MOL CELL T3

What are retroviruses? Structure: ___ ___ molecules. inside ___ protein shells, surrounded by ___ containing viral proteins They are replicated using a ___ ___ What is an ex.?

(+)ssRNA viruses Structure: Two ssRNA molecules. inside two protein shells, surrounded by outer membrane (enveloped virus) containing viral proteins They are replicated using a DNA intermediate ex. HIV

If these bases(C,A,G,U,I) are in the wobble(1st) position if the anticodon then tRNA may recognize codons in the mRNA that have what bases the 3rd position of the codon?

-C(1st anticodon of tRNA)-mRNA must have G in the 3rd position of the codon for tRNA to recognize -A(1st anticodon of tRNA)-mRNA must have U in the 3rd position of the codon for tRNA to recognize -G(1st anticodon of tRNA)-mRNA must have C,U in the 3rd position of the codon for tRNA to recognize -U(1st anticodon of tRNA)-mRNA must have A,G in the 3rd position of the codon for tRNA to recognize -I(1st anticodon of tRNA)-mRNA must have C,A,U in the 3rd position of the codon for tRNA to recognize *I is inosine

If these bases(C,A,G,U) are in the wobble(3rd) position of the codon. What base in the 1st position of the anticodon would allow for the tRNA to recognize it?

-C(3rd position of mRNA)-tRNA must have G,I in the 1st position of the anticodon to recognize -A(3rd position of mRNA)-tRNA must have U,I in the 1st position to recognize -G(3rd position of mRNA)-tRNA must have G,I in the 1st position to recognize -U(3rd position of mRNA)-tRNA must have G,I in the 1st position to recognize

In numbering of mRNA what is 1?

1- This is the beginning of the first codon. Where translation occurs. (often called the start site)

Steps for replication of (+)ssRNA Viruses?(6)

1. (+)ssRNA is translated into a Single Polyprotein 2. Polyprotein is cleaved into smaller proteins that include a RNA-dependent RNA polymerase 3. (+)ssRNA is used to make (-)ssRNA(complementary strand) 4. (-)ssRNA is used along with the RNA-dependent RNA polymerase from the cleaved Polyprotein to make more (+)ssRNA 5. new (+)ssRNA goes through step 1 and 2 and make more viral proteins 6. (+)ssRNA and viral proteins join forming a nucleocapsid

Where does miRNA bind in mRNA?(2) which is more common?

1. 3' UTR of mRNA(common) 2. coding region of mRNA

What is the Mechanism by which siRNA is produced and causes RNA interference and degradation of mRNA?(4) Where does siRNA processing occur?

1. A nuclease called "Dicer" cleaves longer molecules of dsRNA into fragments of 21 or 22 nucleotides called siRNA 2. siRNA (short interfering RNA) are recognized and bound by RNA-induced silencing complex (RISC) 3. The RISC complex then separates the two strands of the siRNA and scours the cytoplasm for complementary RNA sequences(target) and binds to the mRNA 4. The nuclease activity of the RISC complex, sometimes referred to as " Slicer," but more commonly known as an Argonaut (AGO) family member, then degrades the complementary RNAs- inhibiting translation processing occurs in the cytoplasm

What are the steps involved in the process of translating nucleic acid sequences in mRNA into amino acid sequences in proteins?(2) step 1 requires what? links what?forms what bond?forms what molecule? this is called ___of tRNA If an error occurs at either step what is the result?

1. A specific aminoacyl-tRNA synthetase attaches the appropriate amino acid to the appropriate tRNA -requires breaking of ATP to AMP+2Pi -links the amino acid to the adenosine of CCA located at the acceptor stem -forms a high-energy ester bond -this forms an aminoacyl-tRNA -called charging/activation of tRNA 2. A three-base sequence in the tRNA (the anticodon) base-pairs with a codon in mRNA Error results in the wrong amino acid incorporated into the polypeptide chain

If a single stranded DNA or partially replicated DNA is detected at the DNA replication checkpoint what happens?(2) where is the replication checkpoint?

1. ATR associates with replication forks and activates Chk1 kinase. 2. Chk1 phosphorylates and inactivates Cdc25, thereby inhibiting initiation of mitosis Between G2 and M

What is the the exception to the property of "universal" in the genetic code?(3) Most of the exceptions involve what?

1. AUG determines N-formyl methionine in prokaryotes and methionine in eukaryotes 2. small genomes of mitochondria in ciliated protozoans 3. small genome of chloroplasts in Acetabularia, a single-celled eukaryotic plant *Most of the exceptions are changes that cause the reading of normal stop codons as amino acids, NOT an exchange of one amino acid for another

Eukaryotic processing of Pre-RNA to mature RNA consists of what?(3)

1. Addition of 5' cap(capping) 2. Addition of Poly A tail(polyadenylation) 3. Splicing Introns out

RNA Processing in Eukaryotes vs prokaryotes(2)

1. All eukaryotic RNAs (rRNA, tRNA, and mRNA) are processed to produce functional mature RNA but there is no processing of RNAs in prokaryotes 2. Only mature RNAs (rRNA, tRNA, and mRNA) participate in protein synthesis in eukaryotes

What are the types of cell death?(3)

1. Apoptosis -Physiologic form of cell death -it is called programmed cell death 2. Necrosis -Pathologic or accidental cell death -Cells swell and burst releasing their intracellular contents 3. Autophagy -A process of self cannibalism by which a cell recycles its own components to survive under nutrient-deprived condition

What are the steps in the intrinsic(mitochodrial) pathway?(7)

1. Apoptotic signal causes the release of pro-apoptotic Bcl-2 proteins(Bax and Bak} 2. pro-apoptotic Bcl-2 proteins(Bax and Bak} cause the mitochondrion to release Cytochrome C 3. Cytochrome C binds and activates apoptosis promoting activating factor (Apaf 1) 4. Many activated apoptosis promoting activating factor (Apaf 1) join together through a CARD domain to for an apoptosome 5. The Cytochrome C in the apoptosome recruits initiator procaspase-9 and facilitates it's binding to the Apaf 1 in the apoptosome through the CARD domain -this activates the initiator procaspase-9(now called caspase-9) 6. Active Caspase-9 now cleaves and activates activates effector(executioner) pro-caspases: 3, 6, 7(now called caspase3,6,7) 7. activative effector(executioner) caspases: 3, 6, 7 then cause the cleavage of multiple substrates leading to apoptosis

What is the process of Viral Replication?(5)

1. Attachment and Penetration: Receptor mediated endocytosis -for naked viruses: a. Virion recognizes and binds to the receptors on the surface(plasma membrane) of target proteins b. cell membrane invaginates, enclosing the virion in an endocytic vesicle (endosome) c. Viron is release into the cytoplasm -for enveloped viruses: a. proteins on the surface of the envelope recognizes and binds to the receptors on the surface(plasma membrane) of target proteins b. Viral envelope fuses with the plasma membrane dumping the virion into the cytoplasm 2. Un-coating: Disassembly of the virion, enabling expression of viral genes 3. Replication of the viral genome -Viral genome divided into "early" and "late " genes a. Early genes: expressed immediately after infection b. Late genes: promoters not recognized by host polymerase -RNA viruses replicate in the cytoplasm -DNA viruses replicate in the nucleus 4. Assembly and Release of progeny viruses -Virus particle are assembled where the genome replication occurs -Capsid components self-assemble and associate with nucleic acid to form nucleocapsid -for naked viruses: a. nucleocapsid(w/ virion) is released out of the cell -for enveloped viruses: a. virus-specific glycoproteins are synthesized and incorporated into the host cell membrane b. nucleocapsid then bind to these membrane proteins (additional help from viral matrix proteins) c. nucleocapsid is then enveloped by the host cell membrane forming the enveloped -called budding d. enveloped nucleocapsid(w/ virion) is released out of the cell 5. Progeny viruses go and infect other host cells

The large heterodimeric subunit of the mRNA transporter consists of what three separate domains? What are their functions? Which domains recognize the FG repeat motifs of nucleoporins?

1. C-terminal (C) domain 2. middle domain (M) 3. N-terminal domain (N). The M and C domains of NXF1/TAP bind to and help diffuse the RNA as a RNP complex The N-terminal domain has a weak but significant RNA recognition and binding capacity M and C domains recognize the FG repeat motifs of nucleoporins

Biochemical features of apoptosis-DNA fragmentation How does DNA fragmentation occur?(3)

1. CAD (caspase-activated DNase) is bound and inhibited by iCAD 2. an executioner capsase cleaves off iCAD, activating CAD 3. activated CAD fragments DNA

What are the types of CDKs?(4) in order from entry into G1 to end of M aka? What cyclins do they require? for what?

1. CDK4(G1 CDKs) -requires cyclin D for entry into the cell cycle 2. CDK6(G1 CDKs) -requires cyclin D for entry into the cell cycle 3. CDK2(G1/S CDKs and S CDKs -G1/S CDKs requires cyclin E for the passage through the restriction point -S CDKs requires cyclin A for initiation of DNA replication 4. CDK1(M CDKs) -requires cyclin B for entry into mitosis -requires cyclin A for idk?

What are the morphological features of apoptosis?(4)

1. Chromatin condensation 2. Cytoplasmic blebbing -cell detaches its cytoskeleton from the membrane, causing the membrane to swell into spherical bubbles, greatly distorting the shape of the cell 3. Apoptotic bodies 4. Cell shrinkage

What are the 4 principal modifications Membrane and secretory proteins that are synthesized in the ER undergo before reaching their final destination?

1. Covalent addition and processing of carbohydrates 2. Formations of disulfide bonds in the ER and Golgi 3. Proper folding of polypeptide chains and assembly of multisubunit proteins in the ER 4. Specific proteolytic cleavages in the ER, Golgi, and secretory vesicles

Prokaryotic Transcription 1. What happens when glucose is absent and lactose is present? 2. What happens when glucose is present and lactose is absent? 3. What happens both glucose and lactose are absent? 4. What happens both glucose and lactose are present?

1. Crp (plus cyclic AMP) binds, AND lactose is present, hence the LacI repressor is removed from the DNA by binding the inducer. Gene is transcribed 2. Crp is absent and lactose is also absent, hence LacI is still bound. Gene is not transcribed 3. Crp is present, the LacI repressor still blocks transcription. Gene is not transcribed 4. LacI repressor is removed from the DNA. However, glucose is present, hence Crp is absent and RNA polymerase still cannot transcribe the genes. Gene is not transcribed

What regulates cyclin-dependent kinases(CDKs)?(5)

1. Cyclins 2. Phosphorylation and dephosphorylation 3. Cyclin-dependent kinase inhibitors (CKI) 4. Proteolysis 5. Transcription

What does the 3 loops of the tRNA contain?D(1), TψC(3), Anticodon(2) Their function? LOOK at LECTURE 30 SLIDES 17-18 to review tRNA STRUCTURE

1. D loop (arm) of tRNA: -contains: 1. dihydrouridine -aminoacyl-tRNA synthetases use this for recognition of proper tRNA 2. TψC loop (arm) of tRNA -contains: 1. ribothymidine 2. pseudouridne 3. cytodine -recognition of the tRNA by the ribosome. 3. Anticodon loop (arm) of tRNA -contains: 1. codon recognition site (anticodon) 2. inosine(nonstandard amino acid) -base pairs with the codon on a strand of mRNA during translation -aminoacyl-tRNA synthetases use this for recognition of proper tRNA

Eukaryotic Transcription What is RNA Pol II controlled by?(2) What initiates mRNA transcription?

1. DNA bound regulatory proteins far removed from the start of transcription 2. General transcription factors (TFIIA, TFIIB, TFIID (TBP + TAFs), TFIIE, TFIIF, TFIIH,TFIIJ) and RNA pol II (pre-initiation complex) GTFs and RNA Pol II initiate mRNA transcription

Eukaryotic Transcription RNA Pol II is negatively regulated by what 2 proteins? What do they do?

1. DSIF (DRB-sensitivity inducing factor) 2. negative elongation factor ( NELF ), they bind to Pol II and pause transcription of the gene after the transcript has been initiated

What are the Hallmarks of cancer?(7)

1. Disregard normal cell growth control -Self-sufficiency in growth signals -Insensitivity to growth inhibitory signals 2. Resistance to cell suicide or apoptosis 3. Limitless replicative potential: Tumor cells avoid replicative senescence and have unrestricted proliferative capacity 4. Develop angiogenic potential: Tumor cells can stimulate formation of new blood vessels to bring nutrients and oxygen and to access the vasculature for metastasis 5. Ability to invade and metastasize: Invasion and metastasis are the hallmarks of malignant tumors and the root cause of morbidity and mortality 6. Reprogram energy metabolism 7. Escape immune destruction

1. T/F Only the 5' end is important for addition of an amino acid 2. T/F Modified bases are rare in tRNA

1. False, The 3' end is important because it contains the CCA sequence 2. False, tRNA contains many modified bases(ex. dihydrouridine, ribothymidine, pseudouridne, cytodine, inosine)

1. How many tRNA's are there? 2. How many aminoacyl-tRNA synthetases?

1. Fewer than 61(64 possible codons - 3 stop codons), because of wobble -perfect Watson Crick pairing were required, cells would need 61 different tRNAs -Cells tend to only have around 41 or so different tRNA's (the minimum needed is 31 2. 20 aminoacyl-tRNA synthetases

What is the process of splicing?(2)

1. First, the intron and exon are cut apart at the 5′ splice site and the free 5′ end of the intron loops around and is joined to the adenine at the branch site(branch point A) -this is the first Transesterification rxn which makes a 2'-5' Phosphodiester bond -forms a lariat structure -ester bond between the 5'-phosphorus of the intron and 3' oxygen of exon is exchanged for an ester bond with 2' oxygen of branch point A 2. the free 3′ end of the upstream exon displaces the intron from the 3′ splice site and the two exons are joined together. -Second Transesterification rxn (usual 3-5' Phosdiester bond)--- lariat excision The intron is released as a branched lariat structure that is later degraded.

1. What ribosomes synthesize proteins in the non-secretory pathway? 2. What ribosomes synthesize proteins in the secretory Pathway?

1. Free cytoplasmic ribosomes 2. Ribosomes bound to the ER

Eukaryotic Transcription RNA Pol II What are the common upstream elements?(4)

1. GC box 2. CAAT box 3. AP1 element 4. Octamer element

Important points on promoters of an eukaryotic m-RNA coding gene JUST READ

1. Gene: A piece of ds DNA that can be transcribed to produce RNA. 2. A gene has "Top" strand [Generally referred as coding strand]: reads 5'-3' (L-R) 3. A gene has a "Bottom" stand [Generally referred as non-coding or template strand]: reads 3'-5' (L-R) 4. Any of "Top" and "Bottom" strand can be transcribed to produce RNA 5. "Top" or "Bottom" strand will be transcribed if it has promoters at the 5' end and close to the region being transcribed 6. Promoter regions are not transcribed, so promoters are present in the DNA, and also is a part of the gene but not the part of RNA 7. Presence of promoter sequences on a particular DNA strand makes that strand as a coding strand, then the other strand automatically becomes a template strand. 8. Coding strand has the exact same sequence as the RNA sequence (only T is replaced by U) 9. Template strand sequence is complementary to the sequence of RNA or the coding strand

What are the Genetic alternations that lead to cancer?(4)

1. Growth-promoting proto-oncogenes 2. Growth-inhibiting tumor suppressor genes 3. Genes that regulate programmed cell death 4. Genes involved in DNA repair

What are 2 examples of Human Cancer Viruses? -DNA or RNA -Which one is in the retrovius family? About ___ % of cancers related to viral infections

1. Hepatitis C Virus(RNA) 2. Human T-cell Leukemia Virus(RNA)- retrovirus About 12-15 % of cancers related to viral infections

What are some examples of Oncogenic DNA Viruses?(3) -what do they relate to

1. Human Papilloma Virus (HPV) -epithelial cancers 2. Hepatitis B Virus (HBV) -hepatocellular cancers 3. Epstein Barr Virus (EBV) -lymphoid malignancies (B, T cell lymphoma)

What are the Cyclin-dependent kinase inhibitors(4)? what p? What CDK or CDK-cyclin complex does it mess with? inhibit what part of the cell cycle?

