Comprehensive Genetics Review
Purebred Cross
Both parents are "pure" (homozygous). TT x tt = All Tt = All Tall.
Eukaryotic DNA Packaging
eukaryotic DNA is linear and has 7 steps of being condense: Interphase/Chromatin 1)Naked DNA 2)Nucleosome 3)Solenoid 4)Loop M-Phase 5)Rosette 6)Coil 7)Chromatid
Semi-Dominant Lethality
ex. creeper chicken syndrome, familial hypercholesterolemia (FH) in humans L'L' = normal LL' = abnormal LL = lethal
Polydactyly
extra fingers or toes P___ = polydactylous condition pp = normal if 10 people have P___. only 5 will have penetrance of the gene of the 5 with penetrance, the expressivity will vary (some with 1 extra digit vs. some with 8 extra digits)
Following Many Meiotic Events
independent assortment of segregating unit factors 25% chance of each combo (in this particular cross)
Rough Endoplasmic Reticulum (ER)
Exported proteins are made on rough endoplasmic reticula (ER). Rough ER is smooth ER that is embedded with ribosomes (bound ribosomes)
38. List examples of external stimuli that can determine sex in Environmental Sex Determination. List the example of internal stimuli that can determine sex.
External: -light -moisture -temperature -chemical Internal: -hormonal
68. Is fruit fly red and white eye color a sex-linked trait? Is fruit fly normal and vestigial wing type a sex-linked trait?
Eye Color: sex-linked >If the genes are on x chromosomes (sex-linked), reciprocal crosses in the P generation will not give similar results (F1 and F2 ). >ex: drosophila eye color Wing Type: NOT sex-linked >If the genes are on autosomes, reciprocal crosses in the P generation will give similar results (F1 and F2 ). >ex: drosophila wing shape
22. What is a mutagen (aka a mutagenic agent)?
an environmental agent that is capable of inducing a mutation
CDC2 "moves your foot off the break"
analogy -an active complex is the motor running but your foot on the break -CDC2 pushes your foot off the break, allowing for full activation of the transcription factor
26. Describe the fates of the following nuclei in the embryo sac of the female part of a flower: antipodals, polar nuclei, synergids, egg.
antipodals (3): degenerates polar nuclei (2): 1 sperm unites with the two polar nuceli to form endosperm synergids (2): help the pollen nucleus reach the egg cell for fertilization then degenerate egg (1): 1 sperm unites with egg to form zygote/embryo
52. What happens to the graph as the number of additive genes (genes all interacting on the single trait) increases?
as the number of genes interactivity to influence trait increases ∝ the more perfect the curve is and the wider the curve
Centrioles
at the heart of the centrosomes in animal cells are tubelike structures. >Each one is formed from 9 rods >each rod consists of 3 microtubules fused along their length
80. How can recombinant DNA be taken up by a host cell?
before a recombinant DNA molecule can be introduced into a host cell, the host cell must be heat shocked prior to transfer
Tetrads
the paired chromosomes consisting of four chromatids In meiosis, homologous chromosomes pair with each other (i.e., they form tetrads) and crossing-over occurs. In mitosis, neither of these things occur. In metaphase I of meiosis, tetrads align on the metaphase plate. In metaphase of mitosis, individual chromosomes align there.
reaction norm
the pattern of phenotypic expression of a single genotype across a range of environments
1/2 ^n rule
the probability for a specific combination of alleles in one gamete type
Gene Regulation
the process of turning genes on and off ability of an organism to control which genes are transcribed in response to the environment
Phenotypic Ratio
the ratio of phenotypes produced by a cross
Probability
the ratio of the chances favoring an event to the total number of chances for and against the event >expressed as fraction (1/4), decimal (.25), or percentage (25%) >the proportion of times anything will happen out of total times it could happen (particular outcome/possible outcomes) >the probability of anything in a single case is equal to its frequency in the number of cases >the probability for anything with no alternative is 1 (100%) >the sum of all the probabilities of all possible alternatives will equal 1 (100%) (P1 + P2 + P3... = 1) >the probability of something not happening is 1 - the probability that it will: P(not a) = 1 - P(a) >never greater than 1 >known probabilities are not affected by past outcomes, luck, or the law of averages >conditional probabilities may be altered by accumulating data
Genotypic Ratio
the ratio of the genotypes that appear in offspring
44. Can DNA replication and transcription proceed if a pyrimidine dimer is formed?
both replication and transcription are blocked by such dimers (enzymes in these functions cannot cope with dimer structure)
Telomerase
enzyme that helps restore a portion of the telomere with each cell division
41. Cucumber and muskmelon will produce female flowers with exposure to what chemical? Hint: This chemical is also a gas given off by rotting or ripening fruit.
ethylene
46. In the Calvin Bridges model for sex determination in Drosophila melanogaster, how many autosomes are represented by the letter A? Understand how to represent male and female genotypes using this method with the 8 total chromosomes in the fruit fly.
"A" = a set of 3 autosomes >normal fertile female having 8 total chromosomes is designated as 2A2X >normal fertile male having 8 total chromosomes is designated as 2AXY. 2A3X- meta female (AAXXX) 3A3X or 2A2X-female (AAAXXX or AAXX) 4A3X or 3A2X- intersex (AAAAXXX or AAAXX) 2AX or 2AXY- male (AAX or AAXY) 3AXY- metamale (AAAX or AAAXY)
Filial Generation (F1)
"son" and "daughter" generation; the generation or generations after the parental generation
2^n rule (F1)
# of different F1 gametes
3^n rule
# of different F2 genotypes
2^n rule (F2)
# of different F2 phenotypes
4^n rule
# of different F2 progeny
2. Dominant Epistasis
(12:3:1), A epistatic to B,b ex: summer squash fruit color foxglove color 12 A _B_ , A_bb : 3 aaB_ : 1 aabb
3. Dominant and Recessive Epistasis
(13:3), A epistatic to B,b, and/or bb epistatic to A,a ex: chicken color 13 A _B_ , A_bb , aabb : 3 aaB__
5. Duplicate Dominant Epistasis
(15:1), A epistatic to B,b, and/or B epistatic to A,a. ex: shepherd's purse seed capsules 15 A _B_ , A_bb , aaB_ : 1 aabb
1. Recessive Epistasis
(9:3:4) aa epistatic to B,b ex: mice coat pattern and color Labrador retriever color 9 A_B_ : 3 A_bb: 4 aaB_, aabb
4. Duplicate Recessive Epistasis
(9:7), aa epistatic to B,b, and/or bb epistatic to A,a ex: daisy color or white and purple flower color 9 A _B_ : 7 A_bb , aaB_ , aabb
Nucleoli
(plural for nucleolus) form around genetic loci termed Nucleolar Organizing Regions (NORs)
23. Which nucleotides are the pyrimidines?
Cytosine (ONE hydrogenated N) Uracil (TWO hydrogenated Ns) Thymine (methyl group CH3) pyrimidine: single ring "you C.U.T. a piece of pie (py)"
Unbound Ribosomes
Cytosolic or organelle - destined proteins are made on free (unbound; not bound to ER) ribosomes. >Proteins destined for organelles are tagged and are targeted to specific organelles. Only free ribosomes are found in organelles
77. What enzyme forms the covalent linkage between the DNA fragment and the vector's DNA (such as a plasmid)? Hint: this enzyme forms the phophodiester bonds on the sugar phosphate backbone of DNA.
DNA Ligase
43. What enzyme in replication comes back and removes the RNA primer and replaces it with DNA?
DNA Polymerase I >remove and replace the RNA primer with complementary DNA base pairs (5' --> 3' direction) >the physiological function of Pol I is mainly to repair any damage with DNA, but it also serves to connect Okazaki fragments by deleting RNA primers and replacing the strand with DNA.
42. What enzyme primarily adds nucleotides to synthesize the new complementary strand of DNA from the original parent strand in DNA replication? What direction does this enzyme work?
DNA Polymerase III >DNA polymerase III requires a free 3' OH group for initiation of synthesis (purpose of RNA primer) >it can synthesize in only one direction by extending the 3' end of the preexisting nucleotide chain. >DNA polymerase III moves along the template strand in a 3'-5' direction, and the daughter strand is formed in a 5'-3' direction. >initiate DNA synthesis continously in the direction of replication (leading) and dis-continuosly in the opposite direction (lagging) >as well as 3' to 5' exonucleolytic editing of mispaired nucleotides.
DNA Packaging (Prokaryotes)
DNA in prokaryotes is circular and free floating 2 Rounds of Folding 1. Folded Chromosome- condenses 10x fold 2. Super Coiled- condenses another 10x fold (totals to 100 fold)
Nick
DNA is relaxed, available for expression
b. Gene (transcriptional control)
*Primary point of hormonal influence* >The presence of many identical or nearly identical genes in the haploid complement (gene reiteration) permits the corresponding transcripts to be made at a high rate -ex: Xenopus has about 900 ribosomal genes in each somatic cell >The extra-chromosomal replication of ribosomal genes (gene amplification) permits more rapid production of rRNA -ex: The Xenopus ribosomal gene complement is amplified 1000-fold in the oocyte >Specific genes can be activated for transcription. Gene activation is accompanied by changes in the macromolecular structure of the chromosome -ex: different tissues contain different populations of mRNAs -activation of genes on polytene chromosomes is accompanied by "puffing"
Dominant vs. Recessive Alleles
-A dominant allele is always expressed, even if only one copy is present -A recessive allele is only expresses if two copies are present (therefore no dominant allele present)
Gene Interaction
-Although genes may affect phenotypes differently, the expression of a gene will sometimes modify the expression of another gene. -Gene interaction pertains to relationships between alleles belonging to different gene pairs 2 genes --> 1 phenotype
Mitochondrial DNA Syndromes
-Kearns-Sayre Syndrome -Chronic Progressive External Ophthalmoplegia (CPEO) -Myoclonic Epilepsy with ragged-red fibers (MERRF)
Testcross
-To test for genotype (heterozygosity) of a dominant phenotype using a testcross parent (pp), typically described as against pp (homo rec) cross between an organism with an unknown genotype and an organism with a recessive phenotype
Gregor Mendel Pea Experiments
1856-1864, he conducted his garden pea experiments
99. How do you read the DNA sequence after performing the chain termination sequencing in a single tube (using fluorescent dyes)? Are the peaks the sequence of the original DNA strand or its complementary strand sequence?
-all added to one tube, to which are added all four ddNTPs -each ddNTP is labeled with a differently colored fluorescent dye -mixture loaded into one lane -gel is scanned with a laser to fluoresce the dyes, and the fluorescence pattern (series of colored peaks) -read by a sequence machine -each peak represents one deoxyribonucleotide in the sequence -original DNA sequence
Cell Cycle Regulation
-done by to classes of proteins 1) Cyclins 2) Cyclin-dependent kinases [CDKs (ex. CDC Kinase); phosphorylation activity], ex. CDC2 The above two classes of proteins combine to form a complex termed Maturation Promoting Factor (MPF) >these proteins function on a feedback system
Epistatic Gene Interaction
1) One distinct phenotype in each phenotypic classrather than two, although two separate genes are being considered >R/r and P/p in chicken combs 2) "Novel" or new phenotypes may appear in the F1 and/or F2 generations that had not appeared in the P generation >an Rrpp (rose) and rrPp (pea) cross can create rose, pea, walnut (R_P_), and single (rrpp) combs 3) Phenotypic ratio in F2 is altered from classical ratio (9:3:3:1) ex. 9:3:4 in recessive epistasis 12:3:1 in dominant epistasis 13:3 in dominant and recessive epistasis 9:7 in duplicate recessive epstasis 15:1 in duplicate dominant epistasis *note: genotypic ratio in F2 is same as classical ratio 4) "Masking" effect. Masking (non-allelic) is not the same as dominance (allelic).
80. What enzyme causes a tRNA to become "charged" or form a tRNA complex with an amino acid?
1 synthetase catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction: 1. charge the amino acid --> amino acyl-AMP 2. charge the tRNA --> amino acyl - tRNA complex
33. How long is 1 angstrom in centimeters?
1 Å = = 1 * 10^-8 cm
Chicken Comb-type Gene Interaction
1) Phenotypic ratio in F2 remains unaltered from classical ratio. (9:3:3:1) 2) One distinct phenotype (comb shape) in each phenotypic class-rather than two (pea color and shape), although two separate genes are being considered 3) The appearance of "novel" or new phenotypes in the F1 and/or F2 generations that had not appeared in the P generation (chicken only produces novel phenotypes)
Five Forms of Epistasis
1) Recessive 2) Dominant 3) Dominant and Recessive 4) Duplicate Recessive 5) Duplicate Dominant
Binary Fission
1) Replication of single molecule of DNA 2) Each copy attaches to a different area of the cell membrane 3) Replicated chromosomes are segregated into daughter cells following cytokinesis
Two Essential Requirements for Genes
1) it is inherited between generations in such a way that each descendant has a physical copy of this material 2) it provides information to its carriers in respect to structure, function, and other biological attributes
58. What are the four general steps of transcription (in prokaryotes)?
1. Binding- Holoenzyme (RNA Polymerase) binds to promoter site, as specified by sigma subunit and unwinds short stretch of DNA 2. Initiation- Sigma subunit released and transcription begins past promoter site. 3. Elongation- RNA polymerase synthsizes the mRNA strand 4. Termination- the mRNA transcript is finished and RNA polymerase is released from the DNA a) rho-independent b) rho-dependent
Cell Cycle Check Points
1. DNA damage and Size Check- most important (G1) 2. Incomplete DNA synthesis (S) 3. DNA Damage (G2) 4. Incomplete spindle formation (M) *cell cycle is arrested if it does not pass the check points*
88. What enzyme is responsible for the transfer of the amino acid in the P-site to the second amino acid in the A site via peptide bond formation? What is a by-product of peptide bond formation? (Hint: you drink it every day).
1. EF-Tu (elongation factor thermo unstable) binds to 2nd tRNA and facilitates its entry into the A site 2. Peptidyl Transferase catalyzes the peptide bond using GTP >the carboxyl terminus (C-terminus, back) of the 1st amino acid binds to the amino terminus (N-terminus, front) of the 2nd amino acid >forms peptide bond >water is the bi-product (H2O) 3. EF-G (elongation factor G, historically known as translocase) facilitates the translocation of the 2nd tRNA into the P site
36. What are the three general steps of DNA repair?
1. Excision of the defective nucleotide(s) from one strand of the duplex -Endonuclease -DNA Polymerase I 2. Replacement of the missing nucelotide(s) -DNA Polymerase I 3. Ligation of the newly inserted nucleotide(s) to the remainder of the strand -DNA Ligase (phosphoester bond)
Pedigree Analysis Importance
1. Practical applications of the Mendelian principles and the laws of probability are made by human geneticists and by animal breeders in analyzing pedigrees 2. In human genetics, pedigrees are important not only because man has a long generation time and few offspring, but also because, unlike experimental animals, his matings cannot be controlled by a geneticist. 3. Traits with a simple pattern of inheritance may sometimes be traced accurately enough to justify predictions concerning the likelihood of their expression in future children. 4. Examinations of family histories are an important approach in the field of genetic counseling.
28. What are the two main theories of sex determination?
1. Sex is dependent upon genes on the chromosomes. >autosomes >gonosomes (sex chromosomes) 2. Sex is dependent upon the environment (more primitive species) >External Stimuli - Ex. light, moisture, temperature, chemical. >Internal Stimuli - Ex. hormonal
2 Type of Epistasis Metabolic Pathways
1. Step Type > recessive and duplicate recessive 2. Simultaneous > duplicate dominant
97. Understand general protein structure.
1. The amino acid sequence (known as primary structure) ultimately determines the rest of the structure of the protein. 2. The characteristics of the particular sequence of amino acids determine secondary structure -Alpha helix -Beta-pleated sheets 3. Tertiary structure is the folding of these structures into a functional protein. 4. If several proteins combine to form a functional protein (such as hemoglobin) this is known as quaternary structure.
From Cross Results to --> Hypothesis
1. The geneticist must know how much the experimental data he has collected can deviate from his hypothesis and still be regarded as close to expectation. 2. Too much deviation would make the investigator question his hypothesis or discard it entirely. 3. Numerical data are his only means of evaluating ''goodness of fit'' of an experimental result as compared to expectations: use the Chi-Square
93. Which steps in translation require energy (aka GTP)?
1. initiation (w/ initiation factor 2) 2. codon recognition (w/ EF-Tu) 3. transloaction of the tRNA in the A site to the P site (w/ EF-G) 4. disassembly of the ribosome (w/ release factor 1, 2, or 3)
17. What three changes occur when a spermatid differentiates into a mature sperm?
1. loss of cytoplasm 2. addition of flagellum 3. addition of acrosome (all of these aid sperm, lots of traveling to do!)
Chi-Square Example Problem 1
1. observed ratio 2. hypothesis 3. proportion expected in each class 4. number expected in each class 5. observed number in each class 6. calculating chi-square 7. calculating degree of freedom 8. comparing in chi-square table 9. accept or reject hypothesis
Shotgun Approach
1. with the use of one of a variety of more than 100 commonly used restriction endonucleases on a genome, specific DNA fragments can be generated. 2. with the use of sanitation, a genomic library of fragmented genomic DNA can be constructed. the DNA fragments are then cloned, and clones from the genomic library are elected at random and individually sequenced. 3. with the use of computer software, a final base sequence of all the clones from the genomic library is obtained by searching for overlapping base sequences among the clones
Pedigree Analysis and Probability
10. In absence of data to indicate which individuals are carriers, probability becomes the best tool for determining likelihood of expression of a certain trait in a family. 11. It may be necessary to use estimates of the frequency of a gene in the general population. 12. Probability can be based on the family history, which may be recorded in a pedigree chart. (see figure in the next page.)
10. In what year did Watson and Crick publish their DNA structure?
1953- The Watson and Crick DNA Double Helix Evidence for helix (two polynucleotide strands coiled about each other in a spiral): 1) Nitrogenous Base Concentration data -Erwin Chargaff -[Thymine] = [Adenine] -[Cytosine] = [Guanine] 2) X-Ray Crystallographic data -Rosalind Franklin and Maurice Wilkins) -DNA was highly ordered, multiple stranded, and had repeating substructures every 3.4 Å (1 Å = 1 x 10-8 cm). ^^^the Watson & Crick DNA double helix was dependent on these two major pieces of evidence from other scientists
20. In what year did M. Schnös and R. B. Inman demonstrate bidirectional replication in bacteria?
1970 Experiments with transducing phage (lambda) indicate that the circular chromosome of Escherichia coli is replicated in both directions from a fixed origin. -Lambda is a medium size E. coli bacteriophage (virus). -Phage lambda DNA is a common substrate for restriction endonucleases and for generating DNA size marker fragments
23. Why does a pollen grain have two haploid nuclei? What is the purpose of each nuclei?
1n fuses with the polar nuceli to produce the endosperm (3n) 1n fuses with the egg to produce the zygote (2n)
54. How do you determine the number of genes that interact to control a particular quantitative trait (aka what is the formula used in quantitative traits)? What does the letter "n" represent in the formula? Do you set the formula to equal the number of genotypes or phenotypes present in the population in order to solve for "n"?
