Biochemistry Flashcards
blot detect target mRNA in a sample and can be used to assess the degree of gene transcription.
Northern blots
an assay commonly employed to measure the amount of a PROTEIN in body FLUIDS. It can be quantitative, for example, to measure plasma insulin levels.
ELISA (enzyme-linked immunosorbent assay)
blot detect target protein in a sample and can be used to assess the degree of gene translation.
Western blots
Phenylalanine hydroxylase deficiency causes
what disease, what does it require?
PKU, requires THB
Cystathionine synthase
what disease, what does it require
Homocystinuria
requires B6
Proprionyl-CoA carboxylase deficiency causes an inability to digest what? What does it require?
can’t digest VOMIT
requires B7
Methylmalonyl-CoA mutase deficiency causes, what disease, what does it require?
Methylmalonic acidemia
requires B12
Deficient/absent enzyme in Alkaptonuria
Urine/ cartilage turns black
Homogentisate oxidase
Tyr –> Fumurate
intermittent burning pain in the hands and feet and a lack of sweating while engaging in physical activity.
Name the inclusion body found
Ceramide trihexoside
Vomiting, irritable baby with increased muscle tone in all extremities.
His diapers emit a caramel-like odor. Urine studies
are positive for ketone bodies.
What 3 amino acids should be avoided in this baby?
Which one should be given to treat?
Mable Syrup Disease
Isoleucine, Leucine, Valine
(I LiV for Maple Syrup)
Treat with Thiamine
Caused by decreased
branched chain alpha ketoacid DHase (B1)
Maple Syrup Disease
Increases epinephrine through methyl donation
Methionine
Needed for phenylalanine & tyrosine Hydroxylase
also for NTs
Tetrahydrobiopterin (BH4)
Needed for nucleotide production (T, A, G)
Tetrahydrofolates
δ-Aminolevulinate is elevated in
lead poisoning
inhibited dehydratase
Elevated Porphobilinogen
Cause of acute intermittent porphyria
elevated Unconjugated bilirubin
Elevated in hemolysis or when liver can’t
metabolize bilirubin
Elevated Total, Indirect and Direct bilirubin
Alcoholism
Elevated Direct Bilirubin only
Bile Duct Obstruction
Elevated Indirect Bilirubin
Crigler-Najjar
Hemolysis
Elevated Orotic Acid
absent Citrulline
what enzyme is deficient
Ornithine transcarbamylase deficiency
decreased Carbamoyl phosphate synthetase I causes
decreased orotic acid
Elevated liver F1P
what enzyme is deficient
Aldolase B
where is Carbomyl phosphate synthetase I located
Mitochondria
part of urea cycle
where is Carbomyl phosphate synthetase II located
Cytoplasm
for Pyrimidine synthesis
orotic aciduria and acidemia unresponsive to cobalamin or folic acid treatment.
Which enzyme is deficient?
UMP Synthase
HGPRT deficiency
Lesch Nyan Hyperuricemia Gout Pissed off (aggression, self-mutilation) Retardation DysTonia
How to treat Lesch Nyan
Allopurinol
or
Febuxostate
(Block Xanthine Oxidase) Because fucked up purine salvage
COL1A1 and COL1A2 defect
Osteogenesis imperfecta
multiple fractures
Hearing Loss
Tooth abnormalities
blue sclera
Osteogenesis imperfecta
Bones= multiple fractures
I (eye)= blue sclerae
Teeth= dental imperfections
Ear= hearing loss
What collagen is bad in OI
Type 1
COL5A1 and COL5A2 defect
Type 5 collagen
joint/ skin symptoms
Ehlers Danlos
*Defect in collagen
Vascular type
Fragile organs vasculature (Aorta) susceptible to aneurysms
Type III procollagen (COL3A1) defect
Ehler Danlos
impaired copper absorption and transport due to defective protein from ATP7A gene
Menkes
*ATP7B gene is Wilson’s !
Low activity of lysyl oxidase (copper is a necessary cofactor) thus defective collagen
Menkes
Menkes carries an increased risk of what?
Cerebral Aneurysms
FBN1 gene mutation on chromosome 15 (fifteen) results in defective fibrillin, a glycoprotein that forms a sheath around elastin
Marfan
Beta-oxidation of fatty acids, the TCA cycle, and the carboxylation of pyruvate (gluconeogenesis) all occur within the
mitochondria
The enzymes responsible for glycolysis, fatty acid synthesis, and the pentose phosphate pathway reside in the
Cytosol
Pyruvate carboxylase requires
B7 biotin
3-Hydroxy-3-methylglutaryl-CoA (HMG CoA) lyase is a mitochondrial enzyme necessary for ____. It is also responsible for metabolism of the amino acid, _____.
ketogenesis
leucine (ketogenic)
Transketolase is an enzyme of the pentose phosphate pathway that uses _____ as a cofactor
thiamine (vitamin B1)
Medium-chain triglycerides are restricted in __________ deficiency.
a condition characterized by lethargy, seizures, and _______ hypoglycemia following a period of fasting.
medium-chain acyl-CoA dehydrogenase
hypoketotic
Galactose and lactose are excluded from the diet in patients with classic galactosemia (absent ______).
