Genetics Exam III Study Guide

Can mutations in sex cells be inherited?

Chapter 13—Mutation, DNA Repair, and Recombination 

∙ Point mutations vs. Frameshift mutations

o Point Mutation: Only affects one or very few nucleotides, typically changes  one nucleotide for another  

o Frameshift Mutation: Changes the “frame” in which the template strand is  read. Is caused by Indels (Insertions or deletions) of a pair of nucleotides o Therefore, the differences between the two are that point mutations only  affect one nucleotide and frameshift mutations affect more than one  

nucleotide and how the entire code is read.  

∙ Somatic vs. Germline mutations

o Somatic Mutations: Mutation in a non-germline cell that can be passed to  the progeny through cell division

What are some physical and chemical agents that cause mutations?

o Germline Mutations: Inherited genetic mutations in the sex cells

o Therefore, the primary difference between the two is the cells in which they  occur  Don't forget about the age old question of Explain torah's opinion about god.

∙ Spontaneous vs. Induced mutations

o Spontaneous: Occurs without a known cause  

o Induced: Mutation that occurs due to exposure to a chemical or physical  agent that causes changes in the structure of DNA  

∙ Transition vs. Transversion

o Transition: Changes a Purine to a Purine (A ???????? G) or a pyrimidine to a  pyrimidine (C????????T)

o Transversion: Changes a Purine to a Pyrimidine or vice versa  

Which system of testing would be best for testing chemicals as mutagens?

o Purine: Two ring nucleotide  

o Pyrimidine: One ring nucleotide

∙ Mutation via Base Analogs (e.g. 5-bromouracil)

o Inducible mutation

o Base analog: Unnatural purine or pyrimidine bases that differ slightly from  the normal bases and that can be incorporated into nucleic acids  We also discuss several other topics like Is a perfectly competitive market efficient?

o 5-Bromouracil

∙ A pyrimidine  

∙ Thymine analog

∙ Bromine at the 5th position is similar to the methyl (-CH3 ) group in  thymine We also discuss several other topics like What is tacit collusion in oligopoly?

∙ Changes the charge distribution and increases the frequency of  

tautomeric shifts  

∙ In stable Keto form in bonds with adenine

∙ After a tautomeric shift to its enol form it bonds with guanine

∙ In keto form, it causes a G:C ???? A: T transition Don't forget about the age old question of What is the configuration of an electron?

∙ In enol form it causes an A: T ???? G:C transition

∙ Mutations induced by radiation (e.g. thymine dimmers) and superoxides o Ionizing Radiation: X-Rays, gamma rays, and cosmic rays  

∙ High energy

∙ Used for medical diagnoses and penetrate living tissue through  

substantial distances

∙ Cause ionization measured in roentgen units  

∙ Can cause mutation

o Non-ionizing radiation: Ultraviolet light  

∙ Low energy

∙ Penetrate only surface cell

∙ Do not cause ionization but excitation or the movement of electrons in  outer orbitals to higher energy levels  

∙ More likely to cause mutation in single cellular organisms  

o Cells either ionized or excited are more chemically reactive than their normal  forms

o These mutations can cause cancer

∙ Ames Test

o Pages 346 – 348  

o Carcinogens: Mutagenic substances that induce cancer in living cells  o It essentially provides a simple and inexpensive method for detecting the  mutagenicity of chemicals  

o Step 1: Grow Salmonella his auxotroph’s carrying a frameshift mutation  o Step 2: Prepare a solution of the potential mutagen  If you want to learn more check out What is the meaning of respiratory epithelium in the respiratory system?

o Step 3: Spread bacteria on agar medium containing a trace of histidine (plates  skips steps 4 and 5 acting as the control)

o Step 4: Place a solution containing potential mutagen on filter paper disk  o Step 5: Place disk with potential mutagen in experimental plate We also discuss several other topics like What are the steps for a hypothesis test?

o Step 6: Incubate at 37degrees Celsius

∙ Repair Mechanisms (Pages 348-351)

o Light Dependent Repair

∙ Carried out by a light activated enzyme called DNA photolyase  o Excision Repair

∙ Step 1: DNA repair endonuclease or endonuclease-containing enzyme  complex recognizes, binds to, and excises the damaged base or bases  in DNA

∙ Step 2: DNA polymerase fills in the gap by using the undamaged  complementary strand of DNA as template  

