Genetics Final Exam Review (Old material)

What is the most significant nucleotide phosphate and why?

-Triphosphates are the most significant because: i.) they are precursor molecules for nucleic acid synthesis in the cell ii.) adenosine: and guanine triphosphates (ATP and GTP) are essential in cell bioenergetics

List the 3 types of post non-transcriptional processing. Once this occurs this allows what to move out into the cytosol? (pre-mRNA v. mature mRNA)

5' Capping -reaction replaces the triphosphate group at the 5' end of the RNA chain with nucleotide referred to as the 5' cap -5' cap of modified guanosine -helps with mRNA recognition by the ribosome during translation 3' polyadenylation -poly A tail, 100-200 adenines, added to 3' end -mRNA can no longer exist in the cytosol after the poly A tail is added Intron splicing -rejoin remaining RNA pieces -alternative splicing i.) mRNA exons can be spliced together in a different order to produce different base sequences -results in different proteins being translated -intron splicing does not occur in bacteria -the initial eukaryotic gene mRNA is called pre-mRNA, fully processed mRNA is called mature mRNA

What is the ideal phenotypic ration of the F2 generation in a dihybrid cross? What are the conditions that must occur for this ratio to exist?

9:3:3:1 phenotypic ration -pure breed parents crossed in p -heterozygous individuals crossed in F2

Know the 3 types of RNA pol and what they transcribe for

Pol 1 -transcribes all rRNA genes (nonstructural), except 5s rRNA Pol 2 -transcribes all structural genes -synthesizes all mRNAs Pol 3 -transcribes all tRNA genes (nonstructural) and 5s RNA

What part of the cell does transcription occur?

The nucleus

Between the interphase and mitosis, cells can enter a stage called G0, in which they are quiescent

True

DNA synthesis occurs during the S phase of the interphase stage

True

The transitions form one interphase stage to the other are controlled by cell cycle checkpoints

True

The interphase is characterized by the absence of visible chromosomes

True -chromosomes do not become visible until they condense in early prophase

Consider a monohybrid cross between two plants: one is tall and the other is short. You know that tall is the recessive trait and short is the dominant trait, and you see that half of the offspring is tall and half of the offspring is short. What are the genotypes of the parents?

Tt x tt

Epistasis and 6 modifications that can modify the 9:3:3:1 ratio

a. Epistasis: gene interaction, that results in altered phenotypic ratios i.) 6 ways epistasis could affect

What are the three essential components of nucleotides? How many nitrogenous bases are there? Which ones are associated with DNA/RNA?

a.) DNA is a nucleic acid b.) Building blocks of nucleic acids are nucleotides c.) Nucleotides have 3 essential components: i. Nitrogenous base -DNA: A, T, G, C -RNA: A, U, G, C ii. Pentose sugar iii. Phosphate group

What are the differences between gametes of dihybrid cross and unlinked and linked genes?

- A dihybrid of unliked genes will ungergo independent assortment; 4 differnt gamete combinations with equal frequency -A dihybrid of linked genes: no crossing over; the parental combinations (AB and ab, for example) will occur >50% of the time i.) non parental combinations (Ab and aB) will occur <50% of the time

What are Okazaki fragments and how are they combined after being synthesized? Know enzyme involved and what strand they are located on

- Short segments of newly synthesized DNA that are part of a lagging strand and is ligated to other Okazaki fragments to complete lagging strand synthesis -Okazaki fragments are combined via DNA ligase

Define Synteny

-All loci on one chromosome are synthetic regardless of their proximity or interactions in meiosis -Syntenic= on the same ribbon/chromosome

PCR amplification and dye terminator sequencing similarities and differences

-Amplification by PCR doubles the number of copies of the targeted DNA sequence each cycle i.)separation of variable number tandem repeat (VNTR) alleles after PCR amplification -Dye terminator DNA sequencing i.) DNA polymerase is used with fluorescent nucleotides to generate new DNA sequences that can be read by a laser and advanced imaging

Define base stacking, major and minor grooves, and identify the 3 forms of DNA and their properties

-Base stacking: the offspring of adjacent base pairs so that their planes are parallel i.) leads to twist in the double helix -Creates gaps among the sugar-phosphate backbones that partially expose the nucleotides-major and minor grooves i.) the major groove (12A wide) alternates with the minor groove (6A wide) ii.) these grooves are regions where DNA binding proteins can make direct contact with nucleotides -B-DNA: i.) Watson-Crick model, biologically significant conformation ii.) aqueous, low-salt conditions ii.) most common ad has a right-handed twist of the helix (like the A-form) -A-DNA: i.) high-salt or dehydration ii.) bases tilted in relation to the axis iii.) modified major/minor grooves iv.) mainly in vitro conditions v.) occasionally detected in cell and is common in bacteriophage -Z-DNA i.) left-handed double helix, zigzag conformation due to left-handed twist ii.) no major groove -commonly found near transcription start sites (Robert wells and colleagues, 1970)

Complementary Analysis: why is it important and what can it distinguish?

