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Glossary of USMLE Biochem

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which resembles substrate: competitive or noncompetitive inhibitors?
competitive
what type of inhibitor binds at the active site and is overcome by increasing substrate?
competitive
what effect do competitive inhibitors have on Vmax?
none
what effect do noncompetitive inhibitors have on Vmax?
decrease it
what effect do competitive inhibitors have on Km?
increase it
what effect do noncompetitors have on Km?
none
the lower the Km, the higher the _____?
affinity
when does Km = [S]?
at 1/2Vmax
in the cell cycle, which phase is usually the shortest?
mitosis
most cells are at what point in the cell cycle?
G0 - quiescent G1 phase
rapidly dividing cells have a shorter ____?
G1 (growth)
this is the site of synthesis of secretory proteins and N-linked oligosaccharide addition to many proteins
RER
mucus-secreting goblet cells of SI and Ab-secreting plasma cells are rich in what cellular organelle?
RER
nissl substance is not found where?
axon or axon hillock
what do nissl bodies do?
synthesize enzymes (e.g. ChAT) adn peptide neurotransmitters
what is SER for?
site of steroid synthesis and detoxification of drugs and poisons
lipid hepatocytes and steriod-producing cells of the adrenal cortex are rich in what?
SER
where is mannose-6-phosphate added, and what does it do?
golgi - added to specific lysosomal proteins, which targets them to the lysosome
what is I cell disease?
failure of addition of man-6-P to lysosome proteins, causing them to be secreted outside the cell instead of targeted to the lysosome; coarse facial features and restricted joint movement
this is the distribution center of proteins and lipids from the ER to the plasma membrane, lysosomes, and secretory vesicles
golgi
the golgi modifies N-oligosaccharides on what amino acid?
asparagine
golgi adds O-oligosaccharides to residues of what?
serine and threonine
what organelle assembles proteoglycans from proteoglycan core proteins?
golgi
this organelle performs sulfation of sugars in proteoglycans and of selected tyrosine on proteins
golgi
what is the diameter of a microtubule?
24 nm
each dimer in microtubules has how many GTP bound to it?
2
mebendazole/thiabendazole, taxol, griseofulvin, vincristine/vinblastine, and colchicine all act on what structure?
microtubules
this syndrome is characterized by decreased phagocytosis as a result of a microtubule polymerization defect
chediak-higashi syndrome
microtubules are involved in what type of axoplasmic transport?
slow
how many polymerized tubulin dimers are there per circumference in microtubules?
13
this structure consists of a 9+2 arrangement of microtubules
cilia
dynein is reponsible for what direction of movement?
retrograde
kynesin is responsible for what direction of movement?
anterograde
this is an ATPase that links peripheral 9 doublets and causees bending of cilium by differential sliding of doublets
dynein
a high cholesterol or long saturated fatty acid content does what to melting temperature?
increases it
this is the only side of the plasma membrane that contains glycosylated lipids or proteins
noncytoplasmic
this is a major component of RBC membranes, myelin, bile, surfactant, and is also used in the esterification of cholesterol
phosphatidylcholine
H1, alpha1, V1, M1, & M3 are linked to which class of G protein?
Gq (HAVe 1 M&M)
Gq initiates what cascade?
phospholipase C - PIP2 - IP3 - increased intracellular calcium (also PIP2 can yield DAG-PKC)
beta1, beta2, D1, H2, V2 are linked to which class of G protein?
Gs
M2, alpha2, and D2 are linked to what class of G protein?
Gi (MAD 2s)
Gs/Gi stimulate/inhibit what cascade?
adenylyl cyclase - cAMP - PKA
what is the most abundant protein in the body?
collagen
90% of collagen is what type?
type I
this type of collagen is found in bone, tendon, skin, dentin, fascia, cornea, late wound repair
type I
this type of collagen is found in cartilage, vitreous body, nucleus polposus
type II
this type of cartilage is found in skin, blood vessels, uterus, fetal tissue, granulaltion tissue
type III
this type of cartilage is found in basement membrane or basal lamina
type IV
this type of cartilage is found in the epiphyseal plate
type X
where are collagen alpha chains (preprocollagen) translated?
on RER
preprocollagen has the structure Gly-X-Y - what are X and Y?
proline, hydroxyproline, or hydroxylysine
hydroxylation of specific proline and lysine residues in the synthesis of collagen occurs where and requires what?