2n + 1 = the number of phenotypes in the population n = the number of gene pairs interacting to influence the trait/final phenotype if you want to find the number of genes per trait: (#phenotypes - 1)/2 = number of gene pairs
78. How many nucleotides are in a codon?
3 nucleotides 5' --> 3' direction
81. What makes up the initiation complex in translation in prokaryotes (be sure to mention initiation factors)?
30S (prokaryotic ribosomal small subunit) amino-acyl - tRNA complex initiation codon on mRNA (AUG) Initiation Factor Enzymes (IF1, IF2, IF3) (released prior to large subunit attachment and elongation) uses one molecule of GTP for energy
19. What is usually tritiated to track transcription? What is usually tritiated to track replication?
3H = Tritium, a radioactive material 3H-uridine (tritated-uridine) is used to track transcription 3H-deoxythymidine (3H-thymidine) (tritated-deoxythymidine) is used in tracking replication
96. Chain termination sequencing can use radioactive labeling with four different tubes and four different lanes on the gel OR it can be done using one tube and one lane on the electrophoretic gel. How is it possible to use only one tube and lane? What are the ddNTPs labeled with to make this possible?
4 Tubes, 4 Lanes DNA fragments are generated through restriction endonuclease digestion. Those fragments generated by different restriction enzymes are kept isolated from eachother. a. preparation of homogenous single strand of DNA b. label 5' end of ss DNA with 32P (radioactive label) c. divide DNA into 4 separate tubes d. cleavate of specific nucleotides in each one of the four tubes with either A, G, C, or T reagent (restriction endonuclease digestion) to generate short fragments used to sequence DNA e. sequential placement of DNA samples containg the fragments generated by A, G, C, or T digestion into wells at top (cathode end) of four separate adjacent lanes of gel -typical electrophoresis gel -each lane has ddGTP, ddATP, ddCTP, ddTTP -read the gel from bottom to top 1 Tube, 1 Lane -all added to one tube, to which are added all four ddNTPs -each ddNTP is labeled with a differently colored fluorescent dye -mixture loaded into one lane -gel is scanned with a laser to fluoresce the dyes, and the fluorescence pattern (series of colored peaks) -read by a sequence machine -each peak represents one deoxyribonucleotide in the sequence
How many chromosomes do humans have?
46 (23 pairs) in most cells. Gametes have half of this number (23).
8. What is the maximum percentage of crossing over between two genes (aka what is the maximum amount of recombination)?
49.9% (asymptotic curve above 20% recombination) never reaches 50% because then you'd be at Independent Assortment (no linkage, separate chromosomes) OR the genes would be on the very opposite tips of the chromosomes (telomeric) WHY? when the genes are further apart, a double crossover can occur -> reversion back to parental type: AB → AB → AB ab → ba → ab
Pedigree Analysis Recessive vs. Dominant
5. The first step in such an analysis is to determine whether the trait in question is behaving as a dominant or a recessive. 6. Recessive genes are difficult to keep track of because they may remain hidden by their dominant alleles generation after generation. 7. Carriers in the population usually cannot be identified until an expression occurs. 8. Recessives are expressed more frequently in families in which the father and mother are more closely related than they are in the general population. 9. Some phenotypes may behave as dominant in some families and recessive in others.
40. What is the purpose of single-strand binding proteins in DNA replication?
>Interacts with exposed unwound single polynucleotide strands to prevent reannealing and reformation of parent helix >stabilize the unwound region and allow strands separation to serve as template
79. If you have a polypeptide with 8 amino acids, what is the minimum number of nucleotides that coded for that protein?
8 amino acids 1 Start Codon (AUG: Met) + 7 Internal Codons + Stop Codon (UAA, UGA, UAG)= 9 total codons 9 codons * 3 nucleotides per codon = 27 nucelotides (at least) BUT sometimes Met is removed post-translation 10 codons * 3 nucleotides = 30 nucleotides MAX
2. Nucleosome
>146 basepairs of DNA are wrapped around a histone protein (an octamer of 8 separate proteins) >DNA + Histone => Nucleosome >110 angstroms
76. In order for a DNA fragment to be inserted into a specific vector, should both the DNA and the vector be cleaved with the same restriction endonuclease? Why or why not?
>A heterogenous group of DNA segments inserted into a plasmid (vector; ex. pUC18) using EcoRI (makes sticky ends) and DNA ligase. >A vector joined to a desired DNA fragment is a recombinant DNA molecule. >Plasmid and DNA fragment must be exposed to the same restriction enzyme. >the fragmented DNA and vector must be cleaved with the same restriction endonuclease so that they possess the same available sticky ends
Rules that Govern Probability
>Addition Rule - The probability that one of two or more more mutually exclusive events will occur is the sum of their separate probabilities. 1) Mutually exclusive events cannot occur together ex: parents having a baby chance of boy = 0.5 chance of girl = 0.5 chance of boy or girl = 1 = 0.5 + 0.5 >Product Rule - The probability that two or more independent events will occur together is the product of their separate probabilities. 1) Independent events can occur together ex: two parents both hetero for albino having a baby chance of being albino = 0.25 chance of being a girl = 0.5 chance of being an albino girl = 0.25*0.5 = 0.125
38. In DNA replication, what is the function of gyrase?
>An enzyme that induces catalyzes of the ATP-dependent negative super-coiling of DNA >DNA gyrase is a type II topoisomerase >Induces unwinding of the parent helix by introducing negative supercoils ahead of the replication fork
77. Where is the anticodon located? Where is the codon located?
>Anticodons (tRNA) are a set of 3 nucleotides that match in the 3'-->5' order >Codons (mRNA) are read in the 5' --> 3' order
Differences of Prokaryotes and Eukaryotes in Daughter Cell Production
>Binary Fission is exclusive to prokaryotes >whereas mitosis and meiosis are exclusive to eukaryotes
69. What specific molecule is added to the 5' end of eukaryotic pre-mRNA during posttranscriptional modification? What is added to the 3' end? Why do you think these additions are necessary for eukaryotic mRNA?
>Capping of 5' end (i.e., 7-methylquanosine) -The 5' cap is used as a recognition signal for ribosomes to bind to the mRNA. -protects the nascent mRNA from degradation >Addition of poly A tail to 3' end -a poly(A) tail of 150 or more adenine nucleotides is added -plays a role in the stability of the mRNA -protects the mRNA from degradation -aids in the export of the mature mRNA to the cytoplasm -involved in binding proteins involved in initiating translation.
93. Describe the restriction mapping technique. What kinds of enzymes are used? How many tubes will you need? Why?
>DNA sequencing can be accomplished through restriction mapping by multiple or partial endonuclease digestion >Types of Enzymes Used: -EcoRI -HindIII -Bg1II -BstEII -EcoRV (restriction enzyme aka endonuclease) >Restriction maps are created by analyzing the number and length of the DNA fragments produced and piecing them together to construct a complete model >DNA fragments are separated by electrophoresis and mapping by partial endonuclease digestion specifically involves with use of a 32P radioactive marker 1. The first step following the completion of electrophoresis is to add up the sizes of the fragments in each lane. 2. The sum of the individual fragments should equal the size of the original fragment, and each digest's fragments should also sum up to be the same size as each other. # of test tubes = 2n + 1 n= number of enzymes being used ex. 3 enzymes being tested (Bg1II, BstEII, EcoRV) = 2(3)+1 = 7 test tubes Why? you want to test each enzyme individually and in combination with another enzyme + 1 for the marker lane (Lambda x HindIII) (not sure if +1 is all restricting mapping or just some?)
2. Simultaneous Metabolic Pathway
>Duplicate Dominant (15:1)-1 conversion and 2 metabolites (phenotypes)-precursor and final product are different, with no intermediate
8. What organisms did Hershey and Chase use?
>Escherichia coli (also known as E. coli) [seen in yellow] >T2 phage, a bacteriophage (a type of virus) [seen in green]
68. In a Chi-Square goodness of fit test evaluating Hardy-Weinberg Equilibrium/Law (aka that the allele frequencies do not change over the generations) what is the null hypothesis and the alternative hypothesis? What degree of freedom will you use in this particular test? What is the Chi-Square value in the table at that degree of freedom and at P=0.05?
>If x2 < x2 at 0.05 (3.841) with 1 df, then accept Ho (null hypothesis) Null Hypothesis: genotypic and allelic frequencies are in equilibrium # < 3.841 otherwise, reject Ho. accept Ha (alternative hypothesis) Alternative Hypothesis: genotypic and allelic frequencies are NOT in equilibrium # > 3.841
69. If your calculated Chi-Square value is less than the table Chi-Square value, will you accept or reject the null hypothesis? If you accept the null hypothesis, what does that indicate in terms of Hardy-Weinberg Equilibrium/Law?
>If x2 < x2 at 0.05 (3.841) with 1 df, then accept Ho (null hypothesis) if it is LESS than 3.841 you ACCEPT the null hypothesis (genotypic and allelic frequencies are in equilibrium) This means that the population IS IN Hardy-Weinberg equilibrium: - Use when dominance is complete and when there are two phenotypes and three genotypes. -This law states that in large populations, there are the following conditions: A. Frequency of one or two alleles is equal to p^2 B. Frequency of the other alleles is equal to q^2 C. Sum of frequency p + q = 1. D. Mating is random
Pleiotropism
>Many genes (probably most) don't have a single effect and a single function.
Probability: Binomial Expansion
>Many problems in genetics concern not only the probability that a certain event will occur, but also the probability that a certain combination of events will occur. >By expanding the binomial (a + b)^n, we can obtain the chance of various combinations of two independent events happening together. >''a'' = the chance of one event >''b'' = the chance of the alternative event >''n'' = the total number of events being considered. >a = chance for a girl being born = 1/2 >b = chance for a boy being born = 1/2 Assume you want to know the chance of obtaining three girls and a boy. Total number of children is four: so: n = 4 ; (a + b)^4 a^4 + 4a^3b + 6a^2b^2 + 4ab^3 + b^4 coefficient = total # of possible orders of that combo (gggb, gbgg, bggg, etc.) next coefficient = (previous coefficient * a's exponent)/that previous coefficient's position Pick The Term Representing the Combo You Want (3g/1b): The second term (4a^3b) is the one representing three girls and a boy; so by substituting for ''a'' and ''b'' we get: 4 x (1/2)3 x 1/2 = 4/16
13. Describe the Meselson and Stahl experiment proving semiconservative replication including what organism did they use?
>Meselson-Stahl Experiment -supported Watson and Crick's hypothesis that DNA replication was semiconservative (parent strand + daughter strand) -Meselson and Stahl decided the best way to tag the parent DNA would be to change one of the atoms in the parent DNA molecule. -Since nitrogen is found in the nitrogenous bases of each nucleotide, they decided to use an isotope of nitrogen (14N DNA -> 15N DNA) to distinguish between parent and newly copied DNA. -The isotope of nitrogen had an extra neutron in the nucleus, which made it heavier -DNA was extracted periodically and was compared to pure 14N DNA and 15N DNA. After one replication, the DNA was found to have intermediate density. -Semiconservative replication would result in double-stranded DNA with one strand of 15N DNA (parent), and one of 14N DNA (daughter) E. Coli was used in this experiment; the progress of cell division was monitored by microscopic cell counts and by colony assay (so they knew how often E.coli divided)
Polygene
>No complex trait is likely to be produced by a single gene >There is really no one gene for any complex feature >Products (enzymes) from different genes can act on common metabolic or biosynthetic pathways. >When one gene appears to control the properties of a particular trait, it is because the enzyme encoded by that gene acts as the rate-limiting step in a particular pathway
24. One of the two nuclei in the pollen grain divides again to produce two male gametes. What nuclei do each of these two male gametes unite with in the female embryo sac?
>Once a pollen grain lands on the stigma, it will start to germinate (grow) down the style until it reaches the ovary. >When the tube nucleus enters the ovule it will degenerate the synergid nuclei. The antipodal nuclei will break down as well. >One of the nuclei in the pollen grain will go through mitosis again (duplicate). This results in 2 sperm nuclei. >One sperm fertilizes the egg cell--> form a diploid zygote >the other sperm combines with the two polar nuclei of the large central cell of the megagametophyte --> forms a triploid nucleus >The large cell of the gametophyte will then develop into the endosperm, a nutrient-rich tissue which provides nourishment to the developing embryo.
Protein Oscillation Levels
>Oscillations in the level of the protein cyclin were identified in sea urchin eggs, >Cylin rose during interphase and fell during mitosis. >The discovery that cyclin was the only protein that fluctuated during the cell cycle suggested that it might help control the onset of mitosis. >Cyclin is indeed a regulator: it influences the activity of the cdc2 protein (seen on the dotted line), which together with cyclin guides cells into mitosis
Deciding the Genotype of Parents
>Parents: Same phenotype x same phenotype >Progeny: Contrasting phenotype >Based on the above information, you know . . . 1. The phenotype of the parents is dependent upon the dominant gene, and they are heterozygous. 2. The phenotype of the progeny is dependent upon the recessive gene, and the progeny is homozygous recessive. >If the parents are heterozygous and the phenotype of the progeny is dependent upon the dominant gene, the probability that the progeny is homozygous is 1/3 and the probability that the progeny is heterozygous is 2/3.
c. RNA (post-transcriptional control)
>Primary transcripts may require processing to produce active cytoplasmic RNA species -ex: Ribosomal RNA gene transcripts are cleaved to yield rRNA molecules for ribosome assembly >mRNA must be transported from the nucleus to the cytoplasm -ex: The drug cordycepin blocks appearance of new mRNA in the cytoplasm, probably by blocking the synthesis of poly-A terminal required for transport >RNA degradation takes place in both the nucleus and in the cytoplasm -ex: hemoglobin mRNA has a half life of 100 days; whereas the average HeLa cell mRNA has a half life of 2-3 hours >mRNA in the cytoplasm may be "masked" in an inactive form. mRNA must attach to ribosomes for initiation of polypeptide sythesis -ex: maternal mRNA in eggs remain inactive until after fertilization. a variety of initiation factors are involved in attachments of mRNA and initiation of polypeptide synthesis >Translation on polyribosomes may occur at varying rates -ex: the alpha and beta chains of hemoglobin appear to be translated at different rates
41. What enzyme lays down the RNA primer? What is the importance of the primer?
>Primase is an enzyme that binds to the single strand and synthesizes short RNA sequences called primers that are complimentary to the DNA. >Primers serve as a starting point for DNA synthesis -the purpose of primers is to provide a "free" 3'-OH group to which the DNA polymerase III can add dNTPs.
68. What else happens to eukaryotic mRNA (other than splicing) before it is transported to the cytoplasm?
>RNA splicing - removal of non-coding intron (intervening) sequences, between coding exon (expressed) sequences. >Capping of 5' end (i.e., 7-methylquanosine) >Addition of poly A tail to 3' end of pre-mRNA. >pre-mRNA must associate with proteins to get out of the nucleus and into the cytoplasm.
1. Step-Type Metabolic Pathway
>Recessive (9:3:4)-2 conversions and 3 metabolites (phenotypes)-precursor, intermediate, and final product are different. -you first need at least one dom A to get to step 2 (intermediate phenotype) -you next need both dom A and dom B to get to step 3 (final phenotype) >Duplicate Recessive (9:7)-2 conversions and 3 metabolites (phenotypes)-precursor and intermediate are the same, but final product different. -you first need at least one dom A to get to step 2 (even though it is the same phenotype as step one aaB_/aabb) -you next need both dom A and dom B to get to step 3 (final phenotype)
P-Value
>The P value represents the probability that a deviation as great as or greater than that obtained from the experiment will occur by chance alone. >If the P value is small, it is concluded that the deviations are not due entirely to chance, and the hypothesis is rejected. >The null hypothesis (Ho) is rejected, so choose the alternative (H1) hypothesis. > P < .05 >If the P is greater than the predetermined level, the hypothesis is accepted. The null hypothesis (Ho) is accepted. > P > .05
Chi-Square (X^2)
>The chi-square test is a valuable tool that aids the investigator in determining goodness of fit >The test takes into account the size of the sample and the deviations from the expected ratio >It can also be adapted to ratios with different numbers of classes. >The chi-square test is a mechanism by which deviations can be reduced to a single value based on the size of the sample
Degrees of Freedom
>The effect of the number of classes is included in the mathematical concept as degrees of freedom >The number of the degrees of freedom is one less than the number of classes: n-1 ex: 1:1 ratio; 2 numbers in ratio (n=2), 2-1 = 1 = df 9:3:3:1 ratio, 4 numbers in ratio (n=4), 4-1= 3 = df
Chi-Square Table
>When X^2 and the degrees of freedom have been determined, the chi-square table may be consulted for the probability (P) value. >A hypothesis is never proved or disproved solely by a P value but it can indicate that it is unlikely to be true >Results of an experiment are evaluated by the investigator as acceptable or unacceptable with respect to the hypothesis. >The 5 percent point (0.05) on the table is usually chosen as an arbitrary standard for determining the goodness of fit. >Probability at this point is one in twenty that a true hypothesis will be rejected
Probability: Factorials
>When the probability of only a certain combination in a given size group is required, factorials may be employed. >There are products of factors derived from functions by successfully increasing or decreasing by a constant, usually one >Factorial 4 (4!) is the product of 4 x 3 x 2 x l or (4! = 4 x 3 x 2 x l = 24). Factorial 0 (0!) = l and 1! = 0! >The probability of a particular combination may be calculated from the following formula: P = [n!/ x! (n - x)!] * p^x q^(n-x) n = total size of group x = Number in one class (p) n - x = Number in one class (q)
Microtubules
>a hollow fiber made of subunits that contain an alpha- and a beta-tubulin protein. >The cytoplasmic microtubules organized by the centrosome seem to grow out of the pericentriolar material and not directly from the centrioles themselves.
p53 gene
>a tumor-suppressor gene >The p53 protein product functions during the regulation of apoptosis at the G1/S checkpoint in the cell cycle.
