Genetics-mutations

Translesion DNA synthesis

(SOS repair) last ditch effort A translesion DNA Polymerase ---> relaxed base-pairing specificity ---> permits replication past damage

Metacentric

- centromere approximately in middle

Chiasmata

- visible manifestations of cross-over events At least one chiasma is usually essential for proper segregation of each pair.

Cancer

2 heritable properties 1. reproduce in defiance of normal restraints Cells divide at greater rate than wildtype 2. invade and colonize territories normally reserved for other cells Cells tend to displace other cells from their normal position and can invade other areas Cells in this state are said to be transformed Gone from wildtype to transformed state Most cancers derive from single abnormal cell that is able to outgrow its neighbors

DNA Repair

>130 genes have been identified in the human genome associated with DNA repair

Mutation

A change in the order of the bases in an organism's DNA; deletion, insertion, or substitution. only mutations in germ line can be inherited

Frameshift Mutation

A mutation occurring when the number of nucleotides inserted or deleted is not a multiple of three, resulting in the improper grouping of the following nucleotides into codons.

Silent Mutation

A mutation that changes a single nucleotide, but does not change the amino acid created.

Nonsense Mutation

A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.

Missense Mutation

A point mutation in which a codon that specifies an amino acid is mutated into a codon that specifies a different amino acid.

Fragile X syndrome is caused by A) trinucleotide repeats. B) free radicals. C) microdeletions. D) 5-Bromouracil. E) depurination.

A) trinucleotide repeats

Oncogene

Add to number of cells May promote cell cycle progression Inhibits apoptosis Positive regulators of the cell-cycle Inhibit programmed cell-death (apoptosis) Growth factors, transcription factors, signal transduction proteins Proto-oncogenes (c-onc) Virally transported (v-onc)

Indels

Addition or deletion of single base Can be deleterious if it occurs in AA acid sequence

During mutagenic treatment with nitrous acid, an adenine deaminates to form hypoxanthine, which bonds like guanine. The mutational event would be A) AT to CG B) AT to GC C) AT to TA D) GC to AT E) GC to TA

B) AT to GC

Trinucleotide repeat disorders are the result of A) a high rate of mutation throughout the genome. B) extensive duplication of a single codon. C) deviations from the genetic code in human mitochondria. D) tRNAs failing to recognize specific codons. E) transversions of the DNA bases in a coding sequence

B) Extensive duplication of a single codon

Transversion

Base substitution in which a purine replaces a pyrimidine or a pyrimidine replaces a purine

Beads on a string.

Bead = nucleosome String = intervening DNA 10nm in diameter

Mutation caused by acridine

Causes insertions or deletions

G1

Cell is actively growing Transcription, translation Preparing for next phase Enzymes, proteins

Forward mutation

Changes the wild-type phenotype to a mutant phenotype

Base analogs

Chemical Agents E.g., Bromodeoxyuridine and 2-aminopurine higher rate of tautomerization

DIAKINESIS

Condenses further

Cell Cycle

Cyclin CDK drives cell cycle

If an incorrect base is incorporated during DNA synthesis and is not corrected by DNA polymerase, it can be corrected by postreplication repair. This involves A) detection of the mismatch. B) a recognition of the methylation status of the DNA strands. C) a process similar to excision repair. D) All the above. E) None of the above.

D) All of the above

In E. coli a region of a gene with repeats of the sequence CTGG will be prone to A) reversion. B) missense mutation. C) nonsense mutation. D) frameshift mutation. E) amber mutation.

D) Frameshift mutation

S phase

DNA replication chromosome duplication

Mismatch Repair

Detect damage Incorrect base? Remove base Replace DNA

Nucleotide Excision Repair

Detect the damage Assemble the complex Remove the damage Replace DNA

In E. coli, mutation arising during repair is mostly by A) thymine dimer splitting. B) excision repair. C) mismatch repair. D) recombinational repair. E) SOS repair.

