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180 Cards in this Set

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Only histone not in nucleosome core
H1
heterochromatin
Highly Condensed
transcriptionally inactive
Methylation in DNA replication
Hypermethylation
Template strand C and A are methylated for mismatch repair enzymes to distinguish btn old and new strands
hyper- inactivates DNA transcription
Histone acetylation
relaxes DNA coiling, allows for transcription
Acetylation makes DNA Active
Purines
A G
2 rings
Pyrimidines
C T U
1 ring
Guanine has a
Thymine has a
Ketone
meTHYl
How to make uracil
Deamination of cytosine
G-C bond
A-T bond
3 H bonds- stronger
2 H bonds
inc G-C content, inc melting temp
NucleoSide
NucleoTide
base + ribose (Sugar)
base+ribose+phosphaTe, linked by 3-5 phosphodiester bond
AA necessary for purine synthesis
GAG
Glycine
Aspartate
Glutamine
Carbamoyl phosphate involved in 2 metabolic pathways
De novo pyrimidine synthesis
Urea cycle
Ornithine transcarbamoylase (OTC) deficiency
X linked recessive, MC urea cycle dso
OTC key enzyme in urea cycle
Def leads to accumulation of carbamoyl phosphate, which is converted to orotic acid, which is part of pyrimidine synthesis pathway
Inc orotic acid with hyperammonemia
Orotic aciduria
Inability to convert orotic acid to UMP
Inc orotic acid in urine, megaloblastic anemia, FTT
tx oral uridine administration
Adenosine deaminase deficiency
Excess ATP and dATP imbalances nucleotide pool via feedback inhibition of ribonucleotide reductase, prevents DNA synthesis and dec lymphocyte count
major cause of SCID
Lesch-Nyhan syndrome
He's Got Purine Recovery Trouble
X linked recessive
defective purine salvage due to absence of HGPRT, which converts hypoxanthine to IMP and guanine to GMP
excess uric acid production and de novo purine synthesis
ID, self mutilation, aggression, hyperuricemia, gout, choroathetosis
AA encoded by only one codon
Methonine- AUG
Tryptophan- UGG
Severity of damage of DNA mutations
nonsense > missense > silent
Nonsense mutation
early stop codon
Stop the nonsense!
Helicase
Unwinds DNA template at replication fork
DNA topoisomerases
create a nick in helix to relieve supercoils created during replication
Primase
makes RNA primer on which DNA polymerase III can initiate replication
DNA polymerase III
prokaryotic only
5-3 synthesis
proofreads with 3-5 exonuclease
DNA polymerase I
prokaryotic only
degrades RNA primer with 5-3 exonuclease and fills in gap with DNA
DNA ligase
seals
Telomerase
adds DNA to 3' ends of chromosomes to avoid loss of genetic material with every duplication
Xeroderma pigmentosum
nucleotide excision repair is mutated, prevents repair of thymidine dimers due to UV light exposure
What is mutated in HNPCC
DNA mismatch repair
What is mutated in ataxia telangiectasia
Nonhomologous end joining- bringing together 2 ends of DNA fragments
RNA polymerase I makes
rRNA- most numerous RNA, rampant
RNA polymerase II makes
mRNA- largest RNA, massive
RNA polymerase III makes
tRNA- smallest RNA, tiny
alpha amanitin inhibits
RNA polymerase II
causes liver failure
found in death cap mushrooms
Lac operon
When active, E. coli can metabolize lactose
Lactose inhibits repressor
Glucose inhibits activator
Alternative splicing
Different exons can be combined to make unique proteins in different tissues
ex beta thalassemia mutations
Aminoacyl tRNA synthetase
1 per aa, matchmaker, uses ATP
scrutinizes aa before and after it binds to tRNA
CCA
at 3' end of tRNA
Can Carry Amino acids
ATP and GTP in Protein synthesis initiation
ATP- tRNA Activation- charging
GTP- tRNA Gripping and Going places- translocaiton
Rb and p53
inhibit G1 to S progression
mutations in these genes result in unrestrained growth
Cell cycle phases
G - Gap or Growth
S - Synthesis
Mitosis is shortest phase
