intermediate filaments responsible for?
Structure
Examples: vimentin, desmin,cytokeratins, laming, GFAP
What is the most common type of collagen?
I - seen in bone, skin and tendons, dentin, fascia, cornea, late wound repair
What is type II collagen found in?
Cartilage, vitreous body, nucleus pulposus
What is type III collagen found in?
Reticulin- skin,bvs, uterus, fetal tissue, granulation tissue
What is type IV collagen found in?
Basement membrane
What disease is there a defect in type III collagen?
Ehlers-Danlos
What is the structure of procollagen?
Triple helix of 3 collagen alpha chains bound by hydrogen and disulfide bonds
What amino acids are in the alpha chains of collagen?
Glycine, proline, lysine
What is required for the hydroxylation of proline and lysine?
Vitamin C
What cell makes collagen?
Fibroblasts
What happens to procollagen outside of fibroblasts?
The disulfide bonds are cleaved to make insoluble tropocollagen. Then cross-linking between lysine and hydroxylysine via Cu-lysyl oxidase to make collagen fibrils
What’s osteogenesis imperfecta?
An autosomal dominant gene defect resulting in abnormal type I collagen. Specifically, problems forming the triple helix of procollagen
What are the clinical findings in osteogenesis imperfecta?
Multiple fractures
Blue sclera
Hearing loss
Dental problems
What is Ehlers-Danlos syndrome?
Problems with the synthesis of collagen causing hyperextensible skin, easy bruising, and hypermobile joints.
Type I and V are most likely to be affected.
Can be auto Dom or recessive
What other conditions is Ehlers-Danlos associated with?
Berry aneurysms
Joint dislocation
Organ rupture
What is alport syndrome?
X-linked recessive disease resulting in abnormal Type IV collagen
What are the clinical findings in Alport syndrome?
Nephritis
Deafness
Ocular disturbances
What is elastin?
Stretchy protein rich in proline and glycine
What enzyme breaks down elastin?
Elastase
What enzyme inhibits elastase?
Alpha1-antitrypsin
What disease can be caused by excess elastase activity?
Alpha1- antitrypsin deficiency
What is the PCR?
A procedure used to amplify a fragment of DNA.
First, the DNA is denatured, then annealed with premade DNA primer, the elongated with heat stable DNA pol
This process is repeated multiple times for DNA sequence amplification
What is the southern blot used for?
Visualizing DNA segments
DNA is denatured then exposed to radiolabelled DNA probe so that the complementary DNA binds and then it’s visualized
What is the northern blot used for?
Studying mRNA levels
What is the Western blot used for?
Labelled antibody is used to bind relevant protein
What is the southwestern blot?
It identifies DNA-binding proteins using oligonucleotide probes
What are micro arrays?
Thousands of nucleoli acids sequences are arranged in a grid and then DNA or RNA probes are hybridized to the chip. A scanner identifies the amount of complementary binding
What are micro arrays used for?
Gene profiling, forensic analysis, cancer mutation, genetic linkage analysis
Able to detect single nucleotide polymorphisms for a variety of applications.
What is enzyme-linked immunosorbent assay?
A rapid immunologic technique testing for antigen-antibody reactivity
Patient’s blood sample is probed with antigen (indirect) or antibody (direct) to see if the patient has a certain antibody. The added Ag or Ab is attached to a color-generating enzyme that lights up if they do have it
What is the ELISA test used for?
HIV testing. The specificity and sensitivity are 100%
What is FISH - fluorescent in situ hybridization?
A fluorescent DNA or RNA probe binds to specific gene site of interest on chromosomes
What is FISH used for?
Used for localization of genes and visualization of defects
What is the cloning method for DNA?
Isolate the mRNA, exposé to reverse transcriptase to make cDNA.
Insert the cDNA into bacterial plasmids and the bacteria will make it for you
What is the Cre-lox system?
Gene modification at different developmental points using an antibiotic controlled promoter
What is RNA interference?
Using dsRNA synthesized from mRNA of interest and transferring humans with it. The dsRNA separates in Vigo and promotes degradation of the target mRNA causing decreased expression of that gene
What is karytotyping?
A process by which metaphase chromosomes are stained, ordered and numbered so they can be visualized.
Used for looking for chromosomal abnormalities
What is an example of co-dominance?
Blood groups A, B, AB
What is an example of variable expressivity?
2 patients with neurofibromatosis 1
What is an example of incomplete penetrance?
BRCA1 mutation not always resulting in breast or ovarian cancer
What is an example of pleiotropy?
PKU causes seemingly unrelated sx
What is pleiotropy?
When one gene contributed to multiple phenotypic effects
What is imprinting?
Differences in gene expression depending on whether the mutations are maternal or paternal
What is an example of imprinting?
Prader-Willi and angelman’s syndrome
What is an example of anticipation?
Huntington’s disease
What is an example of loss of heterozygosity?
Retinoblastoma
What is a dominant negative mutation?
When a heterozygote produces a nonfunctional altered protein that also prevents the normal gene from functioning
What is linkage disequilibrium?
The tendency for certain alleles at 2 linked loci to occur together more often than expected by chance
What is mosaicism?
When cells in the body differ in genetic makeup due to post fertilization loss of change of genetic info during mitosis
What is locus heterogeneity?