-Complementary analysis distinguishes mutations in the same gene from mutations of different genes -allows the following questions to be asked and answered: i.) do these organisms have mutations in the same or different genes? ii.) how many genes are responsible for the mutations observed? -when genes work in tandem to produce a single product, the process is called complementary gene interaction

What is the main cellular/biological event on which linkage map depends?

-Crossing over

A two-point linkage map is the most effective way to build genetic maps

-False -a 3-point linkage map is the most effective way

Be able to identify monohybrid patterns by Mendel for genotype and phenotype

-GG x gg (pure breeds) - all Gg (heterozygous) -Gg x Gg (heterozygous) - 3:1 phenotypic ratio, 1:2:1 genotype ratio

What is the difference between incomplete dominance and codominance? What are the phenotypic ratios for each case?

-Incomplete dominance/ partial dominance: when heterozygous individuals display intermediate phenotypes between wither homozygous type i.) neither trait is dominant ii.) ex: red and white parents = pink offspring iii.) 1:2:1 phenotypic and genotypic ratio -Codominance: leads to heterozygotes with a different phenotype than that of either homozygote i.) detectable expression of both alleles in the heterozygous ii.) more than one pattern of dominance may exist between different alleles of a gene, for example: AB or O blood type -Example: red and white parents = red and white stripped offspring -1:2:1 phenotypic and genotypic ratio

Know the differences between submetacentric, metacentric, telocentric and acrocentric chromosome and identify the following parts: P arm, Q arm, Centromere, Sister chromatids, telomeres

-Metacentric: middle -Submetacentric: between middle and close to the end -Acrocentric: close to the end -Telocentric chromosomes do not have p or q arms, just 'chromosome arm' -p arm: short arm -q arm: long arm -centromere: in the center

What is pleiotropy?

-Pleiotropy: is the alteration of multiple distinct traits by a mutation in a single gene -often seen in studies of development -Example: sickle cell disease -Ex: in drosophilia, the juvenile hormone influences numerous attributes of development and reduction such as body size, development time, and sexual maturity

Proceeding from the Chromosome Theory of Inheritance, which were the two main candidate molecules for the genetic material?

-Proteins vs nucleic acids -In the 1940's proteins were considered to be the genetic material, but it was later decided that nucleic acids are the carrier of genetic material and are found in the nucleus a.) The chromosomal theory of inheritance states that chromosomes are carriers of genetic material across generations b.) Chromosomes maintain genetic continuity through generations

What are the chemical structure differences between RNA and DNA?

-RNA contains a ribose (A&U, G&C) -DNA contains a deoxyribose (A&T, G&C)

What is needed to make the RNA polymerase holoenzyme?

-RNA polymerase core associates with the transcription initiation fact sigma to form RNA polymerase holoenzyme

What is RNA priming?

-RNA priming is a universal feature of initiation of DNA replication (prokaryotes and eukaryotes)

What are the differences between replicate, reciprocal, and test crosses?

-Replicate cross: producing hundreds of thousands of progeny by repeating each cross several times -Reciprocal cross: same genotypes are crossed but the sexes of the parents are reversed -Medel discovered that monohybrid crosses were NOT sex-dependent. Example: it did not matter whether a tall male plant pollinated a dwarf female plant or vice versa, the results were the same -Test Cross: crosses designed to determine the unknown genotype of an organism (usually between heterozygous or homozygous recessive)

Know the 2 bacterial promoter consensus sequences and the 2 forms of termination

-Sequences i.) Pribnow box or 10-consensus sequence 5'-TATAAT-3' ii.) -35 consensus sequence 5'-TTGACA-3' -Intrinsic termination i.) termination sequences include an inverted repeat, the repeats form into a short-stem-loop structure (hairpin) -Rho-dependent termination i.) requires a different termination sequence and the rho protein ii.) has rho utilization site (also called the rut site) -rho protein attaches to the rut site -protein then moves along the transcript to RNA polymerase -Catalyzes the release of RNA from RNA polymerase which releases the polymerase from DNA -Inverted repeats vs rut site i.) inverted repeats -followed by a string of adenines -results in a hairpin shape ii.)rut site -rho protein bind to mRNA at the rut site -protein moves towards 3' end, releases DNA from RNA polymerase

