FA Biochem I Flashcards
In the chromatin structure, which histones form the octamer, and which ties the nucleosome beads together in a string?
octamer = 2 sets of H2A, H2B, H3, H4 - tie =H1
What amino acid makes up most of the histone octamer?
lysine and arginine
Which type of chromatin is condensed, transcriptionally inactive, sterically inaccessible?
heterochromatin = HighlyCondensed
Which type of chromatin is less condensed, transcriptionally active, sterically accesible
euchromatin
What does PURe As Gold and CUT The Py stand for
purines= A, G pyrimidine = C, T (U)
How many rings do purines have
2 rings
How many rings do pyrimidines have
1 ring
How does cytosine become uracil
deamination
What polar group does guanine have, and what non polar group does thymine have
ketone, methyl
Which bond is stronger AT or CG and why? What is the laboratory consequence of this?
CG- 3 > AT-2 - More CG content, melting point goes up
What 3 amino acids are necessary for purine synthesis
glycine, aspartate, glutamine
What makes up a nucleoside
base + ribose
What makes up a nucleotide
base + ribose + phosphate (3’ -5’) phosphodiester bond
What are purines made from
IMP precursor
What are pyrimidines made from
orotate precursor, with PRPP added later
What is made fir rNucleotides or deoxyrNucleotides and what enzyme is necessary to convert one to the next
ribos first then deoxyribos with ribonucleotide reductase
What two pathways is carbomoyl phosphate involved in, and what enzyme deficiency leads to a build of carbamoyl phosphate leading to what element in pyrimidine synthesis
de novo pyrimidine synthesis and urea, ornithine transcarbamoyl def in the urea cycle leads to a build of CP, then converted to orotic acid in pyrimidine synthesis pathway
Name 5 drugs that interfere with nucleotide synthesis
hydroxyurea - inhibits ribonucleotide reductase, 6 MP - blocks de novo purine synthesis, 5 FU inhibits thymidilate synthase, MTX - inhibits DHFR, Trimethroprin inhibits bacterial DHFR
Inhibition of thymidilate synthase and and DHFR lead to decrease in what substance
dTMP
Which step in the de novo purine and pyrimidine synthesis pathway requires just aspartate
orotic acid to UMP
Which step in the de novo purine and pyrimidine synthesis pathway requires aspartate, glycine, glutamine and THF
Ribose 5-P to PRPP
An inability to convert orotic acid to UMP would be caused by a deficiency either of which two enzymes
orotic acid phosphoribosyltransferase or orotidine 5’-phosphate decarboxylase
How is orotic aciduria inherited
AR
What are the findings in orotic aciduria
inc orotic acid in urine, megaloblastic anemia (does not correct with B12 or folate), failure to thrive
What lab value can distinguish orotic aciduria from ornithine transcarbamoylase def?
OTC has hyperammonemia, orotic aciduira does not
What is the treatment for orotic aciduria
oral uridine administration
What does Adenosine deaminase deficiency cause a build up of, and what does that lead to?
excess ATP, dATP, feeback inhibits ribonucleotide reductase, no DNA synthesis
Adenosine deaminase deficiency is an important cause of what immunodeficiency?
