Flashcards in Biochemistry High Yeild Deck (75)
How is uracil formed?
Deamination of the pyrimidine cytosine.
Uracil is found in RNA and replaces thyamine that binds with adenine.
Which of the nucleotides has a methyl group?
Which three amino acids are needed for the formation of purines?
which group of the nucleotides requires the most steps in synthesis?
Pyrimidines, which are formed from orotic acid.
Purines start with sugar and phosphate and just need a base added.
What can happen when there is an adenosine deaminase deficiency?
Leads to decreasd DNA synthesis due to excessive ATP and dATP balance.
Ultimately lowers lymphocyte counts resulting in SCID.
What is Lesch-Nyhan syndrome?
Defective purine salvage due to absent HGPRT which converts hypoxanthine to IMP and Guanine to GMP.
Results in excessive uric acid production and de novo purine synthesis. X-linked recessive.
Which medication inhibits prokaryotic topoisomerase II and topoisomerase IV?
Prevents the repair of strand breakage in DNA.
What does the enzyme primase do?
Makes an RNA primer that DNA polymerase III can act on to initiate replication.
Where can DNA polymerase III be found?
This is found in prokaryotes only and elongates the leading strand by adding deoxynucleotides to the 3' end.
Thus it has 5'->3' synthesis and 3'->5' proofreading.
What does the DNA polymerase I do?
Found in prokaryotes only.
Degrades the RNA primer and replaces it with DNA.
What does telomerase do?
RNA dependent DNA polymerase that adds DNA to the 3' ends of chromosomes to avoid loss of genetic material with every duplication...
Found in eukaryotes only.
Compare a transition DNA mutation vs a transversion.
Transition is a purine swapped with another purine.
Transversion is a purine swapped for a pyrimidine.
Silent mutation: Nucleotide substitution coding for same amino acid.
Missense mutation: Results in a changed amino acid ex: Sickle cell disease!!!! Glutamic acid swapped for a valine.
Nonsense mutation: Nucleotide substituion resulting in an early stop codon.
Frameshift: Deletion or insertion. Think Duchenne muscular dystrophy!!!
What type of repair occurs in G1 vs G2 phase of growth?
G1 is nuceotide excision repair. Occuring in xeroderma pigmentosum with pyrimidine dimers from UV light.
Mismatch repair occurs in the G2 phase of the cell cycle. Defective in nonpolyposis colorectal cancer.
What is the promoter region?
Site where RNA polymerase II and multiple other transcription factors bind to DNA upstream.
What is the enhancer region?
Stretch of DNA that alters gene expression by binding transcription factors.
Describe RNA pol I
RNA pol II
RNA pol III
RNA pol1 is for rRNA
RNA pol 2 is for mRNA
RNA pol 3 is for tRNA
***Amanitin in mushrooms inhibits RNA pol II.
Rifampin binds RNA polymerase in procaryotes.
Actinomycin D inihibits RNA pol in prokaryotes and eukaryotes.
Describe the ribosomyl locations in elognation.
The A site is the site for incoming aminoacyl-tRNA.
The P site accomodates the growing peptide.
The E site holds the empty tRNA as it Exits.
Moves from the 5' to 3' ends.
What are chaperone proteins?
These are intracellular proteins involved in facilitating/maintaining protein folding.
What are nissle bodies responsible for?
The synthesis of peptide neurotransmitters for ecretion.
Think of mucus goblet cells as well which occurs in the rough endoplasmic reticulum.
mutation in N-acetylglucosaminy-1-phosphotransferase.
Golgi is unable to send things to lysosomes, instead they get secreted and build up.
Signal recognition partecle SRP
Abundant cytosolic robonucleoprotein that traffics proteins from the ribosome to the RER.
When absent, dysfunctional proteins accumulate in the cytosol.
COP I sends from the golgi to the ER. Retrograde.
COP II Sends from the ER to the Cis golgi. Anterograde.
Clathrin: Trans golgi to the lysosomes
What is the role of the peroxisome?
Peroxisomes deal with the catabolism of long chain fatty acids, branched chain fatty acids, and amino acids.
Proteasomes are barrel shaped protein complexes that break down ubiquinated targets.
