Biochemistry Flashcards by Nate Voigtman

what 2 amino acids are histones primarily made from?

lysine and arginine

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which histrone protein is NOT part of the nucleosome core?

H1, this protein attaches to the linker DNA between the beads (nucleosomes)

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differentiate heterochromatin and euchromatin

heterochromatin - highly condensed, transcriptionally inactive

euchromatin - less condensed, transcriptionally active

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where does DNA typically get methylated? what is the result?

on CpG islands

it represses transcription at that location (“M”ethylation makes DNA “M”ute)

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what is the result of histone methylation?

histone methylation also tends to repress transcription, however in a few instances it can actually activate it (histone “M”ethylation “M”ostly makes DNA “M”ute)

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what is the result of histone acetylation?

histone acetylation relaxes the DNA coiling thus allowing for transcription (“A”cetylation “A”ctivates DNA)

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how many rings are in purines? pyrimidines?

which bases are purines? pyrimidines?

purines - 2, A and G

pyrimidines - 1, C, T and U

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how many H-bonds between G-C? A-T?

G-C = 3 H-bonds (therefore stronger/higher boiling point)

A-T = 2 H-bonds

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name 3 amino acids needed for purine synthesis

“GAG” (consequently G and A are purines)
Glycine
Aspartate
Glutamine

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differentiate nucleoSides and nucleoTides

nucleoTides have attached phosphate (via a 3’-5’ phosphodiester bond), nucleoSides do not

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which DNA base contains a methyl group?

thymine (THYmine has a meTHYl)

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what reaction and substrate is used to synthesize uracil?

deamination of cytosine

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what are the steps for de novo purine syntheses?

start with sugar and phosphate (PRPP)

2. add the DNA base

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what are the steps for de novo pyrimidine syntheses?

make a temporary base (orotic acid)
add sugar and phosphate (PRPP)
modify the base

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in de novo nucleotide synthesis, which is made first, ribonucleotides of deoxynucleotides? what enzyme converts the first to the second?

1st is ribonucleotides

ribonucleotide reductase converts them to deoxy…

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name two metabolic pathways the carbamoyl is used in

urea cycle

2. de novo pyrimidine synthesis

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name 10 drugs (anti-cancer and/or antibiotic) that work by interfering with nucleotide synthesis and how they do so (if you’re a badass)

leflunomide (inhibits dihydroorotate dehydrogenase which makes orotic acid [for pyrimidines])
mycophenolate (inhibits IMP dehydrogenase which makes GMP [for purines])
ribavirin (same as #2)
hydroxyurea (inhibits ribonucleotide reductase which makes deoxynucleotides [for pyrimidines])
6-mercaptopurine [6-MP] (inhibit ne dono purine synthesis)
azathioprine (prodrug of #5, same function)
5-fluorouracil [5-FU] (inhibits thymidylate synthesis [for pyrimidines])
methotrexate [MTX] (inhibit dihydrofolate reductase therefore making less dTMP needed for bacteria)
trimethoprim (TMP) (same as #8)
pyrimethamine (same as #8)

page 67 in the book

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purine salvage deficiencies diagram (page 68)

don’t understand diagram…

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how does adenosine deaminase deficiency cause pathology?

adenosine deaminase is mainly involved in the purine metabolism/salvage pathway. this pathway is heavily utilized by lymphocytes as their source of purines (mostly adenosine?). therefore, without purines for DNA synthesis the body can’t produce B or T cells. this is one of the major autosomal recessive caused of SCID

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what is lesch-nyhan syndrome? what are they symptoms? what is its inheritance pattern? what is the treatment?

its a defect in the purine salvage pathway due to a deficiency in HGPRT (Hypoxanthine-Guanine PhosphoRibosylTransferase). it results in excessive uric acid production.

