Genetics

'Model Organisms' are species with special attributes that make them a good example of a biological principle or process. Which of the following attributes would NOT be a good attribute for a model organism to study the principles of meiosis:

the organism's cells only divide by mitosis, never by meiosis

Choose the answer that best completes the statement. Daughter cells of a diploid cell that underwent mitosis are ____________.

diploid (2n)

Karyotypes are pictures of metaphase chromosomes

Extracted from cells and treated with a dye 'Squashed' or 'spread' out of a cell Giemsa (common) - G band pattern Reveals areas of chromosome rich in nucleotide A,T Others- Q bands, R bands, and C bands

Is movement part of synapsis?

'Rapid movements of chromatin axes in zygotene in 5 s intervals.'

Which enzyme is attracted and stabilized by general transcription factors and regulatory transcription factors to initiate transcription?

RNA polymerase II

Gynandromorphs are very rare aneuploid mosaics where up to half of an organism's somatic cells have a different sex chromosome composition and are genetically a different sex. For gynandromorphs of species with XX-XY or ZZ-ZW chromosomal sex determination, which chromosome(s) must have experienced nondisjunction?

A sex chromosome

Telomeres interact with telomerase and shelterin

Active telomerase reverse transcriptase (TERT) extends the telomere Makes a series of DNA repeats on one strand Produces a large looped overhang Shelterin caps the telomere and protects it

Pyrimidines bases include cytosine, thymine, and uracil. Which of the following are purines?

Adenine and guanine

small interfering RNAs (siRNAs) are made from one strand of many double-stranded RNA chunks

After being cleaved by Dicer, many different parts of the double-stranded RNA becomes siRNAs Are often 'phased', creating a siRNA from every 20-24 nt of the dsRNA Can be loaded into RISC to slice or suppress translation siRNAs can become part of RNA-induced transcriptional silencing (RITS) complex and attract a HMET Adds H3K9me3 and epigenetically silences target region

Trisomy 21, the cause of Down's syndrome, is an example of which of the following?

Aneuploidy

Polyploidy is an increase in the total number of homologous chromosomes

Autopolyploidy - doubles a species's normal number of chromosomes Allopolyploidy - doubles an interspecies hybrid's number of chromosomes Interspecies hybrids are normally sterile Foreign chromosomes cannot pair during meiosis Doubling hybrid chromosomes allows meiosis

Mendel hybridized pea plants and tracked traits over generations

Cross = controlled hybridization (mating) Pedigree = mating history that lead to an individual Phenotype = an individual's traits

Mendel's discovery was based on crosses

Crosses = controlled mating P (parental generation) F1 (first filial generation) F2 (second filial generation) Fn (the nth filial generation)... the law of segregation keeps working!

Prophase 1: Crossing over

Crossing over, aka recombination between homologous chromosomes, will happen at chiasmata

Two pairs of 4 histone proteins make up the core of the nucleosome. What molecule is wrapped around the nucleosome 1.65 times?

DNA

Pacific biosciences sequences long molecules with high accuracy using circular sequencing libraries and special nano-wells

DNA fragments are ligated with looped adapters making a circular DNA molecule Each circular molecule is loaded with a DNA polymerase and dropped into a very narrow well with a clear bottom, called a zero-mode waveguide (ZMW) The circular molecule can be up to 20 kbp long Can be amplified using 'rolling circle amplification' to cover the molecule many times ~$0.00000002 / bp (~$60.00 human genome, but many BP will be used to confidently identify the same molecule)

Using modern sequencing, it is possible to collect nucleotide information from many different fragments of full DNA chromosomes. What information identifies a DNA sequence from a putative ORF amongst sequence fragments?

The DNA sequence contains 'ATG' which will be transcribed to 'AUG'

If the F factor episome integrates with the host chromosome and removes some genetic material from the host bacterium when it becomes separate again, what is a potential consequence during conjugation between F+ and F- bacteria?

The F- bacterium will receive new genetic material

Hardy-Weinberg equilibrium predicts stable genotypic and allelic frequencies

The Hardy-Weinberg law models the abundance of alleles and genotypes given strict assumptions Based on Mendelian expectations, traits at Hardy-Weinberg equilibrium will have f(A) = p; f(a) = q f(AA) = p^2; f(Aa) = 2pq; f(aa) = q^2 If a population is at Hardy-Weinberg equilibrium, you can estimate genotypic or allelic frequencies by knowing any of the genotypic or allelic frequencies The chi square goodness-of-fit test (remember me?) evaluates if population observations match Hardy-Weinberg equilibrium

Aneuploidy is the source of several human diseases

Many (most?) aneuploidies are lethal

Variable penetrance or expressivity

Penetrance = correlation between genotype and phenotype Low penetrance phenotypes do not always match genotype (ex. low risk disease factor) Expressivity = variation within the phenotype Traits with variable expressivity can be more or less extreme with the same genotype Many possible causes:Environment, other loci, epigenetics, random chance?

Combining these simple regulatory mechanisms can lead to complex behaviors

Synthetic biology is developing new gene regulatory circuits with sequences (and inspiration) from operons

Roslin Franklin's x-ray crystallography was able to determine precise measurements of the DNA double helix in the B-form secondary structure, including a mirrored symmetry that comes from the two strands of DNA in the double helix, as well as the spacing of nucleotides along the major and minor groove of DNA. What aspects of these measurements would not be changed in an x-ray crystallographic measurement from the Z-form secondary structure of DNA that reverses the direction of the helix?

The x-ray diffraction pattern will still be symmetrical, because DNA is still double-stranded

Chromatin Immunoprecipitation Sequencing (ChIPseq) uses antibodies to identify transcription factor target sequences

Using lab animals, researchers can purify antibodies that attach to a specific protein If the target is a transcription factor, ChIP sequencing identifies the DNA that the transcription factor touches Identifies the consensus sequence of DNA that the transcription factor can bind Identifies the genes and other loci where the the transcription factor binds

Genotypic frequencies represent the proportion of a population with a specific genotype

(genotype) = # individuals with genotype / total # individuals in population Sum of all f(genotypes) = 1 f(AA) + f(Aa) + f(aa) = 1

Most naturally occurring mutations are the result of mistakes during DNA replication

- Base wobble allows mismatched bases to temporarily pair during replication - Strand slippage or looping allows repetitive regions to experience insertions or deletions during replication

Aneuploidy is a change to homologous chromosome number

- Reduction in number: Nullisomy 2n-2 -- loss of a homologous pair Monosomy 2n-1 -- loss of one homologous chromosome - Gain in number: Trisomy 2n+1 -- one extra homologous chromosome Tetrasomy 2n+2 -- an extra homologous chromosome pair

Meiosis has two phases: Meiosis I and Meiosis II

-Meiosis I Paired homologous chromosomes are separated Reduction in number of chromosomes = reduction in 'ploidy' 2n → 1n -Meiosis II Sister chromatids are separated No change in number of chromosomes 1n → 1n

Hemophilia is a disorder that causes excessive bleeding and bruising. The allele that causes hemophilia is X-linked and recessive, only causing symptoms in homozygous and hemizygous individuals. An expecting mother finds out that she is a carrier for hemophilia. The father of the child does not have hemophilia. What is the probability that her unborn child will have hemophilia?

0.25

A fragment from the beginning of the SARS-CoV-2 (COVID19) S protein mRNA reads "aug uuu guu uuu cuu guu uua uug cca cua". How many amino acids does this fragment of the mRNA encode?

10 amino acids

You are studying the binding site of a new transcription factor that binds 100 bp upstream of the TSS. If the TATA box core promoter sequence is found at -25 from the TSS, what is the distance between the TATA box and the binding site of your transcription factor?

100 - 25 = 75 base pairs

Alignment allows comparative genomics and sequence homology

Aligning genome vs genome gives information about the evolution of genomes Sequence homology = sequence similarity that comes from ancestry Synteny = long stretch of homology Homologous genes have similar sequences: Orthologs are genes in two species with the same ancestor Paralogs are unique duplicate sequences found in one species Because of orthology and paralogy, we know many genes come in gene families

Many bacterial genes are regulated in operons

An operon is a DNA sequence that contains: 1) A transcriptional promoter 2) An operator 3) A group of genes in close proximity

Transformation is the uptake of foreign DNA

Bacteria that can take DNA through their cell membranes are 'competent' Competent cells receive DNA near them and become transformants DNA can be self-replicating plasmids, or just fragments of DNA left by dead cells Can recombine with host chromosomes

Some antibiotics target topoisomerases to prevent bacterial growth. Knowing that topoisomerases convert between nicked and supercoiled DNA, what is a reasonable mechanism for how these drugs work?

Bacterial DNA replication requires topoisomerase activity to relax a DNA molecule as it is being replicated and so bacteria cannot reproduce

Bacterial genomes can include circular or linear chromosomes, plasmids, and episomes

Bacterial chromosomes can contain millions of nucleotides and thousands of genes Typically haploid (only one copy of every gene) Plasmids are small circular DNA molecules, separate from the genome Often contain non-essential, conditional information Ex. E. coli virulence plasmids Episomes are plasmids that are able to integrate into bacterial chromosomes

Transduction involves a viral intermediate

Bacteriophages = viruses that infect bacteria and insert their genome into the bacterial cell Viral sequence integration can insert bacterial genes, or recombine with bacterial chromosomes

Reciprocal crosses are useful in determining whether a trait is sex-linked or not. If you constructed reciprocal P, F1, and F2 generation to understand the inheritance of an X-linked, recessive trait, which generation(s) will show different phenotype percentages between the reciprocal pedigrees?

Both F1 and F2

Translocation is the exchange of genetic material between non-homologous chromosomes. Which is the best description of reciprocal translocation?

Both the donor and recipient chromosomes exchange information

CRISPR/Cas9 and engineered Cas9 proteins can also make mutants

CRISPR/Cas9 can produce DNA strand breaks Typically results in deletions Lab designed Cas9-deaminase binds to DNA and can cause nucleotide transversion guideRNA causes binding at specific location, mutations are limited to a nearby region Strategy called 'base editing'

Transcriptional networks are complex and non-hierarchical

ChIPseq and measuring gene expression shows that the same transcription factor can sometimes be a transcriptional repressor and sometimes an activator Most often mostly one or the other Impact on transcription can be contextual, based on other protein interactors

Prophase 1: Leptotene -

Chromosomes condense inside nucleus

Restriction cloning adds sequences together into DNA constructs contained on a vector backbone

Cloning vector = bacterial plasmid with useful features: Origin of replication (Ori) - allows replication of full plasmid (bacterium as a DNA-replication machine) Selectable marker - usually antibiotic resistance Multiple cloning site - region of plasmid with many restriction sites near each other, allows for additive cloning design Bacterial artificial chromosomes (BACs) are vectors that can contain up to 300,000 bp (300kbp) Used in earliest efforts to map and sequence genomes Expression vector = bacterial plasmid with additional features needed for gene expression: Bacterial core promoter Operator TSS+ORF Transcriptional terminator Negative Inducible Repressor of Operator

Mendel's pedigree for Round x wrinkled

Conclusion 1: Although F1 plants are have the Round phenotype they carry the wrinkled allele Evidence -- F2 plants can be wrinkled Corollary 1: Each organism possess two alleles for a trait * Also, traits were not blended, both round and wrinkled could be recovered in F2

Mendel's pedigree for Round x wrinkled 2

Conclusion 2: F1 plants received genetic information from both parents Evidence -- All F1 plants are Round but some F2 plants are wrinkled (wrinkled came back) Corollary 2: Alleles separate when gametes are formed * Alleles separate during meiosis

Which of the following structural variants would be likely to immediately convert a chromosome from a submetacentric configuration to a telocentric configuration?

Deletion of the short arm of the chromosome

Heterochromatin causes banding and knobs in karyotypes

Dense nucleosome packing causes dark C-bands Some genomes have facultative or constitutive heterochromatin (always condensed) Nucleosome packing is regulated by histone protein tail modification Histone modifications are part of epigenetic gene silencing, imprinting, and many traits with variable expressivity or penetrance -- focus of Lecture 19

DNA, RNA, and proteins are the main contenders for genetic material

Deoxyribonucleic acids (DNA) Ribonucleic acids (RNA) Proteins (polypeptides)

New rearrangements can be caused by DNA damage

Double strand breaks (DSB) can be repaired incorrectly and causes a chromosomal rearrangement Sources: Exposure to radiation (ionizing radiation- cosmic rays, gamma rays, x-rays, UV, or some chemical compounds) Errors during DNA replication Many DSBs are created during Meiosis 1 prophase and are a natural part of forming crossovers CRISPR-Cas9 generates DSBs and can (rarely) cause serious chromosomal damage Some rearrangements cause additional chromosomal damage later (mitosis, meiosis)

Eukaryotes use RNA interference (RNAi) to change gene expression when double stranded RNAs are processed into smallRNAs

Double stranded RNA (dsRNA) is detected by Dicer proteins and cleaved into small chunks Mechanism of defense against RNA virus genomes

Sex determination is complicated and not universal amongst living organisms

Environmental sex determination Genic sex determination Chromosomal sex determination

Gene editing by CRISPR-Cas9 involves the formation of double-strand breaks (DSBs) at a targeted region of the genome. Why might gene editing by CRISPR-Cas9 potentially introduce new structural variants?

Errors during the repair of DSBs can lead to chromosomal rearrangements

Primary nondisjunction can lead to later secondary nondisjunction

Extra or unpaired chromosomes do not behave normally during mitosis or meiosis

Differences in DNA molecule size can be visualized with gel electrophoresis

For DNA, typically use cast gels of agarose (very pure agar-agar vegetable gelatin) Smaller molecules move faster, larger molecules move slower Results of a restriction enzyme digestion can be visualized on a gel Also including a separate sample of known DNA sizes (standard or DNA ladder) allows the identification of molecule size in bp

Eukaryotic transcription is conducted in the nucleus and regulation can involve multiple parts of the cell (plasma membrane, cytosol, nucleus, and others)

GAL3 interacts with galactose in the cytoplasm and binds with GAL80 GAL80 with GAL3 cannot enter the nucleus, so GAL4 is allowed to activate transcription **Few signalling molecules enter the nucleus (exceptions: steroid hormones)**

Which term describes the total possible genes and allelic variants within a population?