What's the diference between intermediate filaments and microtubules?
Intermediate filaments give the cell structure and consist of vimentin, desmin, cytokeratin etc.
Microtubules allow for cellular division and movement and consist of cilia, flagella the mitotic spindels etc/
Immotile cilia due to a dynein arm defect resulting in male and female infertility.
Think microtubule cilia problem.
How many sodium are exchanged for potassium at the pump?
Three sodium are pumped out of the cell for two potassium to enter the cell using ATP.
Ouabbain inhibits it by binding the the potassium site.
Type I collagen
Type II collagen
Type III collagen
Type IV collagen
Type I Bone tendon, dentin
Type II Cartwolage
Type III Skin, reticulum, etc.
Type IV Basement membrane, basal lamina etc.
"Type IV under the floor"
Which amino acids are typically used in collagen synthesis?
Lysine and proline.
These are hydroxylated and require vitamin C for proper formation.
Thus Vit C deficiency leads to scurvy and bleeding cums.
note normally collagen is a triple helix of alpha chains.
Autosomal dominant Genetic bone disorder with decreased type I collagen formation.
Look for blue sclerae, hearing loss, dental imperfections etc.
Ehlers Danlos syndrome
Faulty collagen synthesis causing hyperextensible skin, tendency to bleed and hypermobile joints.
Classically a mutation in type V collagen. Vascular type has a deficiency in type III collagen.
Caused by a defect in fibrillin, a glycoprotein that forms a sheath around elastin.
Lack of alpha 1 antitrypsin resulting in excessive elastase activiity.
Wrinkles in the elderly are due to decrease in....
A decrease in colalgen and elastin production.
DNA sample is cleaved into smaller pieces.
Main point is that its checking DNA.
Checks for RNA to study mRNA levels in gene expression.
Labeled antibody binds to a relevant protein.
This can be used as a confirmatory test for HIV after a positive ELISA
Identifies DNA binding proteins.
Uses a test antibody to see if a specific antigen is present.
The antibody is linked to a color generating enzyme.
Test antigen or antibody used to see if a specific antibody or antigen is present.
A secondary antibody couple to a color generating enzyme is then added to detect the antibody-antigen complex.
Metaphase chromosomes stained ordered and coupled based on size etc.
Used to detect chromosome imbalances.
Fluorescence in situ hybridization
Fluorescent DNA or RNA prove binds to specific gene site of interest on chromosomes.
Used to determine the localization of genes and direct visualiztion of anomolies.
One gene contributes to multiple phenotypic effects.
Describe Prader-Willi and Angelman Syndromes
These are both due to mutations or deletions of genes received on the chromosome 15.
Prader Wili is maternal with hyperphagia, obesty, intellectual disability.
Angelmann is on the aternal imprinting resulting in seizures, ataxia, and severe intellecutal disability.
Trinucleotide CAG repeats on chromosome 4.
"Hunting 4 food'
FBN1 gene mutation on chromosoem 15 defective fibrillin.
Connective tissue disorder affecting skeleton, heart, and eyes.
Multiple endocrine neoplasias
Familial tumors of endocrine glands.
Neurofibromatosis type 1
Cafe Au Lait spots!
cutaneous neurofibromas, optic gliomas, pheochromocytomas.
Neurofibromatosis type 2
Bilateral acoustic schwannomas
Juvenile cataracts etc.
Chromosome 22 type 2 = 22!!!
What trisomy is seen in down syndrome?
Look for nuchal translucenc, hypoplastic nasal bone, and hypoplastic nasal bone.
What trisomy is seen in edwards syndrome?
Severe intillectual disability with
ROCKER BOTTOM FEET
Low set ears, clenched hands etc.
This is the second most common trisomy.
What trisomy is seen in Patau Syndrome?
Rocker bottom feet, micropthalmia, cleft lip and cleft palate!
Chromosomal translocation in which the two chromosomes fuse at the centromere and the two short arms are lost.
Congenital microdeletion of long arm of chromosome 7 (elastin gene deleted)
Elfin facies with intellectual diability and hypercalcemia due to vitamin D sensitiivy.