ER; vitamin C
in collagen synthesis, where does glycosylation of pro-alpha-chain lysine residues and formation of procollagen occur?
golgi
what is procollagen?
triple helix of 3 collagen alpha chains
what is formed when procollagen peptidases cleave terminal regions of procollagen? where does this occur?
tropocollagen; occurs outside fibroblasts
collagen fibrils are composed of what?
many staggered tropocollagen molecules that are reinforced by covalent lysine-hydroxylysine cross linkages
the step between pro-alpha-chains and triple helix formation/procollagen does not occur in what disease?
osteogenesis imperfecta
the step between peptide cleavage and collagen fibrils with crosslinks doesn't occur in what syndrome?
ehlers-danlos
vimentin stains what?
connective tissue
what does desmin stain?
muscle
what does cytokeratin stain?
epithelial cells
what do glial fibrillary acid proteins (GFAP) stain?
neuroglia
what do neurofliaments stain?
neurons
fatty acid oxidation (beta-oxidation), acteyl-CoA production, Krebs cycle occur where?
mitochondria
glycolysis, fatty acid synthesis, HMP shunt, protein synthesis (RER), steroid syntheis (SER) occur where?
cytoplasm
where do gluconeogenesis, urea cycle, and heme synthesis occur?
both mitochondria and cytoplasm
the 2 phosphoanhydride bonds in ATP have how many kcal/mol each?
7 kcal/mole
aerobic metabolism of glucose produces how many ATP via malate shuttle?
38 (malate - mal8)
aerobic metabolism of glucose produces how many ATP via G3P shuttle?
36
how many ATP per glucose does anaerobic glycolysis produce?
2
what is ATP composed of?
base (adenine), ribose, 3 phosphoryls, 2 phosphoanhydride bonds
ATP + methionine = ?
S-adenosyl-methionine (SAM)
what does S-adenosyl-methionine do?
transfers methyl units to a wide variety of acceptors (SAM the methyl donor man)
regeneration of methionine (and thus SAM) is dependent on what?
vitamin B12
this yields CAMP via adenylate cyclase
ATP
this yields cGMP via guanylate cyclase
GTP
what is the intermediate between glutamate and GABA? what does it require?
glutamate decarboxylase - requires vitamin B6
choline -> ACh via what?
choline acetyltransferase
arachidonate yields what products via cyclooxygenase/lipoxygenase?
prostaglandins, thromboxanes, leukotrienes
what is the rate-limiting enzyme of glycolysis?
phosphofructokinase
phosphofructokinase catalyzes fructose-6-P to what?
fructose-1,6-bis-P
what reaction does bisphosphoglycerate mutase catalyze?
1,3-BPG to 2,3 BPG
what is NADPH used in?
1. anabolic processes, 2. respiratory burst, 3. P450
this is usually used in catabolic processes to carry reducing equivalents away as NADH
NAD+
this is used in anabolic processes (steroid and fatty acid synthesis) as a supply of reducing equivalents
NADPH - product of the HMP shunt
where is hexokinase found?
throughout the body
where is glucokinase found?
primarily in the liver (gLucokinase-Liver)
this enzyme phosphorylates excess glucose to sequester it in the liver as G6P
glucokinase
what enzyme is feedback inhibited by G6P?
hexokinase
how do RBCS metabolize glucose? what do they depend on?
anaerobically (no mitochondria) - therefore depend solely on glycolysis
what catalyzes D-glucose -> G-6-P?
hexokinase/glucokinase
what catalyzes fructose-6-P -> fructose 1,6-BP?
phoshofructokinase (rate-limiting step)
what inhibits fructose-6-P -> fructose 1,6-BP?