1. Ink4: p15, p16, p18, p19 -messes with CDK4 and CDK6 -inhibits G1 2. Cip1(Cdk2 interacting protein 1): p21 -messes with CDK2-cyclin E complex -inhibits G1 -messes with CDK2-cyclin A complex -inhibits S, and G1 3. Kip1(Kinase inhibitory protein 1): p27 and p57 -messes with CDK2-cyclin E complex -inhibits G1 -messes with CDK2-cyclin A complex -inhibits S, and G1 4. Rb: binds to E2F, preventing transcription of multiple cell cycle gene

What are the 2 pathways by which apoptosis can occur?

1. Intrinsic aka mitochondrial pathway 2. Extrinsic aka receptor-initiated pathway

What are the 2 types of effects viruses have on host cells?

1. Lytic: Infection results in host cell death -Virus inhibits host cells synthetic enzymes, resulting in cell death 2. Lysogenic/ Latency: viral infection does not kill host cell -Viral genome integrated into the host genome -Latent viruses can be activated after months/years -Infected cells can be transformed and induce tumors in animals (tumor viruses)

Translation involves what RNAs?(2) What are their functions?

1. Messenger RNA (mRNA) -carries the genetic information transcribed from DNA in a linear form 2. Transfer RNA (tRNA): -deciphers/decodes codons in mRNA

What are the Pathways for protein targeting in the cell?(2) which one involves an ER targeting sequence?

1. Nonsecretory Pathway 2. Secretory Pathway -has an ER targeting sequence

What are the steps of Peptidyl Chain Elongation in Eukaryotes?(9) a. what is the bond between Met-aa2 in the Met-aa2-tRNA? b. what is the bond between aa2-tRNA in Met-aa2-tRNA?

1. Once the 80S ribosome with Met-tRNAiMet in the ribosome P site is assembled, a ternary complex(EF1alpha(α)-GTP, aa2-tRNAeaa2) bearing the second amino acid (aa2) binds to the A site(loose binding) 2. Hydrolysis of GTP in EF1alpha(α)-GTP to EF1alpha(α)-GDP+Pi -causes a conformational change in the ribosome-binds tighter to aa2-tRNAeaa2 -In the second and subsequent elongation cycles, the tRNA at the E site is ejected as a result of the conformational change 3. EF1alpha(α)-GDP+Pi dissociate 4. The large rRNA catalyzes peptide bond formation between Meti and second amino acid(aa2) 5. EF2-GTP bind to the ribosome 6. Hydrolysis of GTP in EF2-GTP to EF2-GDP+Pi causes another conformational change in the ribosome that results in its translocation one codon along the mRNA and shifts the unacylated tRNAiMet(not longer has Met bound) to the E site and the Met-aa2-tRNA shifts to the P site -peptide bond between Met-aa2 -covalent bond between aa2-tRNA 7. EF2-GDP+Pi dissociates 8. Translocation thus returns the ribosome conformation to a state in which the A site is open and able to accept another aminoacylated tRNA complexed with EF1α·GTP, beginning another cycle of chain elongation 9. The cycle can begin again with binding of a ternary complex bearing aa3 to the now open A site. In the second and subsequent elongation cycles, the tRNA at the E site is ejected during step 2 as a result of the conformational change induced by hydrolysis of GTP in EF1α·GTP a: peptide b: covalent

Eukaryotic Transcription What are the 2 domains of transcription factors(such as activators and repressors)?

1. One that binds to DNA is called DNA-binding domain 2. Another domain that interacts with the transcription apparatus is called activation domain or trans-activation domain or activator domain

What are the types of Endocytosis?(3) a. Which does secretory cells use to to retrieve the membrane material that is added to the plasma membrane during exocytosis?

1. Phagocytosis ("cell eating") is the uptake of solid particles into the cell 2. Pinocytosis ("cell drinking") is nonselective. It can involve uptake of fluid droplets into the cell 3. Receptor-mediated endocytosis is a mechanism for the selective uptake of soluble proteins and other high-molecular-weight materials -Binding is followed by the clustering of receptor-ligand complexes on the cell surface and the formation of an endocytic vesicle a: pinocytosis

How are proto-oncogenes converted to oncogenes?(3)

1. Point mutation -hyperactive or constitutively active protein 2. Gene Amplification -Numerous copies of a protooncogene leads to overproduction of the encoded protein 3. Chromosomal translocation -Inappropriate expression of the gene due to translocation of growth regulatory gene under the control of different promoter -Fusion of two genes produce a hybrid gene encoding a chimeric protein

What are the stages of prokaryotic transcription?(4)

1. Polymerase recognition: The sigma factor recognizes and binds to the -10 and -35 Boxes of the prokaryotic promoter 2. Initiation of transcription: RNA Pol Holoenzyme binds, melts DNA forming a transcription bubble (open complex), transcribes 7-9 bases, sigma factor falls off causing a conformational change to tight binding 3. Elongation of RNA 4. Termination(2 ways)

Prokaryotic Transcription What is positive regulation? What is negative regulation?

1. Positive regulation, an activator protein binds to the DNA in response to a signal, and aids to the binding of RNA polymerase to DNA and thus activates transcription -a signal changes the conformation of an inactive regulator, which then becomes active and binds to the regulatory region of a gene. Its presence aids the binding of the RNA polymerase and helps switch on the gene 2. Negative regulation, a repressor protein binds to the DNA to block the promoter

What are the Four steps of transcription of eukaryotic genes? Where is the difference between Prokaryotic and Eukaryotic?(2)

1. Pre-initiation complex formation 2. Initiation of transcription 3. Elongation of RNA chain 4. Termination of transcription Differences: 1. The first step in Prokaryotic Transcription is Promoter recognition by σ factor of the holoenzyme (RNA polymerase) 2. Termination of transcription Eukaryotic transcription takes place in the cell nucleus. Prokaryotic Termination occurs in the cytoplasm

What are the functions of oligosaccharide side chains attached to glycoproteins?(3)

1. Promote proper folding 2. Confer stability 3. Cell to cell adhesion

What are the steps of the M phase(cell division) of the cell cycle?(7) What happens at each step?

1. Prophase: -Chromosome condensation -Centrosome migration -Mitotic spindle assembles 2. Prometaphase: -Nuclear envelope breakdown -Chromosomes attach to spindle microtubules via kinetochores 4. Metaphase: -Chromosomes move to spindle equator and are aligned at the metaphase plate 5. Anaphase: -Centromeres split -Sister chromatids separate 6. Telophase -Daughter chromosomes arrive at the spindle poles -Nuclear membranes reform -Chromosomes decondense 7. Cytokinesis

What are the 3 steps in the basic mechanism of the secretory pathway?

1. Protein synthesis and translocation across the ER 2. Protein folding and modification inside the ER 3. Protein transport to the Golgi, lysosomes, or cell surface through budding and fusing of vesicles

What are the Three Different RNA Polymerases of eukaryotes? What do they make?

1. RNA polymerase I for class I gene (rDNA) transcription to synthesize rRNA 2. RNA polymerase II for class II genes (protein coding genes) to synthesize mRNA 3. RNA polymerase III for class III genes (tRNA genes,5S rRNA genes, and small RNA genes) to synthesize tRNA, 5S rRNA, small nuclear RNAs(snRNA), and general transcription factors(GTF) *1,2,3,r,m,t *note that RNA Pol III makes tRNA, 5S rRNA, snRNA, and GTF

What some examples of DNA viruses in Higher Organisms?(3) -what do they cause? Are they usually double-stranded or single-stranded?

1. Simian virus SV40: -cancer in monkeys by genome integration 2. Herpesvirus: -sores -genital herpes -chickenpox -infectious mononucleosis 3. Poxviruses Usually dsDNA

What causes RNA silencing and block protein translation and gene expression in Eukaryotes?(2) how? What else also destroys the mRNA in the cytoplasm?

1. Small interfering RNA(siRNA): They have 21 or 22 nucleotides that perfectly pairs with it's target mRNA and induces the CLEAVAGE OF mRNA in the cytoplasm -RNA degradation -INHIBITS TRANSLATION 2. micro RNA(miRNA): They have ~21 nucleotides that imperfectly pairs with it's target mRNA and results in BLOCKING OF TRANSLATION OF mRNA -iINHIBITS TRANSLATION Degradation of mRNA in the cytoplasm by ribonucleases also destroys mRNA

How is mRNA remodeled during nuclear transport?(4)

1. Some mRNA proteins dissociate from nuclear mRNP complexes before export through an NPC 2. The mRNA proteins that did not dissociate earlier are exported through the NPC with the mRNP. Once in the cytoplasm they dissociate and are shuttled back to the nucleus via an NPC 3. In the cytoplasm, the translation initiation factor(eIF4E) replaces the CBC bound to the 5' cap 4. PABPI(poly-A binding protein) replaces PABPII

What are two ways errors are reduced in charging a tRNA? -what inhibits charging/activation of incorrect tRNAs?

1. Specific Active Site: incorrect tRNA binding will inhibit charging the incorrect tRNA 2. aminoacyl-tRNA synthetases have a proofreading activity that checks the fit in their amino acid-binding pocket

Bacteria can become resistant to ribosomally acting antibiotics by mutations that change the target of drug action example?(3)

1. Streptomycin: bacterial resistance can be produced by mutations in the gene for S12, a protein of the small ribosomal subunit to which this antibiotic binds 2. Tetracycline: bacterial resistance can be produced by mutations in the proton pump that introduces tetracycline into the cells 3. Chloramphenicol: bacterial resistance can be produced by mutations in the 50s ribosomal subunit that causes reduced membrane permeability

What are the 3 mRNA-transporters that help diffuse mRNP through the nuclear pore complex? what forms the large heterodimeric subunit of the mRNA transporter? what forms the small heterodimeric subunit of the mRNA transporter?

1. TAP 2. NXF1 3. Nxt1 NXF1 or TAP is the large subunit of mRNA-transporter Nxt1-small subunit

Eukaryotic Transcription RNA Pol II Transcription Factor steps What is the first step?

1. TBP forms part of a transcription factor complex known as TFIID that is needed to recognize promoters specific(TATA box) for RNA polymerase II 2. TFIIA and TFIIB bind next 3. RNA polymerase II itself arrives, accompanied by TFIIF, which helps RNA polymerase bind 4. TFIIH must phosphorylate the CTD(carboxy-terminal domain of RNA polymerase before it can move 5. All the TGFs falls off except TFIIH The binding of TFIID to the TATA box via TBP is the first step of transcription initiation.

What are 3 well characterized Lysosomal Storage Diseases? Which one fatal in early life? Which one is treatable with enzyme replacement therapy? Which one has Less penetrant symptoms that can occur early or late in life?

1. Tay-Sachs Disease -fatal in early life 2. Gaucher Disease- treatable with enzyme replacement therapy 3. Pompe Disease - Less penetrant symptoms can occur early or late in life.

What makes up the promoter region in Prokaryotic Transcription? What is the structure?

1. The -10 box(TATAAT) is a highly conserved 6 base sequence on the coding strand. 2.The 17-19 base sequence representing a defined spacer element is also essential. The -35 box(TTGACA); is also a highly conserved 6 base sequence on the coding strand. 3. The conserved sequences are recognized by DNA-dependent RNA Polymerase with sigma factor bound. 4. The 5-9 base sequence representing a second defined spacer before the start site is also important Structure: -35 box-> 17 to 19 base sequence spacer element-> -10 box->5 to 9 base sequence spacer element-> (it is followed by the startpoint @ the +1 position)

What are the functions of Luminal folding catalysts?(2)

1. They assist in the folding of normal proteins by preventing protein aggregation and by binding to irreversibly misfolded proteins 2. They prevent the formation of dimers

How do proto-oncogenes work?

1. They release growth factors: EGF, PDGF 2. Growth factors bind to Growth factor receptors: EGFR (ErbB), PDGFR which have an intracellular effector region(called protein-tyrosine kinase) which phosphorylates(activates) Intracellular transducer proteins: Ras, Abl(second messengers) 3. Intracellular transducer proteins: Ras, Abl(second messengers) causes Transcription factor: Myc to bind -these transcription factors controls cell division and apoptosis

Eukaryotic Transcription RNA Pol II The assorted transcription factors bind to and recognize specific sequences on the DNA. These DNA sequences are of two major classes are...

1. Those comprising the proximal promoters 2. those that have the enhancer sequence and not the proximal promoter

Explain Replication of dsDNA Viruses in relation to "early" genes and "late" genes

1. Transcription of "early" genes prior to transcription of viral DNA makes "early" mRNAs 2. "early" mRNAs are translated to "early" proteins 3. "early" proteins aid in transcription of virus DNA making "late" mRNAs 4. "late" mRNAs are translated to "late" proteins 5. "late" proteins help the nucleocapsid

What is the process of adding a 3' tail?(6) What is its function

1. Transcripts destined to become mRNA have a tail recognition sequence—AAUAAA—close to the 3′ end, The RNA polymerase that is making the RNA molecule continues past this point 2. Cleavage and polyadenylation specificity factor (CPSF) binds to the AAUAAA sequence 3. Cleavage stimulation factor (CST) binds to the GU-rich tract -lies Beyond the cutting site is 4. CPSF and CST proteins provide a platform for assembly of cleavage factor (CF) and poly(A) polymerase as well as the poly(A)-binding protein (PABP) 5. Once this polyadenylation complex is assembled, the RNA is cut by the cleavage factor (CF) (an endonuclease) and a poly(A) tail is added by the poly(A) polymerase -The tail consists of 100-200 adenine residues 6. PABP stays associated with the mRNA and binds to the poly(A) tail -protects the cap from being cut off function: The poly(A) tail is required for stabilization of mRNA and translation

How is translation terminated in Eukaryotes?(5)

1. Translation is terminated when a ribosome bearing a nascent protein chain reaches a stop codon (UAA, UGA, UAG) 2. eukaryotic release factor 1 (eRF1) enters the ribosomal complex, probably at or near the A site together with eRF3·GTP 3. Hydrolysis of GTP in eRF3-GTP to eRF3-GDP+Pi 4. eRF1, eRF3-GDP+Pi dissociates 5. cleavage of the peptide chain from the tRNA in the P site and release of the tRNAs and dissociation of the two ribosomal subunits

What are the steps in apoptosis that uses components from both pathways that deal with Pro-apoptotic Bcl-2 protein Bid?(6)

1. Tumor Necrosis Factor(TNF) binds to TNF receptor 2. Receptor recruits adapters 3. The adaptors bind with pro-caspase-8 and activates it(now called caspase-8) 4. Activated caspase-8 causes the cleavage of Pro-apoptotic Bcl-2 protein Bid forming Truncated Bid(tBid) 5. Truncated Bid (tBid) translocates to the mitochondria and causes release of cytochrome c 6. Cytochrome c release causes activation of caspase-9 *steps 1-4 relates to extrinsic pathway *steps 5-6 relates to intrinsic pathway

Viruses are divided into groups(classified) based on:(4)

1. Type and structure of nucleic acid -DNA or RNA -single or double-stranded -circular or linear -single or segmented genome 2. Capsid structure -helical vs icosahedral 3. Presence or absence of Lipid envelop 4. Replication Strategy

What are the Stages of spliceosome assembly at 5' splice sites, 3' splice site, and branch site on the pre-mRNA?(7)

1. U1: recognizes and binds to 5' splice site 2. U2AF: recognizes and binds to 3' splice site 3. U2: recognizes and binds the branch site 4. U4 and U6 bind to U2, and U5 binds to the downstream exon 5. A loop forms by association of U1 and U2. 6. U6 displaces U1 from the spliceosome and U4 departs as well 7. splicing

What are the 3 stop codons?

1. UAA 2. UGA 3. UAG You are annoying You go away You are gone

What are the uses of Receptor-Mediated Endocytosis?(3)

1. Uptake of nutritive substances -ex. LDL, and iron-transferrin complex 2. Waste disposal -ex. "worn-out" plasma proteins and hemoglobin-haptoglobin complexes 3. Mucosal transfer:Single-layered epithelia can endocytose a protein on one side and exocytose it on the opposite side(transcytosis) -ex. The secretion of immunoglobulin A (IgA) across mucosal surfaces

1. Do you need a targeting sequence to get in through the inner mitochondrial membrane? 2. Do you need a targeting sequence to get in through the outer mitochondrial membrane?