G1 and G0 are of variable duration
Permanent cells
Remain in G0, regenerate from stem cells
Neurons, skeletal and cardiac muscle, RBCs
Stable (quiescent) cells
Enter G1 from G0 when stimulated
Hepatocytes, lymphocytes
Labile cells
Never enter G0, divide rapidly witha short G1
Bone marrow, gut epithelium, skin, hair follicles
Nucleotide excision repair
Specific endonucleases release oligonucleotide-containing damaged bases
Base excision repair
DNA glycosylase and AP endonuclease remove and repair damaged bases
Nissl bodies
RER in neurons
synthesize enzymes (ex ChAT makes Ach) and peptide Nts
Free ribosomes
site of synthesis of cytosolic and organellar proteins
RER
site of synthesis of secretory exported proteins and of N-linked oligosaccharide addition to many proteins
mucous-secreting goblet cells of SI and ab-secreting plasma cells are rich in RER
SER
steroid synthesis and detox of drugs and poisons
liver hepatocytes and steroid hormone producing cells of adrenal cortex are rich in SER
Golgi
Modifies N-oligosaccharides on asparagine
Adds O-oligosaccharides on serine and threonine
Adds mannose-6-phosphate to proteins for trafficking to lysosomes
Vesicular trafficking proteins
COPI- retrograde- golgi to er
COPII- anterograde- rer to cis golgi
Clathrin- trans golgi to lysosomes, plasma membrane, endosomes
I cell disease
lysosomal storage dso
failure to add M6P to lysosome proteins
coarse facial features, clouded corneas, restricted joint movement, high plasma levels of lysosomal enzymes
Peroxisome
membrane enclosed organelle involved in catabolism of very long fatty acids and aa
Chediak Higashi syndrome
microtubule polymerization defect results in dec fusion of phagosomes and lysosomes
recurrent pyogenic infections, partial albinism and peripheral nureopathy
Kartagener's syndrome
immotile cilia due to dynein arm defect
infertility, bronchiectasis, recurrent sinusitis, situs inversus
Molecular motor proteins
Dynein- retrograde to microtubule + to -
Kinesin- anterograde to microtubule - to +
Type III collagen
Reticulin- skin, blood vessels, uterus, fetal tissue, granulation tissue
defective in Ehlers Danlos- threE D
Type I collagen
bone, skin, tendon, dentin, fascia, cornea, late wound repair
90%
Type II collagen
cartilage, vitreous body, nucleus pulposus
Type IV collagen
Basement membrane or basal lamina
under the floor
Defective in Alport syndrome
Alport syndrome
abnormal type IV collagen
progressive hereditary nephritis, deafness, ocular disturbances
SNoW DRoP
Southern blot= DNA
Northern blot= RNA
Western blot= Protein
Southwestern blot
identifies DNA-binding proteins- ex transcription factors, using labeled oligonucleotide probes
ELISA
enzyme linked immunosorbent assay
rapid immunologic technique testing for antigen-antibody reactivity
can use test antigen or antibody
peroxidase enzyme generates color
intense color reaction indicated positive test results
Cre-lox system
can inducibly manipulate genes at specific developmental points using antibiotic-controlled promoter
ex to study a gene whose deletion causes embryonic death
RNAi
ds RNA synthesized that is complementary to mRNA sequence of interest
when transfected into human cells, dsRNA separates and degrades target mRNA, knocking down gene expression
Mosaicism
occurs when cells in the body differ in genetic makeup due to post-fertilization loss of genetic information during mitosis
come from same zygote
Chimeric
derived from 2 zygotes that subsequently fuse
Locus heterogeneity
mutations at different loci can produce the same phenotype
Marfan's, MEN2B and homocystinuria all cause marfanoid habitus
Heteroplasmy
presence of normal and mutated mtDNA, resulting in variable expression in mitochondrial inherited disease
Frequency of X-linked recessive disease in Hardy Weinberg population in..