Know the difference between sex linked, sex limited, and sex influenced traits? Give a few examples of each

-Sex linked: refers to transmission of genes on sex chromosomes (X or Y linked) Example: fruit flies -Sex limited: occurs in cases where the expression of a specific phenotype in absolutely limited to one sex. Example: breast development is normally limited to females/beard growth is normally limited to males -Sex-Influenced: the sex on an individual influences the expression of a phenotype that is not limited to one sex or another. Example: body hair/muscle mass/ pattern baldness in humans (depends on hormonal construction of the individual) Ex: pattern baldness is caused by an autosomal gene (allele B behaves as dominant in males but recessive in females)

In nice the yellow alllele is lethal when homozygous and dominant to the agouti allele in heterozygotes. In a cross between two yellow mice, what will the phenotype of the offspring be?

1/3 AA agouti, 2/3 AA^Y yellow

C-gene system for coat color and temperature sensitive extremities. Calico cat, etc.

-The C gene (wild type) is responsible for coat color in mammals like cat, rabbits, and mice i.) produces an enzyme, tyrosine, which is active in production of melanin -CC or C (c^ch/c^h/c)= wild type, brown -c^ch = dilute phenotype "leaky", chinchilla: only some of the wildtype shown -c^h= produces Himalayan, temperature sensitive which results in color only on extremities (ears, tail, feet) enzyme loses catalytic function at high temps -c=full recessive null allele, produces no functional enzyme i.) produces albino phenotype in cc homozygotes

Define Linkage

-The proximity of two or more genes on a chromosome -The closer the markers... i.) the lower the probability that they will be separated during meiosis ii.) the greater the probability that they will be inherited together

What are the extensions of Mendelian inheritance?

-There may be more than two alleles for a given gene within a population -Dominance of one allele over another may not be complete -Two or more genes may affect a single trait -The expression of a trait may depend on the interaction of more than one gene and/or the interaction of genes with nongenetic factors (such as environment)

Review 3-point linkage mapping and how to determine parental, SCO, and DCO gametes and what the possible order could be. Be able to determine probability / gamete frequencies of each given m.u.

-Type the highest observed number of gametes=parental type (no crossing over occurs between the genes) -SCOs are the second most frequent, DCO's are the least frequent (because it requires both crossover events) -Steps to determine order 1.) determine the parentals and DCO type gametes 2.) compare parental and DCO to determine which gene is in the middle 3.) with the determined middle gene, perform SCO between the parentals (with the determined middle gene)

Define proband

-the first affected individual who brings a genetic disorder to attention -not necessarily the first affected one in the predigree

Know the steps of DNA replication in their correct order and know the basics for each step

1. unwinding and stabilizing of DNA double helix i.) DNA topoisomerase temporarily relaxes supercoiling and unwinds the helix ii.) helicase breaks hydrogen bonds between nitrogenous bases starting at the origin of replication-2 template strands iii.) single-stranded binding (SSB) protein prevent reannealing of separated strands 2. Initiation of DNA synthesis, synthesis of RNA primers i.) DNA primase synthesizes a short stretch of RNA primers onto existing DNA strands (this gives DNA polymerase the required platform to being copying a DNA strand) 3. Continuous DNA synthesis- leading strand i.) DNA pol 3 synthesizes daughter strands and elongates the strands by adding new complementary nucleotides to the 3' OH end of RNA primer ii.) being made in the same direction as the movement of the replication fork 4. Discontinuous DNA synthesis-lagging strand i.) DNA pol 3 extends the primer by adding new nucleotides; stops each time when it encounters the previously formed fragment 5. Proofreading and correction errors i.) DNA pol 1 removes the RNA primers with 5' to 3' exonuclease activity and replaces RNA nucleotides with DNA ii) DNA ligase joins DNA segments iii.) replication stops when it reaches termination sites (stop codon) iv.) DNA replication process is almost error-free with the help of 3' to 5' exonuclease activity of DNA polymerases (DNA pol 3 proofreads the nucleotides being added and if a nucleotide has been incorrectly added, it recognizes the error, removes the incorrect base, adds the correct nucleotide, and continues on)

During the G1 phase, the cell checks for DNA damages that might have occurred during mitosis

False -G2 phase of interphase checks for completeness of replication, DNA damage, and performs repairs

How many DNA molecules does a chromosome contain in G1, G2, and mitosis?