1. Yes 2. No, because it is permeable

Eukaryotic Transcription What are the 4 types of DNA-binding regulatory protein families can bind to DNA and regulate gene transcription in eukaryotes?

1. Zinc fingers: Steroid hormone receptors. Most common DNA binding motif in human genome. 2. Helix-turn-helix:In eukaryotes, homeodomain proteins which have master control functions in development -Some bacterial repressors 3. Leucine zipper: Motif is an amphipathic a-helix with hydrophobic amino acids concentrated to one side (Leu every 7th position). -Found in many eukaryotic transcription factors and a few prokaryotic proteins 4. Helix-loop-helix: Two a-helical regions linked by a loop of variable length -Common structural motif in proteins implicated in the development of multi-cellular eukaryotic organisms

What is the process of adding a 5' cap?(4) When does this process take place?

1. a phosphatase removes 5' phosphate 2. a guanyl transferase adds GMP by 5' to 5' linkage making the GTP 3. a methyl transferase adds methyl group to guanosine a the 7 position(called cap0) -lower euk and plants only go this far -the cap stabilizes and protects the mRNA from degredation 4.A methyl transferase enzyme also adds methyl groups to 2' hydroxyl oxygen of bases 1 and 2(called cap1 and cap2 respectively) -cap2 is typical of mammals -increase the efficiency of translation takes place shortly after transcription starts

What are the steps in the activation of caspases?(4) REVIEW CELL DEATH SLIDE 17

1. an apoptotic signal results in the production of adaptor proteins 2. adaptor proteins then bind to inactive initiator caspases: 8, 9 -dimerization, activation, and cleavage activates the initiator caspases: 8, 9 3. activated initiator caspases: 8, 9 then activate effector(executioner) caspases: 3, 6, 7 via cleavage 4. activative effector(executioner) caspases: 3, 6, 7 then cause the cleavage of multiple substrates leading to apoptosis

Eukaryotic Transcription What does the promoter for RNA Pol I consist of?(2)

1. an upstream control element 2. Bipartite (a core promoter)

Chloramphenicol 1. What can humans develop form this drug? 2. It is also labelled as a ___ in humans

1. aplastic anemia 2. carcinogen

Tetracycline affects both eukaryotes and prokaryotes 1. why does is it much more more effective in prokaryotes? 2. why is it less effective in humans?

1. bacteria: actively pump tetracycline into their cytoplasm 2. humans: tetracyclineis absorbed into the bone and is sometimes used as a marker for bone growth

What is the process of phagocytosis?(3)

1. binding of a solid particle to a protein in the plasma membrane that functions as a receptor 2. Pseudopods are formed that flow around the particle -requires the reversible depolymerization and repolymerization of actin microfilaments under the plasma membrane 3. The phagocytic vacuole fuses with lysosomes (L), and the particle is digested by lysosomal enzymes

What's the function of a peroxisome?(2)

1. break down fatty acids to be used for forming membranes and as fuel for respiration 2. transfer hydrogen from compounds to oxygen to create hydrogen peroxide and then convert hydrogen peroxide into water

1. The mRNA is read in sets of three-nucleotide sequences, called _____, each of which specifies a particular amino acid 2. The correct tRNA with its attached amino acid is selected at each step because each specific tRNA molecule contains a three-nucleotide sequence, called an _____, that can base-pair with its complementary codon in the mRNA

1. codons 2. anticodon

What are the properties of the Genetic Code?(6)

1. colinear: -The sequence of amino acids in the polypeptide, from amino end to carboxyl end, corresponds exactly to the sequence of their codons in the mRNA, read from 5' to 3'. 2. nonoverlapping and "commaless.": -The codons are aligned without overlap and without empty spaces in between. Each base belongs to one and only one codon. The codon the base belongs to is set by the open reading frame and the start site. 3. It contains 61 amino acid coding codons, including one start codon (AUG), and in addition, 3 (three) stop codons UAA, UAG, and UGA. Commonly referred to as amber (UAG), ochre (UAA) and umber (UGA) 4. unambiguous: -Each codon specifies one and only one amino acid. (for the most part there are some exceptions) 5. degenerate: -More than one codon can code for an amino acid. 6. universal: -The code is identical in prokaryotes and eukaryotes, with the exception of the start codon AUG. AUG determines N-formyl methionine in prokaryotes and methionine in eukaryotes

What is involved in chromosome condensation in the cell cycle?(2)

1. condensins 2. structural maintenance of chromatin (SMC) proteins

What are the steps in the initiation of translation in eukaryotes?(7) In step 1 what forms a ternary complex?

1. eIF1A, eIF2-GTP, Met-tRNAiMet bind to the eIF3-40SrRNA forming the Preinitiation complex(43S complex) -eIF2-GTP, Met-tRNAiMet form the ternary complex 2. eIF4(cap-binding complex-ABEG) bind to the 5' cap of mRNA 3.eIF4(cap-binding complex-ABEG) bound to the 5' cap of mRNA then bind to the Preinitiation complex forming the Initiation complex 4. The associated initiation complex(multicomponent) scans the mRNA, which leads to positioning the small subunit and bound Met-tRNAiMet at the start codon 5. Hydrolysis of GTP in eFI2-GTP to eFI2-GDP+Pi 6. eIF3, eIF1A, eIF2-GDP+Pi, eiF4(cap-binding complex) dissociate -This process uses ATP and converts it to ADP+Pi 8. 60S subunit-eIF6 and eIF5-GTP bind and catalyze the formation of the 80S -GTP bound by eIF5 is hydrolyzed to eIF5-GDP+Pi -when this process is complete, eIF6, eIF5-GDP+Pi dissociate

1. Recognition of stop codon is done by? 2. What monitors the correct recognition of a stop codon?

1. eRF1 2. eRF3

Termination of translation in Eukaryotes requires what types of specific protein release factors(termination factors)?(2) What is their function?

1. eRF1, acts by binding to the ribosomal A site and recognizing stop codons directly 2. eRF3, is a GTP-binding protein. The eRF3·GTP acts in concert with eRF1 to promote cleavage of the peptidyl-tRNA, thus releasing the completed protein chain

What are the steps in the Secretory Pathway?(8) Co-translational or posttranslational?

1. free cytoplasmic ribosomes begin translation of mRNA to protein 2. When the ER signal sequence is made the Signal Recognition Particle(SRP) binds to signal sequence of the nascent protein and the large ribosomal subunit, halting translation 3. The SRP-signal sequence-ribosome complex goes to the Rough ER and binds to a SRP Receptor 4.The SRP receptor orients and brings the large ribosomal subunit in contact with the translocon(a pore in the translocator) -Hydrolysis of 2 molecules of GTP(releases 2 GDP+2Pi) by the SRP and its receptor drive this docking process and cause the dissociation of SRP 5. TRANSLATION RESUMES until Stop sequence is read(go to translation termination steps) 6. signal sequence is no longer needed and is cleaved off by a signal peptidase 7. Soluble secreted proteins are carried from the ER to the Golgi by Transfer Vesicles -dump secretory proteins into Golgi via exocytosis 8. Golgi sorts and packages secretory proteins into Secretory vesicles that carry protein to final location -protein is dumped at it's final location by exocytosis *cotranslational

What are siRNAs important for?(2) What do siRNAs cause?

1. important cellular defense against viral infection 2. excessive transposition by transposons siRNAs causes degradation of mRNA and thus inhibits translation of mRNAs

What are 3 ways that tumors are produced?

1. increased cell division, normal apoptosis 2. normal cell division, decreases apoptosis 3. increased cell division, decreased apoptosis

Why doesn't streptomycin affect humans?(2)

1. it is selective for formyl Methionine 2. humans don't have the small(30S) ribosomal subunit *it inhibits the binding of formyl-Met to 30S subunit

What are the steps in the Extrinsic(receptor-initiated) apoptosis?

1. killer lymphocyte and death ligand(Fas ligand) bind to target cell's death receptor(Fas death receptor) triggering receptor oligomerization 2. Death domain (DD) of the receptors recruits other DD-containing adaptors (e.g., FADD, TRADD) -adaptors contain both DD and death effector domain (DED) 3. The adaptors bind with pro-caspase-8 via DED forming DISC (death-inducing signaling complex) 4. DISC (death-inducing signaling complex) causes autoproteolytic activation of initiator caspase-8 5. Active Caspase-8 now cleaves and activates activates effector(executioner) pro-caspases: 3, 6, 7(now called caspase3,6,7) 6. activative effector(executioner) caspases: 3, 6, 7 then cause the cleavage of multiple substrates leading to apoptosis

What is the process of Receptor-Mediated Endocytosis?(7)

1. ligand binds to receptor 2. patching: formation of a coated pit 3. internalization 4. formation of an acidified endosome -receptor dissociates from ligand 5. receptors and ligands are split into separate vesicles 6. receptor returns to the cell surface, endosome fuses with lysosome 7. ligands are degraded by lysosomal enzymes

What the the three RNAs involved in protein synthesis? What are their roles?

1. mRNA carries information 2. tRNA carries amino acids to the ribosome 3.rRNA forms the peptide bond between the amino-group N on the incoming aa-tRNA and the carboxy-terminal C on the growing protein chain

What is the Mechanism by which miRNA is produced and blocks translation of mRNA Where does miRNA processing occur?

1. miRNA gene is transcribed in the nucleus by RNA pol II into pri-miRNA 2. Drosha processes pri-miRNA into pre-miRNA in the nucleus 3. pre-miRNA exits the nucleus via a Nuclear Pore Complex 4. Dicer processes pre-miRNA in the cytoplasm to produce dsmiRNA 5. dsmiRNA (short interfering RNA) are recognized and bound by miRISC 6. The RISC complex then separates the two strands of the dsmiRNA and scours the cytoplasm for complementary RNA sequences(target) and binds to the mRNA- inhibiting translation processing occurs in the nucleus and cytoplasm

What are the 2 ways of Degradation of mRNA by ribonucleases that inhibit protein translation?

1. poly(A) tails are shortened by deadenylase until it reaches a length of <20 -at this point the interaction with PAB1 is destabilized, leading to weakened interactions between the 5' cap and translation-initiation factors -the deadenylated mRNA can either be decapped and degraded by a 5'-3' ribonuclease or keep the cap and be degraded by a 3'-5' exosome 2. endonuclease cleaves off the poly(A) tail and the mRNA is degraded by a 3'-5' exosome

How does frame-shifting create alternate reading frames?(2) What mutation is observed? is this rare?

1. protein-synthesizing machinery may read four nucleotides as one amino acid and then continue reading triplets 2. protein-synthesizing machinery may back up one base and read all succeeding triplets in the new frame until termination of the chain occurs a frame-shift mutation it is rare

Eukaryotic Transcription RNA Pol II What do cis-acting elements consist of?(2)

1. proximal promoter 2. enhancers

What are the Mechanisms of tumor suppression done by p53?(3)

1. quiescence: Activation of temporary cell cycle arrest 2. senescence: Activation of permanent cell cycle arrest 3. Induction of apoptosis

Tumor Suppressor Genes encode proteins that ...(3) Mutations in Tumor Suppressor Genes → ___ → cellular transformation mutations in Tumor Suppressor Genes are usually dominant or recessive?

1. regulate cell proliferation 2. stimulate cell death 3. trigger cell cycle arrest (p53, pRB); 'Gatekeeper' genes Mutations → complete or partial loss of function → cellular transformation recessive

What are the 2 phenomena significantly increase the overall rate(efficiency) of translation in Eukaryotes?

1. simultaneous translation of a single mRNA molecule by multiple ribosomes 2. rapid recycling of ribosomal subunits after they disengage from the 3′ end of an mRNA

What is makes up the signal-recognition particle (SRP)?(2) what is it's function?

1. small RNA molecule (7SL RNA) 2. 6 protein subunits transiently binds to the ER signal sequence in the nascent protein and the large ribosomal subunit -Binding to the SRP halts translation

How does replication occur in retroviruses?

1. ssRNA is converted to dsDNA -reverse transcriptase uses ssRNA as a template to make a ssDNA -original ssRNA is degraded -ssDNA is used as template to make the second ssDNA resulting in a dsDNA strand 2. dsDNA is permanently inserted into the host genome -Long terminal repeats (LTRs) at the end of the dsDNA participate in integration -integration is random 3. Integrated DNA is transcribed to mRNA using host RNA polymerase 4. Retroviral RNA exits the nucleus and is translated into proteins 5. viral proteins are packaged along with a reverse transcriptase into virus particles 6. Virus particles leave and infect other cells

NF1 gene Neurofibromatosis is associated with ...(3) Loss of Heterozygosity in ___ Recruitment of ___

1. subcutaneous nodules (neurofibromas) 2. light brown spots 3. lisch nodules in the retina Loss of Heterozygosity in Schwann cells Recruitment of mast cells

What are the 2 tRNAmet? Both contain Met, but which one is recognized as the one containing the starting Met?

1. tRNAeMet: e is elongation 2. tRNAiMet: i is initiator -contains the starting Met

Prokaryotic Transcription How does termination occur?(2)

1. ρ-independent(inverted repeats) 2. ρ-dependent(Rho protein)

Eukaryotic Transcription What are the general properties of specific transcription factors?(4)

1.They respond to a stimulus which signals that one or more genes should be turned on 2.Unlike most proteins, transcription factors are capable of entering the nucleus where the genes reside 3.They recognize and bind to a specific sequence on the DNA 4.They also make contact with the transcription apparatus, either directly or indirectly

The ribosome directs elongation of a polypeptide at a rate of ___

3-5 amino acids per second

What must happen to the miss-folded protein before it can be eligible for degradation? degradation is done by the ___

4 of more ubiquitins are attached to the target/miss-folded protein before it can be eligible for degradation degradation is done by the proteasome

What end of the mRNA goes through the Nuclear Pore Complex first?

5'

What is the transcribed RNA structure?

5' UTR-start protein coding sequence-protein coding sequence- end protein coding sequence-3' UTR

A critical aspect of translation initiation is to begin protein synthesis at the start codon, thereby establishing the ___ ___ ___ for the entire mRNA

A critical aspect of translation initiation is to begin protein synthesis at the start codon, thereby establishing the correct reading frame for the entire mRNA

Eukaryotic Transcription RNA Pol II A eukaryotic gene control region consists of a _____ plus _____ T/F-Eukaryotic gene regulatory proteins can control transcription (turn on and off transcription) when bound to DNA far away from the promote The promoter proximal elements occurs within _____BPs (upstream or downstream?)encompassing the____box at ___. ____ box assembles RNA polymerase II and general transcription factors to form pre-initiation complex

A eukaryotic gene control region consists of a promoter(Bipartite) plus regulatory DNA sequences True, this is not true for prokaryotes The promoter proximal elements occurs within ~200bp upstream of +1 site encompassing the TATA box at -30. TATA box assembles RNA polymerase II and general transcription factors to form pre-initiation complex

What are caspases? They are synthesized as ____ that contain 3 domains: 1? 2? 3? What are the members initiator caspases?(3) What are the members effector caspases?(3) What is the difference between initiator caspases and effector caspases?

A family of cysteine proteases that cleave after Aspartate(aspartic acid/ASP/D) residues They are synthesized as inactive proenzymes that contain 3 domains: 1.NH2 terminal proline domain 2. large subunit 3. small subunit initiator caspases: 8, 9, 10 -contain a long pro-domain at the N-terminus effector(executioner) caspases: 3, 6, 7 -contain a short pro-domain at the N-Terminus

A mutation in ___ is the most common in human cancers(more than ___%) What is Li-Fraumeni syndrome? Is it dominantly or recessively inherited?

A mutation in p53 is the most common in human cancers(more than 50%) Li-Fraumeni syndrome is a rare inherited cancer syndome where p53(tumor suppressor) gene is mutated/inactivated Dominantly inherited

A peptide bond forms between the ____-group on the incoming ____and the ____ on the ____. This process is catalyzed by one of the ____

A peptide bond forms between the amino-group on the incoming aa-tRNA and the carboxy-terminal Carbon on the growing protein chain This process is catalyzed by one of the rRNAs

What is the function of APC gene?

APC functions to cause degradation of β-catenin

ATR is for what type of DNA problem?(2) ATM is for what type of DNA damage?(1)

ATR: 1. single stranded DNA(DNA is unreplicated) 2. DNA replication is not complete ATM: 1. double stranded break

What is the sequence of the start codon? This codon sets the ____ ____ of the protein What does it code for?