males
females
males = q
females = q^2
AD
often due to defects in structural genes
AR
often due to enzyme deficiencies
X linked dominant
All female offspring of affected father are diseased
ex hypophosphatemic rickets- vit d resistant rickets- inc phosphate wasting at proximal tubule
X linked recessive
No male to male transmission
Sons of heterozygous mothers have 50% chance of being affected
ADPKD
mutation in PKD1 on chromosome 16, always bilateral, associated with berry aneurysms
FAP
mutation of APC gene on chromosome 5
5 letters in polyp
Familial hypercholesterolemia
hyperlipidemia type IIA
elevated LDL due to defective or absent LDL receptor
Osler Weber Rendu syndrome
hereditary hemorrhagic telangiectasia
inherited dso of blood vessels
telangiectasia, recurrent epistaxis, skin discolor, AVMs
Huntington's dse
dec levels of GABA and Ach in brain, caudate atrophy, gene located on chrom 4, trinucleotide CAG repeat dso, "hunting 4 food"
NF type 1
chromosome 17, cafe au lait spots, neural tumors, lisch nodules, skeletal dso, optic pathway gliomas
NF type 2
chromosome 22, bilateral acoustic schwannomas, juvenile cataracts
von Hippel Lindau disease
3 words for chomosome 3p
deletion of VHL tumor suppressor gene
bilateral renal cell carcinomas, hemangioblastomas or retina/cerebellum/medulla
tuberous sclerosis
adenoma sebaceum, hypopigmented ash leaf spots, cortical and retinal hamartomas, sz, MR, renal cysts and angiomyolipomas, cardiac rhabdomyomas, inc incidence of astrocytomas
CF tx
N-acetylcysteine to loosen mucous plugs- cleaves disulfide bonds within mucous glycoproteins
X linked recessive dsos
Be Wise, Fool's GOLD Heeds Silly Hope
Bruton's agammaglobulinemia, Wiskott-aldrich syndrome, Fabry's dse, G6pd def, Ocular albinism, Lesch nyhan syndrome, Duchennes and beckers muscular dystrophy, Hunter's Syndrome, Hemophilia a and b
Fragile X
X linked defect affecting methylation and expression of FMR1 gene,
eXtra large testes, jaw, ears, CGG repeat dso
Trinucleotide repeat dso
X Girlfriend's- Fragile X CGG
First Aid- Freidreich's Ataxia GAA
Helped Ace- Huntington's CAG
My Test- Myotonic dystrophy CTG
Pregnancy quad screen in Downs
dec alpha fetoprotein, dec estriol, inc beta hCG, inc inhibin A
Pregnancy quad screen in Edward's syndrome (Trisomy 18)
dec alpha fetoprotein, dec estriol, dec beta hCG, normal inhibin A
Pregnancy quad screen in Patau's syndrome (Trisomy 13)
All 4 are normal!
Cri du chat syndrome
congenital microdeletion of short arm of chromosome 5
high pitched crying, microcephaly, VSD
Williams syndrome
congenital microdeletion of 7q, includes elastin gene, elfin facies, hypercalcemia, well developed verbal skills, cardiovascular problems
22q11 deletion
CATCH 22
Cleft palate, Abnormal facies, Thymic aplasia- T cell def, Cardiac defects, Hypocalcemia secondary to parathyroid aplasia
B complex deficiencies often result in
Dermatitis, glossitis, diarrhea
Vit A (retinol)
antioxidant, essential for normal differentiation of epithelial cells into specialized tissue
found in liver and leafy veggies
def- night blindess, dry skin
excess- arthralgias, fatigue, alopecia, skin changes, teratogenic
Vit B1 (Thiamine)
in thiamine pyrophosphate (TPP), a cofactor for several enzymes in decarboxylation rxns required for ATP synthesis
def- impaire glucose breakdown- ATP depletion
Ber1 Ber1, Wenicke Korsakoff
Alpha ketoglutarate DH
Transketolase
Pyruvate DH
required for ATP synthesis
Wernicke Korsakoff
confusion, ophthalmoplegia, ataxia
damage to medial dorsal nuc of thalamus, mammillary bodies
Dry beriberi
polyneuritis, symmetrical muscle wasting
Wet beriberi
high output cardiac failure- dilated cardiomyopathy
edema
Vit B2 (riboflavin)
cofactor in redox
FAD and FMN are derived from riboFlavin, B2 = 2 ATP
def- 2 C's of B2- cheliosis, corneal vascularization
Vit B3 (niacin)
NAD derived from Niacin, B3=3ATP, derived from tryptophan, synthesis requires B6
def- glossitis, severe causes pellagra
excess- facial flushing
Hartnup dse
AR defect in intestinal and renal transporters of neutral AA
dec tryptophan absorption
can cause niacin def- pellagra
3 D's of B3
diarrhea, dermatitis, dementia
Essential AA
PriVaTe TIM HALL
Phe, Val, Thr, Trp, Ile, Met, His, Arg, Leu, Lys
Acidic AA
Aspartic acid
Glutamic acid
Basic AA
Arginine
Histidine
Lysine
Vit B5 (pantothenate)
"pento"thenate
essential component of CoA and fatty acid synthase
def- dermatitis, enteritis, alopecia, adrenal insufficiency
Vit B6 (pyridoxine)
converted to pyridoxal phosphate, used in transamination, synthesis of cystathionine, heme, niacin, and GABA
def- convulsions, hyperirritability, peripheral neuropathy, sideroblastic anemia
Isoniazid
decreases vit b6
Vit B12 (cobalamin)
cofactor for homocysteine methyltransferase and methylmalonyl-CoA mutase, found in animal products
def- macrocytic, megaloblastic anemia, hyperseg polys, neurologic sx
Folate
from FOLiage
coverted to THF
important for synthesis of nitrogenous bases in DNA and RNA
def- macrocytic, megaloblastic anemia, no neuro sx
Most common vit def in US?