G1 stage: if a cell originally has 4 chromosomes there will be 4 DNA molecules G2 stage: if a cell originally has 4 chromosomes and replicates during S phase there will be 8 DNA molecules Mitosis: if a cell originally has 4 chromosomes there will be 4 DNA molecules

Know the three eukaryotic promoter sequences

GC-rich box -5'-GGGCGG-3' -Located at -90 position CAAT box -5'-CAAT-3' -Located at -80 position TATA box or Goldberg Hogness box -5'-TATAAA-3' -Located at -25 position

What is genetics?

Genetics is the science of heredity and the study of how traits and diseases are passed from generation to the next

Explain Medel's tow laws that were discussed in lecture (use examples)

Medel's First Law: Law of Segregation: -Mendel developed this using the law of particulate inheritance -This law states that in the separation into gametes, and the random union of gametes into progeny in predictable proportions Mendel's Second Law: -during gamete formation, the segregation of alleles at one gene is independent of the second gene as well as the other trait

Explain a monad, a dyad, and a tetrad? How many DNA molecules contain in each?

Monad: the monad form consists of a single chromatid, a single piece of DNA containing a centromere and telomeres at the ends Dyad: the dyad consists of 2 identical chromatids (sister chromatids) attached together at the centromere Tetrads: tetrads are the four chromatids that makeup paired homologs in the prophase of the first meiotic division. Present in meiosis 1, prophase 1

How many stages of prophase 1 are there? What happens in Pachynema and Diplonema?

There are 5 stages of prophase 1 1. Leptonema 2. Zygonema 3. Pachynema: where formation of tetrads occurs and crossing over begins; good for characterization and mapping 4. Diplonema: contribution of crossing over (tetrads ad chiasmata); non sister chromatids start to separate but chiasmata keep them still together -crossing over generates new combinations of parental genetic material, is a source of genetic variability, and corrects mutations 5. Diakinesis

Be able to identify patterns of inheritance from pedigrees we discussed in class

X-linked dominant -affected males (hemizygous): all affected daughters, no affected sons -affected female (heterozygous): 50% chance the son will be affected -Heterozygous female + unaffected male: sons and daughters will be equally affected -seen by 100% incidence of affected daughters from their affected father X linked recessive -more males than females are affected -affected males receive the allele from their mother -affected daughters can only come from both parents being affected -seen by 100% incidence of affected sons from an affected mother Y linked -Exclusively patrilineal (from father to son) Autosomal dominant -males and females have the trait in equal proportions -almost always appears in every generation -Individuals with the trait have at least one parent with it ..and if neither parent has it, none of the offspring will have the trait -if the trait is rare (<1%), individuals with the trait are most likely heterozygous -If only one parent has the trait : half of the offspring will have it -if both parents have the trait: some children may not have it (parents are more likely heterozygous) Autosomal recessive -males and females have the trait in equal proportions -trait is typically seen in siblings and can skip generations-pedigree looks bare -individuals with the trait are often from parents that do not show it (parents are heterozygous)... but if both parents have it all their offspring will have it -if trait is rare (<1%) and only 1 parent has it, child can only have it if other parent is heterozygous Cytoplasmic inheritance and mitochondrial disorders -cytoplasmic inheritance: the transmission of genes that occur outside the nucleus (in cytoplasmic organelles, such as mitochondria and chloroplasts) -Maternal inheritance pattern; ALL offspring are affected if mom is -Dads and daughters have different mitochondrial DNA since it is passed on from mom -Disorder must reflect a deficiency in the bioenergetic function of the organelle; there must be a specific mutation in mitochondrial DNA

DNA, RNA, mRNA definitions and structure differences between DNA and RNA

a.) Deoxyribonucleic acid: is the heredity material for all organisms i. DNA is double stranded (DNA double helix or duplex) ii. DNA replication is responsible for the replication of the DNA duplex prior to cell division b.) Ribonucleic Acid (RNA): Used by some viruses i. Ribose + A/U/G/C + phosphate group -mRNA undergoes translation to produce proteins at ribosomes

What are genes, chromosomes, and homologous pairs?

a.) Genes: the physical units of heredity b.) Chromosomes: long molecules of double-stranded DNA and protein which contain genes c.) Homologous pairs: may contain the same or different alleles of the same gene i. Made of maternal and paternal chromosomes ii. Appear in the metaphase 1 of meiosis 1 iii. Do not stick together d.) Sister chromatids i. made out of either maternal or paternal chromosomes e.) Alleles: alternate forms of the same gene i. homozygous: B/B or b/b ii. heterozygous B/b genetic variation: different alleles based on DNA. Example: Darwin finch beaks