AUG This codon sets the "reading frame " of the protein Met

Activation of ___CDK(aka ___) is required for entry into mitosis It is regulated by ____ and ____ inhibited by(1)?what enzyme? activated by(2)?

Activation of M-CDK(aka CDK1) is required for entry into mitosis M-CDK(aka CDK1) is regulated by phosphorylation and dephosphorylation inhib: 1. phosphorylation of Threonine-14 and Tyrosine-15 -enzyme: Wee1 kinase activ: 1. phosphorylation of Threonine-160 -enzyme: CAK(CDK-activating kinase) 2. dephosphorylation of Threonine-14 and Tyrosine-15 -enzyme: Cdc25 phosphatase

Secretory Pathway After synthesis of the protein begins on ___ ribosomes in the ___, a ____ residue ER signal sequence is synthesized What is the general structure of an ER signal sequence?

After synthesis of the protein begins on free ribosomes in the cytosol, a 16-30 residue ER signal sequence is synthesized. N terminus(1 or more (+) charged amino acid) & h core(6-12 hydrophobic residues)) - C Terminus - cargo

Sometimes there can be more than one potential protein start site. this is called ___ ___ ___ This can occur in ___, ___, and ___

Alternative start sites Can Occur in: 1. Eukaryotes 2. Prokaryotes 3. Viral Transcripts

Separation of sister chromatids occur in what phase of the cell cycle? Sister chromatids are held together by ___, a multi-protein complex what enzyme degrades the multi-protein complex and allows the sister chromatids to move to opposite spindle poles? -it is inactive when bound to ___ What are the steps that occur in the Separation of sister chromatids?

Anaphase cohesin Separase -inactive when bound to Securin 1. When Cyclin B-CDK1(M-CDK) becomes activated, it phosphorylates APC(anaphase promoting complex) 2. Phosphorylated APC(anaphase promoting complex) binds to Cdc20 -this activates the proteasomal activity of APC 3. Active APC-Cdc20 complex degrades securin -therefore activating Separase 4. Separase degrades Cohesin allowing sister chromatids to separate and move towards the spindle poles

What are the Anti-apoptotic Bcl-2 family proteins?(4) What are the Pro-apoptotic Bcl-2 family proteins?(4)

Anti-apoptotic Bcl-2 family proteins(pro survival): Bcl-2, Bcl-xl, Bcl-w, Mcl-1 Pro-apoptotic Bcl-2 family proteins: Bax, Bak, Bid, Bok, Bim, Bik, Bmf, Hrk, Puma, Noxa

What are these? 1. Streptomycin 2. Tetracycline 3. Chloramphenicol 4. Cycloheximide 5. Erythromycin 6. Puromysin Answer the following Questions for each of the things above: targets prokaryotes, eukaryotes, or both? binds to small or large subunit? Effects on Protein Synthesis?

Antibiotic Inhibitors of Ribosomal Protein Synthesis *1. Streptomycin -pro -small -inhibits initiation by preventing the binding of formyl-methionine tRNA , causes misreading of mRNA *2. Tetracycline -both but more effective in prok -small -inhibits aminoacyl-tRNA binding by reversibly binding to the A site of the small subunit *3. Chloramphenicol -mainly pro, but can target euk mitochondrial ribosomes -large -inhibits peptidyl transferase 4. Cycloheximide -euk -large -inhibits peptidyl transferase 5. Erythromycin -pro -large -inhibits translocation 6. Puromysin -both -large -terminates elongation

Prokaryotic Transcription What is Rifamycin or Rifampin? What disease are they used to treat? Mutation in RNA polymerase gene causes resistance to Rifamycin therapy in bacteria or mycobacterium that causes __

Antibiotic Rifamycin or Rifampin is an inhibitor of bacterial RNA polymerase but not mammalian RNA polymerases. Therefore, it specifically inhibits bacterial RNA synthesis and thus inhibits bacterial growth Rifampin is used to treat tuberculosis Mutation in RNA polymerase gene causes resistance to Rifamycin therapy in bacteria or mycobacterium that causes Tuberculosis (TB)

What is apoptosis? What does it provide in adults? It plays a critical role in ___

Apoptosis: he removal of unwanted cells during development Provides a defense mechanism in the adult -Eliminates redundant, damaged and infected cells Plays a critical role in tissue homeostasis

The universal rule is used as a strong argument for what? However exceptions to the universal rule argue what?

Argument that life on earth evolved only once Exceptions to the universal code probably were later evolutionary developments; that is, at no single time was the code immutably fixed, although massive changes were not tolerated once a general code began to function early in evolution

What is Autophagy? What is Macroautophagy? -what is the resulting structure? -what is the function of the resulting structure?

Autophagy is the process by which lysosomes digest not only materials from outside the cell but also dispose of worn-out cellular proteins and defective organelles Macroautophagy is the formation of a double membrane that encloses/traps an organelle or a patch of the cytosol The resulting structure is an autophagosome It recycles peroxisomes and parts of the ER but is especially important for the removal of mitochondria

Autophagy recycles what things?(2) Macroautophagy recyckes what things?(3)

Autophagy: 1. Cellular Proteins 2. Organelles Macroautophagy: 1. Organelles 2. Bacteria 3. Viruses

In a normal cell which Pro-apoptotic Bcl-2 protein is inactive? how are the others inactivated? What causes them to be activated in relation to the intrinsic(mitochodrial) pathway?

BH3 only proteins(Bid) the other Pro-apoptotic Bcl-2 proteins are inactivated by interaction with anti-apopototic Bcl-2 proteins(Bcl-2, Bcl-xl, Bcl-w, Mcl-1) an apoptotic signal causes BH3 only proteins(Bid) to inactivate anti-apoptotic Bcl-2 family proteins which activates the other Pro-apoptotic Bcl-2 proteins which aggregate allowing the release of cytochrome C

What represent the first mammalian regulatory protein that inhibits apoptosis?

Bcl-2

NF1 gene What does Neurofibromatosis cause? it progresses to a malignant form called ___

Benign tumors of cell sheaths around nerves in the peripheral nervous system it progresses to a malignant form called neurofibrosarcoma

What is special about branch point A?

Branch point A has only free 2' OH for transesterification reaction

Repetition of the elongation cycle adds amino acids one at a time to the __-terminus of the growing polypeptide until a stop codon is encountered As the nascent polypeptide chain becomes longer, it ____ through a ___ in the ___ ribosomal subunit, exiting at a position opposite of the small subunit

C-terminus As the nascent polypeptide chain becomes longer, it threads through a channel in the large ribosomal subunit, exiting at a position opposite of the small subunit

___ is similar to CDK1

CDC2

What is the most common type of Congenital disorders of glycosylation(CDG)? results in?(8)

CDG-Ia is the most common type of CDG results in: 1. severe psycomotor redtardation 2. hypotonia 3. dysmorphic features 4. failure to thrive 5. liver dysfunction 6. coagulopathy 7. abnormal endocrine functions 8. susceptibility to infection

What are cyclin-dependent protein kinases (CDKs)? What do they require? T/F The cyclic assembly, activation and disassembly of cyclin-CDK complexes are the pivotal events during the cell cycle

CDKs are serine/threonine kinases require Cyclin True

In addition to AUG, what is another initiator codon for methionine in eukaryotes?

CUG

Cell cycle progression requires cyclical activation of ____ T/F The activity of these kinases rises and falls as cells progress through the cell cycle

Cell cycle progression requires cyclical activation of cyclin-dependent protein kinases (CDKs) True

Chromosomal translocation can cause _____of a protein by placing them under the regulatory element of ____ gene. ____ encodes a transcription factor normally induced in response to growth factors In Burkitt's lymphoma, translocation of___ from chromosome ___ to ___ places it close to ___ locus causing unregulated expression of ___ sufficient to drive cell proliferation

Chromosomal translocation can cause overproduction of a protein by placing them under the regulatory element of immunoglobulin gene. c-Myc encodes a transcription factor normally induced in response to growth factors In Burkitt's lymphoma, translocation of c-Myc from chromosome 8 to 14 places it close to immuntoglobin gene(Ig) locus causing unregulated expression of c-Myc sufficient to drive cell proliferation

What are polyribosomes(polysomes)? What is the shape of these?what does this suggest?

Circular structures with mRNA attached to multiple ribosomes bearing nascent growing polypeptide chains Circular shape of polyribosomes suggested the mechanism by which ribosomes recycle efficiently

Prokaryotic Transcription What is a Cistron? What is the ORF? What is the Promoter?

Cistron: structural gene ORF: open reading frame Any sequence of DNA or RNA that could, in theory, encode a protein without interrupted by stop codon prematurely(begins with a start codon and ends with a stop codon) Promoter: RNA polymerase binds to promoter(DNA) and catalyzes RNA synthesis (transcription), they control gene transcription(or expression)

Eukaryotic Transcription of rRNA by RNA polymerase I Clusters of rRNA Genes are located at multiple sites along the DNA. A single transcribed unit of DNA yields an_____ in the ____, a special zone of the nucleus. The ______ is then processed to yield the final ___ and ___ subunits of rRNA.

Clusters of rRNA Genes are located at multiple sites along the DNA. A single transcribed unit of DNA yields an initial 45S RNA molecule in the nucleolus, a special zone of the nucleus. The 45S RNA molecule is then processed to yield the final 18S and 28S subunits of rRNA.

____ bind to DNA in S phase and maintain the linkage between sister chromatids Between G2 and Prophase ___ phosphorylates and activates ___ During Prophase ___ are replaced by ___ except where sister chromatids are held together at the ___ this process is called ___ and occurs in which part of the cell cycle?

Cohesins Between G2 and Prophase Cyclin B-CDK1(M-CDK) phosphorylates and activates condensins During Prophase Cohesins are replaced by Condensins except where sister chromatids are held together at the Centromere called chromosome condensation and it occurs at Prophase

What is Crohn's disease? Ordinarily, intestinal bacteria that have entered the cytoplasm of an intestinal mucosal cell are cleared by a process called ____ via a structure called an ___ But those with the disease have a ___ mutation( __ is replaced by __) in the ____ gene The mutation replaces the amino acid ___ with___ What is the result?

Crohn's disease is an inflammatory bowel disease Ordinarily, intestinal bacteria that have entered the cytoplasm of an intestinal mucosal cell are cleared by a process called macroautophagy via a structure called an autophagosome But those with the disease have a missence mutation(A is replaced by G) in the ATG16L1 gene The mutation replaces Threonine with Alanine impaired sequestration(trapping) of at least some kinds of bacteria in autophagosomes which gives bacteria enough time to trigger an inflammatory response READ OVER THIS IN LECTURE 32 SLIDE

Prokaryotic Transcription What allosteric proteins are required for switching on genes that lactose when lactose is present and glucose is not?(2) How do they work? How do they relate to glucose?

Crp and CAP In order for Crp or CAP to bind to DNA on the Crp or CAP binding site of the regulatory region of the lac operon, Crp or CAP must first binds cAMP. When Crp or CAP binds to cAMP, it forms dimers and the dimers can bind to Crp site of the DNA upstream of the promoter The presence of Crp-cAMP (or CAP-cAMP) helps RNA polymerase bind to the promoter When glucose is present Crp is does not bind to Crp site When glucose is absent Crp binds to Crp site

Curved mRNPs appear to ____ as they pass through nuclear pores. As the mRNA enters the cytoplasm, it rapidly associates with _____, indicating that the _____ mRNA+protein complex(TAP/NXF1 &Nxt1)= ?

Curved mRNPs appear to UNCOIL as they pass through nuclear pores. As the mRNA enters the cytoplasm, it rapidly associates with RIBOSOMES, indicating that the 5' END PASSES THROUGH THE NPC FIRST mRNA+protein complex= mRNPs

Promoter methylation inactivates TSGs DNA can be methylated at ___ base; when its adjacent to ___ Promoter methylation occurs at genomic regions called ___ ___ methylation in gene promoter results in ___ ___

DNA can be methylated at cytosine base; when its adjacent to guanosine [CG] 'CpG island': genomic regions with high density of CG -Present in about 70% of all gene promoters CG methylation in gene promoter results in repressed transcription

The process of transcription is the conversion of ___ to ___

DNA to RNA

What plays an important role in DNA Damage checkpoints?(2) -where is this check point? What plays an important role in DNA Replication checkpoints?(1)

Damage: located between G1 and S 1. ATM (ataxia telangiectasia mutated) 2. p53 Replication: located between G2 and M 1. ATR (AT- and Rad3-related)

Death effector domain (DED) relates to which caspase? Caspase recruitment domain (CARD) relates to which caspase?

Death effector domain (DED): Caspase-8 Caspase recruitment domain (CARD): Caspase-9

Hepatitis B, and C (HBV, HCV) direct mechanism of infection: indirect mechanism of infection:

Direct: Chronic infection Indirect: Viral proteins bind p53 -viral protein of HBV: HBx -=viral protein of HCV: NS5A and NS3

What are Dominant mutations? What are Recessive mutations?

Dominant mutations - Mutation in single allele causes cellular transformation Recessive mutation - mutations in both alleles needed for transformation

What protein Transcribes the genes(cyclin E and cyclin A) needed for S phase transition? What is it inhibited by? What are the steps required to uninhibit?(1-3) what steps follow to allow passage through the Restriction point?(4-5) T/F Cyclin E-Cdk2 and Cyclin A-Cdk2 can further phosphorylate Rb even when growth factors are removed and D-type cyclin levels fall

E2F inhibited by Rb 1. Growth factors use Ras/Raf/MEK/ERK pathway for the synthesis of cyclin D 2. cyclin D activaties G1 CDK which phosphorylates Rb 3. Rb dissociates from E2F 4. E2F transcribes cyclin E and cyclin A 5. cyclin E binds with G1/S CDK for the passage through the restriction point -cyclin A binds with S CDK for initiation of DNA replication True

Epstein Barr Virus (EBV) is an ___ ___ virus Implicated in several malignancies including ...(4) is infection lytic or latent(lysogenic)? Viral proteins ___ and ___ are involved in transformation

EBV is an oncogenic herpes virus Implicated in ... 1. Burkitt lymphoma 2. B-cell lymphomas (in immunocompromised individuals) 3. Nasopharyngeal carcinomas 4. Hodgkin lymphoma infection is latent Viral proteins LMP-1 and EBNA-2 are involved in transformation

Improperly folded proteins that remain in the ER are seen bound to the ____ which assist in proper folding

ER chaperones

Eukaryotic Transcription What do enhancers do? T/F-enhancer must make contact with the transcription apparatus T/F- enhancers and repressors are often found close to the promoter When an enhancer switches a gene on, the DNA between it and the promoter form a ___

Enhancers enhance the initiation of transcription as a result of binding specific transcription factors True, directly or indirectly false, they are found considerable distances away form a loop

Eukaryotes: Large Ribosomal Subunit __S Small Ribosomal Subunit __S Both __S Prokaryotes: Large Ribosomal Subunit __S Small Ribosomal Subunit __S Both __S

Eukaryotes: Large Ribosomal Subunit 60S Small Ribosomal Subunit 40S Both 80S Prokaryotes: Large Ribosomal Subunit 50S Small Ribosomal Subunit 30S Both: 70S

Where is mRNA translated in Eukaryotes? in prokaryotes?

Eukaryotes: cytoplasm Prokaryotes: cytoplasm

The amplification of DNA sequences of a proto-oncogene can cause overproduction of the protein Ex. of gene amplification: (4) What is amplified in neuroblastoma? What is amplified in breast cancer?

Ex. of gene amplification: 1. Myc 2. ErbB2 3. Mdm2 4. Cyclin D N-Myc is amplified in neuroblastoma ErbB2 is amplified in breast cancer

T/F The ER contains proteasomes

False

T/F Most amino acids are encoded by one codon

False -most amino acids are encoded by multiple codons(degenerate)

Prokaryotic Transcription T/F- The first base of the mRNA for a protein-coding gene is A of the AUG codon

False, Between the first base of the mRNA and the first base of the protein coding sequence(A of AUG), there is a short stretch known as 5'-untraslated region (of mRNA) or 5'-UTR

T/F If you completely lack O-glycans(O-linked oligosaccharides) it is lethal

False, it is lethal to me missing N-glycans

T/F dsRNA Viruses are common How are they replicated? What is an example? -what does it look like? -what does it cause?