Galactosemia presents in neonates with jaundice, vomiting, poor feeding, lethargy, hypoglycemia, and _______ accumulation.
galactose-1-phosphate uridyltransferase
galactose-1-phosphate
Fructose and sucrose restriction is the treatment for ________ deficiency.
This condition causes vomiting and hypoglycemia in infants after fruit or juice is introduced.
fructose 1-phosphate aldolase
aldolase B
The major amino acid responsible for transferring nitrogen to the liver for disposal. Requires Vitamin __
Alanine
B6 for transamination
During protein catabolism Alanine carries ammonia to the liver and transfers it to _________ to form glutamate.
Glutamate then transfers the NH3 to the Urea pathway
α-ketoglutarate
Ehlers-Danlos syndrome can be caused by ______ deficiency, which results in impaired cleavage of ______ in the extracellular space.
procollagen peptidase
terminal propeptides
______ deficiency results in impaired tetrahydrobiopterin (BH4) levels, an important cofactor for both phenylalanine hydroxylase and tyrosine hydroxylase.
Although phenylalanine levels can be corrected with dietary restriction, downstream deficiencies of __________ lead to progressive neurologic deterioration and microcephaly (sometimes)
Dihydrobiopterin reductase
dopamine, norepinephrine, epinephrine, and serotonin
____ is used to detect a target PROTEIN or polypeptide from within a mixed sample using gel electrophoresis.
Western blotting
*Potential target proteins are separated by gel electrophoresis. The separated proteins are then transferred to a nitrocellulose membrane and probed with a primary antibody specific for the protein of interest. The membrane is then washed and treated with a (secondary) marked antibody that binds to the primary antibody and can be detected (eg, by colorimetry).
Western blotting is similar to the enzyme-linked immunosorbent assay (ELISA) technique; however, in ELISA the patient’s ____ is tested directly, whereas in Western blotting the proteins are first separated by electrophoresis.
serum
_____ analyzes mRNA via gel electrophoresis
Northern blots
*A sample containing a large number of mRNA molecules is separated via gel electrophoresis. Separated bands are then transferred to a membrane and hybridized with a probe containing a nucleotide sequence complementary to the mRNA of interest.
____ is used to analyze DNA sequences via
restriction endonucleases
gel electrophoresis
radiolabeled DNA probes
Southern blotting
*DNA that is fragmented using restriction endonucleases is separated by gel electrophoresis and transferred to a nitrocellulose membrane. A radiolabeled DNA probe containing a sequence complementary to an area of interest is then used for hybridization. Restriction site mutations can be detected because they alter DNA fragment lengths, thereby altering electrophoresis migration patterns.
____ analysis is similar to Southern and Northern blotting but involves hybridization of a large number of probes at once
Microarray
_____ is a technique that analyzes DNA-BINDING PROTEINS recognized by their ability to bind specific oligonucleotide probes.
Southwestern blotting
H-yperuricemia G-out P-issed off (aggression, self-mutilation) R-etarded (motor/mental) Dys-T-onia
Lesch Nyan
Brittle, kinky hair
growth retardation
hypotonia
cerebral aneurysm risk
Menkes
Compare Menke’s (ATP7A) and Wilson’s (ATP7B)
Menkes = low copper absorption
Wilson’s = High copper absorption
Menkes is inherited in what type of fashion
XLR
Most common cause of death in Marfan?
Aortic Root Aneurysm, rupture, or dissection.
Marfan can cause what type of murmur?
Mitral Valve Prolapse causing a
Systolic Crescendo w/a Mid Systolic Click
Subluxation of lens:
- Up and out
- Down and in
- Marfan (most of the time)
2. Homocystinuria (most of the time)
The hydroxylation of proline and lysine residues in collagen occurs in the ____ and requires vitamin C as a cofactor.
rough endoplasmic reticulum
After formation of the triple helix, ____ molecules are secreted from the cell via the Golgi apparatus.
(pro-alpha-chain helix) procollagen
Terminal Propeptides are cleaved by ____ (space) procollagen peptidase to form insoluble monomers which then self-assemble into collagen fibrils that are subsequently crosslinked via _____.
extracellular space
lysyl oxidase
Collagen Pro alpha Chains are ____ in the RER
Hydroxylated (Lysine and Proline residues)
Proteins destined for the ____ require phosphorylation of specific mannose residues to ensure proper transit through the Golgi apparatus.
lysosome
A Golgi body phosphotransferase enzyme catalyzes the phosphorylation of _____ residues on lysosome-bound proteins, allowing them to traverse the Golgi network
mannose
2-year-old, failure to thrive, developmental delay. recurrent ear infections
coarse facial features, corneal clouding,
hepatosplenomegaly, & restricted joint mobility.