Gene pool

Group I and Group II introns can be found in both eukaryote and prokaryote genomes. If most prokaryotes lack spliceosome machinery, how do these organisms process Group I and Group II introns?

Group I and Group II introns have a complex RNA structure that self-splices

CRISPR-Cas9 is a challenge for current regulatory systems

GuideRNA and DNA template allow many types of edits anywhere in the genome

Fred Griffith showed something in dead bacteria makes non-virulent bacteria cause disease

Heat-killed bacteria transmitted genetic information

Base pairs (bp) and their implications

Hydrogen bonds between purines and pyrimidines make 2 strands 'complementary' Two strands are in an 'antiparallel' arrangement 5'-CGTTAAGC-3'3'-GCAATTCG-5' The second strand is also called the reverse complement Each pair of nucleotides is a 'base pair'

Organelle genetics can lead to uniparental inheritance of traits

If gametes are unequal, largest gamete contributes most of the organelles Organelle genetic traits are matrilinear -- only inherited from the mother's side

Chromosome pairing makes a mess when new polyploids enter meiosis

If multiple chromosomes with similar genes/sequences can pair, will form 'multivalents' Chiasmata connect multiple chromosomes Spindle attachment cannot efficiently reduce chromosome number High chance of aneuploidy and chromosome breakage Potentially leads to loss of genetic information (entire chromosomes or fragments), aka 'genomic shock

Prophase I is the most important for Genetics

In Prophase I, homologous chromosomes pair and exchange genetic information

Applying probability to a dihybrid cross

In a monohybrid cross, you have 2 possible gametes per parent In a dihybrid cross you have 2*2 = 4 possible gametes per parent By using multiplicative and additive probability, you can solve genotypic and phenotypic probabilities for a dihybrid Remember, traits that follow the Law of Segregation have equal chance (0.5 probability) of making gamete

Please complete the statement. If two alleles display ________________ then heterozygous individuals will have a phenotype that is in-between the phenotypes of either the homozygous individuals.

Incomplete dominance

The fly mutant, bicoid (bcd) makes a symmetrical larvae instead of one with a head and tail (anterior and posterior poles)

Injecting bicoid mRNA into different parts of the fly embryo is sufficient to change anterior/posterior polarity

Modern Sanger sequencing uses a mixture of fluorescent terminator nucleotides and reads them as they pass a laser

Instead of a gel, molecules are slowly passed through a microcapillary and converted into a 'chromatogram' Reliably reads around 1000 bps Requires a large amount of DNA ~$0.008 / bp (~$24 million human genome)

If an endosymbiont becomes completely dependent on its host organism and can no longer exist as a free-living organism, what is a reasonable long term impact on the genetics of the endosymbiont?

Isolation from outside individuals of the same species will decrease the occurrence of new allelic variation for the endosymbiont

Phosphorylation is a common protein modification used in gene regulation

Kinases, mutases, or proteins with kinase domains can transfer phosphate groups to or from other proteins Phosphorylation changes the shape of transcription factors and changes DNA binding behavior

Mapping unknown loci using linkage

Linkage analysis -- gene mapping using markers (gene traits or molecular) Common strategy: F2 mapping P generation new trait, Parent1 alleles x no trait, Parent2 alleles Requires allelic variation or polymorphism between parents In F2 (and more advanced generations) only very close Parent1 alleles are still linked

Mixture of organelle genetics can cause genetic mosaicism

Many copies of organelles in a cell If organelles are not genetically identical = heteroplasmy Multiple alleles across organelles Over multiple divisions, organelles randomly assorted Replicative segregation of alleles = phenotypic variability between cells determined by organelle inheritance

DNA → RNA → Protein 2

Mapped out biochemical pathways Each step is controlled by a different enzyme Each enzyme could be mapped to one region of DNA Modern day: more like 1 gene, 1 protein (but many exceptions: splice isoforms, noncoding RNAs, etc.)

Hardy-Weinberg assumption 3: no migration of individuals (no gene flow)

Migration brings new individuals to a population (and the alleles that those individuals carry) Also called gene flow, like mutation, can introduce new alleles to a population Changes allele frequency and populations become more similar

Endosymbiont theory predicts which two eukaryotic organelles were once free living bacteria?

Mitochondria and chloroplasts

Polarity mutants disrupt major axes of organization

Morphogens are substances that regulate pattern formation in organisms Can be hormones (chemical compounds), small peptides (secreted protein fragments), miRNAs, or other signaling molecules Usually require signal transduction to detect morphogen and change gene expression

DNA changes can be used to detect patterns of evolution

Nucleotide diversity, or 𝛑 (pi) is the abundance of DNA mutations within a population or species Protein coding genes can further be studied with synonymous (no effect on protein) vs non-synonymous (probably negative, rarely positive effect on protein) nucleotide changes Reduced nucleotide diversity shows regions that are under directional selection

Charles Darwin

Observed organisms from different islands and saw they shared similar traits But species were specialized to their own habitat

Mitosis

One 2n somatic cell → Two 2n somatic cells Mitosis produces daughter cells with the same number of chromosomes Parent cell = 2n somatic cell Two daughter cells = 2n somatic cells In humans: 2n = 46 chromosomes Parent cell has 2n = 46 chromosomes Two daughter cells have 2n = 46 chromosomes

Long read sequencing technology makes structural variants more accessible

Oxford Nanopore (ONT) and Pacific Biosciences (PacBio) can sequence DNA spanning chromosomal rearrangements Nanopore sequencing reads an entire molecule of DNAUp to a whole chromosome, telomere to telomere

A complementation test determines whether recessive alleles are from the same locus

P: Two homozygous recessive individuals with different alleles If F1 has recessive phenotype, the alleles 'fail to complement each other' and are from the same locus (part of the same allelic series) If F1 has no phenotype, the alleles have been 'complimented' by alleles from a different locus

Which of the following is a correct statement about the difference between paracentric and pericentric inversions?

Paracentric inversions do not contain the centromere; pericentric inversions contain the centromere

Nullisomy (2n-2) requires the fusion of two nullisomic gametes during fertilization. Which of the following is a possible scenario that could lead to a nullisomic individual?

Parent 1 and Parent 2 go through nondisjunction during meiosis

Early genomes were assembled by physical map approaches

Physical or clone-based maps use restriction enzyme cut sites to position portions of the genome relative to each other BACs and YACs (yeast artificial chromosomes-- similar to BACs, but linear and in yeast) stitched together by restriction digest sites A living library of genome fragments Sequenced by Sanger sequencing Overlapping fragments collapsed into contigs of continuous sequence Overlapping contigs collapsed into chromosomes Relatively slow-- a lot of time invested in determining restriction sites

The chemical nature of DNA

Polynucleotide strands of nucleotides with diester bonds in between

Chromosomal sex determination

Prereq: Genic sex determination = sex allelic trait 1 chromosome contains unique information that enhances the production of specific gamete type (promotes one sex) Or suppresses the production of a specific gamete type (inhibits one sex)

DNA structure is organized at three+ levels

Primary structure = nucleotide sequence Secondary structure = double helix (B-form, A-form, etc) Tertiary and quaternary structure = DNA packaging and spatial organization, or topology Interaction between DNA and proteins Can change over the life of the same cell

Probability can predict the outcome of a cross

Probability = likelihood of an event occurring Can be %, fraction, or decimal that is >=0 and <=1 Flipping a normal coin has ½, 0.5, or 50% chance of heads A F1 hybrid Round x wrinkled pea plant (genotype Rr) has a 50% chance of making a gamete carrying Round (R) and 50% chance of making a gamete carrying wrinkled (r) Corollary 3: Alleles separate in equal proportions

Recombination rates between three loci in corn are shown below. What is the order of the genes on the chromosome? Loci Recombination Rates: R and W2 17% R and L2 35% W2 and L2 18%

R, W2, L2

Transcription makes RNA from a DNA template

RNA polymerase creates a complimentary copy of DNA using ribonucleotides (rNTPs) DNA sequences attract many proteins to assemble an RNA polymerase RNA polymerase makes an RNA transcript in the 5' to 3' direction on one DNA strand Information for two transcripts can overlap on opposite sides of DNA, but only one direction is transcribed at a time

With modern availability of DNA sequence data from chromosomes, we observe that the physical map distance between two loci is frequently different from the genetic map distance. What is the most reasonable explanation for this discrepancy?

Recombination rates are not equal all over the chromosome

Transcription of mRNA in eukaryotes involves several transcription factors

Recruitment of RNA polymerase II (RNA pol II) and 'general transcription factors' to a core promoter Specific transcription factors can bind regulatory promoters and distal enhancer sequences Transcriptional repressors make it harder recruit RNA pol II Transcriptional activators make it easier to recruit RNA pol II Transcription factors bind DNA Co-regulators interact with transcription factors

Oswald Avery, Colin MacLeod, and Maclyn McCarty's showed that DNA can transform bacteria

Removed RNA (RNase), Proteins (protease), or DNA (DNase) Only removing DNA stopped transformation DNA must be the molecule behind transformation

Punnett squares visualize outcomes between generations

Represent alleles of the same locus with letter codes

When multiple events MAY happen, add the probability

Rolling a 6-sided die has ⅙+⅙ = 2/6 = ⅓ = 0.3333 chance of 3 OR 4 Corollary 3: Alleles separate in equal proportions A F1 hybrid Round x wrinkled pea plant (genotype Rr) gamete has a 50%+50%=(50%)*2=100% chance of being Round (R) OR wrinkled (r)

Oxford Nanopore sequences single molecules of unlimited length as the DNA passes through protein pores

Smallest, cheapest device 'MinION' has sequenced DNA in space, underwater, in the jungle, all over the place Protein pores are embedded in a charged membrane Sensitive electronics determine when a specific nucleotide passes through the membrane based on its electrical charge Requires an AI model to determine charge to nucleotide conversion; used to be very inaccurate but getting better every year Mostly electronics and chemistry, easiest to prepare and operate Sequencing length is limited by input molecules, small chromosomes can be sequenced telomere-to-telomere ~$0.00000001 / bp (~$30.00 human genome, but need many runs to sequence with confidence)

Model Organisms

Species that have special attributes

Protocol for human insulin in E. coli

Step 1: Clone human insulin gene into bacterial plasmid (A and B separately) Step 2: Transform bacteria with recombinant DNA plasmid Step 3: Express human insulin gene in bacteria Step 4: Extract human insulin chain A and B from bacterial culture and crosslink

PCR (polymerase chain reaction)

Steps: 1) Melting, ~95°C (separates DNA strands) 2) Annealing, ~55°C (allows primers to complement) 3) Extension, ~72°C (Taq polymerase extends primer)...Then repeat! Doubles DNA with each cycle Can create billions of molecules in an afternoon

Species have different chromosome morphologies

Submetacentric- the centromere is not in the middle, two unequal arms Metacentric- the centromere is almost in the middle of the chromosome, making two equal arms Telocentric- the centromere is at the end of the chromosome Acrocentric- the centromere is near one end; one long arm and a nub

You are studying an organism with endosymbionts which are separated from the host organism's cytoplasm by 6 separate cell membranes. What is the simplest explanation for the history of endosymbiosis for this endosymbiont?

The endosymbiont contains an endosymbiont which also contains an endosymbiont; this is a tertiary endosymbiosis

Colchicine is a drug that can prevent chromosomes from separating during cell division and leads to the production of cells with increased chromosome number. Assuming that all other aspects of gamete growth and maturation are not impacted and you are working with an organism with two sets of homologous chromosomes that are not identical, what is the most likely outcome of exposing cells to colchicine during Meiosis II?

The formation of gametes with two sets of identical chromosomes

What information would NOT help determine whether a molecule is DNA or RNA?

The molecule contains a phosphodiester bond

In vitro fertilization (IVF) techniques are used to clone animals from somatic nuclei

The nucleus is removed from an egg and a somatic nucleus is added The new zygote will contain genetic material of the somatic nucleus Can be implanted into a surrogate mother to yield a cloned individual Or cultured in the lab to form tissues or research or regenerative medicine

IVF techniques are used to make genetically modified animals

The nucleus of a fertilized egg can be injected with DNA constructs to make a 'transgenic' or genetically modified individual Constructs need a promoter, CDS, and terminator like normal genes Construct can randomly integrate into the genome and create an individual hemizygous for the new engineered allele

Signal transduction uses receptors to transfer information to another part of the cell

The receptor protein detects a ligand = metabolite, small protein, etc A signal is transferred to another protein that can enter the nucleus and impact transcription involves several intermediate kinases in a 'kinase cascade' Original receptor phosphorylates MAPKKK MAPKKK phosphorylates MAPKK MAPKK phosphorylates MAPK MAPK phosphorylates a transcription factor and changes transcription

Eukaryotic pre-mRNAs are processed by the spliceosome

The spliceosome itself is made of small nuclear RNAs (snRNAs) and proteins together, aka small nuclear ribonucleoprotein particles (snRNPs) 1) Recognizes intron-exon junctions and a 'branch point' 2) One intron-exon junction loops on the branch point 3) This intron loop is called a lariat 4) The spliceosome unites the two exon ends 5) The intron (as a lariat) is released and broken down

Complete the sentence. The only codon that does not encode for amino acids carried by charged tRNAs are ____________________.

The termination codon, UAA, UAG, or UGA

Which of the following is NOT expected for a genetic trait located on the mitochondrial chromosome?

The trait follows the Mendelian segregation ratio of 3:1 in the F2 generation

Which of the following would be an expected change in inheritance if a gene that controls a trait was transferred FROM the mitochondrial genome TO a eukaryotic chromosome?

The trait would switch from matrilineal inheritance to Mendelian 3:1

You are researching the effect of intron retention during late stage brain cancer. Which of the following pieces of information would help you identify that a mRNA transcript resulted from an intron retention alternative splicing event?

The transcript contains sequence information from what is normally an intron

The fly mutant, Antennapedia (Antp) has legs instead of antennae

This dominant mutant shows that the cells that become antennae are 'competent' (were once pluripotent) to form legs Antp maps to transcription factor from the HOX gene family

Genomic selection uses predictions of phenotypic variance to build a model of 'the perfect genotype'

Today, DNA sequencing is cheap; phenotyping (labor, equipment, etc) can be expensive Genomic selection produces animal or plant breeding models using an initial training population

Inversions reverse the order of a chromosome segment

Two types: 1) Paracentric inversions do not include the centromere 2) Pericentric inversions include the centromere Heterozygous inversions cause massive defects in meiosis

Which of the following RNA sequences is most likely from the 3'UTR of an eukaryotic mRNA?

