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Biochemistry II


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Targeting sequence tag that directs proteins to nucleus (polymerase, peroxides)
Targeing Sequence tag that directs proteins to the ER membrane (cell membrane eventually)
Signal peptide sequence
Targeing Sequence tag that directs proteins to the ER lumen surface (point to cytosol eventually)
KDEL sequence (LysAspGluLeu)
Targeting Sequence tag that directs proteins to peroxisomes
keep proteins in unfolded form
chaperones (heat shock proteins)
recognized by proteosomes
ubiquitin-protein conjugate
Shortest phase of the cell cycle
M phase
Longest phase of cell cycle
G1 (or Interphase cumulatively)
activates the start kinase in the G1 phase (cyclin)
cyclin E
Components of start kinase
cyclin E & cdk2 (cyclin-dependent-kinase)
period of intense transcriptional activity with subsequent protein synthesis
G1 phase
cyclin that initiates DNA synthesis
G1 cyclin
most important regulation point in the cell cycle
just prior to S phase
phosphorylates proteins that initiate S phase
G1 cyclin-dependent protein kinase
phase that prepares tetraploid cell for cell division during M phase
G2 phase
requires the M phase kinase to be inactivated
return to interphase
components of MPPF
cyclin B & cdc 2
phosphorylation of these proteins by M phase kinase presumably initiates the condensation of DNA into chromosomes
H1 histones and lamins
cyclin that aids in chromosome formation
cyclin B
second messengers derived by phospholipase C action
DAG (activates PKC), IP3 (opens Ca++ channels)
cell phase when transcription & translation (RNA & Protein synthesis) occurs
G1 phase
Structure of stop sequence of transmembrane proteins
hydrophobic alpha helix
utilizes ATP to phosphorylate discreet target proteins at crucial tyrosine residues
tyrosine kinase
induces internal tyrosine kinase to autophosphorylate itself
target protein of tyrosine kinase
SH2 domain
when phosphorylated, migrates to the nucleus where it modulates transcription of certain genes
target protein
produces secondary messengers by activating PLC & Adenylate Cyclase
enzyme that hydrolyzes PIP2 to DAG & IP3
ADP-ribosylates Gs protein at a crucial arginine residue
cholera toxin
ADP-ribosylates Gi protein at a crucial cysteine residue
pertussis toxin
contains a hormone-binding site and a DNA-binding site
Steroid, Retinoate, & Thyroid hormone receptors
moves to the nucleus where it acts as a transcription factor affecting gene expression
intracellular growth factor-receptor complex (steroids)
constituents of tyrosine kinase receptor
N-terminal ligand binding region, stop sequence (hydrophobic alpha helix), & cytosolic C-terminal catalytic site (autophosphorylation)
general goal of tyrosine kinase cascade
transcription control (gene expression)
consequences of ADP-ribosylated G(alpha)-GTP
inhibited GTPase leading to increased cAMP
binds Ras to plasma membrane
activated by PDGF receptor via Grb2-Sos complex interaction
recruited by stimulation of Raf and MEK kinase
Factors of aging (3)
Free radicals (mutation), glucose (protein modification), growth factors (GH)
phase of the cell cycle that lasts 6-12 hours w/ 2n DNA
G1 phase
phase of the cell cycle that lasts 6-8 hours w/ 2n-4n DNA
S phase
phase of the cell cycle that lasts 3-4 hours w/ 4n DNA
phase of the cell cycle that lasts 1 hour w/ 4n-2n DNA
M phase
phase of the cell cycle that lasts 16-24 hours (non M phase)
growth factor that induces cell division; can become a mutation
mutated gene that turns on G(alpha)-GTP
genetic factor that inhibits growth/division
growth suppressor
permanently stimulated by v-erb B oncogene
tyrosine kinase
oncogene associated with 25% of all cancers and 90% of pancreatic cancer
activity lost if ras is permanently stimulated
viruses that can induce cancer in animals and humans
methods viruses cause cancer (2)
insertion of viral oncogene or promoter (close to oncogene) into host DNA
1st oncogene discovered
develops from formation of Philadelphia chromosomes (chr. 9-22 translocation)
myelogenous leukemia
oncogene turned on by formation of Philadelphia chromosomes
protein products of growth suppressors
check point regulators
tetramer that induces p21 synthesis, inhibiting cyclin/cdk
p53 concentration __________ w/ increasing DNA damage
restricts cells from entering S-phase until damaged DNA is repaired
action of set of genes induced by p53 when cell repair is not possible
proto-oncogene that inhibits apoptosis
protein kinase that phosphorylates pRB
cyclin d-cdk4