ATP, citrate
what promotes fructose-6-P -> fructose 1,6-BP?
AMP, frucotse-2,6-BP
what catalyzes phosphoenolpyruvate -> pyruvate?
pyruvate kinase
what inhibits phosphoenolpyruvate -> pyruvate?
ATP, alanine
what promotes phosphoenolpyruvate -> pyruvate?
fructose-1-6-BP
what catalyzes pyruvate -> acetyl-CoA?
pyruvate dehydrogenase
what inhibits pyruvate -> acetyl-CoA?
ATP, NADH, acetyl-CoA
chronic granulomatous disease is related to a deficiency of what?
NADPH oxidase
deficiencies in hexokinase, glucose phosphate isomerase, aldolase, triosephosphate isomerase, phosphate glycerate kinase, enolase, and pyruvate kinase are associated with what?
hemolytic anemia
what does the pyruvate dehydrogenase complex require?
first 4 B vitamins plus lipoic acid: 1. pyrophosphate (B1, thiamine, TPP) 2. FAD (B2, riboflavin), 3. NAD (B3, niacin), 4. CoA (B5, panthotenate), 5. lipoic acid
pyruvate + NAD+ + CoA -> ???
acetyl-CoA + CO2 + NADH
what happens in pyruvate dehydrogenase deficiency?
causes backup of substrate (pyruvate and alanine), resulting in lactic acidosis - neuro defects
what is the treatment for pyruvate dehydrogenase deficiency?
increase intake of ketogenic nutrients, e.g. high fat content or increased lysine and leucine
what are the only purely ketogenic amino acids?
lysine and leucine
B1 deficiency in alcoholics can lead to what other deficiency?
pyruvate dehydrogenase
how many ATP equivalents are needed to generate glucose from pyruvate?
6 ATP
what serves as a carrier of amino groups from muscle to liver in pyruvate metabolism?
alanine
what does the Cori cycle do?
transfers excess reducing equivalents from RBCs and muscle to liver, allowing muscle to function anaerobically - net 2 ATP
what complex requires the same cofactors as the pyruvate dehydrogenase complex?
alpha-ketoglutarate dehydrogenase complex
how many ATP/acetyl-CoA does the TCA cycle produce?
12
how many NADH per acetyl CoA does the TCA cycle produce? per glucose?
3, 6
how many FADH2 and GTP does the TCA cycle produce per acetyl CoA?
1 of each (2 per glucose)
how many CO2 does the TCA cycle produce per acetyl CoA?
2 (CO2); 4 per glucose
in the electron transport chain, 1 NADH yields what?
3 ATP
in the electron transport chain, 1 FADH2 yields what?
2 ATP
what do rotenone, antimycin A, CN-, CO do?
directly inhibit electron transport, causing a decrease of proton gradient and block of ATP synthesis
what does oligomycin do?
directly inhibits mitochondrial ATPase, causing an increase of proton gradient, but no ATP is produced because electron transport stops
what do uncoupling agents, e.g. 2,4 DNP, do to oxidative phosphorylation?
increase permeability of membrane, causing a decrease of proton gradient and increased O2 consumption; ATP synthesis stops, electron transport continues
what are the irreversible enzymes in gluconeogenesis?
Pathway Produces Fresh Glucose: pyruvate carboxylase, PEP carboxykinase, fructose-1,6-bisphosphatase, glucose-6-phosphatase
what does pyruvate carboxylase catalyze? where does it occur?
pyruvate -> oxaloacetate; in mitochondira
this step of gluconeogenesis requires biotin and ATP, and is activated by acetyl-CoA
pyruvate -> oxaloacetate
what catalyzes oxaloacetate -> phophoenolpyruvate? where does this step of gluconeogenesis occur?
PEP carboxykinase; cytosol
what catalyzes fructose 1,6-bisphophate -> fructose-6-P? where does it occur?
fructose-1,6-bisphosphatase; cytosol
what reaction does glucose-6-phosphatase catalyze?
glucose-6-P -> glucose (in cytosol)
where are the enzymes of gluconeogenesis found?
liver, kidneys, intestinal epithelium (muscle cannot participate in gluconeogenesis)
what do deficiencies of the key gluconeogenesis enzymes cause?
hypoglycemia
what is the role of the pentose phosphate pathway (HMP shunt)?