False, they are rare Replication: virus contains RNA-dependent RNA polymerase, (+) strand used both as a template for (-) strand and for translation (mRNA) ex. Reoviruses (rotavirus) -spherical -2 concentric protein shells -segmented dsRNA -causes infant diarrhea

APC(Adenomatous polyps coli) can result in what type of cancer? Germline mutations in APC associated with susceptibility to ___ T/F Germline mutations in APC are usually non-malignant, but risk of cancer increase significantly after the age 50

Familial Adenomatous polyps (FAP) - heritable colon cancer syndrome Germline mutations in APC associated with susceptibility to develop polyps in the colon True

Chromosomal translocation Formation of ____ genes by recombination of two unrelated chromosomes can activate growth-promoting gene products ___is a tyrosine kinase In ___, ___ gene translocated from chromosome __fuses with ___ gene at chromosome ___ to form ___ chromosome The ____ protein has _____ activity

Formation of hybrid genes by recombination of two unrelated chromosomes can activate growth-promoting gene products Abl is a tyrosine kinase In chronic myelogenous leukemia (CML), Abl gene translocated from chromosome 9 fuses with Bcr gene at chromosome 22 to form Philadelphia chromosome The chimeric protein has intrinsic tyrosine kinase activity

What are the phases of the cell cycle in order? What happens in each? How long does each stage take? Which is a part of interphase?

G1->S or G0->G2->M->back to G1 or G0 G0: Where terminally differentiated cells withdraw from the cell cycle G1: RNA and protein synthesis. - No DNA synthesis -has a Reentry point for cells returning from G0 -has a Restriction Point at the end: cells passing this point is committed to the S Phase -6-12 hrs S: DNA synthesis doubles the amount of DNA in the cell. -RNA and proteins are also synthesized -6-8 hrs G2: RNA and protein synthesis continue - No DNA synthesis -3-4 hrs M: Mitosis(nuclear division) and cytokinesis(cell division) yields 2 daughter cells -1 hr Interphase: G1, S, G2

What enzyme does a glycosylation rxn in galactose metabolism? If this enzyme is deficient what is the result?

GALT result: 1. failure to thrive 2. enlarged liver 3. jaundice 4. cataracts 5. build up of galactose from lactose becomes toxic 6. hypogalactosylation of proteins

Tumour suppressor genes responsible for familial cancer syndromes can be divided into two major categories, known as ____ and ____ What are they each responsible for?

Gatekeeper genes: control growth and division Caretaker genes: DNA repair

What is used as a treatment for non-small cell lung carcinoma?

Gefitinib (Iressa)

What is Glycosylation?

Glycosylation is the reaction in which a carbohydrate, i.e. a glycosyl donor, is attached to a hydroxyl or other functional group of another molecule (a glycosyl acceptor)

What is the process of autocrine growth stimulation? The deregulation of growth factor receptor(PDGF receptor) in proto-oncogenes creates a ____ receptor which keeps the intracellular protein-tyrosine kinase ____ ____

Growth Factors are released and bind to the receptors on the cell that released them causing even more growth factors to be released The deregulation of growth factor receptor(PDGF receptor) in proto-oncogenes creates a Tel/PDGF receptor which keeps the intracellular protein-tyrosine kinase constitutively activated

___ and ___ are over-expressed in people with breast cancer

HER2 and erbb2 are over-expressed in people with breast cancer

What is HIF1α function?(3) When is it activated? It enables the cell to survive under what conditions?

HIF1α - transcription factor - activates genes involved in 1. angiogenesis (new blood vessels) 2. glycolysis and glucose transport 3. erythropoiesis (formation of RBC) HIF1α activated in low oxygen conditions (hypoxia) Enable the cell to survive under hypoxic condition

Human Papilloma Virus (HPV) HPV16 and HPV18 infects cells of ___ ___ -viral genome can be detected in ___% of invasive squamous cell cervical carcinoma ___ and ___ have low malignant potential and causes ___ ___

HPV16 and HPV18 infects cells of squamous epithelia (skin, mucous membrane) -viral genome can be detected in 85% of invasive squamous cell cervical carcinoma HPV6 and HPV11 have low malignant potential and causes genital warts

Hepatitis B, and C Virus (HBV, HCV) are major etiological agents of ___ ___ in ___-related cancer, the viral DNA is integrated into the host cell genome

Hepatitis B, and C Virus (HBV, HCV) are major etiological agents of hepatocellular carcinoma in HBV-related cancer, the viral DNA is integrated into the host cell genome

What was the first targeted biologic therapy for people with breast cancer? What is it?

Herceptin(trastuzumab): a humanized monoclonal antibody against HER2

In the Study of Familial Cancer Cases on retinoblastoma explain... Hereditary retinoblastoma: Sporadic retinoblastoma:

Hereditary retinoblastoma - the 'first hit' or mutation already exist; germline mutation; increased probability of second 'hit'; explains early onset and multiple tumors in both eyes (bilateral) Sporadic retinoblastoma - 'two hits' have to take place in the same cells; somatic mutations; low probability event; explains single tumor in one eye

Human Papilloma Virus (HPV) contains small ___ ___-stranded DNA called ___ It needs ___ host cells Host cell growth maintained by viral protein E6 and E7 ___ binds to p53 - degradation by proteosome ___ binds to pRb - displacement of E2F transcription factor -inactivates ___ -activates ___ and ___ E6/E7 regulated by ___ Results in...(2)

Human Papilloma Virus (HPV) contains small circular single-stranded DNA called episomes It needs dividing host cells Host cell growth maintained by viral protein E6 and E7 E6 binds to p53 - degradation by proteosome E7 binds to pRb - displacement of E2F transcription factor -inactivates CDK inhibitor p21 -activates Cyclin E and A E6/E7 regulated by E2 Results: 1. uncontrolled cell growth 2. viral replication

What is the only human retrovirus implicated in pathogenesis of cancer? It's viral genome contains ___ gene that stimulates viral transcription -transcribes a ___ protein that ...(4)

Human T-Cell Leukemia Virus (HTLV1) It's viral genome contains Tax gene that stimulates viral transcription -transcribes a Tax protein that... *1. stimulates AKT signaling pathway 2. activates NF-κb and cyclin D2 3. inhibits expression of CDK inhibitors *4. inhibits DNA repair (↑genomic instability)

Hyperactive ___ ___ ___ is active in people with leukemia What inhibits it's activity?(2)

Hyperactive Bcr-Abl tyrosine kinase is active in people with leukemia 1. Imatinib mesylate inhibits Bcr-Abl tyrosine kinase activity 2. Gleevec inhibits Bcr-Abl tyrosine kinase activity

In a normal cell ___ is on the ___ leaflet of the plasma membrane But during apoptosis ___ is ___ to the ___ leaflet and binds with the receptor on the surface of a ___ cell

In a normal cell phosphatidylserine is on the inner leaflet of the plasma membrane But during apoptosis phosphatidylserine is translocated to the outer leaflet and binds with the receptor on the surface of a phagocytic cell

In post-translational translocation, a ____ secretory protein is targeted to the ER membrane by interaction of the signal sequence with the translocon. The polypeptide chain is then pulled into the ER by a ____ mechanism that requires ____ T/F In both co-translational and post-translational translocation, a signal peptidase in the ER membrane cleaves the ER signal sequence from a secretory protein soon after the N-terminus enters the lumen

In post-translational translocation, a completed secretory protein is targeted to the ER membrane by interaction of the signal sequence with the translocon. The polypeptide chain is then pulled into the ER by a ratcheting mechanism that requires ATP hydrolysis True

Infectious mononucleosis is caused by ___ it exhibit a ___ latent period; replicate as ___ ___ ___; activated by ___ of other factors

Infectious mononucleosis is caused by Herpesvirus it exhibit a long latent period; replicate as extra-chromosomal circular plasmids; activated by stress of other factors

Initiation of translation occurs when (tRNAeMet or tRNAiMet?) bind to __ site on the ___ ribosomal subunit The other tRNAMet can only bind to the __ site

Initiation of translation occurs when tRNAiMet bind to P site on the small ribosomal subunit The other tRNAMet can only bind to the A site

What is normally found at the wobble position of the anticodon instead of Adenine?

Inosine (a deaminated form of Adenine)

What tRNAs are heavily employed in translation of codons that specify a single amino acid?

Inosine tRNAs

Retroviruses that do not contain an oncogene still cause cancer via a process called ___ ___ -2 ways this can happen Is the Rate of transformation faster or slower when compared to retrovirus containing an oncogene?

Insertional mutagenesis: 1. Promoter insertion: Integrate in the promoter regions of proto-oncogenes 2. Enhancer insertion: Integrated away from the proto-oncogene, LTR's can stimulate expression (enhancer effect) slower

What do Disulfide bonds do? A disulfide bond is a ___ linkage of ___ groups (___), also known as ___ groups Disulfide bonds occur between what amino acids? In eukaryotes, disulfide bonds are only formed where? Disulfide bonds are only found in which proteins?(2)

Intramolecular(with itself) and intermolecular(with another) disulfide bonds help to stabilize the tertiary and quaternary structures of proteins A disulfide bond is a covalent linkage of sulfhydryl groups (-SH), also known as thiol groups occurs between 2 cysteines only formed in the lumen of the ER 1. secretory proteins 2. exoplasmic domains of membrane proteins

'Caretaker' Genes function? Mutations in these genes → inactivation → ____ → cellular transformation mutations in Caretaker' Genes are usually dominant or recessive? What is an example of a disease? -what is mutated?

Involved in maintaining genomic stability (e.g., DNA repair genes) Mutations in these genes → inactivation → increase in spontaneous mutations → cellular transformation recessive ex. Xeroderma Pigmentosum -mutation in nucleotide excision repair

Prokaryotic Transcription Is the Lac Operon inducible or repressible? What metabolites are involved? How do they work?

It is inducible, meaning it is usually turned off(lacI is bound normally bound to lacO), but in the presence of lactose or IPTG it is turned on -presence of inducer such as lactose (or IPTG): lactose binds to the constitutively synthesized repressor (LacI) which prevents its binding to the operator and prevents repression. Transcription of the lac operon starts. The operon is on -absence of inducer (such as lactose or IPTG): lac repressor (LacI protein) binds to the operator and blocks the movement of RNA polymerase at the promoter and there is no transcription (the operon is off). Lactose and IPTG are the inducers

What is the most important source of cholesterol in most cells? What process of endocytosis is used to get this source?

LDL Receptor Mediated Endocytosis

Epstein Barr Virus (EBV) What is the function of LMP-1? What is the function of EBNA-2? What is the function of vIL10?

LMP-1 - mimics activated CD40 receptor - leads to activation of NF-κB, JAK/STAT signaling pathways [proliferation]; activates BCL2 [inhibits apoptosis] EBNA-2 - Notch receptor activation - activates cyclin-D and Src family of protein (proliferation) vIL10 - viral cytokine, inhibits T-cell immune response

What is an example of Negative regulation of prokaryotic gene transcription? How does it work?

Lac Operon When no lactose is available, Lac repressor (LacI) binds to the operator sequence which overlaps the promoter region of this operon. Thus the operon is turned off When lactose (inducer) is present, it binds to lac repressor (LacI) and the repressor is removed from the operator site, and the operon is turned on to start transcriptionx

What is an example of a CDG Type II? leads to what? controlled with?

Leukocyte adhesion deficiency type II leads to frequent infections controlled with the addition of FUCOSE to diet

What are Lysosomes? Function?

Lysosomes(organelles of intracellular digestion) are bags that are filled with hydrolytic enzymes, including glycosidases, proteases, phosphatases, and sulfatases function: breakdown cellular macromolecules, especially macromolecules that are taken up into the cell by phagocytosis, pinocytosis, and receptor-mediated endocytosis

Which domains bind to the NPC? Which domains bind to the mRNA?

M domain and C domain bind to the FG repeats in NPC(technically nucleoporins) N domain binds to the mRNA

What is the most likely sequence of amino acids made from this mRNA sequence? CCCAUGCCCCCUCCA LOOK at Lecture 30 Slide 11 for chart 1. Can a codon code for more than one amino acid? 2. Can an amino acid have more than one codon?

MET-PRO-PRO-PRO -you have to find the start codon first 1. No, (unambiguous rule) 2. Yes, (degenerate rule)

Proteins without a targeting sequence are made by... what ribosome? where are they made? where are they release?

Made by free cytoplasmic ribosomes made in the cytoplasm released in the cytoplasm

Messenger RNA (mRNA) is translated into protein by the joint action of _____ and the ____ What bond is formed between Amino Acids?

Messenger RNA (mRNA) is translated into protein by the joint action of transfer RNA (tRNA) and the ribosome Peptide bond

The Nuclear Pore Complex (NPC) and Its position was determined by ______ of the Nuclear Envelope

Micro-Dissection

Mitochondrial proteins typically pass through the ____ and ____membranes of the ____ to enter the ____ Chloroplast proteins typically pass through the ____ and ___ membranes of the____ ____ to enter the ____ ____

Mitochondrial proteins typically pass through the outer and inner membranes of the mitochondria to enter the matrix Chloroplast proteins typically pass through the outer and inner membranes of the chloroplast envelop to enter the stromal space

Most human cancer viruses are ___viruses What are the differences between these viruses and retroviruses?(2) how do they cause cancer?

Most human cancer viruses are DNA viruses Unlike retroviruses they ... 1. usually do not fully integrate into the host genome 2. no oncogene activation Can cause cancer by *chronic infections(tissue damage and/or stimulating cell division)

Most proteins that are processed through the secretory pathway are ____ What enzyme makes them? via what rxn? what are the precursors for these reactions?

Most proteins that are processed through the secretory pathway are glycoproteins Glycosyl transferases build oligosaccharides on the side chains of serine, threonine, and asparagine in the protein via Glycosylation rxn The precursors for these reactions are nucleotide-activated monosaccharides

What is the difference in the Mutagenic activation of oncogenes and Mutagenic inactivation of tumor suppressor genes?

Mutagenic activation of oncogenes: -gain of function -Mutation of single allele is sufficient to create oncogene Mutagenic inactivation of tumor suppressor genes: -loss of function -need mutation in both alleles to inactivate tumor suppressor genes

Mutations is Proto-oncogenes result in ____ ____ mutations in Proto-oncogenes are usually dominant or recessive?

Mutations → constitutive activation or overexpression (oncogene) → cellular transformation dominant

What is an example of a disease involving defects in mRNA transport? It is an ____ _____ disease caused by an abnormal ___ expansion in the ____ of _____

Myotonic dystrophy type I: toxic RNA causes nuclear retention and disease It is an autosomal dominant disease caused by an abnormal CUG expansion in the 3′ UTR of DMPKCUG+(a DM protein kinase mRNA)

The first Amino Acid is translated at the N terminus or C terminus?

N-Terminus

What are N-linked oligosaccharides bound to? They are synthesized via what rxn? What is the process?(3)

N-linked oligosaccharides are bound to the nitrogen in the side chain of asparagine They are made via N-linked glycosylation process: 1. construction of a mannose-rich oligosaccharide on dolichol phosphate 2. exoglycosidases trims the glucose residues and one or more of the mannose residues from the dolichol phosphate(from the side not bound to the dolichol phosphate) 3. glycosyl transferases then transfer the remaining oligosaccharide from the dolichol phosphate to the side chain of asparagine

What is the function of NF1 gene? Growth factor activation does what to NF1? Mutant NF1 gens is transmitted through germ line in a dominant fashion or recessive fashion? Loss of NF1 results in ____

NF1 functions as a GTPase- activating protein (GAP) -activates the GTPase activity of Ras protein (Ras-GAP) -Inhibits Ras signaling Growth factor activation degrades NF1 which enables Ras signaling dominant fashion Loss of NF1 results in activation of Ras

The M and C domains of the mRNA Exporter contain structural and sequence homologies similar to ____ protein which also interacts with the FG repeats of the nucleoporins. This implies that these domains move the cargo in this case the RNA in a RNP complex through the NPC.

NTF2 protein

What is the Molecular definition of cancer?

