Class Notes (839,470)
Canada (511,354)
Biology (1,309)
BIOL 205 (111)
Kenton Ko (10)
Lecture 6

Lecture 6-November 5.docx

9 Pages

Course Code
BIOL 205
Kenton Ko

This preview shows pages 1,2 and half of page 3. Sign up to view the full 9 pages of the document.
Nov 5/11 – Lecture 6 1. Good mutations Immunity to HIV - 10% copies of Chemokine receptor #5 in human genome have a deletion due to a frameshift - 1% of population homozygous for CCR5 deletion - Having this deletion makes people resistant to HIV EeroMantyranta - Received 7 gold medals - Had 15% more red blood cells than normal which helped him increase O2 capacity by 50% - He had a mutation in erythropoietin receptor that cause increased blood production. 2. Induced mutations mutagenesis - Mutagenesis: production of mutations in the laboratory through exposure to mutagens.\ Incorporation of base analogs - Base analogs: chemical compounds sufficiently similar to normal nitrogen bases of DNA that they’re occasionally incorporated into DNA in place of normal bases. - Once in place, these analogs have different pairing properties that causes a wrong nucleotide to be inserted oppositely - Chemicals that resemble normal nitrogen bases get incorporated into DNA o Ex. 5-bromouracil, normally paired with adenine, it becomes ionized and pairs with guanine instead = transition (AG) o 2- aminopurine2-AP normally paired with T, now pairs with C. (AT GC transition) o 5 bromodeoxyuridine is a derivative of 5-bromouracil that destroys the outside of tumours but not the core. Specific mispairing - Alkylating agents alter bases, it’s not incorporated into DNA but alters it in a way that it’ll form a specific misrepair. EMS - EMS (ethyl methane sulfonate)  add ethyl group rd o Ex. GC AT transition due to elimination of the 3 H bond G can make to C. o TA CG transition NG - NG (nitrosoguanidine)  methyl group Intercalating agents - Planar molecules that mimic base pairs - Slips between bases and causes intersertion or deletion (frameshift) of a single nucleotide pair o Ex. Acridine orange o Proflavin o ICR 191 Base damage - Aflatoxin B1 forms a bulky addition product that is produced by Aspergillus fungus found in peanut butter - It breaks the glycosidic bond and causes base to get removed - This results in a replication block because DNA synthesis won’t proceed past a base that can’t specify its complementary partner. Physical mutagens – Ionized - Includes X rays and gamma rays radiation - Has short wavelength and high energy, thus penetrates deeply into molecules - Causes reactive free radicals that can oxidize DNA - Results in base deletions, single nicks in DNA strands, cross-linking, and chromosomal breaks Non ionizing radiation - Includes UV light Q: Is 6,4 photoproduct and - Has less energy and can’t penetrate deeply into biological molecules cyclobutane pyrimidine dimer both thymine dimer? - Causes formation of cross linked thymine dimers and 6,4-photoproducts - When DNA strand is replicated, this may cause more mutations or DNA breakage. A: They’re both thymine dimers but just more specific names based on where the bonds are. 3. Testing methods for mutagens Ames test - A rat’s liver was ground and centrifuged and liver enzymes were extracted - Liver is used to mimic the mammalian metabolic conditions so that the mutagenic Q: Why would you test the speed potential of metabolites formed by a parent molecule in the hepatic system can be at which mutations revert back, assessed why can’t you test the speed that - A strain of Salmonella typhimurium that can’t synthesize the amino acid histidine mutations occur? Unless you want due to a point mutation is placed in the liver enzymes to find which specific gene is - A carcinogen X is mixed in as well mutated? - The mixture for strain 1, strain 2 and control (no X) is plated and monitored to see when the second mutation for His- His+ takes place. - Some salmonella strains revert through base-pair substitution or frameshift. 