22q11 deletion syndrome
Thymic, parathyrooid and cardiac defects with 3d and 4th branchial pouch disorders.
22q11 deletion syndrome resulting in palate, facial, and cardiac defects.
3rd and 4th branchial pouches do not develop properly.
B1 thiamine (TPP)
B2 Riboflavin (FAD,FMN)
B3 Niacin - NAD+
B5 Pantothenic acid: CoA
B12 and folate are stored in the liver.
which two B vitamins are stored in the liver?
B12 and Folate.
What happens in thiamine deficiencies
B1 deficiencies result in impaired glucose breakdown and ATP depletion worsened with glucose administration.
Will see Wernicke-Korsakof syndrome (confusion, opthalmoplegia, and ataxia) Damage to medial dorsal nucleus of thalamus and mammillary bodies.
Dry Beri-Beri: Polyneuritis, symetrical muscle wasting.
Wet Beri-Beri: High output cardiac failure (dilated cardiomyopathy) and edema
What happens in Riboflavin deficiencies?
Lack fo FAD and FMN in the TCA cycle.
Results in cheilosis (inflammation of the lips, scaling of the corners of the mouth)
And corneal vascularization.
"The two C's of B2"
What happens in niacin deficiencies?
LAck of NAD+ and NADP+ derived from tryptophan!
results in glossitis and pellagra
Diarrhea, dementia, and dermatitis.
What is niacin synthesized from?
Look out for hartnup disease (decreased tryptophan absorption), Malignant carcinoid syndrome (Increased tryptophan metabolism) and isoniazid use (Decreased vitamin B6)
What occurs in Pantothenic acid deficiency?
Vitamin B5 which is essential for Coenzyme A formation and fatty acid synthase.
Deficiency results in enteritis and alopecia, as well as adrenal insufficiency.
What occurs in pyridoxine deficiency?
Vitamin B6 deficiency results in convulsions, hyperirritability, and peripheral neuropathy.
Sideroblastic anemia occurs as well resulting in impaired hemoglobin synthesis and iron excess.
What occurs in Biotin deficincy?
Vitamin B7 a cofactor for carboxylation enzymes
Deficiencies are rare and can cause dermatitis, alopecia, enteritis. Caused by antibiotic use or excessive ingestion of raw egg whites.
What occurs in folate deficiencies?
Vitamin B9 Folate is needed for THF formation needed in DNA and RNA formation. It is absorbed in the jejunum and from foliage.
Deficiencies leads to macrocytic, megaloblastic anemia and hypersegmented polymorphonuclear cells.
Phenytoin, sulfonamides and methotrexate can cause deficiencies.
Where is folate/vitamin B9 absorbed?
Absorbed in the jejunum!
B12 is absorbed in the ileum.
What is the function of vitamin B12/cobalmin?
Cofactor for homocysteine methyltransferase and methylmalonyl-CoA mutase.
Found in animal products stored primarily in the liver. Requires intrinsic factor for absorption in the ileum
What happens in vitamin B12/cobalmin deficiencies?
Macrocytic megaloblastic anemia and hypersegmented PMN's
Associated with increased serum homocysteine and methylmalonic acid levels.
Prolonged deficiency leads to irreversible nerve damage.
Veganism and diphyllobothroum latum infections can cause deficiency in B12.
Describe why vitami C can be used to treat methemoglobinemia.
It serves toreduce Fe3+ to Fe2+
What happens if there is a defciency in vitamin c?
Scurvy, it cannot hydroxylate proline and lysine in collagen without vitamin C.
also effects hair, wound healing, and immune responses.
ALSO without it iron absorption will be decreased.
What does vitamin E do?
Vitamin E is an antioxidant protecting RBC from free radical damage.
Can result in hemolytic anemia, acanthocytosis, muscle weakness, and posterior column and spinocerebellar tract demyelination.
Presents similarly to vitamin B12 deficiency without megaloblastic anemia, hypersegmented neutrophils or increased serum methylmalonic acid levels.
Which vitamin can enhance the anticoagulant effects of warfarin?
What is Kwashiorkor?
Small child with swollen abdomen
Due to decreased plasma oncotic pressure, liver malfunction