Neoplasia is a process(es) by which the normal controlling mechanisms that regulate cell proliferation, differentiation, cell death and senescence are impaired, resulting in progressive growth

Normal warts (benign) -viral DNA exists as episome In transformed cells (cancer) -partial genome integrated into host including ___and ___ genes but not ___

Normal warts (benign) - viral DNA exists as episome In transformed cells (cancer) - partial genome integrated into host including E6 and E7 genes but not E2

Transport of molecules into and out of the cell occurs via ____

Nuclear Pore Complexes (NPC)

Nuclear proteins enter and exit through the ___

Nuclear Protein Complex (NPC)

What are the 6 stages where Eukaryotic gene expression can be controlled? JUST READ

Nucleus: DNA->RNA transcript 1. transcriptional control RNA transcript->mRNA 2. RNA processing control mRNA from nucleus to Cytosol 3. mRNA transport and localization control mRNA->inactive mRNA 4. mRNA degradation control or mRNA->protein 5. translational control protein->inactive protein 6. protein activity control

Nuclear Pore Complex Numerous pore perforate the ____ _____  Each pore is formed from an elaborate structure called _____.  T/F:NPC is one of the largest protein assemblages(60-80 million Da) in the cell Multiple copies of 30 different proteins called _____ are involved in the formation of NPC

Numerous pores perforate the nuclear envelop Each pore is formed from an elaborate structure called Nuclear Pore Complex True Multiple copies of 30 different proteins called NUCLEOPORINS are involved in the formation of NPC

What are O-linked oligosaccharides bound to? where are they synthesized? via what rxn?

O-linked oligosaccharides are bound to the oxygen in the side chains of serine and threonine They are synthesized in the Golgi apparatus via stepwise addition of monosaccharides(type of glycosylation)

Once post transcriptional processing is complete, (ie. Capping, Polyadenylation, Exon splicing, intron removal and methylation), the mRNA message remains associated with ______proteins forming a ___

Once post transcriptional processing is complete, (ie. Capping, Polyadenylation, Exon splicing, intron removal and methylation), the mRNA message remains associated with hnRNP proteins in a messenger ribonuclear protein complex (mRNP)

Once the small ribosomal subunit with its bound Met-tRNAiMet is correctly positioned at the start codon and the ___ bound by eIF2 is hydrolyzed to ___ ___, ___, ___, and ___ then dissociate the small subunit unites with the large (60S) ribosomal subunit in a process catalyzed by ___ and ___ completing formation of an 80S ribosome

Once the small ribosomal subunit with its bound Met-tRNAiMet is correctly positioned at the start codon and the GTP bound by eIF2 is hydrolyzed to GDP eIF1, eIF2, eIF3, and eIF4 then dissociate the small subunit unites with the large (60S) ribosomal subunit in a process catalyzed by eIF5 and eIF6, completing formation of an 80S ribosome

What are Oncogenes? -what do they do? What are proto-oncogenes? First identified through their presence in RNA virus or retrovirus. Hence designated by the prefix "___"(ex___-Src) Cellular counterparts or proto-oncogenes are designated by the prefix "___"(ex___-Src)

Oncogenes: Cancer causing genes -Promote cell growth in the absence of growth-promoting signals Proto-oncogenes: Mutated form of normal cellular genes First identified through their presence in RNA virus or retrovirus. Hence designated by the prefix "v"-v-Src Cellular counterparts or proto-oncogenes are designated by the prefix "c"- c-Src

p27 is for humans as __ is for budding yeast Restriction point is for humans as __ is for budding yeast

P27 = Sic1 Restriction point = START

Pinocytic and endocytic vesicles tend to fuse with each other and with intracellular vesicles to form larger structures called _____, which become ____ to a pH of ____

Pinocytic and endocytic vesicles tend to fuse with each other and with intracellular vesicles to form larger structures called endosomes, which become acidified to a pH of 5 to 6

Point mutation in ___ is the most common abnormality in proto-oncogenes in human. T/F- The frequency of mutation varies with tumor type. A single nucleotide change, which alters codon __ (___ to ____) which changes the amino acid from ___to ___ can contribute to its transforming activity(proto-oncogenes converted to oncogenes)

Point mutation in Ras is the most common abnormality in proto-oncogenes in human. True A single nucleotide change, which alters codon 12 (GGC to GTC) which changes the amino acid from Gly to Val can contribute to its transforming activity

Polymerization occurs through the polymerase by the _____ via ______ _____ on the_____ in the _______ position of the incoming ribonucleotide What bond is formed?

Polymerization occurs through the polymerase by the most recent 5' RNA base's 3' oxygen's via nucleophilic attack on the alpha phosphate in the 5' position of the incoming ribonucleotide A 3'-5' Phosphodiester bond is formed

What is the largest and most complex animal virus?

Poxviruses

Prokaryotic Transcription begins at the __ nucleotide and forms the first ___ bond

Prokaryotic Transcription begins at the +1 nucleotide and forms the first 3'-5' phosphodiester bond

What can inactivate Tumor Suppressor Genes?

Promoter methylation inactivates TSGs

What is the structure of a proteasome? Which part of the structure captures ubiquitinated proteins, denatures them with the help of ATP hydrolysis, and feeds them into the hollow cylinder for degradation? Where are proteasome abundant?(2)

Proteasome is a hollow cylinder whose inner surface is lined with proteases, covered with a large cap on both sides the cap abundant in: 1. cytoplasm 2. nucleus

What is the Viral Envelope? What is it derived from? Helical viruses be enveloped, non-enveloped(naked) or both? Icosahedral viruses can be enveloped, non-enveloped(naked) or both?

Protein-containing lipid membrane around the nucleocapsid Derived from host cell membrane Helical: enveloped Icosahedral: both

Proteins with an organelle-specific targeting sequence are released into the ____ and then ___ into specific locations

Proteins with an organelle-specific targeting sequence are released into the cytosol, and then imported into specific locations

Proto-oncogenes promote ____ Tumor suppressor genes inhibit ____

Proto-oncogenes promote growth Tumor suppressor genes inhibit growth

What can be used to visualize introns?

R-Loop analysis experiment number of R-loops(n)= number of introns n+1= number of exons READ Lecture 28 slide 22-23

What is the final product of gene expression?

RNA

What enzyme copies RNA from DNA?

RNA Polymerase

RNA Viruses are usually ___-stranded and ___ They have ___ genomes dues to ___ ___ ___ how do they avoid host defense?

RNA Viruses are usually single-stranded and enveloped They have small genomes dues to high mutation rates Mutations result in rapid evolution of virus proteins (avoid host defense)

RNA is copied from the DNA ___ strand therefore it has the same sequence as the DNA ___ strand

RNA is copied from the template strand(non-coding/antisense) therefore it has the same sequence as the coding strand(non-template/sense)

What direction is RNA synthesized? RNA Pol reads the template stand in what direction?

RNA is synthesized in 5'-3' direction RNA pol reads the template strand in the 3' to 5' direction

RNA viruses of bacteria are usually (___) ___-stranded RNA

RNA viruses of bacteria are usually (+) ssRNA

Most of the mRNAs are exported from the nucleus to cytoplasm by _______ transport mechanism

Ran-independent transport mechanism

How does loss of RB1 lead to tumor formation?

Rb protein: role in regulating cell cycle -binds and inactivates E2F transcription factor -E2F required for G1 → S transition *Loss of Rb → E2F activation → uncontrolled proliferation

What is the function of ... RB? TP53? NF1? APC? VHL1?

Rb: Retinoblastoma gene -transcriptional repression; control of E2F; G1-checkpoint TP53: p53 transcription factor -regulates cell cycle, apoptosis senescence NF1: neurofibromatosis 1 -Regulates Ras signaling APC: adenomatous polyps coli -Regulates levels of β-catenin VHL1: Von Hippel-Lindau -Ubiquitination of HIFα

What is the difference between pinocytosis and Receptor-mediated endocytosis?

Receptor-mediated endocytosis requires a cell surface receptor to which the endocytosed product binds

What is an example of the involvement of miRNA in the pathogenesis of diseases?

Reduced levels of miRNAs (miR-29a, miR-29b, miR-9) are detected in Alzheimer's disease (AD) These three miRNAs also target mRNA for beta-secretase and prevents its translation Increased beta-secretase activity increases the cleavage of APP to produce amyloid plaques in the brain Therefore, reduced levels of these miRNAs may be responsible for increased beta-secretase activity and the formation of amyloid plaques in AD brain

What is the Restriction point? Where is it located? What happens when cells progress through the Restriction point?(2)

Restriction point is the point where decision to divide takes place it is located at the end of G1 Once cells progress through the restriction point: 1. Cells are committed to proceed through S phase 2.Cells lose their dependency on extracellular factors

What was the first tumor suppressor gene isolated? mutations in these genes can result in...(3)

Retinoblastoma gene (Rb) result in... 1. retinoblastoma 2. osteosarcoma 3. soft-tissue sarcoma

Oncogenic RNA Viruses Retroviruses know to transform cell ___ ___ ___ was the first retrovirus identified to cause cancer in ___ ___ ___ ___contains additional ___(viral sarcoma) gene responsible for abnormal proliferation of infected cells -it is related to a normal cellular gene (___; non-receptor tyrosine protein kinase) Cellular gene is called a ___ when it has the capacity to transform cells

Retroviruses - know to transform cell Rous sarcoma virus (RSV) was the first retrovirus identified to cause cancer in chickens RSV contains additional v-src (viral sarcoma) gene responsible for abnormal proliferation of infected cells -it is related to a normal cellular gene (c-Src; non-receptor tyrosine protein kinase) Cellular gene is called a proto-oncogene when it has the capacity to transform cells

Prokaryotic Transcription: Explain: ρ-dependent termination

Rho accompanies the RNA polymerase as it synthesizes the growing mRNA. Once the RNA polymerase has made the Rho recognition site, Rho binds to this and causes a change in conformation of the RNA polymerase, which then pauses at the termination site. Rho then untwists the newly-formed mRNA strand from the DNA. Subsequently, the mRNA and RNA polymerase fall off the DNA and Rho detaches from the mRNA.

Does the rough or smooth ER receive proteins entering the secretory pathway?

Rough

Selection of the initiating AUG is facilitated by specific surrounding nucleotides called the ___ sequence What is the sequence? What are the 2 most important nucleotides in this sequence that affect translation initiation efficiency?

Selection of the initiating AUG is facilitated by specific surrounding nucleotides called the Kozak sequence (5')ACCaugG(3') 1. A at the 5' 2. G at the 3' *the ends of the Kozak sequence

What can be used as treatment in people in lung cancer where EGFR is active and over-expressed?(3)

Small molecule inhibitors of EGFR: 1. erlotinib 2. lapatinib 3. gefitinib

What is Usage Bias? T/F Certain codons can only be read by certain species

Some amino acids certain codons are preferred to other codons we call this usage bias. False, This does NOT mean that other codons can't be read only that certain species have a preference for particular codon. This means that recombinant eukaryotic proteins can be made in bacteria and will have the same amino acid sequence -ex. we can make human insulin protein in bacteria

What are the 4 base-paired stems of the tRNA? What are the 3 loops of the tRNA?

Stems: 1. Acceptor Stem 2. D Stem 3. Anticodon Stem 4. T Stem Loops: 1. D Loop 2. T ψ(psi) C Loop 3. Anticodon Loop

Prokaryotic Transcription The Stronger promoters means __? Promoter strength is dependent on what?

Stronger promoters means high expression of the gene The strength of a promoter depends partly how closely it matches the ideal consensus -10 and -35 sequence

Suppression of tumorigenicity by ___ ___ ___ of tumor cells with normal cells yields a ____ ____ cell These cells are ___

Suppression of tumorigenicity by cell fusion Fusion of tumor cells with normal cells yields a Nontumorigenic hybrid cell These cells are non-tumorigenic

Eukaryotic Transcription RNA Pol II What are the General transcription factors?(7) function? What is the critical sequence that allows RNA Pol II to recognize the promoter?

TBP: part of TFIID -binds to TATA box TFIID =TBP+TAFs -includes TBP, recognizes Pol II specific promoter(TATA Box) TFIIA -binds upstream of TATA box; required for binding of RNA Pol II to promoter TFIIB -binds downstream of TATA box; required for binding of RNA Pol II to promoter TFIIF -accompanies RNA Pol II as it binds to promoter TFIIE -required for promoter clearance and elongation TFIIH -phosphorylates the tail of RNA Pol II, retained by polymerase during elongation TFIIJ -required for promoter clearance and elongation the TATA Box is the critical sequence that allows RNA polymerase II to recognize the promoter.

The DNA template strand is also called the ___ or ___ The DNA coding strand is also called the ___ or ___

Template: non-coding or antisense Coding: non-template or sense

Eukaryotic processing of Pre-RNA What does the 3' tail consist of? T/F it is preceded by a 3' UTR

The 3'-tail of mRNA consists of a poly (A) tract True

What pathway brings proteins into the cell?

The Endocytic Pathway

Eukaryotic Transcription What is the protein that sits on top of RNA Pol II, provides a contact point for activators/repressors, combines signals from multiple activators and repressors, and sends the final result to the RNA Pol II?

The Mediator Complex Transmits Information to RNA Polymerase

What is the function of the SRP Receptor? What is the translocator?

The SRP receptor orients the ribosome and brings it in contact with a protein translocator The translocator is a donut shaped protein within the ER membrane that contains a protein-lined pore/channel called the translocon

Eukaryotic processing of Pre-RNA What does the 5' cap consist of? it is attached via what type of bond?

The cap consists of guanosine triphosphate attached via a 5'-5' phosphodiester bond, preceding a small 5' UTR

Eukaryotic Transcription RNA Pol I The core promoter is rich in ____ sequences What is UBF1 and SL1 and what role do they play? What is the role of TF1A?

The core promoter is rich in G/C sequences UBF1= Upstream binding factor SL1= Selectivity factor 1 consists of 4 polypeptides one of which is TBP (TATA binding protein)*not TATAAT-for prokaryotes 1. The UBF1 protein recognizes and binds to both the upstream control element and the core promoter(Bipartite) 2. Subsequently, SL1 binds to the DNA in association with UBF1 3. RNA polymerase I binds with the help of general transcription factor TFIA, and transcription commences

The correctly positioned ribosome-Met-tRNAiMet complex can now begin the____ addition of amino acids by the ____ translation of the mRNA. As is the case with initiation, a set of special proteins, termed ___, is required to carry out this process of chain elongation. The key steps in elongation are entry of each succeeding aminoacyl-tRNA with an anticodon ____ to the next codon, formation of a ___ bond, and the movement, or ____, of the ribosome one codon at a time along the mRNA

The correctly positioned ribosome-Met-tRNAiMet complex can now begin the stepwise addition of amino acids by the in-frame translation of the mRNA. As is the case with initiation, a set of special proteins, termed translation elongation factors (EFs)*NOT eIF-which is for initiation*, is required to carry out this process of chain elongation. The key steps in elongation are entry of each succeeding aminoacyl-tRNA with an anticodon complementary to the next codon, formation of a peptide bond, and the movement, or translocation, of the ribosome one codon at a time along the mRNA

The charging/activation of tRNAs form a high energy ester bond What does this bond do?

The energy of this bond subsequently drives formation of the peptide bonds linking adjacent amino acids in a growing polypeptide chain

The genetic code is in a __? 64 possible codons = 61 specific to ____ plus 3 ____ codons

The genetic code is in a triplet 64 possible codons = 61 specific to individual amino acids plus 3 STOP codons

The ___ ___ ___ slides along, or scans, the bound mRNA as the ___ activity of eukaryotic initiation factor ___ unwinds RNA secondary structures that might otherwise interfere with scanning When does scanning stop?

The multicomponent initiation complex slides along, or scans, the bound mRNA as the helicase activity of eukaryotic initiation factor 4A (eIF4A) unwinds RNA secondary structures that might otherwise interfere with scanning. Scanning stops when the tRNAiMet anticodon recognizes the start codon, which is the first AUG downstream from the 5′ end in most eukaryotic mRNAs

The ribosome is composed of ___ different rRNA molecules and as many as ___proteins Eukaryotes: -Large subunit has __ proteins -Small subunit has __ proteins The large subunit contains three rRNAs: -1. __molecule of ___S rRNA(large) -2. __molecule of ___S rRNA -3. __molecule of ___S rRNA The small ribosomal subunit contains ___molecule of ___S rRNA, referred to as ___rRNA.