“HGPRT as a mnemonic for symptoms”

Hyperuricemia
Gout
Pissed off (agression/self mutitation)
Retardation
dysTonia

X-linked recessive

treatment: allopurinol

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explain what the 4 features of the genetic code mean:

unambiguous
degenerate/redundant
commaless/nonoverlapping
universal

unambiguous - each codon only codes for ONE AA
degenerate/redundant - most AAs are encoded by MULTIPLE codons (except MET and TRP)
commaless/nonoverlapping - read continuously from a fixed starting point
universal - the codes is conserved throughout evolution (except in mitochondria)

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DNA replication stuff (page 69)

mostly skipped since I know the hell out of it

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what is the mechanism of action of fluroquinolones?

they inhibit DNA gyrase (prokaryotic topoisomerase II) thus preventing bacterial DNA synthesis

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what is the function of the following enzymes/proteins?

single-stranded binding proteins
primase
DNA pol. I
DNA pol. III

single-stranded binding proteins - prevents DNA strands from rennealing
primase - adds an RNA primer to the DNA for DNA pol. III to bind to
DNA pol. III - elongates leading strand (5’ to 3’) and proofreads in the opposite direction
DNA pol. I - same as pol. III except that is can also remove the RNA primer

(#3 and 4 are PROKARYOTES only)

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differentiate transition and transversion in terms of DNA mutation

transition - purine to purine OR pryimidine to ptrimidine change

transversion - purine to pyrimidine OR vice versa

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differentiate a missense vs. a nonsense mutation

missense - a NT substitution resulting in the change of base (ex. sickle cell disease)

nonsense - a NT substitution resulting in a premature stop codon

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name 3 single strand DNA repair mechanisms and 1 double strand repair mechanism

SS:
1. NER (nucleotide excision repair) - removed damaged nucleotide as well as adjacent NTs and uses template to repair the spot

BER (base excision repair) - removes a single base and replaces it with the correct one (useful in spontaneous/toxic deaminations)
mismatch repair - recognizes and replaces missmatched NTs on a newly synthesized strand

DS:
1. non-homologous end joining - brings together two ends of DNA fragments (useful for DS breaks)

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what is the cause of zeroderma pigmentosum?

a defect in nucleotide excision repair (NER), which prevents the repair of pyrimidine (thymine) dimers caused by UV light

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what is the cause of hereditary nonpolyposis colorectal cancer (HNPCC)??

a defect in DNA mismatch repair

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what is the cause of ataxia telangiectasia?

a defect in non homologous end joining (DS DNA break fixing)

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what are the 3 stop codons?

UGA (U Go Away)
UAA (U Are Away)
UAG (U Are Gone)

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differentiate DNA promoters, enhancers and silencers.

promoters - site where RNA pol. (and other TFs) binds [CAAT and TATA boxes]

enhancers - stretch of DNA that binds TFs which causes increased expression of the gene

silencers - stretch of DNA that binds TFs which causes decreased expression of the gene

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what is the main function of the 3 eukaryotic RNA polymerases?

RNA pol. I - makes rRNA (the larger one)

RNA pol. II - makes mRNA

RNA pol. III - makes tRNA (and the small rRNA)

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what are the 3 sites in a eukaryotic ribosome and what do they do?

“APE”
A site - accepts incoming Aminoacyl-tRNAs
P site - accommodates the growing Peptide
E site - Empties tRNA and Exits

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which cell cycle checkpoints do the following tumor suppressor genes work at?

they BOTH work at the G1 to S checkpoint preventing it from proceeding if there is DNA damage

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what is the cause and symptoms of li-fraumeni syndrome?

caused by a mutation in the p53 tumor suppressor gene. it leads to a susceptibility to developing cancer

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what causes I-cell disease and what are some of the symptoms?

a defect of [a?] phosphotransferase in the golgi. this leads to the inability of the golgi to add mannose-6-phosphate to new proteins which is used as a targeting substituent for lysosomes. the result it that these proteins are excreted from the cell rather than moving to lysosomes.

symptoms:

coarse facial features
clouded corneas
restricted joint movements
high plasma levels of lysosome enzymes
inclusion bodies

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what is a signal recognition protein? what happens if they are deficient?

cytosolic ribonucleoproteins that traffic proteins from the ribosome to the RER. without them, proteins build up in the sytoplasm

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what is the function of the following golgi trafficking proteins?