∙ Step 3: DNA ligase seals the break left by DNA polymerase to  

complete the repair process  

∙ Base excision repair: Remove abnormal or chemically modified bases  from DNA

∙ Can be initiated by a group of enzymes call DNA glycosylases  

that recognize abnormal bases in DNA  

∙ They then cleave the glyosidic bond between the abnormal  

base and 2-Deoxyribose creating AP sites (apurinic or  

apyrimidinic)

∙ AP sites are recognized by endonucleases which act with  

phosphodiesterase to excise the sugar-phosphate groups at  

these sites

∙ DNA polymerase replaces the missing nucleotide per the  

specifications of the complementary strand  

∙ DNA ligase seals it  

∙ Nucleotide excision repair: Pathways remove larger defects like  thymine dimers  

∙ Excinuclease activity begins on either side of the damaged  nucleotide and excises an oligonucleotide containing the  

damaged bases

∙ In E. coli

o Figure shown on page 349

o Requires the product of uvrA, uvrB, and uvrC

o A trimeric protein (2 uvrA and 1 uvrB polypeptide)  

recognizes the defect damaged site and binds to it  

using ATP to bend the DNA at the site of damage.

o UvrA dimer is then released and the UvrC protein bind  

to the UvrB/DNA complex

o UvrC protein cleaves the 4th/5th phosphodiester linkage  

from the damaged 5’ side  

o DNA helicase II releases the excised dodecamer  

o DNA polymerase I fills the gap  

o DNA ligase seals the remaining nick in the DNA

o Mismatch Repair

∙ Repairs mismatched pairs after replication.

∙ Typically, with normal bases  

∙ Detected by identifying the template strand and the new strand  ∙ Based on Methylation process because there is a portion of time  where the template strand is methylated and the newly synthesized  strand is not.

∙ In E. Coli  

∙ Requires the products of mutH, mutS, and mutU (Also uvrD) ∙ MutS protein recognizes mismatches and binds to them to  initiate the repair process

∙ MutH and MutL proteins join the complex  

∙ MutH contains GATC-Specific endonuclease activity and  cleaves the unmethylated strand at the hemi methylated (half  methylated) GATC sites in either the 5’ or 3’

∙ If the incision occurs at the 5’ then a 5’???? 3’ exonuclease  activity (Exonuclease Vii) is needed  

∙ If the incision occurs at the 3’ the 3’????5’ Exonuclease activity  (Exonuclease I)

∙ After the mismatched nucleotide, has been removed from the  

unmethylated strand DNA polymerase III fills the gap and  

DNA ligase seals it.  

o Post replication Repair (E. coli)

∙ When DA polymerase III encounters a thymine dimers its progress is  stopped  

∙ DNA polymerase restarts DNA synthesis past the dimer leaving a gap  In the new strand

∙ Original nucleotide is lost from both strands of the new double helix  ∙ The damaged DNA molecule is repaired by recombination-dependent  repair  

∙ Regulated by recA  

o Stimulates exchange of single strands between

homologous double helices  

o RecA protein binds to a single strand of DNA at the  

gap and mediates it pairing with the homologous  

segment of the sister double helix

∙ Gap in sister Segment is filled by DNA polymerase and sealed  

by DNA ligase  

∙ Thymine dimer stays in template strand but the  

complementary strand is intact  

Chapter 14—Definitions of the Gene 

∙ Beadle and Tatum studies—determination of metabolic pathways through  auxotrophic mutation analysis

o Every gene codes for one and only one enzyme, had to be modified though  and turned into one gene one polypeptide  

∙ Complementation Test (cis/trans)

o Determine whether two mutations associated with a specific phenotype represent two different forms of the same gene (alleles) or are variations of  two different genes.  

o The complementation test is relevant for recessive traits (traits normally not  present in the phenotype due to masking by a dominant allele).

o In instances when two parent organisms each carry two mutant genes in a  homozygous recessive state, causing the recessive trait to be expressed, the  complementation test can determine whether the recessive trait will be  expressed in the next generation.

Chapter 19—Regulation of Gene Expression in Prokaryotes and Their Viruses ∙ General concept of an Operon—components and function (repressor, promoter,  operator, structural genes, inducer, co-repressor, etc.)

