Download ZOMU - ​www.zomuedu.com Regulation of the Cell Cycle, Non

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Regulation of the Cell Cycle, Non-Mendelian Genetics , Protein Synthesis, & Eukaryotic Control of Gene Expression
Regulation of the Cell Cycle (Chapter 12 pgs. 242-248)
● Be able to explain what is being checked at the G1 , G2, and M checkpoint.
G1: ​p53 ​checks integrity of ​DNA​ (to prep for DNA rep), enough ​nutrients/raw materials​, enough ​space​, enough ​energy​,
G2: enough ​energy​, ​organelles​, ​MTOCs​, ​volume​ of cell, integrity of ​DNA
M: if chromosomes are aligned along the ​metaphase plate​ and if all of the ​kinetochore fibers​ are attached to the kinetochores
● Be able to explain how different types of cyclin and CDK’s help to regulate and initiate the next
Cyclin and CDK bind together to form complexes capable of phosphorylating the enzymes necessary in the next step of the cell cycle. [cyclin] fluctuate
and [CDK] respond to changes in [cyclin] by changing levels of activity. Cyclin must activate CDK in order for the CDK to signal the cell that it can go
on.
● phase at each checkpoint.
G1: end of G1 phase; G2: just before M; M: during metaphase and just before anaphase
● Know what each cyclin / CDK combination phosphorylates in order to initiate the next phase of the cell cycle:
G1
G2
M
P53 checks DNA integrity, enough space, enough
raw materials, enough energy
Checks DNA integrity, enough organelles, enough
energy, volume of cell (big enough to divide?),
enough MTOCs
Checks if all chromosomes are aligned at the
metaphase plate and if they are bound by
kinetochore fibers
- enzymes required for DNA replication
Initiator protein, helicase, topoisomerase, ligase,
ssbp, RNA primase, DNA pol III, etc
- enzymes required for cell division
Nuclear lamins (cause dissolving of nuclear
envelope), MTOCs (to form spindle fibers and
organize microtubules), histones (to condense
chromatin into chromatids → disappearance of
nucleolus/nucleoli)
- enzymes required for anaphase
Separase (which separates chromosomes at the
cohesin) and ​kinetochores​ (so that they start pulling
the sister chromatids to the poles)
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G1: if all goes well, cyclin-1 will bind to CDK and form a complex that can phosphorylate the enzymes required for DNA replication
- Phosphorylate initiator protein, single-stranded binding proteins, topoisomerase, helicase, ligase, RNA primase, DNA pol I and III, etc
G2: if all goes well, cyclin-2 will bind to CDK and form the ​mitosis promoting factor​ that can phosphorylate the enzymes required for mitosis
- Phosphorylate nuclear lamins, MTOCs, histones
M: if all goes well, cyclin-m will bind to CDK and phosphorylate ​separase​ and ​kinetochores
Be able to compare and contrast all of the differences between normal and cancerous cells (colorful sheet!)
- require a substratum
- immobile
- apoptosis
- no need for anchorage
- collagenase and pseudopods to move around and dissolve extracellular matrix
- p53 “broken” or RAS protein malfunctioning
- density dependent inhibition
- responds to growth hormones/normal level
- shape determines function
- shorter telomeres
- normal karyotype
- don’t promote angiogenesis
- don’t invade other tissues
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- lack density dependent inhibition
- excess/lack of growth hormones
- no particular shape
- active telomerase enzyme
- nondisjunction
- promote angiogenesis in order to “feed” rapid growth (capillaries)
- invade other tissues
Know the signal transduction pathway that controls moving past the point of no return (G1 checkpoint)
Ligands bind to TKR which triggers a phosphorylation cascade via G protein/Ras protein which leads to the transcription of p53 genes, Ras genes, and
Cyclin genes. Cyclin will be transcribed, translated, and then bound to CDK to form the mitosis-promoting factor which will lead to DNA replication and
eventually cell division.
Be able to explain the significance of p53 , Ras, p21, in the production of a cancerous cell.