COPI
COPII
clathrin

COPI - retrograde transfer between two golgi sacs (from more plasma membrane side to more nuclear/deeper side)
COPII - antergrade transfer between two golgi sacs
clathrin - transfers between the trans-golgi (the plasma membrane side) to lysosomes or the plasma membrane

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list the 3 functions of peroxosomes

catabolism of…:

very-long-chain fatty acids
branched chain fatty acids
amino acids

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what are dyneins and kinesins? what do they do?

they are molecular motor proteins that travel along microtubules.

dyneins move from the + end (growing end) to the - end
kinesins in the opposite direction

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name 5 drugs that act on microtubules and what they’re used for

mnemonic: “Microtubules Get Constructed Very Poorly)

Mebendazole (anti-helminthis)
Griseofulvin (anti-fungal)
Colchicine (anti-gout [and cancer?])
Vincristine/Vinblastine (anti-cancer)
Paclitaxel (anti-cancer)

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what is kartagener syndrome? what causes it? what are some symptoms?

(AKA primary ciliary dyskinesia) is an immobility of cilia due to a defect in dynein (which, in addition to transporting proteins on MTs, can also cause cilia to move by linking adjacent doublets in the 9+2 MT arangment causing them to bend). this lease to immobility of cilia thus causeing:

infertility in both men and women (sperm/uterin tubes)
recurrent respiratory infections
situs inversus (for some odd reason)

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list the targeted cell type for the following immunohistochemical intermediate filament stains:

Vimentin
desmin
cytoketatin
GFAP
neurofilaments

Vimentin - connective tissue
desMin - Muscle
cytoketatin - epithelial cells
GFAP - nueroglia (think reactive astrocytes)
neurofilaments - neurons

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how do cardiac glycosides (digoxin and digitoxin) affect the heart?

they directly inhibit the Na/K pump which indirectly inhibits the Na/Ca exchanger (which normally lets Na in and Ca out) thus leading to an increase in intracellular [Ca]. the increased Ca thus increases the cardiac contractility

list the most common places you’d find collagens type 1-4

“Be (So Totally) Cool, Read Books”

I - Bone (also Skin and Tendons) [defective in osteogeneiss inperfecta type I)

II - Cartilage (“car-two-lage”)

III - Reticular fibers vasculature [defective in the rare vascular form of ehlers-danlose syndrome]

IV - Basement membrane (“four = floor”) [defective in alport syndrome]

what is the most abundant amino acids in collagen?

glycine (proline and lysine are also abundant)

list (generally) the 6 steps of collagen synthesis

synthesis (of amino acid chain)
hydroxylation [defective in scurvy]
glycosylation [defective in osteogenesis imperfecta]
exocytosis (into ECM)
proteolytic processing
cross-linking [defective in ehlers-danlose syndrome]

what causes osteogenesis imperfecta and what are the symptoms?

its an autosomal dominant defect the leads to a decrease in production of type I collagen.

symptoms include:

brittle, easily fractured bones
blue sclerae (due to translucency of CT over the sclera veins)
hearling loss (abnormal ossicles)
dental problems (something to do with dentin)
can have skeletal deformity or limb shortening

what causes ehlers danlose syndrome and what are the symptoms?

a genetic defect in the synthesis of collagen. there are many different types, each with slightly different symptoms but in general they typically include:

hypermobile joints
hypertensible skin
tendency to bleed and easy bruising
aneurism (berry and aortic common)

what is menkes disease? what are the symptoms?

is a connective tissue disease due to impaired copper absorption.

symptoms include:

brittle, “kinky” hair
growth retardation
hypotonia

how do the following conditions relate to the protein elastin?

marfan syndrome
emphysema
age related skin wrinkling

marfan syndrome - caused by a defect in fibrillin which normally sheaths elastin
emphysema - can be caused by a deficiency in alpha-1-antitrypsin (which inhibits elastase, which breaks down elastin resulting in less elastin in tissues)
age related skin wrinkling - caused by decreased production in collagen and elastin

list the what is being analyzed with the following tests:

southern blot
northern blow
western blot
southwestern blot

“SNoW DRoP”