UGC CCA AAA AAA AAA AAA AAA AAA AAA AAA AAA

You are working for a pharmaceutical company that researches drugs which terminate protein translation as a potential cancer treatment. If the drug acts as a synthetic release factor, which of the following biochemical activities should it display?

When added to the actively translating ribosome, the drug causes the dissociation of the polypeptide and the release of ribosomal subunits and tRNAs

Functional genomics works to determine the biological function of genes and proteins

Whole genome sequencing just provides the order of all the nucleotides Genome annotation predicts and records the features of the DNA genome, including genes (UTRs, Introns, Exons, ORFs), miRNAs, transposons, etc.

In many species, histone H3 is exchanged for histone CENP-A in nucleosomes within and around the centromere just before mitotic and meiotic division. Knowing that the spindle will attach to CENP-A during division, what is a likely effect of deleting CENP-A on the inheritance of chromosomes?

Widespread loss of chromosomes because chromosomes without CENP-A will not segregate properly

Choose the answer that best completes the sentence. As opposed to sex chromosomes, are chromosomes that are not involved with sex determination.

autosomes

Allelic frequencies represent the abundance of an allele in a population

f(allele) = # of copies of an allele / total # of alleles at locus in a population Sum of all f(alleles) = 1 f(A) + f(a) = 1

Humans have 2 sets of homologous chromosomes. If having freckles is a dominant trait caused by the F allele and the f allele of the same gene does not cause freckles, what is a possible genotype of someone who does not have freckles?

ff

Transcription has three phases:

initiation, elongation, and termination

mRNA vaccines continued -- translation in action

mRNA vaccines deliver transcripts to dendritic cells in the immune system Ribosomes in the cytoplasm translate the mRNA and make a viral protein (for COVID19, the S glycoprotein - spike protein) Dendritic cells normally detect foreign proteins and present polypeptide fragments to T cells and eventually lead to immunity

Somatic cells

non-reproductive cells (all the other cells)

Prophase 1: Diakinesis

nuclear envelope breaks down; Recombined chromosomes are ready to segregate

Please complete the statement. Episomes are similar to __________ because they can exist as conditional circular chromosomes, but differ because they can integrate with or detach from the host genome.

plasmids

August Weismann amputated tails from multiple generations of mice but found that each new generation of mice were born with tails. What aspects of his work disproved Pangenesis, or the inheritance of acquired traits?

the full body plan of the mouse (including tail) was inherited even though it had acquired a modification (amputation)

the chi-square goodness-of-fit test is a good way of evaluating predictions for the inheritance of a genetic trait. If the P-value for a chi-square goodness-of-fit test is smaller than 0.05, which of the following is NOT true?

we can reject the alternative hypothesis

If the normal order of genes on the Drosophila X chromosome is y w v m r, what would the gene order be if the region containing w and m was inverted?

y m v w r

Coat color of Labrador retrievers follows recessive epistasis. Dogs with genotype P- are able to make a precursor to black and brown pigments; those with genotype pp cannot, and have yellow coats. Among the dogs that can make the precursor, dogs with genotype BB or Bb are black, and dogs with the genotype bb are brown. If two dogs with the genotype BbPp mate, what is the probability that the first three puppies will have yellow fur?

0.2500^3 = 0.0156

Prophase 1: diplotene

bivalent or tetrad of touching homologous chromosomes pairs (with sister chromatids) are visible

Promoters contain a consensus sequence that attracts RNA polymerase

consensus sequence = shared nucleotide sequence between DNA molecules from multiple loci, species, or other samples Bacteria: -10 TATAAT and -35 TTGACA Eukaryotes: -25 TATA box, and more

Many bacterial genes are regulated in operons 2

RNA polymerase will transcribe when operator is not occupied by a transcription factor The group of genes together form a polycistronic mRNA = multiple ORFs on one mRNA Each ORF can be translated into an independent protein

The RNA world hypothesis suggests that RNA molecules preceded DNA and other aspects of modern biochemical systems. What aspect of RNA biology DOES NOT suggest that RNAs are currently capable of independent life?

RNAs are not able to independently replicate themselves

If a human 2n somatic cell has 46 chromosomes, how many chromosomes does a human gamete have?

23 chromosomes

Unlike transcription which converts every DNA base into an RNA base, translation uses multiple RNA bases to specify an amino acid codon. How many RNA bases are used in each codon?

3 RNA bases

After meiosis, how many gametes with unique allele combinations can be produced by a pea plant that is heterozygous for both the round seed and yellow seed phenotypes?

4

RNAs also regulate gene expression

4 possible exons: A, B, C, D Exon B contains a termination or stop codon 1) mRNAs that include exon B encode for a shorter, truncated protein Leads to male development 2) mRNAs that skip exon B encode for a full length protein Leads to female development

Which of the following correctly shows two complementary sequences of DNA?

5'-CGTTAAGC-3' 3'-GCAATTCG-5'

In cats, curled ears result from an allele (Cu) that is dominant over an allele (cu) for normal ears. Black color results from an independently assorting allele (G) that is dominant over an allele for gray (g). Both alleles follow Mendel's Law of Segregation. A gray cat homozygous for curled ears is mated with a homozygous black cat with normal ears. All the F1 cats are black and have curled ears. If two of the F1 cats mate, what phenotypes and proportions are expected in the F2?

9 black fur, curled ears : 3 black fur, normal ears : 3 gray fur, curled ears : 1 gray fur, normal ears

Genetically modified plants and animals are scientifically accepted but socially controversial

A HUGE majority of independent studies show no special risks associated with cultivating or consuming genetically modified organisms Many products made by genetically modified organisms are not controversial ex. recombinant insulin, many pharmaceuticals, rennet for cheese, most vitamins, and others are made by transgenic E.coli or yeast Genetically engineered traits follow the normal rules of genetics Gene flow only within populations Will only increase in frequency if under selection or by genetic drift (random chance)

Culturing and replica plating helps characterize genes in the bacterial genome

A complete medium contains all the substances (sugars, amino acids, etc) that a bacterium needs Auxotroph mutants lack enzymes for synthesizing some compounds Minimal medium will kill auxotrophs, but, wild-type prototrophs will survive Replica plating reveals bacterial cells that can only survive under some conditions

Sex-linked traits

Allele becomes 'linked' to sex (also a trait) Defies Mendel's Law of Independent Assortment Can be linked to any sex chromosome (X-linked, Y-linked, Z-linked, W-linked, etc) First sex linked trait was discovered by Thomas Hunt Morgan in early 1900s

Mendel's second law: The Law of Independent Assortment

Alleles on different chromosomes separate independently ** the Law of Independent Assortment extends the Law of Segregation to traits that are on separate chromosomes **

Heritability is the portion of phenotype that can be explained by Genotype

Broad sense heritability -- proportion of phenotypic variance associated with genotype Narrow sense heritability -- proportion of phenotypic variance associated with specific alleles (additive variance) High heritability traits are primarily determined by genotype alone

Separating phenotypic measurements into groups allows comparison of phenotypes by allele

By comparing mean and standard deviation of two distributions we can determine if they are likely to be from two different populations or samples of the same population An 'unpaired t-test' calculates the probability that the two distributions appear different by random chance

Centromeres are loaded with special histones

CENP-A/CENH3 instead of Histone H3 During mitosis and meiosis, the kinetochore attaches to CENP-A/CENH3 Primary DNA sequence not a good predictor of where the centromere will be

Translocations are exchanges of chromosome segments between non-homologous chromosomes

Can be reciprocal: 2 non-homologous chromosomes exchange material or nonreciprocal: only one chromosome receives a new segment Puts genes from different linkage groups together Heterozygous translocated chromosomes make cross-like structures during meiosis 3 possible outcomes: alternate segregation, adjacent-1 segregation, and adjacent-2 segregation Adjacent-1 and adjacent-2 can produce non-viable gametes Reduces number of viable gametes

Many single cell techniques are based on cell sorting or microfluidics

Cell sorting takes a mixture of cell and separates them into individual reaction tubes Molecules are extracted from each tube separately and processed by whole genome sequencing (DNA), transcriptomics (RNA), or proteomics (protein) But currently, protein detection is limited to a small number of known, highly abundant proteins

Sex chromosomes are inherited according to Mendelian principles

Chromosomes segregate and have 0.5 probability of inheritance XX female x XY male cross produces 1:1 XX female:XY male

'Survival of the fittest' makes new species

Competition for resources makes adapted species accumulate... but how do they become adapted when their ancestors were not? Darwin didn't have the answer... Evolution by natural selection didn't have a mechanism for inherited changes

When multiple events MUST happen, multiply the probability 2

Corollary 3: Alleles separate in equal proportions Two F1 hybrid Round x wrinkled pea plant (genotype Rr) gametes have a 50%^2 = 25% chance of both being Round (R) Corollary 3: Alleles separate in equal proportions Two F1 hybrid Round x wrinkled pea plant (genotype Rr) gametes have a 50%^2 = 25% chance of being #1 Round (R) AND #2 wrinkled (r)

Sometimes you will have combinations of multiplicative and additive probability

Corollary 3: Alleles separate in equal proportions Two F1 hybrid Round x wrinkled pea plant (genotype Rr) gametes have a have a 50%^2 + 50%^2 = 25%+25% = 50% chance of being #1 Round (R) AND #2 wrinkled (r) OR #1 wrinkled (r) AND #2 Round (R)

Sanger sequencing uses terminator reactions to determine nucleotide sequence

DNA polymerase and a primer are used to add deoxyribonucleotides (dNTPs) Different reactions have dideoxyribonucleotides (ddNTPs) that can be added to the 3' end but cannot be extended Results in prematurely terminated molecules that ended with a ddNTP One reaction per nucleotide identifies the base at each position

The hologenome includes DNA from the host chromosomes and all symbionts

DNA sequencing reveals that most organisms have lots of symbionts The microbiome includes endosymbionts and ectosymbionts, on the outside of the host cells

Following the central dogma, DNA changes are the source of new traits

DNA → RNA → Protein → Trait Gene expression = ( → RNA → Protein → Trait ) Actual genes and alleles = DNA Therefore: new trait = new DNA mutant organism = DNA mutation Often, 'wild type' = non mutant trait or allele

Secondary structure of DNA: A B and Z forms

DNA's B form -- Franklin's crystallography reveals a minor groove and a major groove Approximately 10 bp per helix turn But DNA can exist in other conformations A form -- highly compacted Z form -- helix is reversed

Genetics fundamental fact 2: Recombination is the backbone of Genetics

Each parent contributes 1 set of homologous chromosomes Recombination (during Prophase I) exchanges information between homologous chromosome sets Result: offspring has a new combination of genetic information Multiply by many generations: many possible genetic remixes

Chemical mutagens and radiation can induce mutations

Ethyl methanesulfonate (EMS) and N-ethyl-N-nitrosourea (ENU) cause base transversions (substitutions) UV light creates pyrimidine dimers that blocks DNA replication Fast neutrons, X-rays cause DNA strand breaks Imperfect DNA repair leads to mutations

Mature mRNAs consist of a 5'UTR, CDS, and 3'UTR

Eukaryotic RNA-coding region of DNA contains introns, exons, and untranslated regions (UTRs) Only exons are used for translation Exons together = coding sequence (CDS), protein coding region

mRNA vaccines contain an RNA sequence from a target virus gene and are flanked by a 5' cap and 3' polyadenylation sequence. An important requirement for mRNA vaccines is stabilizing the introduced RNA in the cell to allow translation into protein and ultimately an immune response to the virus. What is the a likely explanation for why the 5' cap and 3' polyadenylation sequence are necessary for a viable mRNA vaccine?

Eukaryotic cells degrade RNAs that are missing the 5' cap and 3' polyadenylation and that turnover would reduce the efficacy of the vaccine dose

tRNAs are heavily processed RNAs that carry amino acids

Found in all cells tRNAs use rare ribonucleotides: ribothymidine, pseudouridine Made by modification of primary RNA transcript Complex secondary structure with multiple loop 'arms' Acceptor arm is bonded to amino acid Splicing, modification, and base addition makes a mature tRNA

Biological sex is not the same as gender

Gender includes all the social norms and expectations that categorize humans Mostly up to society, not much to do with biological sex

Properties of chromosomes shape inheritance

Gene is the unit of inheritance Chromosomes are groups of linked genes Cytogenetics studies chromosomes and their properties

Many traits have multiple alleles at the same locus

Gene pool = total possible genes and alleles within a population For 1 locus: each homologous chromosome has one allele, but there could be many possible alleles in the gene pool Alleles may have complicated relationships to each other Allelic series = alleles from the same locus and their relationship to each other

Gene regulation = mechanisms and systems that control the expression of genes

Gene regulation is the many processes that determines which DNA → RNA → Protein at any given moment in a cell

Hardy-Weinberg assumption 4: no genetic drift (large population size)

Genetic drift is a change in allele frequency caused by random chance and low population size Allele frequency variance: s^2 = pq / 2N <- number of individuals High number of individuals, low variance Low number of individuals, high variance Genetic drift can happen when the population shrinksNatural disaster, disease, climate event, habitat destruction, domestication Causes restriction in gene pool = Genetic bottleneck Also when colonizing a new environment = Founder effectPart of why isolated islands have such unusual populations Genetic drift allows fixation of alleles:Allele frequency = 0 or 1 maintained except for mutation or migration

Structural sequencing reveals chromatin packing patterns in nucleus

Hi-C sequencing identifies regions of DNA that are physically close together, topologically-associated domains (TADs) Collecting many interacting DNA fragments shows where chromosomes rest in the nucleus Chromosomes have neighborhoods or territories in the nucleus Centromeres generally hang out on the same side; Telomeres are generally opposite Heterochromatin is mostly on the outside of the nucleus, euchromatin on the inside

Histone modifying enzymes add and remove epigenetic marks from histone tails

Histone deacetylases (HDACs) and histone acyltransferases (HATs) remove and add acetyl groups Histone methyltransferases (HMETs) add or remove methyl groups