1. produces ribose 5P from G6P for nucleotide synthesis 2. produces NADPH from NADP+ for fatty acid and steroid biosynthesis and for maintaining reduced glutathione inside RBCs
all reactions of the HMP shunt occur where?
cytoplasm
how much ATP is used and produced in the HMP shunt?
none
in what sites does the HMP shunt occur?
lactating mammary glands, liver, adrenal cortex - all sites of fatty acid or steroid synthesis
what are the ketogenic essential amino acids?
leucine, lysine
what are the glucogenic/ketogenic essential amino acids?
Ile, Phe, Trp
what are the glucogenic essential amino acids?
Met, Thr, Val, Arg, His
which amino acids are required during periods of growth?
Arg, His
what is the most basic amino acid?
arginine
arginine and lysine are found in high amounts where?
histones, which bind to negatively charged DNA
at body pH (7.4), acidic amino acids aspartic acid (Asp) and glutamic acid (Glu) have what charge?
negative
at body pH, basic amino acids Arg and Lys have what charge?
positive
what net charge does basic amino acid histidine have at body pH?
no net charge
what amino acids have an extra NH3 group?
Arg and Lys
what cycle degrades amino acids into amino groups?
urea cycle
the urea cycle accounts for what percent of nitrogen in urine?
90%
where in the body does the urea cycle take place?
liver
where in the cell does carbamoyl phosphate incorporation (in urea cycle) take place?
mitochondria
all steps of the urea cycle except for carbamoyl phosphate incorporation occur where?
cytosol
histamine is derived from what amino acid?
histidine
porphyrin -> heme comes from what amino acid?
glycine
creatine, urea, and nitric oxide all come from what amino acid?
arginine
GABA is derived from what amino acid?
glutamate
tyrosine (->thyroxine) -> dopa (->melanin) -> dopamine -> NE -> epi originates from what amino acid?
phenylaline
niacin, serotonin, melatonin all come from what amino acid?
tryptophan
what coenzyme is used by pyruvate dehydrogenase to convert pyruvate to acetyl CoA (in the absence of this, pyruvate accumulates and can be converted by lactate dehydrogenase to lactate, which is spilled in the blood causing lactic acidosis)
thiamine
waht do exopeptidases do?
can remove amino acids from the amino- or carboxyl-terminus of a protein
what do endopeptidases do?
cut AA bond within a molecule
what are the essential amino acids?
lysine, isoleucine, leucine, threonine, valine, tryptophan, phenylaline, methionine, histidine (& tyrosine b/c synthesized from phenylaline; arginine required for growth)
what areas of the body don't need insulin for glucose uptake into cells?
brain, RBCs, intestine, cornea, kidney, liver
BRICK L
where are GLUT2 receptors found?
beta cells
where are GLUT4 receptors found?
muscle and fat
what are the anabolic effects of insulin?
(1) increases glucose transport, (2) increases glycogen synthesis and storage, (3) increases TG synthesis and storage, (4) increases Na retention in kidneys, (5) increases protein synthesis
what does glucagon do to glycogen synthase and phosphorylase?
glucagon phosphorylates stuff : turns glycogen synthase OFF and phosphorylase ON
what does insulin do to glycogen synthase and phosphorylase?
insulin dephosphorylates stuff - turns glycogen synthase ON and phosphorylase OFF
where does fatty acid degradation take place?
where its products will be consumed - in the mitochondrion
urine test for ketones does not detect what?
beta-hydroxybutyrate (favored by high redox state)
what are ketone bodies made from?
HMG-CoA
what are ketone bodies metabolized into by the brain?
2 molecules of acetyl-CoA
what catalyzes the rate-limiting step in cholesterol synthesis?