Southern blot - DNA
Northern blot - RNA
Western blot - Protein
southwestern blot - DNA/protein binding (TFs)

define the following genetic terms:

variable expressivity
incomplete penetrance
pleiotropy
locus heterogeneity
allelic heterogeneity
heteroplasmy
uniparental disomy

variable expressivity - the phenotype varies among individuals with the same genotype [neurofibromatosis type I NF1 gene]
incomplete penetrance - not all people with a mutant genotype will show the mutant phenotype [BRCA1 mutation and breast cancer]
pleiotropy - a single gene contributing to multiple phenotypes [PKU]
locus heterogeneity - mutations in different loci producing the same effect [albinism]
allelic heterogeneity - different mutation in same locus produce same phenotype [beta-thalassemia]
heteroplasmy - presence of both normal and mutant mtDNA causing variable expression on mitochondrial diseases
uniparental disomy - a mistake in meiosis resulting in an offspring receiving 2 copies of a chromosome from one parent and none from the other. will not cause anuploidy

what are the symptoms of angelman and prader-willi syndrome and what causes them?

caused by mutation/deletion of a gene on chromosome 15

angelman - mutated gene from mom (dad gene silent)

inappropriate laughter
seizures
ataxia
severe intellectual disability

prader-willi - from dad

obesity
hypogonadism
hypotonia
intellectual disability

skipped page 87

an overview of autosomal dominant diseases

what is the pathophysiology of cystic fibrosis

CF is an autosomal recessive mutation of the CFTR gene on chromosome 17 (frameshift; usually at Phe508).

this protein (mostly found in the lungs and GI tract) works by secreting Cl- into the lungs and GI. when this is defective is leads to a buildup of Cl- in the cell. this causes a large influx of Na+ into the cell (because it’s oppositely changed). the increased ion [ ] in the cell (particularly Na+) causes a large influx of water into the cell as well. the ultimate result is a large buildup of thick, hard to move (because its dryer) mucus in the lungs and GI.

list 11 x-linked recessive diseases

“Be Wise, Fool’s GOLD Heeds Silly HOpe”

Bruton agammaglobulinemia
Wiskott-aldrich syndrome
Fabry disease
G6PD deficiency (a PPP enzyme)
Ocular albinism
Lesch-nyhan disease
Duchenne (and becker) muscular dystrophy
Hunter Syndrome
Hemophilia (type “a” and “b”)
Ornithine transcarbamylase deficiency (a urea cycle disorder)

list the type and site of mutation for the following disease:

duchenne muscular dystrophy
becker muscular dystrophy
myotonic type 1 muscular dystrophy

duchenne muscular dystrophy - FRAMESHIFT mutation in DMD (dystrophin) gene
becker muscular dystrophy - POINT mutation in DMD (dystrophin) gene
myotonic type 1 muscular dystrophy - CTG trinucleotide repeat expansion in DMPK gene

list 3 symptoms of duchenne muscular dystrophy

gowers sign (using arms to stand up)
starts with weakness in pelvic girdle the progresses superiority
pseudohyperthophy of the calf muscles

list 6 symptoms of myotonic type 1 muscular dystrophy (AKA steinert disease)

myotonia (delayed muscular relaxation after voluntary contraction)
muscle wasting
frontal balding
cataracts
testicular atrophy
arrhythmia

what is the cause of fragile x syndrome? what are they symptoms?

is an x-linked defect in the FMR1 (fragile x mental retardation 1) gene caused by a CGG trinucleotide repeat.

symptoms:

large testes, jaw, face and ears
autism
intellectual disability (2nd most common hereditary cause behind downs)
mitral valve prolapse

list 4 diseases caused by trinucleotide repeats and that that repeat is

for the diseases - “Try [trinucleotide] Hunting for MY FRIED Eggs [as in x c’somes]

for the repeats (middle NT) - “X-Girlfriend’s First Aid Helped Ace MY Test”