Different versions of the same gene / locus are called alleles

Homologous chromosomes: A set from mom, a set from dad Two homologous chromosomes = two potential versions of the same gene / locus Homozygous or 'pure breeding' = homologous chromosomes have the same allele Heterozygous = homologous chromosomes have different alleles Genotype = an individual's alleles

Producing human insulin in E.coli

Human insulin is encoded by the INS gene Newly translated protein is long and forms several internal covalent bonds Active insulin is cleaved and processed into two final amino acid chains (A and B) Recombinant insulin synthesis expresses each chain separately E.coli can be cultured in massive bio-reactors Flexible expression system has allowed systematic improvement of insulin-- Glargine insulin has extra amino acids which change its pH and make it 'slow release'

Linked genes do not assort independently

Linked genes are nearby on the same homologous chromosome Linked genes do not assort independently Linkage group = several genes linked to each other

Genetics fundamental fact:

Meiosis produces recombinant gametes

Genetics is essential for modern biology

Meiosis produces recombinant, 1n gametes

Alleles from different loci can interact

Mendel discovered: - Additive loci Independent loci have phenotypes that can be added together F2: 9:3:3:1 phenotypic ratio - Synergistic loci combination of alleles on two loci has different phenotype than either locus alone - Epistatic loci One locus masks, or 'hides' the phenotype of the other The overriding trait 'is epistatic' to the one that is masked

Gregor Mendel's work (1860s) explains the rules of inheritance

Mendel used the Scientific MethodObserve→Hypothesize→Experiment→Analyze→Repeat Many years of observations Created predictive hypothesis before experiment Collected lots of numbers, used math to analyze

Histone proteins have 'tails' that can be modified

Modification changes shape of histone and interaction between nucleosomes H3 <- histone 3, K27 <- lysine (K) in the 27th amino acid position H3K27 Acetylation (H3K27ac) is associated with actively transcribed euchromatin H3K9 trimethylation (H3K9me3) is associated with constitutive heterochromatin (transcriptionally silent)

Hardy-Weinberg assumption 5: no selection of genotypes or alleles

Natural selection and adaptation lead to increased reproductive fitness = increased offspring, increases allele frequency The selection coefficient (s) represents the intensity of natural selection against a genotype Relationship between genotypes and selective pressures depends on nature of allele (dominant, recessive, incomplete dominance, overdominant, underdominant) Over generations, selective pressure leads to a change in allele frequency Directional selection favors one allele over another Balancing or stabilizing selection favors both alleles, but as heterozygotes Purifying or destabilizing selection favors both alleles, but as homozygotes

Linked genes segregate together, but crossing-over produces recombination between their alleles

Nonrecombinant gametes or 'parental gametes' = gametes that match the parental linkage combination Give rise to nonrecombinant progeny or 'parental progeny' Recombinant gametes = gametes that do not match the parental linkage combination Give rise to recombinant progeny Ex. AB/ab x AB/ab Parental gametes: AB or ab Recombinant gametes: aB or Ab

Chi-square test of independence determines if loci are unlinked (independent)

Null hypothesis: variables are independent (loci are unlinked) Alternative hypothesis: variables are not independent (loci are linked) Contingency table is 2x2 or bigger Allele1 genotypes left-to-rightAllele2 genotypes top-to-bottom Same calculation of ꭓ2 as goodness-of-fit Fewer degrees of freedom df = (number of rows - 1) (number of columns - 1)If P < 0.05, reject null; loci are probably linked

Genetics of populations can be described by gene pools

Population = group of individuals that can contribute genetic information to the next generation (can breed together) Gene pool = total genes and alleles available within a population Mathematical representations of gene pools and populations convert natural variation into statistical genetics

All of the following are parts of a mature mRNA EXCEPT:

Promoter sequence (Pro)

RNA world hypothesis suggests that life on Earth could have started with RNA

RNAs can do complex jobs Ribozymes are RNAs with an enzymatic activity RNAs can even replicate other RNAs

Circular plasmids exist in 3 different topologies

Relaxed (nicked) / circular, Linear, and Supercoiled Linearization achieved by restriction endonucleases Enzymatic cut on both strands Supercoiled to nicked regulated by topoisomerases Can be seen with gel electrophoresis Gel electrophoresis separates through a molecular sieve: Smaller molecules migrate faster Supercoiled moves fastest, then linear, and relaxed is slowest

RNA molecules are single stranded

Ribonucleic acid, made of A U C G Uracil is substituted for thymine Many classes of RNAs in a cell - Ribosomal RNAs (rRNAs) Transfer RNAs (rRNAs) Messenger RNAs (mRNAs) Small RNAs (piRNAs, miRNAs, siRNAs, nanoRNAs) Long noncoding RNAs (lncRNAs) And more...

Codons translate three ribonucleotides into an amino acid

Ribonucleotides can be A, U, C, or G (4 possible) If the genetic code used 1 nucleotide: 4 possible amino acids 2 nucleotides: 4^2 = 16 possible amino acids 3 nucleotides: 4^3 = 64 possible amino acids Enough to match common 20 amino acids

Gene regulation can be complex

Several levels of regulation Entire chromosome / set of chromosomes Region of DNA Unprocessed transcript Mature mRNA Unprocessed polypeptide Or final protein

Sex chromosomes are unequal and cannot crossover

Sex chromosomes = homologous chromosomes involved in sex determination Autosomes = homologous chromosomes not primarily involved in sex determination Sex chromosomes pair during meiosis, but no exchange of information or recombination between sex chromosomes Suppressed recombination holds the sex-determining allele on the sex chromosome

Mutations are changes to DNA sequence that make new alleles

Somatic mutations - DNA changes in somatic cells will not be inherited Recall: Genetic mosaicism, chimeras, and sectoring in somatic aneuploidy Germline mutations - DNA changes in germline cells will be inherited

Lethal alleles and meiotic drive

Some allele combinations can be lethal to offspring Lethal genotypes are not observed as adults Some alleles can be lethal to gametes (or other life stages) Gamete lethal alleles have are reduced probability Some alleles improve their probability of making gametes = meiotic drive Meiotic drive alleles are preferentially inherited

Endosymbiont theory predicts that organelles were once independent organisms

Some cells eat by endocytosis (make an endovesicle) What if that cell didn't digest its meal? Cell within another host cell = endosymbiont Endosymbionts are enclosed in two membranes (host endovesicle + endosymbiont cell membrane) Over evolutionary time, host and endosymbiont become mutually dependent = endosymbiosis

Introns are spliced out of eukaryotic mRNAs by the spliceosome

Splicing removes introns Introns are sequences that can be found in DNA but not in mature mRNAs Early experiments created heteroduplex molecules of DNA and the mRNA it encodes and saw introns as loops of folded DNA Bacterial introns are self-splicing (Group I and Group II introns) [Rare] Also found in tRNAs and rRNAs Group II self-splicing introns hypothesized to be an evolutionary precursor to eukaryotic introns (and the spliceosome)

Translation starts at open reading frames (ORFs) and ends at a termination codon

Start codon = AUG Start amino acid = methionine (or formylmethionine in bacteria) Termination codon = UAA, UAG, or UGA No amino acid associated, but instead a protein, Release factor (RF) Afterwards, the polypeptide is released and the ribosome lets go of the mRNA

Selection strength and allele fitness determines how quickly allele frequency will change

The starting allelic diversity and rate of mutation will determine the raw materials The physical environment ('abiotic') or other organisms ('biotic') apply the selective pressure

What DNA feature of the transcriptional unit is the first to be transcribed into an RNA molecule?

The transcriptional start site (TSS)

'The infinitesimal model:' many loci of small effect control quantitative traits

This example has incomplete dominance and is perfectly additive But quantitative traits can display any type of allele interaction

The plant mutant, agamous (ag) has petals instead of stamens and carpels (sexual organs)

This recessive mutant shows that the inner organs of flowers receive special information to make stamens and carpels By looking at double mutants in combination with other floral homeotic genes, it is known that it takes different organs can be defined by a complex of transcription factors These proteins bind DNA together and their combination determines specifically which genes they will regulate

Codons are degenerate = multiple RNA sequences for each amino acid

Translation relies on complementary base pairing between tRNA and RNA 3 RNA bases = sense codon 3 tRNA bases = anticodon But several tRNAs accept multiple sense codons = isoaccepting tRNAs The first two nucleotides the codon are more important Third base = wobble position

If you mated a purebred normal sized chihuahua mated with a purebred teacup (miniature) chihuahua and their heterozygous puppies were smaller than either parent, what kind of dominance are these alleles displaying? (Assume that size is controlled by one gene with two alleles)

Underdominance

Aneuploidy and Polyploidy have a big role in genome evolution

Widespread polyploidy in plants and some animals Historic polyploidy in most taxa (including humans) Increasing the number of copies of genes allows new allelic variation Leads to subfunctionalization, where copies of a gene eventually become distinct

Which of the following would be a reasonable, direct outcome for a mutation that deletes a bacterium's only copy of Isoleucine Aminoacyl-tRNA Synthetase?

Without Isoleucine Aminoacyl-tRNA Synthetase, the bacterium will not be able to charge tRNAs with isoleucine and no proteins containing isoleucine will be produced by translation

trp is a 'negative repressible' operon

Without interacting with tryptophan, the trp repressor cannot bind the trp operator When tryptophan levels are low, transcription is high When tryptophan levels are high, transcription is low

Which of the following is the best definition of Mendel's Law of Independent Assortment?

alleles on different chromosomes segregate independently during inheritance

Which of the following is TRUE about species that follow strict sequential hermaphroditism?

an induvial may produce EITHER sperm or eggs during its lifetime

Prophase 1: Pachytene -

homologous chromosomes zip up into 'synaptonemal complex' of proteins and chromosomal DNA

Which of the following is the best definition of the 'germ plasm' theory of inheritance?

inherited information maintained in the germline and contributed to the next generation through specialized cells

Albino vs pigmented fur color in mice follows the Law of Segregation. If mice in an F1 between a purebred albino mouse and a purebred pigmented (not albino) mouse are ALL pigmented, which of the following is TRUE:

pigmented is dominant over albino

Gamete

reproductive cell (sperm, egg, etc.)

Which of the following cell types are not an example of gametes?

retina cells

Meiosis:

specialized cell divisions that produce gametes from somatic cells

Red-green color blindness in humans is a X-linked trait; an individual will have red-green color blindness with a homozygous recessive or hemizygous genotype. You are working as a genetic counselor for an XY male and XX female couple who want to start a family and would like to know the odds of having a child with color blindness. Neither the man nor the woman are color blind, but both of their biological fathers were color blind. Which statement is true about the probability of color blindness for their children?

their XY male children have a 50% chance of color blindness

You have developed an experimental technique for creating an artificial chromosome in mice with chromosome fragments isolated from another individual. And you think you have isolated the part of the Y chromosome (from the XX-XY sex determination system) that is responsible for male sex determination in mice. Which of the following experiments would prove that you have isolated the region of the Y sex chromosome that is required for male sex determination?

when you add your experimental Y fragment to an XX individual, that mouse begins to produce sperm

The biological species concept defines species by their capacity to mate and exchange genes

'Reproductive isolation' establishes new species Prezygotic isolating mechanisms make mating or fertilization unlikely Ex. Different ecological requirements so individuals would never meet, incompatible reproductive behaviors, organs, or gametes, and others Postzygotic isolating mechanisms make gene flow unlikely Ex. Incompatible maternal environment, unequal or incompatible chromosomes, and others

By comparing the mass of different nucleotides, researchers have found although DNA from all eukaryotes, bacteria, and archaea follow Chargraff's rule, some species have DNA that is richer in some nucleotides than others. If the human genome is made up of approximately 20% guanine, what percentage of adenine is expected? (Remember: DNA is made up of adenine, thymine, guanine, and cytosine)

30%

The figure below shows a generalized structure of an amino acid including 1) the amino group 2) the carboxyl group, 3) the hydrogen atom, and 4) the radical group (side chain). Which part of the amino acid varies amongst the 20 common amino acids found in most organisms?

4) the radical group (side chain)

Mice have 20 pairs of homologous chromosomes. How many total chromosomes would you expect in a mouse that is a monosomic aneuploid for one homologous chromosome?

40-1 = 39 chromosomes

RNAs are modified after transcription

5' Capping and 3' polyadenylation - adding to the beginning or end Splicing - removal of primary transcript sequence Methylation - adding CH3 molecules to the nucleotides Editing - changes to primary sequence at single nucleotides Interaction with proteins/other molecules - loading into a protein complex, attaching amino acids, and more

Please complete the sentence. When single stranded, DNA and RNA molecules are typically written from __________________.

5' to 3'

A wheat plant has 6 alleles of the same gene. What is the minimum number of sets of homologous chromosomes that this wheat plant could have?

6 sets

The figure below contains an image of a hybrid heteroduplex between a mature, fully-processed mRNA molecule and the genomic DNA that was transcribed to produce it. In this hybrid interaction the DNA molecule forms 7 loops (labeled A-G) where the DNA does not pair with the mRNA. How many introns does this DNA sequence contain?

7 introns

You have been characterizing the SARS-CoV-2 (COVID19) E protein involved in forming the lipid envelope of the mature virus and you have determined that the polypeptide encoded by the gene for the E protein is 75 amino acids long. How long is the coding sequence of the E protein mRNA transcript?