4. DNA repair - Since most mutatiosn are deleterious, DNA repair systems are vital to the survival of all organisms - In most cases DNA repair is a multi-step process: 1. Irregularity in DNA structure is detected (i.e. DNA too wide or missing) 2. Abnormal DNA is removed 3. Normal DNA is synthesized - The proofreading function of DNA polymerase 1 and 3 are first defense and most important. Direct Repair - An enzyme recognizes an incorrect alteration in DNA structure and directly converts it back to a correct structure. Photolyase o Ex. Photolyaserepairs Thymine dimers by splitting them through a light- required process called photoreactivation O-6 alkylguaninealkyltransferase o O6-alkylguanine alkyltransferase repairs alkylated bases by transferring the methyl or ethyl group from the G base to a cysteine side change within the alkyltransferase protein which also inactivates alkyltransferase. Base excision repair - A minor base damage is found and DNA glycosylasecleaves base-sugar bond DNA glycosylase - This creates a site that’s missing a purine or pyridine (apurinic/apyrimidimic) AP endonuclease - AP endonuclease makes a cut upstream of AP site dRpase - dRpase (deoxyribophosphodiesterase) removes stretch of DNA Polymerase - Polymerase synthesizes new DNA Ligase - Ligase seals nick. - This requires both strands to be homologous b/c this system exploits the antiparallel complementarity to restore damaged DNA segments to initial undamaged state. - GGR can correct lesions anywhere in the genome and is activated by stalled Global genomic repair (GGR) replication forks Q: Does the complex falls off - NER normally activated when replication fork stalls or is blocked when TFIIH goes on? - A heterodimeric complex recognizes damaged base and recruits TF IIH Diagram seems to show them - TFIIH is a transcription factor with XPB and XPD helicase activity staying on - This 10 protein subunit unwinds DNa, stabilizes it using RPA (Single stranded binding protein) and excises it 2-8 nucleotides from lesion - Poly 5 comes in and synthesizes new strand, and ligase 1 fills in gap o Ex. XPB and XPD are mutated in Xerodermapigmentosum so mutations accumulate in cells and increases risk of skin cancer. Transcription –coupled NER - Repairs transcribed regions - When RNA polymerase is stalled, CSA and CSB recognize the sequence and recruit TFIIH - RNA polymerase, CSA, and CSB falls off and lets TFIIH conduct repair o Ex. Cockayne syndrome has a stalled transcription complex with CSA and CSB mutated and TFIIH can’t bind so the cells undergo apoptosis premature aging Nov 8/11 – Lecture 7 Mismatch repair - Used to repair mismatches missed by the 3’-5’ exonuclease of DNA polymerase III - Lack of this repair system associated with some hereditary forms of colon cancer Process: 1. Mispairing causes a distortion 2. MutS recognizes a mismatched pair 3. MutH recognizes methylated parent strand and nicks GATC methylation site on daughter strand (not methylated yet) 4. UVRa (helicase) binds to nick and unwind DNA and excise it 5. New strand is replaced Q: I’m guessing the replacement is by Pol V or pol 1? Translesion synthesis (SOS - Bypasses lesions at stalled replication forks mechanism) - Pol 3 is stalled at site of damage but DNA continues to be unwound ahead of polymerase. - RecA joins single stranded binding proteins to form stiff filament, acts as a signal to several genes to encode Pol 5. - Pol 3 is released from its clamp when a ubiquitin molecule or PCNA (proliferating cell nuclear antigen) is added to change conformation to let Pol 5 enter because it has a larger active site. - Pol 5 adds a few bases (can’t add too many – it’s error prone) before falling off and being replaced by Pol 3. Double stranded break repair - Caused by X-rays or free radicals 1. Error-prone method: - KU80 and KU70 are part of a protein complex that recognize one end of the double strand, they serve to prevent further damage and recruit other proteins that rim the strand to generate 5’ P and 3’ OH ends required for ligation. - These proteins recognize both ends, trim and bring together and ligates along with DNA ligase 4 2. Error-free method: - Occurs during mitosis - Proteins bind to broken end and 5’ ends are trimmed by endonuclease to expose a single stranded region - RecA/Rad 51 forms long filaments with ssDNA and searches for sister chromatid for homologous sequence - The single strand invades its homolog and uses its complemetntarity to synthesize new sequence. - Ligation fixes any gaps 1. Cancer cells - Cancer cells have a faster division, metabolic rate, can invade new territories, and doesn’t stop growing in response to neighbouring cells (that’s why they pile up on each other) Oncogenes - Gain of function dominant mutations - Proteins encoded by oncogenes are usually activated in tumor cells - Mutation needs to be in only 1 allele and it’ll be dominant and suppress the other allele - Proto-oncogenes are the unmutated form. o Ex. A wt protein that promotes cell cycle progression will be cancerous if an oncogene is there for upregulation o A wt protein that stops apoptosis will never let cells die if oncogenes affect it. ** Oncogenes make proteins more active! Tumor Suppressor genes - Encode proteins whose loss of activity can contribute to a cancerous state - Loss of function – recessive mutations, so for cancer to develop, mutation must be in both alleles o Ex. BRCA1 and BRCA2 for breast cancer o Ex. A wt protein that inhibits cell cycle progression will activate progression when tumor suppressor mutations stop wt from working. ** Tumor suppressor makes inhibitors not inhibit. Proto-oncogenes - Proteins that induce (+vely control) the cell cycle o Ex growth factor receptors o Signal transduction proteins o Transcription regulators - Can also inhibit (-vely control) the apoptotic pathway o Ex. Ras mutation can cause a Rasoncoprotein to be blocked so it’s always on and Ras is constantly produced. 