When mutations at different loci produce the same phenotype
What is an example of locus heterogeneity?
Marfan’s syndrome
Homocystinuria
Albinism
What is heteroplasmy?
Presence of both normal and mutated mtDNA causing a mitochondrial inherited disease of variable expression
Where was the error with heterodisomy?
Meiosis I
Where was the error in isodisomy?
In meiosis II or post zygotes duplication
When should you consider uniparental disomy?
When’s patient presents with an autosomal recessive disorder but there is only one carrier
What are the Hardy Weinberg laws?
No mutation occurring at the locus
Random mating
No selection for any of the genotypes
No migration
What is the frequency of an X-linked recessive disease in males and females using he hardy-Weinberg equation?
Males= q Females = q2
What is Prader-Willi syndrome?
An imprinting error in the parental allele causing it not to be expressed
Chromosome 15 inactivation
What are the clinical findings of Prader-Willi syndrome?
Mental retardation Hyperphagia Obesity Hypogonadism Hypotonia
What is Angelman’s syndrome?
An imprinting error where the maternal allele is not expressed
Chromosome 15
What are the clinical findings of Angelman’s syndrome?
Mental retardation
Seizures
Ataxia
Inappropriate laughter
What percent chance do 2 carrier parents of an auto recessive disease have of having a child with the disease?
25%
What is the pattern of inheritance of CF?
Autosomal recessive
What is the mutation if CF?
Defect in CFTR on ch. 7
CFTR channel actively secretes Cl- in lungs and GI tract and actively resorts Cl- from sweat.
What are the clinical findings of CF?
Abnormally thick mucus of the lungs, pancreas, liver
Recurrent pulmonary infections
Chronic bronchitis, brochiectasis, pancreatic insufficiency
Nasal polyps
Meconium ileus
Infertility in males from absent Vas deferens
What is the test for CF?
Chloride sweat test. Positive if there is increased concentration of chloride
What is the most common lethal genetic disease of the white population?
CF
What is the second most common cause of genetic mental retardation?
Fragile X syndrome
What is the defect in Fragile X syndrome?
X linked defect in the FMR1 gene
What are the clinical findings in Fragile X syndrome?
Marcoorchidism
Long face with a large jaw and large diverted ears
Autism
MVP
What are the trinucleotide repeat expansion diseases?
Huntington’s disease (CAG)
Myotonic dystrophy (CTG)
Friedrich’s ataxia (GAA)
Fragile X syndrome (CGG)
What is the most common genetic cause of mental retardation?
Down’s syndrome
What are the clinical findings in Down’s syndrome?
Flat facies Single simian palmar crease Prominent epicanthal folds Duodenal atresia Gap between 1st 2 toes Congenital heart disease
What is Down’s syndrome associated with?
Increased risk of ALL
Alzheimer’s over 35 yo
What is the chromosomal abnormality of Down’s syndrome due to?
Meiosis nondisjunction associated with increased maternal age
4% due to Robertsonian translocation
1% due to mosaicism
What are the results of the pregnancy quad screen in Down’s syndrome?
Decreased alpha-fetoprotein
Decreased estriol
Increased inhibin A
Increased beta-HCG
What does the ultrasound show in Down’s syndrome?
Increased nuchal? In first trimester lucency
What is Edwards syndrome?
Trisomy 18
Most common trisomy resulting in live birth after Down’s syndrome
Death within the first year
What are the clinical findings of Edwards syndrome?
Severe mental retardation Rocker bottom feet Micrognathia Low set ears Prominent occiput Congenital heart disease
What are the results of pregnancy quad screen in Edwards syndrome?
Decreased alpha-fetoprotein
Decreased beta-HCG
Decreased estriol
Normal inhibin A
What is Patau’s syndrome?
Trisomy 13
What are the clinical findings in Patau’s?
severe mental retardation Rocker bottom feet Microphthalmia Microcephaly Cleft palate Holoprosencephaly Polydactyly Congenital heart disease Death within the first years
What are the pregnancy quad test results of Patau’s?
Decreased beta-HCG
Decreased PAPP-A
Increased nuchal translucency
What is the Robertsonian translocation?
Occurs when the long arms of 2 acrocentric chromosomes fuse at the centromere and the 2 short arms lost.
What is cri-du-chat syndrome?
Congenital micro deletion of the short arm of chromosome 5
What are the clinical findings of cri du chat syndrome?
Microcephaly Mental retardation High-pitched crying/mewing Epicanthal folds Cardiac abnormalities (VSD)
What is Williams syndrome?
Congenital microdeletion of long arm of chromosome 7 including the elastin gene
What are the clinical findings of Williams’s syndrome?
Elfin facies Intellectual disability Hypercalcemia (more sensitivity to vit D) Well developed verbal skills Extreme friendliness with strangers CV problems
What are the features of 22q11 deletion syndromes?
Cleft palate Abnormal facies Thymic aplasia Cardiac defects Hypocalcemia
What is velocardiofacial syndrome?
Palate, facial and cardiac defects
22q11 deletion syndrome
What is DiGeorge syndrome?
Thymic, parathyroid, and cardiac defects
What is the the result of 22q11 deletion syndrome?
Aberrant development of 3rd and 4th bronchial pouches