result of phosphorylation of pRB
dissociation from E2F allowing transcription
induces p21 to bind to cyclinD-cdk4
negative modulator of bcl-2
cell survival oncogene that when translocated causes follicular B cell lymphoma
oncogene that causes leukemia, brain tumors, osteosarcoma, retinoblastoma, and rhabdomyosarcoma
viral oncogene that encodes a truncated form of the EGF receptor (permanently stimulated tyrosine kinase)
region of v-erbB that normally inhibits tyrosine kinase domain
COO- terminal
DNA virus that causes hepatocellular carcinoma
Hepatitis B
DNA virus that causes cervical carcinoma & squamous cell skin carcinoma
DNA virus that causes Burkitt lymphoma and other B cell lymphomas, nasopharyngeal carcinoma
Epstein-Barr virus
RNA Retrovirus that causes adult T cell leukemia
Human T cell lymphotropic virus (HTLV-1)
RNA Retrovirus that causes Karposi sarcoma, lymphomas
oncogene affected by Rous sarcoma virus
src (tyrosine kinase)
oncogene affected by avian erythroblastosis virus
erbB (tyrosine kinase, growth factor receptors)
oncogene affected by Abelson murine leukemia virus
abl (tyrosine kinase)
oncogene affected by Simian sarcoma virus
sis (growth factors)
oncogene affected by Harvey murine sarcoma virus
Ha-ras (Guanyl-nucleotide-binding proteins)
oncogene affected by Kirsten murine sarcoma virus
oncogene affected by FBJ osteosarcoma virus
fos (nuclear proteins)
oncogene affected by Avian myeloblastosis virus
myb (nuclear proteins)
8-14 translated oncogene affected by Avian myelocytomatosis virus (Burkitt lymphoma)
myc (nuclear proteins)
oncogene that produces tyrosine kinase that prevents contact inhibition of cells
formed by reverse transcriptase (complement to RNA template)
properties of trasformed cells by isolated oncogenes
no contact inhibition, rounded shape, piling
toxin produced from a fungus that grows on peanut butter
carcinogen found in whisky and new car interiors
carcinogen used to make plastics
vinyl chloride
retinoblastoma factor that controls growth by reacting w/ E2F
binds to bcl2 in the mitochondria prohibiting apoptosis
inhibiting cdk4 would do what to the S phase of cell replication
genetic basis for cystic fibrosis
CF gene on chromosome 7q encodes CFTR (cystic fibrosis transmembrane regulator) that forms cAMP regulated Cl and Na channels, depleting the airway of water and obstructing lungs and the pancreas
term used to describe disease caused by a reduction (50%) or increase (150%) of the gene product
dosage sensitivity
Which came first; RNA or DNA?
RNA--enzyme capacity & self-splicing
DNA sequences capable of propagating copies of themselves that are inserted in other locations of chromosomes, causing frameshift mutations
transposons (mobile elements)
Cause of Type I neurofibromatosis, familial breast cancer, familial polyposis, and hemophilia A and B
transposon insertion
Introns are precisely removed from the primary mRNA transcript to produce a mature mRNA transcript. This process is called:
Type of mutation that produces a dominant disorder
Gain of function
Type of mutation that produces a recessive disorder
Loss of function
encoded by one gene of chromosome 11
Beta chains of hemoglobin
encoded by two genes of chromosome 16
Alpha chains of hemoglobin
How many genes that code for hemoglobin would a normal person have?
two normal beta genes and four normal alpha genes (6)
condition in which hemoglobin is structurally normal but reduced in quantity
used to diagnose thalassemia and other hemoglobinopathies
Southern blot (change in the number of location of a restriction site; RFLP)
mutation in which a hemoglobin chain is reduced in number, causing the other chain to develop homotetramers
type of thalassemia that has excess beta chains (gamma in the fetus)
alpha thalassemia
clinical consequences of different degrees of alpha thalassemia
1 or 2 alpha-globin genes--silent
3 genes--anemia & splenomegaly
4--hypoxemia, hydrops fetalis
genetic basis for beta thalassemia minor
mutation in one copy of chromosome 11 (heterozygote)
genetic basis of beta thalassemia major (Cooley's anemia)and intermedia
usually produced by a nonsense mutation that gives reduced (beta +) or absent (beta o) beta globins
why are the effects of beta thalassemia major not seen clinically until the age of 2-6 months?
beta globin is not produced until after birth
cause of death in more than 90% of cystic fibrosis patients
chronic lung obstruction by heavy, thick mucus and infection by staph. aureus and pseudomonas aeruginosa.
correlation of genotype and pancreatic and pulmonary function