2. Chromosome numerical variations Polyploidy - Extra complete sets of chromosomes (e.g. 3n triploidy) - Found in some spontaneously aborted human foetuses Aneuploidy - Wrong number of chromosomes - Trisomy (2n + 1) is the presence of an extra copy of one specific chromosome o Other sex chromosome aneuploidies associated with viability are XXY (Klinefelter syndrome) and XYY o Most human autosomal trisomies are embryonic lethals but Ts13 (Patau), 18 (Edwards) and 21 (Down) survive in many cases - Monosomy (2n -1) the absence of one copy of a specific chromosome - Origins of aneuploidy most frequently lie in meiotic nondisjunction, during metaphase as separation occurs or caused by defect in spindle/ centromere. o There are no viable human monosomies except that of the X chromosome (X0 = turner) Q: It makes sense for there to be - Abnormalities and lethality associated with monosomy and trisomy suggest tight no dosage compensation for monosomy but why shouldn’t dosage control with no dosage compensation there be dosage compensation for trisomy? XO Turner Syndrome - Short, low hairline, wide neck due to fold of skin, infertile, brown spots (nevi) - Has undeveloped female characteristics XXY Kleinfelters - Has slightly feminized features such as female type pubic hair, breast development, poor bear growth, and small testes Down Syndrome - An extra chromosome 21 arises from translocations which can be transmitted from parent to child - Nondisjunction can happen during either mitosis or meiosis nd o First division nondisjunction: In the 2 division, one cell is empty and one cndl is full resulting in 2 (n+1) cells and 2 (n-1) or empty cells at the end o 2 Cell nondisjunction: will end up with 2 normal cells and a n+1 and n-1 cell. Nov 9/2011 – Lecture 8 1. Chromosomal structural aberrations Chromosome structure - Chromosomes are single dsDNA molecules - Rearrangements can occur when there are 2 or more double- stranded breaks - Acentric chromosomes: lacking centromere, it is lost and won’t be dragged to either pole at anaphase – it is not inherited - Dicentric : 2 centromeres, pulled in opposite directions and usually break. These chromosomes will be pulled to opposite poles, forming an anaphase bridge which will not be incorporated into either progeny cell Unbalanced rearrangement 1. Deletions - Unbalanced rearrangements changes gene dosage - Deletions can be within a gene (intragenic) or multigenic (many genes) - Can occur through loss or crossing over at repetitive sequences – where a piece loops out and is lost - Cause loss of heterozygosity Balanced Rearrangements 2. Duplications - Can be within the same chromosome or different chromosome, when a gene is duplicated. Q: What is the difference between - Can occur when 2 homologs break and rejoin incorrectly, giving a copy from one crossing over and breakage & homolog to another, creating a duplicate rejoin for duplications? (ref chart) - Or through crossing over, duplication can occur 1. Inversion - Genes change order but this doesn’t remove or duplicate DNA - Genes break and flip or loop and crossover at the incorrect and opposite ends. - 2. Reciprocal Traslocations - 2 non homologous chromosomes break and rejoin 3. Translocation - When another chromosome piece is relocated to your chromosome - When a breakage occurs and the broken strand join
More Less
Unlock Document

Only pages 1,2 and half of page 3 are available for preview. Some parts have been intentionally blurred.

Unlock Document
You're Reading a Preview

Unlock to view full version

Unlock Document

Log In


Join OneClass

Access over 10 million pages of study
documents for 1.3 million courses.

Sign up

Join to view


By registering, I agree to the Terms and Privacy Policies
Already have an account?
Just a few more details

So we can recommend you notes for your school.

Reset Password

Please enter below the email address you registered with and we will send you a link to reset your password.

Add your courses

Get notes from the top students in your class.