Huntington disease - cAg
Myotonic dystrophy - cTg
Friedreich ataxia - gAa
fragile X disease - cGg

list 3 autosomal trisomy disorders and which chromosome they are associated with

“Drinking age = 21, Election age = 18, Puberty = 13”

Down syndrome - 21
Edwards syndrome - 18
Patau syndrome - 13

list some symptoms of down syndrome

trisomy 21

intellectual disability
* 2. characteristic facies
congenital heart disease
* 4. ligamentous laxity
* 5. very high correlation with alzheimer disease
* 6. can have doudinal atresia (blind ended or closed lumen)
* 7. can have hirschprung disease

= unique finding between the 2 other trisomys

list 5 symptoms of edwards syndrome

trisome 18

severe intellectual disability
rocker-bottom feet (upward curved feet)
* 3. low-set Ears
* 4. clenched hands
congenital heart disease (typically death within a year)

= unique finding between the 2 other trisomys

list 5 symptoms of patau syndrome

trisomy 13

severe intellectual disability
rocker-bottom feet (upward curved feet)
* 3. micropthalmia (small eyes)
* 4. cleft liP/Pallate
* 5. holoprosencephaly
* 6. Polydactyly
congenital heart disease (typically death within a year)

= unique finding between the 2 other trisomys

what is robertsonian translocation?

a term for non-reciprical chromosomal translocation between chromosomes. it typically involves chromosomes 13, 14, 15, 21 and 22.

what is cri-du-chat syndrome and what are the symptoms?

a congenital microdeletion of the short arm of chromosome 5.

symptoms:

moderate to severe intellectual disability
microcephaly
high pitched crying/MEWING (like a cat; “cry of the cat”)
cardiac abnormalities (vascular septal defect = defect in wall separating ventricles)
epicanthal folds

what is the cause of williams syndrome and list 5 symptoms

caused by a microdeletion in the long arm of c’some 7 (which includes the elastin gene)

symptoms:

distinctive facies
intellectual disability (with well-developed verbal skills)
hypercalcemia
extreme friendliness with strangers
cardiovascular problems

list the symptoms of 22q11 deletion syndrome and 2 of its presentations

“CATCH-22”

Cleft pallate
Abnormal facies
Thymic aplasia
Cardiac defects
Hypocalcemia (due to parathyroid aplasia [makes PTH which increases [Ca] in blood])

presentations:
1. DiGeorge syndrome - thymic, parathyroid and cardiac symptoms from above

Velocardiofacial syndrome - palate, facial and cardiac symptoms from above

what is the general cause of 22q11 deletion syndrome symptoms

aberrant development of the 3rd and 4th brachial pouches

what are the other names for the following vitamins (and what other molecules are they used to make):

A - retinol
B1 - thiamine [TPP]
B2 - riboflavin [FAD, FMN]
B3 - niacin [NAD+]
B5 - pathothenic acid [CoA]
B6 - pyridoxine [PLP]
B7 - biotin
B9 - folate
B12 - cobalamin
C - ascorbic acid
E - tocopherol/tocotrienol

which 2 water soluable vitamins are stored in the liver

B9 (folate) and B12 (cobalamin). because they are stored in the liver they do NOT wash out of the body as easily as the other water soluble vitamins do

what is the function of vitamin A? what are some symptoms of A deficiency and excess?

(retinol) its an antioxidant, a constituent of visual pigments and is needed for differentiation of epithelial cells to specialized ones

deficiency symptoms:

nyctalopia (night blindness)
xerosis cutis (dry, scaly skin)
alopecia (hair loss)
corneal degeneration
immune supression

excess symptoms:

arthralgias (joint pain)
alopecia
cerebral edema
osteoperosis
pseudotumor cerebri
liver problems
teratogenic

what is the function of vitamin B1? what are some symptoms of B1 deficiency and excess?