69. How can you distinguish a male fruit fly from a female fruit fly?
>males have sex combs >dark abdomen >usually relatively smaller
6. Coil
>one coil is equivalent to 30 rosettes
5. Rosette
>one rosette is equivalent to 6 loops
d. Protein (post-translational control)
>proteins may be storied in vesicles and secreted when required -ex: potentially destructive hydrolytic enzymes are often stored in lysozomes until needed >Proteins may require modification of their covalent structure for activation -ex: proinsulin must be cleaved to form active insulin; proline residues in procollagen must be hydroxylated and partially glycosylated to allow secretion and proper assembly of collagen fibers >Proteins are degraded at different rates -ex: antibodies of one class (IgG) half a half life in the serum of 25 days; whereas antibodies of another class (IgE) have a half life of 2 days
a. Chromosome
>specific chromosomes of chromosomal regions are inactivated by condensation to hetero-chromatin during development >specific chromosomal regions may be activated by translocation -ex: the inactive X chromosome in female mammalian cells is heterochromatic >Specific chromosomes or chromosomal material may be lost during development -ex: genes for the variables and constant regions of antibody molecules may be joined by translocation before they are activated -ex: the somatic cells of Ascaris lack certain chromosomes
97. Why is only a small amount of ddNTPs added to the chain termination sequencing reaction? Describe the competitive exclusion process.
>the higher the concentration of the ddNTP in the reaction, the shorter the products will be, hence, you will get sequence CLOSER to your primer. >With lower concentrations of ddNTP, chain termination will be less likely, and you will get longer products (sequence further AWAY from the primer). >you want the resulting newly synthesized DNA chains will be a mixture of lengths< competitive exclusion: states that two species that compete for the exact same resources cannot stably coexist. -ddNTP wants to attach
4. Loop
>the solenoids are further coiled into looped domains >50,000,000 base pairs
7. Chromatid
>two chromatids (2 chromatids x 10 coils per chromatid) = 20 coils
13. Be able to place genes in order on a chromosome based on the number of testcross progeny. For instance, take genes A, B, and D. Perform two-factor crosses first involving genes A and B, then with genes B and D, and finally A and D. Examine the percentage cross-overs and determine the map unit distances between the genes.
A and D has 10% recombination, 10MU apart B and D has 10% recombination, 10 MU apart if A is 10MU from D and B is 10MU from D then A and B must be 20MU apart
61. List the formulas for determining genotypic frequencies and allelic frequencies.
A and a (allelic frequency) p= frequency of A Fr (A) = p = [2*(#AA) + (#Aa)]/2N q= frequency of a Fr (a) = q = [2*(#aa) + (#Aa)]/ 2N Sum of frequency p + q = 1 Offspring of three genotypes in a definite ratio will be in equilibrium in the next generation in the frequency of: p^2 + 2pq + q^2 = 1 p^2 = # of homozygous dominant individuals (AA) 2pq = # of heterozygous individuals (Aa) q^2 = # of homozygous recessive individuals (aa)
88. What kind of liquid needs to be pored over (and submerges) the gel during gel electrophoresis?
A buffer solution (more precisely, pH buffer or hydrogen ion buffer) is an aqueous solution consisting of a mixture of a weak acid and its conjugate base, or vice versa. >Its pH changes very little when a small amount of strong acid or base is added to it.
Combinations
A combination is a group of objects in which the order is not important. Formula: nCr = N! / [(N-R)! R!] N = number of items R = the number of objects to be combined in which the order is not important
monohybrid cross
A cross between individuals that involves one pair of contrasting traits
monohybrid cross
A cross between individuals that involves one pair of contrasting traits a 1:1 phenotypic ratio
34. Please describe what happens in deletions and insertions.
A deletion or insertion can be of any size. However, deletions or insertions involving one base pair are point mutations. These alterations may radically alter protein function, and may be considered frame shift mutations. Most large DNA insertions will stop gene expression
64. What is a Free Martin in cattle?
A freemartin or free-martin (sometimes martin heifer) is an infertile female mammal with masculinized behavior and non-functioning ovaries. >Genetically the animal is chimeric: Karyotyping of a sample of cells shows XX/XY chromosomes. The animal originates as a female (XX), but acquires the male (XY) component in utero by exchange of some cellular material from a male twin >Externally, the animal appears female, but various aspects of female reproductive development are altered due to acquisition of anti-Müllerian hormone from the male twin
Complex Trait
A genetic trait whose pattern of inheritance cannot be predicted by Mendel's laws of inheritance.
78. What is the polylinker region on a plasmid vector?
A multiple cloning site (MCS, or Polylinker region) is a DNA region within a Plasmid that contains multiple unique Restriction enzyme cut sites. >Plasmids are very useful in biotechnology and one key feature of their use is the multiple cloning site, which allows for foreign DNA to be inserted into the plasmid.
trihybrid cross
a cross involving three traits a 1:1:1:1:1:1:1:1
92. What are polysomes?
A polyribosome is a group of ribosomes bound to an mRNA molecule like "beads" on a "thread". I >t consists of a complex of an mRNA molecule and two or more ribosomes that act to translate mRNA instructions into polypeptides
86. What is Real Time PCR?
A real-time polymerase chain reaction, also known as quantitative Polymerase Chain Reaction, is a laboratory technique of molecular biology based on the polymerase chain reaction. >It monitors the amplification of a targeted DNA molecule during the PCR, not at its end, as in conventional PCR.
Transcription Factors
A regulatory protein that binds to DNA and affects transcription of specific genes.
Centrosome
A structure in animal cells containing centrioles from which the spindle fibers develop. >surrounded by starlike webs of protein filaments are the master architects of cell division. >composed of 2 centrioles
36. What is theta replication?
A theta structure is an intermediate structure formed during the replication of a circular (bacterial) DNA molecule. >Two replication forks can proceed independently (bidirectionally) around the DNA ring point of origin >when viewed from above the structure resembles the Greek letter "theta" (θ).
Epistasis
A type of gene interaction in which one gene alters the phenotypic effects of another gene that is independently inherited
Epistasis
A type of gene interaction in which one gene alters the phenotypic effects of another gene that is independently inherited.
79. Define the term "recombinant DNA."
A vector is a carrier DNA molecule that carries the DNA fragment of interest into the host cell, and when a vector is joined to a DNA fragment, the unit is referred to as a "recombinant DNA molecule"
39. How is depurination damage repaired (recall the three general steps of DNA repair)? Note the specific enzymes involved in each of the repair steps.
A. Excision of depurinated sugar by repair endonuclease B. Insertion of missing nucleotide by DNA polymerase I C. Phosphoester bind formation by DNA ligase
67. Understand how to calculate the expected numbers of individuals of each genotype in the current population using the formerly known allele frequencies and the current population size.
AA = p^2 #AA = p^2(N) Aa = 2pq #Aa = 2pq(N) aa = q^2 #aa = q^2(N)
84. What is the codon for methionine (aka the start codon for translation)?
AUG
7. Who definitively proved in 1952 that DNA was the transforming material?
Alfred Hershey and Martha Chase provided final confirmation that DNA is the "transforming principle"
Gene Interaction
Although genes may affect phenotypes differently, the expression of a gene will sometimes modify the expression of another non-allelic gene ex: comb type in chicken, summer squash shape
Permutations
An arrangement of objects in which the order is important Formula: nCr = N! / [(N-R)!] N = number of items R = the number of objects to be arranged in a specific order
Heterozygous
An organism that has two different alleles for a trait
Homozygous
An organism that has two identical alleles for a trait
45. What sex are parthenogens in birds? What sex are mammalian parthenogens?
Bird Parthenogens: Male (homogametic sex) Mammalian Parthenogens: Female (homogametic sex)
Phenotype
An organism's physical appearance, or visible traits.
49. Define Aneuploid, Euploid, and Polyploid.
Aneuploid: Having an abnormal number of chromosomes -usually the addition or loss of one or two chromosomes -Not having a number that is a multiple of the haploid. >Autosomal ex. Trisomy 21 (Down's Syndrome) >Sex Chromosomal ex. Turner's and Klinefelter's Syndromes. Euploid: Having a chromosome number that is an exact multiple of the haploid number Polyploid: Having more that two homologous sets of chromosomes (more that 2N; ex. 3N, 4N, etc.)
29. What is meant by antiparallelism when talking about DNA structure?
Antiparallel: A term applied to two molecules that are side by side but run in opposite directions. The two strands of DNA are antiparallel. The head of one strand is always laid against the tail of the other strand of DNA. 5' end of the DNA: terminal phosphate group on the 5' carbon of the deoxyribose 3' end of DNA: terminal hydroxyl (OH) group on the 3' carbon of the deoxyribose 5' -------------------------> 3' 3' <------------------------- 5' Why? anti-parallelism allows for proper hydrogen bonding to occur
51. Is mRNA transcribed from the sense (coding) or the antisense (template) strand of DNA? Which direction (5'-3' or 3'-5') does each of these strands run?
Antisense/Template Strand -mRNA is transcribed from the (antisense) template strand -the template strand is read 3' ------> 5' -mRNA is synthesized 5' ------> 3' Sense/Coding Strand -hangs loose -has same sequence as mRNA transcript (except T not U) 5' ------------------- 3' sense/coding strand 3' ------------------- 5' antisense/template strand 5' ------------------- 3' mRNA transcript
Autosomes
Any chromosome that is not a sex chromosome
14. As the distance between two genes increases, there is a tendency for the percent cross over to increase or decrease (circle one).
As the distance between two genes increases, there is a tendency for the percent cross over to increase. 10 m.u. apart = 10% recombination 20 m.u. apart = 20% recombination if two far apart, there will be double-cross over events (reversion back to parental phenotypes)
Gregor Mendel
Augustinian monk and botanist whose experiments in breeding garden peas led to his eventual recognition as founder of the science of genetics (1822-1884)
29. What are the two types of chromosomes?
Autosomes - all chromosomes other than sex chromosomes (same in diploid males and females). Sex chromosomes - Chromosomes particularly concerned with the determination of sex (X and Y and Z & W)
6. In 1944 Avery, MacLeod, and McCarty demonstrated that DNA was the substance that causes bacterial cell transformation. Please describe their experiment-be sure to tell what organism they used.
Avery, MacLeod, and McCarty aso used Streptococcus pneumoniae; using both the IIIS strain and IIR strain -They expanded upon the findings of Frederick Griffith to demonstrate that DNA is the genetic material 1. They prepared cultures containing the heat-killed IIIS strain and then removed lipids and carbohydrates from the solution (using centrifuge, heat kill, and homogenization) 2. Next they treated the solutions with different digestive enzymes (DNase, RNase or protease) to destroy the targeted compound DNase- destroys DNA RNase- destroys RNA Protease- destroys proteins 3. Finally, they introduced living IIR strain cells to the culture to see which cultures would develop transformed IIIS strain bacteria 4. Only in the culture treated with DNase did the S strain bacteria fail to grow (i.e. no DNA = no transformation) This indicated that DNA was the genetic component that was being transferred between cells
34. In the B-Form of DNA (also known as the Watson and Crick form), how many base pairs are there per each turn in the DNA's double helix structure? How many angstroms are there per turn in the DNA? How many angstroms are there between each base pair?
B Form DNA: 10 base pairs per turn 1 complete turn = 34Å 3.4Å between base pairs A Form DNA (more concentrated): ~11 base pair per turn 2.4Å btwn base pairs 1 complete turn = 26.4Å
31. What are the three forms of DNA discussed in class and which is the most common?
B-DNA: the term given for the canonical right-handed DNA helix that is the most common form of DNA A-DNA: typical of laboratory DNA. It is a right-handed double helix fairly similar to the more common B-DNA form. BUT with a shorter, more compact helical structure whose base pairs are not perpendicular to the helix-axis as in B-DNA Z-DNA: a left-handed double helix wherein the sugar-phosphate backbone has a zigzag pattern due to the alternate stacking of bases in anti-conformation and syn conformation
56. What are Barr bodies? Do Barr bodies occur in somatic and/or reproductive cells?
Barr Body: a small, densely staining structure in the cell nuclei of female mammals >consisting of a condensed, inactive X chromosome >It is regarded as diagnostic of genetic femaleness. >found in female somatic cells ONLY
Interphase
Cell grows, performs its normal functions, and prepares for division; consists of G1, S, and G2 phases
48. List the two examples of multiple alleles discussion in class.
Rabbit Fur Color: C, c^ch, c^h, c Blood Type in Humans: IO, IA, IB
26. List examples of chemical mutagens.
Chemical mutagens can (1) penetrate cells and (2) alter the chemical structure of the DNA within the cells. i) Mustard gas ii) Formaldehyde iii) Benzene
7. Describe what is meant by the saying "slipping off the ends."
Chiasmata: The X-shaped, microscopically visible region representing homologous chromatids that have exchanged genetic material through crossing over during meiosis. 1 = chiasma #>1 = chiasmata "slipping off the ends": terminalization of chiasmata -The slipping of chiasmata towards the ends of bivalents is called as terminalisation. They separate along with the cell -When tetrads, which are composed of two pairs of sister chromatids, begin to split the only points of contact are at the chiasmata.
62. Define Chimera.
Chimera: An individual formed from two different cell lines or the fusion of two non-identical fertilized eggs (embryos), but which is composed of cells that all have the genotype of one sex (male or female).
d. Based on the somatic cell hybridization data in your class slides, which chromosome appears to code for the enzyme thymidine kinase?
Chromosome 17
Prophase
Chromosomes become visable, nuclear envelop dissolves, spindle forms -Unit factors in pairs
Metaphase
Chromosomes line up in the middle of the cell
Know how to use this information to determine the configuration of the F1 parent (aka if the F1 parent was cis or trans).
Cis- the two dominant alleles are on the same chromosme and the two recessive alleles are on the same chromosome -parental progeny matches parents phenotype Trans- the dominant and recessive alleles are swapped on the two chromosomes -parental progeny does NOT match parents phenotype -recombinant offspring match parental phenotype
1. What is the definition of a cellular clone? (You also learned about DNA clones).
Clone-all the individuals derived by nonsexual propagation from a single original parent. A clone is a group of identical cells that share a common ancestry, meaning they are derived from the same cell. Clonality implies the state of a cell or a substance being derived from one source or the other.
Molecular Level of Sickle Cell
Co-Dominance Molecular (hemoglobin type) 1/1 normal: HbAHbA 1/2 normal and 1/2 mutant (S): HbAHbS 1/1 mutant (S): HbSHbS
Organism Level of Sickle Cell
Complete Dominance Organism (overall viability) normal: HbAHbA normal: HbAHba anemia (death): HbaHba
5. What are cross-over events? Why are they important? Do cross-over events occur between sister chromatids or between non-sister chromatids?
Cross-Over Event: Process in which homologous chromosomes exchange portions of their chromatids during meiosis (Prophase 1- Pachytene) Importance: resulting in a mixture of parental characteristics in offspring; accounts for genetic variation, because due to the swapping of genetic material during crossing over, the chromatids held together by the centromere are no longer identical. Occurs between: NON-sister chromatids
Eukaryotic Cells
Contain a nucleus and other organelles that are bound by membranes.
55. In a prokaryotic cell, translation can be coupled with transcription. Describe what this means. Why doesn't this occur in a eukaryotic cell?
Coupled -This means that mRNA is translated during transcription, the processes are coupled together -transcription and translation occur in the cytoplasm Independent -In eukaryotic cells translation is independent from transcription -transcription occurs in the nucleus, but translation occurs outside the nucleus -this is because the pre-mRNA goes through additional processes (RNA splicing, Capping of 5' end, Poly-A tail of 3' end, and association with other proteins) before it can leave the nucleus
Backcross
Cross between an F1 individual and one of the parental (P) genotypes, typically described as against PP (homo dom) (pp) or (PP)
dihybrid cross
Cross or mating between organisms involving two pairs of contrasting traits A 1:1:1:1 phenotypic ratio
4. Define crossing-over. Recall that crossing-over occurs during Meiosis I. Does crossingover occur between sister or non-sister chromatids?
Crossing Over: the exchange of chromatin material between non-sister chromatids of homologous chromosomes
38. What occurs during deamination? What nucleotide bases are involved?
Deamination -cytosine, adenine, or guanine -of the 3, cytosine is most susceptivle to deamination, giving rise to uracil -like depurination, deamination is a hydrolytic reaction caused by random thermal collisons of a water molecule with the bond that links the amino group of the base to the pyrimidine or purine ring -the rate of damage to the human genome by this means is about 100 deanimations per day
37. What occurs during Depurination DNA damage? What nucleotide bases are involved? What bond is broken?
Depurination -loss of a purine base (adenine or guanine) -by spontaneous hydrolysis of the glycosidic bond that links it to deoxyribose
Genetic Drift
Differential contribution of genotypes (offspring) to the next generation due to random events. Populations usually small.
55. What is the Mary Lyon Hypothesis?
Dosage Compensation: Inactivation of all but one X chromosome >This allows the dosage relationship between # X and # autosomes to be the same in males and females. >Females (XX) do not express a sex-linked trait more markedly than hemizygous males X Y). >Only one X chromosome required for cell to function - other X chromosomes (1 in normal individuals) are inactivated (more dense and stain darker). >Because X chromosome inactivation does not normally occur in the very early developmental stages of germ cells, each ovum still receives an X chromosome from the female parent. >Because approximately 15 % of X chromosome genes may escape inactivation, sex chromosome aneuploid individuals (ex. XXY and XXX ) can be affected by the over-expression of X chromosome genes.
Who invented PCR and when?
Dr. Kary Mullis in 1983 Kary Banks Mullis (December 28, 1944 - August 7, 2019) was an American biochemist. In recognition of his invention of the polymerase chain reaction (PCR) technique, he shared the 1993 Nobel Prize in Chemistry with Michael Smith and was awarded the Japan Prize in the same year.
Laborador Retriever Recessive Epistasis
E = allows for deposition of either black or brown color in coat ee = prevents deposition of color (black or brown) pigment in coat (epistatic gene pair) B = black skin/lips/nose; b = brown skin/lips/nose
Gene (modern definition)
a section of DNA that determines the amino acid sequence of a polypeptide
15. Who discovered that [A] = [T] and [C] = [G] in DNA? Note that brackets [ ] indicate concentration.
Erwin Chargaff -used nitrogenous base concentration data to match [thymine] = [adenine] [cytosine] = [guanine] ex: 15 T = 15 A 35 C = 35 G
90. How are the bands on the gel visualized? What is ethidium bromide? How can you visualize bands on a gel that has been stained with ethidium bromide?
Ethidium bromide is an intercalating agent commonly used as a fluorescent tag How it it visualized? >It can be used in the gel mixture, the electrophoresis buffer, or to stain the gel after it is run. >Molecules of the dye adhere to DNA strands and fluoresce under UV light, showing you exactly where the bands are within the gel. BUT in a southern blott X-ray film is applied over the top of the filter to produce an autoradiogram that will allow only those bands that have hybridized with the probe to be visualized.
