Biochem Flashcards
what amino acids are histones rich in?
lysine and arginine (+ charged)
what ties nucleosome beads together on a string?
H1 (the only histone that is not in a nucleosome core)
What is methylated during DNA replication
template strand cytosine and adenine (allows for mismatch repair)
What inactivates transcription of DNA
histone methylation
What relaxes DNA coiling, allowing for transcription?
histone acetylation
nucleotides with 2 rings
purines (A, G)
nucleotides with 1 ring
pyrimidines (C, U, T)
which nucleotide has a ketone?
guanine
which nucleotide has a methyl?
thymine
what makes uracil?
deamination of cytosine
amino acids necessary for purine synthesis
GAG (glycine, aspartate, glutamate) and THF
nucleoside
base + ribose
nucleotide
base + ribose + phosphate (linked by 3-5 phosphodiester bond)
de novo purine synthesis
start with sugar + PRPP, add base
de novo pyrimidine synthesis
make temporary base (orotic acid), add sugar + PRPP, modify base
what is required for pyrimidine base production
aspartate
what is carbamoyl phosphate involved in?
de novo pyrimidine synthesis and urea cycle
ornithine transcarbamoylase deficiency
accumulation of carbamoyl phosphate, which is then converted to orotic acid; hyperammonemia
hydroxyurea
interferes with nucleotide synthesis, inhibits ribonucleotide reductase
6-MP
blocks de novo purine sunthesis
5-FU
inhibits thymidylatesynthase
methotrexate
inhibits dihydrofolate reductase
trimethoprim
inhibits bacterial dihydrofolate reductase
what is defective in orotic aciduria?
de novo pyrimidine synthesis (can’t convert orotic acid to UMP) because of defect in UMP synthase (phosphoribosyltransferase or orotidine-5-phosphate decarboxylase)
orotic aciduria inheritance
autosomal recessive
orotic aciduria treatment
oral uridine administration
increased orotic acid in urine, megaloblastic anemia (doesn’t improve with administration of B12 or folic acid), failure to thrive, no hyperammonemia, needle-shaped crystals in urine
orotic aciduria
excess ATP and dATP that inhibits ribonucleotide reductase–>prevents DNA synthesis–>decreases lymphocyte count
adenosine deaminase deficiency (major cause of SCID)
adenosine deaminase deficiency inheritance
autosomal recessive
defective purine salvage due to defective HGPRT–>excess uric acid production
Lesch-Nyhan syndrome
Lesch-Nyhan syndrome inheritance
autosomal recessive
retardation, self-mutilation, aggression, hyperuricemia, gout, choreoathetosis (spastic cerebral palsy)
Lesch-Nyhah syndrome
Lesch-Nyhan syndrome treatment
allopurinol (inhibits xanthine oxidase–>reducesgouty arthritis)
which amino acids are encoded by only 1 codon?
methionine, tryptophan
splice site mutation
frequently results in production of larger proteins with altered function but preserved immune reactivity
unwinds DNA template at replication fork
helicase
prevent strands from reannealing during DNA replication
SSBP
fluoroquionolones
inhibit DNA gyrase (prokaryotic topoisomerase II)
primase
makes RNA primer on which DNA polymerase III can initiate replication
DNA polymerase III
prokaryotic only; 5–>3 synthesis, 3–>5 exonuclease
degrades RNA primer and replaces it with DNA
DNA polymerase I (prokaryotic)
5–>3 exonuclease activity
DNA polymerase I
repairs bulky, helix-distorting lesions
nucleotide excision repair
endonucleases that release oligonucleotide-containing damaged bases
nucleotide excision repair
absence of UV-specific adonuclease
xeroderma pigmentosum (mutated nucleotide excision repair)
glycosylases that recognize and remove damaged bases; important in repair of spontaneous/toxic deamination
base excision repair
defective 3–>5 exonuclease activity (defective mismatch repair)
hereditary nonpolyposis colorectal cancer
mutated homologous end-joining
ataxia telangiectasia
stop codons
UGA, UAA, UAG
what makes rRNA
RNA polymerase I
what makes mRNA
RNA polymerase II (opens DNA at promoter site)
what makes tRNA
RNA polymerase III
alpha amanitin
found in Amanita phalloides, inhibits RNA polymerase II
antibodies to spliceosomal snRNP
SLE
CCA at 3 end
tRNA
tertacycline MOA
bind 30S preventing attachment of aminoacyl-tRNA
prokaryotic 16S rRNA
contains sequence complimentary to shine-delgarno sequence on mRNA
initiation of protein synthesis
activated by GTP hydrolysis
aminoglycosides MOA
bind 30S and inhibit formation of initiation complex
chloramphenicol MOA
binds 50S and inhibits peptidyl transferase
macrolides MOA
bind 50S and prevent release of uncharged tRNA
p27 protein
cell cycle inhibitor, acts during G1, inhibits CDK
CDKs
constitutive and inactive
main tumor suppressors
p53 and hypophosphorylated Rb (inhibit G1-to-S)
permanent cells
neurons, skeletal and cardiac muscle, RBCs
stable cells
hepatocytes, lymphocytes
rER
site of synthesis of secretory proteins, N-linked oligosaccharide addition, synthesize lysosomal proteins
Golgi
modifies N-oligosaccharide on asparagine, sdds O-oligosaccharides on serine and threonine, ads mannose-6-P for trafficking to lysosomes
I-cell disease
lysosomal storage disorder, failure of addition of mannose-6-P to lysosome proteins; abnormal N-acetyl glucosaminotransferase in Golgi
coarse facial features, clouded corneas, restricted joint movement, high plasma levels of lysosomal enzymes
I-cell disease
where does catabolism of very long f.a. and a.a. occur?