dec DNA, dec lymphos leads to SCID
Leysh-Nyhan syndrome is a defect in which enzyme and what are the biochemical results
HGPRT, defective purine salvage, excess uric acid production
What are the findings in Lesch-Nyhan
retardation, self mutilation, aggression, hyperuricemia, gout, choreoathetosis
How is Lesch Neyhan inherited
X-linked recessive
What enzyme converts adenine to AMP
APRT + PRPP
What step of uric acid synthesis does xanthine oxidase catalyze
hypoxanthine to xanthing and xanthine to uric acid
What reaction does adenosine deaminase normally catalyze
adenosine to inosine
What does an umabiguous genetic code refer to
each codon specifies only 1 amino acid
What does degenerate/rundant genetic code refer to
more than 1 codon may code for the same amino acid
What is the exception to genetic redundancy
methionine encode by only 1 codon (AUG)
What does commaless, nonoverlapping genetic code refer to
read from a fixed starting point as a continuous sequence of bases
What does universal genetic code refer to and what are some exception
genetic code is conserved throughout evolution, except for mito, archaebacteria, mycoplasma, and some yeast
What is a silent mutation
same AA, often base change in 3rd position of codon (tRNA wobble)
What is a missense mutation
changed AA (convservative - new AA is similar in chemical structure)
What is a nonsense mutation
change resulting in early stop codon
What is a frame shift
change resulting in misreading of all nucleotides downstream, usually resulting in a truncated nonfxnal protein
What is the order of severity for the different types of mutations
nonsense > missense > silent
Eukaryotic and prokaryotic DNA synthesis is blank and involves both blank and blank strands
semiconservative, continuous and discontinuous strands (okazaki fragments)
For eukaryotes, where does replication begin?
consesus sequenec of base pairs
What is the origin of replication
particular sequence of DNA where replicatino begins - may be single of multiple
Describe the replication fork
Y shaped region along the DNA template where leading nad lagging strands are synthesized
What does helicase do
unwinds DNA template at replcation fork
What do the single stranded binding proteins do
prevent strands from reannealing
What do DNA topoisomerases do
creat a nick in the helix to relieave supercoils created during replication
What does primase do
makes RNA primer on which DNA poly III can initiate replication
What does DNA poly III do?
prokaryotic only - elongates leading strand by adding deoxnucTIDE to the 3’ end. Elongates lagging strand until it reaches primer of preceeding fragment. 3’ to 5’ exonuclease activity “proofreads” each added nucTIDE
What does DNA poly I do?
prokaryotic only - degrades RNA primer and fills in the gap with DNA
What does DNA ligase do
seals.
How do fluoroquinolones work
inhibit DNA gyrase specific for prokaryotic topoisomerase
In which single strand DNA repair mechanism do specific endonucleases release the oligonucTIDE containing bases and DNA poly and ligase fill and reseal, and what disease occures when this is mutated
nucleotide excision repair - xeroderma pigmentosum; unable to repair thymidine dimers caused by UV light
In base excision repaire, what recognizes and removes damaged bases and what cuts the DNA to remove the empty sugar
specific glycosylases, AP endonuclease
In mismatch repair, which strand is recognized and in what hereditary syndrome is this defective
unmethylated, newly synthesized, HNPCC
Is there any requirement for homology in NHEJ
no - its non homologous
In what direction are DNA and RNA synthesized
5’ to 3’
Which carbon bears the triphosphate and the energy source for bond formation
5’ of the incoming nucleotide
What is the target of the 3’ hydroxyl attack
The triphosphate bond
In which direction is protein synthesized
N to C
What is the most abundant type of RNA
rRNA
What is the longest time of RNA and shortest
mRNA, tRNA
What does the start codon code for in eukaryotes and prokaryotes
eu - methionine, pro - formyl-methionine
What are the mRNA stop codons
UGA, UAA and UAG
Which part of the DNA binds RNA polymerase and multiple other TFs upstream from gene locus
promotor - TATA box, and CAAT box, AT rich
What stretch of DNA that alters gene expression by binding of transcription factors
enhancers
This is the site where negative regulators bind
silencers
In eukaryotes, what does RNA poly I make
rRNA
In eukaryotes, what does RNA poly II make
mRNA
In eukaryotes, what does RNA poly III make
tRNA
Which RNA poly opens DNA at promotor site
RNA poly II
RNA poly can’t proofread, but what can it do
initiate chains
In prokaryotes, what does makes the different types of RNA
1 kind with multiple subunits
Why does alpha amanitin cause liver failure and where is it found
inhibits RNA polymerase II, found in death cap mushrooms
What 3 steps in RNA processing occur after transcription
1- capping on 5’ (7-methyguanosine) 2 - polyadenylation on 3’ end 3 - splicing out of introns
What is the initial transcript called and what is the capped and tailed transcript called
initial is heterogenous nuclear RNA, the capped and tailed is called mRNA
Which enzyme involved in RNA synthesis does not require a template
poly A polymerase - signal is AAUAA
What kind of RNA is transported out of the nucleus
only processed RNA
What does the primary transcript combine with to form the spliceosome
snRNPs and other proteins
What shape does the RNA generate during splicing and why?