E) SOS repair

Photoreactivation (Photolyase)

Enzyme detects damage (thymine dimer) and is activated by light. Enzyme breaks the dimer bond and the DNA is repaired. Widespread in nature

Proofreader repair by DNA Polymerase

Error rate = 10-5 Proofreader improves it to 10-7

Molecules that react with DNA

Ethylmethanesulfonate Nitrosoguanidine

Medelian Inheritance

Examination of visible traits and how they are transmitted. 1st systematic, controlled approach to breeding- used common garden pea (many varieties available

Point mutation

Gene mutation involving changes in one or a few nucleotides

BRCA1

Genes associated with certain forms of breast cancer Tumor suppressor gene

Age and DNA repair

Goukassian et al. 2000 Increase in frequency of skin cancer with age Significant decrease in repair of thymine dimers Photolyase expression declines Significant decrease in levels of proteins associated with excision repair Repair mechanisms become less efficient with age

G2

Growth, active transcription One DNA molecule becomes Getting ready for last phase of cell cycle

Mutagen causing base changes from GC to AT(transition) only

Induced mutation- Romouracil

Prophase 1 (meiosis)

Leptotene, Zygotene, Pachytene, Diakenesis

Deamination

Loss of amino group Produces transitions if not at first detected and repaired Cytosine ---------> Uracil which binds with adenine. Detected and removed almost always CG to UA to TA Adenine ----------> Hypoxanthine which binds to cytosine. AT to GC base pair

A base change resulting in a codon specifying a different amino acid

Missense Mutation

M Phase

Mitosis/Meiosis and Cell division Produces two daughter cells

Tautomerization

Mutagen; alternative forms of a base (enol & imino) with different H bonding capabilities produces transitions if replicated twice it results in three wildtypes and one mutant

Induced Mutations

Mutations generated by exposure to certain environmental agents.

Repair of DS breaks

Non-homologous end-joining Causes deletion Homologous recombination Synthesis-dependent strand annealing Uses other chromosome to repair damage

A base change resulting in a stop codon

Nonsense Mutation

P and Q.

P is short arm Q is long arm

An enzyme that repairs thymine dimers in visible light in E. coli

Photolyase

A bacterium E. coli suffered ultraviolet irradiation. In the base-pair sequence shown below, note that the adjacent thymines formed a dimer. What are the requirements, the process, and the outcome of the repair by (a) photoreactivation and (b) general excision repair, if this damage were to be repaired?

Photoreactivation: enzyme detects thymine dimer and is activated by light, enzyme breaks dimer bond, and DNA is repaired General Excision: detect damage, complex created, remove damage, replace DNA

Trinucleotide repeat expansion disorders

PolyQ diseases (CAG ---> Gln) Huntington disease Spinocerebellar ataxia (certain types) Non PolyQ CGG repeat in Fragile-X syndrome

Ionizing radiation

Produces reactive oxygen species(molecules around DNA) that can damage DNA

Eukaryotic Chromosome

Prokaryotic DNA molecule - a near constant state of compaction. Eukaryotic chromosome undergoes periodic structural changes dispersed during interphase to condensed during nuclear division. Each chromosome is a single dsDNA(ds=double stranded) molecule

Spontaneous Mutation

Random change in the DNA arising from errors in replication Not Caused by mutagen Most are corrected by proofreader of DNA polymerase most that aren't corrected are transitions

A postreplication repair system most prone to error

Recombinational Repair

Nucleolar Organizer

Region of rRNA genes

Prophase

Replication and migration of centrioles - responsible for the organization of cytoplasmic microtubules into spindle fibers. Nuclear membrane disappears (pulled apart by microtubules) chromosomes condense through coiling nucleolus disappears Early phase-everything is condensing Late phase- no longer have nuclear envelope

Telophase

Reversal of events that occurred during Prophase.