peroxisome
organelle necessary for heme synthesis
mitochondria
what are microtubules incorporated in
flagella, cilia, mitotic spindles
retrograde to microtubule
dynein
anterograde to microtubule
kinesin
drugs that act on microtubules
mebendazole/thiabendazole (antihelminthic), griseofulvin (antifungal), vincristine/vinblastine, paclitaxel (anti-breast cancer), colchicine
chediak-higashi syndrome
mutation in lysosomal trafficking regulator gene (product is required for microtubule-dependent sorting of endosomal proteins into late multivesicular endosomes)
recurrent pyogenic infections, partial albinism, peripheral neuropathy
cheidak-higashi syndrome
9+2 arrangement of microtubules
cilia
kartagener’s syndrome
immotile cilia due to dynein arm defect
male infertility, decreased female fertility, bronchiectasis, recurrent sinusitis, associated with situs inversus
kartagener’s syndrome
actin and myocin structures
microvilli, muscle contraction, cytokinesis, adherens junctions
microtubule structures
centrioles
vimentin stain
CT
desmin stain
muscle
cytokeratin stain
epithelial cells
GFAP stain
neuroglia
neurofilament stain
neurons
chromogranin A and enolase stain
neuroendocrine
MPO stain
myeloid cells
ouabain
inhibits Na/K pump by binding to K site
digoxin and digitoxin
inhibit Na/K pump–>inhibition of Na/Ca exchange–>increased intracellular Ca–>increased cardiac contractility
most abundant protein in body
collagen
type I collagen
bone, skin, tendon, cornea, late wound repair, defective in osteogenesis imperfecta
type II collagen
cartilage, vitreous body, nucleus pulposus
type III collagen
reticulin: skin, blood vessels, uterus, fetal tissue, granulation tissue. Defective in ehlers-danlos
type IV collagen
basement membrane. Defective in Alport syndrome
fine skin wrinkles
appear secondary to decreased synthesis and net loss of dermal collagen and elastin
the most abundant a.a. in collagen
glycine
collagen synthesis inside fibroblasts
translation of alpha chain Gly-X-Y (proline or lysine); hydroxylation of proline and lysine (requires vitamin C); glycosylation and triple helix formation (defect–>osteogenesis imperfecta); exocytosis
collagen synthesis outside fibroblasts
cleavage of disulfide-rich terminal–>insoluble tropocollagen;c terminal propeptide removal; covalent lysine-hydroxylysine cross-linkage (need Cu; defect–>ehlers-danlos)
osteogenesis imperfecta
autosomal dominant with abnormal type I collagen
multiple fractures, blue sclera (translucency of CT over choroidal veins), hearing loss, small teeth (lack of dentin)
osteogenesis imperfecta; defective bone metrix formation
ehlers-danlos syndrome
hyperextensible skin, tendency to bleed, hypermobile joints, berry aneurysms, organ rupture
alport syndrome
abnormal type IV collagen, usually X-linked recessive
progressive hereditary nephritis and deafness, associated with ocular disturbances
alport syndrome
which a.a. is elastin rich in?
proline and glycine (nonhydroxylated forms)
elastin
cross-linking takes place extracellularly; broken down by elastase (inhibited by alpha1 antitrypsin)
marfan’s syndrome
defect in fibrillin (extracellular matrix protein)
elastin’s plasticity and ability to recoil
attributable to desmosine cross-linking between lysine residues
best method for determining whether a gene is being expressed
northern blot
southwestern blot
identifies DNA-binding proteins
microarrays
used to profile gene expression levels, detect SNPs
indirect ELISA
uses test antigen to see if Ab is present
direct ELISA
uses test Ab to see if antigen is present
FISH
used for specific localization of genes
cre-lox system
can inducibly manipulate genes at specific developmental points using Ab-controlled promoter
pleitropy
one gene contributes to multiple phenotypic effects
imprinting
differences in gene expression depend on whether mutation is of maternal or paternal origin
loss of heterozygosity
if there is a mutation in tumor suppressor gene, complementary allele must be deleted before cancer develops
chimeric pt
derived from 2 zygotes that subsequently fuse
locus heterogeneity
mutations at different loci can produce the same phenotype
heteroplasmy
presence of both normal and mutated mtDNA
mitochondrial syndromes
leber hereditary optic neuropathy: bilateral vision loss; myoclonic epilepsy with ragged red fibers: myoclonic seizures and myopathy associated with exercise; MELAS
uniparental disomy
2 copies of a chromosome from 1 parent. heterodisomy–> meiosis 1 error; isodisomy–>meiosis 2 error or postzygotic chromosomal duplication. Prader-Willi, Angelman
frequency of X-linked recessive disease
males=q, females=q2
prader-willi syndrome
paternal allele is not expressed (chromosome 15)
mental retardation, hyperphagia, obesity, hypogonadism, hypotonia, short stature
prader-willi syndrome
angelman’s syndrome
maternal allele is not expressed (chromosome 15)
mental retardation, seizures, ataxia, inappropriate laughter
angelman’s syndrome