- p53: guardian angel of the cell, acts like a recessive allele for cancerous since both (from both parents) must be damaged in order for cancerous situation
to occur, tumor-suppressor gene; ​if it finds an error​ it will stop the cell cycle, activate repair nuclease/DNA pol I/ligase, or trigger apoptosis
- Ras: gene involved in the signaling of growth hormones; if damaged, will lead to the uncontrolled transcription of cyclin; proto-oncogene → oncogene;
only one needs to be damaged
- p21: directed by p53 aka cyclin-CDK inhibitor and will stop the cell cycle by inhibiting CDK
You should be able to explain why you need at least 3 mutations in order to have a cancerous situation
- both p53 genes (from mom and dad) must be damaged so that the cell’s DNA cannot be repaired and at least one proto-oncogene must be damaged
(uncontrolled activity of Ras/TKR)
- two tumor-suppressor genes and one proto-oncogene must be damaged in order for a cancerous situation to occur.
Genetics (portions of chapters 14 and 15)
● Compare and contrast different Non-Mendelian modes of inheritance to classical Mendelian, inheritance and to each other including . . . Incomplete
Dominance, Multiple allelic, Codominance, Sex-Linked, Autosomal Linked (same chromosome) , Polygenic, Pleiotropic, Environmental, mitochondrial
and Y-linked. (pink sheet)
Non-Mendelian
Mendelian
- incomplete dominance: mix of the two phenotypes
- codominance: both phenotypes expressed
- multiple allelic: multiple possibilities in the gene pool
- sex-linked: associated w/X/Y chromosome
- Autosomal linked: specific to autosomes, show Mendelian inheritance
- Polygenic: attributed to multiple genes
- Pleiotropic: one gene affects multiple traits
- Environmental: setting determines expression
- unlinked
- found on separate chromosomes/>50mu on a chromosome
- only 2 alleles that are clearly d or r
- Mendelian ratios
- Mitochondrial: only from mom
- Y-linked: from father
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Use chi-square analysis (goodness of fit) to reject or not reject null hypothesis of a certain type of inheritance.
- The higher the chi squared value, the more likely you are to reject it
- The p-value is the probability of the results being replicated
- Chi squared value must be lower than the chi-squared value for p = 0.05 to achieve 95% confidence in the experimental data
- If you accept your null hypothesis, that means you are not sure if the results are due to chance/if there is a correlation
- To determine the %recombination/distance btwn genes
Analyze pedigrees and use process of elimination to figure out the type of inheritance
Be able to explain why X-linked recessive disorders are more prevalent in male offspring
- X linked is more common in males bc they only have one X chromosome from their mother so if that’s messed up they don’t have a back-up
Protein Synthesis (Chapter 17) ​https://www.mun.ca/biology/scarr/2250_RNA_translation.html
● Explain the central dogma of informational flow
- Nucleotide sequence/DNA --(transcription)--> RNA (mRNA) --(translation)--> RNA transcript/polypeptide
● Be able to analyze and explain data from Beadle and Tatum classical experiment with mold that helped support the one gene – one enzyme hypothesis
-​ bread mold, ​Neurospora crassa​ was cultured and irradiated to produce organisms with mutant genes and crossed the mutants w/normal ​Neurospora
- some mutant spores required an additional amino acid (Arg) since they had lost use of a specificgene that normally helped produce Arg
- one gene → one enzyme required for the production of Arg (fixed to one polypeptide since enzymes can be made up of multiple proteins/polypeptides)
● Be able to explain that one gene does not always code for one polypeptide, but it always codes
for one RNA transcript
- Doesn’t always code for one polypeptide or protein but always for an RNA transcript
- mRNA, tRNA, rRNA aren’t really considered proteins
● Provide what the small letters mean and the purpose of each of the following types of RNA . . .