Tumor Suppressor Gene

Roles complementary to oncogenes Negative regulators of the cell-cycle(inhibits progression of cell cycle) Promoting cell death

A base change resulting in a codon specifying the same amino acid

Silent Mutation

Anaphase

Sister chromatids separate (disjunction) and migrate to the poles after division of the centromeres chromatids are now chromosomes

Metaphase

Spindle apparatus becomes prominent Chromosomes migrate to the equatorial plane Migration due to binding of spindle fibers (microtubules) and other proteins to centromere and centriole.

Depurination

Spontaneous breaking the glycosidic bond connecting the base to the sugar(causes loss of purine) Apurinic site- ribose sugar that has lost purine Thousands of events per cell cycle Recognized quickly and repaired If it occurs right before DNA replication, a base is randomly incorporated Can produce transversions and translations

Heterochromatin

Stains darker Compacted DNA, less genetic activity In and around centromere and near telomeres

Euchromatin

Stains lighter, less compacted, more genetically active

DIPLOTENE

Synaptonemal complex dissociates Chiasmata(sections where crossing over occurs) appear as homologs begin to separate

The Ames test.

Take mouse liver cells and grind it up to release enzymes Mix with different strains of bacteria that are unable to make histadine If mutant histadine becomes wildtype then it is likely product causes mutations

Rare state of a normal base which may lead to mutation by its faulty base-pairing properties

Tautomere (enol)

Type of mutation in which a purine is substituted for a purine

Transition

Deamination of 5-methylcytosine,

Transition occurs Thymine not recognized as foreign so it is often not corrected

Type of mutation in which a pyrimidine is substituted for a purine

Transversion

p53

Tumor suppressor gene As many as 50% of human tumors are associated with p53 mutations A transcription regulator activated in response to DNA damage Stops cell cycle progression until damage is repaired in response to DNA damage Induces apoptosis What would happen if p53 was not functional

Genomes

Unique set of the DNA of an organism. Size (how many bases) Number of genes in genome (protein coding genes) Chromosome number Chromosome linkage Organelle genomes Mitochondrion - ~17Kbp in vertebrates Chloroplasts - >100Kbp

Homology Dependent Repair

Using the complementary strand to make the repair Nucleotide excision repair Removal and replacement Non-bulky damage

Nucleolus

around area with most transcription

Acrocentric-

centromere is closer to one end

Reverse mutation

changes a mutant phenotype back to the wild-type phenotype

ZYGOTENE

chromosomes SYNAPSE form homologous pairs

Ultraviolet radiation

cross links adjacent pyrimidines, mostly thymine. Creates chemical bond between adjacent pyrimidines on a single strand Consequences for DNA replication mutagenicity of UV light explains why sunlight can cause skin cancer.

Telomeres-

ends Every chromosome has 2

Nucleosome

histone proteins are combined with DNA into repeating subunits 2 each H2A, H2B, H3, H4 = histone octomer DNA wraps around octomer to produce nucleosome

Intercalating agents

mimic base pairs and cause insertions/deletions Insert themselves into the double helix usually ends up causing insertion or deletion

Wildtype

normal, most common phenotype

Slip Strand mispairing

occurs in short repeating sequences during DNA replication Newly synthesized strand may slip DNA polymerase doesn't recognize issue so one strand becomes longer than the other in the second DNA replication Results in addition of one base If template strand slips there will be a deletion, template strand and new synthesized strand becomes shorter by 2 bases

Transitions

purine to purine or pyrimidine to pyrimidine Appear to occur more often than transversions A<-->G T<-->C

Meiosis

reduce the number of chromsomes by half. 2N ----> N 2 separate division cycles (meiosis I and II)

LEPTOTENE -

single thread stage- allows homologous chromosomes to synapse

PACHYTENE

threads are fully synapsed CROSSING-OVER occurs - precise breakage, swapping, and reunion between non-sister chromatids

Histones-

ubiquitous in eukaryotes basic due to arginine and lysine positive charge allows them to bind with negatively charged DNA 5 histone proteins... H1, H2A, H2B, H3, H4

Telocentric-

very close to end but not at very end