The ribosome is composed of 4 different rRNA molecules and as many as 83 proteins Large: 50 proteins Small: 33 proteins The large subunit contains three rRNAs: -1. 1 molecule of large rRNA(28S) -2. 1 molecule of 5S rRNA -3. 1 molecule of 5.8S rRNA The small ribosomal subunit contains 1 molecule of 18S rRNA, referred to as small rRNA

What is the reading frame?

The sequence of codons that runs from a specific start codon to a stop codon

The vast majority of introns initiate with ___ and terminate with ___

The vast majority of introns initiate with GU and terminate with AG

The vast majority of mRNAs can be read in only one frame. Why?

The vast majority of mRNAs, however, can be read in only one frame because stop codons encountered in the other two possible reading frames terminate translation before a functional protein is produced

What happens at the Acceptor Stem? What enzyme does this?

This is where the amino acid is attached when a tRNA is charged/activated by aminoacyl-tRNA synthetase -aminoacyl-tRNA synthetases use this for recognition of proper tRNA

During the first stage of translation, the small and large subunit of the ribosome assemble This process is mediated by a special set of proteins known as ___ It is also ___ dependent, what does this mean?

This process is mediated by a special set of proteins known as translation initiation factors (IFs) The process of translation is generally cap dependent meaning that an mRNA needs a 5'cap

Eukaryotic Transcription What is required for proper functioning eukaryotic RNA polymerases? What are they? Which one relates to which Eukaryotic Polymerase?

Transcription factors: Activators and repressors proteins in eukaryotes -RNA Pol I: TFI -RNA Pol II: TFII -RNA Pol III: TFIII

Translation Initiation Usually Occurs at the First ___ sequence from the ___ End of a mRNA

Translation Initiation Usually Occurs at the First AUG sequence from the 5' End of a mRNA

Translation generally starts ___-___bp after the cap in a space called the ____

Translation generally starts 50 to 100 bp after the cap in a space called the 5' UTR or untranslated region

When the signal-recognition particle (SRP) binds to the ER signal sequence and the large ribosomal subunit, translation is halted What needs to happen for translation to be resumed?

Translation is resumed when the SRP-signal sequence-ribosome complex binds to a SRP-Receptor on the ER membrane

What is Translation?

Translation is the process by which the nucleotide sequence of an mRNA is used as a template to join the amino acids in a polypeptide chain in the correct order RNA->Protein

Eukaryotic Transcription RNA Pol II T/F- A variety of specific transcription factors are needed for expression of certain genes under particular circumstances.

True

T/F A probabilistic analysis indicates that over 60% of human disease-causing mutations affect splicing rather than directly affecting coding sequences

True

T/F Although Adenine is theoretically possible in the wobble position of the anticodon, it is almost never found in nature

True

T/F Any mutation that block proper folding, also blocks movement out of the ER to the Golgi

True

T/F Cancer is a genetic disorder

True

T/F Materials can be transferred from the endosome to the Golgi apparatus

True

T/F Proteins are targeted for cellular location early in the process of creation

True

T/F The 60S ribosomal subunit is aligned with the pore of the translocon in such a way that the growing chain is never exposed to the cytoplasm and is prevented from folding until it reaches the ER lumen

True

T/F The two strands of the DNA to be transcribed are separated locally

True

T/F a primary transcript (pre-mRNA) is NOT allowed to leave the nucleus until the final RNA processing is complete: 5′ cap, 3′ poly(A) tail, and removal of the introns (splicing)

True

T/F All (-)ssRNA Viruses are enveloped Can (-)ssRNA be used to synthesize proteins? -what is the result? steps for replication of (-)ssRNA Viruses?(3)

True (-)ssRNA cannot be used to synthesize proteins -the virus must carry a Viral RNA-dependent RNA polymerase 1. (-)ssRNA from virus is uses the Viral RNA-dependent RNA polymerase to make (+) complementary strand 2a. (-)ssRNA from virus is uses the Viral RNA-dependent RNA polymerase to make more (+) complementary strand -(+)ssmRNA strands are used to code proteins 2b. (+) complementary strand are used to make more (-)ssRNA which are packed into virus particles along with Viral RNA-dependent RNA 3. coded proteins from 2a and virus particle from 2b are joined to make a nucleocapsids

T/F In prokaryotes transcription and translation occur simultaneously T/F mRNAs are only read once

True False, an mRNA is not necessarily only read once. It can be used more than once for protein construction

T/F Cell cycle checkpoints are activated not only during normal cell cycle progression but also in response to internal and external stress signals If DNA damage is detected at these checkpoint what happens?

True If DNA damage is detected, the cell cycle is arrested to allow for repair

T/F Prokaryotic genes are polycistronic What does this mean? What is an example?

True Polycistronic mRNA is a mRNA that encodes several proteins(Several genes are transcribed as single RNA from the same operator and promoter) example: Lac Operon

T/F The message contained within the mRNP must be transported out of the nucleus and into the cytoplasm before it can be utilized by the ribosome to make protein The nucleus is separated from the cytoplasm by __ membranes which form the ___ ___

True The nucleus is separated from the cytoplasm by two membranes which form the nuclear envelope

T/F The first two bases in a codon always follow standard Watson Crick pairing The third base in the codon is the ___ ____

True The third base in the codon is called the wobble position or experiences "wobble" pairing

T/F In cancer, genes are often silenced by promoter methylation T/F Methylation is reversible

True True

Structure of tRNA T/F The exact nucleotide sequence varies among tRNAs The nucleotides sequences fold into what?(2) The ____sequence at the ___ end also is found in all tRNAs What forms an aminoacyl-tRNA? The triplet at the tip of the ____ ____ base-pairs with the corresponding codon in mRNA

True fold into: 1. 4 base-paired stems 2. 3 loops The 5'CCA3' sequence at the 3′ end also is found in all tRNAs Attachment of an amino acid to the 3′ A(the A of CCA^) yields an aminoacyl-tRNA The triplet at the tip of the anticodon loop base-pairs with the corresponding codon in mRNA

T/F The precise linear array of ribonucleotides in groups of three in mRNA specifies the precise linear sequence of amino acids in a polypeptide chain and also signals where synthesis of the chain starts and stops

True(colinear rule)

T/F The Rough ER is the only membrane where secretory proteins are synthesized Why is the Rough ER called "rough"?

True, because the Rough ER has ribosomes bound to it "rough" due to it being densely studded with ribosomes

Eukaryotic Transcription T/F- RNA Pol II can work with just the promoter How do specific transcription factor make contact with the transcription apparatus? T/F- TFII proteins are always SPECIFIC transcription factors because they are always required

True, but it is very inefficient - different upstream elements can increase the efficiency of RNA Pol II binding These usually make contact with the transcription apparatus via TFIID, TFIIB, or TFIIA, not by directly touching RNA polymerase II itself False, they are GENERAL

T/F Once hydrolysis of the GTP in eukaryotic EF2·GTP and subsequent translocations occur the ribosome cannot go back Why?

True, the hydrolysis of the GTP in eukaryotic EF2·GTP is an irreversible process that prevents the ribosome from moving along the RNA in the wrong direction or from translocating down an incorrect number of nucleotides

Eukaryotic Transcription RNA Pol III T/F The promoter is located within the gene itself T/F The recognition sites are located downstream of the start site Transcription of the 5s rRNA and tRNA require what proteins?(2) How do they work?

True, the promoter is located within the gene itself True, the recognition sites are located downstream of the start site Requires TFIIIA and TFIIIB TFIIIC consists of two subunits τA and τB, and binds to the A and B blocks(recognition site over 50BPs downstream of the start site). This induces TFIIIB, which consists of three subunits (Brf1, Bdp1, and TBP), to bind to the promoter near the start site. Only after TFIIIB binds can RNA polymerase III bind. Then transcription start -TFIIIB positions the RNA pol III correctly at the start site *TFIIIA acts in the same way was TFIIIC

T/F The promoters of Eukaryotic Transcription are bipartite in nature What does this mean?

True, there are 2 parts Eukaryotic Transcriptional control 1. Core Promoter 2. Upstream Control Elements

Tumor Suppressor Genes can be found by looking for ___ ___ ___ in tumor cells What are the techniques used to find these?(2) -what do they use?

Tumor Suppressor Genes can be found by looking for Loss Of Heterozygosity in tumor cells *Loss Of Heterozygosity in specific region of cancer cell genome indicates presence of Tumor Suppressor Genes Techniques used to find LOH 1. restriction fragment length polymorphism (RFLP) -use restriction enzymes 2. single nucleotide polymorphisms (SNPs ) -use PCR / sequencing

RNA Tumor Viruses Tumors are caused by ___ ___ of cells done by retroviruses

Tumors are caused by Slow Transformation of cells done by retroviruses

What the 2 types of Congenital disorders of glycosylation(CDG)?

Type 1 disorders - lack entire glycan(sugar chains) Type 2 disorders - structure of the glycan(sugar chain) is altered

If the efforts of the chaperones are not effective, the misfolded protein is marked for degradation via a process called ___ What are the steps?

Ubiquitination 1. ubiquitin-conjugating enzyme (E1) activates ubiquitin and transfers it to the E2 component of a ubiquitin ligase (E2-E3 complex) 2. E3 component of the ubiquitin ligase(E2-E3 complex) recognizes the target/miss-folded protein and transfers the ubiquitin from E2 to the target protein *this process is repeated until 4 of more ubiquitins are attached to the target/miss-folded protein

VHL1 gene encodes for a VHL1 protein that ___ The protein binds to ___ and does what to it? What does bind require? -what enzyme does this? under hypoxia does this protein bind?

VHL1 gene encodes for a VHL1 protein that inhibits HIF1α binds to HIF1α and ubiquitinizes it for degradation binding requires hydroxylation of Proline done by proline hydroxylase under hypoxia the VH1 protein does not bind to HIF1α -HIF1α is now active

VHL1 gene relates to what syndrome ___ mutations found in patients Transcriptional silencing by ___ ___

VHL1: Von Hippel-Lindau syndrome Germline mutations found in patients Transcriptional silencing by promoter methylation

What is the regulator, the adapter, and effector in vertebrates? What about Caenorhabditis elegans? in what order? leads to what?

Vertebrate- Regulator: Bcl-2 Adapter: Apaf-1 Effector: Casp9->Casp3 Caenorhabditis elegans- Regulator: CED-9 Adapter: CED-4 Effector: CED-3 regulator->adapter->effector->death

What is the viral capsid? it can be ___ or ___ -how are they constructed? -where is the viral genome located?

Viral Capsid: Protein shell protecting the genome Helical(rod shaped/cylindrical or coiled): -constructed using *multiple copies of single polypeptide -Viral genome *associated with polypeptide or Icosahedral (spherical or symmetric): -20 triangular faces, constructed using *several different polypeptides (capsomers) -Viral genome located *within the empty space

What are viruses? In order to replicate they rely on the ___ ___ ___ Virus particles (Virion) contains:(3)

Viruses are obligatory intracellular parasites In order to replicate they rely on the host cell machinery Virus particles (Virion) contains: 1.Genetic information, genome (RNA or DNA) 2. A protein shell (capsid) to protect the genome 3. Some viruses have an Envelope (protein-containing lipid bilayer)

Glycosylation deficiencies can result in a congenital muscular dystrophy called ___

Walker-Warburg syndrome

When a normal cell is stimulated through a growth factor receptor, inactive (___-bound) ___ is activated to a ___-bound state. Activated ___ recruits ___ and stimulates the ____ pathway to transmit growth-promoting signals to the nucleus. The mutated ___ protein is permanently activated because of inability to hydrolyze ___, leading to ___ ___ of cells without any ___ ___ The anchoring of ___ to the cell membrane by the ___ moiety is essential for its action

When a normal cell is stimulated through a growth factor receptor, inactive (GDP-bound) RAS is activated to a GTP-bound state. Activated RAS recruits RAF and stimulates the MAP-kinase pathway to transmit growth-promoting signals to the nucleus The mutated RAS protein is permanently activated because of inability to hydrolyze GTP, leading to continuous stimulation of cells without any external trigger. The anchoring of RAS to the cell membrane by the farnesyl moiety is essential for its action

What is Retinoblastoma(Rb)? In inherited retinoblastoma, one defective copy of a ___ ___ ___is genetically transmitted What is Knudson's "two-hit hypothesis" of oncogenesis?

a childhood eye tumor In inherited retinoblastoma, one defective copy of a tumor suppressor gene is genetically transmitted Knudson's "two-hit hypothesis" of oncogenesis: -One genetic change ("first hit") is inherited -Spontaneous mutation ("second hit") in one of the retinal cells which already carry the first mutation

Why does Pre-mRNA splicing need to be accurate within a single base?

a mistake would throw the whole coding sequence out of register and totally scramble the protein sequences

Eukaryotic Transcription What is an example of a promoter mutation that can cause disease?

a mutation of the telomerase reverse transcriptase (TERT) promoter(an important element of telomerase expression) has emerged as a target of cancer-specific mutations

Eukaryotic processing of Pre-RNA What is a newly synthesized RNA molecule called? What does it contain?

a newly synthesized RNA molecule is called a primary transcript (or Pre-RNA) Pre-RNA contains exons, introns, and a tail signal(AAUAAA)

Insertion of Proteins into the ER Membrane The orientation of these proteins are preserved. a. How to you get the N-Terminus in the ER Lumen and C-Terminus in the the cytosol?(2) b. How to you get the C-Terminus in the ER Lumen and N-Terminus in the the cytosol?(1) c. How do you get both C and N Terminuses in the cytosol?(2) REVIEW LECTURE 32 SLIDE 19

a. 1. a terminal ER signal sequence(at N-Term): takes the N-Term into the ER and binds itself to the translocon 2. internal stop-transfer: halts translocation and moves protein out of translocon and anchors it to the membrane -Terminal signal sequence is cleaved off b. 1. a SINGLE internal start-transfer sequence: starts polypeptide transfer and then moves protein out of translocon and anchors it to the membrane(only moves protein out after complete transfer of the polypeptide c 1. a SINGLE internal start-transfer sequence 2. a stop-transfer sequence that prevented complete transfer of the polypeptide through the translocon

a. What protein is responsible for DNA methylation? b. What proteins are used to reverse DNA methylation?

a. DNMT: DNA methyltransferase b. 1. HDAC: histone deacetylase 2. methyltransferase inhibitors

Prokaryotic Transcription What is the Lac Operon is regulated by? What happens in the presence of both?

activated: lactose and IPTG repressed: glucose When both are present, the bacteria prefer breaking down glucose so lacI stays bound to lacO, keeping the Lac Operon turned off

Prokaryotic Transcription What is the true inducer of the Lac Operon?

allo-lactose (not lactose itself)

What allows for a single original DNA sequence to be used to make several different proteins that have distinct but overlapping functions in eukaryotic cells? What is an example?

alternative splicing of exons produce multiple forms of mRNAs Alternative splicing of fibronectin -fibroblasts fibronectin mRNA have EIIIB and EIIIA exons -hepatocyte fibronectin mRNA do not

Some amino acids are so similar structurally, aminoacyl-tRNA synthetases sometimes make mistakes How are these mistakes corrected? In eukaryotes the aminoacyl-tRNA synthetases make about one mistake in every ____ couplings

aminoacyl-tRNA synthetases have a proofreading activity that checks the fit in their amino acid-binding pocket -If the wrong amino acid becomes attached to a tRNA, the bound synthetase catalyzes removal of the amino acid from the tRNA. This crucial function helps guarantee that a tRNA delivers the correct amino acid to the protein-synthesizing machinery In eukaryotes the aminoacyl-tRNA synthetases make about one mistake in every 40,000 couplings

anti-apoptotic Bcl-2 family proteins promotes cancer by ___ ___ Pro-apoptotic Bcl-2 family proteins are over-expressed in ___% of patients with ___ ___ ___ due to ___ ___ between chromosome ___ and chromosome ___ T/F Pro-apoptotic Bcl-2 family proteins was the first protein that was shown to contribute to cancer by inhibiting cell death by inhibiting apoptosis

anti-apoptotic Bcl-2 family proteins promotes cancer by inhibiting apoptosis Pro-apoptotic Bcl-2 family proteins are over-expressed in 85% of patients with B-cell lymphoma due to chromosomal translocation between chromosome 14 and chromosome 18 True

What is the difference between apoptosis and necrosis?

apoptosis: -programmed(body wants to get rid of) -cells are fragmented and phagocytes break down the fragments necrosis: -accidental or pathological -cells swell and burst releasing their intracellular contents