75*3 + 3 (termination codon) = 228 base pairs

Microfluidics use precision fabrication techniques to produce plastic chips with tiny fluid circuits

Allows precision mixing of fluids in multiple simultaneous experiments - 'lab on a chip' Microfluidic approaches can be used on bacteria, isolated cells, or small eukaryotic organisms Chips that use oil and water can produce small liquid droplets emulsions of water in oil Potential for hundreds of thousands of separate reactions in the same test tube

RNAs can have elaborate secondary structure and even do some biochemical jobs

Because RNA is single stranded, internal base pairing makes folds Transfer RNAs (tRNAs) Riboswitches and autocatalytic RNAs Ribosomal RNAs (rRNAs)

Darwin and others (in 1870) believed in Pangenesis- the inheritance of acquired characteristics

Darwin - organisms have 'gemmules,' little particles they absorb from their environment that they transfer to their offspring

Signal transduction underlies several examples of epistasis and pleiotropy

Changing the function of one of the upstream members of a kinase cascade can impact all downstream members If signal transduction pathways use some of the same proteins, changes to the genes for shared components will impact both pathways at the same time (pathway crosstalk)

Regulatory genes affect gene expression

Can encode regulatory RNAs (more info in a couple lectures) Or regulatory proteins, including transcription factors (TFs) Many transcription factors bind DNA Have structures that allow interaction with DNA Other, 'co-regulators' interact and influence the activity of transcription factors

Deletions lose a chromosomal segment

Causes hemizygosity for remaining allele of deleted genes Can reveal a recessive phenotype, also called pseudodominance Used to map genes (deletion mapping) Some genes require two alleles to function, deletion of one allele reveals 'haploinsufficiency,' can be lethal or lead to disease

The plant hormone auxin is used to determine up and down (the apical-basal axis)

Charles and Francis Darwin observed that the tip of a growing plant is required to grow towards the sun Trapping hormone from the tip of a plant in a block of agar then placing it on top of a decapitated stem is sufficient to cause cell elongation Auxin, the molecule behind this behavior is primarily produced in the root of the plant and actively transported towards the growing tip Many morphogens have source-sink relationships Allows long-distance communication between organs, tissues, cells

Mendel's pedigree for Round x wrinkled 3

Conclusion 3: Round is Dominant over wrinkled! Evidence -- All F1 plants are Round, but some (¼) F2 plants are wrinkled recessive alleles disappear in the F1 generation Dominant alleles show in the F1 generation

Eukaryotic transcription by RNA Pol II requires several DNA-protein interactions

Core promoter is binding site for general transcription factors, proteins that are part of the RNA polymerase Further 5', or upstream of core promoter, regulatory promoter sequences attract transcription factors which are specific to a subset of RNA transcript sequences Distal enhancer sequences can attract transcription factors that interact with RNA polymerase at a great distance

The transcriptional unit includes promoter, RNA-coding sequence, and terminator

DNA information necessary to make a transcript: Promoter- attracts RNA polymerase RNA-coding sequence- transcribed into RNA molecule, begins with transcription start site (TSS) Terminator- ends transcription

Nondisjunction of chromosomes can cause aneuploidy and polyploidy

Failure of chromosomes to separate during cell division Potential causes Loss of the centromere (deletion, translocation) Disruption of the spindle (chemicals like colchicine, asbestos) Inefficient spindle attachment (small chromosome, ineffective centromere) In humans, increased chance with mother's age

When multiple events MUST happen, multiply the probability

Flipping a normal coin has ½, 0.5, or 50% chance of heads Flipping twice has ½*½ or (0.5)^2 chance of two heads Flipping seven times has ½*½*½*½*½*½*½ or (0.5)^7 = 0.0078125 chance of seven heads

Modern day: the gene is the unit of heredity

Genes are passed from parents to offspring via gametes

Which organisms can be studied with genetics?

Genetics is the universal language of inheritance Archaea, Bacteria, Eukaryotes (Plants, Animals, Fungi), and Viruses included

PCR allows the amplification of known sequences from even 1 DNA molecule

Highly sensitive technology with many applications Entry point for cloning gene or gene fragment into bacterial vectors Primers can add (leader sequence) or change sequence (site directed mutagenesis) Paired with reverse transcriptase (enzyme which converts mRNA into DNA) RT-PCR can detect gene expression Technology that underlies COVID19 nasal swab

Prophase 1:

Homologous chromosomes will separate with crossovers during Anaphase I

Regions under selection cause 'linkage drag' that also increases frequency of nearby alleles

If strong selection leads to complete fixation or homozygosity of a target allele, linked alleles may become fixed as well Strong selection for an adaptive trait may lead to high frequency of an unrelated trait (or one that might be adaptive under different conditions) Ex. During domestication of plants and animals, linkage drag decreases nucleotide diversity of large regions of chromosomes (many genes)

Conjugation involves sex pili and secreation system

In E. coli the F episome can control conjugation The F factor transfers from F+ to F- individuals If the F factor integrated or recombined with the genome, may transfer genetic information Other plasmids can be transferred by conjugation

Infectious bacterium Agrobacterium tumefaciens is used to transform plants

In the wild, Agrobacterium tumefaciens creates burls, large woody growths on some plants Agrobacterium genetically reprograms plant tissue to make the burl and generate sugars that only Agrobacterium can eat Uses cellular machinery similar to bacterial conjugation proteins to transmit part of the Ti plasmid to a plant cell Researchers have modified the Ti plasmid to use Agrobacterium to insert a gene construct into a plant Removed genes for making a burl and making excess sugars Target construct randomly integrates into the genome and generates a plant cell that is hemizygous for the new engineered allele

Quantitative trait locus (QTL) mapping performs linkage analysis for quantitative traits using markers

Like linkage analysis, QTL mapping uses a bi-parental population but instead, compares phenotypic distributions based on genotype Ex. F2 mapping In many populations F2 phenotypes are intermediate between two parents In some populations F2 phenotypes show 'transgressive variation' with phenotypes outside of what was observed for the parents For intervals between markers, calculates likelihood that alleles separate phenotype into different distributions For intervals between markers, calculates likelihood that alleles separate phenotype into different distributions

Genome evolution involves many types of chromosomal rearrangement

Looking at loci similarity between many species, researchers can predict changes of the genome throughout evolutionary history Humans have 23 chromosome pairs, but ancient chordate precursor is predicted to have 17 chromosome pairs with a long history of rearrangements in between

Many traits do not follow all of Mendel's principles of inheritance

Multiple types of dominance Variable expression Interaction between loci Parental effects

Hardy-Weinberg assumption 2: no mutation of alleles

Mutation is the source of genetic variation Some mutations can convert from one allele to another, or introduce entirely new alleles Changes allele frequency and prevents complete homozygosity Most mutations have no effect, or are negative (deleterious) Mutations are rarely advantageous

Spatial genomics, the final frontier

New technologies allow sequencing of DNA or RNA (and limited proteomics) from thin slices of tissues In the near future, we will be able to characterize gene expression and genetics from single cells, and know where those cells are in the body!

Hardy-Weinberg assumption 1: random mating

Nonrandom mating affects genotypic frequencies, but not allelic frequencies Positive assortative mating = tendency towards inbreeding or self-fertilization Increases homozygous genotypes compared to equilibrium Negative assortative mating = tendency towards outcrossing or mating of unlike individuals Inbreeding coefficient, F is the probability of inheriting identical by descent (familial inheritance) F is between 0, random mating and 1, complete inbreeding Calculating effect of F on genotypic frequencies: f(AA) = p^2 + Fpq; f(Aa) = 2pq - 2Fpq; f(aa) = q^2 + Fpq Inbreeding depression = highly inbred populations display many negative phenotypes Successive generations of inbreeding reveal 'deleterious alleles' that have a negative effect on survival or reproductive fitness But several species primarily inbreed or self fertilize, assumed that they have 'purged' several deleterious alleles from gene pool and are currently homozygous for beneficial alleles

Ex. Single cell RNAseq of the Arabidopsis thaliana root identifies 'cell trajectories'

Plant roots tips have stem cells that are constantly giving rise to new cells that will eventually have their own functions Single cells are processed in droplets RNA is reverse transcribed into barcoded cDNA sequencing library cDNA sequence aligned to the genome Sequencing data that overlaps gene annotations is converted into numerical measurement of gene expression Clustering and data analysis separates cells into groups based on similarity Clusters potentially identify root cell types and intermediates Full single cell gene expression dataset identifies genes that are correlated with changes in cell identity And understanding which genes go up and down as cells mature, or 'a developmental trajectory

Evo-devo considers developmental genetic pathways over evolutionary time

Polyploidy and gene duplication allow new gene function without loss of essential roles Also: changes to regulatory sequences (esp. distal enhancers) can cause new gene regulation and cell identity Changes to the regulation of regulatory genes can quickly lead to organ-level changes from a simple DNA mutations

Single cell sequencing microfluidic experiments mix sequencing library ingredients, cells, and identifying barcodes

Recall: For illumina sequencing, small adapters are ligated to the ends of DNA molecules Barcoding approaches add unique 'barcode sequences' to the adapters Once adapters have been added to the DNA molecule, droplets can be burst and processed together The barcode is now part of that DNA fragment Final sequence will start with barcode and identify the cell it came from Barcode adapters are often tethered to a resin bead or embedded in a gel that can be dissolved in the combined droplet

Recombination frequency is the rate of recombination

Recombination frequency = ( Number of recombinant progeny / total number of progeny ) * 100 Probability of nonrecombinant and recombinant gametes adds to 1.0 Genotypic probability = Prob gamete Parent1 x Prob gamete Parent2

Recombination frequencies are gene mapping units

Recombination frequency is reproducible Some linked pairs have higher recombination frequency than others Hypothesis: genes that are closer together on a chromosome have a lower recombination frequency Recombination frequency = map units (m.u.) = centiMorgans (cM) Genetic maps (cM) can help construct chromosome physical maps (base pairs or nucleotides)

Theta and linear DNA replication

Replication is carried out by a DNA polymerase Always 5' to 3' (adding to the 3' OH) Uses complementarity of free nucleotides (dNTPs) to copy template DNA strand Theta and linear replication are bidirectional and have a leading strand and lagging strand Creates replication bubble / fork

Which term best describes the following phenomenon? After an individual has inherited a nondisjunction, that individual has a greatly increased chance of producing gametes with a new nondisjunction because of errors in meiosis.

Secondary nondisjunction

Transcriptomics sequences cDNAs to perform RNA sequencing

Sequencing approaches work best with DNA templates (but nanopore can process RNAs directly) To understand RNA transcripts, RNAs are reverse transcribed into complementary DNAs or cDNAs by Reverse Transcriptase Aligned RNAseq reads show exon-exon junctions and alternative splicing RNAseq also quantifies transcript abundance / transcriptional activity Transcriptomics is used as a measure of gene expression

Eukaryotes use siRNAs to maintain heterochromatin

Specialized RNA polymerase creates transcripts from repetitive regions, and heterochromatin These transcripts are made into dsRNA by an RNA-directed, RNA polymerase (RDR) dsRNA is processed by RNAi and heterochromatin is maintained

Bacteria exchange genetic information through conjugation, transformation, and transduction

Taking advantage of these systems permits the study of bacterial genes Many bacteria allow homologous recombination between DNA molecules with similar flanking sequences Allows exchange of alleles, or insertion/deletion/rearrangement of genes like with meiotic homologous recombination of chromosomes

Translation's required stages: tRNA charging, Initiation, Elongation, and Termination

The cell expends energy to put amino acids onto the tRNA Done by enzymes called aminoacyl-tRNA synthetases that recognize the tRNA amino acid acceptor stem To initiate translation, the large and small ribosomal subunits must be attached to the ORF Involves several initiation factor proteins, and recognition of the 5' cap and 3' polyA tail in eukaryotes Translation is terminated when a release factor protein binds to a termination codon The polypeptide is released and the ribosome dissociates from the mRNA

CRISPR-Cas9 with a homologous DNA template performs real gene editing

The cell uses DNA repair machinery to fix the DSB Sometimes makes mistakes, deletions, inversions, other rearrangements (like after exposure to x rays) If any nearby DNA molecules share sequence with DNA on both sides of the DSB, DNA repair machinery can conduct homology directed repair (HDR) Pastes new DNA sequence directly into the genome Homologous directed repair requires: 1) Cas9 protein, 2) guideRNA (specific to target site), and 3) DNA template Lipid nanoparticles (like for Moderna COVID19 vaccine) can be used to deliver into a living animal

DNA → RNA → Protein

The central dogma of molecular biology describes the flow of genetic information required to make a trait DNA → RNA → Protein → Trait Alleles = changes to DNA that impact this chain Colinearity of information from DNA, RNA, and Protein RNAs are transcribed from DNA RNAs are translated into Proteins Proteins make traits

BCR-ABL is a mutation caused by the reciprocal translocation of human chromosome 9 and 22. Individuals with a type of cancer called chronic myeloid leukemia (CML) are likely to have the translocated version of BCR-ABL on chromosome 22. Healthy individuals without the translocation have a separate BCR gene on chromosome 22 and separate ABL gene on chromosome 9. Which of the following is NOT likely to be true about BCR-ABL and the chromosome 9 to 22 translocation?

The translocation that causes BCR-ABL is likely to have no effect on meiosis or fertility

How does a cell make more DNA?

Three potential models: Conservative - Double helix does not separate and both strands are copied at once Dispersive - Every replication has a fragmented mixture of old and molecules Semiconservative - One strand from an old molecule is combined with a new strand to make a new double helix (slowest)

Genetic engineering inserts sequences into the genome

Traditional breeding of animals and plants may take years for relatively small changes Improvement depends on allelic variation and recombination To generate new variation, some breeding programs use mutagenic chemicals (EMS, ENU) or radiation which randomly damages the genome Maintaining all the most beneficial alleles and adding more is a juggling act Genetic engineering creates new alleles without altering the rest of the genome (most of the time)

Which of the following are NOT likely consequences of chromosomal structural variation?

Traits are blended together in offspring

Changing chromatin accessibility changes gene expression

flowering to non flowering

Which stage or substage of meiosis will not contain fully recombined homologous chromosomes?

leptotene

Single cell genomics profiles molecules from individual cells

'Bulk' samples extract DNA, RNA, or proteins from groups of cells From tissues up to whole organisms Mixes molecules from many cells Gene regulation leads to different RNA transcripts and proteins in different cell types with different functions Chromatin remodeling expands or contracts access to the genome Single cell techniques isolate cells and prepare miniaturized reactions to characterize their molecular contents Science Magazine 'Breakthrough of the Year' 2018 Applications in immunology, neurology, cancer, development, host-pathogen interaction-- many others!

Anatomy of a chromosome

1- a centromere, constricted region where the spindle attaches to pull chromosomes and sister chromatids during mitosis and meiosis No centromere, no inheritance 2- telomeres, repetitive DNA sequences at the end of the chromosome that stabilize the chromosome ends and prevent fusion between chromosomes 3- origins of replication, where the cellular machinery that copies DNA can begin to copy the chromosome

If a fruit fly gamete is 1n and has 4 chromosomes, how many chromosomes does a fruit fly 2n somatic cell have?