∙ Inducible Operon (Lac)

o Repression/Derepression (allolactose produced by Beta galactosidase (LacZ  product) as inducer)

o Catabolite Repression-glucose dependent, CAP-cAMP complex with  promoter

∙ Identifying plasmids with inserts through LacZ inactivation

∙ Repressible Operon (Trp)

o Polycistronic (Bunch of genes next to each other with only one promoter)  o Tryptophan product inhibits its expression

o Tryptophan operon  

▪ Tryptophan binds to the repressor  

Repressor/Tryptophan binds to operator and expression is turned OFF  ▪ Translation of a small peptide STOPS transcription unless Trp is not  available to complete the peptide.  

o Trp present  

o Trp absent  o http://www.youtube.com/watch?v=8aAYtMa3GFU&feature=related ∙ In Eukaryotes  

o Regulate gene expression by interacting with the promoter  

region  

o Activators and repressors  

o Influenced by external environment  

o Differential gene expression leads to cell specialization

o Temporal regulation

∙ ^ Different Hemoglobin’s based on developmental stages  

∙ Gene Duplication

o Duplication evens create new genes  

o Duplicated gene can evolve a new function  

o Duplication and gene divergence appear to be critical for the evolution of novel  traits  

o Duplication can happen because of recombination errors, DNA replication errors,  transposition, and viral integrations into the genome  

∙ Induction by Biological factors  

o Circulating molecules

▪ Hormones: Cell to cell communication  

∙ Steroids: Small and lipid soluble  

o Steroids can move through the cell membrane  

o Binds to response elements in the promoter region

o Induce transcription

∙ Peptides: Larger in size  

o Binds to cell membrane receptor  

o Activates signal cascade in the cytoplasm  

o Activates a transcription factor  

▪ Pathogens: Foreign antigens  

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Chapter 20—Regulation of Gene Expression in Eukaryotes 

∙ Temporal/Spatial control

o Different gene variants expressed at different times.

∙ Gene families

o Gene duplication creates a group of neighboring genes that take on different  functions (e.g. embryo, fetal and adult globin). Includes pseudogenes, which  are “dead” genes.

∙ Environmental Factors-hormones (steroids, juvenile hormone and honeybee  example)

o Honeybees  

▪ Juvenile Hormone: Transition to foraging influenced by level of  

steroidal hormone, produced by endocrine glands

▪ Social  

∙ When nurse honeybees do not encounter a satisfactory number  

of foragers they transition to foraging (Inhibited by the  

pheromone ethyl oleate which is transferred by foragers when  

they give food to the nurses  

∙

o Hormones - cell to cell communication

▪ Steroids - small and lipid soluble

∙ Steroids can move directly through the cell membrane.

∙ Steroid/receptor complex binds to hormone response elements  

in the promoter region.

∙ Induces transcription → mRNA processing → translation  

∙ *Moves into cell membrane*

▪ Peptides - larger in size  

∙ Hormone binds to a cell membrane receptor

∙ Activates a signal cascade in the cytoplasm

∙ Activates a transcription factor

∙ Induces transcription

∙ → mRNA processing → translation

∙ *Binds to cell membrane*  

o Pathogens

▪ Foreign antigens

∙ Mechanisms of control

o Pre-transcription (Gene amplification, gene dosage, DNA methylation) ∙ Gene dosage

∙ Histones – 100s of gene copies  

o Modification of histones (methylation and acetylation)  

influences DNA packing.

o Tightly packed DNA not expressed.

o Acetylation of histones results in loosening of the  

nucleosomes, which allows transcription to take place.

o Incorrect modifications of histones has recently been  

associated with cancer

o http://www.youtube.com/watch?v=eYrQ0EhVCYA 

o https://www.youtube.com/watch?v=9AfBsTAQ8zs 

∙ Gene amplification

∙ Gene amplification is an increase in the number of DNA  

templates for RNA synthesis.

∙ Example: In amphibian oocytes, the 5.8S, 18S, and 28S  

rRNA genes are amplified by the creation of  

extrachromosomal copies of the genes to allow increased gene  expression. The 5S rRNA genes are present in thousands of  

copies on the chromosomes (gene dosage).

∙ Usually occurs at Cs in consecutive CGs

∙ Methylation (addition of -CH3) in promoter region can prevent  transcription  

∙ Heritable transcription silencing- Imprinting

∙ Imprinted genes expressed in maternal OR paternal allele (Igf2  methylated during oogenesis)

o Transcriptional (transcription factors, response elements, enhancers)  ∙ Basal Transcription factors can bind to response elements in the  promoter region  

∙ Activate transcription

∙ Special Transcription Factors bind to enhancer region (ER) – several  hundred base pairs long (50-1500bp).

∙ Many hormone inducible genes

∙ ER interacts with promoter and assists RNA polymerase binding to  promoter.