82. During translation, what is the first amino acid in eukaryotes? What is the first amino acid in prokaryotes?
Eukaryotes: methionine (met) Prokaryotes: N-formyl methionine (f-met) ^both have start codon of 5'.AUG.3'
64. Know how to determine p and q given the numbers of homozygous recessive individuals present in a population. Understand that knowing the p and q allele frequencies allows you to calculate the percent or frequency of individuals of a particular genotype in the population.
Ex. AA = 21 Aa = 53 aa = 26 N = 100
67. What are exons? What are introns? Which one is spliced out of eukaryotic pre-mRNA during post-transcriptional modifications? Do prokaryotes have introns?
Exon: -a segment of a DNA or RNA molecule containing information coding for a protein or peptide sequence -expressed Intron: -a segment of a DNA or RNA molecule which does not code for proteins and interrupts the sequence of genes -spliced out of eukaryotic pre-mRNA during post-transcriptional modifications prokaryotes do NOT have introns Monocystronic model (only 1 gene), eukaryotic
44. There are several types of parthenogenesis. Please describe facultative and automictic parthenogenesis.
Facultative Parthenogenesis: when a female can produce offspring either sexually or via asexual reproduction >female produces haploid zygote >female produces diploid zygote Automictic Parthenogenesis: a postmeiotic process in which a haploid cell may either duplicate its chromosomes or join with another haploid cell. In both cases, diploid zygotes develop and grow into diploid adults. >The specific form of avian parthenogenesis in which the egg nucleus recombines with the second polar body >female develops haploid egg that fuses with other oocyte
66. In the Promoter region there are three "boxes" that can bind transcription factors called the TATA box, the CAAT box, and the GC box. How do you think they got their names? List these three "boxes" of the Promoter region in order from the farthest to the closest to the transcriptional start site.
Farthest/1st GC box CAAT box TATA box Closest to transcriptional start/3rd "Gotta Commence Transcription" -In the Promoter region, the modular elements, TATA box, CAAT box, and GC box, bind TFs in order to stimulate transcription -named for their base pairings
34. What is the genotype for a person with Turner's syndrome? Is this individual male or female? Are they sterile or fertile?
Female with a missing X chromosome X Sterile
40. Horsetail plant gametophytes sex is also determined by the Environment. Which sex predominates during good growth conditions? The other sex predominates in poor growth conditions.
Female: good growth conditions in environment Male: bad growth conditions in environment
Chi-Square Formulas
Formula for X^2 for a sample consisting of 2 classes: Complex Formula: X^2 = [(O1 - e1)^2 + (O2-e2)^2....]/ e1 e2 O1 = the observed number in the first class e1 = the expected number in the same class as O1 O2 = the observed number for the second class, etc. e2e the expected number in the same class as O2 Simplified formula: X^2 = ∑ d2 , d = O-e >For interpreting X^2 values, the number of classes on which X^2 is based must be considered >It is, therefore, necessary to include the number of classes contributing to a given X^2 in evaluating the ''goodness of fit''
30. How many hydrogen bonds are formed between cytosine and guanine? How many hydrogen bonds form between thymine and adenine?
G ≡≡ C three hydrogen bonds A == T two hydrogen bonds
39. Bonellia veridis the Green Spoonworm has Environmental Sex Determination. Describe what would cause a larva to differentiate into a male. What allows larvae to become female?
Green spoon worms begin life colourless and adrift in a sexually undifferentiated larval state: whether they end up male or female depends on where they settle if bonellia virdis is isolated: female -female will then secrete toxin called bonellin if bonellia virdis larvae is near an adult female (exposed to bonellin): larva will go into the female and develop into a male environmental influence, chemical
89. Describe how gel electrophoresis works. Do smaller or larger DNA fragments move through the gel faster? What charge is DNA? So where would you place the cathode (negative charge) and the anode (positive charge) in relation to a gel with DNA samples placed in the wells?
Gel Electrophoresis 1. DNA fragments are generated through restriction endonuclease digestion. Those fragments generated by different restriction enzymes are kept isolated from eachother. a. preparation of homogenous single strand of DNA b. label 5' end of ss DNA with 32P (radioactive label) c. divide DNA into 4 separate tubes d. cleavate of specific nucleotides in each one of the four tubes with either A, G, C, or T reagent (restriction endonuclease digestion) to generate short fragments used to sequence DNA e. sequential placement of DNA samples containg the fragments generated by A, G, C, or T digestion into wells at top (cathode end) of four separate adjacent lanes of gel 2. Agarose (for separation of large fragments) or polyacrylamide (for separation of small fragments) gels are prepared and placed in a horizontal gel electrophoresis apparatus 3. the fragments produced by different restriction enzymes (different base sequence recognition sites) are loaded into separate lanes (columns) of gel, with the first lane being occupied by a radioactive size marker 4. once separated by size exclusion and electrical charge, fragment positions in each lane can be visualized and photographed with the use of an ethidium bromide label (shines under UV light) Smaller DNA fragments move through the gel faster What charge is DNA? the phosphate group on each DNA nucleotide is NEGATIVELY charged So where would you place the cathode (negative charge) and the anode (positive charge) in relation to a gel with DNA samples placed in the wells? Cathode (-): top of the well Anode (+): bottom of the well, DNA migrates toward positive charge
60. What is gene frequency within a population? How can gene frequency be modified in a population?
Gene Frequency: the relative abundance or relative rarity of a particular gene in a population as compared with its own alleles in a population. >Any gene frequency takes a range from 0(not existent) to 1(the only gene available). A. Gene frequency is determined by the mode of inheritance. B. The variance is due to the frequency of the genes. C. Factors that may modify the gene frequency. 1) Selection - artificial selection. 2) Natural selection - what goes on in nature. Those with more viability continue to reproduce.
3. Define linkage.
Gene Linkage: The association of genes that are physically located on the same chromosome. -Different alleles of different segregating genes that are present together on a particular chromosome in parents tend to remain together on that chromosome in the progeny. -chromosomes that belong to same homologous set have same sequence of genes, but may have different allelic forms of each of those genes (A or a) Locus: The location of a gene on a chromosome. Linkage Group: all of the genes on a single chromosome. >They are inherited as a group; that is, during cell division they act and move as a unit rather than independently. >Each linkage group corresponds to one of the pairs of homologous chromosomes in the genome of that species. Linkage group in one pair of homologs.
14. If Generation 0 is incubated in 15N (heavy) media, and then Generations 1, 2, and 3 are all incubated in 14N (light) media: What density gradient banding pattern DNA is found in Generation 1? What DNA density gradient banding patterns are found in Generation 2 and 3?
Generation 1 band DNA also produced a single band when centrifuged. -However, this band was higher, intermediate in density between the heavy 15N DNA and the lighter 14N DNA Generation 2 would be found with one set of semiconserve and one set of just 14N -When second-generation DNA was centrifuged, it produced two bands -One was in the same position as the intermediate band from the first generation, while the second was higher (appeared to be labeled with only 14N) Generation 3 was majority of 14N -over the third and fourth generations, we'd expect the hybrid band to become progressively fainter (because it would represent a smaller fraction of the total DNA) and the light band to become progressively stronger (because it would represent a larger fraction).
49. Have a general understanding of the immunology associated with blood types. Why can't you give someone with type A blood a blood transfusion using type B blood? What blood type is the universal donor? What blood type is the universal recipient?
Genes I^O (a) - does not produce antigen, allows A and B antibodies to be produced. I^A (A) - produces antigen A, inhibits production of antibody A. I^B (A^B) - produces antigen B, inhibits production of antibody B. Antigen - A substance present on the red blood cells. >Antigen A, antigen B >pegs on RBC Antibody - A substance present in the serum of the blood. >Antibody A, antibody B. Antiserum - A serum that contains a known antibody. >Antiserum A, antiserum B. **Antigen-antibody-reaction - When an antigen (Antigen A) and its corresponding antibody (Antibody A) are brought together. >Type A blood has A agglutinogens and therefore agglutinates with anti-A agglutinins. >Type B blood has B agglutinogens and agglutinates with anti-B serum. >Type AB blood has both A and B agglutinogens and agglutinates with both types of serum >Blood Type O: universal donor >Blood Type AB: universal recipient
Environment's effect on phenotype
Genes play an important part in influencing phenotype, but genes are not the only influence. Environmental conditions, such as temperature and availability of nutrients can affect phenotypes. For example, temperature affects coat color in Siamese cats
Forces Affecting Allele Frequency
Genetic Drift Selection
95. Understand that there are 20 main amino acids and some amino acids share similar properties. List the four major groupings of these 20 amino acids.
Grouping is determined by the R-terminal 1. Nonpolar: hydrophobic 2. Polar Neutral: hydrophilic 3. Polar Positively Charged: basic 4. Polar Negatively Charged: acidic
22. Which nucleotides are the purines?
Guanine (has double bond ==O) Adenine (NO double bond O) purine: double ring
24. Be able to recognize and distinguish the structures of the five different nitrogenous bases.
Guanine (has double bond ==O) Adenine (NO double bond O, --NH2 instead) Cytosine (ONE hydrogenated N) Uracil (TWO hydrogenated Ns) Thymine (methyl group CH3)
61. Define Gynandromorph. What is a bilateral gynandromorph?
Gynandromorph: An individual that developed from a single fertilized egg (embryo) and which is composed of both male and female genotype cells (sexual mosaic). Bilateral Gynandromorph: A gynandromorph can have bilateral asymmetry—one side female and one side male. >Bilateral gynandromorphy arises very early in development, typically when the organism has between 8 and 64 cells. >Later stages produce a more random pattern. >Alternatively, the distribution of male and female tissue can be more haphazard ( non-bilateral)
2. What did Ernst Haeckel propose about the cell nucleus in 1866?
Haeckel proposed that the cell nucleus contains the factors responsible for the transmission of hereditary traits
62. Define the ideal of Hardy-Weinberg Law (equilibrium). What are the five assumptions that must be met in Hardy-Weinberg Law in order for allele frequencies in a population to remain constant over the generations?
Hardy-Weinberg Law - Use when dominance is complete and when there are two phenotypes and three genotypes. >This law states that in large populations, there are the following conditions: A. Frequency of one or two alleles is equal to p^2 . B. Frequency of the other alleles is equal to q^2 . C. Sum of frequency p + q = 1. D. Mating is random. >Offspring of three genotypes in a definite ratio will be in equilibrium in the next generation in the frequency of: p^2 + 2pq + q^2 = 1 >5 Assumptions: 1. No Selection (no difference in fitness) 2. Random Mating 3. No migration (in or out, no gene flow) 4. No mutation 5. No genetic drift (infinitely large population)
Gregor Mendel Published
He read his paper , "Experiments in Plant Hybridization" to the Brunn National History Society in 1865, and it was published in the Proceeding of the Society in 1866
39. What follows gyrase and causes unwinding of the parent helix?
Helicase >Causes unwinding of the parent helix as polymerase moves down parent strand in the 3′ to 5′ direction. >Uses two ATP molecules for energy for each base pair separation
58. Define Hemizygous.
Hemizygous: Having only one allele of a given gene. Ex: X^AY or X^a Y Homozygous Ex: X^AX^A or X^aX^a Heterozygous: Ex: X^AX^a
56. What is heritability? How do you calculate heritability? Distinguish between the unselected population mean, the selected population mean, and the new population mean. Recall that the h2 component of the equation is calculated in decimal form (i.e. 33% is 0.33) and the h2 value does NOT need to be squared. h2 is a representation of the value.
Heritability (h^2) - Degree to which a given trait is controlled by inheritance. h^2 = ∆G/Sd OR h^2 = R/S S = Sd = selection imposed on the trait (can be strong or weak, and is different between selected and unselected population means) S= x̄ reproducing population - x̄ unselected population S= ps-p ps= selected mean p= unselected population mean R = ∆G = response of a population (given by the new population mean after selection) R= x̄ new population - x̄ original population R= pn-p pn= new population mean p= unselected population mean Overall Formulas: R= h^2*S h^2= R/S h^2= (pn-p)/(ps-p)
28. Who in 1927 used x-rays to show that external factors could cause DNA mutations using Drosophila melanogaster?
Hermann J. Muller Muller carried out two experiments with varied doses of X-rays, the second of which used the crossing over suppressor stock ("ClB") he had found in 1919. A clear, quantitative connection between radiation and lethal mutations quickly emerged.
63. What is a Hermaphrodite?
Hermaphrodite: An individual that possesses both male and female gonads, with the social environment usually controlling whether the individual takes on a male or female reproductive role.
9. In the Hershey and Chase experiment, what part of the bacteriophage virus was labeled by radioactive P32 and what part was labeled by S35?
Hershey and Chase used T2 phage, a bacteriophage. The phage infects a bacterium by attaching to it and injecting its genetic material into it. >They labeled the phage DNA with radioactive Phosphorus-32. They then followed the phages while they infected E. coli. >They found that the radioactive element left on the phage's DNA was only in the bacterium, and not in the phage, meaning that the DNA had entered the bacterium. In a second experiment, Hershey and Chase put labels on the phage protein with radioactive Sulfur-35. >After the phage was attached to the bacterium, the radioactive element was found in the phage, but not in the bacterium. >This means that the phage's proteins stayed on the outside of the bacterium. These results showed Hershey and Chase that the genetic material that infects the bacteria is DNA (final confirmation that DNA is the transforming principle)
55. What is heterosis (aka hybrid vigor)? How do you calculate heterosis?
Heterosis - Superiority of heterozygous genotypes in comparison with corresponding homozygous genotypes in respect to one or more traits. Heterosis = [(Avg. of hybrid offspring - Avg. of crossed breeds)/ Avg. of crossed breeds] *100
71. What is a holandric gene? Give an example of a holandric trait.
Holandric Gene: carried on the Y chromosome -only passed by males onto their sons ex: hairy ear rims (pinna)
5. Explain the Holliday Model of Crossing Over. Include the following enzymes in your explanation: a. Endonuclease, DNA binding and/or DNA unwinding proteins (aka gyrase and helicase), proteins such as recA, Exonuclease, DNA polymerase, and DNA ligase
Holliday Model of Crossing Over: -Two Factor Cross: just looking at the relative distance between two genes -cross over only occurs between alleles that are heterozygous (if a b crossed with a b, then the cross would achieve nothing, it would still be the parental type) -occurs between non-sister chromatids -form a recombinant a. Two homologous DNA molecules line up (e.g., two nonsister chromatids line up during meiosis). b. Endonuclease creates cuts/nicks in one strand of both DNAs. c. DNA binding and/or DNA unwinding proteins (aka gyrase and helicase) unwind the DNA from the nicks d. Proteins like recA (recombinantA) cause the cut strands to cross and join homologous strands, forming the Holliday structure (or Holliday junction). -rebinding event -Heteroduplex region is formed by branch migration. e. Exonuclease, DNA ligase, and DNA Polymerase close the nicks by forming new hydrogen bonds into the opposite homolog -Chiasma: the X shaped region f. Rotational event allows top homolog to bend. The bottom homolog bends AND rotates 180degrees AB → AB ab → ba g/h. Endonuclease snaps the rotated chormosomes so now A pairs with b and B pairs with a -this is a transition from parental to recombinant form i. Exonuclease, DNA ligase, and DNA Polymerase form new phosphodiester bonds between the backbones and hydrogen bonds between the nucleotides j. final form of recombinant DNA
33. In mammals, a normal male is the heterogametic sex and a normal female is the homogametic sex. Define heterogametic and homogametic. Which sex is heterogametic in birds (such as chickens)?
Homogametic Sex: produces one kind of gamete in reference to the sex chromosomes. >human females (XX) >bird males (ZZ) Heterogametic Sex: produces two kinds of gametes in reference to the sex chromosomes. >human males (XY) >bird females (ZW)
31. How many autosomes and how many sex chromosomes do humans have? Chickens? Drosophila melanogaster?
Humans: 22 pairs of autosomes 1 pair of sex (23 pairs- 46) Chickens: 38 pairs of autosomes 1 pair of sex (39 pairs- 78) Drosophila melanogaster: 3 pairs of autosomes 1 pair of sex (4 pairs- 8)
Rate Limiting Step
In Transcription rate-limiting steps, which occur during initiation, that control both mean rate and noise in RNA production.
Recessive Lethality
In a cross you remove the lethal offspring that would not be born from the genetic ratio ex. amaurotic idiocy (Tay-Sachs disease); cystic fibrosis in humans ll = lethal L__ = normal
66. What is a reciprocal cross? What is the purpose of doing a reciprocal cross? How do you know if a trait is sex-linked or not?
In genetics, a reciprocal cross is a breeding experiment designed to test the role of parental sex on a given inheritance pattern >All parent organisms must be true breeding to properly carry out such an experiment >AA (fem) X aa (male) AND aa (fem) X AA (male) Purpose: to determine if a trait is sex-linked normal phenotypic ratio: autosomal abnormal phenotypic ratio: sex-linked Identifiers of Sex Linked Traits: 1. Occurs more often in males than females. 2. Gene is transmitted from an affected male through his daughters to 1/2 of his grandsons. 3. Never transmitted from father to son. 4. An affected female had to have an affected father and an affected or carrier mother.
5. Define transformation as it pertains to molecular biology.
In molecular biology and genetics, transformation is the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane(s). "Transforming Principle" is a term given to the substance that could be transferred from non living cells to living cells, causing the living cell to show characteristics of the non living cell.
24. List the three examples of ionizing radiation that could cause mutations in DNA.
Ionizing radiation: short wavelength and high energy i) x-rays ii) alpha (α), beta (β), gamma (γ) radiation α particles = 2 protons and 2 neutrons from nuclei -Ra (radium) (workers licking brushes used in watch dial manufacturing - radium poisoning). β particles = emission of electrons -radioisotopes: 32P, 3H, 35S, 14C, 35Ca γ particles = emission of high energy protons -radioisotopes: 125I, 22Na iii) Cosmic rays Speical Notes: >Dosage of ionizing radiation is cumulative. >Low intensity x long time (chronic dosage) = high intensity x short time (acute dosage).
17. Who in 1963 demonstrated the manner of replication in a bacterial chromosome through autoradiography?
John Cairns demonstrates replicative loops in the DNA of bacterial chromosomes (E. Coli) through autoradiography >Radioactive isotopes decay slowly, releasing particles that appear as black dots on X-ray film. The resulting pictures are called autoradiographs. >Autoradiography: identify the locations and shapes of structures, or to track the movement of molecules in vivo over time. >In 1963, John Cairns demonstrated, using autoradiography, that bacterial chromosomes are circular, and that Y-shaped replication forks are present during DNA replication. 1. E. coli bacteria are cultured in a medium containing thymidine that has been labelled with a radioactive isotope of hydrogen, tritium (3H). 2. During DNA replication, the tritiated thymidine is incorporated into the bacterial chromosome as radioactive thymine. 3. Thin sections of labelled cells are covered with X-ray film. As the tritiated thymine decays, beta particles expose the film in patterns indicating the shape of the DNA molecule. The Cairns technique (labelling with tritiated thymidine followed by autoradiography) can also be used to get information about eukaryotic chromosomes and to measure the length of DNA molecules.