inc. PTH, phosphaturia, inc. urine Ca, inc. urine cAMP, inc. serum Ca, dec. serum PO
primary hyperparathyroidism
dec. PTH, dec. PO & cAMP in urine, dec. serum Ca, inc. serum PO

surgical hypoparathyroidism
inc. PTH, dec. urine PO & cAMP (defective Gs), dec. serum Ca, inc. serum PO

dec. PTH, phosphaturia, inc. urine Ca & cAMP, inc. serum Ca, dec. serum PO

humoral hypercalcemia of malignancy
inc. PTH, dec. phosphate in urine (dec. GFR), dec. serum Ca, inc. serum PO, osteomalacia

chronic renal failure
location of cystic fibrosis gene
chromosome 7q
strux & function of cftr
cAMP-regulated Cl ion channel on epithelial cells (bowel & lungs), involed in Na & Cl transport, causing salt imbalances
relationship between genotype, pancreatic function, & pulmonary function in CF
pancreatic--good correlation,

thalassemia type in which alpha globin chains are deficient (excess beta or gamma chains)
alpha thalassemia
aka--Cooley's anemia
beta thalassemia major
proteins coded for by lac operon
beta galactosidase
lactose permease
inducer of the lac operon protein-coding genes
positive regulator molecule that facilitates polymerase binidng to the lac operon promoter, allowing transcription
CAP-cAMP complex
product of trpR
aporepressor protein
activates aporepressor protein in trp operon
renders promoter for trp synthesis inaccessible to RNA polymerase when bound to operator
aporepressor-trp complex
pairing of leader peptide coding regions on the trp operon that results in a pause
pairing of leader peptide coding regions on the trp operon that results in a antitermination
pairing of leader peptide coding regions on the trp operon that results in termination
main difference of eukaryotes & prokaryotes
prokaryotes have no nuclear MEMBRANE
primary control step in prokaryotic gene expression
What would happen if DNA and histones of transcriptionally inactive cells are mixed with nonhistones of transcriptionally active cells?
first sites to be cut by DNase I
hypersensitive sites
correlation of methylated DNA and transcription
more methylated DNA = less transcription
genes that encode galactose metabolism in yeast
binds to upstream activator sequence-galactose (UASg)
removed from GAL4 by galactose, activating transcription of GAL genes
common to all genes activated by a specific hormone (sequence where steroid-receptor complex binds)
Steroid response element (Res)
location of Res
enhancer region
most significant range of RNA control of processing
mRNA precursors
types of RNA processing control
choice of polyA sites, choice of alternative splice sites
result of Sx1 gene presence in RNA processing
complete tra pre-mRNA(female)
regulation of # of transcripts that exit the nucleus to cytoplasm
transport control
controls rate of protein synthesis rate increase after fertilization
mRNA translation (no new RNA synthesis)
difference between apoB in the liver (B100) and intestine (B48)
codon 2153--liver=CAA, intestine=UAA (stop codon)
shortest phase of cell synthesis
longest phase of cell division
G1 (6-12 hours, 2n DNA)
function of cyclin E
turns on start kinase (cyclin E and cdk2 dimer)
function of cyclin B
activates cdc2 that forms chromosomes (MPPF dimer of cyclin B & cdc2) in M phase
function of cyclin G
activates G cyclin-dependent protein knase to initiate S-phase (most important regulation point)
phase that prepares tetraploid cell for division during M-phase
G2 phase
what phase are DNA and histones synthesized
action of PLC
cleaves PIP2 to IP3 and DAG
activates adenylate cyclase and PLC
G protein alpha subunit
product of PLC that promotes Ca influx
product of PLC that activates PKC
cell cycle lengths
G1--6-12 H, 2n
S---6-8 H, 2n-4n
G2--3-4 H, 4n
M---1 H, 4n-2n
I---16-24 H
result of conversion of a proto-oncogene into an oncogene
cancer (no apoptosis)
most widespread oncogene
most common cancer causing mutation of a tumor suppressor gene
p53 defect
iduces synthesis of p21 that binds and inhibits cyclin cdk
function of blc-2
inhibits apoptosis (proto-oncogene)
binds transcription factor E2F
dephosphorylated pRB
nonreceptor protein-tyrosine kinase oncogene, causes chronic myelogenous leukemia when activated by translocation
cell survival oncogene, causes follicular B cell lymphoma when activated by translocation
nonreceptor protein-tyrosine kinase oncogene, causes brain tumors, leukemia, retinoblastoma, osteosarcoma, and thabdomyosarcoma
tyrosine kinase class oncogene used by Rous sarcoma virus
tyrosine kinase class oncogene used by abelson murine leukemia virus
tyrosine kinase class oncogene used by avian erythoroblastosis virus
Growth factor class oncogene used by simian sarcoma virus
Growth factor class oncogene used by harvey murine sarcoma virus
Growth factor class oncogene used by kirsten murine sarcoma virus
Nuclear protein class oncogene used by FBJ osteosarcoma virus
nuclear protein class oncogene used by avian myeloblastosis virus
nuclear protein class oncogene used by avian myelocytomatosis virus
viral gene that produces reverse transcriptase and integrase
oncogene transformed fibroblast cell properties
no contact inhibition; round shape and disorganized layers
cleavage that results in DNA fragments with a phosphate on 5' ends and hydroxyl on 3' ends
restriction enzymes
DNA library that contains only DNA corresponding to exons
consists of fragments of DNA that are the result of a restriction digest of whole genomic DNA
genomic library
DNA library that utilizes flow cytometry
chromosome-specific library
separates chromosomes according to the proportion of AT base pairs in each one
flow cytometry

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