DSA Readings Flashcards
DNA polymerases
add NT to strand growing in 5 to 3, copying a DNA temp in 3 to 5
Primase
syn RNA primer
Helicase
separate parental DNA strands, unwind double helix
Single strand binding proteins
prevent single strands of DNA from reassociating
topoisomerases
relieve torsional strain on parental duplex caused by unwinding
RNase H
hydrolyzes RNA of DNA RNA hybrids
Flap endonucleases 1
recognizes flap-created by poly z displacing primer as okazaki frag is syn, remove primers
DNA ligase
joins 2 adjacent DNA strands that are bound to the same template, form phosphodiester bond
Proliferating cell nuclear antigen
enhances processivity of DNA poly, binds many proteins at replication fork
Euchromatin vs heterochromatin
eu: loosely packed, hetero: tightly packed
AT and CG bonds
AT: 2 H, CG 3 H connecting bases
what causes DNA strands to seperate
heat and alkali (doesnt cause PD bonds to break, will in RNA)- only separates strands
Ecoli DNA structure
supercoiled and attached to RNA protein core
Nucleosomes
DNA bound to histones, looks like beads on a string- nucleosomes are the beads, bind together- solenoid stucture
Nucleosome core
DNA bound to histones, looks like beads on a string- nucleosomes are the beads with DNA coming from both sides
Euk mRNA general structure
starts with guanine cap at 5 end, start codon, stop codon, poly A tail (cap, tail- added after translation of mRNA)
Ribosome sizes
30S and 50S combine to for E 70S, 55S in mitochondria, 55S in bacteria- target of azithromycin (can also affect mito ribo)
tRNA modified NTs
ribothymine, dihydrouridine, pseudouridine
other RNAs
oligonucleotides: primer for DNA rep, small nuclear ribonucleoproteins: involved in splicing and mod. during maturation of RNA, microRNA: help w reg of gene expression
DNA rep in pro
bidirectional, start at origin of replication, 2 replication forks
DNA poly directions
copy strand 3 to 5, make new 5 to 3
DNA poly bond and energy
ester bond formed between new NT and chain- pyrophosphate released, cleaved- energy that drives polymerization rxn
Processivity
how much an enzyme stays attached to chain, DNA poly has high processivity
Ecoli DNA polyermase III
proofreading, 3 to 5 exonuclease activity
RNA primer
DNA poly needs OH group, needs RNA primer- made by RNA polymerase (primase) that copies the DNA strand
Leading vs lagging strand
lead: continous, 5 to 3
lagg: okazaki frag, 3 to 5, away from fork
Lagging strand process
RNA primer made by pol a and primase, poly S adds DORNT, stops when reach primer of previous fragment- removed by flap endonuclease I and RNase H, gap filled by poly S and ligase
Cigarette smoke mutagen
complex oxidized- form bulky adducts w ganine residues in DNA
UV mutagen
excitation of adjacent pyrimidine bases- form covalent bonds (thymine dimers)
general DNA repair mechanism
distortion removed, DNA poly syn strand 5 to 3, ligase
general DNA repair mechanism bacteria
NT not released, thymine dimer- protoactivate enzyme that cleaves bond using energy from visible light
nucleotide excision repair
mismatched bases or bulky adducts, specific repair endonuclease- cleave bond, remove region, DNA poly, , ligase
base excision repair
damage to single base, glycosylase cleaves N glycosidic bond that joins damaged base to deoxyribose, apurinic/apyrimidinic (AP) endonuclease cleaves sugar phosphate strand- DNA poly, ligase
mismatch repair
mismatch repair enzyme complex find mismatch and replace, in bact- parent strand is acetylated (A), complex goes over new strand before A, dont know how its done in E
General/homologous recombination
2 homo chomo/seg of DNA align- 1 strand of duplex 1 nicked by enzyme, invade strand of duplex 2- form displacement loop, nick duplex 2- displaced strand now base pairs with former partner of invading strand- Holliday structure that can move- cleaved and ligated- chromo w exchanged information
translocation
nonorganic break in chromo- free end reseal with free end of diff broken chromo- can have deleterious effects, seen in cancer
transposable elements
seg of DNA that can move from original position to new location in genome, contains genes for transposase, retrotransposons have these- but RNA used to make double strand copy of DNA and insert into host DNA
Reverse transcriptase
use single strand RNA template to make DNA copy, retrovirus contain to instert bacterial DNA Into host genome