61. In the lac operon model, explain what happens if lactose is present. Explain what happens if lactose is absent.
Lactose is Absent -the repressor protein binds to the operator gene -binding to O prevents transcription Lactose is Present -lactose binds to the repressor protein -the repressor protein goes through a conformational change, and can no longer block transcription -the genes following the operator gene can now be expressed Lac Operon Model: polycistronic, prokaryotic
75. Ribosomes are labeled/named via the Svedberg unit or their sedimentation rate. The total prokaryotic ribosome is 70S. What numbers are the prokaryotic small and large subunits of the ribosome? (Remember Svedberg units are not additive in ribosomes).
Large Subunit: 50S Small Subunit: 30S
76. The eukaryotic ribosome is 80S. What Svedberg units are the eukaryotic small and large ribosomal subunits?
Large Subunit: 60S Small Subunit: 40S
Lethality
Lethal alleles (also referred to as lethal genes or lethals) are alleles that cause the death of the organism that carries them. -They are usually a result of mutations in genes that are essential for growth or development * a gene can be phenotypically dominant but recessive lethal (semidominance)
46. What enzyme connects the sugar phosphate backbone (forms covalent phosphodiester bonds) of the lagging strand and areas where the RNA primer was replaced with DNA nucleotides?
Ligase -facilitates the joining of DNA strands together by catalyzing the formation of phosphodiester bonds (fills the gap between okazaki fragments)
locus
Location of a gene on a chromosome
35. Describe the Major and Minor groves in the B-Form of DNA.
Major Groove occurs where the backbones are far apart Minor Groove occurs where they are close together >The grooves twist around the molecule on opposite sides; the major groove is deep and wide, the minor groove is narrow and shallow >Certain proteins bind to DNA to alter its structure (histone proteins, DNA packaging) or to regulate transcription or replication (copying DNA to DNA) -These proteins bind on the major groove
35. What is the genotype for a person with Klinefelter's Syndrome? Is this individual male or female? Are they sterile or fertile?
Male with an extra X chromosome XXY Sterile
20. Which parts of a flower are the male structures? Which parts are the female structures?
Male: Stamen anther filament Female: Pistil stigma style pollen tube ovary ovule
11. Who in 1958 provided evidence to support the theory of semiconservative replication?
Matthew Meselson and Franklin Stahl
20. Can mutations occur in any cell type?
May occur in any cell A) Somatic- affects individual (cancer) -not heritable (unless asexual reproduction) B) Germ- affects individual but mostly affects offspring -heritable
25. Of the four haploid megaspores that are formed from the diploid megaspore mother cell, how many survive? What happens to the surviving megaspore(s)?
Megaspore: A spore from a heterosporous plant species that develops into a female gametophyte. Egg mother megaspore (2n cell) --> meiosis --> 4 1n cells -- (3 of the 4 die)-> single surviving megaspore --> 3 rounds of mitosis --> a single 8 n cell 3 antipodals 2 polar nuclei 2 synergids 1 egg nucleus 2 n goes to endosperm 1 n goes to zygote 5 n degrade >of the 4 haploid megaspores that are fromed from the diploid megaspore mother cell, only ONE survives >surviving megaspore undergoes mitosis to become egg
8. Are Meiosis I and II reductional division and/or equational division?
Meiosis I - Reductional division (Because the ploidy is reduced from diploid to haploid) Meiosis I 1 X (2N, 4C; G2) ------> 2 X (1N, 2C; no S) Meiosis II - Equational division (analogous to mitosis, in which the sister chromatids are segregated, creating four haploid daughter cells (1n, 1c)) Meiosis II 1 X (1N, 2C) ----------> 2 X (1N, 1C) Final Product 4 X (1N, 1C)
85. Who won the Nobel Prize in 1993 for the use of Taq Polymerase in PCR?
Michael Smith >The Nobel Prize in Chemistry 1993 was awarded "for contributions to the developments of methods within DNA-based chemistry" jointly with one half to Kary B. Mullis
22. Does a diploid microspore mother cell undergo meiotic divisions to become a pollen grain or an egg during sporogenesis?
Microspore: A spore from a heterosporous plant species that develops into a male gametophyte Pollen Grain mother microspore (2n cells) --> 2 meiosis --> 4 1n cells --> 1 mitosis --> 2 1n cells 1n goes to endosperm 1n goes to zygote
3. In 1869 Friedrich Miescher isolates "nuclein" (later known as DNA) from the nuclei of leukocytes. What did he discover about DNA at this time?
Miescher isolated "nuclein" (later known as DNA) from the nuclei of leukocytes (WBC) -he did this just a couple years after the Civil War -he collected large amounts of pus from a local hospital -this was distinctive because the pus cells had carbon, hydrogen, nitrogen, and oxygen but NOT sulfur (which was a major component of many amino acids) -the pus did contain large amounts of phosphorous (which is an essential part of DNA)
Amount of DNA in Organisms
Mitochondrion - 16,000 bp Chloroplast - 120,000 bp Eukaryote Nucleus - 3 billion bp
1. Understand the differences between Mitosis and Meiosis.
Mitosis >a type of cell division that results in two daughter cells each having the same number and kind of chromosomes as the parent nucleus >typical of ordinary tissue growth. Meiosis >a type of cell division that results in four daughter cells each with half the number of chromosomes of the parent cell (reductive division), as in the production of gametes. >(genetics) cell division that produces reproductive cells in sexually reproducing organisms (germ-line cells)
11. N = the number of complete sets of chromosomes or the gene (allele) complement number and C = Amount (mass) of DNA in the nucleus. Describe how the values of N and C change during Mitosis and during Meiosis I and Meiosis II.
Mitosis: 1 X (2N, 4C) --> 2 X (2N, 2C) equational Meiosis I: 1 X (2N, 4C) --> 2 X (1N, 2C) reduction Meiosis II: 1 X (1N, 2C) --> 2 X (1N, 1C) equational
Monozygotic Twins vs. Diozygotic Twins
Monozygotic twins: Twin offspring that have developed from one oocyte >will be the same sex Diozygotic twins: Twin offspring that have developed from two separate oocytes fertilized at the same time >can be the same or different sexes
47. When working with multiple alleles, what formula is used to determine the number of different genotypes possible? What does the letter "n" represent in the formula?
Multiple alleles (more than 2 alleles for a gene in a population) [n (n + 1)] / 2 = the number of genotypes in the population n = the number of alleles in the population for a given gene for rabbits: n = 4 alleles (4(4+1))/2 = (4*5)/2 = (20)/2 = 10 possible genotypes in the population
46. There are the multiple alleles (three or more allelic forms of a gene) present in the population. How many alleles are present per gene in a somatic cell of an individual organism in that population?
Multiple alleles - three or more contrasting genes affecting the expression (phenotypes) of one character (detail of structure) >>>however, only two of these genes may occur in a genotype (somatic cell) >>>and only one is transmitted in a gamete.
17. What is the term for "Sudden, heritable changes in genetic material and the processes by which these changes occur"
Mutation: Sudden, heritable changes in genetic material and the processes by which these changes occur. >Most mutations are lethal and recessive. >These changes are not explained by recombination, but by either change in: • chromosome number [ex., euploidy (diploid, triploid, tetraploid)] • aneuploidy (chromosome # is not an exact multiple of the monoploid; ex., trisomy 21) • chromosomal aberrations [ex., the addition or loss of chromosome segments (ex., deletions, duplications, inversions, translocations)] • changes in individual genes [ex., most common uses of mutation (ex., mutons, where there are point mutations or changes in single base pairs, and, therefore, genes; example of a spontaneous mutation)]
30. What is a point mutation?
Mutations involving changes in single base pairs -substitutions -deletions -insertions
Mitosis is an Equational Division
N = Number of chromosomes in one chromosome set; or allele complement number C = Amount (mass) complement of DNA Mitosis >Equational division (No pairing of homologs) 1 X (2N, 4C; G2) -------> 2 X (2N, 2C; G1)
57. How do you calculate the number of Barr bodies in an organism?
N-1
Nucleolar Organizing Regions (NORs)
NORs are composed of tandem repeats of rRNA genes found in several different chromosomes.
48. Define nondisjunction. What is the implication of a nondisjunction event during Anaphase I?
Nondisjunction: the failure of one or more pairs of homologous chromosomes or sister chromatids to separate normally during nuclear division >usually resulting in an abnormal distribution of chromosomes in the daughter nuclei Nondisjunction in Anaphase 1: >Nondisjunction in meiosis I occurs when the tetrads fail to separate during anaphase I. >At the end of meiosis I, there will be 2 haploid daughter cells, one with n+1 and the other with n-1. Both of these daughter cells will then go on to divide once more in meiosis II, producing 4 daughter cells, 2 with n+1 and 2 with n-1.
51. Quantitative traits exhibit continuous variation (as compared to discrete variation which is a one-or-the-other situation such as "yes" or "no"). What shape does a graph have when the frequency (percentage) of individuals is plotted on the y axis and the quantitative traits (phenotypes) are plotted on the x axis?
Normal Distribution --> bell shaped curve
83. Do all final protein products have a methionine as their first amino acid? Why or why not?
Not all of them. Some proteins do keep methionine, but many remove methionine during post-translation modification of the N-terminus
Four Types of Genes
Nuclear Gene 1) Responds to regulatory signals - makes proteins for export. 2) Responds to internal signals - makes proteins for use in cytoplasm. 3) Makes proteins to be transported into an organelle. Organelle gene 4) Makes proteins for use inside its own organelle.
21. What is the difference between a nucleotide and a nucleoside?
Nucleotide: sugar (ribose or deoxyribose) + nitrogenous base (ATCG) + phosphate Nucleoside: sugar (ribose or deoxyribose) + nitrogenous base (ATCG)
Homologs
One chromosome of each homologous pair comes from the mother (called a maternal chromosome) and one comes from the father (paternal chromsosome). Homologous chromosomes are similiar but not identical. Each carries the same genes in the same order, but the alleles for each trait may not be the same Members of a pair of chromosomes Similar in: -size -shape -centromere location -types of genes that contain
Gene (original definition)
Original Mendelian Definition: -that inherited unit located on chromosomes which determines a biological characteristic -a unit of function and mutation (word coined by Johanssen from "genetics")
45. What is another name for the DNA segments/fragments on the lagging strand?
Ozaki Fragments
87. On the ribosome, what are the full names for the abbreviated P and A sites? When are the P and A sites formed during translation?
P(site)- peptidyl (formed during initiation) A(site)- amino acyl (formed during elongation) E(site)- exit
6. During which stage of Prophase I do cross-over events occur? During which stage of Prophase I are the cross-over events visualized as chiasmata?
Pachytene: cross-over event occurs Diplotene: cross-over visualized as chiasmata
P1 generation
Parental generation; each parent was pure for a given trait.
43. Honey bees that hatch from a fertile egg are females and bees that hatch from an unfertilized egg are males. What term describes when unfertilized eggs become activated and develop into viable individuals as part of the normal life cycle? What other animals have been found to exhibit this phenomenon?
Parthenogenesis: When unfertilized eggs may become activated and develop into viable individuals as part of the normal life cycle. • Parthenogenesis may occur in a number of invertebrate groups (i.e. insects) as well as in scattered vertebrate species (some fishes, a few lizards, and even turkeys). Males (drones): haploid 1N Females (workers and queen): diploid 2N
73. Describe the difference between partial and complete degeneracy.
Partial Degeneracy: changing the third base in a codon from a purine to a purine (G <-> A), or from a pyrimidine to a pyrimidine (C <-> U) Ex. AGU and AGC (pyr.) both code for ser but AGA and AGG (pur.) both code for arg Complete Degeneracy: Any of the four bases may be replaced for the third base in a codon. Ex. GUU, GUC, GUA, or GUG, all code for valine.
Anaphase
Phase of mitosis in which the chromosomes separate and move to opposite ends of the cell -segregation of unit factors during gamete formation, separation of homologs
53. Define polycistronic and monocistronic.
Polycistronic (Polygenic)- 1 mRNA codes for more than one gene -creates multiple protein products that work together -found in prokaryotic transcription Monocistronic (Monogenic)- 1 mRNA codes for a single gene -creates a single gene product -advanced, selective, specific -found in eukaryotic transcription
54. If an mRNA is polycistronic is it prokaryotic or eukaryotic?
Polycistronic- Prokaryotic Monocistronic- Eukaryotic
53. What is another term for multiple genes working in conjunction to influence a single trait?
Polygene Concept or Complex Trait
82. What is the purpose of PCR (Polymerase Chain Reaction)? What happens to the DNA during the PCR reaction? How is a specific segment of DNA amplified?
Polymerase Chain Reaction: cloning WITHOUT the use of a host cell Step 1: The PCR Reaction (~4-5 min): i. Denaturation: The DNA to be amplified is denatured into single strands. This involves heating at 90 - 95°C. ii. Annealing: Temperature is lowered to between 50 and 70°C. This allows DNA primers to bind to denatured (single strands of) DNA. >DNA primers (15 - 30 nucleotides long; synthetic oligonucleotides) bind to sequences that flank the target segment. iii. Extension: Heat-stable DNA Pol (Taq) synthesizes daughter strands complementary to target sequences from primers at 70 to 75°C. Taq adds nucleotides 5' 3'. Step 2: Doubling of number of DNA strands after each full cycle. >25-30 cycles (~3 hours) increases DNA by 1 x 10^6 Step 3: The amplified DNA is recovered: >exposed to a variety of restriction endonucleases for multiple heterogenous cleaving >its sequence analyzed by agarose or polyacrylamide gel electrophoresis (Southern Blotting).
59. Define population genetics.
Population Genetics: dealing the with genetics of individuals that inhabit a particular area
58. Give the definition for a population.
Population: the total of all individuals in a breed or species or as those individuals that inhabit a particular area
70. List the post-transcriptional modifications that occur to a eukaryotic tRNA. What shape is tRNA? What specific sequence is found at the 3' end (where the amino acid attaches to the tRNA)? What unique nucleotide bases are placed in the looped regions?
Post-Transcriptional Modifications -Cut at G on 5' end -Addition of CCA sequence at 3' end (where Amino Acid will attach) -Base modifications (i.e., thymine, pseudouracil) in looped regions -Introns excised from terminal loop (loop w/ stop codon) Shape: clover 3' end: CCA sequence unique nucleotide bases: The structure consists of hydrogen bonded stems and associated loops, which often contain nucleotides with modified bases: -inosine[I] -ribothymidine [T] -pseudouridine[Ψ] -methylguanosine[D]
Mitochondria
Powerhouse of the cell, organelle that is the site of ATP (energy) production >required for growth and development >contains their own DNA, semi-autonomous replication, transcription, and translation >only maternal mitochondria is inherited (in cytoplasm of the egg) >the more active a cell is (muscle or neuron) the more mitochondria present
49. List the precursor nucleotides used in DNA replication. List the precursor nucleotides used in transcription (Hint: think RNA).
Precursor Nucleotides in DNA Replication: >Deoxyadenosine triphosphate (dATP) >Deoxycytidine triphosphate (dCTP) >Deoxyguanosine triphosphate (dGTP) >Deoxythymidine triphosphate (dTTP) deoxyribonucleoside triphosphate precursors; dNTPs Precursor Nucleotides in Transcription: >Adenosine triphosphate (ATP) >Cytidine triphosphate (CTP) >Guanosine triphosphate (GTP) >Uridine triphosphate (UTP) (Uridine and NOT thymine b/c it is RNA) ribonucleoside triphosphate precursors; rNTPs
Mendel's First Law: Law of Segregation
Principle of Allelic Segregation -alleles of each gene segregate (separate) at the time of meiosis (gamete formation), so that half the gametes carry one allele and half carry the other
50. What are the differences in DNA replication between prokaryotes and eukaryotes? (Hint: think about the origin of replication and DNA polymerases). What are the particular functions of the four DNA polymerases found in eukaryotes?
Prokaryotes -Only one point of origin, replication occurs in two opposing directions at the same time -takes place in the cell cytoplasm DNA Polymerase I: replaces the ribonucleotides of the RNA primer with deoxyribonucleotides; filling the gap with DNA DNA Polymerase II: Polymerase activity at 2-4 nucleotides/second -single stranded 3' --- 5' exonuclease activity DNA Polymerase III: polymerase activity 5'---3' at 250-1000 nucleotides/second -endonuclease activity in the 5----3 direction -single stranded 3---5 exonuclease activity -high processivity Eukaryotes -numerous points of origin (bubbles grow with replication fork and eventually meet) -takes place in the cell nucleus Eukaryotic cells contain four DNA polymerases: α, β, γ, ρ a)Polymerases α and ρ (nucleus) are comparable to DNA polymerase III in prokaryotes α- synthesizes lagging strand ρ- synthesizes leading strand b) β functions in DNA repair c) γ is responsible for replication of mitochondrial DNA.
56. How many different RNA polymerases does a prokaryotic cell have? How many different RNA polymerases does a eukaryotic cell have?
Prokaryotic Cell: single RNA polymerase (holoenzyme because its combined w/ sigma unit) Eukaryotic Cell: three different RNA polymerases (NO sigma unit)
Similarities of Prokaryotes and Eukaryotes in Daughter Cell Production
Prokaryotic and eukaryotic cells share three common features regarding daughter cell production: 1) Replication of DNA occurs 2) Separation of replicated chromosomes 3) Cytokinesis
57. List the eukaryotic RNA polymerases used in transcription and what type of RNA they produce.
RNA polymerase I - (inside nucleolus) - makes structural RNA (i.e., rRNA)(ribosomal RNA) RNA polymerase II - (in nucleoplasm) - makes heterogenous nuclear RNAs or hnRNAs (i.e., precursor mRNAs or premRNAs)(messenger RNA) RNA polymerase III - (in nucleoplasm) - makes small adaptor RNAs (i.e., small nuclear RNAs and tRNAs). (transfer RNA)
65. There are two sequences in the DNA that help initiate transcription in eukaryotes. These are Promoters and Enhancers (also known as cis-acting nucleotide sequences). What can Enhancers bind to? What is the purpose of Enhancers? What can Promoters bind to? What is the purpose of Promoters? Is the Enhancer or the Promoter closer to the target gene?