HMG-CoA reductase, which converts HMG CoA to mevalonate
2/3 of plasma cholesterol is esterified by what?
lecithin-cholesterol acyltransferase (LCAT)
what is the role of pancreatic lipase?
degradation of dietary TG in the small intestine
what degrades TG in circulating chylomicrons and VLDLs?
lipoprotein lipase
what is the role of hepatic TG lipase?
degradation of TG remaining in IDL
what degrades TG in stored adipocytes?
hormone-sensitive lipase
what is the role of alipoprotein A-I?
Activates LCAT (A-activate)
which apolipoprotein binds to the LDL receptor?
apo B-100
what is the role of apo C-II
cofactor for lipoprotein lipase
what apolipoprotein mediates extra (remnant) uptake?
apo E (E-extra)
this lipoprotein delivers dietary triglycerides to peripheral tissues and cholesterol to the liver; secreted by intestinal epithelial cells
chylomicron
excess of this lipoprotein causes pancreatitis, lipemia retinalis, and eruptive xanthomas
chylomicron
what apolipoprotein mediates secretion of chylomicrons?
apo B-48
what lipoprotein delivers hepatic triglycerides to peripheral tissues? what is it secreted by?
VLDL - secreted by liver
this lipoprotein is formed in the degradation of VLDL & delivers TG and cholesterol to the liver, where they are degraded to LDL
IDL
what is the role of LDL?
delivers hepatic cholesterol to peripheral tissues
what lipoprotein is formed by lipoprotein lipase modification of VLDL in the peripheral tissue?
LDL
excess of this lipoprotein causes atherosclerosis, xanthomas, and arcus corneae
LDL
what is the role of HDL?
mediates transport of cholesterol from periphery to liver; acts as a repository for apoC and apoE
from where is HDL secreted?
both liver and intestine
what is the first step in heme synthesis? what catalyzes it?
succinyl CoA + glycine … catalyzed by ALA synthetase
what occurs in lead poisoning?
inhibition of ferrochelatase and ALA dehydrase
what accumulates in urine in lead poisoning?
coproporphyrin and ALA
what is deficient in acute intermittent porphyria?
deficiency in uroporphyrinogen I synthetase
what accumulates in acute intermittent porphyria?
porphobilinogen and delta-ALA
what is the deficiency in porphyria cutanea tarda?
uroporphyrinogen decarboxylase
waht accumulates in urine in porphyria cutanea tarda? what else is this associated with?
uroporphyrin accumulates (tea-colored urine); associated with photosensitivity
painful abdomen, pink urine, polyneuropathy, psych disturbances, precipitated by drugs?
symptoms of porphyrias
which form of hemoglobin has a higher affinity for O2?
relaxed form (300x affinity of taut form)
increased Cl-, H+, CO2, 2,3-BPG and temp favor what form of Hb? Which way does the O2 curve shift?
R form; shifts to right, leading to increased O2 unloading
this is an oxidized form of Hb (ferric, Fe3+) that does not bind O2 as readily but has an increased affinity for CN-
methemoglobin
what do you administer in cyanide poisoning?
nitrates to oxidize Hb to methemoglobin form
with what do you treat toxic levels of methemoglobin?
methylene blue
CO2 binding to Hb favors what form?
T (taut)
phospholipids and sphingolipids are what type of molecules? what type of vesicles do they form?
ampiphathic molecules - two hydrophobic tails; form bilayer vesicles
where does beta-oxidation of very long chain fatty acids occur?
peroxisomes
where does degradation of DNA occur?
lysosomes
where does oxidative phosphorylation occur?
mitochondria
where does post-translational modification of proteins occur?
golgi
when NO is released and diffuses into a smooth muscle cell, what does it turn on?
guanylate cyclase, which makes the second messenger cGMP, which triggers smooth muscle relaxation
what synthesized nitric oxide from arginine?
nitric oxide synthase - produces citrulline as a by-product
this is used to form nucleotids by adding a phosphoribosyl group to a nitrogenous base
phosphoribosyltransferase
what covers most microvilli & apparently helps to prevent them from trauma?