Poly used when DNA is damaged 2 continue replication
polymerases L, k, n, l- no 5 exonuclease activity, bypass polymerases
DNA poly a
function in replication and DNA repair, no exo -primase associ with poly a - produces RNA primer, a addes 20 DORNT to RNA and diss from temp (low processivity)
DNA poly b
DNA repain, no exo
DNA poly y
DNA replication in mito, 3 to 5 exo
DNA poly S
*main, replication, DNA repain, 3 to 5 exo
DNA poly E
*main, replication, DNA repair, 3 to 5 exo
DNA poly K, n, z, L
DNA repair, bypass polymerase, no exo
AP-1
heterodimer formed by protein products of fos and jun families of proto oncogenes
MAPK pathway
MAPK induc myc and fos and AP1- act genes involved in cellular prolif and progression through cell cycle (same targets as myc)
C-myc
targets genes in cell prolif and progression through cell cycle, tightly regulated, only expressed during S phase, tumor/cancer- regulation lost, continuous prolif
cyclin CDK
reg through phos and inh proteins- cyclin dependent kinase inhibitors (CKIs slow cell progression by inh cyclin CDK complex)
cdk4 and cdk6
regulatory proteins, constitutively produced throughout cell cycle
cyclin D
syn is induced only after growth factor stimulation, regulatory proteins
retinoblastoma gene product (Rb)
regulatory protein
E2F and proteins induced
regulatory protein, class of transciprtion factors, inh by binding Rb, induce cyclin E, cyclin A, cdc25A
Rb/E2F pathway normal
Rb (tumor suppressor) bind E2F- supp. growth factor simulation- cyclin D induced, bind cdk4 and cdk6 - act protein kinases- target of CD/CDK= Rb, P of RB release from E2F- activation of tranc of genes required for entry to S phase
once E2F is active
lead to prod of cyclin E1-Cdk2- hyperphos Rb protein-keeping inactive, cyclin a-Cdk2 complex- phos and inactivates E2F- signal not present for long
CKIs categories
inh progress through cell cucle, Cip/Kip family and INK4, some induced by DNA damage to halt cell cycle for repair
Cip/Kip
CKIs, p21, p27 and p57, broad specificity and inhib all cyclin CDKs
INK4
CKI, p15, p16, p18, p19, specific for cyclin D -cdk4/6 family
tumor suppressor gene
halt cell cycle if damage, contribute to development of cancer when both copies of gene are inactive
retinoblastoma gene
G1-S phase, reg act of E2F family, inherit mut of Rb gene- 100% of developing retinoblastome (high prob of second allele gain mut)- familial retinoblastoma, dont inherit but develop- sporadic retinoblastoma
p53
TF that regulates cell cycle and apop, loss of both allele f(x) found in more than 50% tumors, level rises in response to DNA damage
p53 process
inc p53, inc transc of p21- inh cyclin CDK- prevent P of Rb- cant enter S phase, inc p53= inc transc of DNA repair enzymes
p53 if dna repaired or nah
repair: induce own downreg through act of mdm2 gene, not repaired: act genes for apop including bax and insulinlike growth factor binding protein 3
Ras
involved in signal transduction for many hormones and growth factors, oncogenic, bind NF1 to Ras- act GTPase domain of Ras- hyro GTP to GDP- inact Ras
Patched and Smoothened
hedgehod class of signaling peptides, patched inhib smoo, binding of HH to pat (tumor suppressor) releases inhib of smoo- act smoo (protooncogene)
Cadherin family of glycoproteins
mediates Ca dependent cell cell adhesion, anchored intracellulary by catenins, which bind actin filaments, loss of E cadherin exp- cancer cells to detach and migrate in metastisis
Apop external vs internal signaling ex
Ex: tumor necrosis factor, deprivation of growth hormone,
In: dec mito integrity, irreparably damaged DNA
Phases of apop
initiation, signal integration, excecution- carried out by proteolytic enzymes called capases
Capases general
cysteine proteases that cleave peptide bond next to an aspartate- activated from procapases to capases by proteolytic cleavage
Initiator capase vs execution capase
In: cleave other procapases, induced by death receptor pathway and mito integrity pathway
Ex: cleave other cellular proteins involved in maintaining cellular integrity
formed elements of blood
rbc, wbc, platelets (hematocrit concentration of formed elements in blood 40%)
blood plasma vs serum
plas: water, plasma proteins, ser: fluid portion of blood leftover after clot forms (plasma)
albumin
imp in maintaining blood and interstitatial fluid VL