Promoters -binds to TFs and RNA Polymerase -Promoters are necessary for transcription initiation -promoters are closer to the target gene Enhancers -ONLY bind to TFs -TFs bend or loop the DNA -this brings distant enhancers and promoters into close proximity to form activated transcription complexes -increasing the overall transcriptional rate -their positions and orientations are not fixed (moveable) -they are general a greater distance from the target gene than promoters -the generically enhance the transcription of surrounding genes
Meiosis Stages
Prophase I, Metaphase I, Anaphase I, Telophase I. Followed by Prophase II, Metaphase II, Anaphase II, Telophase II.
4. Describe the events that occur during the specific stages of Prophase I: a. Leptotene b. Zygotene c. Pachytene d. Diplotene e. Diakinesis
Prophase I: a. Leptotene: the initial condensation and coiling of chromosomes, which appear as very long threadlike structures b. Zygotene: homologous chromosomes have begun to pair and synapse laterally into bivalents or tetrads; beginning of crossing over c. Pachytene: synapsis is complete, bivalents have become shorter and thicker. homologous chromosomes are held tightly into position by synaptonemal complex; crossing over occurs d. Diplotene: the chromosomes of each bivalent begin to undergo repulsion or separate from each other. chiasmata become visible (multiple chiasmata); crossing over is now complete e. Diakinesis: nuclear envelope fragments and nucleoli disperses; chromosomes complete condensing, tetrads ready for metaphase; only one chiasma, maybe less; "slipping off the ends"
43. How specifically does UV light affect/damage DNA? How is this DNA damage repaired?
Pyrimidine Dimer Formation -UV light -formation of a covalent bond between two adjacent pyrimidine bases, usually two thymines Removal -similar mechanism to the first two, except a UV-specific endonuclease is involved in nicking the defective region near the dimer The pathway, using multiple enzymes, which repairs the UV-damage in healthy cells is called nucleotide excision repair.
50. What are quantitative traits? List a few examples of quantitative traits.
Quantitative Traits >may be governed by many genes (perhaps 10-100 or more) >each contributing such a small amount to the phenotype that their individual effects cannot be detected by Mendelian methods. >Genes of this nature are called polygenes. >Thus, more than one gene may contribute to a given trait. >This is where we get the polygene concept as defined at the back of your workbook Examples: >height >weight >life span >skin color
Walnut Comb
R-P-
Rose Comb
R-pp
63. How do each of the three different RNA polymerases terminate transcription in eukaryotes?
RNA Polymerase I (rRNA): -Modified rho-independent. -Strange G-C dyad region (many A's and U's intervening), followed by 26 A's, followed by 16 bases of any kind, followed by UCCACCUGGUC, followed by 3 bases, followed by AGGC. RNA Polymerase II (pre-mRNA): -Termination mechanism unknown -Processing begins before transcription ends -Possibly, processing proteins may literally pull pre-mRNA away and force RNA Pol II off of DNA. RNA Polymerase III (tRNA): -standard rho-independent
60. In prokaryotes, the RNA polymerase is a holoenzyme that consists of two units. What are the two units? What is the purpose of each unit?
RNA polymerase (Holoenzyme) = core unit + σ (sigma unit) σ70 = vegetative, for all RNAs σ60 = nitrogen metabolism σ32 = heat shock proteins Core Unit: performs the primary synthesis actions (reads the antisense strand, creates the mRNA) σ: enables specific binding of RNA polymerase (RNAP) to gene promoters -directs the whole unit to the DNA -released before transcription begins
47. The Calvin Brides model shows how sex is determined based on the ratio of X chromosomes to the number prior to A. Write the values to get a metafemale, a fertile female, an intersex fly, a fertile male (don't forget the Y chromosome), and a metamale.
Ratio of X Chromosomes : Autosome Sets 2A3X- meta female 1.5 3A3X or 2A2X-female 1.0 4A3X - intersex 0.75 3A2X - intersex 0.67 2AX or 2AXY- male 0.5 3AXY- metamale 0.33
40. How is deamination damage repaired? Hint: The first enzyme is different in deamination, but then the steps of repair are exactly the same as in depurination DNA repair.
Repair of deaminated DNA follows a similar course, except that deaminated bases must first be detected and removed 1. this is done by DNA Glycosidase, enzyme that recognize deaminated base and remove it from the DNA by cleaving the glycosidic bond between the base and the deoxyribose sugar 2. The sugar with the missing base is recognized by the same repair endonuclease enzyme that detects depurination damage. 3/4. DNA Polymerase I replaces, and DNA ligase seals
Sister Chromatids
Replicated forms of a chromosome joined together by the centromere and eventually separated during mitosis or meiosis II. Identical copies of a chromosome; full sets of these are created during the S subphase of interphase.
92. What information does restriction mapping and chain termination sequencing give us? Hint: it is in the name.
Restriction Mapping: a method used to map an unknown segment of DNA by breaking it into pieces and then identifying the locations of the breakpoints. >This method relies upon the use of proteins called restriction enzymes, which can cut, or digest, DNA molecules at short, specific sequences called restriction sites. >the breakpoints are labeled using 32P markers Chain Termination Sequence: actual electrophoretic gel generated by chain termination sequencing shows the separation of DNA fragments in the four ddNTP (unlabeled) chain termination lanes >to obtain the 5' --> 3' base sequence of the DNA fragment, the gel is read from the bottom to the top, beginning with the lowest band in any lane >unlabeled by florescents, but still technically labeled by 32P in the gel OR >chain termination sequencing can be done using ddNTPs labeled with fluorescent dyes
27. What is the difference between Ribose (in RNA) and Deoxyribose (in DNA)? Which specific carbon is this difference found?
Ribose (RNA): OH attached to the 2' carbon Deoxyribose (DNA): H attached to the 2' carbon
16. What two people provided X-ray crystallography data about DNA that helped Watson and Crick create their structure of DNA?
Rosalinda Franklin and Maurice Wilkins -discovered DNA was highly ordered, multiple stranded, and had repeating substructures every 3.4Å
50. A human embryo begins with a bipotential gonad (able to differentiate into either the male or the female reproductive tract). Describe the role of the genes SRY and DAX1 in directing the bipotential gonad to differentiate into the male or female reproductive tract.
SRY: gene region >This has been positively identified as the gene encoding the testis determining factor (TDF). >When injected into normal (XX) female mice, it caused them to develop as males. >The gene acts via two established mechanisms: 1. inhibiting p450 2. enhancing mullerian-inhibiting substance DAX1 (gene NR0B1) >an orphan nuclear receptor that regulates adrenal and gonadal development >SRY and DAX-1, interact in early periods of development of the gonadal ridges, expressing both in testicular and ovarian tissue >lack of male sex hormone leads to production of mullerian duct(ovaries)
70. If you wish to select for a particular trait, what three characteristics must the trait possess in the population?
Selection (S): differential contribution of offspring to the next generation due to differences in survivorship or fecundity (reproductive potential). a) artificial - imposed by man b) natural - interaction of environment and genotype. >For selection to occur, trait has to be: 1. Heritable 2. Must have genetic variation 3. Reproductive potential is greater than the carrying capacity - more offspring are produced than are able to live (difference of fitness)
Cellular Level of Sickle Cell
Semi-Dominance Cellular (RBC shape) normal: HbAHbA sickle-cell in low O2 environments (body will produce sickle cells on mountain but more round cells near sea level): HbAHbA' sickle: HbA'HbA'
a. What virus allows the human and mouse cells to fuse to create a hybrid cell? What is the term for the cells when the two cytoplasm fuse? What is the term for the hybrid cell when the human and mouse nuclei fuse?
Sendai Virus: forms little pegs on the cells, allows cells to stick together like Velcro (adhere to one another) Heterokaryon: when the cell cytoplasm fuse -first to form Hybrid Cell or Synkaryon: when the cell nuclei fuse -second to form
37. How is chicken sex determined? What is a rooster's genotype? What is a hen's genotype?
Sex is dependent upon genes on the chromosomes Rooster: XX aka ZZ Hen: XY aka ZW
67. Define sex-linkage.
Sex linkage: is the phenotypic expression of an allele that is dependent on the gender of the individual and is directly tied to the sex chromosomes. >In such cases there is a homogametic sex and a heterogametic sex.
65. Describe the difference between sex-influenced and sex-limited gene expression.
Sex-Influenced Gene Expression: a trait that is caused by a gene whose dominant expression differs in male and females; (e.g., male patterned baldness) Sex-Limited Gene Expression: autosomal genes expressed only in one sex (e.g., hen feathered vs cock feathered)
2. One example discussed in class was somatic cell hybridization fusing human and mouse cells.
Somatic cell hybrids are culture lines that contain the entire complement of the mouse genome and a few human chromosomes. >These culture lines are developed by mixing human and mouse cells in the presence of the Sendai virus. >The virus facilitates the fusing of the two cell types to form a hybrid cell
21. Describe the difference between spontaneous and induced mutations.
Spontaneous mutations • mutations that are not under the control of man • relatively infrequent • occur without a known cause • Due to: -biochemical mistakes during DNA replication -intrinsic errors in DNA repair (which may also be induced by environmental agents ex., lung cancer + smoking, skin cancer + uv irradiation) Induced mutations • mutations produced by man with a mutagen • Due to mutagens like: -ionizing radiation -uv light (solar radiation) -chemicals that react with DNA or RNA -viruses
25. What three components make up a nucleotide?
Sugar + Base + Phosphate -5-carbon (pentose) sugar (ribose:RNA or deoxyribose:DNA) -nitrogenous base (adenine, guanine, cytosine, thymine, or uracil) -one to three phosphate groups
84. What specific polymerase is commonly used for PCR reactions? Why is this polymerase used for this reaction?
Taq DNA Polymerase -used because it is heat-stable -synthesizes daughter strands complementary to target sequences from primers at 70 to 75°C -Taq adds nucleotides 5' 3'.
42. Many reptile species, including Alligator mississippiensis, exhibit a type of Environmental Sex Determination known as Temperature Dependent Sex Determination. Describe Temperature Dependent Sex Determination.
Temperature-dependent sex determination: a type of environmental sex determination in which the temperatures experienced during embryonic/larval development determine the sex of the offspring. 33 degrees- male #<33 and #>33 -female
91. How does translation stop (termination)? Be sure to mention release factors. List the three stop codons. What happens to the ribosome?
Termination happens when a stop codon in the mRNA (UAA, UAG, or UGA) enters the A site. >Stop codons are recognized by proteins called release factors, which fit neatly into the A site (though they aren't tRNAs). >the ribosome separates
2. Contrast the terms tetrad and bivalent when discussing chromosomes.
Tetrad- the association of a pair of homologous chromosomes (4 sister chromatids) physically held together by at least one DNA crossover. -the group of four sister chromatids found within the homologous pair -|||| Bivalent- one pair of chromosomes (sister chromatids) in a tetrad -the pair of two homologous chromosomes found during prophase 1 of meiosis 1 -XX
3. What is a tetrad, a dyad, and a monad when discussing chromosomes in Meiosis?
Tetrad-the association of a pair of homologous chromosomes physically held together by at least one DNA crossover -This physical attachment allows for alignment and segregation of the homologous chromosomes in the first meiotic division. Dyad- consists of 2 identical chromatids (sister chromatids) attached together at the centromere. -Chromosomes are in the dyad form before mitosis, and in the monad form after mitosis. Monad- a single piece of DNA -the monad chromosome
53. What is the function of the p450 aromatase gene?
The SRY protein (TDF) binds the p450 aromatase gene and inhibits its activity. >The p450 aromatase gene has a protein product that converts the male hormone testosterone to the female hormone estradiol.
52. What hormone/substance causes regression of the Mullerian duct?
The SRY protein (TDF) enhances the activity of the gene for: Mullerian Inhibitory Substance (MIS) >induces testicular development and the digression of female reproductive ducts. How? -inhibition of aromatase -decreased estrogens -regression of mullerian duct --> absent female sex structures
1. What is the central motif (dogma) in biology (and specifically molecular biology)?
The central dogma of biology describes how genes are first transcribed to RNA then the mRNA is translated into a corresponding protein sequence. Proteins can then be post-translationally modified, localized to certain locales within the cells, and ultimately degraded
Expressivity
The degree of effect produced by a penetrant genotype. A trait, although penetrant, may be quite variable in its expression
51. The embryonic Mullerian Duct becomes the male or female reproductive tract (circle one). The embryonic Wolffian Duct becomes the male or female reproductive tract (circle one).
The embryonic Mullerian Duct becomes the female reproductive tract. >leads to ovaries The embryonic Wolffian Duct becomes the male reproductive tract. >leads to testes
Nonlinearity of Genes
The most important reason why genetic edges are not additive is that the relation between genetic variation and trait variation is non linear >nonlinearity results because the effect of genetic variation is context dependent, and this makes the effect of simultaneous variation at several genes difficult to predict
72. What is meant when discussing translation by the statement that the genetic code shows degeneracy?
The occurrence of more than one codon for an amino acid (AA). >64 codons, but only 20 different amino acids >Most differ in only the 3rd (3′) base, with the 1st and 2nd being most important for distinguishing the AA Pros: -reduces the possibility of mutation as a result of base pairing errors in transcription and translation of DNA information -thereby increasing genotypic and phenotypic stability -allows for silent mutations
10. What is the map unit distance between two genes (aka what does the map unit distance indicate to a geneticist)?
The percent recombination between two markers indicates the map distance between them: 1% recombination = 1 map unit (m.u.). To determine the map distance between a pair of loci, count the number of SCO and DCO events, and use the following formula [the most common error is to neglect the DCO classes].
Penetrance
The percentage of individuals that show a particular phenotype to any degree among those capable of showing it -Affected by: >modifier genes >epistatic genes >suppressor genes in the rest of an organism's genome or because of modifying effects of the environment
37. Describe the term replication fork.
The replication fork is a very active area where DNA replication takes place. >It is created when DNA helicase unwinds the double helix structure of the DNA. >The replication fork looks like a fork in the road that is composed of a leading strand and a lagging strand of DNA
Homogametic sex
The sex (male or female) that produces gametes that are all alike with regard to sex chromosomes. For example, in the XX-XY sex-determining system, the female produces only X-bearing gametes.
Heterogametic sex
The sex (male or female) that produces two types of gametes with respect to sex chromosomes. For example, in the XX-XY sex-determining system, the male produces both X-bearing and Y-bearing gametes.
Pedigree Analysis
The study of an inherited trait in a group of related individuals to determine the pattern and characteristics of the trait, including: >mode of inheritance >age of onset >phenotypic variability
12. How do you figure out the map unit distance between two genes if the percentage linkage is over 20%?
The two parental types will be most abundant, the four single cross-over (SCO) recombinants will be next while the two double cross-over (DCO) recombinants will be least abundant. To determine the map distance between a pair of loci, count the number of SCO and DCO events, and use the following formula [the most common error is to neglect the DCO classes]. Map distance = % recombination = (# in SCO phenotypes + # in DCO phenotypes x 100) / (total # progeny) or follow the asymptotic curve
64. What are transcription factors in eukaryotic transcription (also known as trans-acting regulatory proteins)? What can transcription factors bind to?
Transcription Factors (TFs) function in the positive regulation of transcription but are not part of RNA polymerase TFs contain two functional domains: i) DNA - binding domain - binds selectively to Promoters and Enhancers. ii) trans- acting domain - involved in protein - protein interactions between TFs and between TFs and RNA Pol in the Promoter
48. Are diphosphate nucleotides or triphosphate nucleotides used as precursors during DNA and RNA replication and transcription? Why?
Triphosphates 2 of the phosphates are used for energy to attach the nucleotide in replication
12. Contrast the two models explaining chromosome separation: Traction Fiber vs. Pac-man.
Two models to explain chromosome separation by spindle fibers: 1. Traction-fiber: >Separation force is produced along the fibers (sliding model). >Best explains separation in metaphase and in meiosis. 2. Pac-man: >Separation forces by disassembly of microtubules at kinetochore (centromere) region. >Best explains separation in mitosis. • One or both models are probably responsible for separation in both mitosis and meiosis.
100. List all of the DNA technologies we discussed that used 32P (radioactive)?
Two screening processes: a) Recombinants (with foreign gene of interest) formed from these are screened by replica plating and autoradiography (32P - cDNA). -nitrocellulos -x-ray film Gel Electrophoresis -label 5' end of single-strand DNA with 32P (radioactive label) -Southern Blotting -Chain termination sequencing using ddNTPs labeled with 32P -restriction mapping using 32P marker
81. Not all host cells will take up the recombinant DNA, so we have to select or screen for cells that have taken up the recombinant DNA (because we aren't interested in host cells that don't contain the DNA of interest). Describe the techniques used to screen if a host cell has taken up your recombinant DNA. Hint: think about antibiotic resistance, X gal media, and replica plating and autoradiography.
Two screening processes: a) Recombinants (with foreign gene of interest) formed from these are screened by replica plating and autoradiography (32P - cDNA). -nitrocellulos -x-ray film b) Bacteria containing recombinant molecules can be screened. DNA segment inserts disrupt lac Z gene in pUC18 causing blue to white color change of colonies grown on Xgal media. Other bacteria can also be excluded by use of ampicillin in media, as the pUC18 vector contains an ampicillin-resistance gene. >Colonies produced from cells containing a recombinant plasmid are white, >whereas colonies from cells containing a nonrecombinant plasmid are blue.
71. What is unique about rRNA post-transcriptional modifications? Is that activity representative of rRNA's future function?
Unique: introns removed by autocatalytic activity of EXON regions -removed by their own exon, not by a spliceosome -this type of RNA has catalytic abilities WITHIN its own sequence -main unique point^^ Unique: the pre-rRNA is combined with proteins that will assist it in its future function of translation Large Subunit: 60S is made up of 5S rRNA, 5.8S rRNA, 28S rRNA as well as 50 other proteins Small Subunit: 40S is made up of 33 proteins as well as 18S rRNA. When the ribosomal subunits have been assembled, they are transported to the cytoplasm.
73. If you are using DNA of known character, you could create a cDNA library to enable you to study parts of the DNA of interest. cDNA is double stranded DNA made from single stranded mRNA of your DNA or gene(s) of interest. Describe the steps (and enzymes) involved in creating double stranded DNA from mRNA. What is unique about the enzyme reverse transcriptase? What enzyme cleaves that final hairpin loop?