lariat shape in order and remove intron precisely and join 2 exons
Which aspect of the spliceosome do patients with lupus make antibodies against
snRNPs
What part of the pre mRNA contains the actual genetic information coding for protein
exons
How many nucTIDEs is a tRNA and what does the secondary sturcture form
75 to 90, cloverleaf
Which end of the tRNA is the amino acid bound to
3’ end (with CCA)
What does aminoacyl tRNA synthetase do the AA before and after it binds to tRNA, and what happens if it’s the wrong the match
scrutinizes, hydrolyzes the bond
What does a mischarge tRNA do
reads usual codon but inserts wrong AA
How do tetracyclines work
bind 30s subunit preventing attachment of aminoacyl-tRNA
Accurate base pairing is required only in the first two nucleotide positions of an mRNA codon, so conds differeing in the 3rd position may code for the same tRNA/AA due to degenerate genetic code
wobble
What initiates protein synthesis
GTP hydrolysis, initiation factors assemble 40S ribosomal subunit with initiator tRNA and are released with mRNA and ribosomal subunit assemble with the complex
What happens in elongation of protein synthesis
Aminoacyl-tRNA binds A site, ribosomal rRNA catalyzes peptide bond formation, transfers growing peptide to AA in A site, ribosome advances 3 nucTIDE toward 3’ end of RNA, moving peptidyl RNA to P side
What happens in termination of proteins synthesis
stop codon is recognized by release factor, and completed protein is released from ribosome
What ribosomes do eukaryotes have
40, 60, 80
What ribosomes do prokaryotes have
30, 50, 70
What is the energy source for tRNA actication (charging)
ATP
What is the energy source for translocation
GTP
How do aminoglycosides work
by inhibiting formation of the initiation complex and cause misreading of mRNA
How does chloramphenicol work
inhibits 50S peptidyltransferase
How do macrolides and clindamycin work
binds 50S, blocking translocation
What is trimming
removal of N or C termal propeptides from zymogens to generate mature proteins
What are covalent alterations
phosphorylation, glycosylation, hydroxylation
What is proteasomal degredation
attachment of ubiquitin to defective proteins tag them for breakdown
What are CDKs
cyclin dependent kinases;constitutive and inactive
What are cyclins
regulatory proteins that control cell cycle events; phase specific; activate CDKs
What are cyclin-CDK complexes
must be both activated and inactivated for cell cycle to progress
Which tumor suppresors inhibit G1 to S progression, where mutations result in unrestrained growth
Rb and p53
How do permanent cells grow and regenerate and what are examples of permanent cells
remain in G0, regenerate from stem cells, neurons, skeletal/cardiac muscle, RBCs
How do stable (quiescent) cells grow and regenerate and what are examples
enter G1 from G0 when stimulated, hepatocytes and lymphocytes
How do labile celss grow and regenerate and what are examples
never go to G0, divide rapidly with a short G1, bone marrow, gut epi, skin, hair follicles
Where are the secretory proteins made and N-linked oligosaccharide addtions put on proteins
RER
Where are cytosolic and organellar proteins made
free ribosomes
What is the RER called in neurons and what is made there
Nissl body, enzyme and NTs
What two cells are particularly rich in RER
mucus secreting globlet cells and antibody secreting plasma cells
What happens at the smooth ER
site of steroid synthesis and detoxification of drugs and poisons
Which cells are rich in smooth ER
liver hepatocytes and steroid producing cells of the adrenal cortex
The golgi apparatus fxns as a distribution center between what organelles in the cell and what does it process
for proteins and lipids from ER to plasma membrane, lysosomes and secretory vesicles
What does the golgi apparatus do on asparagine
modifies N-oligosaccharides
What does the golgi add to serine and threonine residues
O-oligosaccharaides
What does the addition of mannose-6 phosphate do
targets the proteins for lysosome