globulins
a and b globulins - arise from liver and transport sustances
y globulins
arise from plasma cells and include anitbodies
clotting proteins
made by liver, involved in clot formation- prothrombin, fibrinogen
complement proteins
initiate inflammation and destruction of foreign microorganisms
plasma lipoproteins
chylomicrons, VLDL, LDL
chylomicrons
transport triglycerides to liver
VLDL
transport triglycerides from liver to body cells
LDL
transport chol from liver to body
hematopoiesis
development of blood cells
diapedesis
process by which WBC leave BV
WBC categories
granulocytes, agranulocytes
granulocytes
specific granules (specific fx) and azurophilic granules (lysosomes) in cytoplasm
agranulocytes
no azurophilic granules, have specific granules
neutrophils
granulocyte, nucleus arranged in 3 lobes, combating bacterial infection
eosinophils
granulocytes, kills parasitic worms
basophils
granulocytes, lobed nucleus-hidden, immune response
lymphocyte types
t cells, b cells, null cells
t cells
lymphocytes, cellular immune response- rejecting of transplanted organ
b cells
lymphocyte, humoral immune response-production of AB due to antigen
null cells
lymphocyte, circulating stem cells and natural killer cells- kill virus infected cells
monocytes
kidney shaped nuc, macrophages in connective tissue
megakaryocytes
present in boine marrow, appear to be multinucleated- only large lobed nuc
death receptor pathway 2 apop
trimer formed by Fas/CD95, TNF R1 and death receptor 3 bind to TNF 1- TNF receptor complex forms the scaffold for binding 2 molecules of procapase 8 (or 10)-cleave to form active capase 8/10- initiator capase activate execution cap 3, 6, 7
capase 3
also cleaves Bcl 2 protein, Bid- act mitochondrial integrity pathway to apop
mitochondrial integrity pathway to apop
release of cytochrome c from mito (no ETC)- bind Apaf in cyto- Apaf/cyto c binds capase 9 (initiator capase)- activate apoptosome - act cap 3,6,7
Bcl 2 family
integrate pro death and anti death signals, antiapop factors- all 4 domains (BH1-BH4), proapop- 3 domains (BH1-BH3), proapop BH3
antiapop Bcl 2 type proteins
Bcl 2, Bcl L, Bcl w- insert into outer mito memb- antagonize channel forming proapop factors- dec cytochrom c release, can also bind cyto Apaf- cant for apoptosome complex
proapop Bcl 2 families
ion channel forming members, BH3 only members
pro death, ion channel forming members
(Bcl 2) Bax, dimerize with proapop BH3- only memb in outer mito matrix- form ion channel that promotes cyto c release
pro death, BH3 only members
(Bim and Bid) bind to other Bcl 2 family members, form channel, bind Apaf, inactivate antiapop members
cancer signaling pathways that inhibit apop
PDGF/Akt/BAD pathways
BAD/Akt pathway
non phos BAD acts like Bid. binding of growth factor to receptor activates P13K- P and act. serive threonine kinase AKT- act AKT- P/inh of prop apop BH3 only protein BAD- stop apop
BAD/RSK pathway
MAP kinase kinase P/act another protein kinase, RSK- P/inh BAD - no apop
centromere
sister chromatids are held together physically here, region of DNA associates w/ proteins to create kinetochore
prophase
gradual condensation of chromosomes, formation of mitotic spindles, formation of a pair of centromeres
prometaphase
nuclear memb dissolves, chorom attach kinetochores to MT of mitotic spindles
metaphase
equatorial plate
anaphase
chromosomes seperate at centromere
telophase
chromo begin to decondense, nuclear memb begins to reform
spermatogenesus
seminiferous tubules of testes- lines with spermatogenia (develop from primordial germ cells)
sperm
found only after sexual maturity is reached
primary spermatocyte
diploid germ cell that undergoes meiosis I to form 2 haploid secondary spermatocytes - enter meiosis II making 2 spermatids - differentiate into sperm
oogenesis
begin during development as a fetus, ova develop from oogonia cell in ovarian cortex that have decended from the primordial germ cells by a series of 20 mitoses
before ovulation
oocyte rapidly completes meiosis I- one oocyte becomes a secondary oocytes, other becomes a polar body- meiosis II begins to metphase - halts, only completed after fertilizaiton
fertilization
completion of metaphase II- formation of second polar body, chromo of fertilized sperm/egg form pronuclei
most common mutational mechanism
meitoic nondisjunction, primarily in oogenesis
