Biochemistry II
Terms
undefined, object
copy deck
- Targeting sequence tag that directs proteins to nucleus (polymerase, peroxides)
- ProLysLysLysArgVal
- 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
- SerLysPhe
- 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
- EGF
- 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
- G(alpha)-GTP
- enzyme that hydrolyzes PIP2 to DAG & IP3
- PLC
- 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
- Farnacil
- activated by PDGF receptor via Grb2-Sos complex interaction
- Ras
- recruited by stimulation of Raf and MEK kinase
- MAPK
- 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
- G2
- 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)
- Interphase
- growth factor that induces cell division; can become a mutation
- proto-oncogene
- mutated gene that turns on G(alpha)-GTP
- oncogene
- 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
- ras
- activity lost if ras is permanently stimulated
- GTPase
- viruses that can induce cancer in animals and humans
- retrovirus
- methods viruses cause cancer (2)
- insertion of viral oncogene or promoter (close to oncogene) into host DNA
- 1st oncogene discovered
- src
- develops from formation of Philadelphia chromosomes (chr. 9-22 translocation)
- myelogenous leukemia
- oncogene turned on by formation of Philadelphia chromosomes
- abl
- protein products of growth suppressors
- check point regulators
- tetramer that induces p21 synthesis, inhibiting cyclin/cdk
- p53
- p53 concentration __________ w/ increasing DNA damage
- increases
- restricts cells from entering S-phase until damaged DNA is repaired
- p53
- action of set of genes induced by p53 when cell repair is not possible
- apoptosis
- proto-oncogene that inhibits apoptosis
- blc-2
- 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
- p53
- negative modulator of bcl-2
- p53
- cell survival oncogene that when translocated causes follicular B cell lymphoma
- bcl2
- oncogene that causes leukemia, brain tumors, osteosarcoma, retinoblastoma, and rhabdomyosarcoma
- src
- viral oncogene that encodes a truncated form of the EGF receptor (permanently stimulated tyrosine kinase)
- v-erbB
- 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
- Papillomavirus
- 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
- HIV
- 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
- Ki-ras
- 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
- src
- formed by reverse transcriptase (complement to RNA template)
- cDNA
- properties of trasformed cells by isolated oncogenes
- no contact inhibition, rounded shape, piling
- toxin produced from a fungus that grows on peanut butter
- aflatoxin
- carcinogen found in whisky and new car interiors
- diethylnitrosamine
- carcinogen used to make plastics
- vinyl chloride
- retinoblastoma factor that controls growth by reacting w/ E2F
- RB
- binds to bcl2 in the mitochondria prohibiting apoptosis
- bad
- inhibiting cdk4 would do what to the S phase of cell replication
- inhibit
- 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:
- Splicing
- 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
- thalassemias
- 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
- thalassemia
- 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
-
pancreatic--good
pulmonary--variable - 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
diagnosis? - surgical hypoparathyroidism
-
inc. PTH, dec. urine PO & cAMP (defective Gs), dec. serum Ca, inc. serum PO
diagnosis? - pseudohypoparathyroidism
-
dec. PTH, phosphaturia, inc. urine Ca & cAMP, inc. serum Ca, dec. serum PO
diagnosis? - humoral hypercalcemia of malignancy
-
inc. PTH, dec. phosphate in urine (dec. GFR), dec. serum Ca, inc. serum PO, osteomalacia
diagnosis? - 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,
pulmonary--variable - 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
transacetylase - inducer of the lac operon protein-coding genes
- allolactose
- 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
- trp
- 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
- 1:2
- pairing of leader peptide coding regions on the trp operon that results in a antitermination
- 2:3
- pairing of leader peptide coding regions on the trp operon that results in termination
- 3:4
- main difference of eukaryotes & prokaryotes
- prokaryotes have no nuclear MEMBRANE
- primary control step in prokaryotic gene expression
- transcription
- What would happen if DNA and histones of transcriptionally inactive cells are mixed with nonhistones of transcriptionally active cells?
- transcription
- 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
- GAL1, GAL7, GAL10
- binds to upstream activator sequence-galactose (UASg)
- GAL4
- removed from GAL4 by galactose, activating transcription of GAL genes
- GAL80
- 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
- mitosis
- 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
- S
- 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
- IP3
- product of PLC that activates PKC
- DAG
- 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
- Ras
- most common cancer causing mutation of a tumor suppressor gene
- p53 defect
- iduces synthesis of p21 that binds and inhibits cyclin cdk
- p53
- 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
- abl
- cell survival oncogene, causes follicular B cell lymphoma when activated by translocation
- bcl2
- nonreceptor protein-tyrosine kinase oncogene, causes brain tumors, leukemia, retinoblastoma, osteosarcoma, and thabdomyosarcoma
- src
- tyrosine kinase class oncogene used by Rous sarcoma virus
- src
- tyrosine kinase class oncogene used by abelson murine leukemia virus
- abl
- tyrosine kinase class oncogene used by avian erythoroblastosis virus
- erbB
- Growth factor class oncogene used by simian sarcoma virus
- sis
- Growth factor class oncogene used by harvey murine sarcoma virus
- Ha-ras
- Growth factor class oncogene used by kirsten murine sarcoma virus
- Ki-ras
- Nuclear protein class oncogene used by FBJ osteosarcoma virus
- fos
- nuclear protein class oncogene used by avian myeloblastosis virus
- myb
- nuclear protein class oncogene used by avian myelocytomatosis virus
- myc
- viral gene that produces reverse transcriptase and integrase
- pol
- 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
- cDNA
- 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