What does the golgi assemble proteoglycans from
core proteins
what does the golgi do to sugars in proteoglycans and of selected tyrosine on proteins
sulfation
What is I cell disease
inherited lysosomal storage disorder; failure of addition of mannose 6 phosphate to lysosomal proteins, enzymes secreted outside of cell instead of lysosomes
What are the clinical features of I cell diesase
coarse facial features, clouded corneas, restricted joint movements, high plasma levels of lysosomal enzymes, often fatal in childhood
What two proteins make up microtubules and how are they arranged
alpha and beta tubulin, dimers have two GTP bound
In which structures do you find microtubules
flagella, cilia, mitotic spindles
How do microtubules grow and collapse
grows slowly, collapses quickly
Which direction does dynein go
post to neg
Which direction does kinesin go
neg to pos
Which antihelminthe drugs work on microtubules
mebendazole/thiabendazole
Which antifungal drugs work on microtubules
griseofulvin
Which anticancer drugs work on microtubules
vincritsine/vinblastine
Which anti breast cancer drugs work on micortubules
paclitaxel
Which anti gout drugs work on microtubules
colchicine
What is chediak higashi
microtuble polymerization defect causing a dec in phagocytosis results in recurrent pyogenic infections, partial albinism, and peripheral neuropathy
Describe the structure of cilia
9+2 arrangement of microtubules
What is axonemal dynein
ATPase that links peripheral 9 doublets and causes bending of cilium by differential sliding of doublets
What is kartageners syndrome
immotile cilia due to dynein arm defect, male and femail infertile, bronchiectasis, recurrent sinusitis, associated with situs inversus
cytoskeletal elements in micorvilli, muscle contracting fibers, cytokenesis, adherens jxns
actin and myosin
cytoskeletal elements associated with cilia, flagella, mitotic spindle, neurones and centrioles
microtubules
cytoskeletal elements associated with vimenentin, desmin, cytokeratin, glial fibrillary acid protiens (GFAP), neurofilaments
intermediate filaments
What does high cholesterol or long saturated fatty acid content do to the melting temperature and fluidity
inc melt, dec fluidity
What does the vimentin stain for
connective tissue
What does desmin stain for
muscle
What does cytokeratin stain for
epithelial cells
what does GFAP stain for
neuralgia
What do neurofilaments stain for
neurons
Describe the location and fxn of the Na/K ATPase
plasma membrane, 3Na out, 2K in, ATP on cytoplasmic side
How does ouabain work
inhibits the Na/K pump by binding the K side
How do cardia glycosides work
directly inhibit the Na/K pump which leads to indirect inhibition of Na/Ca exchange, inc calcium inside the cell, inc cardiac contractility
What is the most abundant protein in the body
collagen
Type I collagen
Bone, skin, tendon, dentin, fascia, cornea, late wound repair
Type II collagen
cartilage, hyaline, vitreous body, nucleus pulposus
Type III collagen
reticulin - skin, blood vessels, uterus, fetal tissue, granulation tissue
Type IV collagen
basement membrane or basal lamina
Type I bone
bONE
Type II cartilage
carTWOlage
Type IV BM
4 under the floor
What happens in the first stage of collagen synthesis, and where does it happen
RER - translation of alpha chains, usually Gly-X-Y polypeptide (preprocollagen)
What residues are hydroxylated in step 2 of collagen synthesis, and what does this require
proline and lysine, vit C
What does glycosylation of pro alpha chian yield and what is the structure
procollagen, triple helix of 3 alpha collagen chains
In what cell is collagen synthesis initiated
fibroblast
Outside the fibroblast what part of procollagen is cleaved and what is it transformed into
terminal regions, tropocollagen
How are the many staggered tropocollagen molecules reinforced
covalent cross-linking by lysyl oxidase to make collagen fibrils
What does Ehlers Danlos cause and why
faulty collagen synthesis, hyperextensible skin, tendency to bleed, easy bruising, hypermobile joints