How is the the efficiency of translation is greatly increased in Eukaryotes?

binding of mRNA and individual aminoacyl-tRNAs to a ribosome

Abnormally spliced DNMT (DNA methyl transferase) genes is associated with what disease? What is another example?

cancer another example is the Ron(MST1R)- leads to motility of cancer cells

Cell number is regulated not only by cell division but also by ____

cell death

What is Autophagy? Autophagy is caused by ___ such as ____ What is the process?(4)

cell self cannibalism Autophagy is caused by Cellular stresses such as nutrient deprivation 1. Under nutrient deprivation autophagy genes are activated 2. activated autophagy genes initiate the formation of an autophagic vacuole(a membrane bound vesicle) -traps/sequesters cellular organelles 3. autophagic vacuole then fuse and dump sequestered organelles into a lysosome 4. lysosome digest organelles, and the products are used to provide nutrients for the cell

What base in the codon experiences wobble? What base in the anticodon experiences wobble? What's the advantage of having more than one anticodon per tRNA?(wobble pairing)

codon: third anticodon: first Advantage of wobble pairing: it can absorb point mutations

Misfolded membrane and secretory proteins, and unassembled subunits of multimeric proteins, are transported to the ___ for degradation

cytosol

What is more common in virus genomes, single-standed genomes or double-stranded genomes? In single-stranded genomes: -"(+)" strand aka ___ strand ___ -"(-)" strand aka ___ strand ___

double-stranded genomes are most common In single-stranded genomes: -"(+)" strand aka sense strand is directly used for protein synthesis -"(-)" strand aka antisense strand needs to form "(+)" strand first, then the "(+)" strand is used for protein synthesis

endosome fuses with a lysosome to form a ____ ____in which the endocytosed material is digested by lysosomal enzymes

endosome fuses with a lysosome to form a secondary lysosome in which the endocytosed material is digested by lysosomal enzymes

In retinoblastoma the first hit leads to ____ The second hit leads to ___ T/F Probability of two mutational events occurring at the same loci, in the same cell is extremely high How is the second hit usually achieved?(4)

first hit: heterozygosity second hit: loss of heterozygosity False, it is low Second hit(loss of heterozygosity) is achieved through: 1. mitotic recombination 2. Chromosomal non-disjunction (missegregation) 3. translocation 4. gene conversion

For prokaryotes, what is the RNA polymerase made out of? The holoenzyme? The core enzyme? This enzyme makes what?

holoenzyme: α2(2 alpha)β(beta)β'(beta prime)ω(omega)σ(sigma) core:α2ββ'ω synthesize all 3 classes of RNAs (rRNA,tRNA,mRNA)

Where does synthesis begin for all proteins?

in the cytosol

Where does Eukaryotic processing of Pre-RNA to mature RNA take place?

in the nucleus

The area between the large subunit and the small subunit of the ribosome is called the ___ What are the three local domains found at this site?

interface 1. A Site: Aminoacyl-tRNA binding site 2. P site: Peptidyl-tRNA binding site 3. E site: Exit site These are the main sites of interaction for the aminoacyl-tRNA and mRNA within the ribosome, as protein synthesis takes place

Where are introns present? Where are exons present? answer choices DNA, Pre-mRNA, mature mRNA

introns: DNA, Pre-mRNA exons: DNA, Pre-mRNA, and mature mRNA

How does Inosine enable tRNA recognition of proper mRNA?

it can recognize mRNAs that have C, A, or U in the third position of the codon

What is RNA interference(RNAi)? RNAi involves the degradation of ___ or ___ How is RNAi triggered?

it is a sequence specific mechanism for gene silencing that is induced by dsRNA RNAi involves the degradation of dsRNA or ssRNA RNAi is triggered by dsRNA that is fully base-paired and is at least 21-23 base pairs in length(siRNA)

Prokaryotic Transcription What is the structure of the genes encoding the Lac Operon? What are their functions? The Lac Operon mainly is

lacI- promoter for lacI-Crp site-lacP-lacO-lacZ-lacY-lacA-Terminator Lac Operon mainly is lacZ, lacY, and lacA lacI: Lac Repressor Crp site: cyclic AMP receptor proteins/CAP-catabolite activator protein binding site lacP: Promoter for lacZ, lacY, and lacA lacO: Operator- it partly overlaps the lacP and lacZYA(structural genes) lacZ: produces beta-galactosidase that degrades lactose into galactose and glucose LacY: encodes lactose permease , a transport protein LacA: the transacetylase

Prokaryotic Transcription How are the inducers of the Lac Operon processed by the product of the lacZ gene?

lacZ gene makes beta-galactosidase IPTG(iso-propyl-thiogalactoside): is not degraded by beta-galactosidase Lactose: is degraded by beta-galactosidase

Nuclear envelope is maintained by highly organized meshworks of intermediate filaments composed of ___ The nuclear enveloped broken down during what part of the cell cycle? How does this occur?

lamins nuclear envelope breakdown occurs at Prometaphase Cyclin B-CDK1(M-CDK) phosphorylates specific Serine residues in lamins Phosphorylation of lamins causes depolymerization of lamin filaments

Where is the hydrophobic core (h core) located? What is it's function?

located in the N-terminus of the protein directs the ribosome to the Rough ER and initiates translocation of the growing peptide

Where are lysosomal enzymes synthesized? where are they glycosylated? In the ____ they finally acquire a ____ residue on some of their ___-linked oligosaccharides The residue acquired is a ____that route the enzyme to the lysosome

lysosomal enzymes are synthesized at the rough ER become glycosylated in the ER and Golgi apparatus In the Golgi apparatus they finally acquire a mannose-6-phosphate residue on some of their N-linked oligosaccharides The residue acquired is a molecular tag that route the enzyme to the lysosome

mRNA carries genetic information transcribed from DNA in a ____ manner. mRNA is coded into protein by ____ mRNA has only four bases, but there are 20 amino acids Therefore a single base in the mRNA cannot specify an amino acid in a polypeptide. explain the math behind 1 base, 2 bases, and 3 bases

mRNA carries genetic information transcribed from DNA in a linear manner. mRNA is coded into protein by tRNAs mRNA has only four bases, but there are 20 amino acids. Therefore a single base in the mRNA cannot specify an amino acid in a polypeptide -1 base: 4^1= 4 amino acids -2 bases: 4^2= 16 amino acids -3 bases: 4^3= 64 amino acids

Eukaryotic Transcription RNA Pol II main promoter? proximal promoter? where at? What are Proteins that bind to cis-acting elements that increase or decrease transcription called?

main: Bipartite(upstream control element and core promoter-TATA box) proximal: a type of cis-acting element @ -200 to +30 called transcription factors (TFs)

What forms in Metaphase?

metaphase plate

Many miRNAs control mammalian development and its timing What is an example of when there is a mutation? This is caused by?

miRNA plays a role in limb development ex. Dicer is knocked out in mice preventing limb development it is caused by the conditional expression of Cre, which induces the deletion of the Dicer gene

If the ER contains no proteasomes, how are are miss-folded proteins in the ER degraded?

misfolded and damaged proteins can be retrotranslocated from the ER lumen to the cytoplasm, where they are degraded by the ubiquitin-proteasome system

Are all signal peptides the same?

no

What proteins made in the non-secretory pathway?(4) What proteins made in the secretory pathway?(4)

non-secretory pathway: 1. cytoplasmic proteins 2. nuclear proteins 3. mitochondrial proteins 4. chloroplast proteins secretory pathway: 1. plasma membrane proteins 2. ER proteins 3.Golgi proteins 4. lysosomal proteins

In the Somatic cell hybridization experiment, were the hybrids tumorigenic or non-tumorigenic? -Therefore?

non-tumorigenic: therefore we know that the mutation is recessive

What kind of mutation can inactivate a gene in any organism with a base-pair change that converts a codon normally encoding an amino acid into a stop codon? When this occurs early in the reading frame, the resulting _____ protein usually is nonfunctional

nonsense truncated protein

Transport of mature RNA into the eukaryotic cytoplasm from the nucleus is controlled by what protein complex?

nuclear pore complex

In eukaryotic cells, large and small molecules including mature mRNA enter and leave the nucleus via ____

nuclear pore complexes (NPC)

What are the steps in the Ran-independent mechanism of nuclear export of m-RNAs?(6)

nucleus 1. Phosphorylated NpI3(SR protein) binds pre-mRNA at the 5' end 2. When polyadenylation has occurred successfully, Glc7(nuclear phosphatase) dephosphorylates NpI3 -promotes binding of TAP&Nxt1(mRNP exporters) 3. Binding of TAP&Nxt1 allows for diffusion of the mRNP complex through the nuclear pore complex 4. Sky1(cytoplasmic protein kinase) phosphorylates NpI3 5. An RNA Helicase dissociates the phosphorylated NpI3 and TAP/Nxt1 from the mRNA -phosphorylated NpI3 and TAP/Nxt1 are transported back to the nucleus via a nuclear pore complex 6. Transported mRNA is now ready for translation

Following peptide bond synthesis, the ribosome is translocated along the mRNA a distance equal to ___ This translocation step is monitored by ____

one codon This translocation step is monitored by hydrolysis of the GTP in eukaryotic EF2·GTP

Alternative start sites can cause what? is this rare?

overlapping reading frames, as a result, the same nucleotide sequence specifies different amino acids during translation yes

p53 acts as a ___ ___ and induces genes involved in ___ ___ ___ (___), ___ ___ (___) and ___ (___) p53 can also repress expression of genes that ___ ___ ___ (___, ___)

p53 acts as a transcription factor and induces genes involved in cell cycle arrest (p21), DNA repair (GADD45) and apoptosis (Bax) p53 can also repress expression of genes that promote cell survival (e.g., cyclins, anti-apoptotic Bcl-2 proteins)

p53 is induced by ___ ___ such as ___ ___ How does p53 play a role in apoptosis?(4) -via intrinsic(mitochodrial) pathway or Extrinsic(receptor-initiated) pathway?

p53 is induced by cellular stress such as DNA damage 1. ATM associates with double stranded break and activates Chk2 2. Chk2 phosphorylates p53 3. phosphorylated p53 acts as a transcription factor and binds to the promoter region of DNA to allow for the production of Pro-apoptotic Bcl-2 family proteins: Bax Noxa, PUMA 3. Pro-apoptotic Bcl-2 family proteins: Bax Noxa, PUMA go to the mitochondrion and causes the release of Cytochrome C 4. same as intrinsic pathway steps 3-7 via intrinsic(mitochodrial) pathway

How is p53 inactivated by tumor viruses? How is Rb inactivated by tumor viruses?

p53: tumor viruses mess with DNA and cause the production of E6 which ubiquitylize p53 which is then degraded Rb: tumor viruses mess with DNA and cause the production of E7 which inactivates Rb

The binding of Rb protein to E2F is inhibited by ___

phosphorylation

Prokaryotic Transcription What enzyme does the Lac-Operon produce? What does the product do?

produces beta-galactosidase to break down lactose into Galactose and Glucose

Eukaryotic Transcription RNA Pol II Where is the main promoter region? Where are the enhancers?

promoter region(TATA box) is close to the start site enhancers are located far upstream or downstream

Degradation of CDK inhibitors is done by a process called ____ What are the steps of the degradation of the CDK2 inhibitor p27(a type of Kip1) after it binds to CDK2 and prevents initiation of DNA replication?(3)

proteolysis 1. After the cell passes the restriction point CDK2-cyclin E becomes active and phosphorylates p27(a type of Kip1) 2. Phosphorylation of p27 triggers its degradation via the ubiquitin proteasome-mediated pathway 3. Degradation of p27 causes activation of CDK2-cyclin A(S CDK), which then triggers initiation of DNA replication

What experiment in tumor suppressor genes lead to the conclusion that mutations are recessive? What experiment lead to the 'two hit' hypothesis?

recessive: Somatic cell hybridization experiment 'two hit' hypothesis: Study of Familial Cancer Cases

The Study of Familial Cancer Cases was done on what disease? Explain the hypothesis proposed?

retinoblastoma Proposed the 'two hit' hypothesis - that two genetic events have to occur at single loci for tumor formation

What is the most abundant RNA-protein complex in the cell?

ribosome

Cyclin levels rise during interphase or mitosis? Cyclin levels fall during interphase or mitosis?

rise: interphase fall: mitosis

What is the difference in mechanisms for the inhibition of translation between siRNA and miRNA?(2)

siRNA: - perfectly pairs - causes degradation of mRNA miRNA: -imperfectly pairs -does not degrade mRNA

Besides Methylation, what else can result in repressed transcription of Tumor Suppressor Genes? Cancer cells have ____ compared to non-cancerous cell which have ___

silencing Cancer cell have increased methylation at CpG islands compared to non-cancerous cell which have silencing of TSGs

What is the spliceosome? What is it made out of? Where does it assemble?

spliceosome: splicing machinery it is made from small nuclear RNA (snRNA) and their protein partners -snRNA+protein partner=snRNP -snRNA is for base pairing -protein is for cutting an rejoining the spliceosome contains 5 snRNPS 1. U1 2. U2 3. U4 4. U5 6. U6 They assemble at the slice sites located at the intron/exon boundaries

Is the wobble position of tRNA closer to the 5' end or 3' end of tRNA? Is the wobble position of mRNA closer to the 5' end or 3' end of mRNA?

tRNA: 5' mRNA: 3'

Decoding the nucleotide sequence of mRNA into the amino acid sequence of proteins depends on ___ and ____

tRNAs and aminoacyl-tRNA synthetases

Point mutations in 5' splice sites or 3'splice site or at branch point A may not produce functional globin mRNA or protein causing genetic disease like _____

thalassemia

What is the most frequent class on intron in eukaryotic nuclear genes?

the GT-AG (or GU-AG in RNA code) group of introns

What is an example of an RNA that does not get a 3' poly A tail?

the genes and mRNA that encode histones are regarded as "special" and do not get a poly(A) tail but are processed differently

Prokaryotic Transcription: Explain: ρ-independent termination

the inverted repeats at the end of the template DNA are transcribed-the form a hairpin structure When the hairpin structure is followed by a poly U stretch RNA synthesis is terminated because the U-A hydrogen bond between DNA and RNA is weak

the nuclear envelope membrane forms a _______, _______ with numerous associated proteins

the nuclear envelope membrane forms a water-impermeable phospho-lipid bilayer with numerous associated proteins

The sigma factor of the Prokaryotic RNA Pol binds to the ___ box and the ___ box What are the respective sequences? These boxes are a part of the ___ region?

the sigma factor binds to the -10 box (TATAAT box) and to the -35 box (TTGACA box) They are in the promoter region

Tumor Viruses Some animal viruses can permanently alter the host genome, this is called ___ ___ ___ these cells have higher growth rate and can divide indefinitely -resulting in ___ What are Oncoviruses? can they be DNA viruses, RNA viruses or both?

transformation of cells resulting in cancer Oncoviruses: Viruses capable of initiating cancer They can be both

T/F p53 is highly unstable and is present at very low concentration under normal conditions If a double stranded break(caused by chemotherapeutic drugs, gamma irradiation, etc.) is detected at the DNA damage checkpoint what happens?(4) Where are the damage checkpoint?

true 1. ATM associates with double stranded break and activates Chk2 2. Chk2 phosphorylates p53 3. phosphorylated p53 acts as a transcription factor and binds to the promoter region of DNA to allow for the production of p21 4. p21(a Cyclin-dependent kinase inhibitor) inhibits G1/S CDK and S CDK halting the cell cycle to allow for repair or degradation Between G1 and S Also between G2 and M

Upstream is? Downstream is?

upstream: towards the 5' end of the template strand(in the - direction) Downstream: towards the 3' end of the template strand(in the + direction)

What base is different in RNA?

uracil instead of thymine

Eukaryotic Transcription What is an example of an inhibitor or RNA Pol II? What is it produced by? What does it cause?

Αlpha-amanitin is a toxin and inhibitor of RNA polymerase II -Certain mushrooms produce this toxin -Eating those mushrooms causes severe gastrointestinal discomfort and liver damage

What is β-catenin? Loss of APC increases β-catenin levels What happens after?

β-catenin: functions as a proto-oncogene β-catenin translocates to the nucleus and up-regulates cell proliferation