8 chromosomes

Proteins are polypeptide chains built from 20 common amino acids

Amino acids are defined by their side chains Differences in charge (+ or -), size, and structure Peptide bonds link amino acids together to make polypeptides (proteins) Like DNA, proteins have primary, secondary, tertiary, and quaternary structure Structure is very important in determining biochemical function As proteins interact with other molecules, they change shape or conformation and enzymes encourage rare chemical reactions to take place more efficiently

Eukaryotic DNA is wrapped around histones

Chromatin = DNA and all associated proteins Nucleosome = DNA wrapped around proteins called histones 8 histones in each nucleosome 2x H2A, 2x H2B, 2x H3 and 2x H4 Nucleosome = DNA wrapped around proteins called histones 145-147 bp of DNA wraps 1.65 times Little spool of DNA: spread apart nucleosomes = highly accessible DNA = euchromatin condensed nucleosomes = inaccessible DNA = heterochromatin

You are trying to isolate bacteria for bioremediation that can survive exposure to radioactivity and be grown easily in the field on a minimal medium. You prepare a primary culture plate with well-spaced colonies descended from single bacterial cells on a complete medium. If you make a replica plate of all your colonies and stamp it onto 1. A petri plate containing a highly radioactive medium and 2. A petri plate containing a minimal medium without radioactivity, which of the following comparisons will identify putative radioactivity-resistant isolates?

Colonies that grow on plate 1 and plate 2 are resistant to radioactivity and can be cultured on a minimal medium

Genetic material must share the properties of genes

Contain complex information Replicate faithfully Encode the phenotype Must allow variation

Corals are dependent on a dinoflagellate endosymbiont for photosynthesis but eject the dinoflagellate if they become 'bleached' by environmental conditions. What is the likely effect of the loss of this symbiosis on corals?

Corals no longer have the genetic program for photosynthesis in their hologenome and are unable to construct new sugars

Prader-Willi and Angelman Syndrome are human diseases caused by a combination of a deletion on chromosome 15 and either maternal or paternal genomic imprinting of the homologous, intact chromosome 15 respectively. The symptoms of Prader-Willi and Angelman are distinct and caused by different genes, rather than alleles of the same gene. Knowing that genomic imprinting represses expression of genes based on the parent-of-origin, which of the following must be true for these genetic diseases?

Different regions of chromosome 15 are targeted by maternal and paternal imprinting

In which substage of Prophase I are bivalent chromosomes with chiasmata first visible?

Diplotene

DNA replication is semiconservative

E. coli has a generation time of ~20 mins (20 mins between DNA replication events) By spinning DNA extractions in a centrifuge, molecules are separated by density and reveals relative composition of N15 and N14 Results: 1) Labeled molecules changed from being 100% DNA with N15 to 50% N15 in 1 generation 2) N15 decreased by ½ in relative abundance with every generation Conclusion: DNA is ½ old and ½ new every time

Aneuploidy and Polyploidy are changes in chromosome number

Euploidy = cells with the typical number of homologous chromosomes Aneuploidy = change in homologous chromosome number (one, up to a few), increase or decrease Polyploidy = increase in the number of sets of homologous chromosomes (all of them) Like other chromosomal abnormalities, aneuploidy and polyploidy cause problems at meiosis (and sometimes mitosis)

Crossing over during meiosis produces recombinant and parental gametes

Ex. AB/ab individual making gametes In meiosis, one AB sister chromatid crosses over with 1 ab sister chromatid (also, one AB sister chromatid and one ab sister chromatid do not recombine) Four gametes formed: AB, ab, Ab, aB Frequency of recombinant gametes is close to half the frequency of crossing over **Maximum number of recombinant gametes is ~50%**

Biological sex

General biological sex rule: If one gamete is bigger than the other, the bigger gamete is called an egg, made by an ovary The individual that makes the bigger gamete is called female The smaller gamete is called the sperm and made by a male, etc

biological sex

General biological sex rule: If one gamete is bigger than the other, the bigger gamete is called an egg, made by an ovary The individual that makes the bigger gamete is called female The smaller gamete is called the sperm and made by a male, etc Many species are hermaphroditic = produce both gamete types at the same time (they are monecious) Others species have individuals that produce one type of gamete (they are dioecious) Some species are sequentially hermaphroditic, capable of producing male or female gametes during their lifetime, but only producing one type at a time Sex determination = mechanism that establishes which gametes will be produced

Ex. NCBI hosts Basic Local Alignment Search Tool (BLAST), which calculates the most likely relationship between two sequences

Genomic DNA fragments don't always have exactly the same sequence DNA mutants, sequencing errors, related species BLAST algorithm finds the optimal arrangement or alignment of two molecules: the query and the reference Starts with a seed or small word from the query Looks for an exact match between seed and reference From the seed, does next bp match the reference? If so, -0 or +? to alignment score If not, -N to the alignment score Different penalties for different changes (substitution, gap, deletion) Continue to grow sequence against reference Keep score for seed Try new seed and repeat process Highest scoring alignment is the most likely relationship between the two molecules Many more implementations and procedures to speed up and improve alignment, but many follow the same seed-and-grow approach

Homeotic mutants transform tissues from one type to another

Homeotic mutants demonstrate that some developmental processes are decided by transcription factors Changing these critical 'master regulators' of development can reprogram cells from one identity to another Activates or represses target genes responsible for final cell fate

When exposed to the parasite that causes malaria, humans that are heterozygous for sickle cell disease are more likely to remain healthy than individuals that are homozygous for sickle cell disease or homozygous for normal blood cells. What is a term to describe the performance of heterozygous individuals in this case?

Heterozygous advantage

Testcrosses to recessive help determine the genotype

In a complicated pedigree, genotype may not be known Dominant phenotype may come from homozygous or heterozygous genotype Crossing Parent1 with an unknown genotype x homozygous recessive Parent2 helps If Parent1 was heterozygous, next generation will segregate 1:1 for each independent trait (0.5 dominant phenotype, 0.5 recessive phenotype)

Mitochondrial and plastid genes move to the nucleus (over evolutionary time)

In humans, it takes about 3000 genes for functional mitochondria, but only 13 are on the mitochondrial DNA The rest are encoded in the eukaryotic human genome! Endosymbionts transfer genetic information to their host's genome

GAL4 encodes an 'positive inducible' transcriptional activator

In yeast, transcription of enzymes necessary for galactose metabolism are activated only in the presence of galactose The GAL4 transcription factor recognizes a DNA sequence upstream of these DNAs and binds at a distal enhancer When galactose is not present, GAL8 binds GAL4 and blocks the GAL4 'activation domains', parts of the protein required for transcriptional activation When galactose is present, GAL3 interacts with GAL80 and GAL4 is released and activates transcription

Environmental sex determination

Individuals have all the genetic material necessary to produce any gamete type Environmental factors influence which gamete is produced - Temperature: Many reptiles have temperature requirements for sex determination as embryos - Age/size/nutrition: Groupers start out as Female but transition to Male as they age - Ovaries (producing eggs) become testis (producing sperm) An example of sequential hermaphroditism - Social environment: Clownfish live in a single-female, multiple-male social group If the female dies, the next largest male becomes female Its testis become ovaries and produce eggs instead of sperm

The polymerase chain reaction (PCR) uses a thermostable DNA polymerase to copy a targeted DNA sequence in a test tube

Ingredients: DNA templateFree deoxyribonucleotides (dNTPs)DNA primers (complementary to target sequence)DNA polymerase and salts needed for polymerase (Mg2+) Uses Taq polymerase from Thermus aquaticus, heat vent bacterium that can survive extreme temperatures

Starting with the human genome, modern genomes are assembled by a 'shotgun sequencing approach'

Instead of figuring out the restriction digest map first, sequence everything and assemble based on overlapping sequence In 1999 Celera Genomics finished the first draft of the human genome Shotgun sequencing is FAST But requires a lot of computational effort to assemble the genome Requires that most parts of the genome are sequenced multiple times, or have 'high coverage'

Alternative splicing allows the same DNA sequence to produce multiple unique RNA transcripts

Intron retention- intron is not removed Exon skipping- exon is excluded Alternate 5' or 3' splice site- different, non-canonical intron-exon junction Transcripts from the same DNA sequence are called splice isoforms The most abundant is the 'canonical' form Isoforms can be differentially regulated between tissues, made in response to stresses/stimuli, or simultaneously produced in the same cell When isoforms are translated, can lead to different proteins

Illumina uses PCR and reversible fluorescent ddNTPs to simultaneously sequence millions of fragmented molecules

Long DNA molecules are sheared by chemical reactions, physical shearing, or enzymatic processing Ends are repaired and ligated to special Illumina adapters Molecules are elongated one nucleotide at a time, using fluorescent ddNTPs (only one nucleotide is added) A high resolution camera takes a picture of the fluorescence in the flow cell after each elongation Illumina ddNTPs can be chemically reverted into non-fluorescent dNTPs and elongated again Pictures of spots after each nucleotide are used to determine the sequence Reads up to 150 bp from either end of a molecule Reads are relatively short ~$0.00000001 / bp (~$30.00 human genome, but 30x coverage needed for any clinical intervention)

Transcription requires a complex of multiple transcription factors, so changes to chromatin structure impact gene expression

Looser packing = more easily expressed Denser packing = less easily expressed Because this change is independent of DNA sequence, these changes are 'epigenetic' But just like transcription factor-mediated changes, can be dynamic between cells, conditions, and time Major component of cell differentiation in animals and plants

Transposons are DNA sequences that can insert themselves into genes

Mapped the same DNA element (transposon) to multiple chromosome locations Insertion can disrupt gene function, and is reversible Many types and categories of transposons Majority of 'junk DNA' in large genomes Targets of epigenetic silencing, RNAi

Heterozygous paracentric inversions leads to gametes with deletions

Normal and inverted chromosomes form an inversion loop when they pair Recombination in the inverted region produces abnormal chromatids One acentric, with no centromere, cannot segregate into gamete Two have 'dicentric bridge' and have large deletions Will break further during Anaphase I Large deletion can be lethal to recombinant gametes Two parental chromatids lead to nonrecombinant gametes Inheritance of recombinant chromosomes is suppressed Normal and inverted chromosomes form an inversion loop when they pair Recombination in the inverted region produces abnormal chromatids All chromatids have centromeres, but recombinant chromosomes have a large deletion and inverted duplication Large deletion can be lethal to gametes If viable, can cause unequal crossing over in next generation Inheritance of recombinant chromosomes is reduced

Recombinant DNA technology combines DNA sequences as the building blocks for artificial gene constructs

Restriction enzymes or restriction endonucleases cut or 'digest' DNA with specific recognition sequences Part of bacterial defense against viruses Over 800 known restriction enzymes from many different bacteria Name of the enzyme is an abbreviation of the species where it was purified Ex. E. coli EcoRI recognizes 5'-G/AATTC-3' Some restriction enzymes make symmetrical overhanging cuts, 'sticky ends' Staggered ends allow unrelated DNA molecules to be glued together Other restriction enzymes do not make overhanging cuts, 'blunt ends' Blunt ended molecules can be joined without complementarity DNA ligase can make covalent bonds between complementary sticky ends or end-to-end blunt ends Joining two molecules of DNA from different species into one = recombinant DNA

Viruses are nucleic acids wrapped in a protein shell that use other cells to replicate

Retroviruses have an RNA genome DNA viruses have a DNA genome Details of contents are used to classify viruses Viruses genes integrate with the host genome during the lysogenic cycle Viruses replicate during the lytic cycle

Bioinformatics supports the computational needs of genome-scale sequencing and analysis techniques

The National Center for Biotechnology Information (NCBI) and other international organizations help store and display all this sequence information

What information would determine whether a nucleotide is a purine or pyrimidine?

The number of rings in the nucleobase

Cas9-induced alleles leave no identifying information

Traditional transgenics have known sequences introduced during construction (antibiotic resistance, promoter, etc) But Cas9 events do not leave any predictable sequence or scar CRISPR-Cas9 can even re-make naturally occurring alleles DuPont Pioneer used CRISPR to re-create the waxy allele in locally-adapted corn varieties, saving years of crosses and selection -- USDA said 'not GMO'

Which of the following is NOT part of Mendel's Law of Segregation?

Traits are blended together in their offspring

Allosteric transcription factors allow simple regulatory logic

Transcription factors are produced at a separate locus Allosteric = can interact with a biochemical molecule to change conformation, or shape One shape can interact with the operon, one shape can't interact with the operon

Genome-wide association studies (GWAS) directly link phenotype to markers

Uses many distinct lines or individuals and many polymorphisms Assumes that the population of individuals can be traced back through a pedigree Many chances (throughout history) to recombine and break linkage

Viral genes can be studied through transduction

Viral DNA can undergo homologous recombination in the host: if infected with two variants of the same virus, or if cell contains similar DNA sequence Changes to viral genes observed in virus recovered from host

Which of the following is the most likely impact of a chromosomal deletion that removes the core promoter sequence upstream of the transcriptional start site (TSS) of an RNA transcript?