layer of glycocalyx
what is glial fibrillary acidic protein?
intermediate filament found in astrocytes
how are chromatids pulled apart during anaphase?
kinetochore microtuules from each of the two spindle poles attach to teh kinetochore plates of the centromere to pull the chromatids apart during anaphase
gap junctions are made of a hexagonal lattice of tubular rotein subunits called what?
connexons - form hydrophilic channels connecting the cytoplasm of adjacent cells
what structure are sealing strands found in?
tight junctions
what are tonofilaments found in?
desmosomes and hemidesmosomes
what contains type IV collagen, glycoproteins including laminin, and proteoglycans, including heparan sulfate?
basal lamina
what involves unfolding a fully translated protein, transporting it into the mitochondria, and then refolding it using other HSP proteins?
import of mitochondrial proteins from the cytosol into the mitochondria
what type of gene is the Rb gene?
tumor suppressor
what is the role of calreticulin?
binds to misfolded proteins and prevents them from being exported to the golgi
where does synthesis of the LDL receptor begin?
in cytosol on free ribosomes - completed on ribosomes bound to RER
what happens if a protein cannot refold properly?
it is targeted for degradation by proteases
the formation of a junctional complex relies on what?
homotypic interaction between E-cadherin proteins on adjacent cells - initiates the formation of zona adherens, including signaling pathways, which are then activated to initiate the formation of zona occludens and desmosomes
what are microvilli made of?
extensions of bundles of actin filaments, or microfilaments; myosin is associated
during contraction of a skeletal muscle, what maintains its uncontracted length?
A band
what quality control chaperone in the RER binds to misfolded membrane proteins and prevents them form proceeding to the golgi?
calreticulin
what quality control chaperone binds to misfolded soluble proteins and prevents them from going to the golgi?
calnexin
what do antibodies attack in pemphigus vulgaris?
desmoglein
what is the transmembrane cadherin that forms intercellular linkages at desmosomes?
desmoglein
what organelle is responsible for sorting and packaging of proteins?
RER
what protein property is birefringence related to?
beta-pleated sheet secondary structure
the crystalline core of an eosinic granule contains what?
major basic protein - appears to function in the destruction of parasites
name 3 sites where elastic fibers are found
large arteries (esp. aorta), vocal cords, and ligamenta flava (which connect the vertebrae); small amounts also found in skin
acini in what salivary gland are almost pure mucous cells?
sublingual, submandibular, parotid
acini in what salivary gland are a mixture of serous and mucuous cells?
submandibular
acini in what salivary gland are mostly pure serous cells?
parotid
striated muscle under voluntary control is found in what part of the esophagus?
upper third; middle third is roughly half striated and half smooth; lower third contains only smooth
primordial eggs remain stopped in what stage from before birth until ovulation?
diplotene stage of first meotic division
what is the appropriate stain for pneumocystis?
methenamine silver
what cells of the anterior pituitary stain pink?
somatotropes - GH, mammotropes - prolactin
what cells of the anterior pituitary stain blue on H&E?
corticotropes - ACTH, gonadotropes - FSH & LH, thyrotropes - TSH
what is the only site of the kidney in which epithelial cells have a brush border made of microvilli?
proximal convoluted tubule
how do fascial straps (retinacula) and fascial coverings of muscles or muscle groups attach to nearby bones?
blending with the covering periosteum; no deep attachments are made by fascia
what are the three phases of spermatogenesis?
spermatocytogenesis, meiosis, spermiogenesis
what type of cell is the germ cell closest to the basal lamina in the seminiferous tubule?
spermatogonia
what ear structure contains hair cells?
organ of corti (from the cochlear branch of CN VII)
what is a good stain for fungi?
methenamine silver
why is cartilage particularly vulnerable to infection?
because it is relatively avascular - immune system cannot access it effeciently
calcification of what is notorious for producing 'phantom' lung lesions?
hyaline cartilage of the costal cartilages
calcification of what is notorious for producing 'phantom' lung lesions?
hyaline cartilage of the costal cartilages

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