What collagen type is most frequently affected in ehlers danlos and what are common complications
III, joint dislocation, anuerysms, organ rupture
What does osteogenesis imperfecta causes and why
brittle bone disease, most commonly lead AD with abnl type I collagen causing multiple fractures with minimal trauma, blue sclerae due to translucency of connective tissue over the choroid, hearing loss, dental imperfections due to lack of dentin
Which kind of osteogenesis imperfecta is fata in utero or in neonatal period
type II
What does Alports syndrome cause and why
progressive hreditary nephritis and deafness, associated with occular disturbances - due to abnl type IV collagen, usually x-linked recessive
Type IV collagen is an important structural componenet of the BM for which 3 organs
kidney, ears, eyes
Where do you find elastin and what does it do
lungs, large arteries, elastic ligaments, vocal cords, ligamenta flava - stretch.
Which amino acids are elastin rich in
proline and glycine (non glycosylated forms)
Why enzyme breaks down elastin and what enzyme inhibits it
elastase, inhibited by alpha1 antitrypsin
What is the structure of elastin
tropoelastin with fibrillin scafolding
What causes Marfan syndrome
defect in fibrillin
What enzyme def can cause emphysema
alpha1 antitrypsin
What lab procedure is used to amplify desired fragment of DNA and what are the 3 steps
PCR, denaturation, annealing, elongation
What does a southern blot use as its sample
DNA
What does a northern blot use as its sample
RNA
What does a western blot use for its sample
protein
What lab technique is use to profile gene expression levels of thousands of genes simultaneously to study certain diseases and treatments
microarrays
What is the smallest mutation a mircoarray can detect
SNP
What does the ELISA test for
antigen - antibody reactivity - can look for antigen or antibody in patients blood
Fluorescent DNA or RNA probe binds to specific gene of interest - used for specific localization of genes and direct visualization of anomalies, like microdeletions, at molecular level
FISH
What is DNA cloning and how do you do it?
production of a recombinant DNA molecule that is self perpetuating, plasmids, selection, restriction enzyme cleavage, tissue mRNA with reverse transcriptase to make cDNA
What are the two transgenic strategies in mice
constitutive - random insertion of gene into mouse genome and conditional - targeted insertion or deletion of gene through homologous recombination with mouse gene
antbiotic controlled promoter to induciblly manipulate genes at specific developmental points
cre-lox system
What is RNAi used for
dsRNA promotes degradation of target mRNA knocking down gene expression
metaphse chromosomes are stained, ordered and numbered according to morphology, size, arm length ratio, banding pattern
karyotyping
What tissue samples are used for karyotyping
blood, bone marrown, amniotic fluid, placental tissue
What is codominance and give an example
neither of 2 alleles is dominant, blood groups
What is variable expression and what is an example
nature and severity of phenotype vary from 1 individual to another, NF type 1
What is incomplete penetrence and give an example
not all individuals with a mutant genotype show the mutant phenotype
What is pleiotropy and given an example
1 gene had >1 effect on an individuals phenotype, PKU causes many seemingly unrelated symptoms ranging from mental retardation to hair/skin changes
What is imprinting and give an example
differences in phenotype depend on whether the mutation is of maternal or paternal origin, prader-willi and angelman’s syndrome
What is anticipation and give an example
severity of disease worsens or age of onset of disease is earlier in succeeding generations, huntingtons
What is loss of heterozygosity and give an example
if pt inherits or develops a mutation in a tumor suppresor gene, the complementary allele must be deleted/mutated before cancer develops- not true of oncogenes, retinoblastoma