Folate def
seen in alcoholism and pregnancy
can be caused by phenytoin, sulfonamides, MTX
S adenosyl methionine
SAM the methyl donor man
transfers methyl units
required to convert NE to E
Biotin
cofactor for carboxylation enzymes which add a 1-C group
def- rare, dermatitis, alopecia, enteritis, caused by antibiotic use or excessive ingestion of raw eggs
AVIDin in egg whites AVIDly binds biotin, causes def
Vit C (ascorbic acid)
antioxidant, in fruits and veggies, "Absorb"ic acid- facilitates iron absorption, necessary for hydroxylation of proline and lysine in collagen synthesis, and for dopamine beta hydroxylase which converts dopamine to NE
def- scurvy, weakened immune response
excess- NVD, fatigue, sleep problems, inc risk of iron tox in predisposed- ex pts with transfusions, HH
Vit abnormality seen in sarcoidosis?
Vit D excess- inc activation of vit d by epithelioid macrophages, get hypercalcemia, hypercalciuria, loss of appetite, stupor
Vit E
protects Erythrocytes and membranes from free radical damage
def- hemolytic anemia, post column and spinocerebellar tract demyelination, muscle weakness
Vit K
Koagulation
synthesized by intestinal flora
necessary for synthesis of clotting factors II, VII, IX, X, protein C and S
def- inc PT and aPTT but normal bleeding time
Warfarin
vit K antagonist
Vitamins deficient in breast milk
inadequate D, no K
Zinc
essential for activity of many enzymes
def- delayed wound healing, hypogonadism, dec adult hair, dysgeusia- abnml taste, anosmia
Kwashiorkor
protein deficient
MEAL- malnutrition, edema, anemia, liver (fatty)
Marasmus
Muscle wasting
energy malnutrition
Metabolism in mitochondria
FA beta oxidation, acetyl CoA production, TCA cycle, ox phos
Metabolism in cytoplasm
glycolysis, FA synthesis, HMP shunt, protein synthesis in RER, steroid synthesis in SER
Metabolism in both mito and cyto
HUGs take two
Heme synthesis, Urea cycle, Gluconeogenesis
Kinase
uses ATP to add high energy phosphate
Phosphorylase
adds inorganic phosphate without using ATP
Phosphatase
removes phosphate group from substrate
Dehydrogenase
oxidizes substrate
Carboxylase
transfers CO2 groups with help of biotin
Thiamine
cofactor for decarboxylation rxns
Biotin
cofactor for carboxylation rxns
NAD+
from vit B3, used in catabolic processes to carry reducing equivalents away as NADH
NADPH
product of HMP shunt
used in anabolic processes- steroid and FA synthesis- as a supply of reducing equivalents
used in respiratory burst, P-450, glutathione reductase
Hexokinase
phosphorylates glucose to G6P, ubiquitous, high affinity (low Km), low capacity (low Vmax), uninduced by insulin, negative feedback by G6P
Glucokinase
in liver and beta cells of pancreas, low affinity, high capacity, GLUcokinase is a GLUtton- high Vmax because it can't be satisfied, phos excess glucose to sequester it to liver
Fructose 2,6 bisphosphate
stimulates conversion of F-6-P to F-1,6-P, more glycolysis
Fasting state
increase glucagon, inc cAMP, inc protein kinase A, inc FBPase 2, dec PFK 2, less glycolysis
Fed state
increase insulin, dec cAMP, dec protein kinase A, inc PFK 2, dec FBPase2, inc F2,6BP, more glycolysis
Purely Ketogenic AA
Lysine and Leucine
TCA cycle produces
3 NADH, 1 FADH2, 2 CO2, 1 GTP per Acetyl CoA = 12 ATP per acetyl CoA
2 times everything per glucose
Pyruvate to acetyl coA produces