- mRNA: messenger RNA carries genetic info to the ribosome and is found in the cytoplasm
- rRNA: ribosomal RNA is a subunit that makes up the ribozyme/ribosome and is involved in
the translation of mRNA to polypeptide
- tRNA: transfer RNA that inserts an amino acid based on codon/3 nucleotide sequence and
complementary base pairing (it has the anticodon); found in cytoplasm
- snRNA: small nuclear RNA found in nucleus involved in ​splicing primary RNA
- ncRNA: non-coding RNA; not much known; class including miRNA & snRNA
- siRNA: silencing/small-intervening RNA involved in ​gene regulation​/turning them on/off
- miRNA: microRNA is involved in turning genes on/off/​gene regulation
- piRNA: piwi-interacting RNA that code for regulatory proteins that keep stem cells from differentiating
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Be able to explain how the function of each type of RNA is dictated by its unique sequence of nucleotides which sometime dictates the unique shape of
each type of RNA
- rRNA: globular shape makes it ideal to build a ribosome
- tRNA: funky shape that has areas of hydrogen bonding btwn A&U and C&G and areas that are ​methylated​ to ​prevent​ hydrogen bonds from
forming. Shape determines which amino acid the tRNA is going to carry (@​3’ end!​) Anticodon is read 3’-5’ at the opposite end and is
complementary to the codon on the mRNA transcript (what you read instead to determine which a.a. Is attached)
- mRNA: long linear strand of mRNA w/3’poly-A tail and 5’ guanosine cap
Be able to flawlessly use the mRNA codon chart as shown on page 339
Be able to explain in detail transcription including (initiation, elongation and termination)
1) Initiation: initiation complex: promoter region w/DNA bending protein, transcription factors, RNA pol II, activators, enhancer region, TATA box
found in promoter region.
2) Elongation: RNA breaks hydrogen bonds, makes a ​transcription bubble​, reads 3’-> 5’ and builds 5’ -> 3’; follows the template strand and
continues to build complementary to DNA’s template strand
3) Termination: reads termination sequence, stops transcription and ends with a primary RNA transcript
Be able to explain why processing can occur in eukaryotes but not in prokaryotes
- Processing happens in eukaryotes bc transcription and translation do not occur concurrently so
the RNA transcript must be protected and introns must be spliced out
Be able to explain specifics regarding RNA splicing , and cap and tail placement and purposes -POST-TRANSCRIPTIONAL MODIFICATIONS
- Spliceosome binds to specific RNA nucleotide sequences and cuts off introns
- snRNA involved in RNA processing by acting as subunits for the spliceosome and snRNPs
help recog splice sites
- Cap on 5’ (ribosomal recognition) and tail on 3’ end (to lim enzymatic degradation and as a
termination sequence)
- Dynamic factors: transcription factors are specific to cell types; activators and repressors
(types of TF) bind to enhancer regions that may be specificto timing of transcription
Know the structure of a spliceosome and explain how it recognizes introns and catalyzes the reaction
of splicing.
- Spirit fingers recog specific nucleotide sequences (snRNA) and snRNA and snRNP make up
the spliceosome
- Catalyzes splicing w/help of splicing enzymes like snRNP
Know the function of each type of RNA polymerase in eukaryotes (I, II and III)
- RNA pol I: transcribes rRNA
- RNA pol II: transcribes mRNA, snRNA, miRNA; transcribes protein-encoding genes; can bind
to the TATA box to start transcription; changes in RNA pol II affinity can be affected by
enhancers which recruit transcription factors
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- RNA pol III: transcribes tRNA, rRNA
Be able to explain how RNA polymerase II reads and builds
Reads 3’ → 5’ and builds oppo; able to break hydrogen bonds and fix them back together; can build on single-stranded DNA
Explain how RNA polymerase gets the energy to build new RNA strands and explain the complementary base pairing strategy.