(thiamine) used as a cofactor for many DEHYDROGENASE enzymes in the form of TPP (thiamine pyrophosphate). mnemonic “ATP” for the enzymes:
- Alpha-ketogluterate dehudrogenase
- Transketolase
- Pyruvate dehydrogenase
- also branched-chain ketoacid dehydrogenase

(the above mnemonic also works because thiamine deficiency conses ATP depletion)

deficiency symptoms:

ATP depletion due to impaired glucose breakdown (highly aerobic tissues like the heart and brain are affected 1st)
wernicke-korsakoff syndrome (usually from alcoholism malnutrition)
wet and dry beriberi (malnutrition again) [mnemonic = “Ber1Ber1”]

excess symptoms:
-none

what is the cause of wernicke-korsakoff syndrome? what structures are damaged? what is the classic triad of symptoms?

B1 deficiency usually caused by alcoholism induced malnutrition.

the mammillary bodies and dorsal medial nucleus of the thalamus are most commonly damaged

Symptoms:

personality change
confabulation (made up memories)
memory loss

list 2 symptoms for wet and dry beriberi

both caused by B1 (thiamine) deficiency

Wet beriberi

high output cardiac failure (dialated cardiomyopathy)
edema

Dry beriberi

polynephritis
symmetrical muscle wasting

what is the function of vitamin B2? what are some symptoms of B2 deficiency and excess?

(riboflavin) used a components of flavins (FAD and FMN) which are cofactors for red-ox reactions (ex. succinate dehydrogenase in the TCA cycle). mnemonic “B2 = 2ATP [from FAD]”

deficiency symptoms: “the 2 C’s of B2”

cheilosis (inflammation of lips and scaline/fissuring of the corners of the mouth)
corneal vascularization

excess symptoms:
-none

what is the function of vitamin B3? what are some symptoms of B3 deficiency and excess?

(niacin) used as a constituent of NAD+ and NADP+ which are used in red-ox reactions. can also be used to lower levels of VLDL and raise HDL. mnemonic “B3 = 3ATP [from NAD]”

deficiency symptoms: “the 3 D’s of B3”

diarrhea
dementia
dermatitis

excess symptoms:

facial flushing
hyperglycemia
hyperuricemia

what is the function of vitamin B5? what are some symptoms of B5 deficiency and excess?

(pentothenate) used as a component of CoA and for fatty acid synthesis. “B5 = PENTOthenate”

deficiency symptoms:

dermatitis
enteritis
alopecia
adrenal insufficiency

excess symptoms:
-none

what is the function of vitamin B6? what are some symptoms of B6 deficiency and excess?

(pyridoxine) needed for the synthesis of many important molecules including heme, niacin (B3), histamine, serotonin, epinepherine, norepinepherine, dopamine and GABA

deficiency symptoms:

convulsions
hyperirritability
peripherial neuropathy
sideroblastic anemias (due to decreased heme)

excess symptoms:
-none

what is the function of vitamin B7? what are some symptoms of B7 deficiency and excess?

(biotin) cofactor for many CARBOXYLATION enzymes (which add single carbons to molecules) including:
- pyruvate carboxylase
- acetyl-CoA carboxylase
- propionyl-CoA carboxylase

deficiency symptoms: (RARE)

dermatitis
alopecia
enteritis

what is the function of vitamin B9? what are some symptoms of B9 deficiency and excess?

(folic acid) its converted to tetrahydrofolate which is a coenzyme for 1-carbon transfer/methylation reactions needed for the synthesis of nitrogenous bases

deficiency symptoms:

macrocytic and megaloblastic anemia
hypersegmented PMNs on blood smears
glossitis
NO neurological symptoms (like you would see in B12 deficiency)
increased homocystein and normal methylmalonic acid

excess symptoms:
-none

what is the function of vitamin B12? what are some symptoms of B12 deficiency and excess?

(cobalamin) used as a cofactor for two enzymes:
- homocysteine methyltransferase
- methylmalonyl-CoA mutase

deficiency symptoms:

macrocytic and megaloblastic anemia
hypersegmented PMNs on blood smears
parasthesias
subacute combines degeneration (demyelination of dorsal columns as well as lateral CST and spinocerebellar tracts)
increased homocystein AND methylmalonic acid (just homocystein in B9 deficiency)

excess symptoms:
-none

what is the function of vitamin C? what are some symptoms of C deficiency and excess?