1 NADH, 1 CO2
Pyruvate dehydrogenase complex and alpha ketoglutarate complex require cofactors
B1, B2, B3, B5, lipoic acid
TCA cycle order of substrates
Citrate Is Kreb's Starting Substrate For Making Oxaloacetate
Irreversible enzymes in gluconeogenesis
Pathway Produces Fresh Glucose
Pyruvate carboxylase, PEP carboylase, F1,6BPase, G6Pase
Catalase positive spp
Staph aureus
Aspergillus
G6PD deficiency
X linked recessive
dec NADPH, in RBCs leads to hemolytic anemia due to poor RBC defense against oxidizing agents- ex fava beans, sulfonamides, primaquine, anti tb drugs
Heinz bodies- oxidized Hemoglobin precipitated within RBCs
Bite cells from phagocytic removal of Heinz bodies by splenic macrophages
NADPH
produced by G6PD, necessary to reduce glutathione, which in turn detoxifies free radicals and peroxides
Sucrose
glucose + fructose
Lactose
glucose + galactose
Fructose is to Aldolase B as
Galactose is to Uridyl Transferase
FAB GUT
Infantile cataracts
Classic galactosemia
absence of galactose 1 P uridyltransferase
also have FTT jaundice hepatomegaly and MR
Fructose intolerance
deficiency of aldolase B
accum of Fructose 1 P
hypoglycemia, jaundice, cirrhosis, vomiting
Lactase deficiency
bloating, cramps, osmotic diarrhea
Glucogenic AA
Met, Val, Arg, His
Glucogenic/Ketogenic AA
Phe, Thr, Trp, Ile
Ketogenic AA
Lysine, Leucine
Acidic AA
Asp, Glu
Basic AA
Arg, Lys, His
AA found in histones
Arg and Lys
bind negatively charged DNA
Substrates in urea cycle
Ordinarily, Careless Crappers Are Also Frivolous About Urination
Ornithine, Carbamoyl phosphate, Citrulline, Aspartate, Argininosuccinate, Fumarate, Arginine, Urea
Hyperammonemia
excess NH4+ depletes alpha ketoglutarate, leading to inhibition of TCA cycle
Ammonia intoxification
tremor, slurred speech, somnolence, vomiting, cerebral edema, blurred vision
Breakdown products of
Dopamine
NE
E
HVA
VMA
Metanephrine
Phenylketonuria
due to dec in phenylalanine hydroxylase or tetrahydrobiopterin cofactor
tx dec phenylalanine and inc tyrosine
musty body odor, MR, growth retardation, sz, fair skin, eczema
Alkaptonuria
def in homogentisic acid oxidase in degradative pathway of tyrosine to fumarate
dark conenctive tissue, brown pigmented sclera, urine turns black on prolonged exposure to air! arthralgias
Albinism
def in either tyrosinase or defective tyrosine transporters- dec melanin
locus heterogeneity- variable inheritance
Mapsle syrup urine dse
dec alpha ketoacid dehydrogenase, blocked degradation of branched AA- Ile, Leu, Val, causes CNS defects, MR, death
I Love Vermont maple syrup from maple trees with branches
Glycogen bonds at
branches
linkages
alpha (1,6)

alpha (1,4)
Limit dextrin
4 glucose residues in branched configuration
made from glycogen by glycogen phosphorylase
Apolipoprotein B48
mediates chylomicron secretion
Apolipoprotein B100
binds LDL receptor
Apo E
mediates remnant uptake
Apo A-1
Activates LCAT
Apo C-II
LPL cofactor
Hurlers syndrome
deficient in alpha L iduronidase, heparan sulfate and dermatan sulfate accumulate, DD, gargloylism, airway obstruction, corneal clouding, hepatosplenomegaly
Hunters syndrome
XR, deficient in iduronate sulfatase, heparan sulfate and dermatan sulfate accumulate, Milder hurlers sx and aggressive behavior, no corneal clouding
Hunter's see clearly and aim for the X