∙ ER can be far from promoter

∙ ER can be inverted

∙ ER can be upstream or downstream from promoter (different  chromosome)

o Translational (mRNA stability, RNA interference)

∙ mRNA stability

∙ Poly A tail length

∙ 3’ untranslated region (3’UTR)

∙ RNA interference (RNAi).  

∙ Role in gene expression regulation as well as destroying viral  RNA.

∙ MicroRNAs (miRNAs)

∙ Short interfering RNAs (siRNAs)

o Post-Translational (Protein modification, phosphorylation) ∙ Polypeptide degradation

∙ Limited life

∙ Pre-version of protein that must be processed before it is active ∙ Pre-insulin

∙ Endopeptidases activate insulin

∙ Some transcription factors

∙ Phosphorylation

∙ Cleavage

∙ RNA interference in the lab

o Double stranded RNA synthesized in vitro (with RNA polymerization of both  DNA strands).

o Injected or transfected into cells

o One inside knocks out or knocks down gene expression.

o http://www.youtube.com/watch?v=H5udFjWDM3E&feature=related 

Chapter 22—Cancer 

∙ Definition and characteristics of a cancer cell

o Unregulated cell division

o Formation of masses in cell culture instead of a monolayer

o No stable bonding with neighboring cells (metastasis)

o Disorganized cytoskeleton

o Unusual cell surface proteins

o Frequently Aneuploid (abnormal chromosome #s)

o Frequent chromosome level abnormalities (e.g. deletions, duplications, and  translocations)

∙ Cell Cycle Control (checkpoints)/Cancer bypass

o Checkpoints between the different phases of the cell cycle (G1, S, G2 and  M).

o Control is complex—cyclins and cyclin-dependent kinases (CDKs) involved. o Cyclins

∙ Cyclins complex with CDKs enabling them to be active (regulate  

activity of other proteins through phosphorylation- addition of a  

phosphate group).

∙ Concentration of cyclins determines whether cell moves into different  stages of the cell cycle.

∙ When low, the cyclin detaches from the CDK, inhibiting the  

enzyme's kinase activity.

o Cells

∙ START checkpoint in G1 controlled by D-type cyclin and CDK4.

∙ If cyclin D/CDK4 complex is present—commit to S phase and cell  division

∙ If complex disrupted (by proteins that prevent complex forming) will  remain in G1.

∙ Reasons for remaining in G1:

∙ Low nutrient levels

∙ DNA damage -wait for repair (cancer cells do not wait for  

repair- high mutation rate)

∙ Cancer cells often have deregulated checkpoints via:

∙ Mutations in cyclin or CDK genes

∙ Mutations in genes encoding the proteins that respond to  

specific cyclin/CDK complexes

∙ Mutations in proteins that regulate complex formation

∙ Genetic observations—links to cancer

o Evidence for genetic basis:

∙ Clonally inherited—all descendent cells are cancerous.

∙ Viruses can induce cancers (viral genes involved in cancer  

production).

∙ Induced by agents known to cause mutations (can be identified with  the Ames test)

∙ Natural and synthetic- e.g. benzene, nitrosamines, aflatoxin

∙ Cancers tend to run in families (inherited).

∙ All cancers have their basis in genetic defects (either inherited or  acquired somatically during a person’s lifetime).

∙ DNA mutation in key genes

∙ Epigenetic switches that turn key genes on or off

∙

∙ Viruses and oncogenes (v-onc and c-onc)

o V-onc

∙ Rous sarcoma virus

∙ v-src is a kinase -results in host cell growing incessantly

∙ Advantage—to virus—host cell division

∙ Avian sarcoma virus 17

∙ v-jun is a transcription factor

∙ Simian sarcoma virus  

∙ s-src is a growth factor (PDGF)

∙ Avian erythroblastosis virus  

∙ v-erbB is a receptor for a growth factor (EGF receptor)

o C-onc

∙ v-onc usually have normal cellular oncogene homologues, c-onc  (proto-oncogene)

∙ DNA hybridization

∙ Viruses appear to have picked up cellular genes without introns. ∙ c-onc genes that were adjacent to the integrated virus

∙ v-onc gave the virus a selective advantage

∙ Two main types of genes involved (review examples of activities for each type): o proto-oncogene conversion to oncogene

∙ Proto-oncogenes—actively promote cell division

∙ Oncogenes overactive –rapid division

o tumor suppressor genes

∙ Repress cell division

∙ When they are defective they fail to repress cell division

∙ Knudson’s two hit hypotheses

o Must have two mutated alleles for the tumor suppressor genes for cancer to  develop