Deficient phosphorylation of mannose residues (In golgi)
Diagnosis
I cell disease
maximal velocity (Vmax) is unchanged Km increased
Competitive inhibitors
Km unchanged
Vmax decreased
allosteric non-competitive inhibitors
_____ inhibition does not change the apparent Km and cannot be overcome with higher substrate concentrations.
Noncompetitive
Irreversible inhibitors ___ the Vmax
Lower
DNA nucleotide change in Base Pair # that is NOT divisible by 3 is a ____ mutation
frame shift
1 g of protein yields __ Cal
4
Fructose, similar to glucose and galactose, is a ___ sugar and can be detected by a copper reduction test, which nonspecifically detects their presence in urine
reducing
a benign disorder
Asymptomatic
+ urine copper reduction test
Essential fructosuria (fructokinase deficiency)
Northern blots detect target mRNA in a sample and can be used to assess the degree of gene ___.
transcription
*western= translation
Reverse transcription polymerase chain reaction (RT-PCR) is used to detect and quantify levels of ___ in a sample.
mRNA
It uses reverse transcription to create a complementary DNA template that is then amplified using the standard PCR procedure.
RT-PCR
allows direct localization of genes to their respective chromosomes by using a labeled DNA probe complementary to the sequence of interest.
Fluorescence in situ hybridization (FISH)
Beta-oxidation of fatty acids takes place primarily within the
mitochondrial matrix
Malonyl-CoA inhibits ___, preventing the transfer of acyl groups into the mitochondria & Beta Oxidation of Fats
carnitine acyltransferase
High citrate levels causes upregulation of Acetyl-CoA carboxylase. This cytosolic enzyme catalyzes the conversion of acetyl-CoA to _____ in the rate-limiting step of de novo fatty acid synthesis.
malonyl-CoA
High citrate levels causes upregulation of Acetyl-CoA carboxylase. This cytosolic enzyme catalyzes the conversion of acetyl-CoA to malonyl-CoA in the rate-limiting step of de novo ____ synthesis.
fatty acid
High citrate levels causes upregulation of _____ which catalyzes the conversion of Acetyl-CoA to Malonyl-CoA in the rate-limiting step of de novo fatty acid synthesis.
Acetyl-CoA carboxylase
Acetoacetate is a
Ketone body
an intermediate in the TCA cycle. It can be exported out of the mitochondrial matrix and into the cytosol, where it is broken down into acetyl-CoA for use in de novo fatty acid synthesis.
Citrate
This patient developed hypoketotic hypoglycemia after fasting and seizures which is consistent with a deficiency in
medium chain acyl-CoA dehydrogenase
*impaired Beta Oxidation of FA for Ketone bodies
is the primary hormone secreted ACUTELY in response to falling glucose levels
Glucagon
- At the same time, Epinephrine further stimulates glycogenolysis and gluconeogenesis
Prolonged fasting (after a few hours) increases the secretion of _____, a steroid hormone that binds to an intracellular receptor and acts to increase transcription of enzymes involved in gluconeogenesis, lipolysis, and proteolysis.
Cortisol
DNA-binding proteins include transcription factors (Myc, CREB), steroid receptors (cortisol, aldosterone, progesterone), thyroid hormone receptor, fat-soluble vitamin receptors (vitamin D, retinoic acid), and DNA transcription and replication proteins.
just review
Integral membrane proteins contain transmembrane domains composed of alpha helices with hydrophobic amino acid residues ( ___, ___, ___ isoleucine, phenylalanine, tryptophan, methionine, proline, glycine). These transmembrane domains help anchor the protein to the phospholipid bilayer of the cell membrane.
alanine, valine, leucine,
Collagen in the ECM binds ____, which binds to Integrin on the plasma membrane
Fibronectin
organelle remain floating in the cytosol throughout protein synthesis. They are responsible for translating proteins found within the cytosol, nucleosol, peroxisome matrix, and nuclear-encoded mitochondrial proteins
Free ribosomes
Attached ribosomes bind to the RER after protein translation begins. They synthesize most ___ proteins, the integral membrane proteins of the nucleus and cell membrane, and proteins within the ER, Golgi network, and lysosomes.
secretory
Ribosomes attach to the RER via the
translocon
Intracellular receptors that bind steroids, thyroid hormone, and fat-soluble vitamins act directly as transcription factors and contain ___ binding domains which recognize specific DNA sequences
zinc-finger
Calcium-sensing receptors are ___ receptors that regulate the secretion of parathyroid hormone
Gq protein–coupled