Without the promoter, the RNA polymerase enzyme complex will not be assembled and the transcript will no longer be transcribed

Sex Chromosome determination

XX-X0 system - female is XX and male is X0 (only one X)Many insects, arachnids, but also some bats and other mammals ZZ-ZW system - female is ZW and male is ZZW chromosome contains genes necessary for making ovaries and eggsMost birds, some reptiles, fishes XX-XY system - female is XX and male is XYY chromosome contains genes necessary for making testis and sperm (promotes and maintains ovary -> testis conversion) Only found on Y - Sex determining region Y (SRY) promotes testis early in development (in utero) But ovaries are also produced actively... Found on Autosome Chr 3 - Forkhead box protein L2 (FOXL2) promotes ovaries Chromosomal sex determination is not completely rigid There is variation in how chromosomes translate to sex Humans have several possible (rare) sex chromosome number variants

Structures of mRNA can regulate translation

(Most examples in prokaryotes) Riboswitches have interactions between UTR structures and proteins that regulate protein translation Elaborate RNA secondary structure and protein binding block the ORF

Mutations can affect protein codons (and therefore gene expression and/or protein function)

- Missense - New codon substitutes an amino acid Mutant protein may not function properly Ex. change to amino acid necessary for phosphorylation 'phosphodead' kinases which cannot signal 'phosphomimic' kinases which always are shaped like they have been phosphorylated (Ser > Asp). - Nonsense - New codon is a premature stop codon Mutant protein is shorter than usual, or 'truncated' If early in the gene, may also trigger 'nonsense mediated decay' (NMD) Early stop codon leads to removal of all mRNA from this locus If NMD, no mutant protein will accumulate - Synonymous - DNA change, but no new amino acid Because codon usage is 'degenerate' some DNA changes do not impact amino acids No effect on protein and no associated trait, a 'silent mutation' Can be used to look at DNA mutation rates - Frameshift - Insertion or deletion changes all subsequent codons Unless 3 bp are added or removed (one whole codon)

Eukaryotic genetic material isn't all in the nucleus

- Mitochondria - powerhouse of the cell does 'oxidative respiration' Found in almost all eukaryotic species - Plastids - specialized organelles usually for photosynthesis Found in plants, algae, unicellular eukaryotes - Mitochondrial and Plastid genomes also contain DNA ...circular genomes that encode bacterial genes

During elongation, tRNAs interact with codons and add to polypeptide

1) The first tRNA begins at the peptidyl (P) site of the ribosome 2) tRNAs enter at the aminoacyl (A) site of the ribosome based on complementary codon 3) A peptide bond forms between the amino acid at the P site and the A site 4) The ribosome translocates down the mRNA and the oldest tRNA is released when it reaches the exit (E) site of the ribosome 5) Now the A site is available for a new complementary codon interaction

5' capping and 3' polyadenylation

A guanine is added to the 5' end The capping guanine and the next two bases are modified A methyl group (CH3) is added = methylation Required for mRNA stability(uncapped RNAs are detected and degraded) Part of the 3' end is cleaved Replaced with a 3' stretch of multiple adenines, the poly(A) tail Frequently used in molecular biology to recognize eukaryotic mRNAs Non-polyadenylated RNAs are detected and degraded

The Law of Independent Assortment depends on meiosis

Alleles on different homologous chromosomes are segregated separately They can each follow the Law of Segregation 4 possible gametes2 (R or r) *2 (Y or y)

Mendel discovered that not all alleles are equal

An organism's alleles = genotype An organism's traits / appearance = phenotype Mendel figured out special rules that govern how genotype -> phenotype Some alleles are Dominant - control the phenotype even when there is another allele present at the same locus (heterozygous or homozygous) Other alleles are recessive - control the phenotype if there are no other alleles present at the same locus (homozygous only)

Fitness landscapes add the selective pressure on multiple loci

Consider all the different loci in the genome and calculate their selective pressures Fitness or adaptive landscapes calculate optimal allele combinations There can be multiple local 'mountain peaks' with high relative fitness Different populations may reach different optimal fitness

Mendel's first law: The Law of Segregation

Corollary 1: Each organism possesses two alleles for a trait Corollary 2: Alleles separate when gametes are formed Corollary 3: Alleles separate in equal proportions

Mendel's wrinkled trait is caused by a transposon insertion

Disrupts starch debranching enzyme1 (SBE1) Mutant protein cannot convert amylose into amylopectin

Structural variants rearrange a chromosome

Duplications Deletions Inversions Translocations

Meiosis or mitosis substage of nondisjunction leads to different types of aneuploidy Example 1

Ex. Meiosis I nondisjunction of 1 chromosome Homologous chromosomes fail to separate Anaphase I Sister chromatids separate Anaphase II (Meiosis II) Gametes are disomic (2 homologous chromosomes) or nullisomic (0 homologous chromosomes) With normal gamete from other parent -> trisomy 2n+1 (2 from parent1 + 1 from parent2) or monosomy 2n-1 (0 from parent1 + 1 from parent2)

Meiosis or mitosis substage of nondisjunction leads to different types of aneuploidy Example 2

Ex. Meiosis II nondisjunction of 1 chromosome Homologous chromosomes separate Anaphase I Sister chromatids fail to separate from Anaphase II (in one Meiosis II division) Gametes are disomic, nullisomic, or monosomic With normal gamete from other parent -> trisomy 2n+1, monosomy 2n-1, or disomy 2n (normal)

The Chi-Square test checks for random chance in inheritance

For extremely large sample sizes, probability will predict outcome The chi-squared (𝝌2) goodness-of-fit test Null hypothesis: no difference between expected and observed Alternative hypothesis: observations are more different than expected by random chance Marginal distribution test that looks at a 'contingency table' of observed and expected numbers Calculate the 𝝌2 statistic as SUM of (obs - exp)^2 / exp Degrees of freedom, dF (n phenotypes - 1) With 𝝌2 and dF can calculate a P-value, probability of observation by chance If P < 0.05, Reject Null, observations are different from expectations If P >= 0.05, Cannot Reject Null, observations are not statistically different from expectations

microRNAs (miRNAs) are loaded from one strand of one dsRNA chunk into Argonaute proteins (AGO) and impact the expression of other mRNAs

Forms a protein complex called RNA-induced silencing complex (RISC) mRNAs that complement the miRNA in the RISC are silenced Option 1: RISC has 'slicer' activity which destroys the target mRNA Option 2: RISC interferes with translation or mRNA stability miRNAs are made from miRNA genes-- no known function except to produce miRNAs, 'noncoding RNAs'

Mutagenesis experiments help to establish that study gene function

Forward genetics randomly makes mutants in the genome If there is an interesting trait, what is the mutated gene that gives that phenotype? Reverse genetics takes predicted genes and looks at individuals with a mutation in that gene Is there a trait or phenotype associated with mutating that gene?

'Diploidization' is a requirement for stable polyploid genomes

How do so many polyploids survive and reproduce? Mechanisms that encourage simple bivalents or prevent all homologues from crossing over During meiosis, chromosomes pair as 21 neat bivalents If Ph1 is deleted, chromosomes make multivalents instead and chromosome number becomes unstable

CRISPR-Cas9 uses molecular scissors and homologous recombination to defend against viruses

Many bacteria have clustered regularly interspaced short palindromic repeats, or CRISPR arrays of DNA sequences captured from bacteriophages Near CRISPR arrays are Cas genes Cas genes make Cas proteins: Cas1 and Cas2 search for foreign DNA and build new CRISPR repeats The CRISPR array makes crRNAs or guide RNAs Cas9 takes the guide RNA and looks for matching DNA sequences When Cas9 and guide RNA find a match (viral DNA), Cas9 cleaves the DNA and it is degraded Through CRISPR-Cas9, bacteria can become 'immune' to viral sequences For biotechnology applications, researchers design new guide RNAs or modify the activity of Cas9

Evolutionary genetics studies how selection produces new species by changing allele frequencies

Many species possess high levels of genetic variation, created by mutation Neutral-mutation hypothesis = most mutations have no effect on fitness, some have negative impacts on fitness, but rarely mutations have positive impacts on fitness Fitness penalizes negative 'deleterious' alleles, but favors positive alleles

Transcriptional networks are complex and non-hierarchical 2

Many transcription factors regulate hundreds or thousands of genes Target genes can be regulatory genes Can target their own genes or regulators Leads to a complex web of activation or inhibition Gene regulatory networks are filled with logical motifs Feed forward loop amplifies signal Negative feedback loop induces a response and turns it back off again

Looking at multiple loci constructs a genetic map

Maximum distance between two loci is 50 cM (appear unlinked) But they can still be on the same linkage group Add distance between makers to construct a linkage group Very distant loci can experience multiple crossovers 'Three point' crosses can distinguish crossover types

Meiosis: One 2n somatic cell → Four 1n gametes

Meiosis produces daughter cells with the half the number of chromosomes Parent cell = 2n somatic cell Four daughter cells = 1n gametes In humans: 2n = 46 chromosomes Parent cell has 2n = 46 chromosomes Four daughter cells have 1n = 23 chromosomes

Additional types of dominance

Mendel discovered: - Complete dominance Recessive allele only affects the phenotype when homozygous - Incomplete dominance Heterozygote has an intermediate phenotype Alleles are maintained as discrete units (not blended)Homozygotes in the next generation can be original parental type Matches Mendelian F2 genotypic probability (1:2:1), because every genotype has a phenotype - Codominance Heterozygote has a new phenotype that adds both parental alleles Both traits expressed at the same time - Overdominance or underdominance Heterozygous phenotype is more extreme than either parents (over- if above parents' values, under- if below parents' values) Aka. heterozygous advantage possible explanation for heterosis or hybrid vigor, where the F1 generation outperforms the P generation

Biotechnology starts with naturally occurring genes and proteins and puts them to work

Molecular genetics = understanding the DNA and gene regulation necessary for a trait Basic molecular genetics is universal to all organisms Biotechnology replicates these processes, and sometimes modifies them for other purposes In vitro systems can be reproduced in a test tube or other experimental apparatus In vivo systems use a living organism

Today: we use molecular markers for high density maps

Molecular markers alleles may not have associated traits, but still follow rules of inheritance, recombination Some have 'molecular phenotypes,' different sized DNA molecules in the right reaction Others are SNPs or 'single nucleotide polymorphisms,' changes of one DNA base Many have physical map locations (chromosome and DNA nucleotide location in the genome) Molecular biology and DNA sequencing allows direct genotyping of molecular markers

Parent of origin can impact a trait

Morgan discovered: - Sex-linked traits Alleles on a sex chromosome co-segregate with sex - Cytoplasmic inheritance or Extra-nuclear inheritance The egg contributes more cellular machinery than the sperm - Mitochondria and chloroplasts have their own genes Mitochondrial and plastid alleles are inherited matrilineally - Genetic maternal effect The mother's genotype controls the phenotype Offspring genotype is masked by the mother's Alleles are still inherited in the next generation - Genomic imprinting Expression of an allele is controlled by the parent of origin Allele is still present, but has been 'epigenetically' silenced Can be inherited in the silenced state Can be reprogrammed in offspring of the opposite sex Depends on DNA methylation, smallRNAs, and histone modifications, topics of a later lecture

Developmental genetics studies the way that genes orchestrate multicellular growth

Multicellular organisms begin as single cells (zygote) and then produce all their characteristic cells, tissues, and organs Despite unique functions, cells in the same organism all inherit the same genome Early in development embryonic cells are totipotent-- they can become any part of the organism; also called stem cells Most organisms retain small pools of pluripotent cells-- they can become at least two possible cell types

Somatic aneuploidies can result in genetic mosaics

Nondisjunction of a somatic cell during mitosis -> cells and their descendants with different numbers of chromosomes Clones or sectors = groups of cells with same genetics Mosaic or chimera = individual with genetic sectors Involved in cancers and diseases that would be fatal if all cells had nondisjunction If early in development, mitotic sex chromosome nondisjuction can lead to gynandromorphs, individuals with ½ cells that are chromosomally male and ½ cells that are chromosomally female

Messenger RNAs (mRNAs) are transcripts that come from and encode genes

Of all the RNAs, mRNAs carry genetic information Bacterial mRNAs are immediately translated after transcription mRNA modifications (capping, splicing) in bacteria are rare Eukaryotic pre-mRNAs are transcribed then processed in the nucleus

By calculating phenotypic heritability under different conditions, we can estimate environmental control of phenotypes

Phenotype = Genotype x Environment (+ Error) Some phenotypes display a strong environmental influence

Quantitative genetics deals with quantitative traits and multiple genetic loci

Phenotypes are a continuum of values Ex. plant flowering time, human height Complex traits are controlled by multiple loci (they are 'polygenic') Alleles impact the phenotype in an additive way 'The infinitesimal model:' many loci of small effect control quantitative traits

Classical genetics deals with qualitative traits and genetic loci of large effect

Phenotypes fall into discrete categories Ex. Round vs wrinkled, Blood type: A, AB, B, O Simple traits are controlled by one or few genetic loci Alleles change the phenotype in a big way

Proteomics breaks down proteins to characterize peptides and amino acids

Proteins cannot be sequenced like DNA or cDNA Mass spectrometry (MS) identifies proteins by their size 1) Proteins are digested into peptides by the enzyme trypsin 2) Peptides are ionized so they become charged Time of flight (TOF) spectrometry calculates the mass/charge ratio for the peptide Time of flight (TOF) spectrometry calculates the mass/charge ratio for the peptide All the peptides together generate a profile that is characteristic for a given protein Tandem mass spec (MS/MS) captures a peptide and further breaks it down into amino acids to characterize the exact amino acid composition

August Weismann in 1890s - Germ plasm theory disproves Pangenesis

Removed tails from mice generation, after generation But each new mouse was born with a tail Finding: Acquired characteristics are not inherited Finding: Somatic cells (like tails) do not contribute to inheritance Specialized 'germ plasm' cells control heritable traits Today we call these cells the germline and they make gametes Theory: New traits can be inherited if they are in the germ cells / gametes Called these new traits 'mutations'

Gene trees are phylogenetic trees that follow the evolutionary history of gene sequences

Starting with DNA, cDNA, or protein sequences that can be aligned, gene trees predict the most likely relationship between genes Identifies conserved gene features or domains Used to define 'gene families' Reveals gene duplications, whole genome duplications, and potential horizontal gene transfer (movement of genes between species--gene tree does not follow species phylogeny)

Phylogenetic trees use inherited characteristics to represent the differences amongst organisms

Systematics predicts the most likely or 'most parsimonious' relationship between organisms based on important traits Relationship is represented by a phylogenetic tree: branches are evolutionary connections, nodes are evolutionary split points Today, most phylogenetic trees are constructed with molecular characteristics Usually aligned DNA sequences from known loci Knowing rate of DNA mutation can predict approximate age of last common ancestor using a 'molecular clock' approach

Duplications repeat part of the chromosome

Tandem duplications duplicate immediately after the original Displaced duplications add, or insert somewhere else Can cause unequal crossover during meiosis Duplicated genes change allele dosage Allows allelic variation at duplicate, without loss of original allele

You are working in a molecular biology lab that studies both bacterial endosymbionts and their eukaryotic hosts. You blend up your culture of the two species and use a special bead that is covered with polythiamine (polyT, 'TTTTTTTTTT....') molecules to extract RNAs from a culture of your 2 species. Your reaction conditions create a heteroduplex between RNA molecules that are complementary to the polyT sequence on the bead. You then remove the beads with interacting RNAs bound to them. Which of the following is NOT a characteristic of the RNA molecules that interact with the beads?