- Nucleoside triphosphates release lotsa energy; energy is derived from splitting the triphosphate tail into monophosphates and releasing
diphosphates during elongation
Know what UTR stands for and where it is in the RNA transcript
- Region of mRNA upstream of the start codon
- Untranslated region but ​do not​ include introns
- A point before translation that can be monitored to regulate gene expression: initiation of translation can be blocked when regulatory proteins bind
to the UTR and prevent ribosomes from attaching to the UTR and initiate translation
- Also affect lifespan of mRNA
Be able to compare and contrast the primary transcript and final transcript
- Primary transcript has introns, no cap, no tail, no alternative splicing
Be able to explain alternative RNA splicing and its evolutionary significance
- Alternative splicing results in different translated polypeptides/transcripts = variation in gene expression
Know that each exon codes for a specific domain in the final polypeptide/protein
- Exons = codons = amino acids
Be able to explain in detail translation including (initiation, elongation, and termination)
- Translation: mRNA → polypeptide
- Template strand will be read 3’ → 5’
- mRNA will be read 5’ → 3’ which will determine which amino acid attaches
- tRNA will be read 3’ → 5’ and then take the complementary codon (since tRNA
has the anticodon) to determine which amino acid attaches
- Not true but here: Ribosome moves along mRNA from 5’ to 3’ end
1) Initiation: start codon AUG
2) Elongation: EPA sites (exit, peptidyl, aminoacyl) where tRNA goes through to
drop off amino acid
3) Termination: stop codon
Be able to explain how tRNA gets a specific amino acid loaded onto the 3’ end
- amino acids are substrate specific; shape-determined
- Complementary anticodon (3’ → 5’) recog codon (5’ → 3’) and amino acid dropped off and then A pos tRNA shifts to P pos to make room for
another tRNA
Be able to explain what wobble means
- Last position in anticodon can mispair bc of flexibility since there are 64 diff possible amino acid but only 21~ in actuality
Know the purpose of the E, P, and A site on the large ribosomal subunit
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1) Exit site: tRNA leaves
2) Peptidyl site: moves over and site of elongation; catalyzes peptide bond formation; “5’ end”
3) Aminoacyl site is where new tRNA attaches; “3’ end”
Be able to explain how certain polypeptides are targeted to stay in the cytoplasm, be transported to a membrane (organelle or cell), or exit the cell
- Golgi body & vesicles transport, rER/free.bound ribosomes
Be able to explain what each of the following is and the significance of each
- Point mutation: one nucleotide messed up (added/subtracted)
- Substitution: exchange of nucleotides
- Silent mutation: unexpressed mistake. Mishap in nucleotide sequence still codes for the same amino acid
- Missense mutation: a mistake in the nucleotide sequence causes the translation of the wrong amino acid.
- Nonsense mutation: a nucleotide sequence change results in the coding of a stop codon
- Insertions: insert an extra nucleotide
- Deletions: removing a nucleotide
- Frameshift mutations: as a result of an insertion/deletion, all of the successive nucleotides are one or two nucleotides off = all of the codons after the
mutation are affected
- Mutagens: radiation, hormones, environmental factors
Regulation of Eukaryotic Gene Expression (Chapter 18)
● Be able to explain pre-transcriptional control mechanisms, RNA processing, and post translational control mechanisms that are utilized by eukaryotic cells
Pre-transcriptional control mechanisms
RNA processing
Post translational control mechanisms
- long term
- histone packing of chromosomes
- deacetylation of histones: makes histones more +
= more condensed chromatin = ​heterochromatin
- acetylation of histones: makes histones less + =
less condensed chromatin = ​euchromatin​ (more
easily transcribed)
- methylation of DNA (inaccessible for
transcription)
- alternative RNA splicing of mRNA produces diff
mRNA and allows a single gene to encode proteins
specific to a cell/cell stage
- production of short RNA sequences (from
enzymatic RNA processing in nucleus and
cytoplasm) that can bind to complementary sections
of mRNA and prevent translation/degrade sections
of mRNA
- protein processing adn degradation
- eukaryotic polypeptides are processed to become
functional (via regulatory proteins and
phosphorylation)
- cell-surface proteins also transport the proteins to
the correct place = LOTS OF opportunity to
regulate
- cell attached a protein (ubiquitin) to degrade the
protein
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Be able to explain our regulation activity and use specific genes that are turned on or off in red blood cells, intestinal lining cells, smooth muscle cells in
the intestine, and beta cells in the pancreas
- Insulin gene is always off in rbc, intestinal lining cell, and smooth muscle cell
- Ribosome protein, cell growth controller, DNA repair protein, cell resp enzyme, protein synthesis initiator, and fat breakdown enzyme genes are
always on (but can be activated/repressed by TF
- Only intestinal lining cell has gene for lactase available
- Only rbc has hemoglobin B gene available for transcription
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- Only beta cell in pancreas has insulin gene available
- Only smooth muscle cell has actin smooth muscle type gene available
Be able to explain the mechanisms that can turn off certain sections of chromosomes for long period of time and compare and contrast euchromatin and
heterochromatin
- The packaging/(de)acetylation of histones and methylation of DNA are long-term control mechanisms to turn on/off genes on the chromosome
- Euchromatin is available for transcription (looser) (acetylation)
- Heterochromatin is unavailable for transcription (deacetylation and methylation)
Be able to compare general transcription factors and specific transcription factors including purpose and place of DNA attachment.