Use DNA of Known Character 1. isolate and purify mRNA possessing a poly-A (polyadenylated) tail at its 3' end from a cell population 2. combine the polyadenylated mRNA with poly-dT primers, so that the primers bind with the poly-A tails of the mRNA 3. add reverse transcriptase and deoxyribonucleoside triphosphates, which will allow synthesis of a DNA strand (single-stranded cDNA) complementary to the mRNA in the 5'→3' direction away from the primer site. An mRNA-DNA double-stranded hybrid molecule is formed >what is unique about reverse transcriptase: transcribes single-stranded RNA into DNA. >This enzyme is able to synthesize a double helix DNA once the RNA has been reverse transcribed in a first step into a single-strand DNA. 4. use RNAse H to nick and digest the mRNA strand in various places. The remaining undigested RNA pieces will serve as primers for initiation of the synthetic action of DNA polymerase I. 5. use DNA polymerase I to synthesize a second DNA strand and to excise the remaining RNA primer pieces. cDNA (complementary DNA) with a hairpin loop on one end is then formed 6. use S1 nuclease to cleave the hairpin loop and to derive double-stranded cDNA, which can be used in the development of a cDNA library via cloning
b. Once the human and mouse cells are fused, the hybrid cells randomly shed (get rid of) human chromosomes. Geneticists can easily distinguish between the mouse and human chromosomes based on staining. Specific DNA markers can identify what chromosome has a specific sequence present. These markers are complementary to the DNA sequence and can bind to or "hybridize" to the DNA and be recognized such as with specific staining or fluorescence. Based on the cell lines and the media used, this information can be used to determine where certain genes are located (on which human chromosome).
Use a HAT medium for incubation -selective for cells that are both TK+ positive AND HPRT+ positive -human cells are TK+ -mouse cells are HPRT+ -if the synkaryon is formed, the cell will be positive for both >cells are incubated for ~30 generations Clone A: chrom 17, positive for TK+ Clone B: chrom 17 and 3, positive for TK+ Clone C: chrom 17, 3, and 20, positive for TK+ All clones have chromosome 17 in common and all clones are positive for TK+ → so that means that TK+ must be located on chromosome 17
75. The DNA pieces formed from the shotgun approach may be cloned. The DNA is inserted into a vector and placed into a host cell. Define vector and host cell. List at least one example of a vector. List an example of a prokaryotic and a eukaryotic host cell.
Vector: a DNA molecule used as a vehicle to artificially carry foreign genetic material into another cell, where it can be replicated and/or expressed (e.g., pUC18, plasmid, cosmid, Lambda phages) >A vector containing foreign DNA is termed recombinant DNA. >DNA that has been fragmented by a restriction endonuclease (EcoRI makes sticky ends) can be mixed and then ligated (DNA Ligase) with a vector >Recombinant DNA molecule transferred to a host cell (bacterium) Host Cell: A cell that harbors foreign molecules, viruses, or microorganisms. For example, a cell being host to a virus. >A cell that has been introduced with DNA (or RNA), such as a bacterial cell acting as a host cell for the DNA isolated from a bacteriophage >Prokaryotic: E. coli (bacterium) >Eukaryotic: Saccharomyces cerevisiae (yeast) >once inside the host cell, the recombinant vector (recombinant DNA molecule) can undergo replication to produce many copies of clones (up to 500) of the recombinant DNA molecule
27. What else (naturally) has the capability to cause DNA mutations? Hint: It is debatable whether these are considered living or not.
Viruses
Backcross versus Testcross
When an F1 individual is crossed with one of the two parents from which it was derived, it is known as back cross. On the other hand, if an F1 individual is crossed with recessive parent, both phenotypes appear in the progeny. Such back cross with recessive parent is said to be test cross
27. Explain why the endosperm is 3n after fertilization. What is the purpose of the endosperm?
Why 3n? union of a sperm cell with two polar nuclei during double fertilization Function? provides nourishment to the developing embryo in angiosperm seeds.
74. What is the wobble idea? Which nucleotide base positions/locations does wobble occur (mention both the anticodon nucleotide and the codon nucleotide)?
Wobble- The ability of t-RNA anticodons to recognize different codons specifying a certain AA. >occurs between the 1st (5′) base of an anticodon of t-RNA and the 3rd (3′) base of a codon. >Codons (mRNA) are read in the 5' --> 3' order >Anticodons (tRNA) are a set of 3 nucleotides that match in the 3'-->5' order >Hydrogen bonding between anticodon and codon bases at the 1st and 2nd sites of the codon (2nd and 3rd sites of the anticodon) are "tight".
32. Is the X or the Y chromosome larger?
X chromosome is larger
59. Why are normal calico cats always female?
X inactivation (lyon hypothesis/lyonization) >a female cat that is heterozygous for the orange and black coat-color alleles and shows the classic "calico" pattern of orange, black, and white fur X^BX^O >allele for black is expressed in some sections of fur >allele for orange is expressed in some sections of fur >NO BLENDING
36. How is protenor sex determined? What is the sex of a protenor with 1X? With 2X?
XX/X0-> 1:1 ratio of sex in offspring. depends on the random distribution of x chromosome in male gametes. XX = female X__ = male
60. To get a male calico cat, what would his genotype have to be? What aneuploid condition is this in humans?
XXY : male cat -infertile -testicular hypoplasia X^BX^OY Klinefelters syndrome in humans
30. What is the genotype of a normal human male? What is the genotype of a normal human female?
XY -Male has unlike sex chromosomes (heterogametic) (i.e., mammals) XX -Female has like sex chromosomes (homogametic)
66. Allele frequencies in a population can be compared between the generations by using the Chi-square goodness of fit test. What is the formula for the Chi-Square test?
X^2 = Σ(observed - expected)^2/ expected Σ= summation
45. A genetic disorder of DNA repair in which the body's normal ability to remove damage caused by ultraviolet light is deficient. This leads to multiple basaliomas and other skin malignancies at a young age. In severe cases, it is necessary to avoid sunlight. What is the name of this genetic disorder?
Xeroderma Pigmentosum, or XP • A genetic disorder of DNA repair in which the body's normal ability to remove damage caused by ultraviolet (UV) light is deficient. • This leads to multiple basaliomas and other skin malignancies at a young age. In severe cases, it is necessary to avoid sunlight. • Damage to DNA in epidermal cells occurs during exposure to UV light. • The absorption of the high energy light leads to the formation of pyrimidine dimers. • The pathway, using multiple enzymes, which repairs the UV-damage in healthy cells is called nucleotide excision repair. • Briefly, the damage is excised by exonucleases, then the gap is filled by DNA polymerase I and sealed by DNA ligase. • The most common defect in XP is a genetic defect whereby nucleotide excision repair enzymes are mutated, leading to less or no repair of UV-lesions. • Unrepaired damage can lead to mutations, altering the information of the DNA. • If mutations affect important genes, like tumour suppressor genes (e.g. p53) or proto-oncogenes, then this may lead to cancer. • Since in XP patients the frequencies of mutations is much elevated, these patients have a predisposition for cancer.
32. Which DNA form is a left handed helix?
Z form DNA
19. What is the importance of the zona reaction and the vitelline block during fertilization?
Zona Reaction: a modification of the zona pellucida in response to fertilization, which alters the solubility and binding properties of the zona pellucida -Cortical reaction creates barrierat ZP level. -ZP changes to block polyspermy -Polyspermy is the fertilization of oocyte by more than one sperm, resulting in embryo death Vitelline Block- Cortical reaction can alter oocyte membrane, resulting in a vitelline block to prevent additional sperm fusion all together: Female defenses select for ever more aggressive male sperm, however, leading to an evolutionary arms race. On the one hand, polyspermy creates inviable zygotes and lowers female fitness.
Duration of Interphase and Mitosis
a cell will spend 15 hours in interphase, but only 1 hour in mitosis
31. What is a silent mutation?
a change in the sequence of nucleotide bases which constitutes DNA, without a subsequent change in the amino acid or the function of the overall protein. >typically in the 3rd nucleotide (wobble/degeneracy) >Sometimes a single amino acid will change, but if it has the same properties as the amino acid it replaced, little to no change will happen
32. What is a mis-sense mutation?
a change in the third nucleotide is not deleterious (silent mutation) But a change in one of the first two nucleotides in the codon may cause what is known as a mis-sense mutation, which could be detrimental.
Oncogene
a gene that in certain circumstances can transform a cell into a tumor cell
Knockout Gene
a gene used to replace a normal gene that does not produce the protein product of the normal gene
Punnet Square Method
a method of predicting the genotypes and phenotypes of offspring in genetic crosses
70. What cross in chickens will produce offspring that can be distinguished by sex at hatch just by looking at the down (feather) color in the chicks?
a non-barred male (bb) crossed with a true-breeding barred hen (B-) >males have lighter heads, sometimes with a white or yellow spot >females have darker down color often with a black or brown spot or stripes on their heads or with darker stripes on their backs.
Nucleolus
a non-membrane bound structure composed of proteins and nucleic acids that is located within the nucleus.
33. What is a non-sense mutation?
a one-base insertion that changes a codon to a stop codon is considered a nonsense mutation and leads to a truncated protein. >This could greatly decrease the activity of a protein, and could sometimes be lethal. >A suppressor mutation is an addition mutation following a deletion mutation, or a deletion mutation following an addition mutation.
28. What bond forms between a 3'carbon's hydroxyl group and a 5'carbon's phosphate group in the sugar phosphate backbone of DNA or RNA.
a phosphodiester linkage phospho- phosphorous di- two ester- bond connecting the atom doubly bonded to oxygen
Semidominance
a relationship between alleles of a single gene that appears like the blending model of inheritance aka dominance lacking aka incomplete dominance aka intermediate dominance *you canNOT do a test cross with semidominance (RR vs. RR' vs. R'R'), does not work You already know if an organism is heterozygote because they have their own intermediate phenotype. you KNOW a roan is RR'
Complete Dominance
a relationship in which one allele is completely dominant over another Homo dom and heterozygous are indistinguishable *you CAN do a testcross (Rr vs. rr)
21. What is the micropyle in the female part of a flower?
a small opening in the surface of an ovule, through which the pollen tube penetrates, often visible as a small pore in the ripe seed (in seed it is where water enters). simple terms: where the pollen grain grows down into the ovarythe opening
Chromosome
a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.
Meiosis
a type of cell division that results in four daughter cells (1n, haploid) each with half the number of chromosomes of the parent cell (2n, diploid), as in the production of gametes
71. Describe the two main purposes of DNA cloning.
a) Artificial (in vitro) production of commercially important gene products. b) Increasing amounts of DNA that can be used for determining the nucleotide sequence of the gene of interest. -Ex., PCR (polymerase chain reaction)
91. What are the steps of Southern Blotting?
a) Digestion with restriction endonuclease enzymes b) Electrophoresis c) Use of radioactive probe d) Autoradiography (x-ray film) a) Digestion with restriction endonuclease enzymes 1. DNA fragments are generated through restriction endonuclease digestion. Those fragments generated by different restriction enzymes are kept isolated from eachother. a. preparation of homogenous single strand of DNA b. label 5' end of ss DNA with 32P (radioactive label) c. divide DNA into 4 separate tubes d. cleavate of specific nucleotides in each one of the four tubes with either A, G, C, or T reagent (restriction endonuclease digestion) to generate short fragments used to sequence DNA e. sequential placement of DNA samples containg the fragments generated by A, G, C, or T digestion into wells at top (cathode end) of four separate adjacent lanes of gel b) Gel Electrophoresis 2. Agarose (for separation of large fragments) or polyacrylamide (for separation of small fragments) gels are prepared and placed in a horizontal gel electrophoresis apparatus 3. the fragments produced by different restriction enzymes (different base sequence recognition sites) are loaded into separate lanes (columns) of gel, with the first lane being occupied by a radioactive size marker 4. once separated by size exclusion and electrical charge, fragment positions in each lane can be visualized and photographed with the use of an ethidium bromide label 5. the gel is placed underneath a nitrocellulose binding filter and above a wick (sponge) partially immersed in a buffer solution. The upward movement of the buffer, via capillary action, transfers the DNA fragments from the gel onto the nitrocellulose filter 6. the double-stranded DNA fragments on the filter are denatured into single strands by treatment with a denaturation (alkaline) solution c) Use of radioactive probe 7. the filter is then placed in a heat sealed bag with a radioactively labeled single-stranded probe for a minimum of 6 hours at 37°C-42°C the probe will hybridize with the single-stranded fragments on the filter, if their base sequences are complimentary 8. the filter is washed to remove unbound probe, leaving only labeled double-stranded hybrid DNA on the filter d) Autoradiography (x-ray film) 9. the filter is finally dried and X-ray film is applied over the top of the filter to produce an autoradiogram that will allow only those bands that have hybridized with the probe to be visualized. 10. knowing the point at which fragments were cut (corresponding to their respective restriction enzyme lane) and relative positioning of the fragments (bands) to one another on the gel
Simple Rules for Expansion (a+b)^n
a) The power of the binomial chosen (n) is determined by the number of coins, people, etc. you are considering. b) The number of terms in the expansion is n + 1. c) The exponent of ''a'' in any term after the first is one less than in the preceding term; the exponent of ''b'' is one more than in the preceding term. (The exponent of ''a'' in the first term is always ''n'' and there is no ''b'' in the first term.) d) The coefficient of any term after the first is obtained by multiplying the coefficient of the preceding term by the exponent of ''a'' and dividing by the number of terms you have written. (The coefficient of the first term is always one.) e) The coefficient may also be determined by referring to pascals pyramid. f) The sum of the exponents always equals "n".
72. Name the two means by which DNA is derived for cloning.
a) Use DNA of known character: • purified mRNA →single stranded cDNA (reverse transcriptase) • cDNA →double stranded DNA (DNA polymerase 1) • Formation of cDNA library. b) Shot-gun approach: • Use one of a variety of restriction endonucleases (ex. EcoR1) on a genome to generate specific DNA fragments. • shotgun method attaches fragments that match/overlap
62. Describe rho-dependent termination and rho-independent termination of prokaryotic transcription.
a) rho-independent: rich G-C dyad region followed by series of A's and U's (6-8) on RNA transcript causes formation of hairpin structure and consequently causes RNA polymerase to be knocked off. -hair pin kicks it off b) rho-dependent: rho protein (hexamer) binds with RNA transcript at rut site and causes it to fold around it, and upon transclocation and further wrapping pulls the transcript away from the polymerase. -spool of thread: mRNA wraps around protein
6. You perform two-factor crosses between F1 individuals and test-cross parents. Suppose you obtain the genotypic ratios found below in a, b, and c in the offspring among your different crosses. Label the ratios as Independent Assortment, Complete Linkage, or Normal Linkage. a. 6:1:7:2 b. 1:1:1:1 c. 1:1
a. 6:1:7:2- normal linkage b. 1:1:1:1- Independent Assortment c. 1:1- complete linkage Independent Assortment: -No linkage, separate chromosomes -50% parental type progeny -50% recombinant progeny Complete Linkage: -Total linkage, no break between genes -genes are SOOO close together, that recombination is not possible -100% parental type progeny Normal Linkage: -There is some relative distance between genes, some crossing over occurs -dependent on how distant genes are -% parental progeny > % recombinant progeny
83. Name the three main steps in PCR (Polymerase Chain Reaction). This occurs in a machine called a thermal cycler. It takes about 3 hours to run through 25-30 cycles of these three steps: a. _____________ Occurs at 90-95ºC b. _____________ Occurs at 37-70ºC c. _____________ Occurs at 70-75ºC
a. Denaturation Occurs at 90-95ºC b. Annealing Occurs at 37-70ºC c. Extension Occurs at 70-75ºC
15. Place the following terms in order of progression of spermatogenesis: a. Spermatid, Secondary Spermatocyte, Sperm, Spermatogonium, Primary Spermatocyte b. When does the first meiotic division occur? When does the second meiotic division occur? Ex: Which division occurs between the Primary and Secondary Spermatocyte?
a. In Order of Progression: 1. spermatogonium 2. primary spermatocyte 3. secondary spermatocyte(2) 4. spermatids(4) 5. sperm(4) b. I) Spermatocytogenesis: spermatogonium(2N)→mitosis → primary spermatocyte(2N) →first meiotic division → secondary spermatocyte(1N)→second meiotic division→ spermatid(1N) 1x (2N, 4C) → 4x(1N, 1C) "Genetic" II) Spermiogenesis: Spermatid → Spermatozoan (1N, 1C) → (1N, 1C) "Metamorphic" - loss of cytoplasm - addition of flagellum - addition of acrosome (all of these aid sperm, lots of traveling to do!)
16. Place the following terms in order of progression of oogenesis: a. Primary Oocyte, Oogonium, First Polar Body, Second Polar Body, Ovum (Egg), Secondary Oocyte, Ootid b. When does the first meiotic division occur? When does the second meiotic division occur? c. When are the first and second polar bodies formed? In mammals, what triggers the formations of the first and second polar bodies?
a. Order of Progression: 1. oogonium 2. primary oocyte 3. secondary oocyte and first polar body 4. second polar body and ootid 5. ovum(egg) b. FETUS 1. Oogonium (lx) (2n) undergoes cell growth and mitotic division to produce oogonia (nx) (2n). 2. Start of Meiosis I (Prophase I).Transformation of oogonium (1x) (2n) to 1º (primary) oocyte (1x) (2n) by passage through Prophase I up to zygotene/pachytene and cell growth. BIRTH 3. 1º oocyte (2n) arrested in Prophase I (zygotene/pachytene). 4. Growth of follicle, 1º oocyte (2n), and zona pellucida. PUBERTY 5. Pre-ovulatory surge of luteinizing hormone (LH). 6. Resumption of Meiosis I. 7. 1º oocyte (lx) (2n) transformed to 2º oocyte (1x) (1n) and first polar body (1x) (1n) after completion of Meiosis I. 8. 2º oocyte arrested in Meiosis II (Metaphase II) FERTILIZATON 9. Sperm (ln) penetration. 10. Meiosis II resumes. 11. Formation of zygote (2n). 12. Formation of second polar body (1n). 13. First polar body (1n) completes mitotic division to produce two more polar bodies (1n) c. Formation of Polar Bodies: triggered by luteinizing hormone (LH) Puberty: 7. 1º oocyte (lx) (2n) transformed to 2º oocyte (1x) (1n) and first polar body (1x) (1n) after completion of Meiosis I. Fertilization: 12. Formation of second polar body (1n). 13. First polar body (1n) completes mitotic division to produce two more polar bodies (1n)
Centromere Location: close to end
acrocentric
87. Name the two kinds of gels we discussed that are used in gel electrophoresis? Aka what are the gels made of? Hint: you make the gel almost exactly like you make Jello-only you don't have to refrigerate the gel-it solidifies at room temperature.
agarose or polyacrylamide gel electrophoresis (Southern Blotting) Agarose: polysaccharide, generally extracted from certain red seaweed. It is a linear polymer made up of the repeating unit of agarobiose, which is a disaccharide Polyacrylamide Gel: prepared by free radical polymerization of acrylamide and a comonomer crosslinker such as bis-acrylamide. Agarose gels can be used to resolve large fragments of DNA. Polyacrylamide gels are used to separate shorter nucleic acids, generally in the range of 1−1000 base pairs, based on the concentration used.