(ascorbic acid) an antioxidant, facilitates Fe absorption, needed for hydroxylation of proline and lysine in collagen synthesis and needed for the conversion of dopamine to NE

deficiency symptoms:

scurvy (anemia, swollen gums, poor wound healing…)
weakened immune system

excess symptoms:

flu-like symptoms (nausea, vomiting, diarrhea, fatigue)
increased risk of Fe toxicity
kidney stones

what is the function of vitamin D? what are some symptoms of D deficiency and excess?

used to increase intestinal absorption of Ca and phosphate which increases bone mineralization

deficiency symptoms:

rickets (in children)
osteomalacia (in adults)
hypocalcemic tetany

excess symptoms:

hypercalcemia
hypercalciuria
loss of appetite
stupor

what is the function of vitamin E? what are some symptoms of E deficiency and excess?

(tocopherol/tocotrienol) an antioxidant that protects erythrocytes and membranse from free radicals and it can enchance the anticoagulation effect of warfarin. “E is for Erythrocyte”

deficiency symptoms: (can look similar to B12 deficiency)

hemolytic anemia
posterior column and spinocerebellar tract demyelination
acanthocytosis (RBCs becoming “spikey”)

excess symptoms:
-none

what is the function of vitamin K? what are some symptoms of K deficiency and excess?

needed for blood coagulation. used in the activation of clotting factors II, VII, IX, X, protein C and S (warfarin is a vitamin K antagonist)

deficiency symptoms:
-neonatal hemorrhage (increased PT and PTT times because K is made by intestinal flora but neonates have sterile intestines)

excess symptoms:
-none

what is the function of zinc? what are some symptoms of zinc deficiency and excess?

needed for the activity of 100s of enzymes and used in zinc-finger moieties on TFs

deficiency symptoms:

delayed wound healing
hypogonadism
loss of taste and smell
decreased hair in adults

excess symptoms:
-none

what do the following drugs do?

fomepizole
disulfiram

fomepizole - inhibits alcohol dehydrogenase (converts ethanol to acetaldehyde) thus working as an antidote for methanol and ethylene glycol poisoning
disulfiram - inhibits acetaldehyde dehydrogenase (converts acetaldehyde to acetate) thus leading to an increase in acetaldehyde which worsens hang over symptoms. this is used to treat alcoholism

for the following enzymes, list their substrate and produce, where in the cell they are found and the limiting reagent for their reactions

alcohol dehydrogenase
acetaldehyde dehydrogenase

alcohol dehydrogenase - converts ethanol to acetaldehyde, in cytosol
acetaldehyde dehydrogenase - converts acetaldehyde to acetate, in mitochondria

both reactions use energy from NAD+ (thus converting it to NADH) to produce their product. NAD+ is the limiting reagent in these reactions

list 3 other molecules that increase in concentration due to the increased NADH/NAD+ ratio caused by alcohol metabolism and their physiological consiquences

pyruvate - which gets converted to lactate (because there’s more than the cell needs) and contributes to lactic acidosis
oxaloacetate - which gets converted to malate which prevents gluconeogenesis and therefore caused fasting hypoglycemia
glyceraldehyde-3-phosphate - which combines with fatty acids to make triglycerides which contributes to hepatosteatosis (fatty liver)

differentiate kwashiorkor and marasmus and list their symptoms

kwashiorkor - protein malnutrition
"MEAL"
-Malnutrition
-Edema (often distended belly)
-Anemia
-Liver change (fatty)

marasmus - total calorie malnutrition
"Merasmus results in Muscle wasting"
-muscle loss
-subcutaneous fat loss
-visible edema

for the following reactions, list whether they occur in the mitochondria, cytosol or both.