- Activators activate transcription while repressors silence genes
- All genes to be turned on require specific transcription factors
- Initiation complex only need general transcription factors
Be able to explain the purpose of enhancers, silencers, activators, repressors, DNA bending proteins and your close personal friend RNA polymerase II.
- Enhancer: region of DNA that an activator can bind to to increase the likelihood of transcription occurring
- Silencer: when bound by the right transcription factors/repressors, they will repress transcription. Often close to enhancers and only differentiated
by complementary transcription factors
- Activator: transcription factor that binds to enhancer region to promote transcription
- Repressor: transcription factor that binds to silencer region to inhibit transcription
- DNA bending protein: bends DNA
- RNA Pol II: breaks H bonds, repairs DNA, transcribes DNA
Make sure you know how to say TATA correctly or else it will freak out even your bestest of friends!
Be able to compare how multiple genes that are involved in a pathway can all be turned on at the same time even though they are found on different
chromosomes
- Specific transcription factors and their concentrations in the cell determine how frequently genes are turned on/off
Be able to model how microRNAs target and affect mRNA
- microRNA is derived from DNA w/in introns of protein-coding genes/telomeres/anywhere and miRNA begins as a larger RNA transcript that has
been broken down. These short RNA pieces can bind to complementary sections of mRNA and cause it to degrade/
Be able explain the significance of RNAi
- RNA interference = gene silencing caused by short RNA mlc that bind to complementary parts of mRNA in the cytoplasma and block those
sections from translation or lead to their degradation (cleaving)
- Short RNA pieces include miRNA (from DNA and broken down into miRNA) and siRNA (external source of dsRNA that biochemically
transform into siRNA)
Be able to compare different cancer treatment strategies including radiation, chemotherapy, surgery, and immunotherapy.
- Radiation: targeted UV radiation to treat cancerous tumors and ease symptoms. Takes a long time, complications may arise, may be too close to
vital organs
- Chemotherapy: very powerful, treat/slow growth of tumor, ease symptoms. Kills good cells, relapses, repeated rounds, mixtures of poisonous
drugs
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Surgery: removes all traces, debulk helps other treatments, ease symptoms. Not always 100%, surgery complications
Immunotherapy: marks cancer cells to destroy them more easily and boost immune sys. Skin reactions, lymphatic reactions, allergic reactions
Targeted therapy: helps immune sys destroy cancer cell, stops growth/angiogenesis, delivery of toxic substances, may trigger apoptosis of
cancerous cells, starve cells of needed hormones. Resistance, hard to develop (must be cell-spec), fatigue
- Hormone therapy: treat and ease symptoms. Hot flashes, libido
- Stem cell transplant: leukemia, lymphoma, neuroblastoma. Infection, bleeding, antibodies
- Precision medicine: personalized genetic changes, DNA sequencing very spec. Still developing and expensive.
Be able to model a mechanism where a virus can cause a type of cancer
- Tumor viruses: viral integration may donate an oncogene to a cell, disrupt the tumor-suppressor proteins, and inactivate p53 and other
tumor-suppressor proteins = cell more prone to cancer
- Papillomaviruses, Epstein-Barr virus