Chicken vs. Summer Squash
chickens only produce novel phenotypes (4 total) Summer squash produce modified F2 phenotypes (3 total, a single dominant trait where A-bb or B-aa will produce a sphere squash)
15. Does crossing-over occur in male Drosophila melanogaster?
crossing over ONLY occurs in FEMALE drosophila lack of required proteins in the male drosophila before the meiosis process
Fork-line method
determines potential gametes a person can make
95. Chain termination sequencing uses small amounts of dideoxyriboneucleotide triphosphate precursors (ddNTPs). Dideoxy means there are two hydroxyl groups (-OH) missing from the ribose sugar instead of the usual one in DNA (at carbon #2). At which carbon position (#) is the second hydroxyl group missing? Why would this stop/terminate DNA synthesis?
dideoxyriboneucleotide triphosphate precursors (ddNTPs) -missing an OH from the 2' AND 3' carbon -Without the 3' OH, no more nucleotides can be added -DNA polymerase falls off. -The resulting newly synthesized DNA chains will be a mixture of lengths, depending on how long the chain was when a ddNTP was randomly incorporated. -the triphosphate provides energy
Continuous Phenotype
do not fall into discrete classes; a segregating population will show a continuous distribution of phenotypes
Additivity Hypothesis
each factor contributing to a phenotype has a small effect individually; overall phenotype is the collective sum of the contributing factors WRONG in reality we do not know all the contributing factors, so we can only calculate the probability of disease
Addition Rule
forming gametes from parent genotypes
Product Rule
forming progeny genotypes from parent gametes
65. Know how to calculate the probability of a gamete carrying a particular gene. Know how to calculate the probability of particular gametes fusing to form homozygous and heterozygous individuals in that population.
fr(A) = p fr(a) = q frequency of a gamete with a particular phenotype is either: p^2 (AA) pq (Aa) q^2 (aa) if two heterozygotes are mating it is 2pq because the chance of a heterozygous progeny is (2/4)
Dyskeratosis congenita
genetic disease causing accelerated shortening of telomeres. >May result from lowered telomerase activity
The Importance of Context in Genetics
genetic effects can be altered by their surroundings, and this determines the inheritance of traits such as flower color and the likelihood of cancer
Genotype
genetic makeup of an organism
29. Low intensity x long time (chronic dosage) = ?
high intensity x short time (acute dosage).
9. Does pairing of homologous chromosomes occur during Meiosis I, Meiosis II, and/or during Mitosis?
homologous chromosomes ONLY pair during meiosis I -enables crossing over and reduction division
Rules of Plant Height
homozygous recessive individual = 10 cm tall for every dominant allele you add to the genotype of an individual add 10 cm per each dom allele starting with a base of 10 cm
Pleiotropism Example 1
i) strabismus (crossed eyes, nerves in brain have created "snake eyes") and creamy white fur with chocolate stripes in white tigers of the Cincinnati zoo >mutant gene has been accentuated >cross between a Siberian and a Bengal tiger
Individuals and Populations
if individuals can be represented as points on a phenotypic surface, then populations are clouds of points
Pleiotropism Example 2
ii) resistance to malaria and sickle-shaped red blood cells in sickle cell anemia.
4. Who in 1928 found evidence for the transfer of a "transforming principle" between bacterial cells? (Hint: This was the experiment with 3S virulent and 2R non-virulent streptococcus pneumonia strains injected into mice).
in 1928 Frederick Griffith showed evidence for the transfer of a "transforming principle" between bacterial cells -he conducted an experiment involving two strains of the bacterium Streptococcus pneumoniae; one strain was lethal to mice (Living IIIS: virulent) and the other was harmless (Living IIR: avirulent) -when he combined the living IIR (avirulent) with heat-killed IIIS (virulent but now dead) the mouse died -the heat killed IIIS leaked genetic material, which was taken up by IIR, causing it to become virulent -living IIIS cells were recovered
7. In a normal linkage situation, which testcross offspring are the in highest percentage: the parental or the recombinant types? Why? Know how to use this information to determine the configuration of the F1 parent (aka if the F1 parent was cis or trans).
in normal linkage, gametes or testcross progeny that are in the highest percentage are parental types or non-crossovers (N.C.O), whereas those in the lowest percentage are recombinant types or crossovers 0% (CL) < R < 50% (IA) 50% (IA) < P < 100% (CL) ex: R= 40%, P= 60% WHY?- the percentage of recombination is directly related to the distance in microunits between the genes -if genes A and D are 10 microunits apart, then they will have 10% recombinant progeny (up to 20%, then asymptotic curve) -the closer two genes are, the fewer recombinant progeny they can produce -if they are TOO far apart double cross over occurs, revert back to parental type Trans or Cis Parent?
14. Where does oogenesis occur?
in the outermost layers of the ovaries until the mature ovum moves to the fallopian tube
Ribosomal RNA (rRNA)
is transcribed and assembled within the nucleolus
18. What is the acrosome reaction? Why is it important for sperm?
it helps the sperm penetrate the egg and prevents other sperm from invading the egg
44. What is the difference between the leading and the lagging strand in DNA replication?
leading strand: is replicated continuously in the same direction as the moving fork -the free end is the 3' end -DNA polymerase III moves in the 3' --> 5' direction and synthesizes 5' -- 3' DNA -DNA polymerase travels towards the replication fork on this strand lagging strand: is replicated in the opposite direction in the form of short Okazaki fragments -the free end is the 5' end -due to the direction that DNA polymerase III moves, it can only synthesize short fragments -DNA polymerase travels away from the replication fork on this strand, hen returns back toward the replication fork to create another fragment
94. Be able to design an mRNA strand given an antisense (template) DNA strand. Be able to assign amino acids to the particular codons in an mRNA strand (think about the direction of the codon and the anticodon. Are they 5'-3' or 3'-5'? Which directions do they need to be in to be able to complementary bind?)
mRNA 5' AUG UUC GGU ... 3' tRNA 3'UAC5' 3'AAG5' 3'CCA5' mRNA is complimentary to antisense strand mRNA is complimentary to tRNA mRNA is identical (except U not T) to sense strand tRNA order is identical (except U not T) to antisense strand
multihybrid crosses
matings between the F1 progeny of pure breeding parents that differed in two or more unrelated traits/genes
54. What could happen in a male organism if the male sex hormones controlling secondary sex characteristics (testosterone, dihydrotestoterone) are not produced and secreted?
may cause genotypic and phenotypic sex contrast: >Lack of male sex hormone and presence of female sex hormone from ovary: -stimulates development of 2º sexual organs and characteristics (fem). >Presence of male sex hormone from testis: -stimulates development of 2º sexual organs and characteristics (male).
1. Naked DNA
measured in base pairs, linear
Centromere Location: Middle
metacentric
Phenotypic landscapes are ___________________
multidimensional >mutations of the same gene in different individuals will result in different effects. >individuals X and Y have same phenotype, but different alleles for genes A and B >Person X is unaffected, but person Y is dramatically affected. this is due to contour and a nonlinear relationship
c. In the example from class, what kind of mutant are the mouse cells (what gene)? What kind of mutant are the human cells? [Hint: a mutant cell is negative (or lacks) a certain gene.]
mutant cell- negative for a certain gene human cells are HPRT- mouse cells are TK-
Gregor Mendel Importance
no one realized the importance of Mendel's paper during his life. He remained in the monastery until his death in 1884
F2 generation
offspring of the F1 generation
74. What kinds of enzymes does the "shotgun approach" use? List an example of this kind of enzyme.
one of a variety of restriction endonucleases (ex. EcoRI; an enyzme isolated from E. coli, HindIII, BamHI, TaqI) -enzymes that locate a recognition sequence at which they cut both strands of double helical DNA into fragments called restriction fragments -these enzymes serve as natural defenses against invading viruses -bacterium protects its own DNA from a particular restriction enzyme by modifying (ex. methylation) the recognition sequence on its DNA specific for that enzyme
63. Hardy-Weinberg Law utilizes the two equations listed below. Please describe what p and q represent. What do p2, 2pq, and q2 represent? a. p + q = 1 b. p 2 + 2pq + q2 = 1
p + q = 1 p= frequency of dominant allele q= frequency of recessive allele p^2 + 2pq + q^2 = 1 p^2 = # of homozygous dominant individuals (AA) 2pq = # of heterozygous individuals (Aa) q^2 = # of homozygous recessive individuals (aa)
Mitosis
part of eukaryotic cell division during which the cell nucleus divides -ONLY in somatic cells
89. What bond forms between amino acids?
peptide bond
96. Distinguish between the amino end and the carboxyl end of a protein (aka a strand of amino acids).
peptide sequences are written N-terminus (1st) to C-terminus (last), left to right N-terminus has free amino group, positively charged C-terminus has free carboxyl group, negatively charged
Telomere
piece of DNA at the very tip of each cell's chromosomes >susceptible to degradation >associated with cell life ----------------------------------------- (long) >associated with cell life ---------- (short)
26. In a nucleotide, why do you think the carbons in the ribose are numbered with a prime symbol? Ex: 1', 2', 3', 4'?
prime (') is used to denote the positions of carbon on a ring of deoxyribose or ribose. The prime distinguishes places on these two chemicals (the sugar portion of the molecule), rather than places on other parts of DNA or RNA, like phosphate groups or nucleic acids.
Mendel's Second Law
principle of independent assortment -Either allele of one gene pair can enter a gamete with either allele of any other gene pair and all possible combinations are produced in equal proportions ex: pea plants produce yellow or green pods, and round or wrinkled pods, and these are produced in equal proportions. do not affect eachother
Phases of Mitosis
prophase- chromosomes become visible as paired chromatids and the nuclear envelope disappears -mitotic spindles begin to form (centrosome) metaphase- chromosomes line up along metaphase plate (imaginary line) -pulled by mitotic spindles anaphase- chromosomes move away from one another by their centromere (spindles attach to kinetocore portion of the centromere) to opposite poles of the spindle telophase-the chromatids or chromosomes move to opposite ends of the cell and two nuclei are formed
The Stack Method
put the parental allele combos ontop of one another to determine the number of genotypes and phenotypes. use these numbers to determine the genotypic and phenotypic ratios
94. How do you read the DNA sequence on the gel after performing the restriction mapping technique? Which end of the DNA (5' or 3') is at the bottom of the gel? Do you know the first nucleotide using this technique?
read from bottom to top bottom is the least amount of base pairs from restriction site (top is farthest from restriction site) EcoRI cuts DNA at the sequence GTTAAC, so if you know where EcoRI is, you know that the first nucleotide there is a G DOESN'T MATTER
98. How do you read the DNA sequence on the gel after performing the chain termination sequencing using radioactive labeling (so you have four lanes on the gel)? Which end of the DNA (5' or 3') is at the bottom of the gel? Are you reading the sequence of your original DNA strand or its complementary strand off the gel?
read gel from bottom to the top the bottom of the gel is the 5' end you're reading the original DNA strand
10. DNA has been packaged into the loop packaging stage during interphase and progresses to a rosette packaging by the Leptotene stage of Prophase I. What extent is the DNA packaged by the Pachytene stage of Prophase I?
review of DNA packaging: 1. naked DNA 2. Nucelosome 3. Solenoid 4. Loop 5. Rosette 6. Coil 7. Chromatid/chromosome What extent is the DNA packaged by the Pachytene stage of Prophase I? 7. chromatid/chromosome
Pea Comb
rrP-
Single Comb
rrpp
13. Where in the testes does spermatogenesis primarily occur?
seminiferous tubules of the testes
Cell Cycle
series of events that cells go through as they grow and divide G0 (non-dividing) Interphase (G1, S, G2) Mitosis (PMAT)
Gonosomes
sex chromosomes; 23rd pair
35. Are silent mutations, mis-sense mutations, non-sense mutations, and deletions and insertions all also considered point mutations?
silent mutations, mis-sense mutations, and non-sense mutations are all considered point mutations insertions and deletions can be considered point mutations if it involves one base pair, but insertions and deletions can be any size
Co-Dominance
situation in which both alleles of a gene contribute to the phenotype of the organism BOTH are expressed independently, no blending
Polygene Examples
skin color, eye color
47. What enzyme does the drug Ciprofloxacin target and inhibit in a bacterial cell? (Hint: this inhibition prevents the bacteria from replicating its DNA).
specifically targets an enzyme called DNA gyrase in bacteria. >This enzyme relaxes tightly wound chromosomal DNA, thereby allowing DNA replication to proceed >by inhibiting gyrase DNA replication can not occur
Centromere Location: between middle and end
submetacentric
18. What radioactive material is commonly used in autoradiography?
sulfur-35 (sulfur is in proteins, used in Hershey & Chase) hydrogen-3 (used by Cairns) carbon-14 125-iodine phosphorus-32 (phosphorous is in DNA, used in Hershey & Chase) >In Cairns' method, E. coli bacteria are cultured in a medium containing thymidine that has been labelled with a radioactive isotope of hydrogen, tritium (3H). (35S, 3H, 14C, 125I and 32P, respectively)
Centromere Location: at end
telocentric
86. Where in the full ribosome (which site) does the second amino acid bind with the help of an elongation factor?
the A-site (amino acyl site) -site of all incoming amino acids
85. During translation, where does the first "charged" tRNA molecule (aka tRNA containing methionine or formyl-methionine) bind in the ribosome (which site)?
the P-site (peptidyl site)
phenotypic plasticity
the ability of an organism to change its phenotype in response to changes in the environment.
Test Cross Ratio
the amount of 1s in the ratio = 2^n n = # of heterozygous test pairs in consideration
52. How is the mRNA different from the sense (coding) strand?
the coding/sense strand has the same sequence as mRNA transcript EXCEPT it posses T (DNA) instead of U (RNA)
allele
the different forms of a gene; could be dominant or recessive
Environmental Genetic Interaction
the environment (ex. diet) of an organism can affect how severely a gene is expressed. Epigenetics ex. Severity of atherosclerosis in genetically selected birds (for high blood cholesterol concentration Chol. added to diet: -if HL -> severe -if LL -> moderate No chol. diet: -if HL -> moderate -if LL -> low
59. If no free hydroxyl group on the 3' carbon on ribose and no primer are necessary for initiation of transcription, what causes the initiation of transcription in prokaryotes and eukaryotes?
the holoenzyme binding to the promoter site
3. Solenoid
the nucleosomes are coiled further into a solenoid fiber >300 angstroms (30nm)
n
the number of different heterozygous gene pairs in an F1 genotype
"Genetics"
the term "genetics" (Greek- to generate) was coined by William Bateson in 1905
57. As selection occurs on a quantitative trait, will the curve become narrower or wider?
the wider the curve, the more loci affecting the trait, polygenic BUTTTTT as selection proceeds, curve gets narrower and narrower
The #^n Rule Exception
these rules only work with heterozygosity. otherwise the stack method can be used to determine phenotypes and genotypes.
Discontinuous Phenotypes
traits with only a few possible phenotypes that fall into discrete classes; phenotype is controlled by one or only a few genes (ex.: tall or short pea plants; red, pink or white snapdragon flowers).
90. An elongation factor also aids in the translocation step. What happens during translocation? Which direction (3' to 5' or 5' to 3') does translocation occur (think about the mRNA)?
translocation is the process that advances the mRNA-tRNA moiety on the ribosome, to allow the next codon to move into the decoding center All mRNAs are read in the 5´ to 3´ direction
Epiloia
tuberous sclerosis -is a dominantly inherited congential disease -includes: >Adenoma sebaceum (angiofibromas involving sebaceous glands) and benign tumor-like malformations in the nervous system, heart, and kidneys >epilepsy >mental retardation this is a dominant lethal trait
25. What is an example of non-ionizing radiation that can cause mutations?
ultraviolet light
11. When does the percentage cross over equal the map unit distance?
up to 20%
16. Please explain the importance of a three factor cross. Consider double cross-over events.
very useful for genes that exceed 20 m.u. distance between them A third gene that maps between two other loci can be used to identify two-factor crosses that might otherwise go undetected due to the occurrence of double crossovers in addition, this allows one to order the three factors involved or part of a linkage group (whats on outside, whats on middle) It will also help correct the underestimation, at least in part, of the mapping distance between two factors which would have been estimated based on a two factor cross
41. Deamination and depurination events are considered hydrolytic reactions. What molecule causes the DNA damage?
water (H2O)
42. When DNA ligase repairs a phosphodiester bond in the sugar phosphate backbone of DNA, what molecule is produced?
water (H2O)
12. What is semiconservative replication?
when the double stranded DNA helix is replicated, each of the two new double-stranded DNA helices consisted of one strand from the original helix and one newly synthesized. -parent strand and daughter strand
Dominant Lethality
whenever lethal allele is expressed, individual dies. therefore no cross can be performed ex. epiloia in humans L__ = lethal ll = normal
Mice Recessive Epistasis
white is the precursor trait aa (BB, Bb, bb) if gene a is dominant (A)--> you get a colored intermediate bb (Aa, AA) if gene b is dominant (B) --> you get an agouti final product A_B_
9. How do you calculate the percentage cross-over/recombination when given the numbers of each of the genotypes of the offspring resulting from a cross between an F1 parent and a testcross parent?
you take the total percentage of recombinant offspring (# of genotype/N) N= total # of offspring AD: 45% ad: 45% Ad: 5% aD: 5% 10% recombination
23. What is the minimal level of DNA base pair mistakes allowed naturally without causing problems associated with mutations?
• Mistakes in DNA nucleotide (base pair) selection are corrected to some extent by DNA polymerase activity • a minimal level of mistakes (1 x 10^-10 = errors/synthesized nucleotide) may still normally go unrepaired. • The level of this occurrence may be increased by environmental mutagenic agents.
19. Mutations are usually lethal and recessive. When could a mutation be a good thing?
• Mutations introduce variation (alleles) and, thus, help drive natural selection. • Mutations are the basic source of all genetic variation. • However, too many mutations would disrupt the normal transmission of genetic material from generation to generation.
18. We went over an example of a mutation involving chromosome 22 and chromosome 9 in humans. This mutation involved translocation (a type of aberration) where chromosome 22 becomes abnormally shortened which leads to CML (chronic myeloid leukemia). What is the name of the shortened chromosome 22 that causes this disease?
• Philadelphia chromosome (Ph chromosome) is an abnormality that causes chronic myeloid leukemia (CML) in humans. • The Ph chromosome is chromosome 22 that has become involved in a translocation (an exchange of material) with chromosome 9. • In this mutational process, chromosome 22 becomes abnormally shortened. • This translocation takes place in a single bone marrow cell, and through clonal expansion of this one mutant cell, gives rise to CML. Chronic myelogenous leukemia (CML) is an uncommon type of cancer of the bone marrow — the spongy tissue inside bones where blood cells are made. CML causes an increased number of white blood cells in the blood