The bead-bound RNAs come from the bacterial endosymbiont

Prophase 1: Zygotene -

homologous chromosomes begin to pair = undergo 'synapsis'

lac is a 'negative inducible' operon

lacI, the lac repressor is transcribed and translated from a separate locus When lacI protein binds to the lac operon, lac operon transcription is suppressed = lacI acts as a transcriptional repressor When lactose is available in the cell, a small amount is converted into allolactose When allolactose binds to lacI, lacI changes shape and cannot repress the lac operon lacZ, lacY, and lacA are transcribed by RNA polymerase in a polycistronic mRNAThese genes are 'induced' by lactose lacZ translates into a beta-galactosidase enzyme that can convert lactose into glucose and galactose, which the cell uses for primary metabolism If lacZ converts enough lactose into glucose and galactose, or the cell is no longer in the presence of lactose, allolactose levels will fall and lacI transcription factors can bind the lac operator and repress transcription

Ribosomes contain spliced and methylated rRNAs

rRNAs are the most abundant RNAs in the cell (~80% of total RNAs) Ribosomes contain two subunits of rRNA and proteins rRNAs are spliced then methylated at several locations

Bacteria and viruses are diverse and numerous

~10 trillion bacterial cells in every human, 10x more than human cells! Genes in human gut bacteria outnumber human genes by 150-fold Few bacteria and viruses can be cultured in the lab DNA sequencing suggests tens of thousands of bacteria and viruses in every gram of soil Complex community ecology and interactions with other species Bacteria and viruses do not use meiosis, but have other methods of exchanging genetic material that we use to study inheritance and gene function

Which of the following statements about Punnett squares is TRUE?

gametes from parent1 are represented top to bottom and gametes from parent2 are represented left to right along the Punnett square

Some cells do not divide mitotically after G2 of interphase and instead enter 'endoreduplication,' a special cell cycle where the DNA content of the cell continues to double without the cell dividing. Cells which have undergone endoreduplication have been measured at 4n, 8n, 16n, 32n, and even 64n instead of the typical 2n DNA content. Knowing that gametes have 1n DNA content, which of the following statements about endoreduplicated cells must be TRUE?

germline cells are prohibited from entering endoreduplication

Mendel's Law of Segregation assumes that every allele is inherited in equal proportions. However, some alleles cause a phenomenon called meiotic drive, where that allele is preferentially inherited over another allele at a probability greater than 0.5. Ab10 is a dominant allele that causes meiotic drive in corn. What type of cross would allow you to calculate the preferential inheritance of Ab10 over its recessive allele wt?

heterozygous Ab10 x homozygous wt

Red eye vs purple eye and normal wing vs vestigal wing are linked fruit fly traits that were studied by Thomas Hunt Morgan and his students. In the P generation, Morgan mated red eye, normal wing (pr+vg+/pr+vg+) flies with purple eye, vestigal wing (prvg/prvg) flies to make an F1 that was 100% red eye, normal wing (pr+vg+/prvg). Morgan performed a testcross that mated an F1 individual with a purple eye, vestigal wing (prvg/prvg) fly. The phenotypes of the progeny were 1339 red eye, normal wing, 1195 purple eye, vestigal wing, 151 red eye, vestigal wing, and 154 purple eye, normal wing. What is the recombination frequency between the eye color and wing type loci?

( 151 + 154 ) / ( 1339 + 1195 + 151 + 154 ) * 100 = 10.74%

You are collecting unfertilized eggs (gametes) from chickens that are F1 hybrids heterozygous for white feathers vs black feathers, an allelic trait that follows the law of segregation. If you pick up 6 eggs, what is the probability that ALL 6 eggs will carry the black feather allele?

(0.5)^6 = 0.0156

Alkaptonuria is a metabolic disorder in which affected persons produce black urine. Alkaptonuria results from an allele (a) that is recessive to the allele for normal metabolism (A) and follows the Law of Segregation and Law of Independent Assortment. Sally has normal metabolism, but her brother has alkaptonuria. Sally's father has alkaptonuria, and her mother has normal metabolism. If Sally's parents have another child, what is the probability that this child will have alkaptonuria?

0.5

Chickens have ZZ-ZW chromosomal sex determination. When you mate a ZW female with a ZZ male chicken, what is the probability that their offspring will inherit the W chromosome?

0.5

The following two genotypes are crossed: Aa Bb Cc dd Ee × Aa bb Cc Dd Ee. All loci follow the Law of Segregation and the Law of Independent Assortment. What proportion of the progeny of this cross will have the genotype Aa Bb Cc Dd Ee?

0.5*0.5*0.5*0.5*0.5 = 0.03125

You have made a perfect model system for human eye color using mice with 10 loci that follow the law of segregation and the law of independent assortment. According to probability, what proportion of F2 mice will be heterozygous at all loci?

0.5^10

Red (R) vs yellow (r) tomato fruit color is determined by a single locus that follows the law of segregation. Red is dominant over yellow. If you started with homozygous red and homozygous yellow fruit parents in the P generation, what is the ratio of genotypes you would expect to see in the F2 generation?

1 RR: 2 Rr: 1 rr

Albino (c) vs pigmented (C) fur color in mice follows the Law of Segregation. Albino is recessive to pigmented. If you looked at 40 F2 mice descended from a purebred albino x purebred pigmented cross, how many albino mice would you expect?

10 albino mice (25%)

Human somatic cells have 2 sets of homologous chromosomes. What is the maximum number of alleles that an individual can have at one locus?

2 alleles

Although human eye color is a complex trait that involves multiple genes, pigments, and patterns, current evidence has identified 10 contributing genetic loci. If each of these loci follow the Law of Segregation and Law of Independent Assortment, and each possesses 1 dominant and 1 recessive allele, how many possible phenotypes are expected?

2^10 = 1024 eye colors

Domesticated upland cotton (Gossypium hirsutum) is an allopolyploid formed from a hybrid between a wild African and a wild American cotton species estimated to have taken place about 1 million years ago. The African ancestor had a 2n = 26 chromosome count and the American ancestor had a 2n = 26 chromosome count. All chromosomes from the two ancestors were preserved and can be identified in modern upland cotton today. What is the chromosome number in upland cotton?

2n = 52

In the pearl-millet plant, color is determined by three alleles at a single locus: Rp1 (red), Rp2 (purple), and rp (green). Red is dominant over purple and green, and purple is dominant over green (Rp1>Rp2>rp). Give the expected phenotype ratios of offspring produced by crossing a red Rp1/Rp2 individual with a red Rp1/rp individual.

3 red : 1 purple

Sturtevant published the first chromosomal linkage map with 6 genes. Of these, yellow body miniature wings, and rudimentary wings appear in the same linkage group, in that order. yellow body and miniature wings are 33.7 cM away from each other, miniature wings and rudimentary wings are 23.9 cM away from each other. Which of the following is the predicted genetic distance between yellow body and rudimentary wings? Are yellow body and rudimentary wings inherited as if they are unlinked or linked?

33.7 + 23.9 = 57.6 cM; they appear unlinked

If the normal gene order on a chromosome is A B C D E F G, which of the following represents a displaced duplication?

A B C D E F B C G

The Meselson-Stahl experiment was instrumental in determining the overall model of DNA replication. Which model of DNA replication did that experiment support?

DNA replication is semi-conservative with each new helix created from one old strand and one new strand of complementary DNA

Shell coiling of the snail Lymnaea peregra results from a genetic maternal effect. An autosomal allele for a right-handed, or dextral, shell (s+) is dominant over the allele for a left-handed, or sinistral, shell (s). A pet snail called Martha is sinistral and reproduces only as a female (the snails are hermaphroditic). Indicate which of the following statements is true:

All the offspring produced by Martha must be sinistral.

Please complete the statement. _______________ is when nondisjunction of an interspecies hybrid creates a polyploid genome.

Allopolyploidy

How does meiosis lead to the exchange of genetic information between homologous chromosomes?

During Prophase I some chiasmata form crossovers where chromosome pairs touch each other

You are analyzing genotype information collected from a cross with two genes. You calculated a chi-squared value to see if the results of your cross matched the ratios predicted for Mendelian inheritance. You calculated degrees of freedom = 3 and P-value = 0.0333. Now you are wondering if your results match expectations for two independent genes. What parts of your analysis will not be changed by switching to a test of independence?

Chi-squared statistic

Individuals can have type A blood, type B blood, but also can express type A and blood type B traits expressed simultaneously. These multiple alleles belong to the same locus. The ability for both type A and type B alleles to be expressed simultaneously is an example of which of the following?

Codominance

Which of the following is a way that bacteria can transmit genetic information without using an intermediate or requiring uptake of DNA?

Conjugation

Please complete the statement. Traits with variable __________ can be more or less extreme even with the same genotype.

Expressivity

You are a fancy chicken enthusiast. You want to mate your favorite homozygous chicken with black feathers with another that is homozygous for a speckled feather trait called splash. You know that these traits are both alleles of the same locus and black feathers are recessive to splash. If splash exhibits incomplete dominance over black, in which filial generation or set of crosses could you observe black, splash, and the incomplete dominant phenotype in the offspring?

F2

Mendelian genetics provides a mechanism for the inheritance of traits which was predicted by Charles Darwin's Theory of Evolution by Natural Selection. Which aspects of evolution did Mendel's experiments with peas NOT address? (Note: These have all since been addressed and support the theory of evolution)

How are new alleles or traits produced?

Although CRISPR-Cas systems are found in over 40% of known bacteria, few strains that are used in lab or industrial settings have functional CRISPR-Cas loci. Researchers believe that this correlation may be due to the way that Cas proteins interact with transformation of plasmids and other DNA fragments, which is commonly required in lab or industrial applications. Which of the following is the most reasonable hypothesis for how functional CRISPR-Cas loci may negatively impact transformation of plasmids and other DNA fragments?

If Cas1 and Cas2 interact with the plasmid or DNA fragment, they could assemble a new CRISPR array and guide RNA to target Cas9 to cleave the plasmid or DNA fragment, destroying it

When any Chinese hamster with white spots is crossed with another hamster that has no spots, approximately 1/2 of the offspring have white spots and 1/2 have no spots. When any two hamsters with white spots are crossed, 2/3 of the offspring possess white spots and 1/3 have no spots. What does this F2 phenotypic ratio suggest about individuals homozygous for the white spot allele?

It is lethal for hamsters to have two copies of the white spot allele and they are never observed

The cell contains several types or species of RNAs. Which of the following is the RNA species that contains genetic information?

Messenger RNA (mRNA)

Mosaic variegated aneuploidy (MVA) is a rare human recessive disease characterized by growth retardation, microcephaly, and childhood cancer. Individuals with MVA have a rare allele of the BUB1B gene that can cause premature chromatid separation during mitosis. If MVA is caused by the formation of somatic aneuploidy, which of the following is the most likely cause of the disease phenotypes?

Nondisjunction during somatic mitosis led to multiple sectors of cells with too many or too few chromosomes, causing illness

Bananas (Musa spp.) are an autopolyploid with three identical sets of chromosomes (triploid, 3n=33). Which of the following is a possible scenario that could lead to a triploid autopolyploid?

Parent 1 is the same species as Parent 2 and Parent 1 experiences nondisjunction, doubling the number of chromosomes contributed from Parent 1

Genome wide association studies or GWAS take advantage of historical recombination events in the ancestry of individuals to make associations between phenotypes and loci. Many GWAS approaches try to account for recent relatedness or population structure within an experiment through statistical or experimental design considerations. Why might recent relatedness affect an association study?

Recently related individuals will have linkage between markers that are not truly contributing to the phenotype

Centromeres are required for a chromosome or chromatid to properly migrate during mitosis and meiosis. Which of the following is the most likely impact on the inheritance of a chromosomal deletion that removes the centromere?

The chromosome cannot attach to the spindle properly so the deletion cannot be inherited

Recombination is repressed by a chromosomal inversion because of the loss of recombinant gametes. If an inversion includes two separate genes A and B, what is the most likely impact of the inversion on the observed genetic map between A and B?

The map distance between A and B will be close to 0 cM

In a ZZ-ZW chromosomal sex determination system, which chromosome has unique information required for female sex determination?

W

Some organisms have a complex life cycle where the cells that are produced by meiosis do not directly mature into the gametes, but instead divide to create a multicellular, completely 1n life form. Which of the CANNOT be true about organisms with this type of life cycle?

after the initial cell made by meiosis, additional cells of the 1n phase are made by meiosis

Choose the answer that best completes the statement. "Alternative" versions of the same gene are called ____________.

alleles

Labrador retrievers are dogs with many different possible coat colors. The difference between a black and a chocolate color coat is controlled by alleles of the same gene, B and b. Chocolate Labradors have a brown coat and their genotype is always bb. Black Labradors have a black coat and their genotype can be BB or Bb. Which statement about the b allele is TRUE?

b is recessive to B

In cucumbers, orange fruit color (R) is dominant over cream fruit color (r). A cucumber plant homozygous for orange fruit is crossed with a plant homozygous for cream fruit. F1 individuals are intercrossed to produce the F2 and study the inheritance of this trait. For this pedigree, what are the genotypes and phenotypes of the individuals in the P generation?

homozygous orange (RR) and homozygous cream (rr)

Global weather patterns and seasonal temperature are predicted to become more unstable and increase overall. The eggs of painted turtles (Chrysemys picta) use environmental temperature during sex determination (temperature-dependent sex determination or TSD) to irreversibly determine their sex. Which of the following is NOT an anticipated way that TSD species may be immediately impacted by climate change?

increased adult transition from male to female

Please complete the statement. If two genes are linked that implies that they are ________.

on the same chromosome

Which of the following is TRUE about sex chromosomes?

recombination between X-Y or Z-W chromosomes pairs is suppressed

The chi-square statistic is calculated as the sum of the squared differences between observed values and expected values divided by expected values (SUM [(obs - exp)^2 / exp], ∑ ( o b s − e x p ) 2 e x p ). The chi-squared statistic can be applied to complicated crosses with any number of phenotypic or genotypic categories. What part of this equation allows the chi-squared statistic to accomplish this?

the chi-square value is the sum of the individual differences between observed values and expected values, no matter how many categories are being tested

Mendel's Law of Segregation expects each trait to be controlled by one locus. However some alleles exhibit pleiotropy, where one allele causes several traits in the same individual. What is the difference in the inheritance pattern of a single recessive allele that causes two traits vs two separate recessive alleles that each control one trait?

the single pleiotropic allele will control two phenotypes in 1/4 of the F2 generation, but two separate recessive alleles will control two phenotypes in 1/16 of the F2