TCA cycle
gylcolysis
fatty acid synthesis
heme synthesis
beta (fatty acid) oxidation
HMP shunt
acetyl-CoA production
urea cycle
oxidative phosphorylation
protein synthesis
steroid synthesis
gluconeogenesis
cholesterol synthesis

TCA cycle - mitochondria
gylcolysis - cytosol
fatty acid synthesis - mitochondria
heme synthesis - both
beta (fatty acid) oxidation - mitochondria
HMP shunt - cytosol
acetyl-CoA production - cytosol
urea cycle - both
oxidative phosphorylation - mitochondria
protein synthesis - cytosol
steroid synthesis - cytosol
gluconeogenesis - both
cholesterol synthesis - cytosol

for both = “HUGs take 2 (ie. both)”

rate limiting enzymes on page 99. probably important but I’m skipping it

too much shit to write down

what is the NET ATP production per glucose for aerobic metabolism? what about anaerobic?

aerobic - 32ATP

anaerobic - 2ATP

how does arsenic affect ATP production?

it causes glycolysis to produce 0 net ATP

for the following carrier molecules, list what they are carrying when activated

ATP
NADH, NADPH, FADH2
CoA, lipoamide
biotin
tetrahydrofolates
SAM
TPP

ATP - phosphoryl groups
NADH, NADPH, FADH2 - electrons
CoA, lipoamide - acyl groups
biotin - CO2
tetrahydrofolates - 1-carbon units
SAM - CH3 groups
TPP - aldehydes

list ALL the net products of glycolysis

2 pyruvate
2 ATP
2 NADH
2 H+
2 H2O

page 102 has some glycolysis regulation info.

maybe i’ll review it later

list the reagents and products of the pyruvate dehydrogenase complex

pyruvate + NAD+ + CoA = acetyl-CoA + CO2 + NADH

name the 5 cofactors required for the pyruvate dehydrogenase complex to function

pyrophosphate (B1/thiamine, TPP)
FAD (B2/riboflavin)
NAD (B3/niacin)
CoA (B5/pantothenate)
lipoic acid [arsenic inhibits this]

what is the result of pyruvate dehydrogenase complex deficiency and what are the symptoms?

it causes a buildup of pyruvate which gets converted to lactate and alanine

symptoms:

neurological defects
lactic acidosis
increases serum alanine

what are the products of the 4 different pyruvate metabolism pathways?

acetyl-CoA - used for the TCA cycle
oxaloacetate - used to replenish the TCA cycle
lactate
alanine

list the NET end products of the TCA cycle (per 1 acetyl-CoA)

3 NADH
1 FADH2
2 CO2
1 GTP

list the 8 major molecules used in the TCA cycle and how many carbons each one has

“Citrate Is Kreb’s Starting Substrate For Making Oxaloacetate”

Citrate (6; it gets 2 from acetly-CoA)
Isocitrate (6)
alpha-Ketogluterate (5)
Succinyl-CoA (4)
Succinate (4)
Fumarate (4)
Malate (4)
Oxaloacetate (4)

for each of the following molecules going through the electron transport chain, how many ATP is produced by ATP synthase

NADH
FADH2

NADH - 2.5 ATP

2. FADH2 - 1.5 ATP (because it enters the chain at complex II at a lower energy level)

list 4 molecules/drugs that interfere with the electron transport chain and 1 that directly interferes with ATP synthase

ETC disruptors (decreased proton gradient therefore no ATP)

rotenone
cyanide
antimycin A
CO

ATP synthasea disruptors (increased proton gradient because ETC is still working but no ATP because this enzyme is not functional)
1. oligomycin

list 3 mitochondrial uncoupling agents and how they work

they work by making the membrane of the mitochondria more permeable to protons thus destroying the gradient needed for ATP synthesis. the ETC however, is still functioning, which results in increased heat production.

2,4-dinitrophenol (used illicitly for weight loss)
aspirin (to a smaller degree, overdose causes fever)
thermogenin in brown fat

list the 4 irreversible enzymes in gluconeogenesis

“[gluconeogenesis] Pathway Produces Fresh Glucose”

Pyruvate carboxylase
Phosphoenolpyruvate carboxykinase
Fructose-1,6-bisphosphatase
Glucose-6-phosphatase

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